mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 22:59:07 +09:00
initial commit
This commit is contained in:
@@ -0,0 +1,69 @@
|
||||
% GARRAY wrap the GPU functions for user so that CPU and GPU code is identical
|
||||
%
|
||||
% array = Garray(array)
|
||||
%
|
||||
% ** array numerical array
|
||||
% returns
|
||||
% ++ array GPU numerical array
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
function array = Garray(array)
|
||||
|
||||
global use_gpu
|
||||
array = utils.Garray(array, use_gpu);
|
||||
|
||||
end
|
||||
@@ -0,0 +1,75 @@
|
||||
% GFUN wrap the arrayfun function so that CPU and GPU code is identical
|
||||
% when GPU is not available, assume that matlab dimension expansion is enough
|
||||
%
|
||||
% varargout = Gfun(varargin)
|
||||
%
|
||||
% ** varargin {function, arguments, ...}
|
||||
% returns
|
||||
% ++ varargout outputs
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function varargout = Gfun(varargin)
|
||||
import core.*
|
||||
global use_gpu
|
||||
varargout = cell(nargout,1);
|
||||
if use_gpu
|
||||
[varargout{:}] = arrayfun(varargin{:});
|
||||
else
|
||||
[varargout{:}] = varargin{1}(varargin{2:end});
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,70 @@
|
||||
% GGATHER wrap the GPU functions for user so that CPU and GPU code is identical
|
||||
%
|
||||
% array = Ggather(array)
|
||||
%
|
||||
% ** array GPU array
|
||||
% returns
|
||||
% ++ array CPU array
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function array = Ggather(array)
|
||||
global use_gpu
|
||||
if use_gpu
|
||||
array = gather(array);
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,73 @@
|
||||
% GPAGEFUN wrapper around GPU pagefun function to get similar functionality for GPU and CPU arrays
|
||||
% out = Gpagefun(fun, varargin)
|
||||
%
|
||||
% ** varargin {function, arguments, ...}
|
||||
% returns
|
||||
% ++ varargout outputs
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function out = Gpagefun(fun, varargin)
|
||||
% wrapper around GPU pagefun function
|
||||
if isa(varargin{1}, 'gpuArray')
|
||||
out = pagefun(fun,varargin{:});
|
||||
else
|
||||
Npages = size(varargin{1},3);
|
||||
for ii = 1:Npages
|
||||
out(:,:,ii) = fun(varargin{1}(:,:,ii), varargin{2}(:,:,ii));
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,97 @@
|
||||
% GZEROS wrap the GPU functions for user so that CPU and GPU code is identical
|
||||
%
|
||||
% array = Gzeros(varargin)
|
||||
%
|
||||
% ** varargin identical to "zeros"
|
||||
% returns
|
||||
% ++ array identical to "zeros", only created on GPU if possible
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function array = Gzeros(varargin)
|
||||
global use_gpu
|
||||
|
||||
% if islogical(varargin{end}) && varargin{end} == true
|
||||
% type = single(1i); % directly create complex array !!
|
||||
% else
|
||||
% type = single(1);
|
||||
% end
|
||||
%
|
||||
if length(varargin) > 1 && islogical(varargin{end})
|
||||
varargin = varargin(1:end-1);
|
||||
isComplex = true;
|
||||
else
|
||||
isComplex = false;
|
||||
end
|
||||
% if use_gpu
|
||||
% % move this scalar to GPU to tell matlab what we want
|
||||
% type = gpuArray(type);
|
||||
% end
|
||||
%
|
||||
% array = zeros(varargin{:}, 'like', type);
|
||||
|
||||
if use_gpu
|
||||
array = gpuArray.zeros(varargin{:}, 'single');
|
||||
else
|
||||
array = zeros(varargin{:}, 'single');
|
||||
end
|
||||
|
||||
if isComplex
|
||||
array = complex(array);
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,90 @@
|
||||
% CHECK_AVAIL_MEMORY check and possibly report the available GPU memory
|
||||
%
|
||||
% memory_out = check_avail_memory(show)
|
||||
%
|
||||
% ** show (bool) if true, print results
|
||||
% returns
|
||||
% ++ memory_out (scalar) availible GPU memory in GB
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function memory_out = check_avail_memory(show)
|
||||
|
||||
import utils.verbose
|
||||
|
||||
if nargin == 0; show = false; end
|
||||
global use_gpu gpu
|
||||
if isempty(use_gpu); use_gpu = false; end
|
||||
if use_gpu
|
||||
memory = gpu.AvailableMemory / gpu.TotalMemory;
|
||||
if memory < 0.03
|
||||
error('MATLAB:LowGPUMem','Low gpu memory : %3.0f%%', memory*100)
|
||||
elseif (show && memory < 0.2) || verbose()> 2
|
||||
if verbose()> 4
|
||||
dbstack(1)
|
||||
end
|
||||
verbose(4,'Free gpu memory: %3.3g%%', gpu.AvailableMemory / gpu.TotalMemory*100)
|
||||
end
|
||||
if nargout
|
||||
memory_out = gpu.AvailableMemory / 1e9;
|
||||
end
|
||||
else
|
||||
if nargout
|
||||
memory_out = 1;
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,157 @@
|
||||
% ESTIMATE_REQUIRED_GPU_MEMORY Estimate GPU memory required to run reconstruction with provided parameters
|
||||
%
|
||||
% [required_mem , data_mem, object_mem, required_fft_mem] = ...
|
||||
% estimate_required_GPU_memory(self, par)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% returns
|
||||
% ++ required_mem total required mem
|
||||
% ++ data_mem mem to store data
|
||||
% ++ object_mem mem to store object
|
||||
% ++ required_fft_mem mem to run FFT
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [required_mem , data_mem, object_mem, required_fft_mem] = estimate_req_memory(self, par, grouping)
|
||||
% estimate how much GPU memoty will be needed to run the code
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
if nargin < 3
|
||||
grouping = par.grouping;
|
||||
end
|
||||
if par.gpu_id < 1
|
||||
% ie no GPU is used
|
||||
required_mem = nan; data_mem = nan; object_mem = nan; required_fft_mem = nan;
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
required_mem = 0;
|
||||
data_mem = 0;
|
||||
object_mem = 0;
|
||||
verbose(2, 'Checking available GPU memory ID:%i', par.gpu_id)
|
||||
if par.keep_on_gpu
|
||||
data_class = class(self.diffraction);
|
||||
switch data_class
|
||||
case 'single'
|
||||
byte_size = 4;
|
||||
case 'uint16'
|
||||
byte_size = 2;
|
||||
case {'uint8','int8'}
|
||||
byte_size = 1;
|
||||
end
|
||||
% keep data on GPU
|
||||
data_mem = data_mem + prod(self.Np_p)*self.Npos*byte_size / 2^(2*par.upsampling_data_factor); % self.diffraction can be either cell or array, so the size is calculated from par
|
||||
data_mem = data_mem + numel(self.mask); % bool (uint8 in matlab)
|
||||
data_mem = data_mem + numel(self.noise)*4; % single
|
||||
% keep views on GPU
|
||||
if any(strcmpi(par.method, {'DM'}))
|
||||
required_mem = required_mem + 8*prod(self.Np_p)*self.Npos*par.probe_modes;
|
||||
end
|
||||
end
|
||||
% very empirical guess , assuming FFT memory requirement ~6*8*numel(x)
|
||||
required_fft_mem = (2)*6*8*prod(self.Np_p)*grouping; % empirically tested
|
||||
required_mem = required_mem + required_fft_mem;
|
||||
|
||||
% basic arrays: obj_proj, chi
|
||||
% add for multiple layers by ZC
|
||||
if isfield(par,'Nlayers')
|
||||
Nlayers=par.Nlayers;
|
||||
else
|
||||
Nlayers=1;
|
||||
end
|
||||
|
||||
required_mem = required_mem + 2*4*2*prod(self.Np_p)*grouping*par.Nmodes; % added Nmodes by ZC
|
||||
|
||||
% multilayers of probe added by ZC
|
||||
required_mem = required_mem + 2*4*prod(self.Np_p)*Nlayers*grouping*par.Nmodes + 2*4*prod(self.Np_p)*(grouping+par.Nmodes-1);
|
||||
|
||||
if any(~isinf([par.probe_position_search, par.probe_fourier_shift_search]))
|
||||
% memory needed to keep a probe for each position in the grouping
|
||||
required_mem = required_mem + 2*4*prod(self.Np_p)*grouping;
|
||||
end
|
||||
if is_method(par, 'PIE') && par.variable_probe
|
||||
% size of probe stored for each scan position
|
||||
required_mem = required_mem + 4*2*prod(self.Np_p)*self.Npos;
|
||||
end
|
||||
|
||||
if is_method(par, 'ML') && par.momentum
|
||||
% account for data stored for momentum estimate
|
||||
momentum_mem = 2 + 1 ; % 2 previous steps + velocity map
|
||||
object_mem = object_mem + momentum_mem*4*2*prod(self.Np_o)*numel(self.object);
|
||||
end
|
||||
if is_method(par, 'ML') && par.accelerated_gradients_start < par.number_iterations
|
||||
% account for data stored for accelerated gradient
|
||||
object_mem = object_mem + 2*4*2*prod(self.Np_o)*numel(self.object);
|
||||
end
|
||||
if ~par.share_probe
|
||||
% size of probe stored for each scan position
|
||||
required_mem = required_mem + 4*2*prod(self.Np_p)*grouping;
|
||||
end
|
||||
if par.apply_subpix_shift || par.variable_probe
|
||||
% memory needed for subpixel shifted probe
|
||||
required_mem = required_mem + 4*2*prod(self.Np_p)*grouping*par.Nmodes; % add par.Nmodes by ZC
|
||||
end
|
||||
% size of the object, object update, local object illumination,
|
||||
% total object illumination
|
||||
object_mem = object_mem + 4*prod(self.Np_o) * ( (2+2+1)*numel(self.object) );
|
||||
|
||||
% add object and data
|
||||
required_mem = required_mem + data_mem;
|
||||
required_mem = required_mem+object_mem;
|
||||
end
|
||||
@@ -0,0 +1,147 @@
|
||||
% ESTIMATE_REQUIRED_GPU_MEMORY Estimate GPU memory required to run reconstruction with provided parameters
|
||||
%
|
||||
% [required_mem , data_mem, object_mem, required_fft_mem] = ...
|
||||
% estimate_required_GPU_memory(self, par)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% returns
|
||||
% ++ required_mem total required mem
|
||||
% ++ data_mem mem to store data
|
||||
% ++ object_mem mem to store object
|
||||
% ++ required_fft_mem mem to run FFT
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [required_mem , data_mem, object_mem, required_fft_mem] = estimate_req_memory(self, par, grouping)
|
||||
% estimate how much GPU memoty will be needed to run the code
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
if nargin < 3
|
||||
grouping = par.grouping;
|
||||
end
|
||||
if par.gpu_id < 1
|
||||
% ie no GPU is used
|
||||
required_mem = nan; data_mem = nan; object_mem = nan; required_fft_mem = nan;
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
required_mem = 0;
|
||||
data_mem = 0;
|
||||
object_mem = 0;
|
||||
verbose(2, 'Checking available GPU memory ID:%i', par.gpu_id)
|
||||
if par.keep_on_gpu
|
||||
data_class = class(self.diffraction);
|
||||
switch data_class
|
||||
case 'single'
|
||||
byte_size = 4;
|
||||
case 'uint16'
|
||||
byte_size = 2;
|
||||
case {'uint8','int8'}
|
||||
byte_size = 1;
|
||||
end
|
||||
% keep data on GPU
|
||||
data_mem = data_mem + prod(self.Np_p)*self.Npos*byte_size / 2^(2*par.upsampling_data_factor); % self.diffraction can be either cell or array, so the size is calculated from par
|
||||
data_mem = data_mem + numel(self.mask); % bool (uint8 in matlab)
|
||||
data_mem = data_mem + numel(self.noise)*4; % single
|
||||
% keep views on GPU
|
||||
if any(strcmpi(par.method, {'DM'}))
|
||||
required_mem = required_mem + 8*prod(self.Np_p)*self.Npos*par.probe_modes;
|
||||
end
|
||||
end
|
||||
% very empirical guess , assuming FFT memory requirement ~6*8*numel(x)
|
||||
required_fft_mem = (2)*6*8*prod(self.Np_p)*grouping; % empirically tested
|
||||
required_mem = required_mem + required_fft_mem;
|
||||
|
||||
% basic arrays: obj_proj, chi
|
||||
required_mem = required_mem + 2*4*2*prod(self.Np_p)*grouping;
|
||||
|
||||
if any(~isinf([par.probe_position_search, par.probe_fourier_shift_search]))
|
||||
% memory needed to keep a probe for each position in the grouping
|
||||
required_mem = required_mem + 2*4*prod(self.Np_p)*grouping;
|
||||
end
|
||||
if is_method(par, 'PIE') && par.variable_probe
|
||||
% size of probe stored for each scan position
|
||||
required_mem = required_mem + 4*2*prod(self.Np_p)*self.Npos;
|
||||
end
|
||||
|
||||
if is_method(par, 'ML') && par.momentum
|
||||
% account for data stored for momentum estimate
|
||||
momentum_mem = 2 + 1 ; % 2 previous steps + velocity map
|
||||
object_mem = object_mem + momentum_mem*4*2*prod(self.Np_o)*numel(self.object);
|
||||
end
|
||||
if is_method(par, 'ML') && par.accelerated_gradients_start < par.number_iterations
|
||||
% account for data stored for accelerated gradient
|
||||
object_mem = object_mem + 2*4*2*prod(self.Np_o)*numel(self.object);
|
||||
end
|
||||
if ~par.share_probe
|
||||
% size of probe stored for each scan position
|
||||
required_mem = required_mem + 4*2*prod(self.Np_p)*grouping;
|
||||
end
|
||||
if par.apply_subpix_shift || par.variable_probe
|
||||
% memory needed for subpixel shifted probe
|
||||
required_mem = required_mem + 4*2*prod(self.Np_p)*grouping;
|
||||
end
|
||||
% size of the object, object update, local object illumination,
|
||||
% total object illumination
|
||||
object_mem = object_mem + 4*prod(self.Np_o) * ( (2+2+1)*numel(self.object) );
|
||||
|
||||
% add object and data
|
||||
required_mem = required_mem + data_mem;
|
||||
required_mem = required_mem+object_mem;
|
||||
end
|
||||
@@ -0,0 +1,107 @@
|
||||
% INITIALIZE wrap the GPU functions for user so that CPU and GPU code is identical
|
||||
%
|
||||
% param = initialize(param)
|
||||
%
|
||||
% ** par structure containing parameters for the engines
|
||||
% returns
|
||||
% ++ par updated structure containing parameters for the engines
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
function param= initialize(param)
|
||||
import utils.verbose
|
||||
|
||||
global use_gpu gpu
|
||||
if exist('gpuArray', 'class') && param.use_gpu && gpuDeviceCount
|
||||
verbose(2, 'Initializing GPU %i ... ', param.gpu_id )
|
||||
try
|
||||
gpu= gpuDevice;
|
||||
catch err
|
||||
if strcmp(err.identifier,'parallel:gpu:array:NoPCTLicense')
|
||||
disp('No free licences for parallel toolbox')
|
||||
pause(10)
|
||||
gpu= gpuDevice;
|
||||
else
|
||||
rethrow(err)
|
||||
end
|
||||
end
|
||||
if ~isempty(param.gpu_id) && gpu.Index ~= param.gpu_id
|
||||
gpu= gpuDevice(param.gpu_id);
|
||||
else
|
||||
% let matlab choose, useful for parfor
|
||||
end
|
||||
verbose(1, 'GPU %i initialized ... ', gpu.Index )
|
||||
param.gpu_id = gpu.Index;
|
||||
|
||||
use_gpu = true;
|
||||
elseif ~param.use_gpu
|
||||
use_gpu = false;
|
||||
verbose(0,'Using CPU implementation, calculation can be slower')
|
||||
gpu = [];
|
||||
elseif param.use_gpu && gpuDeviceCount==0
|
||||
warning('No GPU devices available, switching to CPU ... ')
|
||||
use_gpu = false;
|
||||
end
|
||||
|
||||
param.use_gpu = use_gpu;
|
||||
|
||||
% initial persistent variables in Garray
|
||||
utils.Garray([], use_gpu);
|
||||
|
||||
end
|
||||
@@ -0,0 +1,105 @@
|
||||
% MOVE_FROM_GPU gather reconstruction back from GPU to RAM
|
||||
%
|
||||
% self = move_from_gpu(self, move_from_GPU = true)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** move_from_GPU (bool) if true (default), data will be gathered from GPU
|
||||
% returns:
|
||||
% ** self structure containing outputs
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
function self = move_from_gpu(self, move_from_GPU)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
for i = 1:length(self.modes)
|
||||
for field = {'weights', 'ASM_factor', 'cASM_factor', 'FAR_factor', 'cFAR_factor'}
|
||||
if isfield(self.modes{i}, field{1})
|
||||
self.modes{i}.(field{1}) = [];
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
for field = {'probe_support', 'background', 'intensity_corr', 'probe_fourier_shift', 'probe_evolution'}
|
||||
if isfield(self, field{1})
|
||||
self.(field{1}) = Ggather(self.(field{1}));
|
||||
end
|
||||
end
|
||||
|
||||
if nargin < 2 || move_from_GPU
|
||||
self.diffraction = Ggather(self.diffraction);
|
||||
self.noise = Ggather(self.noise);
|
||||
self.mask = Ggather(self.mask);
|
||||
end
|
||||
|
||||
|
||||
for i = 1:numel(self.probe)
|
||||
self.probe{i} = Ggather(self.probe{i});
|
||||
end
|
||||
for i = 1:numel(self.object)
|
||||
self.object{i} = Ggather(self.object{i});
|
||||
end
|
||||
for i = 1:numel(self.illum_sum)
|
||||
self.illum_sum{i} = Ggather(self.illum_sum{i});
|
||||
end
|
||||
if isfield(self, 'phase')
|
||||
for i = 1:length(self.phase)
|
||||
self.phase{i} = Ggather(self.phase{i});
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,141 @@
|
||||
% MOVE_TO_GPU move reconstruction from RAM to GPU
|
||||
%
|
||||
% [self, cache] = move_to_gpu(self,cache, move_data, split_data)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** move_data (bool) if true (default), data will be moved on GPU as well
|
||||
% ** split_data if the data grouping is fixed, the data will be stored in cell for each group separatelly, important for large datasets
|
||||
%
|
||||
% returns:
|
||||
% ++ self self structure moved to GPU
|
||||
% ++ cache cache structure moved to GPU
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
function [self, cache] = move_to_gpu(self,cache, move_data, split_data)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.*
|
||||
|
||||
verbose(0, 'Moving data to GPU')
|
||||
verbose(0, 'Free GPU memory %3.2fGB', check_avail_memory)
|
||||
|
||||
for i = 1:numel(self.probe)
|
||||
self.probe{i} = complex(Garray(self.probe{i}));
|
||||
end
|
||||
|
||||
for i = 1:numel(self.object)
|
||||
self.object{i} = complex(Garray(self.object{i}));
|
||||
end
|
||||
if isfield(self, 'phase')
|
||||
for i = 1:length(self.phase)
|
||||
self.phase{i} = Garray(self.phase{i});
|
||||
end
|
||||
end
|
||||
|
||||
for i = 1:length(self.modes)
|
||||
for field = {'weights','probe_rel_intensity', ...
|
||||
'ASM_factor', 'cASM_factor', ...
|
||||
'FAR_factor', 'cFAR_factor', ...
|
||||
'probe_support', 'probe_support', ...
|
||||
'support_back_propagation_factor', 'support_propagation_factor'}
|
||||
try self.modes{i}.(field{1}) = Garray(self.modes{i}.(field{1}));end
|
||||
end
|
||||
end
|
||||
|
||||
% verbose(0, 'Free GPU memory %g ', check_avail_memory)
|
||||
for field = {'deconv_matrix', 'probe_support', 'background', 'mask'}
|
||||
try self.(field{1}) = Garray(self.(field{1}));end
|
||||
end
|
||||
for field = { 'apodwin', 'background_profile', 'background_weight', 'US_diffraction', 'V_diffraction', 'MAX_ILLUM', 'blur_kernel'}
|
||||
try cache.(field{1}) = Garray(cache.(field{1}));end
|
||||
end
|
||||
for i = 1:numel(cache.illum_sum_0)
|
||||
cache.illum_sum_0{i} = Garray(cache.illum_sum_0{i});
|
||||
end
|
||||
|
||||
check_avail_memory
|
||||
if nargin < 2 || move_data
|
||||
if split_data
|
||||
% split data into cells for each scan -> avoid memory
|
||||
% limitations for too many joined scans and make data loading
|
||||
% faster
|
||||
if isfield(cache, 'preloaded_indices_compact')
|
||||
assert(length(cache.preloaded_indices_compact) == 1, 'Dataset splitting implemented only for single set, use MLc method or smaller dataset')
|
||||
ind = cache.preloaded_indices_compact{1}.indices;
|
||||
elseif isfield(cache, 'preloaded_indices_simple')
|
||||
assert(length(cache.preloaded_indices_simple) == 1, 'Dataset splitting implemented only for single set, use MLc method or smaller dataset')
|
||||
ind = cache.preloaded_indices_simple{1}.indices;
|
||||
else
|
||||
error('Data splitting implemented only for DM or MLc solvers ')
|
||||
end
|
||||
for ii = 1:length(ind)
|
||||
diffraction{ii} = Garray(self.diffraction(:,:,ind{ii}));
|
||||
end
|
||||
self.diffraction = diffraction;
|
||||
else
|
||||
self.diffraction = Garray(self.diffraction);
|
||||
end
|
||||
self.noise = Garray(self.noise);
|
||||
self.mask = Garray(self.mask);
|
||||
end
|
||||
|
||||
verbose(0, 'Data moved to GPU')
|
||||
verbose(0, 'Free GPU memory %3.2fGB', check_avail_memory)
|
||||
|
||||
end
|
||||
@@ -0,0 +1,216 @@
|
||||
% ADD_MOMENTUM_OBJECT speed up convergence by adding momentum / integral term into the
|
||||
% update direction for the MLc method
|
||||
%
|
||||
% [self, cache] = add_momentum_object(self, cache, par, object_upd_sum, iter, fourier_error)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** object_upd_sum cell of arrays containing update direction from the LSQML method
|
||||
% ** iter current iteation numebr
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
|
||||
function [self, cache] = add_momentum_object(self, cache, par, object_upd_sum, iter, fourier_error, beta_object)
|
||||
|
||||
import utils.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
|
||||
verbose(1, 'Adding momentum to object')
|
||||
|
||||
|
||||
object_modes = size(self.object,1);
|
||||
|
||||
% create velocity maps in the first iterations
|
||||
if iter == par.object_change_start
|
||||
cache.object_upd_sum = cell(object_modes,1);
|
||||
for ll = 1:object_modes
|
||||
for jj = 1:par.Nlayers
|
||||
cache.velocity_map_object{ll,jj} = Gzeros(self.Np_o);
|
||||
cache.object_upd_sum{ll,jj} = [];
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
% store previous update directions
|
||||
for ll = 1:object_modes
|
||||
for jj = 1:par.Nlayers
|
||||
upd = object_upd_sum{ll,jj}(cache.object_ROI{:})* mean(beta_object(:,jj));
|
||||
upd = upd / norm2(upd);
|
||||
cache.object_upd_sum{ll,jj} = [cache.object_upd_sum{ll,jj}, {upd}];
|
||||
end
|
||||
end
|
||||
|
||||
% how many steps are stored to calculate optimal friction
|
||||
momentum_memory = 2;
|
||||
|
||||
% use Fourier error to avoid issues with convergence
|
||||
ind_compare = find(all(~isnan(fourier_error),2),3,'last');
|
||||
if length(ind_compare) > 2
|
||||
merr = mean(fourier_error,2);
|
||||
ferr_ok = max(merr(ind_compare([1,2]))) > min(merr(ind_compare([2,3])));
|
||||
else
|
||||
ferr_ok = true;
|
||||
end
|
||||
|
||||
if iter > momentum_memory+par.object_change_start
|
||||
for ll = 1:object_modes
|
||||
for jj = 1:par.Nlayers
|
||||
cache.object_upd_sum{ll,jj}(1) = []; % delete the oldest stored object update
|
||||
corr_level = nan;
|
||||
|
||||
if ferr_ok
|
||||
% caculate correlation between updated to estimate optimal
|
||||
% friction, !! NOTE that cache.object_upd_sum contains only the
|
||||
% object_ROI region !!
|
||||
%
|
||||
switch momentum_memory
|
||||
case 2, [aux{1}, aux{2}] = compare_upd_directions_2(cache.object_upd_sum{ll,jj}{:});
|
||||
case 3, [aux{1}, aux{2}, aux{3}] = compare_upd_directions_2(cache.object_upd_sum{ll,jj}{:});
|
||||
othewise, error('Not implemented')
|
||||
end
|
||||
for kk = 1:momentum_memory
|
||||
corr_level(kk) = real(Ggather(mean2(aux{kk})));
|
||||
end
|
||||
end
|
||||
|
||||
if ferr_ok && all(corr_level > 0 )
|
||||
|
||||
|
||||
% estimate optimal friction from previous steps
|
||||
poly_fit = polyfit(0:momentum_memory,[0,log(corr_level)],1);
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
gain = par.momentum; % smaller -> lower relative speed (less momentum)
|
||||
friction = 0.5*max(-poly_fit(1),0); % smaller -> longer memory, more momentum
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
% update object by the momentum gradient
|
||||
[self.object{ll,jj}, cache.velocity_map_object{ll,jj}] = update_momentum(self.object{ll,jj}, cache.velocity_map_object{ll,jj}, object_upd_sum{ll,jj}, friction, gain, cache.illum_sum_0{ll}, cache.MAX_ILLUM(ll));
|
||||
else
|
||||
% error was increased or updates are not well correlated, skip acceleration
|
||||
gain = 0; friction = inf;
|
||||
cache.velocity_map_object{ll,jj} = cache.velocity_map_object{ll,jj}/2;
|
||||
end
|
||||
|
||||
if verbose()> 1
|
||||
norm_upd = norm2(object_upd_sum{ll,jj});
|
||||
norm_vmap = norm2(gain.*cache.velocity_map_object{ll,jj});
|
||||
verbose(2,['Object %i Corr=', repmat('1:%5.2f ',1,momentum_memory)],ll, corr_level )
|
||||
verbose(0, 'Momentum: friction=%3.1e \tacceleration %1.1fx',friction, 1+norm_vmap/norm_upd)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
% plotting.smart_figure(25454)
|
||||
% img = cat(1,cat(2, cache.velocity_map_object{:}) .* cat(2,cache.illum_sum_0{:}), cat(2, object_upd_sum{:}) .* cat(2,cache.illum_sum_0{:}));
|
||||
% aimg = abs(img);
|
||||
% img = min(aimg, quantile(aimg(:), 0.99)) .* img ./ (aimg+1e-3);
|
||||
% plotting.imagesc3D(img(1:4:end, 1:4:end))
|
||||
% axis off image xy
|
||||
% drawnow
|
||||
|
||||
try
|
||||
if verbose()> 2
|
||||
plotting.smart_figure(121)
|
||||
subplot(1,2,1)
|
||||
plotting.imagesc3D(cache.velocity_map_object{1,1})
|
||||
axis off image
|
||||
title(sprintf('Velocity, iter=%i', iter))
|
||||
subplot(1,2,2)
|
||||
plotting.imagesc3D(object_upd_sum{1,1})
|
||||
axis off image
|
||||
title('Gradient')
|
||||
drawnow
|
||||
end
|
||||
catch
|
||||
keyboard
|
||||
end
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
function [object, Vmap] = update_momentum(object, Vmap, Vmap_upd, friction, gain, weight, w_max)
|
||||
% auxiliary function
|
||||
weight = weight ./ (0.1*w_max+weight);
|
||||
Vmap = (1-friction)*Vmap + Vmap_upd;
|
||||
object = object + weight.*gain.*Vmap;
|
||||
end
|
||||
|
||||
function [out1, out2] = compare_upd_directions_2(upd1, upd2, upd3)
|
||||
% compare updates
|
||||
upd3 = conj(upd3);
|
||||
out2 = upd1 .* upd3;
|
||||
out1 = upd2 .* upd3;
|
||||
end
|
||||
function [out1, out2, out3] = compare_upd_directions_3(upd1, upd2, upd3, upd4)
|
||||
% compare updates
|
||||
upd4 = conj(upd4);
|
||||
out3 = upd1 .* upd4;
|
||||
out2 = upd2 .* upd4;
|
||||
out1 = upd3 .* upd4;
|
||||
end
|
||||
@@ -0,0 +1,197 @@
|
||||
% ADD_MOMENTUM_PROBE speed up convergence by adding momentum / integral term into the
|
||||
% update direction for the MLc method
|
||||
%
|
||||
% [self, cache] = add_momentum_probe(self, cache, par, probe_upd, iter, fourier_error)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** probe_upd cell of arrays containing update direction from the LSQML method
|
||||
% ** iter current iteation numebr
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
|
||||
function [self, cache] = add_momentum_probe(self, cache, par, probe_upd, iter, fourier_error, beta_probe)
|
||||
|
||||
import utils.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
|
||||
verbose(1, 'Adding momentum to probe')
|
||||
|
||||
Nmodes = size(self.probe,1);
|
||||
% create velocity maps in the first iterations
|
||||
if iter == par.probe_change_start
|
||||
cache.probe_upd_sum = cell(Nmodes,1);
|
||||
for ll = 1:Nmodes
|
||||
cache.velocity_map_probe{ll} = Gzeros(self.Np_p);
|
||||
cache.probe_upd_sum{ll} = [];
|
||||
end
|
||||
end
|
||||
|
||||
% store previous update directions
|
||||
for ll = 1:Nmodes
|
||||
probe_upd{ll} = probe_upd{ll}(:,:,:,1); % accelerate only the fundamental probe in the variable probe extension
|
||||
probe_upd{ll} = probe_upd{ll} .* mean(beta_probe(:));
|
||||
upd = probe_upd{ll} ./ (norm2(probe_upd{ll})+eps);
|
||||
cache.probe_upd_sum{ll} = [cache.probe_upd_sum{ll}, {upd}];
|
||||
end
|
||||
|
||||
% how many steps are stored to calculate optimal friction
|
||||
momentum_memory = 3;
|
||||
|
||||
if iter > momentum_memory+par.probe_change_start
|
||||
for ll = 1:Nmodes
|
||||
probe_modes= size(self.probe{ll},3);
|
||||
cache.probe_upd_sum{ll}(1) = []; % delete the oldest stored probe update
|
||||
% caculate correlation between updated to estimate optimal
|
||||
% friction,
|
||||
|
||||
[aux{1}, aux{2}, aux{3}] = compare_upd_directions(cache.probe_upd_sum{ll}{:});
|
||||
for kk = 1:momentum_memory
|
||||
corr_level(kk,:) = real(Ggather(mean2(aux{kk})));
|
||||
end
|
||||
|
||||
|
||||
% use Fourier error to avoid issues with convergence
|
||||
ind_compare = find(all(~isnan(fourier_error),2),3,'last');
|
||||
if length(ind_compare) > 2
|
||||
merr = mean(fourier_error,2);
|
||||
ferr_ok = max(merr(ind_compare([1,2]))) > min(merr(ind_compare([2,3])));
|
||||
else
|
||||
ferr_ok = true;
|
||||
end
|
||||
|
||||
if all(corr_level(:) > 0 ) && ferr_ok
|
||||
|
||||
try
|
||||
% estimate optimal friction from previous steps
|
||||
poly_fit = polyfit(repmat(0:momentum_memory,probe_modes,1),[zeros(1,probe_modes);log(corr_level)]',1);
|
||||
catch
|
||||
keyboard
|
||||
end
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
gain = par.momentum; % smaller -> lower relative speed (less momentum)
|
||||
friction = 0.5*max(-poly_fit(1),0); % smaller -> longer memory, more momentum
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
% update probe by the momentum gradient , accelerate only the fundamental probe in the variable probe extension
|
||||
[self.probe{ll}(:,:,:,1), cache.velocity_map_probe{ll}] = update_momentum(self.probe{ll}(:,:,:,1), cache.velocity_map_probe{ll}, probe_upd{ll}, friction, gain);
|
||||
else
|
||||
% error was increased or updates are not well correlated, skip acceleration
|
||||
gain = 0; friction = inf;
|
||||
cache.velocity_map_probe{ll} = cache.velocity_map_probe{ll}/2;
|
||||
end
|
||||
|
||||
if verbose() > 0
|
||||
norm_upd = mean(norm2(probe_upd{ll}));
|
||||
norm_vmap = eps+mean(norm2(gain.*cache.velocity_map_probe{ll}));
|
||||
verbose(2,['Probe %i Corr=', repmat('1:%5.2f ',1,momentum_memory)],ll, corr_level(:,1) )
|
||||
verbose(0, 'Momentum: friction=%3.1e \tacceleration %1.1fx',friction(:,1), 1+norm_vmap./norm_upd(1))
|
||||
end
|
||||
end
|
||||
|
||||
% plotting.smart_figure(25454)
|
||||
% img = cat(1,cat(2, cache.velocity_map_probe{:}) .* cat(2,cache.illum_sum_0{:}), cat(2, probe_upd_sum{:}) .* cat(2,cache.illum_sum_0{:}));
|
||||
% aimg = abs(img);
|
||||
% img = min(aimg, quantile(aimg(:), 0.99)) .* img ./ (aimg+1e-3);
|
||||
% plotting.imagesc3D(img(1:4:end, 1:4:end))
|
||||
% axis off image xy
|
||||
% drawnow
|
||||
|
||||
try
|
||||
if verbose() > 2
|
||||
plotting.smart_figure(1213)
|
||||
subplot(1,2,1)
|
||||
plotting.imagesc3D(cache.velocity_map_probe{1,1})
|
||||
axis off image
|
||||
title(sprintf('Velocity, iter=%i, norm=%g', iter, norm2(cache.velocity_map_probe{1,1})))
|
||||
subplot(1,2,2)
|
||||
plotting.imagesc3D(probe_upd{1})
|
||||
axis off image
|
||||
title(sprintf('Gradient, norm=%g',norm2(probe_upd{1})))
|
||||
drawnow
|
||||
end
|
||||
catch
|
||||
keyboard
|
||||
end
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
function [probe, Vmap] = update_momentum(probe, Vmap, Vmap_upd, friction, gain)
|
||||
% auxiliary function
|
||||
Vmap = (1-friction)*Vmap + Vmap_upd;
|
||||
probe = probe + gain.*Vmap;
|
||||
end
|
||||
function [out1, out2, out3] = compare_upd_directions(upd1, upd2, upd3, upd4)
|
||||
% compare updates
|
||||
upd4 = conj(upd4);
|
||||
out3 = upd1 .* upd4;
|
||||
out2 = upd2 .* upd4;
|
||||
out1 = upd3 .* upd4;
|
||||
end
|
||||
@@ -0,0 +1,97 @@
|
||||
% GET_FORWARD_MODEL from the provided object and probe calculate the exit wave
|
||||
%
|
||||
% [self, probe, obj_proj, psi] = get_forward_model(self, obj_proj, par, cache, g_ind, p_ind, scan_ids, layer_ids)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** obj_proj [Nx,Ny,N] array, just a preallocated array on GPU, can be empty
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** g_ind indices corresponding to the current group that is solved in parallel
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
% ** scan_ids determines to which scan correponds each of the position
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
%
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ probe either [Nx,Nx,1] or [Nx,Nx,N] aarray of shared probe or variable probe that differs for each position
|
||||
% ++ obj_proj [Nx,Ny,N] array, views of the object for each scan position
|
||||
% ++ psi [Nx,Ny,N] array, complex valued exit-wave (psi = P*O)
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
function [self, probe, obj_proj, psi] = get_forward_model(self, obj_proj, par, cache, g_ind, p_ind, scan_ids, layer_ids)
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.LSQML.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import plotting.*
|
||||
|
||||
if isempty(obj_proj{1})
|
||||
for ll = 1:par.object_modes
|
||||
obj_proj{ll} = Gzeros([self.Np_p, 0], true);
|
||||
end
|
||||
end
|
||||
|
||||
% allocate memory for probes. Added by ZC
|
||||
% probe = self.probe;
|
||||
if par.Nlayers > 1
|
||||
probe=cell(par.probe_modes,par.Nlayers+1);
|
||||
end
|
||||
|
||||
% get illumination probe
|
||||
for ll = 1:par.probe_modes
|
||||
if (ll == 1 && (par.variable_probe || par.variable_intensity))
|
||||
% add variable probe (OPRP) part into the constant illumination
|
||||
probe{ll,1} = get_variable_probe(self.probe{ll}, self.probe_evolution(g_ind,:),p_ind{ll});
|
||||
else
|
||||
% store the normal (constant) probe(s)
|
||||
probe{ll,1} = self.probe{min(ll,end)}(:,:,min(end,p_ind{ll}),1);
|
||||
end
|
||||
|
||||
if (ll == 1 && par.apply_subpix_shift && isinf(self.z_distance(end))) || is_used(par,'fly_scan')
|
||||
% only in farfield mode
|
||||
probe{ll,1} = apply_subpx_shift(probe{ll,1}, self.modes{min(end,ll)}.sub_px_shift(g_ind,:) );
|
||||
end
|
||||
if (ll == 1)
|
||||
probe{ll,1} = apply_subpx_shift_fft(probe{ll,1}, self.modes{1}.probe_fourier_shift(g_ind,:));
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
% allocate memory for psi. Added by ZC
|
||||
psi=cell(max(par.object_modes, par.probe_modes),1);
|
||||
|
||||
% get projection of the object and probe
|
||||
for layer = 1:par.Nlayers
|
||||
for ll = 1:max(par.object_modes, par.probe_modes)
|
||||
llo = min(ll, par.object_modes);
|
||||
llp = min(ll, par.probe_modes);
|
||||
% get objects projections
|
||||
obj_proj{llo} = get_views(self.object, obj_proj{llo},layer_ids(layer),llo, g_ind, cache, scan_ids,[]);
|
||||
if (ll == 1 && par.apply_subpix_shift && ~isinf(self.z_distance(end)))
|
||||
% only in nearfield mode , apply shift in the opposite direction
|
||||
obj_proj{ll} = apply_subpx_shift(obj_proj{ll} .* cache.apodwin, -self.modes{min(end,ll)}.sub_px_shift(g_ind,:) ) ./ cache.apodwin;
|
||||
end
|
||||
|
||||
% get exitwave after each layer
|
||||
psi{ll} = probe{llp,layer} .* obj_proj{llo};
|
||||
%modified by YJ: no need to do another propagation after the
|
||||
%last object layer
|
||||
if layer < par.Nlayers
|
||||
% fourier propagation
|
||||
[psi{ll}] = fwd_fourier_proj(psi{ll} , self.modes{layer}, g_ind);
|
||||
if par.Nlayers > 1
|
||||
probe{llp,layer+1} = psi{llp};
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
% At this point, psi is the exit wave after the last object layer
|
||||
% Now propagate the wave function to far-field (detector) plane
|
||||
% This is same as using fwd_fourier_proj w. distance = inf and no camera angle refinement
|
||||
for ll= 1:max(par.object_modes, par.probe_modes)
|
||||
psi{ll} = fft2_safe(psi{ll}); % fully farfield
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,143 @@
|
||||
% GET_OPTIMAL_LSQ_STEP calculate the optimal step lenght for given update directions and chi array
|
||||
%
|
||||
% [beta_probe, beta_object] = get_optimal_LSQ_step(self,chi,dO,dP,O,P, p_ind, par)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** chi [Nx,Ny,N] array, difference between original and updated exit-wave
|
||||
% ** dO [Nx,Ny,N] array, object update direction
|
||||
% ** dP [Nx,Ny,N] array, probe update direction
|
||||
% ** O [Nx,Ny,N] array, object views
|
||||
% ** P [Nx,Ny,1] or [Nx,Ny,N] array, single or variable probe
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
% ** par structure containing parameters for the engines
|
||||
%
|
||||
% returns:
|
||||
% ++ beta_probe optimal probe step
|
||||
% ++ beta_object optimal object step
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
function [beta_probe, beta_object] = get_optimal_LSQ_step(self,chi,dO,dP,O,P, p_ind, par)
|
||||
|
||||
% find optimal step in the LSQ sense
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
global gpu use_gpu
|
||||
if ~isempty(gpu); wait(gpu); end
|
||||
|
||||
grouping = size(chi,3);
|
||||
lambda_0 = eps(single(1)) / prod(self.Np_p);
|
||||
|
||||
lambda_LSQ = 0.1; % add some small regularization to avoid instabilities
|
||||
|
||||
|
||||
if use_gpu
|
||||
% fast mex based CUDA version
|
||||
if size(dP,3) == grouping
|
||||
p_ind = 1:grouping; % one update for each position
|
||||
elseif size(dP,3) == 1 && numel(p_ind) == 1
|
||||
p_ind = ones(size(chi,3),1); % use only the one update given
|
||||
elseif max(p_ind) <= size(dP,3) && numel(p_ind) == grouping
|
||||
|
||||
else
|
||||
warning('Checkme, untested option')
|
||||
keyboard
|
||||
end
|
||||
try
|
||||
[AA, Atb] = get_LSQ_step_mex(chi,dO,dP,O,P,lambda_0, uint8(p_ind));
|
||||
catch err
|
||||
if any(strcmp(err.identifier, { 'MATLAB:UndefinedFunction','MATLAB:mex:ErrInvalidMEXFile'}))
|
||||
path = fullfile(replace(mfilename('fullpath'), mfilename, ''), 'private');
|
||||
mexcuda('-output', [path, '/get_LSQ_step_mex'], [path, '/get_LSQ_step_mex.cu'])
|
||||
|
||||
[AA, Atb] = get_LSQ_step_mex(chi,dO,dP,O,P,lambda_0, uint8(p_ind));
|
||||
else
|
||||
rethrow(err)
|
||||
end
|
||||
end
|
||||
|
||||
AA = Ggather(AA);
|
||||
Atb = Ggather(Atb);
|
||||
% is seems to be faster to get it first from GPU and then apply some
|
||||
% oprations because the matrices are too small
|
||||
AA = sum(AA,4);
|
||||
Atb = sum(Atb,4);
|
||||
AA = AA + lambda_LSQ*diag(diag(mean(AA,3)));
|
||||
% the system of equations is so small that solving on CPU is good enough
|
||||
[x1, x2] = solve_LSQ(AA(1,1,:), AA(2,1,:), AA(1,2,:), AA(2,2,:), Atb(1,1,:), Atb(2,1,:));
|
||||
LSQ_step = cat(1, x1, x2);
|
||||
else
|
||||
|
||||
|
||||
if ~( par.share_probe || length(unique(p_ind)) == 1 )
|
||||
% in case of multiple scans !!
|
||||
% replicate the update back to the original dP size
|
||||
dP = dP(:,:,p_ind);
|
||||
end
|
||||
tic
|
||||
% prevent ill posed inversion, ideally it should be Garray(mean(abs(AA1)+abs(AA4))/2) but it i show
|
||||
[AA1,AA2,AA4, Atb1,Atb2] = ...
|
||||
Gfun(@get_optimal_step_lsq, chi,dO,dP,...
|
||||
O,P, lambda_0);
|
||||
|
||||
AA1 = sum2(AA1);
|
||||
AA2 = sum2(AA2);
|
||||
AA4 = sum2(AA4);
|
||||
Atb1 = sum2(Atb1);
|
||||
Atb2 = sum2(Atb2);
|
||||
|
||||
% it seems faster to solve it on GPU than using pagefun on GPU
|
||||
AA1 = Ggather(AA1);AA2 = Ggather(AA2);AA4 = Ggather(AA4);Atb1 = Ggather(Atb1);Atb2 = Ggather(Atb2);
|
||||
AA3 = conj(AA2);
|
||||
|
||||
lambda = 0.5; % add some small regularization to avoid unstabilities
|
||||
I = lambda*[mean(AA1), mean(AA4)];
|
||||
|
||||
AA = [ AA1+I(1), AA2; AA3, AA4+I(2)];
|
||||
Atb= [ Atb1; Atb2];
|
||||
|
||||
[x1, x2] = solve_LSQ(AA(1,1,:), AA(2,1,:), AA(1,2,:), AA(2,2,:), Atb(1,1,:), Atb(2,1,:));
|
||||
LSQ_step = cat(1, x1, x2);
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
LSQ_step = max(0, real(LSQ_step));
|
||||
LSQ_step = Ggather(LSQ_step);
|
||||
|
||||
% prevent unwanted oscilation of step gets too high
|
||||
beta_probe = LSQ_step(2,1,:);
|
||||
beta_object = LSQ_step(1,1,:);
|
||||
|
||||
beta_probe = (par.beta_probe *par.beta_LSQ)* beta_probe;
|
||||
beta_object = (par.beta_object*par.beta_LSQ)* beta_object;
|
||||
|
||||
end
|
||||
|
||||
function [AA1,AA2,AA4, Atb1,Atb2] = ...
|
||||
get_optimal_step_lsq(chi,dO,dP,O,P, lambda)
|
||||
% fast kernel for estimation of optimal P and object steps
|
||||
dOP = dO.*P;
|
||||
dPO = dP.*O;
|
||||
cdOP = conj(dOP);
|
||||
cdPO = conj(dPO);
|
||||
|
||||
AA1 = real(dOP .* cdOP)+lambda;
|
||||
AA2 = (dOP .* cdPO);
|
||||
AA4 = real(dPO .* cdPO)+lambda;
|
||||
Atb1 = real(cdOP .* chi);
|
||||
Atb2 = real(cdPO .* chi);
|
||||
end
|
||||
|
||||
|
||||
function [x1, x2] = solve_LSQ(AA1, AA2, AA3, AA4, Atb1, Atb2)
|
||||
% GPU kernel to solve simple 2x2 system of equations
|
||||
det = (AA1.*AA4 - AA2.*AA3);
|
||||
x1 = -conj(AA2.*Atb2-AA4.*Atb1) ./ det;
|
||||
x2 = conj(AA1.*Atb2-AA3.*Atb1) ./ det;
|
||||
end
|
||||
|
||||
|
||||
@@ -0,0 +1,89 @@
|
||||
% GET_VARIABLE_PROBE calculate variable probe for given mean/var probe and its evolution inputs
|
||||
%
|
||||
% probe = get_variable_probe(probe, probe_evolution, p_ind)
|
||||
%
|
||||
% ** probe [Nx,Ny,probe_modes,variable_modes] array, variable probe
|
||||
% ** probe_evolution [Npos,variable_modes] array containing evolution of the varaible modes for each position
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
%
|
||||
% returns:
|
||||
% ++ probe [Nx,Ny,N] array, a different probe for each scan position
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
function probe = get_variable_probe(probe, probe_evolution, p_ind)
|
||||
|
||||
Np_p = [size(probe,1),size(probe,2)];
|
||||
|
||||
probe = probe(:,:,p_ind,:);
|
||||
|
||||
if length(p_ind) == 1 % in case that only single probe is called
|
||||
probe = reshape(probe,prod(Np_p),[]);
|
||||
probe = reshape(probe * probe_evolution', Np_p(1), Np_p(2), []);
|
||||
else % in case multiple scans with unshared probe
|
||||
probe_out = 0;
|
||||
for ii = 1:size(probe,4)
|
||||
probe_out = probe_out + probe(:,:,:,ii).*reshape(probe_evolution(:,ii),1,1,[]);
|
||||
end
|
||||
probe = probe_out;
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,465 @@
|
||||
/*
|
||||
Set complex views to complex object
|
||||
mexcuda -output +engines/+GPU/get_optimal_LSQ_step_mex +engines/+GPU/get_optimal_LSQ_step_mex.cu
|
||||
*/
|
||||
|
||||
#include "mex.h"
|
||||
#include "gpu/mxGPUArray.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <iostream>
|
||||
#include <list>
|
||||
|
||||
typedef const unsigned int cuint;
|
||||
typedef const uint16_T cuint16;
|
||||
#define MAX_BLOCK_DIM_SIZE 65535
|
||||
|
||||
|
||||
/*
|
||||
* Device code
|
||||
*/
|
||||
|
||||
// allocate shared memory so that all functions can see it
|
||||
extern __shared__ float sdata[];
|
||||
const unsigned int MAX_IND_READ = 10000;
|
||||
__constant__ uint8_T gC_pind[MAX_IND_READ];
|
||||
|
||||
|
||||
int checkLastError(char * msg)
|
||||
{
|
||||
cudaError_t cudaStatus = cudaGetLastError();
|
||||
if (cudaStatus != cudaSuccess) {
|
||||
char err[512];
|
||||
sprintf(err, "get_optimal_LSQ_step_ker failed \n %s: %s. \n", msg, cudaGetErrorString(cudaStatus));
|
||||
mexPrintf(err);
|
||||
return 1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/*********** fast inplace version of LSQ step calculation *************/
|
||||
|
||||
template <unsigned int blockSize>
|
||||
__device__ void calculate_AA_matrix( const float2 *P_f, const float2 *O_f,const float2 *dP_f, const float2 *dO_f, const float2 *chi_f,
|
||||
float &AA1, float2 &AA2,float2 &AA3, float &AA4,
|
||||
float &Atb1, float &Atb2 , const float lambda,
|
||||
cuint Np_x, cuint Np_y, cuint Npixz, cuint idz,
|
||||
cuint Nblocks, const bool single_probe, cuint id, cuint tid)
|
||||
{
|
||||
|
||||
float2 dO, dP, O, P, chi;
|
||||
// load to local memory
|
||||
cuint id3 = id + Np_x*Np_y*idz;
|
||||
O = O_f[id3] ;
|
||||
dO = dO_f[id3] ;
|
||||
chi = chi_f[id3];
|
||||
|
||||
if (single_probe) {
|
||||
// single shared 2D probe
|
||||
P = P_f[id];
|
||||
dP = dP_f[id];
|
||||
} else {
|
||||
// unshared probe => size(dp,3) == Nscans
|
||||
dP = dP_f[id + (gC_pind[idz]-1)*Np_x*Np_y];
|
||||
// position in 3D array
|
||||
P = P_f[id3];
|
||||
}
|
||||
|
||||
// make auxiliary variables
|
||||
float2 dOP, dPO, cdPO, cdOP;
|
||||
|
||||
// dOP = dO.*P;
|
||||
dOP.x = dO.x * P.x - dO.y * P.y;
|
||||
dOP.y = dO.y * P.x + dO.x * P.y;
|
||||
|
||||
// dPO = dP.*O;
|
||||
dPO.x = dP.x * O.x - dP.y * O.y;
|
||||
dPO.y = dP.y * O.x + dP.x * O.y;
|
||||
|
||||
// cdOP = conj(dOP);
|
||||
cdOP.x = dOP.x;
|
||||
cdOP.y = -dOP.y;
|
||||
|
||||
// cdPO = conj(dPO);
|
||||
cdPO.x = dPO.x;
|
||||
cdPO.y = -dPO.y;
|
||||
|
||||
// AA1 = abs(dOP).^2+lambda;
|
||||
AA1 = dOP.x * dOP.x + dOP.y * dOP.y ;
|
||||
|
||||
// AA2 = (dOP .* cdPO);
|
||||
AA2.x = dOP.x * cdPO.x - dOP.y * cdPO.y ;
|
||||
AA2.y = dOP.x * cdPO.y + dOP.x * cdPO.y ;
|
||||
|
||||
// AA3 = conj(AA2);
|
||||
AA3.x = AA2.x;
|
||||
AA3.y = -AA2.y;
|
||||
|
||||
// AA4 = abs(dPO)^2+lambda;
|
||||
AA4 = dPO.x * dPO.x + dPO.y * dPO.y ;
|
||||
|
||||
// Atb1 = real(cdOP .* chi);
|
||||
Atb1 = cdOP.x*chi.x - cdOP.y*chi.y;
|
||||
|
||||
// Atb2 = real(cdPO .* chi);
|
||||
Atb2 = cdPO.x*chi.x - cdPO.y*chi.y;
|
||||
|
||||
|
||||
// add to the shared gpu memory
|
||||
sdata[tid ] = AA1;
|
||||
sdata[tid+ blockSize] = AA2.x;
|
||||
sdata[tid+2*blockSize] = AA2.y;
|
||||
sdata[tid+3*blockSize] = AA3.x;
|
||||
sdata[tid+4*blockSize] = AA3.y;
|
||||
sdata[tid+5*blockSize] = AA4;
|
||||
sdata[tid+6*blockSize] = Atb1;
|
||||
sdata[tid+7*blockSize] = Atb2;
|
||||
}
|
||||
|
||||
template <unsigned int blockSize>
|
||||
__device__ void add_to_shared_array( cuint tid, cuint offset )
|
||||
{
|
||||
// another loop unrolling
|
||||
sdata[tid + 0*blockSize] += sdata[tid + 0*blockSize + offset];
|
||||
sdata[tid + 1*blockSize] += sdata[tid + 1*blockSize + offset];
|
||||
sdata[tid + 2*blockSize] += sdata[tid + 2*blockSize + offset];
|
||||
sdata[tid + 3*blockSize] += sdata[tid + 3*blockSize + offset];
|
||||
sdata[tid + 4*blockSize] += sdata[tid + 4*blockSize + offset];
|
||||
sdata[tid + 5*blockSize] += sdata[tid + 5*blockSize + offset];
|
||||
sdata[tid + 6*blockSize] += sdata[tid + 6*blockSize + offset];
|
||||
sdata[tid + 7*blockSize] += sdata[tid + 7*blockSize + offset];
|
||||
}
|
||||
|
||||
|
||||
template <unsigned int blockSize>
|
||||
__device__ void reduce_shared_array( cuint tid )
|
||||
{
|
||||
// do reduction in shared mem using unrolled loops
|
||||
if (blockSize >= 1024){ if (tid < 512) { add_to_shared_array<blockSize>(tid,512); } __syncthreads(); }
|
||||
if (blockSize >= 512) { if (tid < 256) { add_to_shared_array<blockSize>(tid,256); } __syncthreads(); }
|
||||
if (blockSize >= 256) { if (tid < 128) { add_to_shared_array<blockSize>(tid,128); } __syncthreads(); }
|
||||
if (blockSize >= 128) { if (tid < 64) { add_to_shared_array<blockSize>(tid,64); } __syncthreads(); }
|
||||
// why not do the same for all
|
||||
if (blockSize >= 64) { if (tid < 32) { add_to_shared_array<blockSize>(tid,32); } __syncthreads(); }
|
||||
if (blockSize >= 32) { if (tid < 16) { add_to_shared_array<blockSize>(tid,16); } __syncthreads(); }
|
||||
if (blockSize >= 16) { if (tid < 8) { add_to_shared_array<blockSize>(tid,8); } __syncthreads(); }
|
||||
if (blockSize >= 8) { if (tid < 4) { add_to_shared_array<blockSize>(tid,4); } __syncthreads(); }
|
||||
if (blockSize >= 4) { if (tid < 2) { add_to_shared_array<blockSize>(tid,2); } __syncthreads(); }
|
||||
if (blockSize >= 2) { if (tid < 1) { add_to_shared_array<blockSize>(tid,1); } __syncthreads(); }
|
||||
}
|
||||
|
||||
|
||||
// fast kernel for estimation of optimal probe and object steps
|
||||
|
||||
template <unsigned int blockSize>
|
||||
__global__ void get_optimal_LSQ_step_ker( float2 const * P_f, float2 const * O_f,float2 const * dP_f, float2 const * dO_f,
|
||||
float2 const * chi_f, const float lambda,
|
||||
float2 * AA, float * Atb, cuint Np_x,cuint Np_y, cuint Npixz, cuint Nblocks, const bool single_probe) {
|
||||
|
||||
const mwSize tid = threadIdx.x;
|
||||
// do only every second block
|
||||
//cuint i = blockIdx.x*(blockSize*2) + threadIdx.x;
|
||||
const mwSize i = blockIdx.x*(blockDim.x) + threadIdx.x;
|
||||
|
||||
const mwSize N2 = Np_x*Np_y;
|
||||
mwSize AA_page_id, Atb_page_id;
|
||||
|
||||
float2 AA2, AA3;
|
||||
float AA1, AA4, Atb1, Atb2;
|
||||
|
||||
for(int n = 0; n < 8; n++)
|
||||
sdata[tid + n*blockSize ] = 0 ;
|
||||
|
||||
|
||||
if(i < N2)
|
||||
{
|
||||
|
||||
//for(int n = 0; n < 8*blockSize; n++)
|
||||
// sdata[n] = 0 ;
|
||||
|
||||
|
||||
// Page in a 3D matrix
|
||||
for(int idz = 0; idz < Npixz; idz++)
|
||||
{
|
||||
unsigned int ii = i ;
|
||||
|
||||
// empty the share memory
|
||||
for(int n = 0; n < 8; n++)
|
||||
sdata[tid + n*blockSize ] = 0 ;
|
||||
|
||||
|
||||
|
||||
// get coeficients for the AA matrix + right size Atb vector and add them to the shared array
|
||||
calculate_AA_matrix<blockSize>(P_f ,O_f ,dP_f ,dO_f ,chi_f ,
|
||||
AA1, AA2, AA3, AA4, Atb1, Atb2, lambda, Np_x, Np_y, Npixz, idz, Nblocks,single_probe, ii, tid);
|
||||
|
||||
|
||||
__syncthreads();
|
||||
|
||||
|
||||
// reduce the shared memory data
|
||||
reduce_shared_array<blockSize>( tid );
|
||||
|
||||
|
||||
// write result for this block to global mem
|
||||
if (tid == 0) {
|
||||
// store data to the AA matrix
|
||||
AA_page_id = 4*idz + 4*Npixz*blockIdx.x;
|
||||
Atb_page_id = 2*idz + 2*Npixz*blockIdx.x;
|
||||
|
||||
AA[ 0 + AA_page_id].x = sdata[0*blockSize];
|
||||
AA[ 0 + AA_page_id].y = 0; // needs to be set to zero or initalized to zero when created
|
||||
|
||||
AA[ 1 + AA_page_id].x = sdata[1*blockSize];
|
||||
AA[ 1 + AA_page_id].y = sdata[2*blockSize];
|
||||
AA[ 2 + AA_page_id].x = sdata[3*blockSize];
|
||||
AA[ 2 + AA_page_id].y = sdata[4*blockSize];
|
||||
AA[ 3 + AA_page_id].x = sdata[5*blockSize];
|
||||
AA[ 3 + AA_page_id].y = 0;
|
||||
|
||||
Atb[ 0 + Atb_page_id] = sdata[6*blockSize];
|
||||
Atb[ 1 + Atb_page_id] = sdata[7*blockSize];
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
unsigned int nextPow2( unsigned int x ) {
|
||||
--x;
|
||||
x |= x >> 1;
|
||||
x |= x >> 2;
|
||||
x |= x >> 4;
|
||||
x |= x >> 8;
|
||||
x |= x >> 16;
|
||||
return ++x;
|
||||
}
|
||||
|
||||
void getNumBlocksAndThreads(int n, int maxBlocks, int maxThreads, int &blocks, int &threads)
|
||||
{
|
||||
threads = (n < maxThreads*2) ? nextPow2((n + 1)/ 2) : maxThreads;
|
||||
blocks = (n + (threads * 2 - 1)) / (threads * 2);
|
||||
blocks = min(maxBlocks, blocks);
|
||||
}
|
||||
|
||||
|
||||
|
||||
void mexFunction(int nlhs, mxArray *plhs[],
|
||||
int nrhs, const mxArray *prhs[])
|
||||
{
|
||||
char const * const errId = "parallel:gpu:mexGPUExample:InvalidInput";
|
||||
char const * const errMsg = "Invalid input to MEX file.";
|
||||
|
||||
|
||||
// Check for proper number of arguments.
|
||||
|
||||
if (nrhs != 7)
|
||||
mexErrMsgTxt("Seven input arguments required");
|
||||
|
||||
|
||||
|
||||
const mxGPUArray * m_chi = mxGPUCreateFromMxArray(prhs[0]);
|
||||
if ((mxGPUGetClassID(m_chi) != mxSINGLE_CLASS) || (mxGPUGetComplexity(m_chi) != mxCOMPLEX)) {
|
||||
mexPrintf("m_chi\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const float2 * p_chi = (float2 *)mxGPUGetDataReadOnly(m_chi);
|
||||
|
||||
const mxGPUArray * m_dO = mxGPUCreateFromMxArray(prhs[1]);
|
||||
if ((mxGPUGetClassID(m_dO) != mxSINGLE_CLASS) || (mxGPUGetComplexity(m_dO) != mxCOMPLEX)) {
|
||||
mexPrintf("m_dO\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const float2 * p_dO = (float2 *)mxGPUGetDataReadOnly(m_dO);
|
||||
|
||||
const mxGPUArray * m_dP = mxGPUCreateFromMxArray(prhs[2]);
|
||||
if ((mxGPUGetClassID(m_dP) != mxSINGLE_CLASS) || (mxGPUGetComplexity(m_dP) != mxCOMPLEX)) {
|
||||
mexPrintf("m_dP\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const float2 * p_dP = (float2 *)mxGPUGetDataReadOnly(m_dP);
|
||||
|
||||
const mxGPUArray * m_O = mxGPUCreateFromMxArray(prhs[3]);
|
||||
if ((mxGPUGetClassID(m_O) != mxSINGLE_CLASS) || (mxGPUGetComplexity(m_O) != mxCOMPLEX)) {
|
||||
mexPrintf("m_O\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const float2 * p_O = (float2 *)mxGPUGetDataReadOnly(m_O);
|
||||
|
||||
const mxGPUArray * m_P = mxGPUCreateFromMxArray(prhs[4]);
|
||||
if ((mxGPUGetClassID(m_P) != mxSINGLE_CLASS) || (mxGPUGetComplexity(m_P) != mxCOMPLEX)) {
|
||||
mexPrintf("m_P\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const float2 * p_P = (float2 *)mxGPUGetDataReadOnly(m_P);
|
||||
|
||||
const mxGPUArray * m_P_ind = mxGPUCreateFromMxArray(prhs[6]);
|
||||
if (mxGPUGetClassID(m_P_ind) != mxUINT8_CLASS) {
|
||||
mexPrintf("m_P_ind class %i\n", mxGPUGetClassID(m_P_ind));
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const uint8_T * p_P_ind = (uint8_T *)mxGPUGetDataReadOnly(m_P_ind);
|
||||
const unsigned int Npos = mxGPUGetNumberOfElements(m_P_ind);
|
||||
|
||||
if (Npos > MAX_IND_READ) {
|
||||
mexErrMsgIdAndTxt(errId, "Maximal size of input block exceeded");
|
||||
}
|
||||
|
||||
|
||||
// Get dimension of probe and object
|
||||
const unsigned int Ndims = (unsigned int)mxGPUGetNumberOfDimensions(m_chi);
|
||||
if (Ndims != 3) {
|
||||
mexErrMsgIdAndTxt(errId, "Inputs has to be 3 dimensional\n");
|
||||
}
|
||||
const mwSize * Npix = mxGPUGetDimensions(m_chi);
|
||||
const mwSize * Npix_probe = mxGPUGetDimensions(m_P);
|
||||
const mwSize * Npix_probe_upd = mxGPUGetDimensions(m_dP);
|
||||
const mwSize Ndims_probe = mxGPUGetNumberOfDimensions(m_P);
|
||||
const mwSize Ndims_probe_upd = mxGPUGetNumberOfDimensions(m_dP);
|
||||
|
||||
if ((Npix[2] != Npos)) {
|
||||
mexErrMsgIdAndTxt(errId, "Number of probe indices has to match size of inputs (%i vs %i) \n", Npix[2], Npos);
|
||||
}
|
||||
if ((Npix_probe[2] != Npix[2]) && (Ndims_probe != 2)) {
|
||||
mexErrMsgIdAndTxt(errId, "Dimension of probe has to match size of inputs (%i vs %i) \n", Npix_probe[2], Npix[2]);
|
||||
}
|
||||
|
||||
|
||||
float lambda = mxGetScalar(prhs[5]);
|
||||
|
||||
|
||||
|
||||
const bool single_probe =Ndims_probe == 2 ;
|
||||
|
||||
|
||||
|
||||
cudaMemcpyToSymbol(gC_pind, p_P_ind, Npos*sizeof(uint8_T), 0, cudaMemcpyHostToDevice);
|
||||
checkLastError("after cudaMemcpyToSymbol pos");
|
||||
|
||||
// Choose a reasonably sized number of threads in each dimension for the block.
|
||||
int maxThreads = 1024; // number of threads per block, does not work with 1024, I dont know why
|
||||
int threads = 0, blocks = 0;
|
||||
|
||||
cuint n = Npix[0]*Npix[1];
|
||||
|
||||
threads = (n < maxThreads) ? nextPow2((n + 1)/ 2) : maxThreads;
|
||||
blocks = (n + (threads - 1)) / (threads );
|
||||
|
||||
|
||||
|
||||
dim3 dimBlock(threads, 1, 1);
|
||||
dim3 dimGrid(blocks, 1, 1);
|
||||
|
||||
// allocation size needed for shared GPU memory , it needs to reduce 2 float2 elements and 4 float elements
|
||||
int smemSize = 8* threads * sizeof(float);
|
||||
|
||||
//mexPrintf("threads %i blocks %i smemSize %i \n", threads, blocks, smemSize);
|
||||
|
||||
|
||||
// allocate output fields
|
||||
mwSize matrix_size[4] = {2,2,Npix[2],blocks};
|
||||
mxGPUArray * m_AA = mxGPUCreateGPUArray(
|
||||
4,
|
||||
matrix_size,
|
||||
mxSINGLE_CLASS,
|
||||
mxCOMPLEX,
|
||||
MX_GPU_DO_NOT_INITIALIZE); // MX_GPU_DO_NOT_INITIALIZE , MX_GPU_INITIALIZE_VALUES
|
||||
float2 * p_AA = (float2 *)mxGPUGetData(m_AA);
|
||||
|
||||
mwSize vector_size[4] = {2,1,Npix[2],blocks};
|
||||
mxGPUArray * m_Atb = mxGPUCreateGPUArray(
|
||||
4,
|
||||
vector_size,
|
||||
mxSINGLE_CLASS,
|
||||
mxREAL,
|
||||
MX_GPU_DO_NOT_INITIALIZE);
|
||||
float * p_Atb = (float *)mxGPUGetData(m_Atb);
|
||||
|
||||
|
||||
|
||||
checkLastError("after dimThread");
|
||||
switch (threads)
|
||||
{
|
||||
case 1024:
|
||||
get_optimal_LSQ_step_ker< 1024><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 512:
|
||||
get_optimal_LSQ_step_ker< 512><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 256:
|
||||
get_optimal_LSQ_step_ker< 256><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 128:
|
||||
get_optimal_LSQ_step_ker< 128><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 64:
|
||||
get_optimal_LSQ_step_ker< 64><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 32:
|
||||
get_optimal_LSQ_step_ker< 32><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 16:
|
||||
get_optimal_LSQ_step_ker< 16><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 8:
|
||||
get_optimal_LSQ_step_ker< 8><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 4:
|
||||
get_optimal_LSQ_step_ker< 4><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 2:
|
||||
get_optimal_LSQ_step_ker< 2><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
case 1:
|
||||
get_optimal_LSQ_step_ker< 1><<< dimGrid, dimBlock, smemSize>>>( p_P, p_O,p_dP, p_dO, p_chi, lambda,
|
||||
p_AA, p_Atb, Npix[0], Npix[1], Npix[2], blocks, single_probe);
|
||||
break;
|
||||
}
|
||||
|
||||
|
||||
checkLastError("after kernel");
|
||||
|
||||
|
||||
cudaThreadSynchronize();
|
||||
|
||||
|
||||
checkLastError("after kernel");
|
||||
|
||||
// Wrap the result up as a MATLAB gpuArray for return.
|
||||
plhs[0] = mxGPUCreateMxArrayOnGPU(m_AA);
|
||||
plhs[1] = mxGPUCreateMxArrayOnGPU(m_Atb);
|
||||
|
||||
|
||||
mxGPUDestroyGPUArray(m_P);
|
||||
mxGPUDestroyGPUArray(m_O);
|
||||
mxGPUDestroyGPUArray(m_dP);
|
||||
mxGPUDestroyGPUArray(m_dO);
|
||||
mxGPUDestroyGPUArray(m_chi);
|
||||
mxGPUDestroyGPUArray(m_AA);
|
||||
mxGPUDestroyGPUArray(m_Atb);
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,136 @@
|
||||
% REFINE_OBJECT_UPDATE calculate improved update direction
|
||||
% apply "overlap" constraint to get better estimate of the update direction
|
||||
%
|
||||
% [object_upd_sum,object_update_proj, cache] = ...
|
||||
% refine_object_update(self, object_update_proj,object_upd_sum,layer_ids,scan_ids,g_ind,par, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** object_update_proj [Nx, Ny, N] array, estimate of the object update for each scan position, ie conj(P)*chi
|
||||
% ** object_upd_sum cell of object sized arrays containg previous optimal updates
|
||||
% ** g_ind indices corresponding to the current group that is solved in parallel
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
% ** scan_ids determines to which scan correponds each of the position
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ object_upd_sum cell of object sized arrays containg updated optimal update
|
||||
% ++ object_update_proj [Nx, Ny, N] array, estimate of the refiend object update for each scan position,
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [object_upd_sum,object_update_proj, cache] = ...
|
||||
refine_object_update(self, object_update_proj,object_upd_sum,layer_ids,scan_ids,g_ind,par, cache)
|
||||
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
if par.share_object
|
||||
obj_ids = 1;
|
||||
else
|
||||
obj_ids = unique(scan_ids);
|
||||
end
|
||||
|
||||
if ~isinf(self.z_distance)
|
||||
% only in nearfield mode , apply shift in the opposite direction
|
||||
object_update_proj = apply_subpx_shift(object_update_proj .* cache.apodwin, self.modes{1}.sub_px_shift(g_ind,:) ) ./ cache.apodwin;
|
||||
end
|
||||
|
||||
|
||||
% calculate update direction
|
||||
% apply "overlap" constraint to get better estimate
|
||||
% of the update directin
|
||||
if is_method(par, 'MLs')
|
||||
for ll_tmp = obj_ids; object_upd_sum{ll_tmp,layer_ids}(:) = eps*1i; end
|
||||
end
|
||||
if par.delta_p == 0 % || par.Nlayers > 1 % layer_ids > 1
|
||||
%no preconditioner as in the original ML method
|
||||
object_upd_sum = set_views(object_upd_sum,object_update_proj,layer_ids,obj_ids, g_ind, cache, scan_ids);
|
||||
|
||||
%plotting.smart_figure(1231)
|
||||
%plotting.imagesc3D(object_upd_sum{1,layer_ids})
|
||||
%drawnow
|
||||
|
||||
object_update_proj = get_views(object_upd_sum,object_update_proj,layer_ids,obj_ids, g_ind, cache, scan_ids);
|
||||
elseif par.delta_p > 0
|
||||
% damped LSQ method (preconditioned update)
|
||||
object_upd_sum = set_views(object_upd_sum,object_update_proj,layer_ids,obj_ids, g_ind, cache, scan_ids);
|
||||
for ll_tmp = obj_ids
|
||||
object_upd_precond{ll_tmp,1} = Gfun(@object_sum_update_Gfun, object_upd_sum{ll_tmp,layer_ids}, cache.illum_sum_0{ll_tmp},cache.MAX_ILLUM(ll_tmp)*(par.delta_p));
|
||||
end
|
||||
object_update_proj = get_views(object_upd_precond,object_update_proj,1,obj_ids, g_ind, cache, scan_ids);
|
||||
if is_method(par, 'MLs')
|
||||
object_upd_sum(:,layer_ids) = object_upd_precond(obj_ids);
|
||||
end
|
||||
else
|
||||
error('Unimplemented option')
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
function object_upd_sum = object_sum_update_Gfun(object_upd_sum, obj_illum_sq_sum, max)
|
||||
% final update is just weighted mean of the updared object views
|
||||
object_upd_sum = object_upd_sum ./ sqrt(obj_illum_sq_sum.^2+ max.^2);
|
||||
end
|
||||
@@ -0,0 +1,139 @@
|
||||
% REFINE_PROBE_UPDATE calculate improved update direction
|
||||
% apply "overlap" constraint to get better estimate of the update direction
|
||||
% also updates the variable probe estimate
|
||||
%
|
||||
% [ self,m_probe_update, probe_update, cache] = ...
|
||||
% refine_probe_update(self, obj_proj, probe_update, chi,layer_ids,probe_id,p_ind,g_ind, par, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** obj_proj [Nx, Ny, N] array, estimate of the object update for each scan position, ie conj(P)*chi
|
||||
% ** probe_update cell of object sized arrays containg previous optimal updates
|
||||
% ** chi indices corresponding to the current group that is solved in parallel
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
% ** probe_id id of incoherent probe mode
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
% ** g_ind indices corresponding to the current group that is solved in parallel
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ object_upd_sum cell of object sized arrays containg updated optimal update
|
||||
% ++ object_update_proj [Nx, Ny, N] array, estimate of the refiend object update for each scan position,
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [ self,m_probe_update, probe_update, cache] = ...
|
||||
refine_probe_update(self, obj_proj, probe_update, chi,layer_ids,probe_id,p_ind,g_ind, par, cache)
|
||||
% get probe update direction
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.LSQML.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
if layer_ids > 1 % in case of multilayer object
|
||||
m_probe_update = [];
|
||||
return
|
||||
end
|
||||
|
||||
if (probe_id == 1 && par.apply_subpix_shift && isinf(self.z_distance(end))) || is_used(par,'fly_scan')
|
||||
probe_update = apply_subpx_shift(probe_update , -self.modes{min(end,probe_id)}.sub_px_shift(g_ind,:) );
|
||||
end
|
||||
if probe_id == 1
|
||||
probe_update = apply_subpx_shift_fft(probe_update, -self.modes{min(end,probe_id)}.probe_fourier_shift(g_ind,:));
|
||||
end
|
||||
|
||||
|
||||
if par.share_probe || length(unique(p_ind)) == 1
|
||||
% BETTER WAY: assume that sum(|obj_proj|^2,3) is close to 1
|
||||
% and additionally use weighting based on confidence given by illum_sum_0
|
||||
% => apriory weighting giving less importance to the less
|
||||
% illuminated regions
|
||||
%weight_proj = cache.illum_sum_0{1} ./ (cache.illum_sum_0{1}+0.01*cache.MAX_ILLUM(1));
|
||||
%weight_proj = get_views({weight_proj},[],1,1, g_ind, cache);
|
||||
%m_probe_update = mean( weight_proj.* probe_update,3);
|
||||
% or originally was used simple average , good for object >> probe
|
||||
m_probe_update = mean(probe_update,3); % calculate single update for all current positions
|
||||
else % unshared probe and multiple scans in one group (ie shared object)
|
||||
probe_ids = unique(p_ind);
|
||||
m_probe_update = Gzeros([self.Np_p,length(probe_ids)], true);
|
||||
for probe_id =probe_ids(:)'
|
||||
m_probe_update(:,:,probe_id) = mean(probe_update(:,:,p_ind == probe_id),3); % calculate one update for each scan
|
||||
end
|
||||
end
|
||||
|
||||
if (par.variable_probe || par.variable_intensity) && probe_id == 1
|
||||
% ORTHOGONAL PROBE RELAXATION (OPRP) EXTENSION - allow
|
||||
% variable probe wavefront
|
||||
% Odstrcil, M., et al. "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369.
|
||||
% iterate over all sub probes
|
||||
[self.probe{probe_id}, self.probe_evolution] = ...
|
||||
update_variable_probe(self, self.probe{probe_id}, self.probe_evolution, m_probe_update,probe_update, obj_proj, chi,cache.illum_sum_0{probe_id}, p_ind, g_ind, cache, par);
|
||||
end
|
||||
|
||||
% % apply probe constraints
|
||||
% if probe_id == 1 && (check_option(self,'probe_support') || check_option(self,'probe_support_fft'))
|
||||
% m_probe_update = apply_probe_contraints(m_probe_update, self.modes{probe_id});
|
||||
% end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,162 @@
|
||||
% UPDATE_OBJECT calculate improved update direction
|
||||
% apply "overlap" constraint to get better estimate of the update direction
|
||||
%
|
||||
% [object, object_upd_sum] = update_object(self, object, object_upd_sum, layer,object_ids, g_ind, scan_ids, par, cache, beta_object)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** object cell of object arrays
|
||||
% ** object_upd_sum cell of object sized arrays containg previous optimal updates
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
% ** object_ids id of incoherent object mode (not implemented)
|
||||
% ** g_ind indices corresponding to the current group that is solved in parallel
|
||||
% ** scan_ids determines to which scan correponds each of the position
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** beta_object (scalar) relaxation parameter of the update step
|
||||
%
|
||||
% returns:
|
||||
% ++ object cell of object arrays, after update
|
||||
% ++ object_upd_sum cell of object sized arrays containg updated optimal update
|
||||
%
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the foobject_idswing acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the foobject_idswing copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [object, object_upd_sum] = update_object(self, object, object_upd_sum, layer,object_ids, g_ind, scan_ids, par, cache, beta_object)
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
if par.share_object
|
||||
obj_ids = 1;
|
||||
else
|
||||
obj_ids = unique([scan_ids{:}]);
|
||||
end
|
||||
% take single optimal value, works well for most of samples
|
||||
% it is possible to use different weighting for each scan position but
|
||||
% it may become less stable in some cases -> robusness is preferred
|
||||
|
||||
% in case of the MLc method take minimum of the LSQ updates from all
|
||||
% subsets
|
||||
if is_method(par, 'MLc')
|
||||
% preconditioner should be applied on the total sum of all object_upd_sum
|
||||
if par.delta_p > 0 % && par.Nlayers == 1
|
||||
for kk = obj_ids
|
||||
object_upd_sum{kk,layer} = Gfun(@object_sum_update_Gfun, object_upd_sum{kk,layer}, cache.illum_sum_0{kk},cache.MAX_ILLUM(kk)*(par.delta_p));
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
% calculate optimal step, apply at least different step for each object (scan)
|
||||
for i = 1:length(g_ind)
|
||||
for kk = obj_ids
|
||||
ind = g_ind{i}(scan_ids{i} == kk);
|
||||
if isempty(ind)
|
||||
beta_object_avg(i,kk) = nan;
|
||||
else
|
||||
beta_object_avg(i,kk) = trimmean(beta_object(ind, layer), 10); %20240929 SK Edit
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
% take the most pesimistic estimate of the per object
|
||||
beta_object_avg=nanmin(beta_object_avg,[],1);
|
||||
|
||||
|
||||
% update each of the objects separately
|
||||
for kk = obj_ids
|
||||
if beta_object_avg(kk) > 0
|
||||
object_upd_sum{kk,layer} = object_upd_sum{kk,layer}*beta_object_avg(kk);
|
||||
object{kk,layer} = object{kk,layer}+object_upd_sum{kk,layer};
|
||||
end
|
||||
end
|
||||
|
||||
if verbose()> 3
|
||||
% show applied subsets (update amplitude) and probe update amplitude
|
||||
plotting.smart_figure(11)
|
||||
Nobj = size(object_upd_sum,1);
|
||||
for ll = 1:Nobj
|
||||
subplot(Nobj,2,1+Nobj*(ll-1))
|
||||
cla()
|
||||
o = object_upd_sum{ll,layer}(cache.object_ROI{:});
|
||||
o = min(abs(o), quantile(abs(o(:)), 0.999)) .* o ./ abs(o);
|
||||
plotting.imagesc3D(o);
|
||||
axis image xy off
|
||||
hold all
|
||||
fprintf('Object update norm: %g\n', norm2(object_upd_sum{ll,layer}(cache.object_ROI{:})))
|
||||
% try
|
||||
% for k = 1:length(g_ind)
|
||||
% for i = unique(scan_ids{k})
|
||||
% plot(self.probe_positions_0(g_ind{k}(scan_ids{k}==i),1)+self.Np_o(2)/2,self.probe_positions_0(g_ind{k}(scan_ids{k}==i),2)+self.Np_o(1)/2, '.')
|
||||
% end
|
||||
% end
|
||||
% end
|
||||
end
|
||||
title('Object update')
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
function object_upd_sum = object_sum_update_Gfun(object_upd_sum, obj_illum_sq_sum, max)
|
||||
% final update is just weighted mean of the updared object views
|
||||
object_upd_sum = object_upd_sum ./ sqrt(obj_illum_sq_sum.^2+ max.^2);
|
||||
end
|
||||
@@ -0,0 +1,125 @@
|
||||
% UPDATE_PROBE calculate improved update direction
|
||||
% apply "overlap" constraint to get better estimate of the update direction
|
||||
%
|
||||
% probe = update_probe(probe, m_probe_update, par, p_ind, g_ind, beta_probe, Nind)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** object_update_proj [Nx, Ny, N] array, estimate of the object update for each scan position, ie conj(P)*chi
|
||||
% ** object_upd_sum cell of object sized arrays containg previous optimal updates
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
% ** g_ind indices corresponding to the current group that is solved in parallel
|
||||
% ** beta_probe (scalar) relaxation parameter of the update step
|
||||
% ** Nind (int) number of groups that are solved serially
|
||||
|
||||
% returns:
|
||||
% ++ probe cell of the updated probes
|
||||
%
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function probe = update_probe(probe, m_probe_update, par, p_ind, g_ind, beta_probe, Nind)
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.verbose
|
||||
|
||||
%% update probe
|
||||
beta_probe = beta_probe(g_ind);
|
||||
probe_ids = unique(p_ind);
|
||||
if is_method(par, 'MLc')
|
||||
beta_probe = beta_probe / Nind; % in order to make the compact version closer to original ML method, the accumulated probe step per iteration should be 1
|
||||
end
|
||||
|
||||
if (par.share_probe || par.Nscans == 1) && size(probe,3)==1
|
||||
% most simple case, no multiprobe needed
|
||||
probe = probe + m_probe_update .* mean(beta_probe);
|
||||
elseif length(probe_ids) == 1
|
||||
% variable probe extension with shared probe
|
||||
probe(:,:,probe_ids,1) = probe(:,:,probe_ids,1) + m_probe_update .* mean(beta_probe);
|
||||
else % unshared probe
|
||||
% update each of the probes separately
|
||||
for id = probe_ids(:)'
|
||||
ind = p_ind == id;
|
||||
beta = mean(beta_probe(ind));
|
||||
probe(:,:,id,1) = Gfun(@upd_probe_Gfun, probe(:,:,id,1),m_probe_update(:,:,min(end,id)), beta);
|
||||
end
|
||||
end
|
||||
|
||||
if verbose()> 3
|
||||
% show applied subsets (update amplitude) and probe update
|
||||
% amplitude
|
||||
plotting.smart_figure(11)
|
||||
probe_modes = size(m_probe_update,3);
|
||||
for ll = 1:probe_modes
|
||||
subplot(probe_modes,2,2+probe_modes*(ll-1))
|
||||
p = fftshift(fft2(fftshift(m_probe_update(:,:,ll))));
|
||||
p = min(abs(p), quantile(abs(p(:)), 0.999)) .* p ./ abs(p);
|
||||
plotting.imagesc3D(p);
|
||||
axis off image xy
|
||||
end
|
||||
title('Probe update')
|
||||
colormap bone
|
||||
drawnow
|
||||
end
|
||||
end
|
||||
|
||||
function probe = upd_probe_Gfun(probe,probe_update, alpha_p)
|
||||
probe = probe + alpha_p.*probe_update;
|
||||
end
|
||||
@@ -0,0 +1,224 @@
|
||||
% UPDATE_VARIABLE_PROBE approximation of the OPRP method to get only the first orthogonal
|
||||
% vector describing the probe
|
||||
%
|
||||
% [probe, probe_evolution] = ...
|
||||
% update_variable_probe(self,probe, probe_evolution, m_probe_update,probe_update, obj_proj, chi, weights, p_ind, g_ind, cache, par)
|
||||
%
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** probe [Nx,Nx,probe_modes,variable_modes] variable probe modes
|
||||
% ** probe_evolution [Npos,variable_modes] array containing evolution of the varaible modes for each position
|
||||
% ** m_probe_update precalculated value of mean(dP,3)
|
||||
% ** probe_update probe update, ie conj(O)*chi
|
||||
% ** obj_proj [Nx,Ny,N] array, views of the object for each scan position
|
||||
% ** chi [Nx,Ny,N] array, difference between original and updated exit-wave
|
||||
% ** weights array of relaxation values for object pixel, reduce weight of regions with weak illumination in the variable probe calculation
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
% ** g_ind indices corresponding to the current group that is solved in parallel
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** par structure containing parameters for the engines
|
||||
%
|
||||
% returns:
|
||||
% ++ probe [Nx,Nx,probe_modes,variable_modes] updated variable modes
|
||||
% ++ probe_evolution [Npos,variable_modes] updated array containing evolution of the varaible modes for each position
|
||||
%
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [probe, probe_evolution] = ...
|
||||
update_variable_probe(self,probe, probe_evolution, m_probe_update,probe_update, obj_proj, chi, weights, p_ind, g_ind, cache, par)
|
||||
|
||||
import math.*
|
||||
import plotting.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
|
||||
uids = unique(p_ind);
|
||||
for kk = uids
|
||||
if length(uids) == 1 % single or shared probe between the scans
|
||||
% avoid memory copy is possible
|
||||
probe_update_tmp = probe_update;
|
||||
chi_tmp = chi;
|
||||
obj_proj_tmp = obj_proj;
|
||||
g_ind_tmp = g_ind;
|
||||
block_size = length(g_ind);
|
||||
else
|
||||
% otherwise
|
||||
block_ind = p_ind == kk;
|
||||
probe_update_tmp = probe_update(:,:,block_ind);
|
||||
obj_proj_tmp = obj_proj(:,:,block_ind);
|
||||
chi_tmp = chi(:,:,block_ind);
|
||||
g_ind_tmp = g_ind(block_ind);
|
||||
block_size= sum(block_ind);
|
||||
end
|
||||
|
||||
|
||||
if par.variable_probe
|
||||
% use some relaxation to avoid too faster changes
|
||||
relax_U = min(0.1,block_size/self.Npos);
|
||||
relax_V = 1;
|
||||
% make probe_update_tmp orthogonal to the average update
|
||||
probe_update_tmp = probe_update_tmp - m_probe_update(:,:,min(end,kk));
|
||||
|
||||
for ii = 1:par.variable_probe_modes
|
||||
var_probe = probe(:,:,kk,1+ii);
|
||||
probe_evol = probe_evolution(g_ind_tmp,1+ii); % evolution of the 1th SVD mode coeficient
|
||||
|
||||
[var_probe,probe_evol,probe_update_tmp] = get_first_SVD_mode(probe_update_tmp, var_probe, probe_evol,relax_U,relax_V, obj_proj_tmp, chi_tmp);
|
||||
if ii < par.variable_probe_modes
|
||||
% subtract projection of the updated var_probe from the
|
||||
% probe_update_tmp to enforce orthogonality between the
|
||||
% modes
|
||||
projection = sum2(probe_update_tmp .* conj(var_probe)) ./ sum2(abs(var_probe).^2);
|
||||
probe_update_tmp = probe_update_tmp - projection .* var_probe;
|
||||
end
|
||||
% return the updated vector to the probe array
|
||||
probe(:,:,kk,1+ii) = var_probe;
|
||||
probe_evolution(g_ind_tmp,1+ii) = probe_evol;
|
||||
end
|
||||
|
||||
end
|
||||
if par. variable_intensity
|
||||
% correction to account for variable intensity
|
||||
mean_probe = probe(:,:,kk,1);
|
||||
% compare P*0 and chi to estimate best update of the intensity
|
||||
[nom, denom] = Gfun(@get_coefs_intensity,chi_tmp, mean_probe, obj_proj_tmp);
|
||||
|
||||
probe_evolution(g_ind_tmp,1) = probe_evolution(g_ind_tmp,1) + 0.1* squeeze(Ggather(sum2(nom)./ sum2(denom)));
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if any(g_ind==1) && utils.verbose() > 3
|
||||
self.probe{1} = probe;
|
||||
self.probe_evolution = probe_evolution;
|
||||
plot_variable_probe(self, par)
|
||||
drawnow
|
||||
end
|
||||
end
|
||||
|
||||
function [var_probe,probe_evol, probe_update] = get_first_SVD_mode(probe_update, var_probe, probe_evol, relax_U,relax_V, obj_proj, chi)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import plotting.*
|
||||
|
||||
|
||||
|
||||
% get a weighting function => avoid effect of too strong noise
|
||||
% around edges of the reconstructed region => improve robustness againts outliers
|
||||
% weights = weights / max2(weights);
|
||||
% weight_proj = get_views( weights, Gzeros(size(chi)),1,1, g_ind, cache);
|
||||
weight_proj = 1;
|
||||
|
||||
%% calculate terms needed to calculate update of the variable probe
|
||||
% => U term in SVD decomposition
|
||||
[resid, proj, probe_update] = Gfun(@get_SVD_update,probe_update, weight_proj, var_probe, reshape(probe_evol,1,1,[]), norm(probe_evol));
|
||||
% get update the variable probe
|
||||
var_probe_upd = mean( resid .* mean2(proj), 3);
|
||||
% apply update, prevent too large changes at the beginning of the covergence
|
||||
var_probe = var_probe + relax_U*var_probe_upd / norm2(var_probe_upd);
|
||||
|
||||
%% equivalent but much slower code
|
||||
%[U,S,V] = svd(reshape(weight_proj.*(probe_update - m_probe_update), prod(self.Np_p),[]), 0);
|
||||
%var_probe = var_probe + relax_U*reshape(U(:,1), self.Np_p);
|
||||
|
||||
% keep the eigenprobe normalized
|
||||
var_probe = var_probe ./ norm2(var_probe);
|
||||
|
||||
%% calculate optimal OPRP evolution coeficients
|
||||
[num, denum] = Gfun(@get_SVD_evol,var_probe, obj_proj, chi);
|
||||
num =Ggather(mean2(num));
|
||||
denum = Ggather(mean2(denum));
|
||||
% perform relaxed update => improve robustness againts outliers
|
||||
probe_evol_upd = squeeze(num ./ (denum + 0.1*mean(denum,3))); % caclulate regularized update
|
||||
% add to the coefficients that are already used in the currently
|
||||
% used probe{1} variable
|
||||
|
||||
probe_evol = probe_evol + relax_V*probe_evol_upd;
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
%% GPU kernel merging
|
||||
|
||||
% SVD approximation => calculation of U
|
||||
function [resid, proj, probe_update] = get_SVD_update(probe_update, weight_proj, var_probe, probe_evol, probe_evol_norm)
|
||||
resid = weight_proj .* probe_update;
|
||||
proj = (real(conj(resid) .* var_probe)+ probe_evol) / probe_evol_norm^2;
|
||||
end
|
||||
|
||||
% SVD approximation => calculation of S*V
|
||||
function [num, denum] = get_SVD_evol(var_probe, obj_proj, chi)
|
||||
psi = var_probe .* obj_proj;
|
||||
denum = abs( psi ).^2;
|
||||
num = real(chi .* conj(psi));
|
||||
end
|
||||
|
||||
function [nom1, denom1] = get_coefs_intensity(xi, P, O)
|
||||
OP = O.*P;
|
||||
nom1 = real(conj(OP) .* xi);
|
||||
denom1 = abs(OP).^2;
|
||||
end
|
||||
|
||||
|
||||
@@ -0,0 +1,123 @@
|
||||
% APPLY_SVD_FILTER The core of the variable probe (OPRP) code:
|
||||
% find SVD decomposition and limit the probe into several orthogonal
|
||||
% modes
|
||||
% additional prior knowledge can be also included
|
||||
%
|
||||
% [probe, probe_evolution] = apply_SVD_filter(probe, Nmodes, mode)
|
||||
%
|
||||
% ** probe [Nx,Ny,N] variable probe for each position
|
||||
% ** Nmodes (int) number of variable modes
|
||||
% ** mode structure containing parameters for selected probe mode
|
||||
% returns
|
||||
% ++ probe [Nx,Ny,variable_modes] variable probe modes
|
||||
% ++ probe_evolution [Npos,variable_modes] updated array containing evolution of the varaible modes for each position
|
||||
%
|
||||
% see also: engines.GPU_MS.PIE
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [probe, probe_evolution] = apply_SVD_filter(probe, Nmodes, mode)
|
||||
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
|
||||
Np = size(probe);
|
||||
|
||||
[U,S,V] = fsvd(reshape((probe),[],Np(3)) ,Nmodes);
|
||||
% if any(diag(S.^2)/sum(diag(S.^2)) < 1e-3) % 2e-3 is the weakest that FSVD can recover
|
||||
% try
|
||||
% warning('Running full SVD (maybe use less OPR modes) (weak modes %i/%i) ', Ggather(sum(diag(S.^2)/sum(diag(S.^2)) < 2e-3)), Nmodes)
|
||||
% [U,S,V] = svd(reshape((probe),[],Np(3)) ,0);
|
||||
% U = single(U(:,1:Nmodes));
|
||||
% S = single(S(1:Nmodes,1:Nmodes));
|
||||
% V = single(V(:,1:Nmodes));
|
||||
% catch
|
||||
% keyboard
|
||||
% end
|
||||
% end
|
||||
|
||||
U = reshape(U, Np(1),Np(2),1,[]);
|
||||
U = apply_probe_contraints(U, mode);
|
||||
|
||||
|
||||
V(:,1) = mean(V(:,1)) + 0.99*(V(:,1) - mean(V(:,1)));
|
||||
V(:,2:end) = mean(V(:,2:end)) + 0.99*(V(:,2:end) - mean(V(:,2:end)));
|
||||
|
||||
%% remove outliers
|
||||
aV = abs(V);
|
||||
MAX = quantile(aV,0.99);
|
||||
V = min(aV, MAX) .* (V ./ (aV+1e-3));
|
||||
|
||||
probe_evolution = (S*V').';
|
||||
probe = U;
|
||||
|
||||
|
||||
avg = mean(abs(probe_evolution(:,1)),1);
|
||||
|
||||
probe = probe*avg;
|
||||
probe_evolution = probe_evolution / avg;
|
||||
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,329 @@
|
||||
% FOURIER_RING_CORRELATION simplified but faster version of the FRC code
|
||||
%
|
||||
% [score, object] = fourier_ring_correlation(object_1, object_2, varargin)
|
||||
%
|
||||
% ** object_1 array reconstructed object
|
||||
% ** object_2 array reconstructed object from an independend scan
|
||||
% ** varargin see code for more details
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [score, object] = fourier_ring_correlation(object_1, object_2, varargin)
|
||||
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import plotting.*
|
||||
|
||||
par = inputParser;
|
||||
par.addParameter('px_scale', 1 , @isnumeric )
|
||||
par.addParameter('auto_crop', false, @islogical )
|
||||
par.addParameter('plot_results', true , @islogical ) % use white background
|
||||
par.addParameter('smoothing', 0 , @isnumeric ) % smooth over N pixels
|
||||
par.addParameter('Nrings', 20 , @isnumeric ) % smooth over N pixels
|
||||
par.addParameter('crop', 0 , @isnumeric ) % crop image by N pixels
|
||||
par.addParameter('flip_horizontal', false , @islogical ) % flip second image horizontally
|
||||
par.addParameter('fft_phase_removal_guess', false , @islogical ) % flip second image horizontally
|
||||
par.addParameter('weights', {} , @iscell ) % cell array of weights
|
||||
par.addParameter('find_shift', true, @islogical ) % cell array of weights
|
||||
|
||||
par.parse(varargin{:})
|
||||
r = par.Results;
|
||||
|
||||
if r.flip_horizontal
|
||||
object_2 = fliplr(object_2);
|
||||
end
|
||||
|
||||
Npix = min(size(object_1), size(object_2));
|
||||
|
||||
object = {object_1, object_2};
|
||||
|
||||
if r.crop > 0
|
||||
for ii = 1:2
|
||||
object{ii} = crop_pad(object{ii}, Npix-r.crop);
|
||||
end
|
||||
if ~isempty(r.weights)
|
||||
for ii = 1:2
|
||||
r.weights{ii} = crop_pad(r.weights{ii}, Npix-r.crop);
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
Npix = min(size(object{1}), size(object{2}));
|
||||
|
||||
for ii = 1:2
|
||||
object{ii} = object{ii} / mean(abs(object{1}(:)) );
|
||||
|
||||
W{ii} = tukeywin(Npix(1), 0.2) .* tukeywin(Npix(2),0.2)';
|
||||
if ~isempty(r.weights)
|
||||
W{ii} = W{ii} .* single(r.weights{ii});
|
||||
end
|
||||
end
|
||||
|
||||
score.shift = [0,0];
|
||||
|
||||
|
||||
if r.find_shift
|
||||
for kk = 1:4
|
||||
Npix = size(object{1});
|
||||
[X,Y] = meshgrid(-Npix(2)/2+1:Npix(2)/2,-Npix(1)/2+1:Npix(1)/2);
|
||||
object{1} = utils.stabilize_phase(object{1}, object{2}, 'fourier_guess', r.fft_phase_removal_guess);
|
||||
|
||||
for ii = 1:2
|
||||
phasor{ii} = object{ii} ./ (abs(object{ii}) + 1e-3*mean(abs(object{ii}(:))));
|
||||
fobject{ii} = fft2(single(W{ii}.*(phasor{ii}-mean(phasor{ii}(:)))));
|
||||
end
|
||||
|
||||
|
||||
% high pass filter
|
||||
Wf = Garray(fftshift(exp(- 1./ ((X.^2+Y.^2)/(Npix(1)/50)^2))));
|
||||
|
||||
[output] = utils.dftregistration( Wf.* fobject{1}, Wf.* fobject{2},100);
|
||||
object{2} = imshift_fft(object{2}, output(4), output(3));
|
||||
|
||||
|
||||
ROI = { (1+max(0,ceil(output(3)))):(Npix(1)+min(0, floor(output(3)))) , ...
|
||||
(1+max(0,ceil(output(4)))):(Npix(2)+min(0, floor(output(4))))};
|
||||
|
||||
object{1} = object{1}(ROI{:});
|
||||
object{2} = object{2}(ROI{:});
|
||||
for j = 1:2
|
||||
W{j} = W{j}(ROI{:});
|
||||
end
|
||||
|
||||
verbose(3,'Image shifted by %g %g px', output([4,3]))
|
||||
score.shift = score.shift + Ggather([output(4), output(3)]);
|
||||
|
||||
% subplot(1,2,1)
|
||||
% plotting.imagesc3D(object{1}); axis off image
|
||||
% subplot(1,2,2)
|
||||
% plotting.imagesc3D(object{2}); axis off image
|
||||
% drawnow
|
||||
|
||||
if all(abs(output(3:4)) < 0.5)
|
||||
break
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
Npix = size(object{1});
|
||||
|
||||
[object{1}] = utils.stabilize_phase(object{1}, object{2}, abs(object{2}), 'binning', 4 , 'fourier_guess', r.fft_phase_removal_guess);
|
||||
|
||||
if r.flip_horizontal
|
||||
score.shift(1) = -score.shift(1);
|
||||
end
|
||||
|
||||
for ii = 1:2
|
||||
object{ii} = object{ii} ./ mean(abs(object{ii}(:)));
|
||||
end
|
||||
|
||||
W = sqrt(W{1} .* W{2});
|
||||
ROI_compare = get_ROI(W>0.1*max(W(:))); % compare only the reliable ROIs
|
||||
|
||||
W = tukeywin(length(ROI_compare{1}),0.2) .* tukeywin(length(ROI_compare{2}),0.2)';
|
||||
|
||||
for ii = 1:2
|
||||
fobject{ii} = fft2(W.*object{ii}(ROI_compare{:}));
|
||||
end
|
||||
|
||||
|
||||
|
||||
for ii = 1:2
|
||||
fobject{ii} = fftshift(fobject{ii});
|
||||
fobject_norm{ii} = abs(fobject{ii}).^2;
|
||||
end
|
||||
fcorr = fobject{1} .* conj(fobject{2});
|
||||
|
||||
binning = ceil(Npix/2 / r.Nrings);
|
||||
fcorr = conv2(fcorr, ones(binning) / prod(binning), 'same');
|
||||
fcorr = fcorr(1:binning(1):end, 1:binning(2):end);
|
||||
for ii = 1:2
|
||||
fobject_norm{ii} = conv2(fobject_norm{ii}, ones(binning) / prod(binning), 'same');
|
||||
fobject_norm{ii} = fobject_norm{ii}(1:binning(1):end, 1:binning(2):end);
|
||||
end
|
||||
|
||||
Npix= size(fcorr);
|
||||
|
||||
|
||||
x = single(-Npix(2)/2+0.5:Npix(2)/2-0.5)/(Npix(2)/2);
|
||||
y = single(-Npix(1)/2+0.5:Npix(1)/2-0.5)/(Npix(1)/2);
|
||||
if length(r.px_scale) > 1 && r.px_scale(1) > r.px_scale(2)
|
||||
y = y .* r.px_scale(2) / r.px_scale(1);
|
||||
elseif length(r.px_scale) > 1 && r.px_scale(1) < r.px_scale(2)
|
||||
x = x .* r.px_scale(1) / r.px_scale(2);
|
||||
end
|
||||
[X,Y] = meshgrid(x, y);
|
||||
|
||||
|
||||
R_mat = sqrt(X.^2 + Y.^2);
|
||||
|
||||
Rmax = 0.98;
|
||||
R0 = 0.01;
|
||||
R_all = linspace(R0, Rmax, min(r.Nrings, min(Npix)));
|
||||
|
||||
for ii = 1:(length(R_all)-1)
|
||||
R = R_all(ii);
|
||||
|
||||
ring = find((R_mat > R_all(ii)) & (R_mat < R_all(ii+1)));
|
||||
|
||||
fcorr_values{1}(ii) = abs(sum(fcorr(ring)) ./ sqrt(sum(fobject_norm{1}(ring)) .* sum(fobject_norm{2}(ring))));
|
||||
|
||||
n_values(ii) = length(ring); % sum(ring(:));
|
||||
|
||||
end
|
||||
|
||||
spatial_freq = R_all(1:end-1);
|
||||
|
||||
n_values = n_values .* prod(binning);
|
||||
% 1-bit curve
|
||||
T = (0.5+2.41./sqrt(n_values)) ./ (1.5+1.41./sqrt(n_values));
|
||||
% 1/2 bit curve
|
||||
% T = (0.21+1.91 ./sqrt(n_values)) ./ (1.21+0.91./sqrt(n_values));
|
||||
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
fcorr_values{1} = Ggather(fcorr_values{1});
|
||||
|
||||
AUC = nanmean(fcorr_values{1}); % area undear curve criterion
|
||||
score.AUC = AUC;
|
||||
score.thresh = T;
|
||||
score.FRC = fcorr_values{1};
|
||||
|
||||
|
||||
score.spatial_freq = spatial_freq;
|
||||
score.SSNR = 2 * score.FRC ./ (1-score.FRC);
|
||||
|
||||
score.SNR_avg = nansum(score.SSNR .* spatial_freq) / sum(spatial_freq);
|
||||
|
||||
|
||||
Ts = smooth(T);
|
||||
if r.smoothing > 0
|
||||
score.FRC = imgaussfilt(score.FRC,r.smoothing);
|
||||
end
|
||||
[x0,y0,iout,jout] = intersections(spatial_freq,score.FRC,spatial_freq, Ts,false);
|
||||
|
||||
if all(score.FRC >= Ts')
|
||||
score.resolution = 1;
|
||||
elseif all(score.FRC <= Ts')
|
||||
score.resolution = 0;
|
||||
elseif any(x0 > 0.1)
|
||||
score.resolution = min(x0(x0 > 0.1));
|
||||
else
|
||||
score.resolution = min(x0);
|
||||
end
|
||||
|
||||
|
||||
|
||||
if r.plot_results
|
||||
subplot(1,2,1)
|
||||
hold all
|
||||
b = plot(spatial_freq,score.FRC+randn*0.1,'LineWidth', 2);
|
||||
h = plot(spatial_freq, Ts, 'k--', 'LineWidth', 2);
|
||||
plot(x0, y0, 'o')
|
||||
xlabel('Spatial frequency / Nyquist')
|
||||
% ylabel('FRC')
|
||||
ylabel(sprintf('Fourier ring correlation, AUC=%3.3g', AUC))
|
||||
hold off
|
||||
ylim([0,1])
|
||||
xlim([0,1])
|
||||
% r = vline(resolution, '-k');
|
||||
legend([b, h], 'FRC', '1 bit threshold','Location','Best');
|
||||
grid on
|
||||
|
||||
subplot(1,2,2)
|
||||
hold all
|
||||
plot(score.spatial_freq, score.SSNR);
|
||||
try; vline(score.resolution); end
|
||||
hline(1)
|
||||
set(gca, 'yscale', 'log')
|
||||
hold off
|
||||
grid on
|
||||
ylabel(sprintf('Spectral SNR, SNR_{avg}=%3.3g', score.SNR_avg))
|
||||
|
||||
|
||||
% width = 10;
|
||||
% aspect_ratio=4/3;
|
||||
% height = width / aspect_ratio;
|
||||
% % set size of the resulting image
|
||||
% set(gcf, 'PaperPosition', [1.5 1.5 width height]);
|
||||
plotting.suptitle(sprintf('Resolution=%.3gnm AuC=%.3g', min(r.px_scale) / score.resolution * 1e9,AUC))
|
||||
|
||||
end
|
||||
|
||||
|
||||
verbose(3,'AUC %g', score.AUC)
|
||||
verbose(3,'SNR %g', score.SNR_avg)
|
||||
verbose(3,'resolution %g (%g nm)', score.resolution, min(r.px_scale) / score.resolution*1e9)
|
||||
|
||||
try
|
||||
verbose('SSNR 0.1 %g 0.5 %g, 0.9 %g \n', log10(quantile(score.SSNR, [0.1, 0.5, 0.9] )))
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,213 @@
|
||||
% ONLINE_FSC_ESTIMATE online estimation of the fourier shell correlation curve to estimation of optimal convergence
|
||||
% compare two scans and estimate FSC and other statistics
|
||||
%
|
||||
% score = online_FSC_estimate(self, par, cache, score_0, iter)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** score_0 [] or a structure with outputs from previous online estimation of FSC curve
|
||||
%
|
||||
% returns:
|
||||
% ++ score structure with outputs from online estimation of FSC curve
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function score = online_FSC_estimate(self, par, cache, score_0, iter)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import plotting.*
|
||||
import engines.GPU_MS.*
|
||||
|
||||
if check_option(self, 'object_orig')
|
||||
self.object{end+1,1} = cat(3,self.object_orig{1,:});
|
||||
end
|
||||
|
||||
compared_indices = (2:size(self.object,1))-1;
|
||||
|
||||
% take product of the reconstructed images, eDOF
|
||||
%% refererene image
|
||||
selected_ROI = cache.object_ROI;
|
||||
selected_ROI{2} = selected_ROI{2}(ceil(end/10):floor(end*9/10));
|
||||
obj{1} = cat(3, self.object{1,:});
|
||||
obj{1} = Garray(obj{1});
|
||||
|
||||
for ll = compared_indices
|
||||
%% compared image
|
||||
% take product of the reconstructed images, eDOF
|
||||
obj_compared = cat(3,self.object{ll+1,:});
|
||||
if ~isempty(score_0) && ~isempty(score_0{ll})
|
||||
obj_compared = imshift_fft(obj_compared, score_0{ll}.shift);
|
||||
end
|
||||
obj{2} = Garray(obj_compared);
|
||||
|
||||
%% get at least some empirical esitmation of reliability -> for selection of compared ROI
|
||||
for kk = 1:2
|
||||
ind = [1,min(ll+1, length(cache.illum_sum_0))];
|
||||
W{kk} = cache.illum_sum_0{ind(kk)}(selected_ROI{:});
|
||||
W{kk} = W{kk} > 0.5*mean(W{kk});
|
||||
% W{kk} = imfill(W{kk}, 'holes');
|
||||
if any(W{kk}(:)==0)
|
||||
Npix = size(W{kk});
|
||||
downscale = 10;
|
||||
W{kk} = real(utils.interpolateFT(W{kk}, ceil(Npix / downscale)));
|
||||
try; W{kk} = Garray(imerode( Ggather(W{kk})>0.1, strel('disk', ceil(self.Np_p(1)/8/downscale)))); end
|
||||
W{kk} = (utils.imgaussfilt3_conv(W{kk}, mean(self.Np_p)/8/downscale));
|
||||
W{kk} = max(0,real(utils.interpolateFT(W{kk},Npix)));
|
||||
end
|
||||
end
|
||||
clear obj_0
|
||||
Wshared = sqrt(W{1}.*W{2});
|
||||
for kk = 1:2
|
||||
W{kk} = Wshared;
|
||||
end
|
||||
|
||||
if size(obj{1},3) > 1 ||size(obj{2},3) > 1
|
||||
Nl_shifts = 4;
|
||||
else
|
||||
Nl_shifts = 1;
|
||||
end
|
||||
|
||||
for kk = 1:Nl_shifts
|
||||
|
||||
for ii = 1:2
|
||||
Nlayers = size(obj{ii},3);
|
||||
horiz_shifts = linspace(-(kk-1), (kk-1), Nlayers)';
|
||||
shift = [horiz_shifts, zeros(Nlayers,1)];
|
||||
if kk > 1 && ii == 1
|
||||
shift = shift - score{ll,kk-1}.shift;
|
||||
end
|
||||
% apply different shift on each layer -> minic rotation
|
||||
obj_tmp{ii} = prod(imshift_fft(obj{ii}, shift),3);
|
||||
obj_tmp{ii} = obj_tmp{ii}(selected_ROI{:});
|
||||
end
|
||||
|
||||
[score{ll,kk},obj_out] = analysis.fourier_ring_correlation(obj_tmp{:},...
|
||||
'smoothing', 1, 'crop', ceil(self.Np_p / 4) , 'plot_results', false, 'px_scale', self.pixel_size, 'weights', W);
|
||||
|
||||
|
||||
if ~isempty(score_0) && ~isempty(score_0{ll})
|
||||
score{ll,kk}.shift = score{ll,kk}.shift + score_0{ll}.shift ;
|
||||
end
|
||||
|
||||
if ll == compared_indices(end) && verbose > 2
|
||||
plotting.smart_figure(2121)
|
||||
img = angle(cat(3,obj_out{:}));
|
||||
plotting.imagesc3D(img); axis off image xy ;
|
||||
caxis(Ggather(math.sp_quantile(img, [0.01, 0.99],10)))
|
||||
title('Aligned frames used for FSC estimation')
|
||||
drawnow
|
||||
end
|
||||
|
||||
% fprintf('========== total object shift ====== %g %g\n', score{end}.shift)
|
||||
score{ll,kk}.iter = iter;
|
||||
score{ll,kk}.positions = self.modes{1}.probe_positions;
|
||||
score{ll,kk}.positions_0 = self.modes{1}.probe_positions_0;
|
||||
%score{ll,kk}.intensity = self.modes{1}.weights;
|
||||
score{ll,kk}.probe_fourier_shift = self.modes{1}.probe_fourier_shift;
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
plotting.smart_figure(4554)
|
||||
clf
|
||||
subplot(1,2,1)
|
||||
linestyle = {'-','--',':'};
|
||||
hold all
|
||||
for kk = 1:Nl_shifts
|
||||
for ll = compared_indices
|
||||
if isempty(score{ll,kk}); continue; end
|
||||
b(ll) = plot(score{ll,kk}.spatial_freq,score{ll,kk}.FRC,linestyle{1+mod(ll-1,end)},'LineWidth', 2);
|
||||
legend_names{ll} = sprintf('FRC scans 1 vs %i', ll+1);
|
||||
end
|
||||
h = plot(score{ll,1}.spatial_freq, score{ll,1}.thresh, 'k--', 'LineWidth', 2);
|
||||
end
|
||||
xlabel('Spatial frequency / Nyquist')
|
||||
ylabel(sprintf('Fourier ring correlation, AUC=%3.3g', score{ll,1}.AUC))
|
||||
hold off
|
||||
ylim([0,1])
|
||||
xlim([0,1])
|
||||
|
||||
legend([b, h], legend_names{:}, '1 bit threshold','Location','Best');
|
||||
grid on
|
||||
|
||||
|
||||
subplot(1,2,2)
|
||||
hold all
|
||||
for kk = 1:Nl_shifts
|
||||
for ll = compared_indices
|
||||
if isempty(score{ll,kk}); continue; end
|
||||
score{ll,kk}.SSNR(~isfinite(score{ll}.SSNR) | score{ll,kk}.SSNR <= 0) = nan;
|
||||
plot(score{ll,kk}.spatial_freq, score{ll,kk}.SSNR);
|
||||
end
|
||||
end
|
||||
hline(1)
|
||||
set(gca, 'yscale', 'log')
|
||||
hold off
|
||||
grid on
|
||||
ylabel(sprintf('Spectral SNR, SNR_{avg}=%3.3g', score{ll,1}.SNR_avg))
|
||||
plotting.suptitle(sprintf('Resolution %3.3gnm', mean(self.pixel_size) / score{ll,1}.resolution * 1e9))
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,77 @@
|
||||
% PLOT_BACKGROUND_INTENSITY plot estiamtion of background for each of the scan positions
|
||||
%
|
||||
% plot_background_intensity(self,probe, background)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** probe structure containing parameters for the engines
|
||||
% ** probe [Nx,Ny,variable_modes] complex array with probe
|
||||
% ** background [Npos,1] array with background intensity
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_background_intensity(self,probe, background)
|
||||
plotting.smart_figure(11231)
|
||||
subplot(1,2,1)
|
||||
show_spatial_distribution(self.probe_positions_0, background, false, false)
|
||||
axis off image
|
||||
colorbar
|
||||
title('Background distribution')
|
||||
subplot(1,2,2)
|
||||
imagesc(abs(probe))
|
||||
axis off image
|
||||
end
|
||||
@@ -0,0 +1,97 @@
|
||||
% PLOT_FRC_ANALYSIS plot evolution of the resolution and SNR estimated from the FRC
|
||||
%
|
||||
% plot_frc_analysis(score, par)
|
||||
%
|
||||
% ** score structure with outputs from online estimation of FSC curve
|
||||
% ** par structure containing parameters for the engines
|
||||
%
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_frc_analysis(score, par)
|
||||
N = size(score,1)-1;
|
||||
resolution = nan(N,1);
|
||||
for i = 1:N
|
||||
iteration(i) = score{i+1,1}.iter;
|
||||
try; resolution(i) = score{i+1,1}.resolution; end
|
||||
SNR(i) = score{i+1,1}.SNR_avg;
|
||||
AUC(i) = score{i+1,1}.AUC;
|
||||
end
|
||||
plotting.smart_figure(123132)
|
||||
subplot(1,3,1)
|
||||
semilogx(iteration, medfilt1(resolution, 'truncate'))
|
||||
xlim([1, par.number_iterations])
|
||||
xlabel('Iteration')
|
||||
ylabel('Spatial frequency/Nyquist')
|
||||
title('FRC resolution')
|
||||
grid on
|
||||
subplot(1,3,2)
|
||||
semilogx(iteration, medfilt1(SNR, 'truncate' ))
|
||||
xlim([1, par.number_iterations])
|
||||
xlabel('Iteration')
|
||||
ylabel('SNR')
|
||||
title('Average signal to noise ratio')
|
||||
grid on
|
||||
subplot(1,3,3)
|
||||
semilogx(iteration, medfilt1(AUC, 'truncate' ))
|
||||
xlim([1, par.number_iterations])
|
||||
xlabel('Iteration')
|
||||
ylabel('AUC')
|
||||
title('Area under FRC curve')
|
||||
grid on
|
||||
plotting.suptitle('Fourier ring resolution analysis')
|
||||
end
|
||||
@@ -0,0 +1,292 @@
|
||||
% PLOT_GEOM_CORRECTIONS plot position refinement statistics - position errors, directions and weights
|
||||
%
|
||||
% plot_geom_corrections(self, mode, object, iter, par, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** mode structure containing reconstruction parameters related to the selected incoherent mode
|
||||
% ** object cell of arrays, reconstructed object
|
||||
% ** iter current iteration number
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
|
||||
% FUNCTION plot_geom_corrections(self, mode, object, iter, par, cache)
|
||||
% plot positiones updates
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_geom_corrections(self, mode, object, iter, par, cache)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import plotting.*
|
||||
import utils.*
|
||||
|
||||
pos = mode.probe_positions;
|
||||
pos_0 = self.probe_positions_0;
|
||||
|
||||
|
||||
Nplots = 4*(iter >= par.probe_position_search && ~isempty(par.probe_geometry_model)) ...
|
||||
+ (iter >= par.estimate_NF_distance) + ...
|
||||
(iter >= par.detector_rotation_search) + ...
|
||||
(iter >= par.detector_scale_search);
|
||||
|
||||
|
||||
if ~ishandle(16165)
|
||||
plotting.smart_figure(16165)
|
||||
set(gcf,'Outerposition',[100 100 Nplots*330 400]) %[left, bottom, width, height
|
||||
else
|
||||
plotting.smart_figure(16165)
|
||||
end
|
||||
|
||||
plot_id = 0;
|
||||
|
||||
if iter >= par.probe_position_search && ~isempty(par.probe_geometry_model)
|
||||
clf()
|
||||
x_iters=[par.probe_position_search:iter]; % correction of iteration index in x-axis by ZC
|
||||
subplot(1,Nplots,1)
|
||||
hold all
|
||||
plot(x_iters,mode.scales , '-'); axis tight
|
||||
ylabel('Relative pixel scaling correction [-]')
|
||||
xlabel('Iteration')
|
||||
hold off
|
||||
grid on
|
||||
title('Scales')
|
||||
subplot(1,Nplots,2)
|
||||
plot(x_iters,mode.rotation , '-'); axis tight
|
||||
ylabel('Rotation [deg]')
|
||||
title('Rotation')
|
||||
xlabel('Iteration')
|
||||
grid on
|
||||
subplot(1,Nplots,3)
|
||||
plot(x_iters,mode.shear , '-'); axis tight
|
||||
ylabel('Shear [deg]')
|
||||
title('Shear')
|
||||
xlabel('Iteration')
|
||||
grid on
|
||||
subplot(1,Nplots,4)
|
||||
plot(x_iters,mode.asymmetry*100 , '-'); axis tight
|
||||
ylabel('Asymmetry [%]')
|
||||
title('Asymmetry')
|
||||
xlabel('Iteration')
|
||||
grid on
|
||||
plot_id = 4;
|
||||
end
|
||||
|
||||
if iter >= par.estimate_NF_distance
|
||||
subplot(1,Nplots,plot_id+1)
|
||||
plot(mode.distances * 1e6 , '-');
|
||||
axis tight
|
||||
grid on
|
||||
ylabel('Propagation distance [um]')
|
||||
title('Nearfield propagation distance')
|
||||
xlabel('Iteration')
|
||||
plot_id = plot_id + 1;
|
||||
end
|
||||
|
||||
if iter >= par.detector_rotation_search
|
||||
subplot(1,Nplots,plot_id+1)
|
||||
plot(mode.probe_rotation,'-');
|
||||
axis tight
|
||||
grid on
|
||||
ylabel('Detector rotation angle [deg]')
|
||||
title('Detector rotation')
|
||||
xlabel('Iteration')
|
||||
plot_id = plot_id + 1;
|
||||
end
|
||||
|
||||
if iter >= par.detector_scale_search
|
||||
subplot(1,Nplots,plot_id+1)
|
||||
plot((1+mode.probe_scale_upd),'-');
|
||||
axis tight
|
||||
grid on
|
||||
ylabel('Detector optimal scaling [-]')
|
||||
title('Relative pixel scale')
|
||||
xlabel('Iteration')
|
||||
plot_id = plot_id + 1;
|
||||
end
|
||||
|
||||
plotting.suptitle('Evolution of geometry parameters')
|
||||
|
||||
%modified by YJ: remove check_option(par, 'probe_geometry_model') to
|
||||
%plot position correction even without geom refinement
|
||||
%if iter >= par.probe_position_search && check_option(par, 'probe_geometry_model')
|
||||
if iter >= par.probe_position_search
|
||||
%modified by YJ for electron pty
|
||||
if isfield(par,'beam_source') && strcmp(par.beam_source, 'electron')
|
||||
unitFactor = 1;
|
||||
scaleFactor = 0.1;
|
||||
unitLabel = 'A';
|
||||
else %X-ray
|
||||
unitFactor = 1e9;
|
||||
scaleFactor = 1e6;
|
||||
unitLabel = 'nm';
|
||||
end
|
||||
% substract the geometry model to show only residuum
|
||||
pos_err = pos - mode.probe_positions_model ;
|
||||
|
||||
% subtract average error per scan
|
||||
for kk = 1:par.Nscans
|
||||
ind = self.reconstruct_ind{kk};
|
||||
pos_err(ind,:) = pos_err(ind,:) - mean(pos_err(ind,:));
|
||||
end
|
||||
pos = pos+ self.Np_o([2,1])/2;
|
||||
|
||||
marker_colors = {'r', 'b', 'g', 'k'};
|
||||
scale = self.pixel_size*scaleFactor;
|
||||
plotting.smart_figure(455454)
|
||||
clf()
|
||||
subplot(2,2,1)
|
||||
aobject = angle(object);
|
||||
range = sp_quantile(aobject(cache.object_ROI{:}), [1e-3, 1-1e-3],10);
|
||||
aobject = (aobject - range(1)) / (range(2) - range(1));
|
||||
grids = {(-ceil(self.Np_o(2)/2):ceil(self.Np_o(2)/2)-1)*scale(2), ...
|
||||
(-ceil(self.Np_o(1)/2):ceil(self.Np_o(1)/2)-1)*scale(1)};
|
||||
imagesc(grids{:}, aobject, [-2, 1]); % reduce contrast
|
||||
colormap bone
|
||||
axis xy
|
||||
hold on
|
||||
if isfield(par,'beam_source') && strcmp(par.beam_source, 'electron')
|
||||
ylabel('Position [nm]')
|
||||
else
|
||||
ylabel('Position [\mum]')
|
||||
end
|
||||
pos_scales = (pos-self.Np_o([2,1])/2) .* scale([2,1]);
|
||||
for i = 1:length(self.reconstruct_ind)
|
||||
id = self.reconstruct_ind{i};
|
||||
if any(mode.probe_positions_weight)
|
||||
% plot importance
|
||||
scatter(pos_scales(id,1), pos_scales(id,2), max(mode.probe_positions_weight(id,:),[],2)*20, marker_colors{1+mod(i,4)})
|
||||
end
|
||||
mean_err = mean(std(pos_err));
|
||||
range = max(pos) - min(pos);
|
||||
up = 0.02 * min(range) / mean_err;
|
||||
rounding_order = 10^floor(log10(up));
|
||||
up = ceil(up / rounding_order)*rounding_order;
|
||||
quiver( pos_scales(id,1), pos_scales(id,2), scale(1)*pos_err(id,1)*up, scale(2)*pos_err(id,2)*up, 0, marker_colors{1+mod(i,4)})
|
||||
end
|
||||
hold off
|
||||
axis equal xy tight
|
||||
range = [min(pos_scales(:,1)), max(pos_scales(:,1)), min(pos_scales(:,2)), max(pos_scales(:,2))];
|
||||
axis(range)
|
||||
title(sprintf('Position errors, upscaled %ix', up))
|
||||
|
||||
subplot(2,2,3)
|
||||
plot(mean(mode.probe_positions_weight,2), 'b.-')
|
||||
ylim([0, max(mean(mode.probe_positions_weight,2))])
|
||||
hold all
|
||||
for i = 1:length(self.reconstruct_ind)
|
||||
vline(self.reconstruct_ind{i}(end), '-r')
|
||||
end
|
||||
hold off
|
||||
axis tight
|
||||
ylabel('Importance weights')
|
||||
xlabel('Position #')
|
||||
title('Relative importance weights for geometry model')
|
||||
|
||||
subplot(2,2,2)
|
||||
yyaxis left
|
||||
h = plot(pos_err(:,1), 'w.');
|
||||
axis tight
|
||||
ylabel('Position error [px]')
|
||||
yyaxis right
|
||||
plot(pos_err(:,1)*self.pixel_size(2)*unitFactor, 'b.-')
|
||||
axis tight
|
||||
xlabel('Position #')
|
||||
ylabel(strcat('Position error [',unitLabel,']'))
|
||||
|
||||
hold all
|
||||
for i = 1:length(self.reconstruct_ind)
|
||||
vline(self.reconstruct_ind{i}(end), '-r')
|
||||
end
|
||||
hold off
|
||||
title( 'Horizontal')
|
||||
grid on
|
||||
%legend({sprintf('STD=%3.2g nm', std(pos_err(:,1)*self.pixel_size(2)*1e9) )})
|
||||
legend({sprintf(strcat('STD=%3.2g ',unitLabel), std(pos_err(:,1)*self.pixel_size(2)*unitFactor) )})
|
||||
|
||||
subplot(2,2,4)
|
||||
yyaxis left
|
||||
h = plot(pos_err(:,2), 'w.');
|
||||
ylabel('Position error [px]')
|
||||
axis tight
|
||||
yyaxis right
|
||||
plot(pos_err(:,2)*self.pixel_size(1)*unitFactor, 'b.-')
|
||||
axis tight
|
||||
%ylabel('Position error [nm]')
|
||||
ylabel(strcat('Position error [',unitLabel,']'))
|
||||
|
||||
xlabel('Position #')
|
||||
hold all
|
||||
title( 'Vertical')
|
||||
legend({sprintf(strcat('STD=%3.2g ',unitLabel), std(pos_err(:,2)*self.pixel_size(1)*unitFactor) )})
|
||||
grid on
|
||||
|
||||
for i = 1:length(self.reconstruct_ind)
|
||||
vline(self.reconstruct_ind{i}(end), '-r')
|
||||
end
|
||||
hold off
|
||||
plotting.suptitle('Random position errors after subtraction of geometry model')
|
||||
|
||||
try
|
||||
if length(self.reconstruct_ind) == 2 && verbose() > 1 && length(self.reconstruct_ind{1}) == length(self.reconstruct_ind{2})
|
||||
disp('Correlation between two scans')
|
||||
corr( pos_err(self.reconstruct_ind{1},:), pos_err(self.reconstruct_ind{2},:) )
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,81 @@
|
||||
% PLOT_GEOM_CORRECTIONS plot evolution of intensity correction
|
||||
%
|
||||
% plot_geom_corrections(self)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
%
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_intensity_corr(self)
|
||||
|
||||
plotting.smart_figure(131231)
|
||||
subplot(1,2,1)
|
||||
corr = abs(self.intensity_corr/median(self.intensity_corr));
|
||||
plot(corr)
|
||||
axis([1,self.Npos, 0, max(corr)])
|
||||
title('Intensity evolution')
|
||||
subplot(1,2,2)
|
||||
show_spatial_distribution(self.probe_positions_0, abs( self.intensity_corr), false, false)
|
||||
axis off image
|
||||
colorbar
|
||||
title('Intensity distribution')
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
@@ -0,0 +1,145 @@
|
||||
% PLOT_OBJECT_MODES incoherent object modes / layers / objects belonging to multiple scans
|
||||
%
|
||||
% plot_object_modes(self, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent object{ii}:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_object_modes(self, cache)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import utils.*
|
||||
import math.*
|
||||
import plotting.*
|
||||
|
||||
[Nscans,Nlayers] = size(self.object);
|
||||
ROI = cache.object_ROI;
|
||||
|
||||
for ii = 1:Nscans
|
||||
object{ii} = cat(3,self.object{ii,:});
|
||||
object{ii} = Ggather(object{ii}(ROI{:},:));
|
||||
illum{ii} = cache.illum_sum_0{ii}(ROI{:});
|
||||
end
|
||||
|
||||
plotting.smart_figure(302809)
|
||||
kk = 1;
|
||||
scale = self.pixel_size;
|
||||
|
||||
Np_o = [size(object{1},1),size(object{1},2)];
|
||||
Np_o(2) = Np_o(2) * Nlayers;
|
||||
|
||||
for ii = 1:Nscans
|
||||
|
||||
grids = {(-ceil(Np_o(2)/2):ceil(Np_o(2)/2)-1)*scale(2), ...
|
||||
(-ceil(Np_o(1)/2):ceil(Np_o(1)/2)-1)*scale(1)};
|
||||
|
||||
amp_obj = abs(object{ii});
|
||||
% consider only the illuminated region
|
||||
ROI_mask = illum{ii} >= 0.5*quantile(illum{ii}(:), 0.9);
|
||||
[ROI] = get_ROI(ROI_mask);
|
||||
|
||||
ROI_mask = repmat(ROI_mask,1,1,size(amp_obj,3));
|
||||
RANGE_amp = sp_quantile(amp_obj(ROI_mask),[5e-3,1-5e-3], 4)';
|
||||
|
||||
RANGE_amp(2) = max(RANGE_amp(2), RANGE_amp(1)+1e-6);
|
||||
|
||||
[~, gamma] = stabilize_phase(object{ii}(ROI{:},:));
|
||||
ang_object = -angle(object{ii}.*gamma);
|
||||
RANGE_angle = sp_quantile(ang_object(ROI_mask),[1e-3,1-1e-3], 4)';
|
||||
|
||||
for jj = 1:Nlayers
|
||||
% avoid plotting residua in not illuminated regions for object{ii}
|
||||
resid_mask = cache.illum_sum_0{ii}(ROI{:})/ cache.MAX_ILLUM(ii) > 0.1;
|
||||
resid_mask = imfill(gather(resid_mask), 'holes'); % gpuArray and imfill seems to be very unstable
|
||||
residues = resid_mask(2:end,2:end) & (abs(utils.findresidues(object{ii}(:,:,jj))) > 0.1);
|
||||
[X,Y] = find(residues);
|
||||
end
|
||||
|
||||
ax(2*kk-1)=subplot(2,Nscans,ii);
|
||||
imagesc(grids{:},reshape(amp_obj, Np_o))
|
||||
if diff(RANGE_amp)>0;caxis(RANGE_amp); end
|
||||
title(sprintf('Scan %i (L:%i)', ii, jj))
|
||||
ylabel(sprintf('Amplitude - <%3.2g ; %3.2g>', RANGE_amp))
|
||||
axis xy tight image
|
||||
colormap bone
|
||||
set(gca,'TickLength',[0 0])
|
||||
set(gca,'XTick',[],'YTick',[])
|
||||
|
||||
|
||||
ax(2*kk)=subplot(2,Nscans,Nscans+kk);
|
||||
imagesc(grids{:},reshape(ang_object, Np_o))
|
||||
|
||||
hold all
|
||||
plot(Y,X,'or')
|
||||
hold off
|
||||
if diff(RANGE_angle)>0; caxis((RANGE_angle')); end
|
||||
ylabel(sprintf('Phase - <%3.2g ; %3.2g>', RANGE_angle))
|
||||
axis xy tight image
|
||||
colormap bone
|
||||
set(gca,'TickLength',[0 0])
|
||||
set(gca,'XTick',[],'YTick',[])
|
||||
kk = kk + 1 ;
|
||||
|
||||
end
|
||||
linkaxes(ax, 'xy')
|
||||
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,137 @@
|
||||
% PLOT_PROBE_MODES plot incoherent probe modes
|
||||
%
|
||||
% plot_probe_modes(self, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent probe:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_probe_modes(self, par)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.*
|
||||
import math.*
|
||||
import plotting.*
|
||||
|
||||
for i = 1:par.probe_modes
|
||||
power(i) = Ggather(mean2(abs(self.probe{i}(:,:,1)).^2));
|
||||
end
|
||||
power = power / sum(power);
|
||||
|
||||
grids = {(-ceil(self.Np_p(2)/2):ceil(self.Np_p(2)/2)-1)*self.pixel_size(2), ...
|
||||
(-ceil(self.Np_p(1)/2):ceil(self.Np_p(1)/2)-1)*self.pixel_size(1)};
|
||||
|
||||
|
||||
plotting.smart_figure(46456)
|
||||
|
||||
for i = 1:par.probe_modes
|
||||
mode = Ggather(mean(mean(self.probe{i},3),4));
|
||||
|
||||
ax(2*i-1)=subplot(2,par.probe_modes,i);
|
||||
RANGE = sp_quantile(abs(mode),[1e-3,1-5e-3], 4)';
|
||||
RANGE(2) = max(RANGE(2), RANGE(1)+1e-6);
|
||||
amode = abs(mode);
|
||||
imagesc3D(grids{:},amode)
|
||||
if diff(RANGE)>0;caxis(RANGE); end
|
||||
title(sprintf('Mode %i, P:%3.2g', i, power(i)))
|
||||
ylabel(sprintf('Amplitude - <%3.2g ; %3.2g>', RANGE))
|
||||
axis image xy
|
||||
colormap bone
|
||||
set(gca,'TickLength',[0 0])
|
||||
set(gca,'XTick',[],'YTick',[])
|
||||
|
||||
|
||||
ax(2*i)=subplot(2,par.probe_modes,par.probe_modes+i);
|
||||
arg = -angle(utils.stabilize_phase(mode));
|
||||
RANGE_arg = sp_quantile(arg,[1e-3,1-1e-3], 4)';
|
||||
imagesc3D(grids{:},arg )
|
||||
if diff(RANGE_arg)>0; caxis((RANGE_arg')); end
|
||||
ylabel(sprintf('Phase - <%3.2g ; %3.2g>', RANGE_arg))
|
||||
axis image xy
|
||||
colormap bone
|
||||
set(gca,'TickLength',[0 0])
|
||||
set(gca,'XTick',[],'YTick',[])
|
||||
end
|
||||
linkaxes(ax, 'xy')
|
||||
|
||||
|
||||
if par.probe_modes > par.Nscans % dont run for multiscan
|
||||
reconstruct_ind = [self.reconstruct_ind{:}];
|
||||
if par.variable_probe
|
||||
plotting.smart_figure(id+1)
|
||||
clf
|
||||
power = power / sum(power);
|
||||
for i = 1:length(self.probe)
|
||||
pos = self.probe{i}.probe_positions;
|
||||
pos = pos(:,[2,1]);
|
||||
pos(:,1) = -pos(:,1);
|
||||
subplot(2,1,1)
|
||||
hold all
|
||||
plot(power(i))
|
||||
hold off
|
||||
title('Variable incoherent probe')
|
||||
xlabel('Normalized mode power')
|
||||
subplot(2,par.probe_modes,par.probe_modes+i)
|
||||
scatter(pos(reconstruct_ind,:),gather(W(reconstruct_ind)), 20);
|
||||
axis off image
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,181 @@
|
||||
% PLOT_RESULTS show current reconstruction and errors during ptychography
|
||||
%
|
||||
% plot_results(self, cache, par, fourier_error,probe_positions)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
% ** probe_positions array [Npos,2] with probe positions for the main coherence mode
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function plot_results(self, cache, par, fourier_error,probe_positions)
|
||||
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.*
|
||||
import math.*
|
||||
import plotting.*
|
||||
|
||||
likelihood = lower(par.likelihood);
|
||||
|
||||
try
|
||||
verbose(1,'Plotting ... ')
|
||||
Np_o = self.Np_o;
|
||||
Npos = length(probe_positions);
|
||||
reconstruct_ind = [self.reconstruct_ind{:}];
|
||||
ind = find(any(~isnan(fourier_error),2));
|
||||
|
||||
probe = Ggather(self.probe{1}(:,:,1,1));
|
||||
% show extended DoF projection through layers of first scan
|
||||
object = prod(cat(3,self.object{1,:}),3);
|
||||
|
||||
if par.fourier_ptycho
|
||||
object = fft2(fftshift(object));
|
||||
end
|
||||
object = object(cache.object_ROI{:});
|
||||
|
||||
plotting.smart_figure(10)
|
||||
clf()
|
||||
number_iterations = size(fourier_error,1);
|
||||
ha = tight_subplot(2,2,[.01 .01],[.01 .01],[.01 .01]);
|
||||
axes(ha(1))
|
||||
|
||||
|
||||
pixel_size = self.pixel_size .* cosd(par.sample_rotation_angles([1,2]));
|
||||
params = {'scale', pixel_size,'enhance_contrast', true};
|
||||
probe_positions = probe_positions - repmat([mean(cache.object_ROI{2})-Np_o(2)/2, mean(cache.object_ROI{1})-Np_o(1)/2],Npos,1);
|
||||
|
||||
imagesc_hsv(object ,params{:});
|
||||
|
||||
if ~par.fourier_ptycho
|
||||
% avoid plotting residua in not illuminated regions
|
||||
resid_mask = cache.illum_sum_0{1}(cache.object_ROI{:})/ cache.MAX_ILLUM(1) > 0.1;
|
||||
% find residua to plot
|
||||
residues = resid_mask(2:end, 2:end) & (abs(utils.findresidues(object)) > 0.1);
|
||||
|
||||
[X,Y] = find(residues);
|
||||
if length(probe_positions) < 2e3
|
||||
points = probe_positions(reconstruct_ind, :);
|
||||
hold all
|
||||
plot(points(:,1)*pixel_size(2)*1e6, points(:,2)*pixel_size(1)*1e6, '.w')
|
||||
plot((Y-size(object,2)/2)*pixel_size(2)*1e6,(X-size(object,1)/2)*pixel_size(1)*1e6,'ow')
|
||||
hold off
|
||||
end
|
||||
end
|
||||
|
||||
axis xy
|
||||
ylabel('Reconstruction in fake colors')
|
||||
axes(ha(3))
|
||||
probe = utils.prop_free_nf(probe, self.lambda, sum(self.z_distance(1:end-1))/2, self.pixel_size);
|
||||
imagesc_hsv(probe, params{:} );
|
||||
|
||||
|
||||
axis xy
|
||||
ylabel('Contrast enhanced probe')
|
||||
subplot(2,2,2)
|
||||
fourier_error(fourier_error == 0) = nan;
|
||||
|
||||
|
||||
if strcmpi(likelihood, 'poisson')
|
||||
fourier_error = (bsxfun(@minus, fourier_error, fourier_error(1,:)));
|
||||
end
|
||||
if ~isempty(ind) %if there is somethign to plot
|
||||
hold all
|
||||
plot(ind, fourier_error(ind,reconstruct_ind), '-')
|
||||
ind_missing = ~ismember(1:self.Npos, reconstruct_ind);
|
||||
if any(ind_missing)
|
||||
plot(ind, fourier_error(ind,ind_missing), '--')
|
||||
end
|
||||
plot(ind, nanmean(fourier_error(ind,~ind_missing)'),'k', 'LineWidth', 3)
|
||||
plot(ind, nanmedian(fourier_error(ind,~ind_missing)'),'k--', 'LineWidth', 3)
|
||||
hold off
|
||||
grid on
|
||||
set(gca, 'xscale', 'log')
|
||||
if strcmpi(likelihood, 'L1')
|
||||
set(gca, 'yscale', 'log')
|
||||
end
|
||||
xlim([1, number_iterations])
|
||||
% ignore the first iteration error in plotting
|
||||
try ylim([min2(fourier_error(2:end,:)), max2(fourier_error(2:end,:))]); end
|
||||
|
||||
switch likelihood
|
||||
case 'poisson', title('Relative neg-likelihood change');
|
||||
case 'l1', title('Fourier error');
|
||||
end
|
||||
end
|
||||
subplot(2,2,4)
|
||||
if length(ind) > 1
|
||||
err = fourier_error(ind(end) , reconstruct_ind) ;
|
||||
pos = pixel_size([2,1]).*probe_positions(reconstruct_ind,:);
|
||||
%% compatibility with the CPU code
|
||||
pos(:,2) = -pos(:,2);
|
||||
show_spatial_distribution(Ggather(pos), Ggather(err), false, length(probe_positions) < 2e3)
|
||||
axis off equal
|
||||
end
|
||||
title('Spatial distribution of error')
|
||||
|
||||
|
||||
catch err
|
||||
warning('Error during plotting: %s', err.message)
|
||||
keyboard
|
||||
disp('plotting failed')
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,110 @@
|
||||
% PLOT_VARIABLE_PROBE plot SVD decomposition of the probes to show their differences
|
||||
%
|
||||
% plot_variable_probe(self, par)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
function plot_variable_probe(self, par)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import plotting.*
|
||||
import math.*
|
||||
|
||||
|
||||
probe = self.probe{1};
|
||||
|
||||
% probe = fftshift_2D(fft2( fftshift_2D( self.probe{1})));
|
||||
|
||||
probe_evolution= real(self.probe_evolution);
|
||||
|
||||
plotting.smart_figure(12131)
|
||||
ax(1)=subplot(2,1+par.variable_probe_modes,1);
|
||||
imagesc_hsv(probe(:,:,:,1))
|
||||
axis xy off
|
||||
title('Constant mode')
|
||||
for ii = 1:par.variable_probe_modes
|
||||
ax(ii+1)=subplot(2,1+par.variable_probe_modes,1+ii);
|
||||
imagesc_hsv(probe(:,:,:,1+ii))
|
||||
axis xy off
|
||||
title(sprintf('Variable mode %i', ii))
|
||||
end
|
||||
|
||||
subplot(2,1,2)
|
||||
plot( probe_evolution(:,1)-1 , 'k' );
|
||||
hold on
|
||||
plot( probe_evolution(:,2:end))
|
||||
hold off
|
||||
for kk = 1:length(self.reconstruct_ind)
|
||||
vline(self.reconstruct_ind{kk}(end),'r--')
|
||||
end
|
||||
hold off
|
||||
axis tight
|
||||
if par.variable_probe && par.variable_intensity
|
||||
legend({'Intensity correction', 'Variable mode evol'}, 'Location', 'best')
|
||||
elseif par.variable_intensity
|
||||
legend({'Intensity correction'}, 'Location', 'best')
|
||||
else
|
||||
legend({'Variable mode evol'}, 'Location', 'best')
|
||||
end
|
||||
xlabel('Position #')
|
||||
ylabel('Relative mode importance')
|
||||
title('Evolution of each variable probe mode')
|
||||
linkaxes(ax, 'xy');
|
||||
|
||||
end
|
||||
@@ -0,0 +1,202 @@
|
||||
% IMAGESC_HSV for plotting complex valued arrays , similar to imagesc3D but with more options
|
||||
% imagesc_hsv(varargin)
|
||||
%
|
||||
% ** varargin see the code
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function imagesc_hsv(varargin)
|
||||
|
||||
import utils.*
|
||||
import math.*
|
||||
|
||||
par = inputParser;
|
||||
par.addOptional('data', [])
|
||||
par.addParameter('scale', nan , @isnumeric )
|
||||
par.addParameter('clim', [] , @isnumeric )
|
||||
par.addParameter('inverse', false , @islogical ) % use white background
|
||||
par.addParameter('show_ROI', false , @islogical ) % show only intersting area
|
||||
par.addParameter('points', [] , @isnumeric ) % plot dots
|
||||
par.addParameter('enhance_contrast', false , @islogical ) % plot dots
|
||||
par.addParameter('axis', [] , @isnumeric ) % plot dots
|
||||
par.addParameter('stabilize_phase', true , @islogical ) % plot dots
|
||||
par.addParameter('show', true , @islogical ) % plot dots
|
||||
|
||||
par.parse(varargin{:})
|
||||
r = par.Results;
|
||||
data = r.data;
|
||||
clim = r.clim;
|
||||
|
||||
if all(data(:) == 0)
|
||||
warning('Empty data to plot')
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
|
||||
[W,H] = size(data);
|
||||
|
||||
if ~isempty(r.axis)
|
||||
X = linspace(r.axis(1),r.axis(2),W)*1e6;
|
||||
Y = linspace(r.axis(3),r.axis(4),H)*1e6;
|
||||
else
|
||||
if ~isnan(r.scale)
|
||||
scale = ones(2,1).*r.scale(:);
|
||||
X = [-W/2:W/2-1]* scale(1)*1e6;
|
||||
Y = [-H/2:H/2-1]* scale(2)*1e6;
|
||||
else
|
||||
X = 1:W; Y = 1:H;
|
||||
end
|
||||
end
|
||||
if r.show_ROI
|
||||
asum = abs(sum(data,3));
|
||||
try
|
||||
T1 = (graythresh_new((sum(asum,1))));
|
||||
T2 = (graythresh_new((sum(asum,2))));
|
||||
asum(:,sum(asum,1) < T1) = 0;
|
||||
asum(sum(asum,2) < T2,:) = 0;
|
||||
[ROI] = get_ROI(asum > 0.01*quantile(asum(:), 0.99), 0);
|
||||
data = data(ROI{:});
|
||||
X = X(ROI{1});
|
||||
Y = Y(ROI{2});
|
||||
catch
|
||||
warning('ROI estimation failed')
|
||||
end
|
||||
end
|
||||
[W,H] = size(data);
|
||||
|
||||
if ~isempty(clim)
|
||||
ind_min = abs(data) < clim(1);
|
||||
ind_max = abs(data) > clim(2);
|
||||
data(ind_min) = data(ind_min) ./ abs(data(ind_min)) * clim(1);
|
||||
data(ind_max) = data(ind_max) ./ abs(data(ind_max)) * clim(2);
|
||||
end
|
||||
|
||||
adata = abs(data);
|
||||
|
||||
|
||||
|
||||
alpha = 1e-3;
|
||||
tmp= sort(adata(:));
|
||||
MAX = tmp(ceil(end*(1-alpha)));
|
||||
ind = adata > MAX;
|
||||
data(ind) = MAX * data(ind) ./ abs(data(ind));
|
||||
if r.enhance_contrast
|
||||
data = data ./ sqrt(alpha+abs(data));
|
||||
clim = sqrt(clim);
|
||||
end
|
||||
if r.stabilize_phase
|
||||
data = stabilize_phase(data, abs(data), abs(data), 'remove_ramp', false);
|
||||
end
|
||||
|
||||
adata = abs(data);
|
||||
|
||||
if isempty(clim)
|
||||
range = sp_quantile(adata(:), [1e-2, 1-1e-2],10);
|
||||
else
|
||||
range = clim;
|
||||
end
|
||||
|
||||
adata = (adata - range(1) ) ./ ( range(2) - range(1) );
|
||||
ang_data = angle(data);
|
||||
|
||||
if r.enhance_contrast && r.stabilize_phase
|
||||
ang_range = max(abs(sp_quantile(ang_data(:), [1e-2, 1-1e-2],10)));
|
||||
ang_range = max(1e-3, ang_range);
|
||||
ang_data = 2*pi*ang_data ./ (2* ang_range);
|
||||
end
|
||||
|
||||
|
||||
if r.inverse
|
||||
hue = mod(ang_data+1.5*pi, 2*pi)/(2*pi);
|
||||
hsv_data = [ hue(:) , adata(:), ones(W*H,1) ];
|
||||
else
|
||||
hue = mod(ang_data+2.5*pi, 2*pi)/(2*pi);
|
||||
hsv_data = [ hue(:) , ones(W*H,1), adata(:) ];
|
||||
end
|
||||
hsv_data = min(max(0, hsv_data),1);
|
||||
|
||||
|
||||
rgb_data = hsv2rgb(hsv_data);
|
||||
|
||||
rgb_data = reshape(rgb_data, W,H,3);
|
||||
rgb_data = min(1,rgb_data);
|
||||
|
||||
|
||||
if r.show
|
||||
hh = imagesc(Y,X, rgb_data );
|
||||
axis image
|
||||
end
|
||||
|
||||
|
||||
if r.show
|
||||
% Get the parent Axes of the image
|
||||
axis image
|
||||
|
||||
if ~isempty(r.points) && ~any(isnan(r.scale))
|
||||
hold on
|
||||
points = r.scale.*1e6.*r.points;
|
||||
plot( points(:,1),points(:,2), '.w')
|
||||
hold off
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,369 @@
|
||||
function [x0,y0,iout,jout] = intersections(x1,y1,x2,y2,robust)
|
||||
%INTERSECTIONS Intersections of curves.
|
||||
% Computes the (x,y) locations where two curves intersect. The curves
|
||||
% can be broken with NaNs or have vertical segments.
|
||||
%
|
||||
% Example:
|
||||
% [X0,Y0] = intersections(X1,Y1,X2,Y2,ROBUST);
|
||||
%
|
||||
% where X1 and Y1 are equal-length vectors of at least two points and
|
||||
% represent curve 1. Similarly, X2 and Y2 represent curve 2.
|
||||
% X0 and Y0 are column vectors containing the points at which the two
|
||||
% curves intersect.
|
||||
%
|
||||
% ROBUST (optional) set to 1 or true means to use a slight variation of the
|
||||
% algorithm that might return duplicates of some intersection points, and
|
||||
% then remove those duplicates. The default is true, but since the
|
||||
% algorithm is slightly slower you can set it to false if you know that
|
||||
% your curves don't intersect at any segment boundaries. Also, the robust
|
||||
% version properly handles parallel and overlapping segments.
|
||||
%
|
||||
% The algorithm can return two additional vectors that indicate which
|
||||
% segment pairs contain intersections and where they are:
|
||||
%
|
||||
% [X0,Y0,I,J] = intersections(X1,Y1,X2,Y2,ROBUST);
|
||||
%
|
||||
% For each element of the vector I, I(k) = (segment number of (X1,Y1)) +
|
||||
% (how far along this segment the intersection is). For example, if I(k) =
|
||||
% 45.25 then the intersection lies a quarter of the way between the line
|
||||
% segment connecting (X1(45),Y1(45)) and (X1(46),Y1(46)). Similarly for
|
||||
% the vector J and the segments in (X2,Y2).
|
||||
%
|
||||
% You can also get intersections of a curve with itself. Simply pass in
|
||||
% only one curve, i.e.,
|
||||
%
|
||||
% [X0,Y0] = intersections(X1,Y1,ROBUST);
|
||||
%
|
||||
% where, as before, ROBUST is optional.
|
||||
|
||||
% Version: 2.0, 25 May 2017
|
||||
% Author: Douglas M. Schwarz
|
||||
% Email: dmschwarz=ieee*org, dmschwarz=urgrad*rochester*edu
|
||||
% Real_email = regexprep(Email,{'=','*'},{'@','.'})
|
||||
|
||||
|
||||
% Theory of operation:
|
||||
%
|
||||
% Given two line segments, L1 and L2,
|
||||
%
|
||||
% L1 endpoints: (x1(1),y1(1)) and (x1(2),y1(2))
|
||||
% L2 endpoints: (x2(1),y2(1)) and (x2(2),y2(2))
|
||||
%
|
||||
% we can write four equations with four unknowns and then solve them. The
|
||||
% four unknowns are t1, t2, x0 and y0, where (x0,y0) is the intersection of
|
||||
% L1 and L2, t1 is the distance from the starting point of L1 to the
|
||||
% intersection relative to the length of L1 and t2 is the distance from the
|
||||
% starting point of L2 to the intersection relative to the length of L2.
|
||||
%
|
||||
% So, the four equations are
|
||||
%
|
||||
% (x1(2) - x1(1))*t1 = x0 - x1(1)
|
||||
% (x2(2) - x2(1))*t2 = x0 - x2(1)
|
||||
% (y1(2) - y1(1))*t1 = y0 - y1(1)
|
||||
% (y2(2) - y2(1))*t2 = y0 - y2(1)
|
||||
%
|
||||
% Rearranging and writing in matrix form,
|
||||
%
|
||||
% [x1(2)-x1(1) 0 -1 0; [t1; [-x1(1);
|
||||
% 0 x2(2)-x2(1) -1 0; * t2; = -x2(1);
|
||||
% y1(2)-y1(1) 0 0 -1; x0; -y1(1);
|
||||
% 0 y2(2)-y2(1) 0 -1] y0] -y2(1)]
|
||||
%
|
||||
% Let's call that A*T = B. We can solve for T with T = A\B.
|
||||
%
|
||||
% Once we have our solution we just have to look at t1 and t2 to determine
|
||||
% whether L1 and L2 intersect. If 0 <= t1 < 1 and 0 <= t2 < 1 then the two
|
||||
% line segments cross and we can include (x0,y0) in the output.
|
||||
%
|
||||
% In principle, we have to perform this computation on every pair of line
|
||||
% segments in the input data. This can be quite a large number of pairs so
|
||||
% we will reduce it by doing a simple preliminary check to eliminate line
|
||||
% segment pairs that could not possibly cross. The check is to look at the
|
||||
% smallest enclosing rectangles (with sides parallel to the axes) for each
|
||||
% line segment pair and see if they overlap. If they do then we have to
|
||||
% compute t1 and t2 (via the A\B computation) to see if the line segments
|
||||
% cross, but if they don't then the line segments cannot cross. In a
|
||||
% typical application, this technique will eliminate most of the potential
|
||||
% line segment pairs.
|
||||
|
||||
%
|
||||
%
|
||||
% Copyright (c) 2017, Douglas M. Schwarz
|
||||
% All rights reserved.
|
||||
%
|
||||
% Redistribution and use in source and binary forms, with or without
|
||||
% modification, are permitted provided that the following conditions are
|
||||
% met:
|
||||
%
|
||||
% * Redistributions of source code must retain the above copyright
|
||||
% notice, this list of conditions and the following disclaimer.
|
||||
% * Redistributions in binary form must reproduce the above copyright
|
||||
% notice, this list of conditions and the following disclaimer in
|
||||
% the documentation and/or other materials provided with the distribution
|
||||
%
|
||||
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
|
||||
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
|
||||
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
|
||||
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
|
||||
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
|
||||
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
||||
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
% POSSIBILITY OF SUCH DAMAGE.
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
% Input checks.
|
||||
if verLessThan('matlab','7.13')
|
||||
error(nargchk(2,5,nargin)) %#ok<NCHKN>
|
||||
else
|
||||
narginchk(2,5)
|
||||
end
|
||||
|
||||
% Adjustments based on number of arguments.
|
||||
switch nargin
|
||||
case 2
|
||||
robust = true;
|
||||
x2 = x1;
|
||||
y2 = y1;
|
||||
self_intersect = true;
|
||||
case 3
|
||||
robust = x2;
|
||||
x2 = x1;
|
||||
y2 = y1;
|
||||
self_intersect = true;
|
||||
case 4
|
||||
robust = true;
|
||||
self_intersect = false;
|
||||
case 5
|
||||
self_intersect = false;
|
||||
end
|
||||
|
||||
% x1 and y1 must be vectors with same number of points (at least 2).
|
||||
if sum(size(x1) > 1) ~= 1 || sum(size(y1) > 1) ~= 1 || ...
|
||||
length(x1) ~= length(y1)
|
||||
error('X1 and Y1 must be equal-length vectors of at least 2 points.')
|
||||
end
|
||||
% x2 and y2 must be vectors with same number of points (at least 2).
|
||||
if sum(size(x2) > 1) ~= 1 || sum(size(y2) > 1) ~= 1 || ...
|
||||
length(x2) ~= length(y2)
|
||||
error('X2 and Y2 must be equal-length vectors of at least 2 points.')
|
||||
end
|
||||
|
||||
|
||||
% Force all inputs to be column vectors.
|
||||
x1 = x1(:);
|
||||
y1 = y1(:);
|
||||
x2 = x2(:);
|
||||
y2 = y2(:);
|
||||
|
||||
% Compute number of line segments in each curve and some differences we'll
|
||||
% need later.
|
||||
n1 = length(x1) - 1;
|
||||
n2 = length(x2) - 1;
|
||||
xy1 = [x1 y1];
|
||||
xy2 = [x2 y2];
|
||||
dxy1 = diff(xy1);
|
||||
dxy2 = diff(xy2);
|
||||
|
||||
|
||||
% Determine the combinations of i and j where the rectangle enclosing the
|
||||
% i'th line segment of curve 1 overlaps with the rectangle enclosing the
|
||||
% j'th line segment of curve 2.
|
||||
|
||||
% Original method that works in old MATLAB versions, but is slower than
|
||||
% using binary singleton expansion (explicit or implicit).
|
||||
% [i,j] = find( ...
|
||||
% repmat(mvmin(x1),1,n2) <= repmat(mvmax(x2).',n1,1) & ...
|
||||
% repmat(mvmax(x1),1,n2) >= repmat(mvmin(x2).',n1,1) & ...
|
||||
% repmat(mvmin(y1),1,n2) <= repmat(mvmax(y2).',n1,1) & ...
|
||||
% repmat(mvmax(y1),1,n2) >= repmat(mvmin(y2).',n1,1));
|
||||
|
||||
% Select an algorithm based on MATLAB version and number of line
|
||||
% segments in each curve. We want to avoid forming large matrices for
|
||||
% large numbers of line segments. If the matrices are not too large,
|
||||
% choose the best method available for the MATLAB version.
|
||||
if n1 > 1000 || n2 > 1000 || verLessThan('matlab','7.4')
|
||||
% Determine which curve has the most line segments.
|
||||
if n1 >= n2
|
||||
% Curve 1 has more segments, loop over segments of curve 2.
|
||||
ijc = cell(1,n2);
|
||||
min_x1 = mvmin(x1);
|
||||
max_x1 = mvmax(x1);
|
||||
min_y1 = mvmin(y1);
|
||||
max_y1 = mvmax(y1);
|
||||
for k = 1:n2
|
||||
k1 = k + 1;
|
||||
ijc{k} = find( ...
|
||||
min_x1 <= max(x2(k),x2(k1)) & max_x1 >= min(x2(k),x2(k1)) & ...
|
||||
min_y1 <= max(y2(k),y2(k1)) & max_y1 >= min(y2(k),y2(k1)));
|
||||
ijc{k}(:,2) = k;
|
||||
end
|
||||
ij = vertcat(ijc{:});
|
||||
i = ij(:,1);
|
||||
j = ij(:,2);
|
||||
else
|
||||
% Curve 2 has more segments, loop over segments of curve 1.
|
||||
ijc = cell(1,n1);
|
||||
min_x2 = mvmin(x2);
|
||||
max_x2 = mvmax(x2);
|
||||
min_y2 = mvmin(y2);
|
||||
max_y2 = mvmax(y2);
|
||||
for k = 1:n1
|
||||
k1 = k + 1;
|
||||
ijc{k}(:,2) = find( ...
|
||||
min_x2 <= max(x1(k),x1(k1)) & max_x2 >= min(x1(k),x1(k1)) & ...
|
||||
min_y2 <= max(y1(k),y1(k1)) & max_y2 >= min(y1(k),y1(k1)));
|
||||
ijc{k}(:,1) = k;
|
||||
end
|
||||
ij = vertcat(ijc{:});
|
||||
i = ij(:,1);
|
||||
j = ij(:,2);
|
||||
end
|
||||
|
||||
elseif verLessThan('matlab','9.1')
|
||||
% Use bsxfun.
|
||||
[i,j] = find( ...
|
||||
bsxfun(@le,mvmin(x1),mvmax(x2).') & ...
|
||||
bsxfun(@ge,mvmax(x1),mvmin(x2).') & ...
|
||||
bsxfun(@le,mvmin(y1),mvmax(y2).') & ...
|
||||
bsxfun(@ge,mvmax(y1),mvmin(y2).'));
|
||||
|
||||
else
|
||||
% Use implicit expansion.
|
||||
[i,j] = find( ...
|
||||
mvmin(x1) <= mvmax(x2).' & mvmax(x1) >= mvmin(x2).' & ...
|
||||
mvmin(y1) <= mvmax(y2).' & mvmax(y1) >= mvmin(y2).');
|
||||
|
||||
end
|
||||
|
||||
|
||||
% Find segments pairs which have at least one vertex = NaN and remove them.
|
||||
% This line is a fast way of finding such segment pairs. We take
|
||||
% advantage of the fact that NaNs propagate through calculations, in
|
||||
% particular subtraction (in the calculation of dxy1 and dxy2, which we
|
||||
% need anyway) and addition.
|
||||
% At the same time we can remove redundant combinations of i and j in the
|
||||
% case of finding intersections of a line with itself.
|
||||
if self_intersect
|
||||
remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)) | j <= i + 1;
|
||||
else
|
||||
remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2));
|
||||
end
|
||||
i(remove) = [];
|
||||
j(remove) = [];
|
||||
|
||||
% Initialize matrices. We'll put the T's and B's in matrices and use them
|
||||
% one column at a time. AA is a 3-D extension of A where we'll use one
|
||||
% plane at a time.
|
||||
n = length(i);
|
||||
T = zeros(4,n);
|
||||
AA = zeros(4,4,n);
|
||||
AA([1 2],3,:) = -1;
|
||||
AA([3 4],4,:) = -1;
|
||||
AA([1 3],1,:) = dxy1(i,:).';
|
||||
AA([2 4],2,:) = dxy2(j,:).';
|
||||
B = -[x1(i) x2(j) y1(i) y2(j)].';
|
||||
|
||||
% Loop through possibilities. Trap singularity warning and then use
|
||||
% lastwarn to see if that plane of AA is near singular. Process any such
|
||||
% segment pairs to determine if they are colinear (overlap) or merely
|
||||
% parallel. That test consists of checking to see if one of the endpoints
|
||||
% of the curve 2 segment lies on the curve 1 segment. This is done by
|
||||
% checking the cross product
|
||||
%
|
||||
% (x1(2),y1(2)) - (x1(1),y1(1)) x (x2(2),y2(2)) - (x1(1),y1(1)).
|
||||
%
|
||||
% If this is close to zero then the segments overlap.
|
||||
|
||||
% If the robust option is false then we assume no two segment pairs are
|
||||
% parallel and just go ahead and do the computation. If A is ever singular
|
||||
% a warning will appear. This is faster and obviously you should use it
|
||||
% only when you know you will never have overlapping or parallel segment
|
||||
% pairs.
|
||||
|
||||
if robust
|
||||
overlap = false(n,1);
|
||||
warning_state = warning('off','MATLAB:singularMatrix');
|
||||
% Use try-catch to guarantee original warning state is restored.
|
||||
try
|
||||
lastwarn('')
|
||||
for k = 1:n
|
||||
T(:,k) = AA(:,:,k)\B(:,k);
|
||||
[unused,last_warn] = lastwarn; %#ok<ASGLU>
|
||||
lastwarn('')
|
||||
if strcmp(last_warn,'MATLAB:singularMatrix')
|
||||
% Force in_range(k) to be false.
|
||||
T(1,k) = NaN;
|
||||
% Determine if these segments overlap or are just parallel.
|
||||
overlap(k) = rcond([dxy1(i(k),:);xy2(j(k),:) - xy1(i(k),:)]) < eps;
|
||||
end
|
||||
end
|
||||
warning(warning_state)
|
||||
catch err
|
||||
warning(warning_state)
|
||||
rethrow(err)
|
||||
end
|
||||
% Find where t1 and t2 are between 0 and 1 and return the corresponding
|
||||
% x0 and y0 values.
|
||||
in_range = (T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) <= 1 & T(2,:) <= 1).';
|
||||
% For overlapping segment pairs the algorithm will return an
|
||||
% intersection point that is at the center of the overlapping region.
|
||||
if any(overlap)
|
||||
ia = i(overlap);
|
||||
ja = j(overlap);
|
||||
% set x0 and y0 to middle of overlapping region.
|
||||
T(3,overlap) = (max(min(x1(ia),x1(ia+1)),min(x2(ja),x2(ja+1))) + ...
|
||||
min(max(x1(ia),x1(ia+1)),max(x2(ja),x2(ja+1)))).'/2;
|
||||
T(4,overlap) = (max(min(y1(ia),y1(ia+1)),min(y2(ja),y2(ja+1))) + ...
|
||||
min(max(y1(ia),y1(ia+1)),max(y2(ja),y2(ja+1)))).'/2;
|
||||
selected = in_range | overlap;
|
||||
else
|
||||
selected = in_range;
|
||||
end
|
||||
xy0 = T(3:4,selected).';
|
||||
|
||||
% Remove duplicate intersection points.
|
||||
[xy0,index] = unique(xy0,'rows');
|
||||
x0 = xy0(:,1);
|
||||
y0 = xy0(:,2);
|
||||
|
||||
% Compute how far along each line segment the intersections are.
|
||||
if nargout > 2
|
||||
sel_index = find(selected);
|
||||
sel = sel_index(index);
|
||||
iout = i(sel) + T(1,sel).';
|
||||
jout = j(sel) + T(2,sel).';
|
||||
end
|
||||
else % non-robust option
|
||||
for k = 1:n
|
||||
[L,U] = lu(AA(:,:,k));
|
||||
T(:,k) = U\(L\B(:,k));
|
||||
end
|
||||
|
||||
% Find where t1 and t2 are between 0 and 1 and return the corresponding
|
||||
% x0 and y0 values.
|
||||
in_range = (T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) < 1 & T(2,:) < 1).';
|
||||
x0 = T(3,in_range).';
|
||||
y0 = T(4,in_range).';
|
||||
|
||||
% Compute how far along each line segment the intersections are.
|
||||
if nargout > 2
|
||||
iout = i(in_range) + T(1,in_range).';
|
||||
jout = j(in_range) + T(2,in_range).';
|
||||
end
|
||||
end
|
||||
|
||||
% Plot the results (useful for debugging).
|
||||
% plot(x1,y1,x2,y2,x0,y0,'ok');
|
||||
|
||||
function y = mvmin(x)
|
||||
% Faster implementation of movmin(x,k) when k = 1.
|
||||
y = min(x(1:end-1),x(2:end));
|
||||
|
||||
function y = mvmax(x)
|
||||
% Faster implementation of movmax(x,k) when k = 1.
|
||||
y = max(x(1:end-1),x(2:end));
|
||||
@@ -0,0 +1,115 @@
|
||||
% SHOW_SPATIAL_DISTRIBUTION plot distribution of a variable, you can also use scatter or scatter_hsv
|
||||
%
|
||||
% show_spatial_distribution(pos, values, symmetrize, plot_points, range, px_scale )
|
||||
%
|
||||
% ** pos positions for each value
|
||||
% ** val plotted values
|
||||
% ** symmetrize (bool) if true make the caxis symmetric around 0
|
||||
% ** plot_points (bool) if true plot the positions where are provided values located
|
||||
% ** range array 2x1 of min / max range
|
||||
% ** px_scale size of a single pixel
|
||||
|
||||
%
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function show_spatial_distribution(pos, values, symmetrize, plot_points, range, px_scale )
|
||||
|
||||
|
||||
pos = double(pos);
|
||||
values = squeeze(double(values));
|
||||
if nargin < 3; symmetrize = false; end
|
||||
if nargin < 4; plot_points = true; end
|
||||
if nargin < 5 || isempty(range); range = [min(values(:)), max(values(:))]; end
|
||||
if nargin < 6; px_scale = 1; end
|
||||
|
||||
if range(1) == range(2)
|
||||
range(1) = 0;
|
||||
range(2) = max(range(1),1);
|
||||
range = sort(range);
|
||||
end
|
||||
|
||||
% remove missing data
|
||||
missing = isnan(values);
|
||||
pos(missing,:) = [];
|
||||
values(missing) = [];
|
||||
|
||||
ax = [min(pos(:,1)), max(pos(:,1)), min(pos(:,2)), max(pos(:,2))];
|
||||
N = max(100, 4*sqrt(length(pos)));
|
||||
XI = linspace(ax(1), ax(2), N);
|
||||
YI = linspace(ax(3), ax(4), N)';
|
||||
warning('off','all')
|
||||
Z = griddata(pos(:,1),pos(:,2),real(values),XI,YI,'linear');
|
||||
if ~isreal(values)
|
||||
Z = Z + 1i*griddata(pos(:,1),pos(:,2),imag(values),XI,YI,'linear');
|
||||
end
|
||||
warning('on','all')
|
||||
|
||||
|
||||
if isreal(Z)
|
||||
imagesc(px_scale*XI, px_scale*YI, Z, range)
|
||||
colormap gray
|
||||
else
|
||||
imagesc_hsv(Z)
|
||||
end
|
||||
if plot_points
|
||||
hold on
|
||||
plot(px_scale*pos(:,1), px_scale*pos(:,2), 'wo')
|
||||
hold off
|
||||
axis equal tight
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,129 @@
|
||||
% PTYCHO_PLOT_WRAPPER wrapper around the default ptychoshelves plotting routine
|
||||
%
|
||||
% ptycho_plot_wrapper(self, par, fourier_error)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
|
||||
%% PLOTTING
|
||||
function ptycho_plot_wrapper(self, par, fourier_error)
|
||||
%% wrapper to the cSAXS default plotting function
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
p = par.p;
|
||||
p.object_size = ceil(p.object_size .* ( self.Np_p ./ p.asize)); % modify the size in case of presolver with different probe size
|
||||
p.asize = self.Np_p;
|
||||
|
||||
p.numobjs = size(self.object,1);
|
||||
Nlayers = size(self.object,2);
|
||||
p.object = {};
|
||||
for ii = 1:p.numobjs
|
||||
p.object_size(ii,:) = self.Np_o;
|
||||
p.object{ii} = [];
|
||||
for jj = 1:Nlayers
|
||||
p.object{ii}(:,:,1,jj) = Ggather(utils.crop_pad(self.object{ii,jj}, p.object_size));
|
||||
end
|
||||
end
|
||||
p.object_modes = par.object_modes;
|
||||
p.probe_modes = par.probe_modes;
|
||||
p.probes = [];
|
||||
for ii = 1:p.probe_modes
|
||||
p.probes(:,:,:,ii) = Ggather(self.probe{ii}(:,:,:,1));
|
||||
end
|
||||
p.dx_spec=[self.pixel_size]/self.relative_pixel_scale;
|
||||
p.engines = {struct()};
|
||||
|
||||
iterations = Ggather(find(any(~isnan(fourier_error),2)));
|
||||
p.engines{1}.error_metric_final = struct();
|
||||
p.engines{1}.error_metric_final.iteration=iterations;
|
||||
p.engines{1}.error_metric_final.value = Ggather(fourier_error( iterations,:));
|
||||
p.engines{1}.error_metric_final.method = par.method;
|
||||
p.engines{1}.error_metric_final.err_metric = par.likelihood;
|
||||
|
||||
position_offset = 1+floor((p.object_size-self.Np_p)/2);
|
||||
for ii = 1:p.numscans
|
||||
ind = p.scanidxs{ii};
|
||||
p.positions(ind,:) = self.modes{1}.probe_positions(ind,[2,1]) + position_offset(p.share_object_ID(ii),:);
|
||||
end
|
||||
|
||||
p.plot.extratitlestring = '';
|
||||
p.plot.show_only_FOV = true;
|
||||
p.plot.mask_bool = false;
|
||||
p.plot.log_scale = [1 1];
|
||||
p.plot.subplwinobj_dir = 'vertical';
|
||||
p.plot.show_layers = true;
|
||||
p.plot.residua = true;
|
||||
|
||||
if isempty(p.plot.obtitlestring)
|
||||
p.plot.obtitlestring = [core.generate_scan_name(p) ' '];
|
||||
end
|
||||
if isempty(p.plot.prtitlestring)
|
||||
p.plot.prtitlestring = [core.generate_scan_name(p) ' '];
|
||||
end
|
||||
|
||||
if par.share_object
|
||||
p.share_object_ID = ones(p.numobjs,1);
|
||||
else
|
||||
p.share_object_ID = 1:p.numobjs;
|
||||
end
|
||||
core.analysis.plot_results(p, 'final', true)
|
||||
|
||||
end
|
||||
@@ -0,0 +1,241 @@
|
||||
% REPORT_REFINED_GEOMETRY report results of the geometry refinenement in a readable way
|
||||
%
|
||||
% p = report_refined_geometry(self, param, p)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** param structure containing parameters for the engines
|
||||
% ** p ptychoshelves p structure
|
||||
%
|
||||
% returns:
|
||||
% ** p updated ptychoshelves p structure
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function p = report_refined_geometry(self, param, p)
|
||||
|
||||
import utils.*
|
||||
scale = 1;
|
||||
|
||||
%% GENERATE REPORT ABOUT GEOMETRY REFINEMENT
|
||||
if isempty(p.affine_matrix)
|
||||
p.affine_matrix = diag([1,1]);
|
||||
end
|
||||
% aux function for printing results
|
||||
mat2str=@(matrix)sprintf(' [%.4g , %.4g ; %.4g , %.4g ] ', reshape(matrix',[],1));
|
||||
|
||||
|
||||
if ~isempty(self.affine_matrix) && param.probe_position_search < param.number_iterations && ~isempty(param.probe_geometry_model)
|
||||
for ii = 1:length(self.affine_matrix)
|
||||
self.affine_matrix{ii} = rot90(self.affine_matrix{ii},2)'; % rotation is important to match the coordinates with other engines
|
||||
end
|
||||
|
||||
for ii = 1:length(self.affine_matrix)
|
||||
p.affine_matrix_refined{ii} = p.affine_matrix * self.affine_matrix{ii};
|
||||
end
|
||||
if param.Nscans == 2 && param.share_object && param.mirror_objects
|
||||
%% use mirrored scans to refine scanning geometry
|
||||
verbose(0, '========================================================= ')
|
||||
verbose(0, '==== Geometry parameters for shared 0/180 deg scans ===== ')
|
||||
verbose(0, '========================================================= ')
|
||||
verbose(0, '')
|
||||
% find difference between 0 and 180 ,
|
||||
affine_mat_relative = sqrtm(self.affine_matrix{1} * self.affine_matrix{2})*p.affine_matrix;
|
||||
% keep only nondiagonal terms
|
||||
affine_mat_relative = eye(2) + (1-eye(2)).*affine_mat_relative;
|
||||
|
||||
verbose(0, '=============== RELATIVE (0vs180deg) GEOMETRY REFINEMENT ===============')
|
||||
verbose(0, '(apply p.affine_matrix manually to your template)')
|
||||
verbose(0, 'p.affine_matrix = %s ', mat2str(affine_mat_relative))
|
||||
[~, ~, rotation, shear] = math.decompose_affine_matrix(affine_mat_relative);
|
||||
verbose(0, 'This correponds to the following parameters: [rotation=%.3fdeg , shear=%.3fdeg] ', [rotation, shear])
|
||||
|
||||
% find affine matrix that stays contant when moving from 0 to
|
||||
% 180 deg, include also the diagonal terms from original affine
|
||||
% matrix
|
||||
affine_mat_global = sqrtm(self.affine_matrix{1} * ( [1,-1;-1,1] .* self.affine_matrix{2}));
|
||||
affine_mat_global = affine_mat_global* diag(diag(p.affine_matrix));
|
||||
|
||||
verbose(0, '====================================================================================')
|
||||
verbose(0, '')
|
||||
|
||||
scale = mean(diag(affine_mat_global));
|
||||
|
||||
else
|
||||
%% use conventional scans to refine scanning geometry
|
||||
median_affine_matrix = median(cat(3,p.affine_matrix_refined{:}),3);
|
||||
verbose(0, '')
|
||||
verbose(0, '========= 2D PTYCHO GEOMETRY REFINEMENT, apply manually to your template ===========')
|
||||
verbose(0, 'p.affine_matrix = %s' , mat2str(median_affine_matrix))
|
||||
verbose(0, '====================================================================================')
|
||||
verbose(0, '')
|
||||
verbose(0, 'Advanced: ======================== AFFINE CORRECTION OF SCANNER AXIS ====================')
|
||||
verbose(0, 'Advanced: (for control system of piezo scanner, important for calibration of cSAXS fast FZP scanner)')
|
||||
verbose(0, 'Advanced: correction_matrix = inv(p.affine_matrix) = %s ', mat2str(inv(median_affine_matrix)))
|
||||
verbose(0, 'Advanced: ===============================================================================')
|
||||
verbose(0, 'Note: Use scans at 0 and 180 deg with eng.share_object == true && eng.mirror_objects == true to get estimation of the 0vs180deg affine matrix requied for ptychotomography')
|
||||
verbose(0, '')
|
||||
verbose(0, '')
|
||||
verbose(0, '==== Geometry parameters for each scan===== ')
|
||||
for ii = 1:length(p.affine_matrix_refined)
|
||||
[scale, asymmetry, rotation, shear] = math.decompose_affine_matrix(p.affine_matrix_refined{ii});
|
||||
verbose(0, 'Scan #%i: [scale=%.4f , asymmetry=%.3f , rotation=%.3fdeg , shear=%.3fdeg, shift = %.1f %.1fpx ] ', [p.scan_number(ii), scale, asymmetry, rotation, shear, self.shift_scans(:,ii)'])
|
||||
end
|
||||
scale = mean(diag(median_affine_matrix));
|
||||
end
|
||||
|
||||
%% evaluate results if the simulated geometry
|
||||
if isfield(p,'simulation') && check_option(p.simulation,'affine_matrix')
|
||||
% report for simulation
|
||||
verbose(-2, '')
|
||||
verbose(-2, '========== IDEAL AFFINE MATRIX vs RECONSTRUCTED AFFINE MATRIX ====')
|
||||
verbose(-2, 'ideal_affine_matrix = %s ', mat2str(p.simulation.affine_matrix))
|
||||
if param.Nscans == 2 && param.share_object && param.mirror_objects
|
||||
affine_mat = diag(diag(affine_mat_global)) + affine_mat_relative - eye(2);
|
||||
else
|
||||
affine_mat = median_affine_matrix;
|
||||
end
|
||||
verbose(-2, 'refined_affine_matrix = %s ', mat2str(affine_mat))
|
||||
verbose(-2, '==================================================================')
|
||||
verbose(-2, '')
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if param.number_iterations > param.detector_rotation_search && ~isempty(param.probe_geometry_model)
|
||||
if isfield(p,'simulation') && check_option(p.simulation,'sample_rotation_angles')
|
||||
% report for simulation
|
||||
verbose(-2, '')
|
||||
verbose(-2, '==== SIMULATION: IDEAL vs RECONSTRUCTED DETECTOR ROTATION CORRECTION =======')
|
||||
verbose(-2, 'ideal camera rotation = %.3f deg reconstructed camera rotation = %.3f deg', p.simulation.sample_rotation_angles(3), self.detector_rotation(1))
|
||||
verbose(-2, '=============================================================================')
|
||||
verbose(-2, '')
|
||||
else
|
||||
% report for real data
|
||||
verbose(0, '')
|
||||
verbose(0, '========== RECONSTRUCTED DETECTOR ROTATION CORRECTION =====================')
|
||||
verbose(0, '(misalignement between detector and the rotation axis, correct by camera rotation)')
|
||||
verbose(0, 'Reconstructed camera rotation = %.3f deg', self.detector_rotation(1) + param.sample_rotation_angles(3))
|
||||
verbose(0, '=============================================================================')
|
||||
verbose(0, '')
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if param.number_iterations > param.detector_scale_search && ~isempty(param.probe_geometry_model)
|
||||
if isfield(p,'simulation') && isfield(p.simulation, 'affine_matrix') && param.detector_scale_search
|
||||
% report for simulation
|
||||
verbose(-2, '')
|
||||
verbose(-2, '============ SIMULATION: IDEAL vs RECONSTRUCTED DETECTOR SCALE =============')
|
||||
if check_option(p.simulation, 'z')
|
||||
scale_z = p.z / p.simulation.z;
|
||||
else
|
||||
scale_z = 1;
|
||||
end
|
||||
verbose(-2, 'ideal scale = %.3f reconstructed scale = %.3f ', 1/(mean(diag(p.simulation.affine_matrix)) * scale_z), scale/self.detector_scale)
|
||||
verbose(-2, '=============================================================================')
|
||||
verbose(-2, '')
|
||||
else
|
||||
% report for real data
|
||||
verbose(0, '')
|
||||
verbose(0, '========== RECONSTRUCTED DETECTOR SCALE CORRECTION ========================')
|
||||
verbose(0, '(relative scaling error of the provided reconstruction pixel p.dx_spec )')
|
||||
verbose(0, 'reconstructed scale = %.3f ', scale/self.detector_scale)
|
||||
verbose(0, '=============================================================================')
|
||||
verbose(0, '')
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if isinf(self.z_distance) && ...
|
||||
((param.detector_scale_search < param.number_iterations) ...
|
||||
|| (param.probe_position_search < param.number_iterations && any(ismember(param.probe_geometry_model, 'scale'))))
|
||||
|
||||
verbose(-2, '')
|
||||
verbose(-2, '========== RECONSTRUCTED DETECTOR DISTANCE CORRECTION =====================')
|
||||
|
||||
if isfield(p,'simulation') && check_option(p.simulation, 'z')
|
||||
% report for simulation
|
||||
verbose(-2, '==== Compare ideal (simulated) distance and distance refined by ptychography')
|
||||
if isfield(p.simulation, 'affine_matrix')
|
||||
aff_corr_scale = mean(diag(p.simulation.affine_matrix));
|
||||
else
|
||||
aff_corr_scale = 1;
|
||||
end
|
||||
verbose(-2, 'ideal camera distance = %.4f estimated camera distance = %.4f', p.simulation.z/aff_corr_scale, p.z / (scale * self.detector_scale))
|
||||
else
|
||||
% report for measurements
|
||||
verbose(-2, '(needs to be corrected by adjusting p.z parameter in the template)')
|
||||
verbose(-2, '==== Scale error corresponds to the following p.z value')
|
||||
verbose(-2, 'p.z = %.4f (error=%.2g%%)', p.z/(scale*self.detector_scale), 100*(1/(scale*self.detector_scale)-1))
|
||||
if param.probe_position_search < param.number_iterations && ~isempty(param.probe_geometry_model)
|
||||
verbose(0, '(corrected p.affine_matrix to be used with the new p.z value, add manually to your template)')
|
||||
if exist('median_affine_matrix', 'var')
|
||||
affine_mat = median_affine_matrix;
|
||||
else
|
||||
affine_mat = affine_mat_relative;
|
||||
end
|
||||
verbose(0, 'p.affine_matrix = %s ', mat2str(affine_mat / (scale/self.detector_scale) ))
|
||||
end
|
||||
end
|
||||
verbose(-2, '=============================================================================')
|
||||
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,178 @@
|
||||
% INITIAL_CHECKS check if the inputs are valid or try to correct them
|
||||
%
|
||||
% [self,par] = initial_checks(self, par)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ par structure containing parameters for the engines
|
||||
|
||||
function [self,par] = check_inputs(self, par)
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
[self.Np_o(1),self.Np_o(2),~] = size(self.object{1});
|
||||
[self.Np_p(1),self.Np_p(2),~] = size(self.probe{1});
|
||||
par.Nrec = 1;
|
||||
par.Nscans = length(self.reconstruct_ind);
|
||||
|
||||
if ischar(par.extension)
|
||||
par.extension = {par.extension};
|
||||
end
|
||||
|
||||
for ii = 1:numel(self.object)
|
||||
assert(all(isfinite(self.object{ii}(:))), 'Provided object contains nan / inf')
|
||||
end
|
||||
|
||||
for ii = 1:numel(self.probe)
|
||||
assert(all(isfinite(self.probe{ii}(:))), 'Provided probes contain nan / inf')
|
||||
end
|
||||
|
||||
Np_d = size(self.diffraction);
|
||||
if any(self.Np_p ~= Np_d(1:2)) % && isempty(self.modF_ROI)
|
||||
error('Size of probe and data is different')
|
||||
end
|
||||
|
||||
tmp = self.diffraction(1:self.Np_p(1)*7:end); % get some small sample
|
||||
tmp = tmp * 2^(par.upsampling_data_factor*2); % remove upsampling effects
|
||||
if par.compress_data && max(abs((tmp - round(tmp)))) > 0.2
|
||||
verbose(1,'Data are not integers, cannot use compression')
|
||||
par.compress_data = false;
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%% accelerated solver %%%%%%%%%%%%%%%%%%%
|
||||
if par.accelerated_gradients_start < par.number_iterations && ~is_method(par, 'MLs')
|
||||
verbose(3, 'accelerated_gradients_start < number_iterations is supported only for MLc engine')
|
||||
par. accelerated_gradients_start = inf;
|
||||
end
|
||||
|
||||
% if par.accelerated_gradients_start < par.number_iterations && par.momentum > 0 && is_method(par, 'ML')
|
||||
% error('accelerated_gradients_start < inf cannot be used if momemtum > 0 ')
|
||||
% end
|
||||
|
||||
%%%%%%%%%%%%% variable probe %%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if ~par.variable_probe
|
||||
par.variable_probe_modes = 0;
|
||||
end
|
||||
|
||||
if par.variable_probe && par.variable_probe_modes > 0 && ~is_method(par, {'PIE', 'ML'})
|
||||
warning('Variable probe implemented only for PIE and ML')
|
||||
par.variable_probe = false;
|
||||
end
|
||||
|
||||
if par.variable_probe && par.variable_probe_modes == 0
|
||||
error('Choose more than 0 variable_probe_modes for OPRP')
|
||||
par.variable_probe_modes = 1;
|
||||
end
|
||||
|
||||
if par.variable_probe && ~par.share_probe && is_method(par, 'PIE')
|
||||
par.share_probe = true;
|
||||
% variable probe means automatically shared variable probe
|
||||
end
|
||||
|
||||
if ~is_method(par, {'PIE', 'ML'}) && strcmpi(par.likelihood, 'poisson')
|
||||
warning('Poisson likelihood supported only for PIE methods')
|
||||
par.likelihood = 'L1';
|
||||
end
|
||||
|
||||
if ~ismember(lower( par.likelihood), {'l1','poisson'})
|
||||
error('Unsupported error estimation')
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%% check if position correction is allowed
|
||||
if ~ is_method(par, {'PIE', 'ML'}) && par.probe_position_search < par.number_iterations
|
||||
verbose(2, 'Position correction supported only for PIE/ML methods ')
|
||||
par.probe_position_search = inf;
|
||||
end
|
||||
|
||||
if any(~ismember(par.probe_geometry_model, {'scale', 'asymmetry', 'rotation', 'shear'}))
|
||||
missing_option = setdiff(par.probe_geometry_model, {'scale', 'asymmetry', 'rotation', 'shear'} );
|
||||
error('Unsupported geometry model option: "%s"', missing_option{1})
|
||||
end
|
||||
|
||||
if par.probe_position_search < par.number_iterations && par.detector_scale_search < par.number_iterations && any(ismember(par.probe_geometry_model,'scale'))
|
||||
error('Do not use probe_position_search with probe_geometry_model==''scale'' and detector_scale_search together')
|
||||
end
|
||||
|
||||
%%%%%% checks for the multilayer method %%%%%%%%%%%%%%%%
|
||||
%Note: self.z_distance is first initialized in load_from_p.m, where a
|
||||
%vacuum layer is appended: self.z_distance = [p.delta_z, inf] for far-field
|
||||
par.Nlayers = length(self.z_distance);
|
||||
if par.Nlayers > 1 && isinf(self.z_distance(end))
|
||||
% Added by ZC: exclude the last vacuum (inf) layer for multisluce
|
||||
par.Nlayers = par.Nlayers - 1;
|
||||
end
|
||||
|
||||
assert(sum(~isfinite(self.z_distance)) <= 1, 'Provided distanced of layers are not possible to be used')
|
||||
|
||||
if par.Nlayers > 1 && ~is_method(par, {'PIE', 'ML'})
|
||||
error('Multilayer extension is supported only for PIE/ML methods')
|
||||
end
|
||||
|
||||
% Added by ZC. allow user to specify the layer used for position correction
|
||||
if ~isfield(par,'layer4pos') || isempty(par.layer4pos)
|
||||
par.layer4pos = ceil(par.Nlayers/2);
|
||||
end
|
||||
|
||||
%%%%%%%%%% fast scanning %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if is_used(par, 'fly_scan') && ~is_method(par, {'PIE', 'ML'})
|
||||
error('Fly scan is supported only for PIE/ML methods')
|
||||
end
|
||||
|
||||
if is_used(par, 'fly_scan')
|
||||
if par.Nmodes == 1
|
||||
warning('Flyscan has no effect with a single mode')
|
||||
par.extension = setdiff(par.extension, 'fly_scan');
|
||||
par.apply_subpix_shift= true;
|
||||
end
|
||||
par.Nrec = par.Nmodes;
|
||||
% par.apply_multimodal_update = true;
|
||||
end
|
||||
|
||||
%%%%%%%% nearfield %%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if par.estimate_NF_distance < par.number_iterations && isinf(self.z_distance(end))
|
||||
error('estimate_NF_distance valid only for nearfield mode')
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%% OTHER %%%%%%%%%%%%%%%%%%%%
|
||||
if strcmpi(par.likelihood, 'poisson') && par.background_detection && ~isinf(par.background_detection)
|
||||
error('Background detection does not work well with Poisson likelihood')
|
||||
end
|
||||
|
||||
if prod(self.Np_p) *self.Npos > intmax('int32') && par.keep_on_gpu && is_method(par, {'MLs', 'ePIE'})
|
||||
warning('Dataset as more than 2147483647 elements (max of int32). Set par.keep_on_gpu to false')
|
||||
par.keep_on_gpu = false;
|
||||
end
|
||||
|
||||
if any(self.noise(:) == 0) && par.relax_noise
|
||||
warning('Some values of expected noise are 0')
|
||||
self.noise = max(0.5, self.noise);
|
||||
end
|
||||
|
||||
if par.Nrec > max([par.Nmodes, par.probe_modes , par.object_modes])
|
||||
warning('Number of modes is too high')
|
||||
end
|
||||
|
||||
if length(self.probe_positions) ~= self.Npos
|
||||
self.probe_positions = [];
|
||||
end
|
||||
|
||||
if par.mirror_objects && par.Nscans ~= 2
|
||||
error('Object mirroring is supported only for two scans')
|
||||
end
|
||||
|
||||
%%%%%% position correction %%%%%
|
||||
if ~is_method(par, {'PIE', 'ML'}) && par.probe_position_search < par.number_iterations
|
||||
warning('Position corrections works only for PIE/ML methods')
|
||||
end
|
||||
|
||||
if is_method(par, {'PIE', 'ML'}) && par.probe_position_search < par.number_iterations && ~(par.apply_subpix_shift || is_used(par,'fly_scan'))
|
||||
verbose(2,'Subpixel shifting is strongly recommended for position refinement => enforcing par.apply_subpix_shift = true')
|
||||
par.apply_subpix_shift = true;
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,131 @@
|
||||
% INITIALIZE generate list of default parameters
|
||||
% [param] = initialize
|
||||
%
|
||||
%
|
||||
% returns:
|
||||
% ++ param structure containing parameters for the engines
|
||||
|
||||
function [param] = get_defaults
|
||||
|
||||
%%%%%%%%%%%%%% GPU SETTINGS %%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
param.use_gpu = true; % use GPU if possible
|
||||
param.keep_on_gpu = true; % keep the data all the time on GPU
|
||||
param.compress_data = true; % apply online compress on the GPU data
|
||||
param.gpu_id = []; % default GPU id, [] means choosen by matlab
|
||||
param.check_gpu_load = true;
|
||||
param.obj_size_limit_on_gpu = inf; % maximum object size (in MB) allowed on gpu. Automatically use cpu if exceed the limit.
|
||||
|
||||
%% basic recontruction parameters
|
||||
%% PIE
|
||||
param.beta_object = 1;
|
||||
param.beta_probe = 1; % step size, faster convergence , more instable ??
|
||||
%% DM
|
||||
param.pfft_relaxation = 0.1;
|
||||
param.probe_inertia = 0.3; % add inertia to the probe reconstruction to avoid oscilations
|
||||
%% general
|
||||
param.share_probe = true;
|
||||
param.share_object = false;
|
||||
param.delta = 0; % press values to zero out of the probe area !! illim < max*delta is removed
|
||||
param.relax_noise = 0.0; % relaxation for noise, lower => slower convergence, more robust
|
||||
param.positivity_constraint_object = 0; % enforce weak positivity in object
|
||||
param.amplitude_threshold_object = inf; % enforce maximum amplitude to object. Values larger than the threshold is set to 1
|
||||
param.Nmodes = 1; % number of multi apertures , always better to start wih one !!
|
||||
param.probe_modes = 1; % number of probes
|
||||
param.object_modes = 1; % number of multi apertures , always better to start wih one !!
|
||||
param.probe_change_start = 1; % iteration when the probe reconstruction is started
|
||||
param.object_change_start = 1;% iteration when the object reconstruction is started
|
||||
param.number_iterations = 300 ;
|
||||
param.grouping = inf;
|
||||
param.method = 'MLs';
|
||||
param.likelihood = 'L1' ; % l1 or poisson, - choose which likelihood should be used for solver, poisson is suported only for PIE
|
||||
param.verbose_level = 1;
|
||||
param.plot_results_every = 50;
|
||||
|
||||
|
||||
%tilted_sample_LB : I don't think this is needed
|
||||
|
||||
param.tilt_x = 0.0; %%LB
|
||||
param.tilt_y = 0.0; %%LB
|
||||
|
||||
|
||||
param.remove_residues = false; % autodetect and remove phase residua
|
||||
param.extension = '';
|
||||
|
||||
%% data handling
|
||||
param.upsampling_data_factor = 0; % assume that the data were created by upsampling using function utils.unbinning
|
||||
|
||||
param.damped_mask = 5e-3; % if damped_mask = 0 -> do nothing, if 1>x>0 -> push masked regions weakly towards measured magnitude value in each iteration
|
||||
|
||||
param.background_detection = false;
|
||||
param.background_width = inf;
|
||||
|
||||
%% ADVANCED OPTIONS
|
||||
|
||||
param.object_regular = [0, 0]; % enforce smoothness !!!, use between [0-0.1 ]
|
||||
param.remove_object_ambiguity = true; % remove intensity ambiguity between the object and the probes
|
||||
param.variable_probe = false; % Use SVD to account for variable illumination during a single (coupled) scan
|
||||
param.apply_subpix_shift = false; % apply FFT-based subpixel shift, important for good position refinement but it is slow
|
||||
|
||||
param.probe_geometry_model = {'scale', 'asymmetry', 'rotation', 'shear'}; % list of free parameters in the geometry model
|
||||
param.probe_position_search = inf;
|
||||
param.apply_relaxed_position_constraint = true; %added by YJ: allow position update without geom model constraint
|
||||
param.update_pos_weight_every = inf; %added by YJ: allow position weight to be updated multiple times. Default = inf: only calculate once
|
||||
param.max_pos_update_shift = 0.1; %added by YJ: allow user to specify the maximum position update allowed in each iteration. Default = 0.1 (pixel).
|
||||
param.probe_position_search_momentum = 0; % added by YJ. enable momentum acceleration for position correction. Default = 0: no acceleration.
|
||||
|
||||
param.probe_fourier_shift_search = inf;
|
||||
param.estimate_NF_distance = inf;
|
||||
param.detector_rotation_search = inf; % rotation of the detector axis with respect to the sample axis, similar as rotation option in the position refinement geometry model but works also for 0/180deg rotation shared scans
|
||||
param.detector_scale_search = inf; % pixel scale of the detector, can be used to refine propagation distance in ptycho
|
||||
|
||||
param.apply_multimodal_update = false; % use thibault modes to get higher signal, it can cause isses, not real gain if blur method is used
|
||||
param.probe_backpropagate = 0;
|
||||
param.beta_LSQ = 0.9; % use predictive step length
|
||||
param.delta_p = 0.1; % LSQ damping constant
|
||||
param.variable_probe_modes = 1; % OPRP settings
|
||||
param.variable_probe_smooth = 0;% OPRP settings
|
||||
param.variable_intensity = false; % account fort variable intensity
|
||||
param.relaxed_object_constrain = 0; % enforce known object (inputs.object_orig)
|
||||
param.probe_position_error_max = 10e-9; % max expected error of the stages
|
||||
param.probe_fourier_shift_search = inf;
|
||||
param.momentum = 0; % use mementume accelerated gradient decsent method
|
||||
|
||||
param.regularize_layers = 0; % 0<R<1 -> apply regularization on the reconstructed layers
|
||||
param.preshift_ML_probe = true; % multilayer ptycho extension: if true, assume that the provided probe is reconstructed in center of the sample.
|
||||
param.layer4pos = []; % Added by ZC. speficy which layer is used for position correction
|
||||
param.init_layer_select = []; % Added by YJ. Select layers in the initial object for pre-processing If empty (default): use all layers.
|
||||
param.init_layer_preprocess = ''; % Added by YJ. Specify how to pre-process initial layers
|
||||
% '' or 'all' (default): use all layers (do nothing)
|
||||
% 'avg': average all layers
|
||||
% 'avg1': keep one averaged layer
|
||||
% 'interp': interpolate layers using spline method. Need to specify desired depths in init_layer_interp
|
||||
param.init_layer_interp = []; % Specify desired depths for interpolation. The depths of initial are [1:Nlayer_init]. If empty (default), no interpolation
|
||||
param.init_layer_append_mode = ''; % Added by YJ. Specify how to initialize extra layers
|
||||
% '' or 'vac' (default): add vacuum layers
|
||||
% 'edge': append 1st or last layers
|
||||
% 'avg': append averaged layer
|
||||
param.init_layer_scaling_factor = 1; % Added by YJ. Scale all layers. Default: 1 (no scaling). Useful when delta_z is changed
|
||||
|
||||
param.initial_probe_rescaling = true; % find the optimal scaling correction for the provided probe guess in the initial iteration
|
||||
param.accelerated_gradients_start = inf; % use accelerated gradients to speed up the convergence
|
||||
param.align_shared_objects = false; % align multiple objects from various scans
|
||||
|
||||
% extra analysis
|
||||
param.get_fsc_score = false; % measure evolution of the Fourier ring correlation during convergence
|
||||
param.mirror_objects = false; % mirror objects, useful for 0/180deg scan sharing
|
||||
param.align_shared_objects = false; % align the objects before sharing them onto single one
|
||||
|
||||
% fly scans
|
||||
param.flyscan_offset = 0;
|
||||
param.flyscan_dutycycle = 1;
|
||||
%rng('default');
|
||||
%rng('shuffle');
|
||||
|
||||
% convergence check - stop reconstruction if fourier error is larger than the previous one by given (relative) threshold.
|
||||
param.fourier_error_threshold = inf; % default: no convergence check.
|
||||
|
||||
% I/O
|
||||
param.save_init_probe = false; % Added by YJ. If true, save initial probe function in the .mat output file. Default is false.
|
||||
param.save_images = {'obj_ph','obj_ph_sum','obj_ph_stack','probe'}; % Added by YJ. Save intermediate results as tiff images.
|
||||
% Options: {'obj_ph','obj_ph_sum','obj_ph_stack','obj_mag','obj_ph_sum','obj_mag_stack','probe_mag','probe'}
|
||||
end
|
||||
@@ -0,0 +1,161 @@
|
||||
% GET_PARALLEL_BLOCKS Find the optimal groups to be solved in parallel on GPU/CPU
|
||||
%
|
||||
%[cache, par] = get_parallel_blocks(self, par, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ par structure containing parameters for the engines
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
function [cache, par] = get_parallel_blocks(self, par, cache)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%% FIND MAXIMAL GROUP SIZE IF GPU IS USED %
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
grouping_0 = par.grouping;
|
||||
|
||||
par.grouping = round(min(self.Npos, par.grouping));
|
||||
|
||||
global gpu
|
||||
|
||||
if par.use_gpu
|
||||
%% !! very empirical estimation of the GPU memory requirements !!!
|
||||
% use the estimated memory requirements to prevent low memory issues
|
||||
|
||||
[required_mem_constant] = estimate_req_memory(self, par, 0);
|
||||
[required_mem] = estimate_req_memory(self, par, 1);
|
||||
% precheck size of the block and try to optimize size of the groups
|
||||
% allowed for given GPU
|
||||
max_group_size = floor( (gpu.AvailableMemory - required_mem_constant) ./ (required_mem - required_mem_constant));
|
||||
max_group_size = min(self.Npos, max_group_size);
|
||||
verbose(1,'Maximal possible grouping %i', max_group_size);
|
||||
|
||||
% if group size was set to infinity, is the maximal group size possible
|
||||
if isinf(grouping_0)
|
||||
par.grouping= max_group_size;
|
||||
else
|
||||
% otherwise use max_group_size as a top limit
|
||||
par.grouping = min(par.grouping, max_group_size);
|
||||
end
|
||||
|
||||
% adjust grouping to minimize overhead -> make the group sizes more
|
||||
% equal
|
||||
if is_method(par, {'ML', 'PIE'})
|
||||
% allows to calculate several scans together
|
||||
par.grouping = ceil(self.Npos/ceil(self.Npos/par.grouping));
|
||||
else
|
||||
% consider each scan separatelly
|
||||
Npos_scan = cellfun(@length, self.reconstruct_ind);
|
||||
par.grouping = max(ceil(Npos_scan./ceil(Npos_scan./par.grouping)));
|
||||
end
|
||||
|
||||
if par.grouping ~= grouping_0
|
||||
verbose(1,'Optimal grouping was changed from %i to %i ', grouping_0, par.grouping);
|
||||
end
|
||||
if par.grouping < 1
|
||||
error('Too low memory, use smaller dataset or try ePIE')
|
||||
end
|
||||
|
||||
verbose(1,'Selected grouping %i', par.grouping);
|
||||
|
||||
else
|
||||
if is_method(par, {'DM', 'ML'})
|
||||
par.grouping = self.Npos;
|
||||
end
|
||||
end
|
||||
|
||||
% precalculate distance matrix for pseudo ePIE / hPIE / MLs to get
|
||||
% least overlapping indices
|
||||
if is_method(par, {'ML', 'PIE'})
|
||||
if self.Npos/par.Nscans < 1e3 %added by YJ to save memory
|
||||
for ll = 1:par.Nscans
|
||||
dist_mat = single(distmat(self.probe_positions_0(self.reconstruct_ind{ll},:)));
|
||||
dist_mat(dist_mat==0 | dist_mat > max(self.Np_p)/2) = inf;
|
||||
cache.distances_matrix{ll} = dist_mat;
|
||||
end
|
||||
end
|
||||
end
|
||||
if is_method(par, 'MLc')
|
||||
% get higly overlapping subsets of indices for PIE / ML
|
||||
[cache.preloaded_indices_compact{1}.indices,cache.preloaded_indices_compact{1}.scan_ids] = ...
|
||||
get_close_indices(self, cache, par );
|
||||
elseif is_method(par, {'MLs', 'PIE'})
|
||||
% preload order of indices , generate several of them to add randomness
|
||||
for i = 1:min(par.number_iterations,10)
|
||||
[cache.preloaded_indices_sparse{i}.indices,cache.preloaded_indices_sparse{i}.scan_ids] = ...
|
||||
get_nonoverlapping_indices(self, cache, par );
|
||||
end
|
||||
end
|
||||
% get just some predefined sets of indices - RAAR, DM , !! order
|
||||
% does not matter
|
||||
[cache.preloaded_indices_simple{1}.indices,cache.preloaded_indices_simple{1}.scan_ids] = ...
|
||||
get_scanning_indices(self, cache, par );
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,696 @@
|
||||
% INITIALIZE_SOLVER initialize GPU ptycho reconstruction, generate cache values, fftshift data, etc
|
||||
%
|
||||
% [self, cache] = initialize_solver(self,par)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
|
||||
function [self, cache] = init_solver(self,par)
|
||||
|
||||
import engines.GPU_MS.shared.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import plotting.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
verbose(struct('prefix','GPU/CPU_MS-engine-init'))
|
||||
|
||||
par.Nscans = length(self.reconstruct_ind); %number of scans
|
||||
cache.skip_ind = setdiff(1:self.Npos,[self.reconstruct_ind{:}]); % wrong datasets to skip
|
||||
|
||||
if ~any(self.probe_support(:))
|
||||
self.probe_support = [];
|
||||
end
|
||||
%% avoid probe to be larger than a certain oversampling !!!!
|
||||
if isempty(self.probe_support)
|
||||
par.probe_backpropagate = 0;
|
||||
end
|
||||
|
||||
if ~isempty(self.background) && any(self.background(:) > 0)
|
||||
Background = self.background;
|
||||
elseif par.background_detection
|
||||
Background = 0;
|
||||
else
|
||||
Background = []; % array of background light
|
||||
end
|
||||
|
||||
Noise = [];
|
||||
%% prepare data / noise / mask
|
||||
if par.relax_noise && ~isempty(self.noise) && strcmp(par.likelihood, 'L1')
|
||||
Noise = self.noise;
|
||||
Noise = (sqrt(posit(self.diffraction + Noise)) - sqrt(posit(self.diffraction - Noise)))/2;
|
||||
Noise(self.diffraction == 0) = 1;
|
||||
disp('Using measured noise')
|
||||
Noise = max(0.5, Noise);
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%% PREPARE MASK AND DATA %%%%%%%%%%%%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%% prepare mask , note that bool in matlab has size of uint8 !!
|
||||
cache.mask_indices = [];
|
||||
if any(self.mask(:))
|
||||
Mask = [];
|
||||
% single mask
|
||||
if all(all(mean(self.mask,3) == self.mask(:,:,1)))
|
||||
Mask = self.mask(:,:,1);
|
||||
else
|
||||
% mask for each scan
|
||||
for ll = 1:par.Nscans
|
||||
ind = self.reconstruct_ind{ll};
|
||||
%if there is only one repeated mask over whole scan
|
||||
if all(all(all(bsxfun(@eq, self.mask(:,:,ind), self.mask(:,:,ind(1))))))
|
||||
Mask(:,:,ll) = self.mask(:,:,ind(1));
|
||||
end
|
||||
cache.mask_indices(ind) = ll;
|
||||
end
|
||||
end
|
||||
if isempty(Mask)
|
||||
% mask for each position
|
||||
Mask = self.mask; % otherwise just store original
|
||||
cache.mask_indices(ind) = 1:self.Npos;
|
||||
end
|
||||
% important to save memory
|
||||
if all(Mask(:) == 1 | Mask(:) == 0)
|
||||
Mask = logical(Mask );
|
||||
else
|
||||
Mask = uint8(Mask*255); % if there are nonlogical values in mask, store them as uint8 to save memory
|
||||
end
|
||||
else
|
||||
Mask = [];
|
||||
end
|
||||
|
||||
%% prepare diffraction data
|
||||
Diffraction = self.diffraction; % diffraction is intensity, not amplitude, comment by ZC
|
||||
if par.upsampling_data_factor
|
||||
% downsample the data down to original size to save memory
|
||||
Diffraction = utils.binning_2D(Diffraction, 2^par.upsampling_data_factor) * (2^(2*par.upsampling_data_factor));
|
||||
if ~isempty(Mask)
|
||||
Mask = utils.binning_2D(Mask, 2^par.upsampling_data_factor) == 1;
|
||||
end
|
||||
end
|
||||
|
||||
Diffraction = single(max(0,Diffraction));
|
||||
|
||||
|
||||
if ~isempty(Mask)
|
||||
if size(Mask,3) == par.Nscans && par.Nscans > 1
|
||||
for ll = 1:par.Nscans
|
||||
ind = self.reconstruct_ind{ll};
|
||||
Diffraction(:,:,ind) = Diffraction(:,:,ind) .* ~Mask(:,:,ll);
|
||||
end
|
||||
else
|
||||
Diffraction = Diffraction .* ~Mask;
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if ~isinf(self.z_distance(end)) % && mod(Ninf,2)~=0
|
||||
% assume inputs already fftshifted, but in case of nearfield
|
||||
% fftshift it back for the ASM propagator
|
||||
Noise = fftshift_2D(Noise);
|
||||
Diffraction = fftshift_2D(Diffraction);
|
||||
Mask = fftshift_2D(Mask);
|
||||
end
|
||||
|
||||
|
||||
%%%% compress data if requested %%%%%%
|
||||
if par.compress_data
|
||||
DATA_MAX = quantile(max2(abs(Diffraction)), 1-1e-2);
|
||||
C_factor_0 = 2; % compression factor >=2 seems to be safe, >=4 is pratically lossless
|
||||
if par.compress_data == 1 || DATA_MAX < 2^(2*8) / C_factor_0^2
|
||||
Diffraction = sqrt(single(Diffraction));
|
||||
if DATA_MAX < 2^(2*8) / C_factor_0^2
|
||||
% simple sqrt compression to 8 bits
|
||||
verbose(1, 'Online data compression to 8-bits')
|
||||
Diffraction = uint8(C_factor_0*Diffraction);
|
||||
cache.C_factor = C_factor_0;
|
||||
elseif DATA_MAX < 2^(2*16) / 16^2
|
||||
% failsafe option: sqrt compression to 16 bits
|
||||
verbose(1, 'Online data compression to 16-bits')
|
||||
cache.C_factor = 16; % use compression factor 16, to be super safe just because we have space
|
||||
Diffraction = uint16(cache.C_factor*Diffraction);
|
||||
else
|
||||
error('Online compression will fail')
|
||||
end
|
||||
elseif par.compress_data == 2
|
||||
% SVD subtraction compression to 8 bits (failsafe is compression to 16bits)
|
||||
% additionally remove some SVD modes
|
||||
Diffraction = sqrt(single(Diffraction));
|
||||
Nmodes = par.Nscans;
|
||||
[U,S,V] = fsvd(reshape(Diffraction,prod(self.Np_p),[]), Nmodes);
|
||||
ind_relevant = diag(S).^2/sum(diag(S).^2) > 1e-2; % more than 1% of power
|
||||
cache.US_diffraction = (U(:,ind_relevant)*S(ind_relevant,ind_relevant));
|
||||
cache.V_diffraction = V(:,ind_relevant);
|
||||
svd_Diffraction = round(reshape(cache.US_diffraction*cache.V_diffraction',[self.Np_p, self.Npos]));
|
||||
|
||||
%% compress
|
||||
cDiffraction = single(Diffraction) - svd_Diffraction;
|
||||
% reestimate optimal compression factor to keep values < 128
|
||||
C_factor = min(C_factor_0, 128/quantile(max2(abs(cDiffraction)), 1-1e-2));
|
||||
if C_factor > 3
|
||||
verbose(1, 'Online data compression to 8-bits + SVD')
|
||||
cache.C_factor = C_factor;
|
||||
cache.US_diffraction = cache.US_diffraction;
|
||||
cache.V_diffraction = cache.V_diffraction*C_factor;
|
||||
Diffraction = int8(cDiffraction*C_factor);
|
||||
elseif DATA_MAX < 2^(2*16) / 16^2
|
||||
% sqrt compression to 16 bits
|
||||
%warning(sprintf('Too high online compression of data, it may cause problems\n Compression factor is %2.2f but should be >= 2\n Switching from 8 to 16bits',C_factor))
|
||||
verbose(1, 'Online data compression to 16-bits')
|
||||
C_factor = 16;
|
||||
cache.C_factor = C_factor;
|
||||
Diffraction = uint16(C_factor*Diffraction);
|
||||
else
|
||||
error('Online compression will fail')
|
||||
end
|
||||
|
||||
clear svd_Diffraction cDiffraction
|
||||
|
||||
else
|
||||
error('Unimplented level of compression')
|
||||
end
|
||||
else
|
||||
% precalculate sqrt from the data, store as singles
|
||||
Diffraction = sqrt(single(max(0,Diffraction))); % diffraction is amplitude, comment by ZC
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% write back the data arrays
|
||||
self.diffraction = Diffraction; % diffraction is amplitude, comment by ZC
|
||||
self.mask = Mask;
|
||||
self.noise = Noise;
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%% PREPARE GEOMETRY, PROPAGATION, MODES%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
% precalculate ASM factor for propagation distance recovery
|
||||
[ASM_difference] = near_field_evolution_gradient(self.Np_p, self.lambda, self.pixel_size .*self.Np_p );
|
||||
cache.ASM_difference = fftshift(ASM_difference);
|
||||
|
||||
% custom propagator to account for tilted plane sample - this chuck is
|
||||
% basically not used since the lines bellow are commented out - LB
|
||||
if any(par.p.sample_rotation_angles(1:2)) && check_option(par.p, 'apply_tilted_plane_correction', 'propagation')
|
||||
% get propagators to the tilted plane
|
||||
[tilted_plane_propagate_fwd, tilted_plane_propagate_back] = ...
|
||||
get_tilted_plane_propagators(Garray(self.probe{1}), ...
|
||||
[par.p.sample_rotation_angles(1:2),0],...
|
||||
self.lambda, self.pixel_size);
|
||||
else
|
||||
tilted_plane_propagate_fwd = []; tilted_plane_propagate_back = [];
|
||||
end
|
||||
|
||||
|
||||
if ~iscell(self.affine_matrix)
|
||||
self.affine_matrix = {self.affine_matrix};
|
||||
end
|
||||
|
||||
%Note: par.Nmodes is # of probe modes (p.probe_modes). Assigned in
|
||||
%load_from_p.m
|
||||
% modes = cell(max(par.Nmodes, par.Nlayers),1);
|
||||
modes = cell(par.Nlayers,1); % corrected by Zhen Chen
|
||||
|
||||
%Comment by YJ: par.Nmodes seems to be # of modes for A-fly scan
|
||||
% for i = 1:max(par.Nmodes, par.Nlayers)
|
||||
%par.Nlayers equals to the # of slices in the object (excluding the
|
||||
%vacuum layer)
|
||||
for i = 1:par.Nlayers % modified by ZC
|
||||
verbose(2,'Creating new modes files ')
|
||||
modes{i}.lambda = self.lambda;
|
||||
|
||||
% decompose affine matrix into scale, asymmetry, rotation, shear
|
||||
%affine = scale*[1+asym/2,0; 0,1-asym/2]*[cosd(rot), sind(rot); -sind(rot), cosd(rot)] * [1,0;tand(shear),1];
|
||||
|
||||
affine_matrix = self.affine_matrix{min(i,end)};
|
||||
[scale, asymmetry, rotation, shear] = decompose_affine_matrix(affine_matrix);
|
||||
|
||||
% store initial geometry parameters
|
||||
modes{i}.scales = repmat(scale, 1,par.Nscans);
|
||||
modes{i}.asymmetry = repmat(asymmetry, 1,par.Nscans);
|
||||
modes{i}.shear = repmat(shear, 1,par.Nscans);
|
||||
modes{i}.rotation = repmat(rotation, 1,par.Nscans);
|
||||
modes{i}.affine_matrix = repmat(affine_matrix, 1,1,par.Nscans);
|
||||
modes{i}.shift_scans = zeros(2, par.Nscans);
|
||||
modes{i}.probe_scale_upd = 0;
|
||||
modes{i}.probe_rotation = ones(1,par.Nscans) * par.sample_rotation_angles(3); % one rotation per scan
|
||||
if par.mirror_objects
|
||||
modes{i}.probe_rotation = modes{i}.probe_rotation .* [1,-1]; % flip the coordinates for mirrored object (ie 0 vs 180deg rotation)
|
||||
end
|
||||
modes{i}.probe_rotation_all = zeros(self.Npos,1);
|
||||
for jj = 1:par.Nscans
|
||||
modes{i}.probe_rotation_all(self.reconstruct_ind{jj}) = modes{i}.probe_rotation(jj); % one rotation per scan
|
||||
end
|
||||
|
||||
distance = self.z_distance(min(end,i));
|
||||
|
||||
if ~isinf(distance)
|
||||
verbose(2, 'Layer %i distance %g um ', i, distance*1e6 )
|
||||
end
|
||||
modes{i}.distances = distance;
|
||||
if is_used(par, 'fly_scan') && (~isfield(modes{i}, 'probe_positions') || isempty(modes{i}.probe_positions) )
|
||||
%% get positions for fly scans
|
||||
self = prepare_flyscan_positions(self, par);
|
||||
modes{i}.probe_positions = self.modes{i}.probe_positions; %added by YJ. seems like a bug
|
||||
modes{i}.probe_positions_0 = self.probe_positions_0; %added by YJ. seems like a bug
|
||||
else
|
||||
%% get positions for normal tomo
|
||||
try % try to reuse the positions of there are saved
|
||||
modes{i}.probe_positions = self.modes{i}.probe_positions;
|
||||
verbose(2,'Using saved positions')
|
||||
catch
|
||||
if (modes{i}.scales(end) == modes{1}.scales(end)) && ~isempty(self.probe_positions)
|
||||
modes{i}.probe_positions = self.probe_positions;
|
||||
verbose(0,'Using saved positions')
|
||||
else
|
||||
verbose(2,'Using original positions')
|
||||
modes{i}.probe_positions = (affine_matrix*self.probe_positions_0')';
|
||||
end
|
||||
end
|
||||
try
|
||||
modes{i}.probe_positions_0 = self.modes{i}.probe_positions_0;
|
||||
catch
|
||||
modes{i}.probe_positions_0 = self.probe_positions_0;
|
||||
end
|
||||
|
||||
end
|
||||
modes{i}.probe_positions_update = { zeros(size(modes{i}.probe_positions)) };
|
||||
modes{i}.probe_positions_all = {modes{i}.probe_positions};
|
||||
modes{i}.probe_positions_weight = zeros(self.Npos, 1);
|
||||
if isfield(self, 'probe_fourier_shift') && ~isempty(self.probe_fourier_shift) && i == 1
|
||||
modes{i}.probe_fourier_shift = self.probe_fourier_shift;
|
||||
else
|
||||
modes{i}.probe_fourier_shift = zeros(self.Npos,2);
|
||||
end
|
||||
|
||||
if ~isempty(self.probe_support) && i <= par.Nrec
|
||||
modes{i}.probe_support = self.probe_support;
|
||||
if i == 1
|
||||
verbose(2,'Using real-space probe support')
|
||||
end
|
||||
else
|
||||
modes{i}.probe_support = [];
|
||||
end
|
||||
|
||||
if ~isempty(self.probe_support_fft) && i <= par.Nrec && ~check_option(par,'probe_support_tem')
|
||||
modes{i}.probe_support_fft = fftshift(self.probe_support_fft);
|
||||
if i == 1
|
||||
verbose(2,'Using far-field probe support')
|
||||
end
|
||||
elseif check_option(par,'probe_support_tem') % not shift for TEM aperture, by Zhen Chen
|
||||
modes{i}.probe_support_fft = self.probe_support_fft;
|
||||
else
|
||||
modes{i}.probe_support_fft = [];
|
||||
end
|
||||
|
||||
F = mean( self.pixel_size)^2 .* mean(self.Np_p) / (modes{i}.lambda * modes{i}.distances);
|
||||
if F ~= 0
|
||||
verbose(3,'Nearfield propagation: Fresnel number/Npix %3.3g', F)
|
||||
end
|
||||
scale = modes{i}.scales(end);
|
||||
modes{i}.ASM_factor = [] ;
|
||||
modes{i}.cASM_factor = [] ;
|
||||
|
||||
if ~isinf(modes{i}.distances(end)) % Forward Fresnel propagator in k-space, ASM, commented by ZC
|
||||
%% near field factor
|
||||
%ASM = exp( modes{i}.distances(end)* cache.ASM_difference);
|
||||
% modified by YJ: use H instead of dH (which is an approximation)
|
||||
%[~,ASM,~,~] = near_field_evolution(ones(self.Np_p), modes{i}.distances(end), self.lambda, self.pixel_size .*self.Np_p, true );
|
||||
tiltx = par.tilt_x*1e-3;
|
||||
tilty = par.tilt_y*1e-3;
|
||||
[~,ASM,~,~] = near_field_evolution(ones(self.Np_p), modes{i}.distances(end), self.lambda, self.pixel_size .*self.Np_p, true,tiltx,tilty );
|
||||
ASM = fftshift(ASM);
|
||||
modes{i}.ASM_factor = ASM;
|
||||
modes{i}.cASM_factor = conj(ASM);
|
||||
end
|
||||
|
||||
%% far field factor
|
||||
modes{i}.FAR_factor = [];
|
||||
modes{i}.cFAR_factor = conj(modes{i}.FAR_factor);
|
||||
|
||||
if isinf( par.probe_backpropagate)
|
||||
modes{i}.support_fwd_propagation_factor = inf;
|
||||
modes{i}.support_back_propagation_factor = -inf;
|
||||
elseif par.probe_backpropagate ~= 0
|
||||
[~, modes{i}.support_fwd_propagation_factor] = utils.prop_free_nf( self.probe{1}(:,:,1), par.probe_backpropagate,...
|
||||
modes{i}.lambda, self.pixel_size ./ scale );
|
||||
|
||||
modes{i}.support_fwd_propagation_factor = fftshift( modes{i}.support_fwd_propagation_factor );
|
||||
modes{i}.support_back_propagation_factor = conj(modes{i}.support_fwd_propagation_factor);
|
||||
else
|
||||
modes{i}.support_fwd_propagation_factor = [];
|
||||
modes{i}.support_back_propagation_factor = [];
|
||||
end
|
||||
|
||||
%I am a bit confused on why this is commented out?? - the tilted
|
||||
%plane propogators are caleed in the ptycho solver
|
||||
% modes{i}.tilted_plane_propagate_fwd = tilted_plane_propagate_fwd;
|
||||
%modes{i}.tilted_plane_propagate_back = tilted_plane_propagate_back;
|
||||
modes{i}.tilted_plane_propagate_fwd = [];
|
||||
modes{i}.tilted_plane_propagate_back = [];
|
||||
end
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%% PREPARE PROBES, INCOHERENT MODES %%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
probe_0 = mean(self.probe{1},3);
|
||||
probe = cell(1,par.probe_modes); % Added by ZC and fixed by YJ
|
||||
for i = 1:par.probe_modes
|
||||
try
|
||||
probe{i} = self.probe{i};
|
||||
%% test if the probe size ok for the variable probe settings etc
|
||||
assert( size(probe{i},4) == 1+par.variable_probe_modes || ...
|
||||
~(par.variable_probe) || i > 1)
|
||||
assert((size(probe{i},3) ==1 || par.variable_probe) || ...
|
||||
(size(probe{i},3) == par.Nscans && ~par.share_probe) ) % no variable prob extension and multiple probes used
|
||||
assert(size(probe{i},3) == par.Nscans || par.share_probe || par.variable_probe, 'Wrong probe size for not shared probe option')
|
||||
catch
|
||||
if i <= par.Nrec || is_used(par, 'fly_scan')
|
||||
verbose(2, 'Creating probe')
|
||||
|
||||
if ~par.share_probe && size(probe{i},3) == 1
|
||||
% dont share probe between scans
|
||||
probe{i} = repmat(probe_0,[1,1,par.Nscans]);
|
||||
end
|
||||
if (par.variable_probe && par.variable_probe_modes > 0) && i == 1
|
||||
verbose(2,'Creating variable probe ')
|
||||
probe{i}(:,:,:,2:1+par.variable_probe_modes) = ...
|
||||
randn([self.Np_p, size(probe{i},3), par.variable_probe_modes])+randn([self.Np_p,size(probe{i},3), par.variable_probe_modes])*1i;
|
||||
continue
|
||||
end
|
||||
end
|
||||
if length(probe) < i % none of above
|
||||
% simply create slightly shifted modes in fourier domain, it is useful for
|
||||
% inital guess of incoherent modes after orthogonalization
|
||||
step = median(diff(self.probe_positions_0));
|
||||
probe{i} = 0.01*fftshift(imshift_fft(fftshift(probe_0), randn, randn, false));
|
||||
end
|
||||
|
||||
% fill the unreconstructed positions if the OPRP method is used
|
||||
if par.variable_probe && is_method(par, 'PIE') && i ==1
|
||||
ind_wrong = setdiff(1:self.Npos, [self.reconstruct_ind{:}]);
|
||||
probe{i}(:,:,ind_wrong) = repmat(mean(probe{i},3),1,1,length(ind_wrong));
|
||||
end
|
||||
end
|
||||
end
|
||||
if par.probe_modes > par.Nrec
|
||||
% orthogonalization of incoherent probe modes
|
||||
if is_used(par, 'fly_scan')
|
||||
probe_tmp = probe;
|
||||
% orthogonalize the modes with all the other shifted modes
|
||||
for i = 1:par.Nrec
|
||||
dx = median(modes{i}.probe_positions - modes{1}.probe_positions);
|
||||
probe_tmp{i} = imshift_fft(probe_tmp{i}, dx);
|
||||
end
|
||||
probe_tmp = ortho_modes(probe_tmp); % perform othogonalization
|
||||
probe(1+par.Nrec:par.probe_modes) = probe_tmp(1+par.Nrec:par.probe_modes);
|
||||
else
|
||||
ind = [1,1+par.Nrec:par.probe_modes]; % skip polyvave/multilayer probe_tmp
|
||||
probe(ind) = ortho_modes_eig(probe(ind)); %% slightly better
|
||||
end
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%% PREPARE OBJECT, MULTILAYER OBJECT %%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%% updated illumination
|
||||
aprobe2 = abs(self.probe{1}(:,:,1)).^2;
|
||||
for ll = 1:par.Nscans
|
||||
if par.share_object
|
||||
ind = [self.reconstruct_ind{:}];
|
||||
else
|
||||
ind = self.reconstruct_ind{ll};
|
||||
end
|
||||
[cache.oROI_s{1}] = find_reconstruction_ROI( modes{1}.probe_positions,self.Np_o, self.Np_p);
|
||||
% avoid oscilations by adding momentum term
|
||||
illum_sum_0{ll} = Ggather(set_views(Gzeros(self.Np_o), Garray(aprobe2), 1,1, ind, cache));
|
||||
end
|
||||
|
||||
%% multilayer extension
|
||||
% modified by YJ for more dynamic initialization
|
||||
|
||||
% Step 1: choose specific layers from initial object file
|
||||
N_layer_input_obj = size(self.object,2);
|
||||
par.init_layer_select(par.init_layer_select<0) = [];
|
||||
par.init_layer_select(par.init_layer_select>N_layer_input_obj) = [];
|
||||
if ~isempty(par.init_layer_select)
|
||||
object_temp = cell(size(self.object,1),length(par.init_layer_select));
|
||||
for ll = 1:par.Nscans
|
||||
for jj=1:length(par.init_layer_select)
|
||||
object_temp{ll,jj} = self.object{ll,par.init_layer_select(jj)};
|
||||
end
|
||||
end
|
||||
self.object = object_temp;
|
||||
end
|
||||
|
||||
% Step 2: pre-process layers
|
||||
switch par.init_layer_preprocess
|
||||
case 'avg' % only use the averaged layer
|
||||
verbose(0,'Average initial layers')
|
||||
for ll = 1:par.Nscans
|
||||
obj_avg = prod(cat(3,self.object{ll,:}),3);
|
||||
obj_avg = abs(obj_avg).*exp(1i*phase_unwrap(angle(obj_avg))/size(self.object,2));
|
||||
for jj=1:size(self.object,2)
|
||||
self.object{ll,jj} = obj_avg;
|
||||
end
|
||||
end
|
||||
case 'avg1' % only use the averaged layer
|
||||
verbose(0,'Average initial layers and only keep one')
|
||||
object_temp = cell(size(self.object,1),1);
|
||||
for ll = 1:par.Nscans
|
||||
obj_avg = prod(cat(3,self.object{ll,:}),3);
|
||||
obj_avg = abs(obj_avg).*exp(1i*phase_unwrap(angle(obj_avg))/size(self.object,2));
|
||||
object_temp{ll,1} = obj_avg;
|
||||
end
|
||||
self.object = object_temp;
|
||||
case 'interp' % interpolate layers
|
||||
if ~isempty(par.init_layer_interp)
|
||||
verbose(0,'Interpolate %d initial layers to %d layers', size(self.object,2), length(par.init_layer_interp))
|
||||
for ll = 1:par.Nscans
|
||||
obj_temp = cat(3,self.object{ll,:});
|
||||
[N_obj_y,N_obj_x,N_obj_z] = size(obj_temp);
|
||||
[X,Y,Z] = meshgrid(linspace(1,N_obj_x,N_obj_x),linspace(1,N_obj_y,N_obj_y),linspace(1,N_obj_z,N_obj_z));
|
||||
[Xq,Yq,Zq] = meshgrid(linspace(1,N_obj_x,N_obj_x),linspace(1,N_obj_y,N_obj_y),par.init_layer_interp);
|
||||
obj_temp = interp3(X,Y,Z,obj_temp,Xq,Yq,Zq,'spline');
|
||||
for jj=1:size(obj_temp,3)
|
||||
self.object{ll,jj} = obj_temp(:,:,jj);
|
||||
end
|
||||
end
|
||||
end
|
||||
case {'','all'} % default: keep all layers
|
||||
% nothing to do
|
||||
otherwise
|
||||
error('Invalid init_layer_preprocess!')
|
||||
end
|
||||
|
||||
% Step 3: add or remove layers based on par.Nlayers
|
||||
if size(self.object,2) > par.Nlayers
|
||||
warning('Initial object has more layers than Nlayers')
|
||||
for ll = 1:par.Nscans
|
||||
self.object{ll,1} = prod(cat(3,self.object{ll,:}),3);
|
||||
end
|
||||
self.object(:,2:end) = [];
|
||||
end
|
||||
|
||||
if size(self.object,2) < par.Nlayers
|
||||
N_add = par.Nlayers - size(self.object,2);
|
||||
verbose(0,'Add %d more layers from %d layer(s)', N_add, size(self.object,2))
|
||||
for ll = 1:size(self.object,1) %loop over scans
|
||||
obj{ll} = self.object(ll,:);
|
||||
switch par.init_layer_append_mode
|
||||
case 'avg' %Not sure when this is useful, but I'll keep it for now
|
||||
verbose(0,'Append averaged layer')
|
||||
obj_pre = prod(cat(3,self.object{ll,:}),3);
|
||||
obj_pre = abs(obj_pre).*exp(1i*phase_unwrap(angle(obj_pre))/size(self.object,2));
|
||||
obj_post = obj_pre;
|
||||
case 'edge'
|
||||
verbose(0,'Append 1st/last layer')
|
||||
obj_pre = self.object{ll,1};
|
||||
obj_post = self.object{ll,end};
|
||||
case {'','vac'}
|
||||
verbose(0,'Append vacuum layer')
|
||||
%obj_pre = ones(self.Np_o, 'single') + 1e-9i*randn(self.Np_o, 'single');
|
||||
obj_pre = ones(self.Np_o, 'single');
|
||||
obj_post = obj_pre;
|
||||
otherwise
|
||||
error('Invalid init_layer_append_mode!')
|
||||
end
|
||||
for ii = 1:N_add
|
||||
if mod(ii, 2) == 1
|
||||
obj{ll}{end+1} = obj_post; % add slice at the end
|
||||
else
|
||||
obj{ll}(2:end+1) = obj{ll};
|
||||
obj{ll}{1} = obj_pre; % add slice at the beginning
|
||||
end
|
||||
end
|
||||
end
|
||||
self.object = cat(1, obj{:}); %combine all scans
|
||||
end
|
||||
|
||||
% if object has more layers but only one is needed
|
||||
if size(self.object,2) > 1 && par.Nlayers == 1
|
||||
for ll = 1:par.Nscans
|
||||
object{ll,1} = prod(cat(3,self.object{ll,:}),3);
|
||||
end
|
||||
self.object = object;
|
||||
end
|
||||
|
||||
% At this point: size(self.object,3) should equal to par.Nlayers
|
||||
%{
|
||||
%% MO's code, should be useless now. I'll keep it for now in case of
|
||||
bugs in steps 1-3.
|
||||
for j = 1:par.Nlayers
|
||||
for i = 1:max(1, par.Nscans * ~par.share_object) % loop over scans
|
||||
try
|
||||
object{i,j} = self.object{min(end,i),j};
|
||||
object{i,j}(1);
|
||||
catch
|
||||
verbose(0, 'add transparent slice') % add extra layers
|
||||
%% add fully transparent slice at the end
|
||||
object{i,j} = ones(self.Np_o, 'single');
|
||||
if size(self.object,2) == 1
|
||||
% swap order of the new layers to keep the original
|
||||
% reconstruction in center
|
||||
object(i,:) = object(i,end:-1:1);
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
%}
|
||||
% Step 4: assign self.object to object and rescale layers if needed
|
||||
if par.init_layer_scaling_factor~=1
|
||||
verbose(0,'Rescale each layer by %f', par.init_layer_scaling_factor)
|
||||
end
|
||||
for j = 1:par.Nlayers
|
||||
for i = 1:max(1, par.Nscans * ~par.share_object) % loop over scans
|
||||
if par.init_layer_scaling_factor~=1
|
||||
object_temp = self.object{min(end,i),j};
|
||||
object_temp_ph = phase_unwrap(angle(object_temp))*par.init_layer_scaling_factor;
|
||||
object{i,j} = abs(object_temp).*exp(1i.*object_temp_ph);
|
||||
else
|
||||
object{i,j} = self.object{min(end,i),j};
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
for i = 1:numel(object)
|
||||
object{i} = single(object{i});
|
||||
object{i} = complex(object{i});
|
||||
end
|
||||
|
||||
for i = 1:numel(probe)
|
||||
probe{i} = single(probe{i});
|
||||
probe{i} = complex(probe{i});
|
||||
end
|
||||
|
||||
%% STORE RESULTS TO SELF CLASS
|
||||
self.object = object;
|
||||
self.probe = probe;
|
||||
self.modes = modes;
|
||||
self.diffraction = Diffraction;
|
||||
self.noise = Noise;
|
||||
self.mask = Mask;
|
||||
self.background = reshape(Background,1,1,[]);
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%%%%%% PRECALCULATE USEFUL VALUES %%%%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
if ~isfield(self, 'probe_evolution' )
|
||||
% initial coefficients for OPRP approximation
|
||||
self.probe_evolution(:,1) = ones(self.Npos,1); % first mode is constant
|
||||
end
|
||||
new_probe_modes_ind = 1+(size(self.probe_evolution,2):par.variable_probe_modes);
|
||||
self.probe_evolution(:,new_probe_modes_ind) = 1e-6*randn(self.Npos,length(new_probe_modes_ind));
|
||||
|
||||
if par.variable_probe
|
||||
pnorm = norm2(self.probe{1});
|
||||
self.probe{1}(:,:,:,2:end) = self.probe{1}(:,:,:,2:end) ./ pnorm(1,1,:,2:end);
|
||||
self.probe_evolution(:,2:end) = self.probe_evolution(:,2:end) .* squeeze(mean(pnorm(1,1,:,2:end),3))';
|
||||
end
|
||||
|
||||
|
||||
if par.background_detection || ~isempty(self.background)
|
||||
%% auto-estimate background correction distribution
|
||||
if isempty(self.mask)
|
||||
mask = 0;
|
||||
else
|
||||
mask = self.mask;
|
||||
end
|
||||
if par.background_detection
|
||||
background_weight = sum(self.diffraction.^2,3) ./ max(1,sum(~mask,3));
|
||||
background_weight = imgaussfilt(background_weight,1);
|
||||
background_weight = 1./sqrt(max(1e-3, background_weight)) .* ~any(mask,3);
|
||||
background_weight = max(0,background_weight - 0.3*mean(background_weight(:)));
|
||||
cache.background_weight = ( fftshift_2D(background_weight / sum2(background_weight)));
|
||||
end
|
||||
|
||||
if isinf(par.background_width)
|
||||
cache.background_profile = 1;
|
||||
else
|
||||
mdiffr = Garray(fftshift(mean(get_modulus(self,cache,1:self.Npos,false).^2,3)));
|
||||
|
||||
W = par.background_width;
|
||||
X = (-self.Np_p(1):self.Np_p(1)-1);
|
||||
Y = (-self.Np_p(2):self.Np_p(2)-1);
|
||||
[X,Y] = meshgrid(X,Y);
|
||||
|
||||
background_profile = exp(-sqrt( (X/W(1)).^2 +(Y/W(1)).^2));
|
||||
background_profile = conv2(mdiffr,background_profile, 'same');
|
||||
background_profile = background_profile / max2(background_profile);
|
||||
|
||||
background_profile = utils.crop_pad(background_profile,self.Np_p);
|
||||
cache.background_profile = gather(fftshift(background_profile));
|
||||
|
||||
end
|
||||
|
||||
if ~isempty(self.diffraction_deform_matrix)
|
||||
apply_deform = @(x,D)single(reshape(full(D * double(reshape(x,[],size(x,3)))), size(x)));
|
||||
% apply deformation effects caused by tilted sample , be sure to enforce the mask before
|
||||
% interpolation, the hotpixels can spread around after the correction
|
||||
if isscalar(cache.background_profile)
|
||||
cache.background_profile = ones(self.Np_p, 'single');
|
||||
end
|
||||
cache.background_profile = apply_deform(cache.background_profile, self.diffraction_deform_matrix');
|
||||
end
|
||||
else
|
||||
cache.background_profile_weight = 1;
|
||||
end
|
||||
|
||||
for ll = 1:par.Nscans
|
||||
illum_sum_0{ll} = Ggather(illum_sum_0{ll});
|
||||
cache.MAX_ILLUM(ll) = max(illum_sum_0{ll}(:));
|
||||
cache.illum_sum_0{ll} = illum_sum_0{ll};
|
||||
end
|
||||
|
||||
%% precalculate illumination ROIs
|
||||
cache = precalculate_ROI(self,cache, Ggather(sqrt(aprobe2)));
|
||||
|
||||
%% prepare mask needed for subpixel shifts of object views
|
||||
cache.apodwin = single(0.1+0.9*tukeywin(self.Np_p(1),0.05) .* tukeywin(self.Np_p(2), 0.05)');
|
||||
|
||||
if par.initial_probe_rescaling
|
||||
%% initial rescaling of probe intensity , just a very rough guess
|
||||
% modified by ZC, propagate probe to far field
|
||||
mean_aPsi = mean2(abs(fft2_safe(self.probe{1}(:,:,1))).^2);
|
||||
% old method: self.modes{end} is the vaccum layer
|
||||
%mean_aPsi = mean2(abs(fwd_fourier_proj(self.probe{1}(:,:,1), self.modes{end})).^2);
|
||||
|
||||
mean_diffraction_intensity = mean(mean2(self.diffraction(:,:,randi(self.Npos, [10,1])).^2)); % take roughly average intensity % bug fixed by Zhen Chen, previous no ^2
|
||||
|
||||
for ii = 1:par.probe_modes
|
||||
self.probe{ii} = self.probe{ii} * sqrt( mean_diffraction_intensity / mean_aPsi);
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,457 @@
|
||||
% LOAD_FROM_P load parameters from the p-structure to param and self structures for GPU
|
||||
% engine
|
||||
%
|
||||
% [self, param] = load_from_p(self, param, p)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** param structure containing parameters for the engines
|
||||
% ** p ptychoshelves p structure
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ++ param structure containing parameters for the engines
|
||||
|
||||
function [self, param, p] = load_from_p(param, p)
|
||||
import math.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
|
||||
[Np_p(1),Np_p(2),Npos] = size( p.fmag);
|
||||
self.reconstruct_ind = p.scanidxs;
|
||||
|
||||
%% load default variables with different name from the main ptycho code
|
||||
param.Nmodes = p.probe_modes;
|
||||
param.plot_results_every = p.plot.interval;
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% additional features added by YJ
|
||||
%for output intermediated results,
|
||||
param.fout = p.fout;
|
||||
if isfield(p, 'save_results_every')
|
||||
param.save_results_every = p.save_results_every;
|
||||
if param.save_results_every<=p.number_iterations
|
||||
verbose(0, 'Intermediate results will be saved in the directory below every %i iterations.', param.save_results_every)
|
||||
verbose(0,param.fout)
|
||||
end
|
||||
end
|
||||
if isfield(p, 'extraPrintInfo')
|
||||
param.extraPrintInfo = p.extraPrintInfo;
|
||||
end
|
||||
if isfield(p, 'affine_matrix')
|
||||
param.affine_matrix_init = p.affine_matrix;
|
||||
end
|
||||
if isfield(p, 'beam_source')
|
||||
param.beam_source = p.beam_source;
|
||||
end
|
||||
if isfield(p, 'TV_lambda')
|
||||
param.TV_lambda = p.TV_lambda;
|
||||
end
|
||||
|
||||
if isfield(p,'avg_photon_threshold') && p.avg_photon_threshold>=0
|
||||
avg_photon_threshold = p.avg_photon_threshold;
|
||||
else %default
|
||||
if isfield(param,'beam_source') && strcmp(param.beam_source,'electron')
|
||||
avg_photon_threshold = 0.0001;
|
||||
else
|
||||
avg_photon_threshold = 0.01;
|
||||
end
|
||||
end
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%
|
||||
% if defined in p, use from p otherwise use defaults in param
|
||||
try;param.object_regular = p.reg_mu; end
|
||||
try;param.probe_inertia = p.probe_regularization; end
|
||||
|
||||
param.tilt_x = p.tilt_x; %%LB
|
||||
param.tilt_y = p.tilt_y; %%LB
|
||||
|
||||
|
||||
if check_option(p,'opt_errmetric','poisson')
|
||||
param.likelihood = 'poisson';
|
||||
else
|
||||
param.likelihood = 'L1';
|
||||
end
|
||||
if get_option(p,'background_width') && get_option(p,'binning')
|
||||
param.background_width = param.background_width / 2^p.binning;
|
||||
end
|
||||
|
||||
%% load variables from the main ptycho code and merge it with the defaults
|
||||
for field = fieldnames(param)'
|
||||
field = field{1};
|
||||
if isfield(p, field)
|
||||
param.(field) = p.(field);
|
||||
end
|
||||
end
|
||||
|
||||
% set verbosity for GPU engine
|
||||
param.verbose_level = max(-2,p.verbose_level-2); % adjust verbosity for GPU code , verbose_level 0 is enough for commmon use
|
||||
verbose(param.verbose_level)
|
||||
|
||||
% load additional reconstructed parameters , otherwise use default
|
||||
for item = {{'background',[]}, {'intensity_corr',[]}, {'probe_fourier_shift',[]}, {'rotation',0},{'shear',0},{'relative_pixel_scale',1}}
|
||||
item = item{1};
|
||||
if isfield(p, item{1}) && ~isempty(p.(item{1}))
|
||||
self.(item{1}) = p.(item{1});
|
||||
else
|
||||
self.(item{1}) = item{2};
|
||||
end
|
||||
end
|
||||
if any(ismember(fieldnames(p), {'shear', 'rotation', 'relative_pixel_scale'})) && isfield(p, 'positions_0')
|
||||
warning('Reseting probe positions to original values')
|
||||
p.positions = p.positions_0;
|
||||
p = rmfield(p, 'positions_0');
|
||||
end
|
||||
|
||||
if isempty(p.affine_matrix)
|
||||
p.affine_matrix = diag([1,1]);
|
||||
end
|
||||
|
||||
self.diffraction_deform_matrix = [];
|
||||
|
||||
if ~check_option(p,'asize_presolve')
|
||||
param.Np_p_presolve = [];
|
||||
else
|
||||
param.Np_p_presolve = min(p.asize_presolve, p.asize);
|
||||
end
|
||||
|
||||
% Other parameters
|
||||
param.fourier_ptycho = check_option(p,'fourier_ptycho');
|
||||
param.upsampling_data_factor = p.detector.upsampling;
|
||||
|
||||
% Offaxis ptychography correction
|
||||
if check_option(p, 'sample_rotation_angles')
|
||||
param. sample_rotation_angles = p.sample_rotation_angles; % 3x1 vector rotation around [X,Y,beam] axes in degrees , apply a correction accounting for tilted plane oR the sample and ewald sphere curvature (high NA correction)
|
||||
else
|
||||
param. sample_rotation_angles = [0,0,0]; % conventional ptychography
|
||||
end
|
||||
|
||||
self.pixel_size = p.dx_spec;
|
||||
self.Np_p = Np_p;
|
||||
Nscans = length(self.reconstruct_ind);
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% load probes%%%%%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
if param.share_probe
|
||||
p.share_probe_ID(:) = 1; % enforce single object if sharing is requested
|
||||
end
|
||||
|
||||
% normalization for consistency with the other CPU engines
|
||||
probes = single(p.probes ./ (prod(sqrt(Np_p))*2*p.renorm));
|
||||
|
||||
% force to a column cell convenient for multilayer, Added by ZC
|
||||
%self.probe = cell (min(p.probe_modes, size(probes,4)),1);
|
||||
for i = 1:min(p.probe_modes, size(probes,4))
|
||||
% variable probe
|
||||
if isfield(p, 'probe_PCA') && ~isempty(p.probe_PCA) && i == 1 && size(p.probe_PCA.eigen_vec,1) == p.asize(1) && param.variable_probe && is_method(param, 'PIE')
|
||||
verbose(1,'Loading PCA probe (%i)', i)
|
||||
self.probe{i} = reshape(p.probe_PCA.eigen_vec,prod(p.asize),[]) * p.probe_PCA.evolution' /(prod(sqrt(Np_p))*2*p.renorm);% normalization for consistency with the CPU code;
|
||||
elseif isfield(p, 'probe_variable') && ~isempty(p.probe_variable) && i == 1 && size(p.probe_variable.eigen_vec,1) == p.asize(1) && param.variable_probe && is_method(param, 'ML')
|
||||
% ML methods, OPRP approx
|
||||
verbose(0,'Loading variable probe (%i)', i)
|
||||
% constant part
|
||||
self.probe{i}(:,:,:,1) = probes(:,:,:,1);
|
||||
% variable part
|
||||
self.probe{i}(:,:,:,2) = p.probe_variable.eigen_vec /(prod(sqrt(Np_p))*2*p.renorm);
|
||||
% evolution of the variable part
|
||||
self.probe_evolution = p.probe_variable.evolution ;
|
||||
assert(length(self.probe_evolution)==Npos, 'Wrong size of variable probe coefficients')
|
||||
else
|
||||
% constant probe
|
||||
verbose(1,'Loading constant probe (%i)', i)
|
||||
if param.share_probe
|
||||
self.probe{i} = mean(probes(:,:,:,i),3);
|
||||
else
|
||||
if size(p.probes,3) == Nscans
|
||||
% one probe for each scan
|
||||
self.probe{i} = probes(:,:,:,i);
|
||||
else
|
||||
% rather take only first to avoid issues
|
||||
self.probe{i} = probes(:,:,1,i);
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% prepare support contraints%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
% provide estimate of the probe support
|
||||
if check_option(p, 'probe_mask') && check_option(p,'use_probe_support') && any(p.probe_mask)
|
||||
self.probe_support = ~p.probe_mask;
|
||||
elseif check_option(p,'probe_support_radius') && p.probe_support_radius < sqrt(2)
|
||||
% very useful for DM code
|
||||
[X,Y] = meshgrid((-p.asize(2)/2+1:p.asize(2)/2)/p.asize(2), (-p.asize(1)/2+1:p.asize(1)/2)/p.asize(1));
|
||||
self.probe_support = sqrt(X.^2+Y.^2) < p.probe_support_radius/2;
|
||||
else
|
||||
self.probe_support = [];
|
||||
end
|
||||
|
||||
% estimate of the probe support in detector plane
|
||||
if check_option(p,'probe_support_fft') && ~check_option(p, 'prop_regime', 'nearfield') && ~check_option(p,'probe_support_tem') % exclude TEM aperture mask by ZC
|
||||
if ~check_option(p.model, 'probe_focal_length') && ~check_option(p.model, 'probe_outer_zone_width')
|
||||
error('Missing model.probe_focal_length and model.probe_outer_zone_width of Fresnel zone plate' )
|
||||
end
|
||||
if ~check_option(p.model, 'probe_outer_zone_width')
|
||||
p.model.probe_outer_zone_width = p.lambda * p.model.probe_focal_length / p.model.probe_diameter;
|
||||
end
|
||||
FZP_cone_diameter = p.lambda* p.z/(p.model.probe_outer_zone_width * p.ds);
|
||||
% add some extra space
|
||||
FZP_cone_diameter = FZP_cone_diameter * 1.2;
|
||||
[X,Y] = meshgrid(-p.asize(2)/2+1:p.asize(2)/2, -p.asize(1)/2+1:p.asize(1)/2);
|
||||
self.probe_support_fft = utils.imgaussfilt2_fft(sqrt(X.^2+Y.^2) < FZP_cone_diameter/2, FZP_cone_diameter/50);
|
||||
af_probe = sqrt(abs(fftshift(fft2(self.probe{1}(:,:,1)))));
|
||||
[cx, cy] = center(max(0,af_probe-0.1*max(af_probe(:))));
|
||||
self.probe_support_fft = imshift_fast(self.probe_support_fft, -cx, -cy,[], 'nearest');
|
||||
self.probe_support_fft = max(0, min(1, self.probe_support_fft));
|
||||
verbose(1, 'Using farfield probe support constraint')
|
||||
elseif check_option(p,'probe_support_tem') % TEM aperture mask by ZC
|
||||
mask_dp=abs(fft2(p.probe_initial));
|
||||
mask_dp(mask_dp>1.0)=1;
|
||||
mask_dp(mask_dp<0.1)=0;
|
||||
self.probe_support_fft = logical(mask_dp);
|
||||
else
|
||||
self.probe_support_fft = [];
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% load object%%%%%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
if param.share_object
|
||||
p.share_object_ID(:) = 1; % enforce single object if sharing is requested
|
||||
end
|
||||
|
||||
% correct positions for sample tilt
|
||||
positions = p.positions ;
|
||||
if isfield(p, 'positions_0')
|
||||
positions_0 = p.positions_0 ;
|
||||
end
|
||||
|
||||
verbose(1, 'Load and pad object and probe')
|
||||
% update current size of the object
|
||||
for i = 1:length(p.object)
|
||||
for j = 1:size(p.object{i},4) % load multiple layers of the object
|
||||
self.object{i,j} = p.object{i}(:,:,1,j);
|
||||
end
|
||||
p.object_size(i,:) = size(self.object{i,1});
|
||||
end
|
||||
|
||||
% calculate optimal size !! find minimal object to fit all scans
|
||||
Np_o = max(p.object_size,[],1);
|
||||
|
||||
% expand object size if the probe p
|
||||
if p.number_iterations > check_option(p, 'probe_position_search') && is_method(param, {'ML', 'PIE'})
|
||||
extra = 0.2; % add plenty of extra space for geometry refinement
|
||||
else
|
||||
extra = 0.05; % do just a little of extra space
|
||||
end
|
||||
|
||||
% shift the positions to account for the expanded object size AND
|
||||
% center them !!! (GPU code assumes positions to be centered, better for scale / probe positions are unknown)
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% load positions %%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
for i = unique(p.share_object_ID)
|
||||
ind = [self.reconstruct_ind{p.share_object_ID == i}];
|
||||
position_offset = 1+floor((max(positions(ind,:))-min(positions(ind,:)))/2 + min(positions(ind,:)) );
|
||||
if isfield(p, 'positions_0')
|
||||
self.probe_positions_0(ind,:) = positions_0(ind,:) - position_offset;
|
||||
self.probe_positions(ind,:) = positions(ind,:) - position_offset;
|
||||
else
|
||||
self.probe_positions_0(ind,:) = positions(ind,:) - position_offset;
|
||||
self.probe_positions = [];
|
||||
end
|
||||
end
|
||||
|
||||
% get object extent
|
||||
self.Np_o = max(Np_o, ceil((1+extra) * ( self.Np_p + (max(self.probe_positions_0) - min(self.probe_positions_0)) )));
|
||||
% store object size without padding, useful for plotting
|
||||
p.object_size = max(p.object_size, ceil(( self.Np_p + (max(self.probe_positions_0) - min(self.probe_positions_0)) )));
|
||||
self.probe_positions_0 = self.probe_positions_0(:,[2,1]); %swap x&y axis
|
||||
|
||||
if ~isempty(self.probe_positions)
|
||||
self.probe_positions = self.probe_positions(:,[2,1]);
|
||||
end
|
||||
self.Npos = Npos;
|
||||
|
||||
% only a relative correction with respect to the affine matrix already
|
||||
% applied in p-struct
|
||||
for ii = 1:Nscans
|
||||
self.affine_matrix{ii} = diag([1,1]);
|
||||
end
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% adjust object %%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%
|
||||
for i = 1:size(self.object,1)
|
||||
for layer = 1:size(self.object,2)
|
||||
% if needed expand the object to allow position refinement
|
||||
% and shift for consistency with the CPU code
|
||||
self.object{i,layer} = imshift_fast(self.object{i,layer},1,1,self.Np_o, 'nearest', mean(self.object{i,layer}(:)));
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%% load data, mask noise %%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
verbose(1, 'Preparing data and masks')
|
||||
assert(all(isfinite(p.fmag(:))), 'Provide p.fmag contains NaN/Inf')
|
||||
self.noise = [];
|
||||
self.diffraction = (single(p.fmag .* p.fmask) / single(p.renorm) ).^2;
|
||||
self.mask = (~p.fmask);
|
||||
|
||||
if check_option(p, 'damped_mask')
|
||||
% if relaxed mask is used, try to fill the smallest gaps (hot pixels) by neighbors
|
||||
mask_ind = find(self.mask);
|
||||
self.diffraction(mask_ind) = self.diffraction(min(mask_ind+1, numel(self.diffraction)));
|
||||
end
|
||||
|
||||
low_photon_count_dp = sum(sum(self.diffraction)) / prod(p.asize) < avg_photon_threshold;
|
||||
if any(low_photon_count_dp)
|
||||
error('%0.2f%% diffraction patterns has average photon count < %f', sum(low_photon_count_dp)/size(self.diffraction,3)*100, avg_photon_threshold)
|
||||
end
|
||||
|
||||
%% automatic data centering / flipping / tilted plane correction
|
||||
if check_option(p, 'auto_center_data') || check_option(p, 'custom_data_flip') || check_option(p, 'sample_rotation_angles')
|
||||
self.diffraction = fftshift_2D(self.diffraction);
|
||||
self.mask = fftshift_2D(self.mask);
|
||||
warning on
|
||||
warning off backtrace
|
||||
|
||||
if check_option(p, 'auto_center_data')
|
||||
warning('Enforcing automatic data centering')
|
||||
for ii = 1:Nscans
|
||||
[x0,y0]=math.center(abs(fftshift(fft2(fftshift(self.probe{1}(:,:,min(end,ii)))))));
|
||||
W = mean2(self.diffraction(:,:,self.reconstruct_ind{ii}));
|
||||
W = ((W - min(W)) / (max(W)-min(W))).^4; % give more weight to the more transpared regions (air)
|
||||
avg_pattern = mean(W.*sqrt(max(0,single(self.diffraction(:,:,self.reconstruct_ind{ii})))),3);
|
||||
[x,y]=math.center(avg_pattern);
|
||||
x = round(x-x0); y = round(y-y0);
|
||||
self.diffraction(:,:,self.reconstruct_ind{ii}) = imshift_fast(self.diffraction(:,:,self.reconstruct_ind{ii}),x,y);
|
||||
self.mask(:,:,self.reconstruct_ind{ii}) = imshift_fast(self.mask(:,:,self.reconstruct_ind{ii}), x,y);
|
||||
fprintf('Data in scan %i shifted by %i %i pixels\n', ii, x,y);
|
||||
end
|
||||
if ~isempty(self.probe_support_fft )
|
||||
self.probe_support_fft = imshift_fast(self.probe_support_fft , x,y);
|
||||
end
|
||||
end
|
||||
|
||||
% apply custom flip of the diffraction data
|
||||
if check_option(p, 'custom_data_flip') && any(p.custom_data_flip)
|
||||
warning('Applying custom data flip: %i %i %i ', p.custom_data_flip(1), p.custom_data_flip(2), p.custom_data_flip(3))
|
||||
if p.custom_data_flip(1)
|
||||
self.diffraction = flipud(self.diffraction);
|
||||
self.mask = flipud(self.mask);
|
||||
end
|
||||
if p.custom_data_flip(2)
|
||||
self.diffraction = fliplr(self.diffraction);
|
||||
self.mask = fliplr(self.mask);
|
||||
end
|
||||
if p.custom_data_flip(3)
|
||||
self.diffraction = permute(self.diffraction, [2,1,3]);
|
||||
self.mask = permute(self.mask, [2,1,3]);
|
||||
end
|
||||
end
|
||||
|
||||
%
|
||||
if isfield(p, 'sample_rotation_angles') && any(p.sample_rotation_angles) && check_option(p, 'apply_tilted_plane_correction', 'diffraction')
|
||||
%% OFFAXIS PTYCHOGRAPHY CORRECTION
|
||||
if utils.verbose > -1
|
||||
warning('Applying tilted plane correction: %3.5g %3.3g %3.3g\n Note that current implementation assumes low NA illumination, if this is not true, the central diffraction cone can be malformed', p.sample_rotation_angles(1), p.sample_rotation_angles(2), p.sample_rotation_angles(3))
|
||||
end
|
||||
% create matrix of deformation to apply effects similar to
|
||||
deform_mat = get_tilted_plane_correction_matrix(max(self.Np_p), ...
|
||||
p.z ,p.detectors{1}.pixel_size, ...
|
||||
p.sample_rotation_angles(1),...
|
||||
p.sample_rotation_angles(2),...
|
||||
p.sample_rotation_angles(3));
|
||||
if self.Np_p(1) ~= self.Np_p(2)
|
||||
% quick fix for asymmetric probe dimensions
|
||||
blank = true(self.Np_p);
|
||||
blank_ind = find(utils.crop_pad(blank,[ max(self.Np_p), max(self.Np_p)]));
|
||||
deform_mat = deform_mat(blank_ind,blank_ind);
|
||||
end
|
||||
|
||||
apply_deform = @(x,D)single(reshape(full(D * double(reshape(x,[],size(x,3)))), size(x)));
|
||||
plotting.smart_figure(3423)
|
||||
ax(1)=subplot(1,2,1);
|
||||
imagesc(log(1+max(self.diffraction, [],3))); axis off image xy ; colormap(plotting.franzmap)
|
||||
title('Diffraction BEFORE tilted plane correction')
|
||||
% apply deformation effects caused by tilted sample , be sure to enforce the mask before
|
||||
% interpolation, the hotpixels can spread around after the correction
|
||||
self.diffraction = apply_deform(self.diffraction .* ~self.mask, deform_mat');
|
||||
self.mask = apply_deform(self.mask, deform_mat') > 0;
|
||||
% plotting.imagesc3D(log(1+max(self.diffraction,[],3))); grid on
|
||||
ax(2)=subplot(1,2,2);
|
||||
imagesc(log(1+max(self.diffraction, [],3))); axis off image xy ; colormap(plotting.franzmap)
|
||||
title('Diffraction AFTER tilted plane correction')
|
||||
plotting.suptitle('Effect of tilted ptychography correction')
|
||||
linkaxes(ax, 'xy')
|
||||
drawnow
|
||||
self.diffraction_deform_matrix = deform_mat;
|
||||
end
|
||||
|
||||
warning on
|
||||
|
||||
self.diffraction = ifftshift_2D(self.diffraction);
|
||||
self.mask = ifftshift_2D(self.mask);
|
||||
end
|
||||
|
||||
self.filename = [p.detector.data_prefix, p.run_name];
|
||||
|
||||
% other basic parameters
|
||||
self.path = '';
|
||||
if check_option(p, 'prop_regime', 'nearfield')
|
||||
self.z_distance = p.z;
|
||||
else
|
||||
self.z_distance = inf; % farfield
|
||||
end
|
||||
% multilayer extension
|
||||
if isfield(p, 'delta_z')
|
||||
assert(all(isfinite(p.delta_z)), 'Some of the provided layer distanced delta_z is not finite' )
|
||||
self.z_distance = [p.delta_z(:)', self.z_distance];
|
||||
end
|
||||
|
||||
self.lambda = p.lambda;
|
||||
if check_option(p,'diff_pattern_blur')
|
||||
self.diff_pattern_blur=p.diff_pattern_blur;
|
||||
else
|
||||
self.diff_pattern_blur = 0; % incoherent smoothing
|
||||
end
|
||||
self.modes = [];
|
||||
|
||||
% keep p structure for plotting purposes
|
||||
param.p = p;
|
||||
|
||||
% if requested, shift the average probe to center and shift the object
|
||||
% to correspond to the probe shift
|
||||
if check_option(p, 'auto_center_probe')
|
||||
[x,y] = center(mean(abs(self.probe{1}(:,:,:,1))));
|
||||
for ii = 1:numel(self.probe)
|
||||
self.probe{ii} = imshift_fft(self.probe{ii}, -x,-y);
|
||||
end
|
||||
for ii = 1:numel(self.object)
|
||||
self.object{ii} = imshift_fft(self.object{ii}, -x, -y);
|
||||
end
|
||||
end
|
||||
|
||||
% check if all is ok (remove in future !!!)
|
||||
positions = self.probe_positions_0(:,[2,1]);
|
||||
positions = bsxfun(@plus, positions, ceil(self.Np_o/2-self.Np_p/2));
|
||||
positions = round(positions);
|
||||
range = ([min(positions(:,1)), max(positions(:,1))+ Np_p(1), min(positions(:,2)), max(positions(:,2))+ Np_p(2)]);
|
||||
if range(1) < 0 || range(2) > self.Np_o(1) || range(3) < 0 || range(4) > self.Np_o(2)
|
||||
warning('Object size is too small, not enough space for probes !! ')
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,113 @@
|
||||
% PREPARE_FLYSCAN_POSITIONS from finit number of measured position interpolate possitions for each
|
||||
% measured frame when fly scan is used
|
||||
%
|
||||
% self = prepare_flyscan_positions(self, par)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function self = prepare_flyscan_positions(self, par)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import plotting.*
|
||||
|
||||
|
||||
jumps = diff(self.probe_positions_0);
|
||||
step = median(jumps,1);
|
||||
jumps = sum(abs(jumps),2);
|
||||
% empirical condition
|
||||
jumps = find(jumps > 10*median(jumps));
|
||||
if length(jumps) < par.Nscans
|
||||
% assume that smooth path is used
|
||||
%% ADVANCED FLY SCAN - SPIRAL
|
||||
for ii = 1:par.Nscans
|
||||
assert(~any(isfinite(par.probe_position_search)), 'Position refinement and fly scans not suported')
|
||||
|
||||
ind = self.reconstruct_ind{ii};
|
||||
pos = self.probe_positions_0(ind,:);
|
||||
[ang, rad] = cart2pol(pos(:,1)-pos(1,1), pos(:,2)-pos(1,2));
|
||||
ang = unwrap(ang);
|
||||
% get interpolate d positions of the sub probes
|
||||
ang_all = ang + (par.flyscan_offset -0.5+linspace(0,par.flyscan_dutycycle*(par.Nmodes-1)/par.Nmodes, par.Nmodes) ).*[diff(ang);0];
|
||||
rad_all = interp1(ang, rad, ang_all, 'pchip');
|
||||
[X,Y] = pol2cart(ang_all, rad_all);
|
||||
|
||||
for ll = 1:par.Nmodes
|
||||
self.modes{ll}.probe_positions(ind,:) = pos(1,1:2) + [X(:,ll), Y(:,ll)];
|
||||
if iter == 1; self.probe{ll} = self.probe{1}; end
|
||||
end
|
||||
end
|
||||
else
|
||||
%% ADVANCED FLY SCAN - LINE SCAN
|
||||
% interpolate the other modes into new positions
|
||||
pos = self.modes{1}.probe_positions;
|
||||
for ll = 1:par.Nmodes
|
||||
ratio = par.flyscan_dutycycle*(ll-1)/par.Nmodes;
|
||||
self.modes{ll}.probe_positions = pos(min((1:self.Npos)+1,self.Npos),:)*ratio + (1-ratio)*pos;
|
||||
if ~isempty(jumps)
|
||||
% expected step continuation
|
||||
self.modes{ll}.probe_positions(jumps,:) = bsxfun(@plus, self.modes{ll}.probe_positions(jumps-1,:),step);
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,157 @@
|
||||
% DISTMAT Compute a Distance Matrix for One or Two Sets of Points
|
||||
%
|
||||
%
|
||||
%
|
||||
% Copyright (c) 2015, Joseph Kirk
|
||||
% All rights reserved.
|
||||
%
|
||||
% Redistribution and use in source and binary forms, with or without
|
||||
% modification, are permitted provided that the following conditions are
|
||||
% met:
|
||||
%
|
||||
% * Redistributions of source code must retain the above copyright
|
||||
% notice, this list of conditions and the following disclaimer.
|
||||
% * Redistributions in binary form must reproduce the above copyright
|
||||
% notice, this list of conditions and the following disclaimer in
|
||||
% the documentation and/or other materials provided with the distribution
|
||||
%
|
||||
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
|
||||
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
|
||||
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
|
||||
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
|
||||
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
|
||||
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
||||
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
% POSSIBILITY OF SUCH DAMAGE.
|
||||
%
|
||||
|
||||
% Filename: distmat.m
|
||||
%
|
||||
% Description: Computes a matrix of pair-wise distances between points in
|
||||
% A and B, using one of {euclidean,cityblock,chessboard} methods
|
||||
%
|
||||
% Author:
|
||||
% Joseph Kirk
|
||||
% jdkirk630@gmail.com
|
||||
%
|
||||
% Date: 02/27/15
|
||||
%
|
||||
% Release: 2.0
|
||||
%
|
||||
% Inputs:
|
||||
% A - (required) MxD matrix where M is the number of points in D dimensions
|
||||
% B - (optional) NxD matrix where N is the number of points in D dimensions
|
||||
% if not provided, B is set to A by default
|
||||
% METHOD - (optional) string specifying one of the following distance methods:
|
||||
% 'euclidean' Euclidean distance (default)
|
||||
% 'taxicab','manhattan','cityblock' Manhattan distance
|
||||
% 'chebyshev','chessboard','chess' Chebyshev distance
|
||||
% 'grid','diag' Diagonal grid distance
|
||||
%
|
||||
% Outputs:
|
||||
% DMAT - MxN matrix of pair-wise distances between points in A and B
|
||||
%
|
||||
% Usage:
|
||||
% dmat = distmat(a)
|
||||
% -or-
|
||||
% dmat = distmat(a,b)
|
||||
% -or-
|
||||
% dmat = distmat(a,method)
|
||||
% -or-
|
||||
% dmat = distmat(a,b,method)
|
||||
%
|
||||
% Example:
|
||||
% % Pairwise Euclidean distances within a single set of 2D points
|
||||
% xy = 10*rand(25,2); % 25 points in 2D
|
||||
% dmat = distmat(xy);
|
||||
% figure; plot(xy(:,1),xy(:,2),'.');
|
||||
% for i=1:25, text(xy(i,1),xy(i,2),[' ' num2str(i)]); end
|
||||
% figure; imagesc(dmat); colorbar
|
||||
%
|
||||
% Example:
|
||||
% % Pairwise Manhattan distances within a single set of 2D points
|
||||
% xy = 10*rand(25,2); % 25 points in 2D
|
||||
% dmat = distmat(xy,'cityblock');
|
||||
% figure; plot(xy(:,1),xy(:,2),'.');
|
||||
% for i=1:25, text(xy(i,1),xy(i,2),[' ' num2str(i)]); end
|
||||
% figure; imagesc(dmat); colorbar
|
||||
%
|
||||
% Example:
|
||||
% % Pairwise Chebyshev distances within a single set of 2D points
|
||||
% xy = 10*rand(25,2); % 25 points in 2D
|
||||
% dmat = distmat(xy,'chebyshev');
|
||||
% figure; plot(xy(:,1),xy(:,2),'.');
|
||||
% for i=1:25, text(xy(i,1),xy(i,2),[' ' num2str(i)]); end
|
||||
% figure; imagesc(dmat); colorbar
|
||||
%
|
||||
% Example:
|
||||
% % Inter-point Euclidean distances for 2D points
|
||||
% xy = 10*rand(15,2); % 15 points in 2D
|
||||
% uv = 10*rand(25,2); % 25 points in 2D
|
||||
% dmat = distmat(xy,uv);
|
||||
% figure; plot(xy(:,1),xy(:,2),'.');
|
||||
% for i=1:15, text(xy(i,1),xy(i,2),[' ' num2str(i)]); end
|
||||
% figure; plot(uv(:,1),uv(:,2),'.');
|
||||
% for i=1:25, text(uv(i,1),uv(i,2),[' ' num2str(i)]); end
|
||||
% figure; imagesc(dmat); colorbar
|
||||
%
|
||||
% See also:
|
||||
%
|
||||
function dmat = distmat(a,varargin)
|
||||
|
||||
|
||||
% Set defaults
|
||||
method = 'euclidean';
|
||||
b = a;
|
||||
|
||||
% Error check primary input
|
||||
if ~isnumeric(a)
|
||||
error('Expecting a matrix of floating point values for A input.');
|
||||
end
|
||||
|
||||
% Process optional inputs
|
||||
for var = varargin
|
||||
arg = var{1};
|
||||
if ischar(arg)
|
||||
method = arg;
|
||||
elseif ~isempty(arg)
|
||||
b = arg;
|
||||
end
|
||||
end
|
||||
|
||||
% Check input dimensionality
|
||||
[na,aDims] = size(a);
|
||||
[nb,bDims] = size(b);
|
||||
if (aDims ~= bDims)
|
||||
error('Input matrices must have the same dimensionality.');
|
||||
end
|
||||
|
||||
% Create index matrices
|
||||
[j,i] = meshgrid(1:nb,1:na);
|
||||
|
||||
% Compute array of inter-point differences
|
||||
delta = a(i,:) - b(j,:);
|
||||
|
||||
% Compute distance by specified method
|
||||
dmat = zeros(na,nb);
|
||||
switch lower(method)
|
||||
case {'euclidean','euclid'}
|
||||
% Euclidean distance
|
||||
dmat(:) = sqrt(sum(delta.^2,2));
|
||||
case {'cityblock','city','block','manhattan','taxicab','taxi'}
|
||||
% Cityblock distance
|
||||
dmat(:) = sum(abs(delta),2);
|
||||
case {'chebyshev','cheby','chessboard','chess'}
|
||||
% Chebyshev distance
|
||||
dmat(:) = max(abs(delta),[],2);
|
||||
case {'grid','diag'}
|
||||
dmat(:) = max(abs(delta),[],2) + (sqrt(2) - 1)*min(abs(delta),[],2);
|
||||
otherwise
|
||||
error('Unrecognized distance method %s',method);
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,300 @@
|
||||
% GET_CLOSE_INDICES simple based method to select indices for DM
|
||||
% !! GPU needs the sets to be with similar , ideally the same sizes !!!
|
||||
%
|
||||
% [indices_out, scan_ids_out] = get_close_indices(self, cache, par )
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ indices_out cell of arrays, contain indices of positions processed in parallel
|
||||
% ++ scan_ids_out cell of arrays, contain scan numbers for each position
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [indices_out, scan_ids_out] = get_close_indices(self, cache, par )
|
||||
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
grouping = par.grouping;
|
||||
|
||||
% in case of a shared scan join together all positions to find the optimal groups
|
||||
group_across_scans = true;
|
||||
|
||||
|
||||
if par.share_object && group_across_scans
|
||||
Nsets = 1;
|
||||
else
|
||||
Nsets = par.Nscans;
|
||||
end
|
||||
cluster_refinement_time = 0;
|
||||
cluster_time = 0;
|
||||
|
||||
% in simplest case process all positions together
|
||||
if Nsets == 1 && grouping >= self.Npos
|
||||
indices_out = {[self.reconstruct_ind{:}]};
|
||||
scan_ids_out{1} = [];
|
||||
for ii = 1:length(self.reconstruct_ind)
|
||||
scan_ids_out{1} = [scan_ids_out{1}; ii*ones(length(self.reconstruct_ind{ii}),1)];
|
||||
end
|
||||
return
|
||||
end
|
||||
|
||||
%rng default
|
||||
|
||||
for kk = 1:Nsets
|
||||
% take them sequentially but with random offset
|
||||
if par.share_object && group_across_scans
|
||||
% join all indices into one large set if the object is shared
|
||||
indices_0 = [self.reconstruct_ind{:}];
|
||||
for ii = 1:length(self.reconstruct_ind)
|
||||
scans_0(self.reconstruct_ind{ii}) = ii;
|
||||
end
|
||||
else
|
||||
indices_0 = self.reconstruct_ind{kk};
|
||||
scans_0 = kk * ones(size(indices_0)); % scan number
|
||||
end
|
||||
N = length(indices_0);
|
||||
Ngroups=ceil(N/grouping);
|
||||
positions = self.probe_positions_0(indices_0,:);
|
||||
Npos = length(positions);
|
||||
|
||||
% get initial set distribution
|
||||
[groups, C, sum_D, D] = get_best_kmeans(positions, Ngroups);
|
||||
|
||||
iter = 0;
|
||||
t0 = tic;
|
||||
|
||||
while true
|
||||
iter= iter +1;
|
||||
[nbins,bins] = hist(groups, unique(groups));
|
||||
% if less than 2 types of groups are present, finish
|
||||
Ngroups_sizes = length(unique(nbins));
|
||||
% try to find distribution with most similar sets sizes, if not
|
||||
% easy, end with suboptimal distribution after 50 iterations
|
||||
if ( Ngroups_sizes <= max(2, ceil(iter/1e3)) && (Ngroups*grouping ~= N || iter > 1e3 )) ...
|
||||
|| Ngroups_sizes == 1 % choose suboptimal solution if better is not found soon
|
||||
break
|
||||
end
|
||||
|
||||
% find group with lowest number of members , add new points into
|
||||
% this group
|
||||
min_group = bins(argmin(nbins));
|
||||
large_groups = bins(nbins>grouping);
|
||||
if isempty(large_groups) || any(ismember(min_group, large_groups)) ; break; end
|
||||
% choose closest position from the largest group to be moved to the
|
||||
% smallest group
|
||||
ind_large = (D(:,min_group) == min(D(ismember(groups, large_groups), min_group)));
|
||||
|
||||
groups(ind_large) = min_group;
|
||||
|
||||
end
|
||||
|
||||
% remove empty groups
|
||||
ugroups = unique(groups);
|
||||
Ngroups = length(ugroups);
|
||||
groups = sum((1:Ngroups) .*(groups == ugroups'),2);
|
||||
|
||||
|
||||
|
||||
cluster_time = cluster_time + toc(t0);
|
||||
|
||||
|
||||
for ii = 1:Ngroups
|
||||
C(ii,:) = median(positions(groups == ii,:));
|
||||
end
|
||||
for ii = 1:Ngroups
|
||||
D(:,ii) = (sum((positions - C(ii,:)).^2,2));
|
||||
end
|
||||
|
||||
|
||||
t0 = tic;
|
||||
%% find more compact refinement
|
||||
% find the most distanced points
|
||||
[~,sind] = sort(D,2);
|
||||
% positions to be improved -> find the best matching group
|
||||
optimal_group = sind(:,1);
|
||||
|
||||
nonoptimal_ratio_0 = 1;
|
||||
|
||||
for iter = 1:10
|
||||
ind_switch = (groups ~= optimal_group);
|
||||
nonoptimal_ratio = sum(ind_switch) / numel(ind_switch);
|
||||
if nonoptimal_ratio > 0
|
||||
verbose(0, 'Indexes to be switched: %3.2g%% positions', nonoptimal_ratio * 100)
|
||||
end
|
||||
|
||||
if nonoptimal_ratio >= nonoptimal_ratio_0
|
||||
break
|
||||
end
|
||||
nonoptimal_ratio_0 = nonoptimal_ratio;
|
||||
|
||||
max_dist_0 = inf;
|
||||
for i = 1:sum(ind_switch)
|
||||
% calculate distance for each point from its group center
|
||||
center_dist = (D(sub2ind(size(D), (1:Npos)', groups)));
|
||||
max_dist_0 = max(center_dist(ind_switch));
|
||||
% start from the worst case
|
||||
ind_worse = find(max(center_dist(ind_switch)) == center_dist, 1, 'first');
|
||||
% initial group
|
||||
group_old = groups(ind_worse);
|
||||
% better fitting group
|
||||
group_new = optimal_group(ind_worse);
|
||||
% position to be switched in the new group
|
||||
ind_new = find(D(:,group_old) == min(D(groups == group_new, group_old)), 1, 'first');
|
||||
% switch the group members
|
||||
groups(ind_worse) = group_new;
|
||||
groups(ind_new) = group_old;
|
||||
ind_switch([ind_worse, ind_new]) = 0;
|
||||
if all(ind_switch == 0)
|
||||
break
|
||||
end
|
||||
end
|
||||
|
||||
% ind_switch = (groups ~= sind(:,1));
|
||||
% for ii = Ngroups
|
||||
% clf
|
||||
% hold all;
|
||||
% ind = groups == ii;
|
||||
% ax = plot(self.probe_positions_0(ind & ind_switch, 1), self.probe_positions_0(ind & ind_switch, 2), 'o');
|
||||
% ax2 = plot(self.probe_positions_0(ind & ~ind_switch, 1), self.probe_positions_0(ind & ~ind_switch, 2), 'x');
|
||||
% try; ax2.Color = ax.Color; end
|
||||
% plot(C(ii,1),C(ii,2),'x','Linewidth', 2)
|
||||
% % drawnow
|
||||
% % pause(1)
|
||||
% end
|
||||
% title(num2str(iter))
|
||||
% axis tight equal
|
||||
% pause(1)
|
||||
%
|
||||
end
|
||||
|
||||
cluster_refinement_time = cluster_refinement_time + toc(t0);
|
||||
|
||||
|
||||
%% optimally sort the indices to help GPU
|
||||
[nbins,bins] = hist(groups, unique(groups));
|
||||
[~,ind] = sort(nbins,2,'descend');
|
||||
for ii = 1:length(bins)
|
||||
indices{kk}{ii} = indices_0((groups == bins(ind(ii))));
|
||||
scan_ids{kk}{ii} = scans_0((groups == bins(ind(ii))));
|
||||
end
|
||||
verbose(2,'=== Number of cluster sizes %i', length(unique(nbins)))
|
||||
end
|
||||
|
||||
verbose(0,'=== Position clusters found in %i iterations in %3.2gs', iter, cluster_time)
|
||||
verbose(0,'=== Position clusters refined in %i iterations in %3.2gs', iter, cluster_refinement_time)
|
||||
|
||||
|
||||
%rng shuffle
|
||||
|
||||
if verbose() > 1 && Ngroups_sizes > 1
|
||||
warning('Unequal group sizes, it may cause slower calculation')
|
||||
end
|
||||
|
||||
|
||||
indices_out = horzcat(indices{:});
|
||||
scan_ids_out = horzcat(scan_ids{:});
|
||||
|
||||
|
||||
if Ngroups == 1 && Nsets == 1
|
||||
%% merge groups from multiple scans into larger chunks if grouping is too large
|
||||
indices_out = {horzcat(indices_out{:})};
|
||||
scan_ids_out = {horzcat(scan_ids_out{:})};
|
||||
end
|
||||
|
||||
|
||||
|
||||
%% sort them to minimize allocation of new projection matrices
|
||||
Nitems = cellfun(@length, indices_out);
|
||||
|
||||
if all(max(Nitems) - min(Nitems) <= 1) && all(Nitems > 100)
|
||||
% just neglect one scanning position to keep the bunches with the same
|
||||
% size -> faster run on GPU
|
||||
for i = 1:length(indices_out)
|
||||
indices_out{i} = indices_out{i}(1:min(Nitems));
|
||||
scan_ids_out{i} = scan_ids_out{i}(1:min(Nitems));
|
||||
end
|
||||
else
|
||||
[~,ind] = sort(Nitems(:),1,'descend' );
|
||||
indices_out = indices_out(ind);
|
||||
scan_ids_out = scan_ids_out(ind);
|
||||
end
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
function [groups, C, sum_D, D] = get_best_kmeans(positions, Ngroups)
|
||||
% make several guesses to get better Kmean distribution
|
||||
warning('off','stats:kmeans:FailedToConverge')
|
||||
for i = 1:10
|
||||
[groups{i}, C{i}, sum_D{i}, D{i}] = kmeans(positions, Ngroups);
|
||||
nbins = hist(groups{i}, unique(groups{i}));
|
||||
score(i) = std(nbins);
|
||||
end
|
||||
best = math.argmin(score);
|
||||
groups = groups{best};
|
||||
C = C{best};
|
||||
sum_D = sum_D{best};
|
||||
D = D{best};
|
||||
end
|
||||
|
||||
@@ -0,0 +1,203 @@
|
||||
% GET_NONOVERLAPPING_INDICES a heuristic based method to select pseudorandom indices of non overlapping regions
|
||||
% Note: It can be slow for large number of scanning positions
|
||||
%
|
||||
% [indices_out, scan_ids_out] = get_nonoverlapping_indices(self, cache, par )
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ indices_out cell of arrays, contain indices of positions processed in parallel
|
||||
% ++ scan_ids_out cell of arrays, contain scan numbers for each position
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [indices_out, scan_ids_out] = get_nonoverlapping_indices(self, cache, par )
|
||||
|
||||
% find groups accross the scans in order to further minimize overlap
|
||||
group_across_scans = true; %need to be true for sharing object amongs scans
|
||||
|
||||
if group_across_scans
|
||||
% divide the grouping equally over all the scans
|
||||
grouping = ceil(par.grouping/par.Nscans);
|
||||
else
|
||||
grouping = par.grouping;
|
||||
end
|
||||
max_groups = 0;
|
||||
|
||||
for kk = 1:par.Nscans
|
||||
|
||||
% setdiff sort the indices by size
|
||||
indices_0 = self.reconstruct_ind{kk}; % remove unwanted from the decision process
|
||||
ind_start(kk) = min(indices_0)-1;
|
||||
indices_0 = indices_0 - ind_start(kk); %
|
||||
Npos_tmp=length(indices_0);
|
||||
% randomly permutate the indices
|
||||
indices_0 = indices_0(randperm(Npos_tmp));
|
||||
max_groups = max(max_groups, ceil(Npos_tmp/grouping));
|
||||
% fill it with some initial random guess
|
||||
for ii = 1:ceil(Npos_tmp/grouping)
|
||||
indices{kk}{ii} = indices_0(1+(ii-1)*grouping : min(Npos_tmp,ii*grouping));
|
||||
end
|
||||
|
||||
% no need for this method ot it calculation would be too long -> use
|
||||
% just the random initial guess
|
||||
if (self.Npos/par.Nscans > 1e3 ) || (grouping == 1) || ~isfield(cache, 'distances_matrix')
|
||||
%%%for ii = 1:length(indices{1}) %why length(indices{1})? Bug?
|
||||
for ii = 1:length(indices{kk}) %modified by YJ to prevent error when different scans have differernt number of positions
|
||||
scan_ids{kk}{ii} = ones(1,length(indices{kk}{ii}))*kk; % note their scan origin
|
||||
end
|
||||
continue
|
||||
end % hope that for large number of positions the random statistics will be enough
|
||||
|
||||
try
|
||||
|
||||
update_score = 0;
|
||||
for i = 1:ceil(Npos_tmp/grouping)-1
|
||||
id = indices{kk}{i};
|
||||
dist_mat_small = cache.distances_matrix{kk}(id,id);
|
||||
for ii = 0:2*length(indices{kk}{i+1}) % go twice through all positions
|
||||
j = 1+mod(ii, length(indices{kk}{i+1}));
|
||||
min_dist = 1./sum(1./dist_mat_small.^2); % find the shortest distance between the probes
|
||||
if all(isinf(min_dist)) % all(isnan(min_dist))
|
||||
break
|
||||
end
|
||||
[~,min_dist_ind] = min(min_dist);
|
||||
% make a swap with the j position in i+1 index array
|
||||
tmp = indices{kk}{i+1}(j);
|
||||
indices{kk}{i+1}(j) = indices{kk}{i}(min_dist_ind);
|
||||
indices{kk}{i}(min_dist_ind) = tmp;
|
||||
|
||||
|
||||
% update distance matrix
|
||||
dist_mat_small_update = cache.distances_matrix{kk}(tmp,indices{kk}{i});
|
||||
dist_mat_small(min_dist_ind,:) = dist_mat_small_update';
|
||||
dist_mat_small(:,min_dist_ind) = dist_mat_small_update;
|
||||
end
|
||||
update_score = update_score +j;
|
||||
end
|
||||
catch
|
||||
keyboard
|
||||
end
|
||||
|
||||
|
||||
% fill the last group by the skip indieces but do not expand it
|
||||
skip_ind = cache.skip_ind(randperm(length(cache.skip_ind)));
|
||||
indices{kk}{end} = [indices{kk}{end}, skip_ind(1:min(end, grouping-length(indices{kk}{end})))]; % join skip_ind back to the last (smallest) set
|
||||
|
||||
for ii = 1:length(indices{kk})
|
||||
scan_ids{kk}{ii} = ones(1,length(indices{kk}{ii}))*kk; % note their scan origin
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if group_across_scans
|
||||
indices_out = cell(max_groups,1);
|
||||
scan_ids_out = cell(max_groups,1);
|
||||
%% merge groups from difference scans into larger chunks if required
|
||||
for ii = 1:max_groups
|
||||
indices_out{ii} = [];
|
||||
scan_ids_out{ii} = [];
|
||||
% from each scan add one group
|
||||
for kk = 1:par.Nscans
|
||||
if ii <= length(indices{kk})
|
||||
indices_out{ii} = [indices_out{ii}, indices{kk}{ii}+ind_start(kk)];
|
||||
scan_ids_out{ii} = [scan_ids_out{ii}, scan_ids{kk}{ii}];
|
||||
end
|
||||
end
|
||||
if length(scan_ids_out) > 1 && length(scan_ids_out{end}) < grouping / 10
|
||||
% if the a group is too small, merge it with the previous to
|
||||
% reduce the overhead
|
||||
indices_out{end-1} = [indices_out{end-1}, indices_out{end}];
|
||||
scan_ids_out{end-1} = [scan_ids_out{end-1}, scan_ids_out{end}];
|
||||
scan_ids_out(end) = []; indices_out(end) = [];
|
||||
end
|
||||
end
|
||||
else
|
||||
indices_out = {};
|
||||
for ii = 1:par.Nscans
|
||||
for kk = 1:length(indices{ii})
|
||||
indices_out = [indices_out, indices{ii}{kk}+ind_start(ii)];
|
||||
end
|
||||
end
|
||||
scan_ids_out = [scan_ids{:}]';
|
||||
|
||||
end
|
||||
|
||||
%% sort them to minimize allocation of new projection matrices
|
||||
Nitems = cellfun(@length, indices_out);
|
||||
|
||||
if all(max(Nitems) - min(Nitems) <= 1) && all(Nitems > 100)
|
||||
% just neglect one scanning position to keep the bunches with the same
|
||||
% size -> faster run on GPU
|
||||
for i = 1:length(indices_out)
|
||||
indices_out{i} = indices_out{i}(1:min(Nitems));
|
||||
scan_ids_out{i} = scan_ids_out{i}(1:min(Nitems));
|
||||
end
|
||||
else
|
||||
[~,ind] = sort(Nitems(:),1,'descend' );
|
||||
indices_out = indices_out(ind);
|
||||
scan_ids_out = scan_ids_out(ind);
|
||||
end
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,147 @@
|
||||
% GET_SCANNING_INDICES simple based method to select indices for DM
|
||||
%
|
||||
% [indices_out, scan_ids_out] = get_scanning_indices(self, cache, par )
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ indices_out cell of arrays, contain indices of positions processed in parallel
|
||||
% ++ scan_ids_out cell of arrays, contain scan numbers for each position
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
function [indices_out, scan_ids_out] = get_scanning_indices(self, cache, par )
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
|
||||
grouping = par.grouping;
|
||||
max_groups = 0;
|
||||
|
||||
if self.Npos == grouping && par.Nscans == 1
|
||||
indices_out = self.reconstruct_ind;
|
||||
scan_ids_out = {ones(self.Npos,1)};
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
for kk = 1:par.Nscans
|
||||
N = length(self.reconstruct_ind{kk});
|
||||
|
||||
% !! indices ordering has to be always the same for DM !!!
|
||||
|
||||
indices_0 = self.reconstruct_ind{kk};
|
||||
|
||||
max_groups = max(max_groups, ceil(N/grouping));
|
||||
|
||||
for ii = 1:ceil(N/grouping)
|
||||
indices{kk}{ii} = indices_0(1+(ii-1)*grouping : min(end,ii*grouping));
|
||||
end
|
||||
% fill the last group by the skip indices but do not expand it
|
||||
skip_ind = cache.skip_ind(randperm(length(cache.skip_ind)));
|
||||
indices{kk}{end} = [indices{kk}{end}, skip_ind(1:min(end, grouping-length(indices{kk}{end})))]; % join skip_ind back to the last (smallest) set
|
||||
for ii = 1:length(indices{kk})
|
||||
scan_ids{kk}{ii} = kk * ones(1,length(indices{kk}{ii})); % note their scan origin
|
||||
end
|
||||
end
|
||||
|
||||
% how many scans should be merged to reach the desired grouping
|
||||
Njoin = ceil(par.grouping / (self.Npos/par.Nscans));
|
||||
|
||||
|
||||
if Njoin > 1 && par.Nscans > 1 && is_method(par, {'PIE', 'ML'})
|
||||
% join several scan to improve performance
|
||||
indices_out = cell(ceil(par.Nscans/Njoin),1);
|
||||
scan_ids_out = cell(ceil(par.Nscans/Njoin),1);
|
||||
%% merge groups from difference scans into larger chunks
|
||||
for kk = 1:ceil(par.Nscans/Njoin)
|
||||
indices_out{kk} = [];
|
||||
scan_ids_out{kk} = [];
|
||||
for ii = 1:Njoin
|
||||
if kk+(ii-1)*ceil(par.Nscans/Njoin) <= par.Nscans
|
||||
indices_out{kk} = [indices_out{kk}, indices{kk+(ii-1)*ceil(par.Nscans/Njoin)}{1}];
|
||||
scan_ids_out{kk} = [scan_ids_out{kk}, scan_ids{kk+(ii-1)*ceil(par.Nscans/Njoin)}{1}];
|
||||
end
|
||||
end
|
||||
end
|
||||
else
|
||||
indices_out = horzcat(indices{:});
|
||||
scan_ids_out = horzcat(scan_ids{:});
|
||||
end
|
||||
|
||||
|
||||
%% sort them to minimize allocation of new projection matrices
|
||||
Nitems = cellfun(@length, indices_out);
|
||||
|
||||
if all(max(Nitems) - min(Nitems) <= 1) && all(Nitems > 100)
|
||||
% just neglect one scanning position to keep the bunches with the same
|
||||
% size -> faster run on GPU
|
||||
for i = 1:length(indices_out)
|
||||
indices_out{i} = indices_out{i}(1:min(Nitems));
|
||||
scan_ids_out{i} = scan_ids_out{i}(1:min(Nitems));
|
||||
end
|
||||
else
|
||||
[~,ind] = sort(Nitems(:),1,'descend' );
|
||||
indices_out = indices_out(ind);
|
||||
scan_ids_out = scan_ids_out(ind);
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,167 @@
|
||||
% RESCALE_INPUTS multigrid scheme method
|
||||
%
|
||||
% self = rescale_inputs(self, Np_p_new, rescale_data)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** Np_p_new new size of the rescaled dataset
|
||||
% ** rescale_data true -> rescale also data + mask + noise arrays
|
||||
%
|
||||
% returns:
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
function self = rescale_inputs(self, Np_p_new, rescale_data)
|
||||
|
||||
import utils.*
|
||||
import math.*
|
||||
|
||||
if isempty(Np_p_new)
|
||||
return
|
||||
end
|
||||
|
||||
scale = Np_p_new ./ self.Np_p;
|
||||
|
||||
if all(scale == 1)
|
||||
return
|
||||
end
|
||||
|
||||
self.modes = [];
|
||||
|
||||
if ~isempty(self.diffraction_deform_matrix)
|
||||
verbose(1,'Rescalling with diffraction_deform_matrix is not implemented')
|
||||
self.diffraction_deform_matrix = [];
|
||||
end
|
||||
|
||||
self.Np_p = ceil(self.Np_p.*scale);
|
||||
self.Np_o = ceil(self.Np_o.*scale);
|
||||
|
||||
if ~isempty(self.probe_positions) && any(self.probe_positions(:) ~= self.probe_positions_0(:))
|
||||
self.probe_positions = scale([2,1]) .* self.probe_positions;
|
||||
else
|
||||
self.probe_positions = [];
|
||||
end
|
||||
self.probe_positions_0 = scale([2,1]) .* self.probe_positions_0;
|
||||
self.pixel_size = self.pixel_size ./ scale;
|
||||
|
||||
for i = 1:length(self.probe)
|
||||
% scale also intensity
|
||||
self.probe{i} = interpolateFT_addnoise(self.probe{i}, self.Np_p, 1 )./prod(scale);
|
||||
end
|
||||
|
||||
for i = 1:numel(self.object)
|
||||
self.object{i} = interpolateFT_addnoise(self.object{i}, self.Np_o , 1);
|
||||
end
|
||||
|
||||
if ~isempty(self.probe_support)
|
||||
self.probe_support = interpolateFT( self.probe_support, self.Np_p) ;
|
||||
end
|
||||
if ~isempty(self.probe_support_fft)
|
||||
self.probe_support_fft = crop_pad( self.probe_support_fft, self.Np_p) ;
|
||||
end
|
||||
|
||||
|
||||
if rescale_data
|
||||
self.diffraction = fftshift_2D(self.diffraction);
|
||||
self.diffraction = crop_pad(self.diffraction, self.Np_p);
|
||||
self.diffraction = ifftshift_2D(self.diffraction);
|
||||
|
||||
% force mask empty by Zhen Chen
|
||||
self.mask=[];
|
||||
if ~isempty(self.mask)
|
||||
fill_value = 0.9; % fill value in case of ptychographic "super resolution"
|
||||
self.mask = fftshift_2D(self.mask);
|
||||
self.mask = crop_pad(self.mask, self.Np_p, fill_value);
|
||||
self.mask = ifftshift_2D(self.mask);
|
||||
end
|
||||
if ~isempty(self.noise)
|
||||
self.noise = fftshift_2D(self.noise);
|
||||
self.noise = crop_pad(self.noise, self.Np_p);
|
||||
self.noise = ifftshift_2D(self.noise);
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
function [ imout ] = interpolateFT_addnoise(im,outsize, noise_amplitude)
|
||||
% fill the empty regions in the FFT interpolated data by some weak
|
||||
% random noise
|
||||
import math.fftshift_2D
|
||||
import math.ifftshift_2D
|
||||
import utils.crop_pad
|
||||
|
||||
|
||||
Nout = outsize;
|
||||
Nin = size(im);
|
||||
|
||||
imFT = fftshift_2D(fft2(im));
|
||||
|
||||
imout = crop_pad(imFT, outsize);
|
||||
|
||||
% add noise to avoid correlation between upsampled imaged from
|
||||
% interpolation artefacts
|
||||
imout = imout + noise_amplitude * randn(outsize).*mean(min(abs(imFT)));
|
||||
|
||||
imout = ifft2(ifftshift_2D(imout))*(Nout(1)*Nout(2)/(Nin(1)*Nin(2)));
|
||||
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,177 @@
|
||||
% SAVE_TO_P save parameters and recosntrutions from param and self structures to the p-structure
|
||||
%
|
||||
% p_out = save_to_p(self, param, p, fourier_error)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** param structure containing parameters for the engines
|
||||
% ** p ptychoshelves p structure
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
%
|
||||
% returns:
|
||||
% ** p_out updated ptychoshelves p structure
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function p_out = save_to_p(self, param, p, fourier_error)
|
||||
|
||||
import utils.*
|
||||
Np_p = self.Np_p;
|
||||
|
||||
p_out = p;
|
||||
|
||||
|
||||
%% return calculated values back to the main code (p-structure)
|
||||
p_out.probe_modes = length(self.probe);
|
||||
p_out.numprobs = size(self.probe{1},3);
|
||||
for ll = 1:p_out.probe_modes
|
||||
if size(self.probe{ll},3) == self.Npos
|
||||
% classical OPRP method
|
||||
for ii = 1:p.numscans
|
||||
probes(:,:,ii,ll) = mean(self.probe{ll}(:,:,self.reconstruct_ind{ii}),3);
|
||||
end
|
||||
% save the variable modes
|
||||
[X,V] = extract_PCA(self.probe{ll}, param.variable_probe_modes);
|
||||
p_out.probe_PCA.eigen_vec = X * (prod(sqrt(Np_p))*2*p.renorm);% normalization for consistency with the CPU code
|
||||
p_out.probe_PCA.evolution = V;
|
||||
else
|
||||
% store constant part
|
||||
probes(:,:,1:size(self.probe{ll},3),ll) = self.probe{ll}(:,:,:,1);
|
||||
if ndims(self.probe{ll}) == 4
|
||||
p_ind = zeros(self.Npos,1);
|
||||
for kk = 1:length(self.reconstruct_ind)
|
||||
p_ind = p_ind + kk*ismember(1:self.Npos, self.reconstruct_ind{kk})';
|
||||
end
|
||||
p_out.probe_variable.eigen_vec = self.probe{ll}(:,:,:,2) * (prod(sqrt(Np_p))*2*p.renorm);% normalization for consistency with the CPU code
|
||||
p_out.probe_variable.evolution = self.probe_evolution;
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
% normalization for consistency with the CPU code
|
||||
probes = probes * (prod(sqrt(Np_p))*2*p.renorm);
|
||||
p_out.probes = probes;
|
||||
|
||||
|
||||
position_offset = 1+floor((p.object_size-self.Np_p)/2);
|
||||
|
||||
% for consistency with the CPU code revert the object to the original size
|
||||
p_out.numobjs = size(self.object,1);
|
||||
p_out.object = cell(1,p_out.numobjs);
|
||||
for i = 1:p_out.numobjs
|
||||
obj_size = p.object_size(min(end,p.share_object_ID(i)),:);
|
||||
p_out.object{i} = single([]);
|
||||
for layer = 1:param.Nlayers
|
||||
p_out.object{i}(:,:,1,layer) = imshift_fast(self.object{i,layer}, -1,-1, obj_size, 'nearest', mean(self.object{i,layer}(:)));
|
||||
end
|
||||
end
|
||||
|
||||
for i = 1:p.numscans
|
||||
id = p.share_object_ID(i);
|
||||
obj_size = p.object_size(min(end,id),:);
|
||||
p_out.illum_sum{id} = imshift_fast(self.illum_sum{id}, -1,-1, obj_size, 'nearest');
|
||||
end
|
||||
|
||||
if param.probe_position_search < param.number_iterations
|
||||
% store the refined positions
|
||||
p_out.positions = self.probe_positions(:,[2,1]);
|
||||
% return to the original coordinates
|
||||
p_out.positions_0 = self.probe_positions_0(:,[2,1]);
|
||||
for i = 1:length(self.reconstruct_ind)
|
||||
ind = self.reconstruct_ind{i};
|
||||
p_out.positions(ind,:) = p_out.positions(ind,:) + position_offset(p.share_object_ID(i),:);
|
||||
p_out.positions_0(ind,:) = p_out.positions_0(ind,:) + position_offset(p.share_object_ID(i),:);
|
||||
end
|
||||
else
|
||||
for i = 1:length(self.reconstruct_ind)
|
||||
ind = self.reconstruct_ind{i};
|
||||
if ~isempty(self.probe_positions)
|
||||
p_out.positions(ind,:) = self.probe_positions(ind,[2,1]) + position_offset(p.share_object_ID(i),:);
|
||||
else
|
||||
p_out.positions(ind,:) = self.probe_positions_0(ind,[2,1]) + position_offset(p.share_object_ID(i),:);
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
if param.probe_position_search < param.number_iterations || param.detector_rotation_search < param.number_iterations || param.detector_scale_search < param.number_iterations
|
||||
p_out = engines.GPU_MS.analysis.report_refined_geometry(self, param, p_out);
|
||||
end
|
||||
|
||||
|
||||
% save additional reconstructed parameters
|
||||
for item = {'background', 'intensity_corr', 'probe_fourier_shift' }
|
||||
try
|
||||
p_out.(item{1}) = self.(item{1});
|
||||
end
|
||||
end
|
||||
|
||||
% save error metrics
|
||||
ind_ok = any(~isnan(fourier_error),2); % plot only the reported values
|
||||
p_out.error_metric.value = nanmean(fourier_error(ind_ok,:),2);
|
||||
p_out.error_metric.iteration = find(ind_ok);
|
||||
if strcmp(param.likelihood,'poisson' )
|
||||
p_out.error_metric.err_metric = 'poisson';
|
||||
else
|
||||
p_out.error_metric.err_metric = 'L1';
|
||||
end
|
||||
p_out.error_metric.method = ['GPU-',param.method, ' metric:' , param.likelihood ];
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,136 @@
|
||||
% self = align_objects(self )
|
||||
% align all provided object arrays and apply the same shift on the
|
||||
% corresponding probe so that the scans can be used for shared object
|
||||
% reconstructions
|
||||
%
|
||||
% Inputs:
|
||||
% self main data structure
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function self = align_objects(self)
|
||||
|
||||
import engines.GPU_MS.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
|
||||
cache.skip_ind = [];
|
||||
[cache.oROI_s{1},cache.oROI{1}] = shared.find_reconstruction_ROI( self.probe_positions_0,self.Np_o, self.Np_p);
|
||||
cache.object_ROI = {ceil(self.Np_p(1)/2):self.Np_o(1)-ceil(self.Np_p(1)/2), ...
|
||||
ceil(self.Np_p(2)/2):self.Np_o(2)-ceil(self.Np_p(2)/2)};
|
||||
|
||||
Nobj = size(self.object,1);
|
||||
shift = [0,0];
|
||||
obj1 = prod(cat(3,self.object{1,:}),3);
|
||||
obj1 = Ggather(obj1(cache.object_ROI{:}));
|
||||
|
||||
for ll = 1:Nobj
|
||||
obj2 = prod(cat(3,self.object{ll,:}),3);
|
||||
obj2 = Ggather(obj2(cache.object_ROI{:}));
|
||||
[score(ll), object_aligned{ll}] = analysis.fourier_ring_correlation(obj1,obj2,...
|
||||
'smoothing', 5, 'crop', self.Np_p/4, 'plot_results', false);
|
||||
shift(ll,:) = score(ll).shift;
|
||||
end
|
||||
|
||||
if any([score(:).AUC] < 0.3)
|
||||
warning('Alignment of scans %i vs scan %i propably failed, FRC resolution is %3.3g of Nyquist frequency limit', 1, ll, score.resolution)
|
||||
figure(56476)
|
||||
subplot(1,Nobj,1)
|
||||
plotting.imagesc3D(angle(object_aligned{1}{1})); axis off image
|
||||
grid on
|
||||
for ll = 1:Nobj
|
||||
subplot(1,Nobj,ll)
|
||||
plotting.imagesc3D(angle(object_aligned{ll}{2})); axis off image xy
|
||||
grid on
|
||||
end
|
||||
plotting.suptitle('Objects after alignement, check visually the estimated alignement')
|
||||
colormap bone
|
||||
disp('Estimated shifts between the aligned objects')
|
||||
disp(shift )
|
||||
end
|
||||
|
||||
shift = shift - mean(shift,1);
|
||||
|
||||
|
||||
self.Np_o = self.Np_o + 2*ceil(max(abs(shift(:,[2,1])),[],1));
|
||||
for layer = 1:size(self.object,2)
|
||||
for ll = 1:Nobj
|
||||
% make them all the same size
|
||||
self.object{ll,layer} = crop_pad(self.object{ll,layer}, self.Np_o, mean(self.object{ll,layer}(:)));
|
||||
self.object{ll,layer} = utils.imshift_fft(self.object{ll,layer}, shift(ll,:));
|
||||
end
|
||||
end
|
||||
if utils.verbose > -1 && any(max(abs(shift) ./ self.Np_p([2,1])) > 0.25)
|
||||
warning off backtrace
|
||||
id = math.argmax(max(abs(shift),[],2));
|
||||
|
||||
warning('Alignement of two mirrored scans resulted in maximal probe shift of %3.3g %3.3gpx, \n!! this is more than 50%% of the probe diameter !! \nconsider using better alignement between 0deg and 180deg scans ', -shift(id,1), shift(id,2))
|
||||
warning on backtrace
|
||||
end
|
||||
|
||||
|
||||
for ii = 1:length(self.probe)
|
||||
for ll = 1:Nobj
|
||||
% apply shift to the probe as well, if needed, replicate the
|
||||
% probe
|
||||
probe{ii}(:,:,ll,:) = utils.imshift_fft(self.probe{ii}(:,:,min(end,ll),:), shift(ll,:));
|
||||
end
|
||||
end
|
||||
self.probe = probe ;
|
||||
|
||||
end
|
||||
@@ -0,0 +1,66 @@
|
||||
% APPLY_PROBE_CONTRAINTS apply support constrains on the probe in the real space, fourier space or any other
|
||||
% plane if provided, it useds factor in mode.support_back_propagation_factor to perform ASM propagation
|
||||
%
|
||||
% probe = apply_probe_contraints(probe, mode)
|
||||
%
|
||||
% ** probe complex array with probe / probes
|
||||
% ** mode structure containing parameters for selected probe mode
|
||||
%
|
||||
% returns:
|
||||
% ** probe complex array with probe / probes
|
||||
%
|
||||
%
|
||||
|
||||
function probe = apply_probe_contraints(probe, mode)
|
||||
import math.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
|
||||
if ~isempty(mode.probe_support)
|
||||
% apply support contraint in real space (ir nearfield propagated )
|
||||
if ~isempty(mode.support_fwd_propagation_factor)
|
||||
if isscalar(mode.support_fwd_propagation_factor) && isinf(mode.support_fwd_propagation_factor)
|
||||
probe = fftshift_2D(fft2(fftshift_2D(probe))); % propagate to infinity
|
||||
else
|
||||
probe = ifft2(fft2(probe) .* mode.support_propagation_factor);
|
||||
end
|
||||
end
|
||||
|
||||
%% apply real-space support
|
||||
probe = probe .* mode.probe_support;
|
||||
|
||||
if ~isempty(mode.support_back_propagation_factor)
|
||||
if isscalar(mode.support_back_propagation_factor) && isinf(mode.support_back_propagation_factor)
|
||||
probe = fftshift_2D(ifft2(fftshift_2D(probe))); % propagate to infinity
|
||||
else
|
||||
probe = ifft2(fft2(probe).* mode.support_back_propagation_factor);
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
Np_p = size(probe);
|
||||
|
||||
if mode.probe_scale_upd(end) > 0 && ~isempty(mode.probe_scale_window)
|
||||
% apply windowing to avoid boundary issues when subpixel probe
|
||||
% rescaling is used
|
||||
probe = probe .* mode.probe_scale_window ;
|
||||
end
|
||||
if ~isempty(mode.probe_support_fft) || mode.probe_scale_upd(end) ~= 0
|
||||
%% apply contraint in the detector plane
|
||||
|
||||
% propagate probe on the detector
|
||||
probe = fwd_fourier_proj(probe, mode);
|
||||
|
||||
if ~isempty(mode.probe_support_fft)
|
||||
probe = probe .* mode.probe_support_fft;
|
||||
end
|
||||
if mode.probe_scale_upd(end) < 0 && ~isempty(mode.probe_scale_window)
|
||||
probe = probe .* mode.probe_scale_window ;
|
||||
end
|
||||
|
||||
% propagate probe back to the sample plane
|
||||
probe = back_fourier_proj(probe, mode);
|
||||
end
|
||||
end
|
||||
|
||||
@@ -0,0 +1,111 @@
|
||||
% APPLY_SUBPX_SHIFT subpixel probe shifting , equivalent just a bit faster than imshift_fft
|
||||
%
|
||||
% img = apply_subpx_shift(img, shift)
|
||||
% apply_subpx_shift() will reset persitent variables that are created on GPU to avoid overhead with CPU / GPU transfer
|
||||
%
|
||||
%
|
||||
% ** img stack images
|
||||
% ** shift (N,2) array of shifts
|
||||
% returns
|
||||
% ++ img shifted image stack
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for maximum likelihood:
|
||||
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
|
||||
% (doi: 10.1088/1367-2630/14/6/063004),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% (doi: 10.1364/OE.24.029089).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function img = apply_subpx_shift(img, shift)
|
||||
% subpixel probe shifting
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
persistent xgrid ygrid
|
||||
if nargin == 0
|
||||
xgrid = [];
|
||||
return
|
||||
end
|
||||
if all(shift(:) == 0); return ; end
|
||||
global use_gpu
|
||||
|
||||
|
||||
shift = single(shift);
|
||||
x = reshape(shift(:,1),1,1,[]);
|
||||
y = reshape(shift(:,2),1,1,[]);
|
||||
|
||||
|
||||
Np = size(img);
|
||||
|
||||
if size(img,3) ~= size(shift,1) && use_gpu
|
||||
% ugly trick making matlab GPU FFT faster
|
||||
img = repmat(img,1,1,size(shift,1));
|
||||
end
|
||||
img = fft2_safe(img);
|
||||
|
||||
if isempty(xgrid)
|
||||
% matlab seems to need quite a lot of time to generate it -> preallocate
|
||||
xgrid = Garray(fftshift((0:Np(2)-1)'/Np(2))-0.5)';
|
||||
ygrid = Garray(fftshift((0:Np(1)-1)'/Np(1))-0.5);
|
||||
end
|
||||
|
||||
if use_gpu
|
||||
img = Gfun(@apply_shift_Gfun,img,x,y,xgrid, ygrid);
|
||||
else
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times, x,xgrid)));
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times,y,ygrid)));
|
||||
end
|
||||
img = ifft2_safe(img);
|
||||
end
|
||||
|
||||
function img = apply_shift_Gfun(img,x,y,xgrid, ygrid)
|
||||
img = img .* exp((-2i*pi)*(x*xgrid+y*ygrid));
|
||||
end
|
||||
@@ -0,0 +1,98 @@
|
||||
% APPLY_SUBPX_SHIFT_FFT fast shifting in fourier space (ie apply phase ramp )
|
||||
%
|
||||
% img = apply_subpx_shift_fft(img, shift)
|
||||
%
|
||||
% ** img stack images
|
||||
% ** shift (N,2) array of shifts
|
||||
% returns
|
||||
% ++ img shifted image stack
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for maximum likelihood:
|
||||
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
|
||||
% (doi: 10.1088/1367-2630/14/6/063004),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% (doi: 10.1364/OE.24.029089).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function img = apply_subpx_shift_fft(img, shift)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
if all(shift(:) == 0); return ; end
|
||||
global use_gpu
|
||||
persistent grid
|
||||
|
||||
shift = Garray(shift);
|
||||
|
||||
x = reshape(shift(:,1),1,1,[]);
|
||||
y = reshape(shift(:,2),1,1,[]);
|
||||
|
||||
|
||||
Np = size(img);
|
||||
|
||||
if Np(1) ~= Np(2); error('Not implemented'); end
|
||||
grid = Garray((0:Np(1)-1)'/Np(1)-0.5);
|
||||
|
||||
if isempty(grid)
|
||||
grid = Garray((0:Np(1)-1)'/Np(1)-0.5);
|
||||
end
|
||||
|
||||
if use_gpu
|
||||
img = Gfun(@apply_shift_Gfun,img,x,y,grid', grid);
|
||||
else
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times,x,grid')));
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times,y,grid)));
|
||||
end
|
||||
end
|
||||
|
||||
function img = apply_shift_Gfun(img,x,y,xgrid, ygrid)
|
||||
img = img .* exp((-2i*pi)*(x*xgrid+y*ygrid));
|
||||
end
|
||||
@@ -0,0 +1,111 @@
|
||||
% BACK_FOURIER_PROJ back propagate to the sample plane
|
||||
%
|
||||
% Psi = back_fourier_proj(Psi, mode)
|
||||
%
|
||||
% ** Psi [Nx,Ny,N] array, propagated complex valued exit-wave Psi = F(P*O)
|
||||
% ** mode structure containing parameters for selected probe mode
|
||||
%
|
||||
% returns
|
||||
% ++ psi [Nx,Ny,N] array, back-propagated complex valued exit-wave
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [Psi, fmask] = back_fourier_proj(Psi, mode, ind)
|
||||
import engines.GPU_MS.shared.*
|
||||
fmask = [];
|
||||
|
||||
try
|
||||
if mode.distances(end) == 0
|
||||
% no propagation
|
||||
elseif mode.distances(end) == inf
|
||||
Psi = ifft2_safe(Psi); % fully farfield
|
||||
% Psi = fftshift_2D(ifft2_safe(fftshift_2D(Psi))); % fully farfield
|
||||
elseif mode.distances(end) == -inf
|
||||
Psi = fft2_safe(Psi); % fully farfield forward
|
||||
elseif ~isempty(mode.cFAR_factor) % almost far field
|
||||
Psi = fftshift_2D(ifft2_safe(fftshift_2D(Psi)));
|
||||
Psi = bsxfun(@times, Psi, mode.cFAR_factor);
|
||||
elseif ~isempty(mode.cASM_factor) % near field
|
||||
Psi = fft2_safe(Psi);
|
||||
Psi = Psi .* mode.cASM_factor;
|
||||
Psi = ifft2_safe( Psi );
|
||||
else
|
||||
error('Not implemented')
|
||||
end
|
||||
if mode.probe_scale_upd(end) ~= 0
|
||||
% apply scaling to the probe , used for camera distance refinement
|
||||
Psi = utils.imrescale_frft(Psi,1/(1+mode.probe_scale_upd(end)));
|
||||
end
|
||||
if nargin > 2 && any(mode.probe_rotation_all)
|
||||
% apply rotation to the probe , used for camera angle refinement
|
||||
Psi = utils.imrotate_ax_fft(Psi,mode.probe_rotation_all(ind),3);
|
||||
end
|
||||
if ~isempty(mode.tilted_plane_propagate_fwd)
|
||||
% propagate to tilted plane of the sample (if provided)
|
||||
Psi = mode.tilted_plane_propagate_fwd(Psi);
|
||||
end
|
||||
catch err
|
||||
if utils.verbose() > 0
|
||||
warning(err.message)
|
||||
keyboard
|
||||
else
|
||||
rethrow(err)
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,104 @@
|
||||
% CLEAN_RESIDUA, try to use 2D FFT unwrapping to remove phase residua
|
||||
%
|
||||
% self = clean_residua(self)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% returns:
|
||||
% ++ self self-like structure with final reconstruction
|
||||
%
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function self = clean_residua(self, cache)
|
||||
|
||||
ker = gausswin(7) .* gausswin(7)';
|
||||
ker = ker / math.sum2(ker);
|
||||
|
||||
for ii = 1:numel(self.object)
|
||||
object = self.object{ii};
|
||||
Nresid(ii) = sum(sum(abs(utils.findresidues(object(cache.object_ROI{:}))) > 0.5));
|
||||
if Nresid(ii) == 0
|
||||
continue
|
||||
end
|
||||
|
||||
utils.verbose(1,'Detected %i residua, trying to remove', Nresid(ii))
|
||||
|
||||
amp = abs(object);
|
||||
|
||||
phase = 0;
|
||||
W = 2*(1-1./(1+cache.illum_sum_0{1}/max(max(cache.illum_sum_0{1}))));
|
||||
mean_amp = math.sum2(amp .* W) / math.sum2(W);
|
||||
W = W .* amp / mean_amp;
|
||||
for jj = 1:2
|
||||
phase = phase + math.unwrap2D_fft2(object,[],0,W,0);
|
||||
object = exp(-1i*phase) .* object;
|
||||
end
|
||||
|
||||
phase = convn( phase, ker, 'same');
|
||||
|
||||
%plotting.smart_figure(54655);
|
||||
%imagesc(angle(exp(-1i*phase) .* self.object{ii}))
|
||||
|
||||
self.object{ii} = exp(1i*phase)*mean_amp; % remove amplitude information, it is easy to recover
|
||||
end
|
||||
if sum(Nresid)
|
||||
utils.verbose(1,'Removing residua will result in low\n frequency errors in phase and amplitude, \n !! run DM again with current results as initial guess !!')
|
||||
end
|
||||
|
||||
% imagesc(utils.findresidues( self.object{ii} ))
|
||||
end
|
||||
@@ -0,0 +1,75 @@
|
||||
% EXTRACT_PCA Extract N principal compenents of 3D array x using SVD
|
||||
%
|
||||
% [X,V] = extract_PCA(x, N)
|
||||
%
|
||||
% ** x ND array
|
||||
% ** N number of SVD modes
|
||||
% returns:
|
||||
% ++ X principal components
|
||||
% ++ V principal weights
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
function [X,V] = extract_PCA(x, N)
|
||||
[U,S,V] = fsvd(reshape(x,[],size(x,3)), N);
|
||||
X = U*S;
|
||||
X = reshape(X, size(x,1), size(x,2),[]);
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,94 @@
|
||||
% FFT2_SAFE wrapper around fft2, in case of low memory it will try to repeat Ntimes before giving up
|
||||
%
|
||||
% x = fft2_safe(x)
|
||||
%
|
||||
% ** x input array
|
||||
% returns:
|
||||
% ++ x 2D fft array
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function x = fft2_safe(x)
|
||||
|
||||
|
||||
low_mem_errs = {'id:parallel:gpu:array:OOMForOperation',...
|
||||
'id:MATLAB:LowGPUMem','MATLAB:LowGPUMem',...
|
||||
'parallel:gpu:array:OOM',...
|
||||
'parallel:gpu:device:UnknownCUDAError', ...
|
||||
'parallel:gpu:array:OOMForOperation', ...
|
||||
'parallel:gpu:array:FFTInternalError'};
|
||||
|
||||
N = 5;
|
||||
for i = 1:N
|
||||
try
|
||||
x = fft2(x);
|
||||
break
|
||||
catch ME
|
||||
if ~any(strcmpi(ME.identifier, low_mem_errs))
|
||||
disp(N)
|
||||
rethrow(ME)
|
||||
end
|
||||
pause(1)
|
||||
end
|
||||
warning('FFT was not able to allocate enough memory')
|
||||
gpuDevice
|
||||
dbstack
|
||||
rethrow(ME)
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,209 @@
|
||||
% FIND_GEOM_CORRECTION use current probe positions estimates to update geometry model and
|
||||
% improve the new probe positions
|
||||
%
|
||||
% [self] = find_geom_correction(self,cache, par, iter, best_mode_id, update_position_weight)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** iter current iteration
|
||||
% ** best_mode_id strongest mode id
|
||||
% ** update_position_weight update_position_weight
|
||||
%
|
||||
% returns:
|
||||
% ++ self self-like structure with final reconstruction
|
||||
%
|
||||
%
|
||||
function [self] = find_geom_correction(self,cache, par, iter, best_mode_id, update_position_weight)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import utils.*
|
||||
import math.*
|
||||
|
||||
mode = self.modes{best_mode_id};
|
||||
|
||||
%% constrain the detector rotation
|
||||
|
||||
% store only the single update per scan
|
||||
if iter > par.detector_rotation_search
|
||||
for ii = 1:length(self.reconstruct_ind)
|
||||
ind = self.reconstruct_ind{ii};
|
||||
mrot(ii) = mean(mode.probe_rotation_all(ind));
|
||||
end
|
||||
if par.mirror_objects
|
||||
% enforce zero average rotation if two mirror scans are provided
|
||||
mrot = mrot - mean(mrot);
|
||||
end
|
||||
for ii = 1:length(self.reconstruct_ind)
|
||||
mode.probe_rotation_all(ind) = mrot(ii) ;
|
||||
end
|
||||
mode.probe_rotation(end+1,:) = mrot;
|
||||
end
|
||||
|
||||
|
||||
if iter <= par.probe_position_search
|
||||
self.modes{best_mode_id} = mode;
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
pos = mode.probe_positions;
|
||||
pos_0 = mode.probe_positions_0;
|
||||
|
||||
|
||||
%if all(isnan(mode.probe_positions_weight(:))) || all(mode.probe_positions_weight(:)==0)
|
||||
if update_position_weight %modified by YJ. add this option so users can update poisition weights more than once
|
||||
%% EMPIRICAL ESTIMATION OF POSITION RELIABILITY
|
||||
verbose(1,'EMPIRICAL ESTIMATION OF POSITION RELIABILITY\n')
|
||||
illum = utils.crop_pad(abs(self.probe{1}(:,:,1)).^2, self.Np_p/2);
|
||||
total_variation = zeros(self.Npos,2, 'single');
|
||||
|
||||
for ii = 1:par.Nscans
|
||||
o_tmp = self.object{min(end,ii), par.layer4pos};
|
||||
o_tmp = o_tmp ./ max2(abs(o_tmp(cache.object_ROI{:})));
|
||||
% keep it more memory effecient (important for GPU !! )
|
||||
Npos = length(self.reconstruct_ind{ii});
|
||||
for jj = 1:ceil(Npos/par.grouping)
|
||||
ind = 1+(jj-1)*par.grouping:min(Npos, jj*par.grouping);
|
||||
obj_proj = get_views(o_tmp,[],1,1,self.reconstruct_ind{ii}(ind),cache);
|
||||
obj_proj = utils.crop_pad(obj_proj, self.Np_p/2);
|
||||
|
||||
[nx, ny,~] = size(obj_proj);
|
||||
[X,Y] = meshgrid(-ny/2:ny/2-1, -nx/2:nx/2-1);
|
||||
% suppress edge effects of the FFT derivatives
|
||||
spatial_filter = exp(-(X.^16+Y.^16)/(min(nx,ny)/2.2)^16);
|
||||
obj_proj = obj_proj.* spatial_filter;
|
||||
[dX, dY] = get_img_grad(obj_proj);
|
||||
clear obj_proj
|
||||
illum_proj = get_views(utils.imgaussfilt2_fft(cache.illum_sum_0{min(ii,end)},self.Np_p/10),[],1,1,self.reconstruct_ind{ii}(ind),cache);
|
||||
illum_proj = utils.crop_pad(illum_proj, self.Np_p/2);
|
||||
|
||||
dX = abs(dX) .* illum_proj.* illum;
|
||||
dY = abs(dY) .* illum_proj.* illum;
|
||||
clear illum_proj
|
||||
total_variation(self.reconstruct_ind{ii}(ind),:) = Ggather(sqrt(squeeze([mean2(dX),mean2(dY)]))');
|
||||
clear dX dY
|
||||
end
|
||||
end
|
||||
mode.probe_positions_weight = total_variation.^4./mean(total_variation.^4);
|
||||
end
|
||||
|
||||
probe_positions_weight = double(mode.probe_positions_weight);
|
||||
jj = size(mode.scales,1)+1;
|
||||
|
||||
% find geometry for each scan separatelly
|
||||
for ii = 1:par.Nscans
|
||||
ind = self.reconstruct_ind{ii};
|
||||
C0 = mode.affine_matrix(:,:,ii) - eye(2);
|
||||
C0 = C0(:);
|
||||
|
||||
if par.Nscans > 1 && par.share_object
|
||||
% it the case of multiple scans allow also freedom of coordinates shifts
|
||||
pos_fun = @(C)(( [1+C(1), C(2); C(3), 1+C(4)]*pos_0(ind,:)')' + C([5,6])' );
|
||||
if isfield(mode, 'shift_scans' ) && size(mode.shift_scans,2)>=ii
|
||||
C0(5:6) = mode.shift_scans(:,ii);
|
||||
else
|
||||
C0(5:6) = 0;
|
||||
end
|
||||
else
|
||||
pos_fun = @(C)(( [1+C(1), C(2); C(3), 1+C(4)]*pos_0(ind,:)')' );
|
||||
end
|
||||
|
||||
err_fun = @(C)( probe_positions_weight(ind,:) .* (pos(ind,:) - pos_fun(C)));
|
||||
|
||||
options = optimoptions('lsqnonlin','Display','off');
|
||||
%C(:,ii) = lsqnonlin( err_fun, C0,[],[],options) ;
|
||||
%% modified by YJ to avoid fitting error
|
||||
try
|
||||
C(:,ii) = lsqnonlin( err_fun, C0,[],[],options);
|
||||
catch
|
||||
disp('Fitting error during geom correction...')
|
||||
C(:,ii) = [0,0,0,0,0,0];
|
||||
end
|
||||
%% restrict the geometry model only to the allowed degreed of freedom
|
||||
% ===================================================================
|
||||
M{ii} = reshape(C(1:4,ii),2,2)+eye(2);
|
||||
M_fit = M; %added by YJ to keep track of estimated affine matrix
|
||||
[scale, asymmetry, rotation, shear] = decompose_affine_matrix(M{ii});
|
||||
if ~ismember('scale', par.probe_geometry_model)
|
||||
scale = 1;
|
||||
end
|
||||
if ~ismember('asymmetry', par.probe_geometry_model)
|
||||
asymmetry = 0;
|
||||
end
|
||||
if ~ismember('rotation', par.probe_geometry_model)
|
||||
rotation = 0;
|
||||
end
|
||||
if ~ismember('shear', par.probe_geometry_model)
|
||||
shear = 0;
|
||||
end
|
||||
M{ii} = compose_affine_matrix(scale, asymmetry, rotation, shear);
|
||||
% ===================================================================
|
||||
mode.scales(jj,ii) = scale;
|
||||
mode.asymmetry(jj,ii) = asymmetry;
|
||||
mode.rotation(jj,ii) = rotation;
|
||||
mode.shear(jj,ii) = shear;
|
||||
|
||||
if par.Nscans > 1 && par.share_object
|
||||
mode.shift_scans(:,ii) = C(5:6,ii);
|
||||
else
|
||||
mode.shift_scans(:,ii) = [0,0];
|
||||
end
|
||||
|
||||
% store initial guess
|
||||
mode.affine_matrix(:,:,ii) = M{ii};
|
||||
|
||||
% calculate ideal model positions
|
||||
pos_model(ind,:) = pos_fun([reshape(M{ii} - eye(2), [],1); mode.shift_scans(:,ii)]);
|
||||
|
||||
end
|
||||
|
||||
self.affine_matrix = M;
|
||||
self.affine_matrix_fit = M_fit; %added by YJ to keep track of estimated affine matrix
|
||||
|
||||
verbose(2,['----- Geom. correction ', repmat('%3.3g ', 1,length(C))], C)
|
||||
|
||||
% use average
|
||||
resid_pos= pos - pos_model;
|
||||
|
||||
% ignore errors in the global shift of the positions
|
||||
for ii = 1:par.Nscans
|
||||
ind = self.reconstruct_ind{ii};
|
||||
resid_pos(ind,:) = resid_pos(ind,:) - mean(resid_pos(ind,:));
|
||||
end
|
||||
|
||||
err = abs(resid_pos);
|
||||
|
||||
max_err = par.probe_position_error_max ./ self.pixel_size .* self.relative_pixel_scale;
|
||||
|
||||
verbose(1, '==== AVG position error %3.2g px MAX error %3.2g LIMIT %3.2g px ', mean(err(:)), max(err(:)), max(max_err))
|
||||
|
||||
%modified by YJ: add par.apply_relaxed_position_constraint to allow position update without constraints from geometry model.
|
||||
%Useful if there are big jumps in positions
|
||||
if par.apply_relaxed_position_constraint
|
||||
%% apply only relaxed constrain on the probe positions !!!
|
||||
relax = 0.1;
|
||||
% constrain more the probes in flat regions
|
||||
W = relax*(1- (probe_positions_weight./ (1+probe_positions_weight)));
|
||||
% penalize positions that are further than max_err from origin
|
||||
W = min(10*relax, W+max(0,err - max_err).^2 ./ max_err.^2 ); % avoid travel larger than max error
|
||||
else
|
||||
W=0; %no geom model imposed to regularize positions
|
||||
end
|
||||
|
||||
% allow free movement in depenence on realibility and max allowed error
|
||||
pos_new = pos .*(1-W)+W.*pos_model;
|
||||
|
||||
mode.probe_positions = pos_new;
|
||||
mode.probe_positions_model = pos_model;
|
||||
|
||||
if any(isnan(mode.probe_positions(:)))
|
||||
keyboard
|
||||
end
|
||||
|
||||
self.modes{best_mode_id} = mode;
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,106 @@
|
||||
% FIND_RECONSTRUCTION_ROI precalculate the reconstruction regions for CPU and GPU
|
||||
%
|
||||
% [oROI, oROI_vec, sub_px_shift] = find_reconstruction_ROI( positions,Np_o, Np_p )
|
||||
%
|
||||
% ** positions Npox*2 vector of scanning positions
|
||||
% ** Np_o object size
|
||||
% ** Np_p probe size
|
||||
%
|
||||
% returns:
|
||||
% ++ oROI cell array contaning range for each view
|
||||
% ++ oROI_vec cell array contaning range for each view in vector shape
|
||||
% ++ sub_px_shift subpixel rounding errors, used for subpixel shift
|
||||
%
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
|
||||
function [oROI, oROI_vec, sub_px_shift] = find_reconstruction_ROI( positions,Np_o, Np_p )
|
||||
|
||||
positions = positions(:,[2,1]);
|
||||
positions = positions + ceil(Np_o/2-Np_p/2);
|
||||
sub_px_shift = positions - round(positions);
|
||||
|
||||
sub_px_shift = sub_px_shift(:,[2,1]); % return to the original XY coordinates
|
||||
|
||||
positions = round(positions);
|
||||
|
||||
range = [min(positions), max(positions)+ Np_p];
|
||||
|
||||
if any(range(1:2) < 0) || any(range(3:4) > Np_o)
|
||||
error('Object size is too small, not enough space for probes !! \nposition range: %i %i %i %i, \nobject size: %i %i ', range(1), range(2), range(3), range(4), Np_o(1), Np_o(2))
|
||||
end
|
||||
|
||||
oROI = cell(2,1);
|
||||
for dim = 1:2
|
||||
oROI{dim} = [positions(:,dim),positions(:,dim)+ Np_p(dim)-1]-1;
|
||||
oROI{dim} = uint32(oROI{dim});
|
||||
end
|
||||
|
||||
if nargout > 1
|
||||
Npos = length(positions);
|
||||
oROI_vec = cell(Npos,2);
|
||||
for ii = 1:Npos
|
||||
for i = 1:2
|
||||
oROI_vec{ii,i} = oROI{i}(ii,1):oROI{i}(ii,2);
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,150 @@
|
||||
% self = flip_mirror_scan(self, align_objects )
|
||||
% join two scans obtained at 0 and 180 degrees to get a better estiamte
|
||||
% of geometry errors
|
||||
%
|
||||
% Inputs:
|
||||
% self main data structure
|
||||
% align_objects find optimal shifts between the scans to match the 0 and 180 deg scan
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function self = flip_mirror_scan(self, align_objects)
|
||||
|
||||
|
||||
import engines.GPU_MS.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
if nargin < 2
|
||||
align_objects = true; % find optimal shifts between the scans to match the 0 and 180 deg scan
|
||||
end
|
||||
|
||||
verbose(1,'=== Flipping 2nd scan ==== ')
|
||||
|
||||
assert(length(self.reconstruct_ind) == 2, 'Two mirrored (0vs180deg) scans are required')
|
||||
|
||||
for layer = 1:size(self.object,2)
|
||||
self.object{2,layer} = fliplr(self.object{min(end,2),layer});
|
||||
end
|
||||
|
||||
|
||||
ind = self.reconstruct_ind{2};
|
||||
|
||||
|
||||
%% FLIP THE 2ND SCAN POSITIONS
|
||||
% keep the position distance from the reconstruction edge
|
||||
|
||||
|
||||
self.probe_positions_0 = flip_positions(self, self.probe_positions_0, ind);
|
||||
if ~isempty(self.probe_positions)
|
||||
self.probe_positions = flip_positions(self, self.probe_positions, ind);
|
||||
end
|
||||
|
||||
|
||||
%% flip other inputs
|
||||
for ii = 1:length(self.probe)
|
||||
self.probe{ii}(:,:,2,:) = fliplr(self.probe{ii}(:,:,min(end,2),:));
|
||||
end
|
||||
|
||||
if ~isempty(self.diffraction)
|
||||
self.diffraction(:,:,ind) = fliplr(self.diffraction(:,:,ind));
|
||||
end
|
||||
if ~isempty(self.mask)
|
||||
if size(self.mask,3) == 1
|
||||
self.mask = repmat(self.mask, 1, 1, self.Npos);
|
||||
end
|
||||
self.mask(:,:,ind) = fliplr(self.mask(:,:,ind));
|
||||
end
|
||||
|
||||
if isfield(self, 'affine_matrix')
|
||||
% flip nondiagonal terms of the affine matrix for account for the flipping
|
||||
self.affine_matrix{2} = self.affine_matrix{2} .* [1,-1; -1,1];
|
||||
end
|
||||
|
||||
|
||||
|
||||
if align_objects
|
||||
% using crosscorrelation find optimal shift between objects
|
||||
self = shared.align_objects(self);
|
||||
else
|
||||
|
||||
% move the probe back to the center of the asize
|
||||
for ii = 1:2
|
||||
[cx, cy] = math.center(abs(self.probe{1}(:,:,ii,1)).^2);
|
||||
self.probe{1}(:,:,ii,:) = utils.imshift_fft(self.probe{1}(:,:,ii,:), -cx, -cy);
|
||||
self.object{ii} = utils.imshift_fft(self.object{ii}, -cx, -cy);
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
function pos_0 = flip_positions(self, pos_0, ind)
|
||||
% flip positions so that the flipped object does not move after
|
||||
% reconstruction
|
||||
pos = pos_0(ind,1);
|
||||
offset = ceil(self.Np_o(2)/2-self.Np_p(2)/2);
|
||||
pos = -(pos + offset);
|
||||
left_offset = -max(pos);
|
||||
right_offset = self.Np_o(2) -max(pos)-self.Np_p(2) ;
|
||||
pos = pos + right_offset - left_offset;
|
||||
pos = pos - offset;
|
||||
pos_0(ind,1) = pos ;
|
||||
|
||||
end
|
||||
@@ -0,0 +1,107 @@
|
||||
% FWD_FOURIER_PROJ forward propagate to the detector plane
|
||||
% Psi = fwd_fourier_proj(Psi, mode)
|
||||
%
|
||||
% ** psi [Nx,Ny,N] array, back-propagated complex valued exit-wave
|
||||
% ** mode structure containing parameters for selected probe mode
|
||||
%
|
||||
% returns
|
||||
% ++ Psi [Nx,Ny,N] array, propagated complex valued exit-wave Psi = F(P*O)
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [Psi] = fwd_fourier_proj(Psi, mode, ind)
|
||||
import engines.GPU_MS.shared.*
|
||||
try
|
||||
if ~isempty(mode.tilted_plane_propagate_back)
|
||||
% propagate from tilted plane of the sample to flat plane of the detector (if provided)
|
||||
Psi = mode.tilted_plane_propagate_back(Psi);
|
||||
end
|
||||
if nargin > 2 && any(mode.probe_rotation_all)
|
||||
% apply rotation to the probe , used for camera angle refinement
|
||||
Psi = utils.imrotate_ax_fft(Psi,-mode.probe_rotation_all(ind),3);
|
||||
end
|
||||
if mode.probe_scale_upd(end) ~= 0
|
||||
% apply scaling to the probe , used for camera distance refinement
|
||||
Psi = utils.imrescale_frft(Psi,1+mode.probe_scale_upd(end));
|
||||
end
|
||||
if mode.distances(end) == 0
|
||||
% no propagation
|
||||
elseif mode.distances(end) == inf
|
||||
Psi = fft2_safe(Psi); % fully farfield
|
||||
% Psi = fftshift_2D(fft2_safe(fftshift_2D(Psi))); % fully farfield
|
||||
elseif mode.distances(end) == -inf
|
||||
Psi = ifft2_safe(Psi); % fully farfield backward
|
||||
elseif ~isempty(mode.FAR_factor) % almost far field
|
||||
Psi = bsxfun(@times, Psi, mode.FAR_factor);
|
||||
Psi = fftshift_2D(fft2_safe(fftshift_2D(Psi)));
|
||||
elseif ~isempty(mode.ASM_factor) % near field transformation
|
||||
Psi = fft2_safe(Psi);
|
||||
Psi = Psi .* mode.ASM_factor;
|
||||
Psi = ifft2_safe(Psi);
|
||||
else
|
||||
error('Not implemented')
|
||||
end
|
||||
catch err
|
||||
if utils.verbose()> 0
|
||||
warning(err.message)
|
||||
keyboard
|
||||
else
|
||||
rethrow(err)
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,125 @@
|
||||
% GET_ROI find optimal rectange containing the logical mask
|
||||
%
|
||||
% ROI = get_ROI(mask, extent = 0, type = 'any')
|
||||
%
|
||||
% ** mask logical array
|
||||
% ** extend (scalar) relative increase of the found range
|
||||
% ** type (string) odd, even, pow2, any
|
||||
%
|
||||
% returns:
|
||||
% ++ ROI smallest ROI that contains the mask
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [ROI] = get_ROI(mask, extent, type)
|
||||
|
||||
if all(mask(:) == 0)
|
||||
error('Empty mask')
|
||||
end
|
||||
|
||||
if nargin < 3
|
||||
type = 'any';
|
||||
end
|
||||
if nargin == 1
|
||||
extent = 0.25;
|
||||
end
|
||||
|
||||
[W,H] = size(mask);
|
||||
if ~islogical(mask)
|
||||
error('Not implemented')
|
||||
end
|
||||
|
||||
x = any(mask,2);
|
||||
y = any(mask,1);
|
||||
coord = [find(x, 1,'first'), find(x, 1,'last'), find(y, 1,'first'), find(y, 1,'last')];
|
||||
|
||||
w = (coord(2) - coord(1));
|
||||
h = (coord(4) - coord(3));
|
||||
Cx = (coord(2) +coord(1))/2;
|
||||
Cy = (coord(4) + coord(3))/2;
|
||||
|
||||
|
||||
coord(1) = floor(Cx - ceil( (0.5 + extent) *w )) ;
|
||||
coord(2) = ceil(Cx + ceil((0.5 + extent) * w )) ;
|
||||
coord(3) = floor(Cy - ceil((0.5 + extent) * h )) ;
|
||||
coord(4) = ceil(Cy + ceil((0.5 + extent) * h )) ;
|
||||
|
||||
switch type
|
||||
case 'odd'
|
||||
coord(2) = coord(1) + floor((coord(2) - coord(1))/2)*2;
|
||||
coord(4) = coord(3) + floor((coord(4) - coord(3))/2)*2;
|
||||
case 'even'
|
||||
coord(2) = coord(1) + ceil((coord(2) - coord(1))/2)*2-1;
|
||||
coord(4) = coord(3) + ceil((coord(4) - coord(3))/2)*2-1;
|
||||
case 'pow2'
|
||||
w = 2^(nextpow2( coord(2) - coord(1))-2);
|
||||
h = 2^(nextpow2( coord(4) - coord(3))-2);
|
||||
Cx = (coord(2) +coord(1))/2;
|
||||
Cy = (coord(4) + coord(3))/2;
|
||||
coord(1) = round(Cx - w) ;
|
||||
coord(2) = round(Cx + w-1) ;
|
||||
coord(3) = round(Cy - h) ;
|
||||
coord(4) = round(Cy + h-1) ;
|
||||
end
|
||||
|
||||
coord(coord < 1) = 1;
|
||||
if coord(2) > W ; coord(2) = W; end
|
||||
if coord(4) > H ; coord(4) = H; end
|
||||
|
||||
ROI = {coord(1):coord(2), coord(3):coord(4)};
|
||||
|
||||
end
|
||||
@@ -0,0 +1,92 @@
|
||||
% GET_MASK get mask for current list of indices ind
|
||||
%
|
||||
% mask = get_mask(self,mask_indices, ind, damped_mask)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** mask_indices indices that determine which mask is needed for each scan position
|
||||
% ** ind currenly processed indices
|
||||
% ** damped_mask relaxation constant that push masked values weakly to the measured value, useful for missing pixels when the data were fixed by nearest neighbor
|
||||
%
|
||||
% returns:
|
||||
% ++ mask prepared mask array (true == ignored values)
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function mask = get_mask(self,mask_indices, ind, damped_mask)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
|
||||
mask = [];
|
||||
if ~isempty(self.mask)
|
||||
if size(self.mask, 3) == 1
|
||||
mask = self.mask;
|
||||
else
|
||||
mask = self.mask(:,:,mask_indices(ind));
|
||||
end
|
||||
end
|
||||
mask = Garray(mask);
|
||||
if (isa(mask, 'gpuArray') && strcmpi(classUnderlying(mask), 'uint8')) || isa(mask, 'uint8')
|
||||
mask = single(mask)/ 255; % convert back to singles from the storage class
|
||||
end
|
||||
|
||||
% push masked regions towards data value (ie towards zero)
|
||||
if nargin == 4 && damped_mask > 0
|
||||
mask = mask .* single(1-damped_mask);
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,123 @@
|
||||
% GET_MODULUS load and prepare data for current positions ind
|
||||
%
|
||||
% modF = get_modulus(self, cache, ind, move_to_gpu = true, bunch_id)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** ind currenly processed indices
|
||||
% ** move_to_gpu (bool) if the data should be moved on GPU or left on CPU , default == true
|
||||
% ** bunch_id number of the processed bunch, used only if the positions are stored as a list of cells with data
|
||||
%
|
||||
% returns:
|
||||
% ++ modF prepared modulus data
|
||||
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function modF = get_modulus(self, cache, ind, move_to_gpu, bunch_id)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.*
|
||||
|
||||
if ~iscell(self.diffraction)
|
||||
% if diffraction is just array, load block ind
|
||||
modF = self.diffraction(:,:,ind);
|
||||
else
|
||||
% load from cell array
|
||||
modF = self.diffraction{bunch_id};
|
||||
end
|
||||
|
||||
if isa(modF, 'gpuArray')
|
||||
data_class = classUnderlying(modF);
|
||||
else
|
||||
data_class = class(modF);
|
||||
end
|
||||
|
||||
if nargin < 4 || move_to_gpu
|
||||
% load on GPU if not there yet
|
||||
modF = Garray(modF);
|
||||
end
|
||||
switch data_class
|
||||
case {'uint16', 'uint8'} % simple sqrt lossy online compression
|
||||
modF = single(modF)/ cache.C_factor;
|
||||
verbose(5, 'UINT8/16 lossy compression')
|
||||
case 'int8'
|
||||
% lossy compression
|
||||
modF = single(modF) ;
|
||||
if size(cache.US_diffraction,2) == 1 && isa(modF, 'gpuArray')
|
||||
% 1 SVD mode - run merged kernel
|
||||
modF = Gfun(@decompress_N1,modF, reshape(cache.US_diffraction,self.Np_p),...
|
||||
reshape(cache.V_diffraction(ind),1,1,[]), cache.C_factor);
|
||||
else % mode SVD modes
|
||||
modF = modF + round(reshape(cache.US_diffraction*cache.V_diffraction(ind,:)', size(modF)));
|
||||
modF = modF / cache.C_factor;
|
||||
end
|
||||
verbose(5, 'SVD INT8 lossy compression')
|
||||
case 'single'
|
||||
|
||||
otherwise
|
||||
error('Not implemented class %s', data_class)
|
||||
end
|
||||
end
|
||||
|
||||
function modF = decompress_N1(modF, US, V, C)
|
||||
modF = modF + round(US .* V);
|
||||
modF = modF / C;
|
||||
end
|
||||
|
||||
@@ -0,0 +1,76 @@
|
||||
% GET_NOISE load and prepare noise estimate for current positions ind
|
||||
%
|
||||
% noise = get_noise(self, par, g_ind)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** g_ind processed indices
|
||||
%
|
||||
% returns:
|
||||
% ++ noise noise intensity for selected frames
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function noise = get_noise(self, par, g_ind)
|
||||
|
||||
if par.relax_noise && ~isempty(self.noise)
|
||||
noise = self.noise(:,:,g_ind);
|
||||
else
|
||||
noise = [];
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,85 @@
|
||||
% GET_OBJECT_EXTENT estimate the minimal area surrounding all the probe positions
|
||||
%
|
||||
% Np_o_new = get_object_extent(Np_p, probe_positions, extra_padding)
|
||||
%
|
||||
% ** Np_p proeb size
|
||||
% ** probe_positions (Npos,2) vector of probe positions
|
||||
% ** extra_padding relative extra padding of the estimated project size
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function Np_o_new = get_object_extent(Np_p, probe_positions, extra_padding)
|
||||
|
||||
probe = ones(Np_p);
|
||||
Np_o = [1e5, 1e5];
|
||||
Npos = size(probe_positions,1);
|
||||
Np_p = size(probe);
|
||||
probe_positions = bsxfun(@minus, probe_positions, (max(probe_positions)+min(probe_positions))/2 );
|
||||
[oROI] = engines.GPU_MS.shared.find_reconstruction_ROI(probe_positions, Np_o, Np_p );
|
||||
|
||||
Range = [Np_o, 0,0];
|
||||
for i = 1:Npos
|
||||
Range(1) = min(Range(1), oROI{1}(i,1));
|
||||
Range(2) = min(Range(2), oROI{2}(i,1));
|
||||
Range(3) = max(Range(3), oROI{1}(i,2));
|
||||
Range(4) = max(Range(4), oROI{2}(i,2));
|
||||
end
|
||||
Np_o_new = [Range(3) - Range(1), Range(4) - Range(2)];
|
||||
Np_o_new= ceil(Np_o_new*(1+extra_padding));
|
||||
|
||||
end
|
||||
@@ -0,0 +1,199 @@
|
||||
% GET_VIEWS extract view for each the provided positions and indices
|
||||
%
|
||||
% obj_proj = get_views(object, obj_proj,layer_ids,object_id, indices, cache, scan_ids, skip_ind)
|
||||
%
|
||||
% ** object [Nx_o, Ny_o] array or cells containing object
|
||||
% ** obj_proj [Nx_o, Ny_o, N] preallocated array for the views
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
% ** object_id id of the object, ie scan or incoherent mode
|
||||
% ** indices processed positions
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** scan_ids determines to which scan correponds each of the position
|
||||
% ** skip_ind list of indices to be skipped
|
||||
%
|
||||
% returns:
|
||||
% ++ obj_proj [Nx_p, Ny_p, N] array with the object views
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function obj_proj = get_views(object, obj_proj,layer_ids,object_id, indices, cache, scan_ids, skip_ind)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import utils.verbose
|
||||
global use_gpu
|
||||
|
||||
Np_p = [size(obj_proj,1),size(obj_proj,2)];
|
||||
|
||||
if size(obj_proj,3) ~= numel(indices) || isempty(obj_proj)
|
||||
% in the last iter, number of items may not be equal to grouping
|
||||
if isempty(obj_proj)
|
||||
obj_proj = Gzeros([Np_p, numel(indices)], true);
|
||||
else
|
||||
% should be tiny bit faster
|
||||
obj_proj = zeros([Np_p, numel(indices)], 'like', obj_proj);
|
||||
end
|
||||
end
|
||||
|
||||
if nargin < 8
|
||||
skip_ind = [];
|
||||
end
|
||||
skip_ind = [skip_ind, cache.skip_ind];
|
||||
|
||||
|
||||
if nargin > 6
|
||||
%% !!! call recursivelly -> wrapper for multiscan version !!!!
|
||||
|
||||
% get unique IDs of the scans
|
||||
if isempty(scan_ids)
|
||||
unq_scans = [];
|
||||
elseif all(scan_ids == scan_ids(1))
|
||||
unq_scans = scan_ids(1);
|
||||
else
|
||||
unq_scans = unique(scan_ids);
|
||||
end
|
||||
if (length(unq_scans)> 1 || length(object) > 1 ) && iscell(object)
|
||||
if ~isempty(use_gpu) && use_gpu && isa(object{object_id(1)}, 'gpuArray') && isa(obj_proj, 'gpuArray')
|
||||
% object_modes > 1 not implemented yet
|
||||
if size(object,1) == 1
|
||||
% shared object or single object
|
||||
ind_ok{1} = uint16(1:length(indices));
|
||||
else
|
||||
for kk = 1:size(object,1)
|
||||
ind_ok{kk} = uint16(find(scan_ids == kk));
|
||||
end
|
||||
end
|
||||
% feed data directly to the GPU mex without splitting
|
||||
obj_proj = get_views_gpu(object(:,layer_ids),obj_proj,cache.oROI_s{min(end,object_id(1))}, indices, ind_ok);
|
||||
else
|
||||
% if GPU not available use this "wrapper" around single
|
||||
% set_projection function
|
||||
for kk = unq_scans
|
||||
ind = scan_ids == kk;
|
||||
skip_ind = indices(~ind); % avoid going through these indices
|
||||
obj_proj = get_views(object{kk,layer_ids},obj_proj, 1, object_id, indices, cache, [], skip_ind);
|
||||
end
|
||||
end
|
||||
return
|
||||
end
|
||||
end
|
||||
|
||||
object_id = object_id(1);
|
||||
try
|
||||
if iscell(object)
|
||||
object = object{object_id, layer_ids};
|
||||
end
|
||||
catch
|
||||
keyboard
|
||||
end
|
||||
|
||||
if ~isempty(cache.skip_ind) && ~isempty(skip_ind)
|
||||
ind_ok = uint16(find(~ismember(indices, [cache.skip_ind,skip_ind]))); % skip wrong patterns
|
||||
else
|
||||
ind_ok = uint16(1:length(indices));
|
||||
end
|
||||
|
||||
|
||||
if isempty(obj_proj)
|
||||
Np_p = [length(cache.oROI{min(object_id,end)}{1,1}), length(cache.oROI{min(object_id,end)}{1,2})];
|
||||
obj_proj = Gzeros([Np_p, length(ind_ok)], true);
|
||||
end
|
||||
|
||||
|
||||
if isa(object, 'gpuArray')
|
||||
%% USE CUDA MEX FOR GPU
|
||||
obj_proj = get_views_gpu(object,obj_proj,cache.oROI_s{min(end,object_id)}, indices, ind_ok);
|
||||
else
|
||||
%% USE CPU
|
||||
positions = int32([cache.oROI_s{min(end,object_id)}{1}(indices,1), cache.oROI_s{min(end,object_id)}{2}(indices,1)]);
|
||||
obj_proj = utils.get_from_3D_projection(obj_proj,object, positions, ind_ok);
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
function obj_proj = get_views_gpu(object, obj_proj, ROI, ind, ind_ok)
|
||||
% Description: simple method to get GPU based projections from object
|
||||
import utils.verbose
|
||||
% mexcuda -output +engines/+GPU_MS/get_views_gpu_mex +engines/+GPU/get_views_gpu_mex.cu
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
|
||||
%% do not return matrices, write directly into obj_proj !!!
|
||||
x = uint16(ROI{1}(ind,1));
|
||||
y = uint16(ROI{2}(ind,1));
|
||||
|
||||
if ~iscell(object); object = {Garray(complex(object))}; end
|
||||
if ~iscell(ind_ok); ind_ok = {Garray(uint16(ind_ok))}; end
|
||||
obj_proj = complex(Garray(obj_proj));
|
||||
try
|
||||
get_views_gpu_mex( obj_proj, object,x,y, ind_ok);
|
||||
catch err
|
||||
verbose(0, 'Recompilation of MEX functions ... ')
|
||||
if any(strcmp(err.identifier, { 'MATLAB:UndefinedFunction','MATLAB:mex:ErrInvalidMEXFile'}))
|
||||
path = replace(mfilename('fullpath'), mfilename, '');
|
||||
mexcuda('-output', [path,'private/get_views_gpu_mex'], [path, 'private/get_views_gpu_mex.cu'])
|
||||
|
||||
get_views_gpu_mex( obj_proj, object,x,y, ind_ok);
|
||||
else
|
||||
rethrow(err)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
@@ -0,0 +1,91 @@
|
||||
% IFFT2_SAFE wrapper around fft2, in case of low memory it will try to repeat 5-times before giving up
|
||||
% ** x input array
|
||||
%
|
||||
% x = ifft2_safe(x)
|
||||
%
|
||||
% ** x input stacked array
|
||||
% returns:
|
||||
% ++ x 2D fft array
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function x = ifft2_safe(x)
|
||||
|
||||
low_mem_errs = {'id:parallel:gpu:array:OOMForOperation',...
|
||||
'id:MATLAB:LowGPUMem','MATLAB:LowGPUMem',...
|
||||
'parallel:gpu:array:OOM',...
|
||||
'parallel:gpu:device:UnknownCUDAError', ...
|
||||
'parallel:gpu:array:OOMForOperation',...
|
||||
'parallel:gpu:array:FFTInternalError'};
|
||||
|
||||
N = 5;
|
||||
for i = 1:N
|
||||
try
|
||||
x = ifft2(x);
|
||||
break
|
||||
catch ME
|
||||
if ~any(strcmpi(ME.identifier, low_mem_errs))
|
||||
rethrow(ME)
|
||||
end
|
||||
pause(1)
|
||||
end
|
||||
warning('FFT was not able to allocate enough memory')
|
||||
gpuDevice
|
||||
dbstack
|
||||
rethrow(ME)
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,78 @@
|
||||
% IS_METHOD try if the method match or at least partially match
|
||||
%
|
||||
% match = is_method(par, method)
|
||||
%
|
||||
% ** par parameter structure
|
||||
% ** method method name , even partial will work
|
||||
% returns
|
||||
% ++ match (bool) if the current method and string "method" at least partialyl match
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
function match = is_method(par, method)
|
||||
match = 0;
|
||||
if ~iscell(method)
|
||||
method = {method};
|
||||
end
|
||||
try
|
||||
for i = 1:length(method)
|
||||
match = match || contains(lower(par.method), lower(method{i}));
|
||||
end
|
||||
catch
|
||||
keyboard
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,89 @@
|
||||
% IS_USED Check if the extension/extensions is set to be used
|
||||
%
|
||||
% used = is_used(param, extension)
|
||||
% Example: is_used(param, {'ext1', 'ext2'})
|
||||
%
|
||||
% ++ param parametrer structure
|
||||
% ++ extension string or cell of the extension names
|
||||
% returns:
|
||||
% ** used bool if method is used
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
function used = is_used(param, extension)
|
||||
|
||||
if ~isfield(param, 'extension'); used = false; return ; end
|
||||
|
||||
if ~iscell(param.extension) && ~iscell(extension)
|
||||
used = strcmpi(param.extension, extension);
|
||||
else
|
||||
if ~iscell(extension)
|
||||
extension = {extension};
|
||||
end
|
||||
if ~iscell( param.extension)
|
||||
param.extension = {param.extension};
|
||||
end
|
||||
used = false;
|
||||
for i = 1:length(param.extension)
|
||||
for j = 1:length(extension)
|
||||
used = used | strcmpi(param.extension{i}, extension{j});
|
||||
if used; break; end
|
||||
end
|
||||
if used; break; end
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,135 @@
|
||||
% FUNCTION [u_1, H, h, dH] = near_field_evolution(u_0, z, lambda, extent, use_ASM_only)
|
||||
% Description: nearfield evolution function, it automatically swithc
|
||||
% between ASM and Fraunhofer propagation
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [u_1, H, h, dH] = near_field_evolution(u_0, z, lambda, extent, use_ASM_only,tiltx,tilty)
|
||||
|
||||
|
||||
H = [];
|
||||
h = [];
|
||||
u_1 = [];
|
||||
dH = [];
|
||||
|
||||
|
||||
if nargin < 5
|
||||
use_ASM_only = false;
|
||||
end
|
||||
|
||||
if nargin < 7
|
||||
tiltx = 0;
|
||||
tilty = 0;
|
||||
end
|
||||
|
||||
extent = extent(:)' .* ones(1,2);
|
||||
if z == 0
|
||||
H = 1;
|
||||
u_1 = u_0;
|
||||
return
|
||||
end
|
||||
if z == inf
|
||||
return
|
||||
end
|
||||
|
||||
Npix = size(u_0);
|
||||
|
||||
xgrid = (0.5+(-Npix(1)/2:Npix(1)/2-1))/Npix(1);
|
||||
ygrid = (0.5+(-Npix(2)/2:Npix(2)/2-1))/Npix(2);
|
||||
|
||||
k = 2 * pi / lambda(1);
|
||||
|
||||
% Undesamplling parameter
|
||||
F = mean( extent.^2 ./ (lambda(1) .* z .* Npix ));
|
||||
|
||||
%if abs(F) < 1 && ~use_ASM_only
|
||||
if abs(F) < 1 && ~use_ASM_only && tiltx == 0 && tilty == 0
|
||||
% farfield propagation
|
||||
warning('Farfield regime, F/Npix=%g', F )
|
||||
Xrange = xgrid*extent(1);
|
||||
Yrange = ygrid*extent(2);
|
||||
[X,Y] = meshgrid(Xrange, Yrange);
|
||||
h = exp(1i*k*z +1i*k/(2*z) * (X'.^2 + Y'.^2));
|
||||
|
||||
% this serves as low pass filter for the far nearfield
|
||||
H = ifftshift(fft2(fftshift(h)));
|
||||
H = H / abs(H(end/2+1, end/2+1)); % renormalize to conserve flux in image
|
||||
|
||||
else
|
||||
% standard ASM
|
||||
%kx = 2 * pi .*xgrid / extent(1) * Npix(1) ;
|
||||
%ky = 2 * pi .*ygrid / extent(2) * Npix(2);
|
||||
kx = xgrid / extent(1) * Npix(1) ;
|
||||
ky = ygrid / extent(2) * Npix(2);
|
||||
[Kx, Ky] = meshgrid(kx, ky);
|
||||
k2 = Kx'.^2 + Ky'.^2;
|
||||
|
||||
%dH = ( -1i*(Kx'.^2+Ky'.^2)/(2*k) );
|
||||
|
||||
dH = (-2*pi*1i*k2/(2*k) ); %dH is not used anywhere in the code I think
|
||||
|
||||
%H = exp( 1i*z*sqrt( k^2 - Kx'.^2-Ky'.^2)); % it make it a bit more sensitive to z distance
|
||||
% i don;t know if what yi had made sense to me
|
||||
H = exp(-1i*pi*lambda*z*k2 + 2i*pi*z*(Kx'.*tan(-tiltx) + Ky'.*tan(-tilty)) );
|
||||
|
||||
h = [];
|
||||
end
|
||||
|
||||
|
||||
u_1 = ifft2( bsxfun(@times, ifftshift(H), fft2(u_0)));
|
||||
end
|
||||
|
||||
@@ -0,0 +1,89 @@
|
||||
% NEAR_FIELD_EVOLUTION_GRADIENT Gradient of the nearfield evolution function, useful for calcualteion of the optimal propagation
|
||||
% distance
|
||||
%
|
||||
% [dH] = near_field_evolution_gradient(Npix, lambda, extent)
|
||||
%
|
||||
% ** Npix size of the propagated window
|
||||
% lambda wavelenght
|
||||
% extend lateral size of the window
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [dH] = near_field_evolution_gradient(Npix, lambda, extent)
|
||||
|
||||
|
||||
extent = extent(:)' .* ones(1,2);
|
||||
|
||||
|
||||
xgrid = (0.5+(-Npix(1)/2:Npix(1)/2-1))/Npix(1);
|
||||
ygrid = (0.5+(-Npix(2)/2:Npix(2)/2-1))/Npix(2);
|
||||
|
||||
k = 2 * pi / lambda(1);
|
||||
|
||||
|
||||
% standard ASM
|
||||
kx = 2 * pi .*xgrid / extent(1) * Npix(1) ;
|
||||
ky = 2 * pi .*ygrid / extent(2) * Npix(2);
|
||||
[Kx, Ky] = meshgrid(kx, ky);
|
||||
|
||||
dH = ( -1i*(Kx'.^2+Ky'.^2)/(2*k) );
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,90 @@
|
||||
% ORTHO_MODES return orthogonal modes, without any normalization , expect cells
|
||||
%
|
||||
% x = ortho_modes(x)
|
||||
%
|
||||
% ** x cell array with probes to be orthogonalized
|
||||
%
|
||||
% returns:
|
||||
% ++ x orthogonalized set
|
||||
%
|
||||
%
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function x = ortho_modes(x)
|
||||
|
||||
for i = 1:length(x)
|
||||
power(i) = sum2(abs( mean(x{i},3)).^2);
|
||||
for j = 1:i-1
|
||||
mx_j = mean(x{j},3);
|
||||
mx_i = mean(x{i},3);
|
||||
proj = sum2(mx_i .* conj(mx_j)) ...
|
||||
/ sum2(abs(mx_j).^2);
|
||||
x{i} = x{i} - proj * mx_j;
|
||||
end
|
||||
end
|
||||
% sort them, should improve convergence
|
||||
[~,ind]=sort(-power);
|
||||
x(2:end) = x(ind(2:end));
|
||||
end
|
||||
|
||||
%% added by YJ
|
||||
|
||||
function x = sum2(x)
|
||||
x = sum(sum(x,1),2);
|
||||
end
|
||||
|
||||
@@ -0,0 +1,97 @@
|
||||
% ORTHO_MODES_EIG orthogonal modes using eigen values
|
||||
%
|
||||
% x = ortho_modes_eig(x)
|
||||
%
|
||||
% ** x cell array with probes to be orthogonalized
|
||||
%
|
||||
% returns:
|
||||
% ++ x orthogonalized set
|
||||
%
|
||||
%
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function x = ortho_modes_eig(x)
|
||||
|
||||
N = length(x);
|
||||
Np = [size(x{1},1),size(x{1},2)];
|
||||
for i = 1:N
|
||||
x_tmp{i} = mean(x{i}(:,:,:,1),3);
|
||||
end
|
||||
A = zeros(N,N, class(x{1}));
|
||||
for i = 1:N
|
||||
for j = 1:N
|
||||
A(i,j) = (x_tmp{i}(:)'* x_tmp{j}(:));
|
||||
end
|
||||
end
|
||||
[v,d] = eig(A);
|
||||
[~,di] = sort(-abs(diag(d)));
|
||||
|
||||
for j = 1:N
|
||||
x_new{j} = zeros(Np, class(x{1}));
|
||||
for i = 1:N
|
||||
x_new{j} = x_new{j} + x{i}*v(i,j);
|
||||
end
|
||||
end
|
||||
%% sort by energy
|
||||
x_new = x_new(di);
|
||||
|
||||
% dont update the first one (it may interefere with OPR method)
|
||||
x(2:end) = x_new(2:end);
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,85 @@
|
||||
% PRECALCULATE_ROI precalculate the views areas for given probe_positions for faster calculations
|
||||
%
|
||||
% cache = precalculate_ROI(self, cache, probe)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** probe complex array with the current probe, used to estimate probe smallest support
|
||||
% returns:
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function cache = precalculate_ROI(self, cache, probe)
|
||||
|
||||
import math.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
|
||||
object_ROI = {round(self.Np_o(1)/2+(min(self.probe_positions_0(:,2)):max(self.probe_positions_0(:,2)))), ...
|
||||
round(self.Np_o(2)/2+(min(self.probe_positions_0(:,1)):max(self.probe_positions_0(:,1))))};
|
||||
|
||||
|
||||
Np = size(probe,1);
|
||||
|
||||
[~, fftshift_idx] = fftshift_2D(probe);
|
||||
|
||||
cache.object_ROI = object_ROI;
|
||||
cache.fftshift_idx = fftshift_idx;
|
||||
|
||||
end
|
||||
@@ -0,0 +1,168 @@
|
||||
/*
|
||||
*
|
||||
*
|
||||
|
||||
Academic License Agreement
|
||||
|
||||
Source Code
|
||||
|
||||
Introduction
|
||||
• This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
|
||||
Terms and Conditions of the LICENSE
|
||||
1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
hereinafter set out and until termination of this license as set forth below.
|
||||
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
another computing language:
|
||||
"Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
Scherrer Institut, Switzerland."
|
||||
|
||||
Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
(doi: 10.1126/science.1158573),
|
||||
for mixed coherent modes:
|
||||
P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
for LSQ-ML method
|
||||
M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
for OPRP method
|
||||
M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
and/or for multislice:
|
||||
E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
*
|
||||
Compilation from Matlab:
|
||||
maybe a tiny bit faster code is generated by
|
||||
mex -O COPTIMFLAGS='-O2' LDOPTIMFLAGS='-O2' CFLAGS="\$CFLAGS -fopenmp" LDFLAGS="\$LDFLAGS -fopenmp" get_views_cpu_mex.cpp
|
||||
|
||||
Usage from Matlab:
|
||||
get_views_cpu_mex(object,obj_proj,positions, ind_ok);
|
||||
|
||||
This code in matlab:
|
||||
asize = size(probe);
|
||||
for i=ind_ok
|
||||
Indy = positions(i,1) + (1:asize(1));
|
||||
Indx = positions(i,2) + (1:asize(2));
|
||||
ob(Indy,Indx) = ob(Indy,Indx) + probe;
|
||||
end
|
||||
*/
|
||||
|
||||
#include "mex.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <omp.h>
|
||||
|
||||
void mexFunction(int nlhs, mxArray *plhs[],
|
||||
int nrhs, const mxArray *prhs[])
|
||||
{
|
||||
int i;
|
||||
|
||||
/* Check for proper number of arguments. */
|
||||
if (nrhs != 4)
|
||||
mexErrMsgTxt("Four input arguments required: get_views_cpu_mex(object,obj_proj,positions,ind_ok)");
|
||||
else if (nlhs != 0)
|
||||
mexErrMsgTxt("No output argument has to be specified.");
|
||||
|
||||
/* Input must be of type single. */
|
||||
for (i=0; i < 2; i++) {
|
||||
if (mxIsSingle(prhs[i]) != 1){
|
||||
printf(" Input %d is not single\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
/* Input must be of type int32. */
|
||||
for (i=2; i<nrhs; i++){
|
||||
if (mxIsInt32(prhs[i]) != 1){
|
||||
printf("Input %d is not integer\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
|
||||
/* It cannot be one-dimensional */
|
||||
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
|
||||
printf("The 1st input argument must have at least two dimensions.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
|
||||
}
|
||||
/* It cannot be more than 3-dimensional */
|
||||
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
|
||||
printf("The 1st input argument must have at most three dimensions.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
|
||||
}
|
||||
/* Check that arrays are complex */
|
||||
if(mxIsComplex(prhs[0]) != 1) {
|
||||
printf("object input argument must be complex-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
|
||||
}
|
||||
if(mxIsComplex(prhs[1]) != 1) {
|
||||
printf("probe input argument must be complex-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
|
||||
}
|
||||
|
||||
float *object_r, *object_i, *projection_r,*projection_i;
|
||||
const int *positions;
|
||||
positions = (int*)mxGetData(prhs[2]);
|
||||
object_r = (float*)mxGetData(prhs[0]);
|
||||
projection_r = (float*)mxGetData(prhs[1]);
|
||||
|
||||
/* get pointers to input data */
|
||||
object_i = (float*)mxGetImagData(prhs[0]);
|
||||
projection_i = (float*)mxGetImagData(prhs[1]);
|
||||
|
||||
|
||||
/* Get dimension of probe and object */
|
||||
const mwSize Ndims = mxGetNumberOfDimensions(prhs[1]);
|
||||
const mwSize * dims = mxGetDimensions(prhs[1]);
|
||||
const mwSize No_y = mxGetM(prhs[0]);
|
||||
const mwSize No_x = mxGetN(prhs[0]);
|
||||
const mwSize Np_y = dims[0];
|
||||
const mwSize Np_x = dims[1];
|
||||
const mwSize Npos = mxGetM(prhs[2]);
|
||||
|
||||
if((Npos > dims[2])) {
|
||||
printf("wrong size of update / positions %i", Ndims);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
|
||||
}
|
||||
|
||||
mwSize id_small, id_large, pos, col, row;
|
||||
#pragma omp parallel for private(pos,col, row, id_small, id_large)
|
||||
for (pos=0;pos<Npos;pos++){
|
||||
for (col=0;col<Np_x;col++) {
|
||||
for (row=0;row<Np_y;row++) {
|
||||
id_small = row + col*Np_y + Np_y*Np_x*pos;
|
||||
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
|
||||
projection_r[id_small] = object_r[id_large];
|
||||
projection_i[id_small] = object_i[id_large];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return;
|
||||
}
|
||||
@@ -0,0 +1,260 @@
|
||||
/*
|
||||
Get complex views from complex object
|
||||
mexcuda -output +engines/+GPU/+shared/private/get_views_gpu_mex +engines/+GPU/+shared/private/get_views_gpu_mex.cu
|
||||
*/
|
||||
|
||||
#include "mex.h"
|
||||
#include "gpu/mxGPUArray.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
typedef const unsigned int cuint;
|
||||
typedef const uint16_T cuint16;
|
||||
|
||||
// unfortunatelly ~10800 is the maximum of const memory
|
||||
const unsigned int MAX_IND_READ = 10800;
|
||||
__constant__ uint16_T gC_ind_read[MAX_IND_READ];
|
||||
__constant__ uint16_T gC_pos_X[MAX_IND_READ];
|
||||
__constant__ uint16_T gC_pos_Y[MAX_IND_READ];
|
||||
|
||||
|
||||
#define MAX(x,y) (x>y?x:y);
|
||||
#define MIN(x,y) (x<y?x:y);
|
||||
#define ABS(x) (x>0?x:-x);
|
||||
|
||||
|
||||
int checkLastError(char * msg)
|
||||
{
|
||||
cudaError_t cudaStatus = cudaGetLastError();
|
||||
if (cudaStatus != cudaSuccess) {
|
||||
char err[512];
|
||||
sprintf(err, "getprojection failed \n %s: %s. \n", msg, cudaGetErrorString(cudaStatus));
|
||||
mexPrintf(err);
|
||||
return 1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Device code
|
||||
*/
|
||||
/*********** fast const memory based version ***************/
|
||||
|
||||
__global__ void readFromArray_c_fast(float2 * sarray, const float2 * larray,
|
||||
cuint Np_px,cuint Np_py, cuint Np_pz,cuint Np_ox, cuint Np_oy,
|
||||
cuint Npos) {
|
||||
// Location in a 3D matrix
|
||||
int idx= blockIdx.x * blockDim.x + threadIdx.x;
|
||||
int idy= blockIdx.y * blockDim.y + threadIdx.y;
|
||||
int id = blockIdx.z * blockDim.z + threadIdx.z;
|
||||
|
||||
if ( idx < Np_px & idy < Np_py & id < Npos)
|
||||
{
|
||||
int idz = gC_ind_read[id]-1; // go only through some of the indices
|
||||
int id_large = gC_pos_X[idz]+idx + Np_ox*(gC_pos_Y[idz]+idy);
|
||||
int id_small = idx + Np_px*idy + Np_px*Np_py*idz ;
|
||||
sarray[ id_small ].x = larray[ id_large ].x ;
|
||||
sarray[ id_small ].y = larray[ id_large ].y ;
|
||||
}
|
||||
}
|
||||
/*********** global memory based version ***************/
|
||||
|
||||
__global__ void readFromArray_c(float2 * sarray, const float2 * larray, cuint16* ind_read, cuint16* pos_X, cuint16* posY,
|
||||
cuint Np_px,cuint Np_py, cuint Np_pz,cuint Np_ox, cuint Np_oy,
|
||||
cuint Npos) {
|
||||
// Location in a 3D matrix
|
||||
int idx= blockIdx.x * blockDim.x + threadIdx.x;
|
||||
int idy= blockIdx.y * blockDim.y + threadIdx.y;
|
||||
int id = blockIdx.z * blockDim.z + threadIdx.z;
|
||||
|
||||
if ( idx < Np_px & idy < Np_py & id < Npos)
|
||||
{
|
||||
int idz = ind_read[id]-1; // go only through some of the indices
|
||||
int id_large = pos_X[idz]+idx + Np_ox*(posY[idz]+idy);
|
||||
int id_small = idx + Np_px*idy + Np_px*Np_py*idz ;
|
||||
sarray[ id_small ].x = larray[ id_large ].x ;
|
||||
sarray[ id_small ].y = larray[ id_large ].y ;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void mexFunction(int nlhs, mxArray *plhs[],
|
||||
int nrhs, const mxArray *prhs[])
|
||||
{
|
||||
int i ;
|
||||
char const * const errId = "parallel:gpu:mexGPUExample:InvalidInput";
|
||||
char const * const errMsg = "Invalid input to MEX file.";
|
||||
|
||||
/* Initialize the MathWorks GPU API. */
|
||||
//mxInitGPU();
|
||||
|
||||
/* Check for proper number of arguments. */
|
||||
if (nrhs != 5)
|
||||
mexErrMsgTxt("Five input arguments required");
|
||||
|
||||
|
||||
for (i=0; i < 2; i++) {
|
||||
if ( !mxIsGPUArray(prhs[i]) && !mxIsCell(prhs[i]) ){
|
||||
printf("Input %d is not GPU array / cell \n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// load positions
|
||||
|
||||
|
||||
const mxGPUArray * m_positions_x = mxGPUCreateFromMxArray(prhs[2]);
|
||||
if ((mxGPUGetClassID(m_positions_x) != mxUINT16_CLASS)) {
|
||||
mexPrintf("m_positions_x\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const cuint16 * p_positions_x = (cuint16 *)mxGPUGetDataReadOnly(m_positions_x);
|
||||
|
||||
const mxGPUArray * m_positions_y = mxGPUCreateFromMxArray(prhs[3]);
|
||||
if ((mxGPUGetClassID(m_positions_y) != mxUINT16_CLASS)) {
|
||||
mexPrintf("m_positions_y\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const cuint16 * p_positions_y = (cuint16 *)mxGPUGetDataReadOnly(m_positions_y);
|
||||
|
||||
|
||||
/**** copy of the array is the slowest operation *****/
|
||||
// Now it is writting directly into the input field !!!
|
||||
//mxGPUArray * m_obj_proj = mxGPUCopyFromMxArray(prhs[0]);
|
||||
mxGPUArray * m_obj_proj = const_cast<mxGPUArray*>(mxGPUCreateFromMxArray(prhs[0])); //
|
||||
if ((mxGPUGetClassID(m_obj_proj) != mxSINGLE_CLASS)) {
|
||||
mexPrintf("m_obj_proj\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
if (mxGPUGetComplexity(m_obj_proj) != mxCOMPLEX) {
|
||||
mexPrintf("m_obj_proj is not complex \n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
float2 * p_obj_proj = (float2 *)mxGPUGetData(m_obj_proj);
|
||||
|
||||
|
||||
if (!mxIsCell(prhs[1]) || !mxIsCell(prhs[4]))
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Object and indices has to be in cell/cells !! ");
|
||||
if (mxGetNumberOfElements(prhs[1]) != mxGetNumberOfElements(prhs[4]))
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Number of objects != number of indices ");
|
||||
|
||||
|
||||
/* Get dimension of probe and object */
|
||||
const unsigned int Ndims = (unsigned int)mxGPUGetNumberOfDimensions(m_obj_proj);
|
||||
|
||||
|
||||
cuint Ncells = mxGetNumberOfElements(prhs[1]);
|
||||
const unsigned int Np_pp = mxGPUGetNumberOfElements(m_positions_x);
|
||||
|
||||
|
||||
if (Np_pp < MAX_IND_READ) {
|
||||
cudaMemcpyToSymbol(gC_pos_X, p_positions_x, Np_pp*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
|
||||
cudaMemcpyToSymbol(gC_pos_Y, p_positions_y, Np_pp*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
|
||||
checkLastError("after cudaMemcpyToSymbol pos");
|
||||
}
|
||||
|
||||
for (int l=0; l<Ncells; l++)
|
||||
{
|
||||
// read the cell content
|
||||
mxArray * mx_object = mxGetCell(prhs[1],l);
|
||||
mxArray * mx_ind = mxGetCell(prhs[4],l);
|
||||
int N_ok = mxGetNumberOfElements(mx_ind);
|
||||
if(N_ok == 0)
|
||||
continue;
|
||||
|
||||
const mxGPUArray * m_object = mxGPUCreateFromMxArray(mx_object);
|
||||
if ((mxGPUGetClassID(m_object) != mxSINGLE_CLASS)) {
|
||||
mexPrintf("m_object\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
if (mxGPUGetComplexity(m_object) != mxCOMPLEX) {
|
||||
mexPrintf("m_object is not complex \n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const float2 * p_object = (float2 *)mxGPUGetDataReadOnly(m_object);
|
||||
|
||||
|
||||
const mxGPUArray * m_ind_ok = mxGPUCreateFromMxArray(mx_ind);
|
||||
if ((mxGPUGetClassID(m_ind_ok) != mxUINT16_CLASS)) {
|
||||
mexPrintf("m_ind_ok\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const cuint16 * p_ind_ok = (cuint16 *)mxGPUGetDataReadOnly(m_ind_ok);
|
||||
|
||||
const mwSize * Np_o = mxGPUGetDimensions(m_object);
|
||||
const mwSize * Np_p = mxGPUGetDimensions(m_obj_proj);
|
||||
const unsigned int Npos = mxGPUGetNumberOfElements(m_ind_ok);
|
||||
|
||||
|
||||
|
||||
// mexPrintf("Ndims %i Np_o %i %i Np_p %i %i %i Npos %i \n " ,Ndims,Np_o[0],Np_o[1],Np_p[0],Np_p[1],Np_p[2],Npos);
|
||||
|
||||
|
||||
|
||||
|
||||
if (Ndims == 3 && Npos > Np_p[2]) {
|
||||
printf("wrong size of update / positions %i", Ndims);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
|
||||
}
|
||||
|
||||
|
||||
|
||||
// Choose a reasonably sized number of threads in each dimension for the block.
|
||||
int const threadsPerBlockEachDim = 32;
|
||||
// Compute the thread block and grid sizes based on the board dimensions.
|
||||
int const blocksPerGrid_M = (Np_p[0] + threadsPerBlockEachDim - 1) / threadsPerBlockEachDim;
|
||||
int const blocksPerGrid_N = (Np_p[1] + threadsPerBlockEachDim - 1) / threadsPerBlockEachDim;
|
||||
int const blocksPerGrid_O = Npos;
|
||||
|
||||
// mexPrintf("Threads %i %i %i \n ", blocksPerGrid_M, blocksPerGrid_N, blocksPerGrid_O);
|
||||
|
||||
dim3 const dimBlock(blocksPerGrid_M, blocksPerGrid_N, blocksPerGrid_O);
|
||||
dim3 const dimThread(threadsPerBlockEachDim, threadsPerBlockEachDim, 1);
|
||||
|
||||
|
||||
checkLastError("after dimThread");
|
||||
|
||||
//mexPrintf("Blocks %i %i %i \n ", dimThread.x, dimThread.y, dimThread.z);
|
||||
|
||||
if (Np_pp > MAX_IND_READ) {
|
||||
//mexPrintf( "More than %i positions may be slow \n", MAX_IND_READ);
|
||||
} else {
|
||||
cudaMemcpyToSymbol(gC_ind_read, p_ind_ok, Npos*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
|
||||
checkLastError("after cudaMemcpyToSymbol pos");
|
||||
}
|
||||
|
||||
checkLastError("after cudaMemcpyToSymbol");
|
||||
|
||||
|
||||
//============= run the kernel ======================
|
||||
if (Npos < MAX_IND_READ)
|
||||
readFromArray_c_fast<<<dimBlock, dimThread>>>(p_obj_proj,p_object, Np_p[0],Np_p[1],Np_p[2],Np_o[0],Np_o[1], Npos);
|
||||
else
|
||||
readFromArray_c<<<dimBlock, dimThread>>>(p_obj_proj,p_object,p_ind_ok, p_positions_x,p_positions_y,Np_p[0],Np_p[1],Np_p[2],Np_o[0],Np_o[1], Npos);
|
||||
|
||||
|
||||
checkLastError("after kernel");
|
||||
|
||||
|
||||
mxGPUDestroyGPUArray(m_object);
|
||||
mxGPUDestroyGPUArray(m_ind_ok);
|
||||
|
||||
|
||||
}
|
||||
|
||||
cudaThreadSynchronize();
|
||||
|
||||
|
||||
// plhs[0] = mxGPUCreateMxArrayOnGPU(m_obj_proj);
|
||||
mxGPUDestroyGPUArray(m_obj_proj);
|
||||
mxGPUDestroyGPUArray(m_positions_x);
|
||||
mxGPUDestroyGPUArray(m_positions_y);
|
||||
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,193 @@
|
||||
/*
|
||||
*
|
||||
*Academic License Agreement
|
||||
|
||||
Source Code
|
||||
|
||||
Introduction
|
||||
• This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
|
||||
Terms and Conditions of the LICENSE
|
||||
1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
hereinafter set out and until termination of this license as set forth below.
|
||||
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
another computing language:
|
||||
"Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
Scherrer Institut, Switzerland."
|
||||
|
||||
Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
(doi: 10.1126/science.1158573),
|
||||
for mixed coherent modes:
|
||||
P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
for LSQ-ML method
|
||||
M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
for OPRP method
|
||||
M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
and/or for multislice:
|
||||
E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
*
|
||||
*
|
||||
Compilation from Matlab:
|
||||
maybe a tiny bit faster code is generated by
|
||||
mex -O COPTIMFLAGS='-O2' LDOPTIMFLAGS='-O2' set_views_cpu_mex.c
|
||||
|
||||
Usage from Matlab:
|
||||
set_views_cpu_mex(probe,object,positions, Npos);
|
||||
|
||||
This code in matlab:
|
||||
asize = size(probe);
|
||||
for i=1:Npos
|
||||
Indy = positions(i,1) + (1:asize(1));
|
||||
Indx = positions(i,2) + (1:asize(2));
|
||||
ob(Indy,Indx) = ob(Indy,Indx) + probe;
|
||||
end
|
||||
*/
|
||||
|
||||
#include "mex.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <omp.h>
|
||||
|
||||
|
||||
void mexFunction(int nlhs, mxArray *plhs[],
|
||||
int nrhs, const mxArray *prhs[])
|
||||
{
|
||||
int i;
|
||||
|
||||
/* Check for proper number of arguments. */
|
||||
if (nrhs != 4)
|
||||
mexErrMsgTxt("Four input arguments required: set_views_cpu_mex(probe,object,positions,Npos)");
|
||||
else if (nlhs != 0)
|
||||
mexErrMsgTxt("No output argument has to be specified.");
|
||||
|
||||
/* Input must be of type single. */
|
||||
for (i=0; i < 2; i++) {
|
||||
if (mxIsSingle(prhs[i]) != 1){
|
||||
printf("Input %d is not single\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
/* Input must be of type int32. */
|
||||
for (i=2; i<nrhs; i++){
|
||||
if (mxIsInt32(prhs[i]) != 1){
|
||||
printf("Input %d is not integer\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
|
||||
/* It cannot be one-dimensional */
|
||||
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
|
||||
printf("The 1st input argument must have at least two dimensions.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
|
||||
}
|
||||
/* It cannot be more than 3-dimensional */
|
||||
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
|
||||
printf("The 1st input argument must have at most three dimensions.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
|
||||
}
|
||||
// /* Check that arrays are complex */
|
||||
// if(mxIsComplex(prhs[0]) != 1) {
|
||||
// printf("object input argument must be complex-valued.");
|
||||
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
|
||||
// }
|
||||
// if(mxIsComplex(prhs[1]) != 1) {
|
||||
// printf("probe input argument must be complex-valued.");
|
||||
// mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
|
||||
// }
|
||||
|
||||
float *object_r, *object_i, *probe_r,*probe_i;
|
||||
const int *positions, *ind_ok;
|
||||
bool cprobe, cobject;
|
||||
|
||||
cobject = mxIsComplex(prhs[0]);
|
||||
cprobe = mxIsComplex(prhs[1]);
|
||||
if( cobject != cobject)
|
||||
{
|
||||
printf("probe/object input argument must be complex/real-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected both complex / real arrays");
|
||||
}
|
||||
|
||||
ind_ok = (int*)mxGetData(prhs[3]);
|
||||
positions = (int*)mxGetData(prhs[2]);
|
||||
object_r = (float*)mxGetData(prhs[0]);
|
||||
probe_r = (float*)mxGetData(prhs[1]);
|
||||
if(cprobe)
|
||||
{
|
||||
/* get pointers to input data */
|
||||
object_i = (float*)mxGetImagData(prhs[0]);
|
||||
probe_i = (float*)mxGetImagData(prhs[1]);
|
||||
}
|
||||
|
||||
|
||||
/* Get dimension of probe and object */
|
||||
const mwSize Ndims = mxGetNumberOfDimensions(prhs[1]);
|
||||
const mwSize * dims = mxGetDimensions(prhs[1]);
|
||||
const mwSize No_y = mxGetM(prhs[0]);
|
||||
const mwSize No_x = mxGetN(prhs[0]);
|
||||
const mwSize Np_y = dims[0];
|
||||
const mwSize Np_x = dims[1];
|
||||
const mwSize Npos = mxGetM(prhs[2]);
|
||||
|
||||
if((mxGetM(prhs[2]) != dims[2]) && (Ndims == 3)) {
|
||||
printf("wrong size of update / positions %i", Ndims);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
|
||||
}
|
||||
|
||||
mwSize id_small, id_large, pos, col, row, o, p;
|
||||
bool flat_probe = Ndims == 2;
|
||||
|
||||
|
||||
#pragma omp parallel for private(p,pos, col, row, id_small, id_large)
|
||||
for (p=0;p<Npos;p++){
|
||||
pos = ind_ok[p]-1;
|
||||
for (col=0;col<Np_x;col++) {
|
||||
for (row=0;row<Np_y;row++) {
|
||||
if(flat_probe)
|
||||
id_small = row + col*Np_y;
|
||||
else
|
||||
id_small = row + col*Np_y + Np_y*Np_x*pos;
|
||||
|
||||
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
|
||||
|
||||
#pragma omp atomic
|
||||
object_r[id_large] += probe_r[id_small];
|
||||
if(cprobe)
|
||||
#pragma omp atomic
|
||||
object_i[id_large] += probe_i[id_small];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return;
|
||||
}
|
||||
@@ -0,0 +1,182 @@
|
||||
/*
|
||||
*
|
||||
*Academic License Agreement
|
||||
|
||||
Source Code
|
||||
|
||||
Introduction
|
||||
• This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
|
||||
Terms and Conditions of the LICENSE
|
||||
1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
hereinafter set out and until termination of this license as set forth below.
|
||||
2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
"IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
another computing language:
|
||||
"Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
Scherrer Institut, Switzerland."
|
||||
|
||||
Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
(doi: 10.1126/science.1158573),
|
||||
for mixed coherent modes:
|
||||
P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
for LSQ-ML method
|
||||
M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
for OPRP method
|
||||
M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
and/or for multislice:
|
||||
E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
© All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
*
|
||||
*
|
||||
Compilation from Matlab:
|
||||
maybe a tiny bit faster code is generated by
|
||||
mex -O COPTIMFLAGS='-O2' LDOPTIMFLAGS='-O2' set_views_cpu_mex_rc.cpp
|
||||
|
||||
Usage from Matlab:
|
||||
set_views_cpu_mex(probe,object,positions, Npos);
|
||||
|
||||
This code in matlab:
|
||||
asize = size(probe);
|
||||
for i=1:Npos
|
||||
Indy = positions(i,1) + (1:asize(1));
|
||||
Indx = positions(i,2) + (1:asize(2));
|
||||
ob(Indy,Indx) = ob(Indy,Indx) + probe;
|
||||
end
|
||||
*/
|
||||
|
||||
#include "mex.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <omp.h>
|
||||
|
||||
|
||||
void mexFunction(int nlhs, mxArray *plhs[],
|
||||
int nrhs, const mxArray *prhs[])
|
||||
{
|
||||
int i;
|
||||
|
||||
/* Check for proper number of arguments. */
|
||||
if (nrhs != 6)
|
||||
mexErrMsgTxt("Six input arguments required: set_views_cpu_mex_rc(object,obj_upd, illum, illum_upd, positions,ind_ok)");
|
||||
else if (nlhs != 0)
|
||||
mexErrMsgTxt("No output argument has to be specified.");
|
||||
|
||||
/* Input must be of type single. */
|
||||
for (i=0; i < 4; i++) {
|
||||
if (mxIsSingle(prhs[i]) != 1){
|
||||
printf("Input %d is not single\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
/* Input must be of type int32. */
|
||||
for (i=4; i<nrhs; i++){
|
||||
if (mxIsInt32(prhs[i]) != 1){
|
||||
printf("Input %d is not integer\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
|
||||
/* Check that arrays are complex */
|
||||
if(mxIsComplex(prhs[0]) != 1) {
|
||||
printf("first input argument must be complex-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
|
||||
}
|
||||
if(mxIsComplex(prhs[1]) == 1) {
|
||||
printf("second input argument must be real-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected real arrays");
|
||||
}
|
||||
if(mxIsComplex(prhs[2]) != 1) {
|
||||
printf("third input argument must be complex-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected complex arrays");
|
||||
}
|
||||
if(mxIsComplex(prhs[3]) == 1) {
|
||||
printf("fourth input argument must be real-valued.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Expected real arrays");
|
||||
}
|
||||
|
||||
|
||||
|
||||
float *object_r, *object_i, *probe_r,*probe_i, *illum_r, *illum_upd;
|
||||
const int *positions, *ind_ok;
|
||||
bool cprobe, cobject;
|
||||
|
||||
positions = (int*)mxGetData(prhs[4]);
|
||||
ind_ok = (int*)mxGetData(prhs[5]);
|
||||
object_r = (float*)mxGetData(prhs[0]);
|
||||
object_i = (float*)mxGetImagData(prhs[0]);
|
||||
illum_r = (float*)mxGetData(prhs[1]);
|
||||
probe_r = (float*)mxGetData(prhs[2]);
|
||||
probe_i = (float*)mxGetImagData(prhs[2]);
|
||||
illum_upd = (float*)mxGetData(prhs[3]);
|
||||
|
||||
|
||||
|
||||
/* Get dimension of probe and object */
|
||||
const mwSize Ndims = mxGetNumberOfDimensions(prhs[2]);
|
||||
const mwSize * dims = mxGetDimensions(prhs[2]);
|
||||
const mwSize No_y = mxGetM(prhs[0]);
|
||||
const mwSize No_x = mxGetN(prhs[0]);
|
||||
const mwSize Np_y = dims[0];
|
||||
const mwSize Np_x = dims[1];
|
||||
const mwSize Npos = mxGetNumberOfElements(prhs[5]);
|
||||
|
||||
|
||||
if(mxGetM(prhs[4]) != dims[2]) {
|
||||
printf("wrong size of update / positions %i", Ndims);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
|
||||
}
|
||||
|
||||
// mexPrintf("O %i %i P %i %i N %i \n ", No_y, No_x, Np_y, Np_x, Npos);
|
||||
|
||||
mwSize id_small, id_small_3D, id_large, pos, col, row, p;
|
||||
|
||||
#pragma omp parallel for private(p,pos, col, row, id_small,id_small_3D, id_large)
|
||||
for (p=0;p<Npos;p++){
|
||||
pos = ind_ok[p]-1;
|
||||
for (col=0;col<Np_x;col++) {
|
||||
for (row=0;row<Np_y;row++) {
|
||||
id_small = row + col*Np_y;
|
||||
id_small_3D = id_small + Np_y*Np_x*pos;
|
||||
id_large = row + positions[pos] + (col+positions[pos+Npos])*No_y;
|
||||
#pragma omp atomic
|
||||
object_r[id_large] += probe_r[id_small_3D];
|
||||
#pragma omp atomic
|
||||
object_i[id_large] += probe_i[id_small_3D];
|
||||
#pragma omp atomic
|
||||
illum_r[id_large] += illum_upd[id_small];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return;
|
||||
}
|
||||
@@ -0,0 +1,303 @@
|
||||
/*
|
||||
Set complex views to complex object
|
||||
mexcuda -output +engines/+GPU/+shared/private/set_views_gpu_mex +engines/+GPU/+shared/private/set_views_gpu_mex.cu
|
||||
*/
|
||||
|
||||
#include "mex.h"
|
||||
#include "gpu/mxGPUArray.h"
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
|
||||
typedef const unsigned int cuint;
|
||||
typedef const uint16_T cuint16;
|
||||
|
||||
// unfortunatelly ~10800 is the maximum of const memory
|
||||
const unsigned int MAX_IND_READ = 10800;
|
||||
static const unsigned MAX_IND_READ_DEV = MAX_IND_READ;
|
||||
__constant__ uint16_T gC_ind_read[MAX_IND_READ_DEV];
|
||||
__constant__ uint16_T gC_pos_X[MAX_IND_READ_DEV];
|
||||
__constant__ uint16_T gC_pos_Y[MAX_IND_READ_DEV];
|
||||
|
||||
|
||||
int checkLastError(char * msg)
|
||||
{
|
||||
cudaError_t cudaStatus = cudaGetLastError();
|
||||
if (cudaStatus != cudaSuccess) {
|
||||
char err[512];
|
||||
sprintf(err, "setprojection failed \n %s: %s. \n", msg, cudaGetErrorString(cudaStatus));
|
||||
mexPrintf(err);
|
||||
return 1;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Device code
|
||||
*/
|
||||
|
||||
/*********** reduction of object projection array to single object ***************/
|
||||
template <bool useGlobal>
|
||||
__global__ void addToArray_r( float const * sarray, float * larray, cuint16* ind_read, cuint16* pos_X, cuint16* posY,
|
||||
cuint Np_px,cuint Np_py, cuint Np_pz,cuint Np_ox, cuint Np_oy,
|
||||
cuint Npos, const bool isFlat) {
|
||||
// Location in a 3D matrix
|
||||
int idx= blockIdx.x * blockDim.x + threadIdx.x;
|
||||
int idy= blockIdx.y * blockDim.y + threadIdx.y;
|
||||
if ( idx < Np_px & idy < Np_py ) {
|
||||
int idz, id_large;
|
||||
float sarray_val;
|
||||
for(int id = 0; id < Npos; id++)
|
||||
{
|
||||
if (useGlobal) {
|
||||
// fast const memory based version
|
||||
idz = gC_ind_read[id]-1; // go only through some of the indices
|
||||
id_large = gC_pos_X[idz]+idx + Np_ox*(gC_pos_Y[idz]+idy);
|
||||
} else {
|
||||
// slower global memory based version
|
||||
idz = ind_read[id]-1; // go only through some of the indices
|
||||
id_large = pos_X[idz]+idx + Np_ox*(posY[idz]+idy);
|
||||
}
|
||||
int id_small = idx + Np_px*idy ;
|
||||
if (!isFlat)
|
||||
id_small = id_small + Np_px*Np_py*idz ;
|
||||
|
||||
// prevent extra memory load
|
||||
sarray_val = (isFlat && (idz > 0)) ? sarray_val: sarray[ id_small ];
|
||||
|
||||
//larray[id_large] += sarray_val;
|
||||
//__syncthreads();
|
||||
|
||||
// slowest step, without atomicAdd it misses some values
|
||||
atomicAdd(&larray[id_large] ,sarray_val);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
template <bool useGlobal>
|
||||
__global__ void addToArray_c( float2 const * sarray, float2 * larray, cuint16* ind_read, cuint16* pos_X, cuint16* posY,
|
||||
cuint Np_px,cuint Np_py, cuint Np_pz,cuint Np_ox, cuint Np_oy,
|
||||
cuint Npos, const bool isFlat) {
|
||||
// Location in a 3D matrix
|
||||
int idx= blockIdx.x * blockDim.x + threadIdx.x;
|
||||
int idy= blockIdx.y * blockDim.y + threadIdx.y;
|
||||
if ( idx < Np_px & idy < Np_py ) {
|
||||
int idz, id_large;
|
||||
float2 sarray_val;
|
||||
for(int id = 0; id < Npos; id++)
|
||||
{
|
||||
if (useGlobal) {
|
||||
// fast const memory based version
|
||||
idz = gC_ind_read[id]-1; // go only through some of the indices
|
||||
id_large = gC_pos_X[idz]+idx + Np_ox*(gC_pos_Y[idz]+idy);
|
||||
} else {
|
||||
// slower global memory based version
|
||||
idz = ind_read[id]-1; // go only through some of the indices
|
||||
id_large = pos_X[idz]+idx + Np_ox*(posY[idz]+idy);
|
||||
}
|
||||
int id_small = idx + Np_px*idy ;
|
||||
if (!isFlat)
|
||||
id_small = id_small + Np_px*Np_py*idz ;
|
||||
|
||||
// prevent extra memory load
|
||||
sarray_val = (isFlat && (idz > 0)) ? sarray_val: sarray[ id_small ];
|
||||
|
||||
|
||||
//larray[id_large].x += sarray_val.x;
|
||||
//larray[id_large].y += sarray_val.y;
|
||||
//__syncthreads();
|
||||
|
||||
// slowest step, without atomicAdd it misses some values
|
||||
atomicAdd(&larray[id_large].x ,sarray_val.x);
|
||||
atomicAdd(&larray[id_large].y ,sarray_val.y);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void mexFunction(int nlhs, mxArray *plhs[],
|
||||
int nrhs, const mxArray *prhs[])
|
||||
{
|
||||
|
||||
|
||||
int i ;
|
||||
char const * const errId = "parallel:gpu:mexGPUExample:InvalidInput";
|
||||
char const * const errMsg = "Invalid input to MEX file.";
|
||||
|
||||
// Check for proper number of arguments.
|
||||
if (nrhs != 5)
|
||||
mexErrMsgTxt("Five input arguments required");
|
||||
|
||||
|
||||
// Input must be of type single.
|
||||
for (i=0; i < 2; i++) {
|
||||
if ( !mxIsGPUArray(prhs[i]) && !mxIsCell(prhs[i]) ){
|
||||
printf("Input %d is not cell array\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type.");
|
||||
}
|
||||
}
|
||||
// Input must be of type int16.
|
||||
for (i=2; i<4; i++){
|
||||
if (mxIsUint16(prhs[i]) != 1){
|
||||
printf("Input %d is not integer\n",i+1);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Inputs must be of correct type uint16.");
|
||||
}
|
||||
}
|
||||
|
||||
// It cannot be one-dimensional
|
||||
if(mxGetNumberOfDimensions(prhs[0]) < 2) {
|
||||
printf("The 1st input argument must have at least two dimensions.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
|
||||
}
|
||||
// It cannot be more than 3-dimensional
|
||||
if(mxGetNumberOfDimensions(prhs[0]) > 3) {
|
||||
printf("The 1st input argument must have at most three dimensions.");
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong number of dimensions");
|
||||
}
|
||||
// Check that arrays are complex
|
||||
|
||||
const mxGPUArray * m_obj_proj = mxGPUCreateFromMxArray(prhs[0]);
|
||||
if ((mxGPUGetClassID(m_obj_proj) != mxSINGLE_CLASS)) {
|
||||
mexPrintf("m_obj_proj\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
|
||||
const mxGPUArray * m_positions_x = mxGPUCreateFromMxArray(prhs[2]);
|
||||
if ((mxGPUGetClassID(m_positions_x) != mxUINT16_CLASS)) {
|
||||
mexPrintf("m_positions_x\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const uint16_T * p_positions_x = (uint16_T *)mxGPUGetDataReadOnly(m_positions_x);
|
||||
|
||||
const mxGPUArray * m_positions_y = mxGPUCreateFromMxArray(prhs[3]);
|
||||
if ((mxGPUGetClassID(m_positions_y) != mxUINT16_CLASS)) {
|
||||
mexPrintf("m_positions_y\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const uint16_T * p_positions_y = (uint16_T *)mxGPUGetDataReadOnly(m_positions_y);
|
||||
|
||||
if (!mxIsCell(prhs[1]) || !mxIsCell(prhs[4]))
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Object and indices has to be in cell/cells !! ");
|
||||
if (mxGetNumberOfElements(prhs[1]) != mxGetNumberOfElements(prhs[4]))
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","Number of objects != number of indices ");
|
||||
|
||||
cuint Ncells = mxGetNumberOfElements(prhs[1]);
|
||||
const unsigned int Np_pp = mxGPUGetNumberOfElements(m_positions_y);
|
||||
|
||||
if (Np_pp < MAX_IND_READ) {
|
||||
cudaMemcpyToSymbol(gC_pos_X, p_positions_x, Np_pp*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
|
||||
cudaMemcpyToSymbol(gC_pos_Y, p_positions_y, Np_pp*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
|
||||
checkLastError("after cudaMemcpyToSymbol pos");
|
||||
}
|
||||
|
||||
for (int l=0; l<Ncells; l++)
|
||||
{
|
||||
|
||||
// read the cell content
|
||||
mxArray * mx_object = mxGetCell(prhs[1],l);
|
||||
mxArray * mx_ind = mxGetCell(prhs[4],l);
|
||||
|
||||
int N_ok = mxGetNumberOfElements(mx_ind);
|
||||
if(N_ok == 0)
|
||||
continue;
|
||||
|
||||
mxGPUArray * m_object = const_cast<mxGPUArray*>(mxGPUCreateFromMxArray(mx_object)); // mxGPUCopyFromMxArray(prhs[1]);
|
||||
if ((mxGPUGetClassID(m_object) != mxSINGLE_CLASS)) {
|
||||
mexPrintf("m_object\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
|
||||
if (mxGPUGetComplexity(m_object) != mxGPUGetComplexity(m_obj_proj)) {
|
||||
mexPrintf("m_object and m_obj_proj complexity has to be the same \n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
|
||||
|
||||
|
||||
const mxGPUArray * m_ind_ok = mxGPUCreateFromMxArray(mx_ind);
|
||||
if ((mxGPUGetClassID(m_ind_ok) != mxUINT16_CLASS)) {
|
||||
mexPrintf("m_ind_ok\n");
|
||||
mexErrMsgIdAndTxt(errId, errMsg);
|
||||
}
|
||||
const uint16_T * p_ind_ok = (uint16_T *)mxGPUGetDataReadOnly(m_ind_ok);
|
||||
|
||||
|
||||
|
||||
// Get dimension of probe and object
|
||||
const unsigned int Ndims = (unsigned int)mxGPUGetNumberOfDimensions(m_obj_proj);
|
||||
const mwSize * Np_o = mxGPUGetDimensions(m_object);
|
||||
const mwSize * Np_p = mxGPUGetDimensions(m_obj_proj);
|
||||
const unsigned int Npos = mxGPUGetNumberOfElements(m_ind_ok);
|
||||
|
||||
//mexPrintf("Ndims %i Np_o %i %i Np_p %i %i %i Npos %i \n " ,Ndims,Np_o[0],Np_o[1],Np_p[0],Np_p[1],Np_p[3],Npos);
|
||||
|
||||
|
||||
|
||||
|
||||
if (Ndims == 3 && Npos > Np_p[2]) {
|
||||
printf("wrong size of update / positions %i", Ndims);
|
||||
mexErrMsgIdAndTxt("MexError:ptycho","wrong size of update / positions");
|
||||
}
|
||||
|
||||
|
||||
if (Npos > MAX_IND_READ) {
|
||||
//mexPrintf( "More than %i positions may be slow \n", MAX_IND_READ);
|
||||
} else {
|
||||
cudaMemcpyToSymbol(gC_ind_read, p_ind_ok, Npos*sizeof(uint16_T), 0, cudaMemcpyHostToDevice);
|
||||
checkLastError("after cudaMemcpyToSymbol pos");
|
||||
}
|
||||
|
||||
|
||||
// Choose a reasonably sized number of threads in each dimension for the block.
|
||||
int const threadsPerBlockEachDim = 32;
|
||||
// Compute the thread block and grid sizes based on the board dimensions.
|
||||
int const blocksPerGrid_M = (Np_p[0] + threadsPerBlockEachDim - 1) / threadsPerBlockEachDim;
|
||||
int const blocksPerGrid_N = (Np_p[1] + threadsPerBlockEachDim - 1) / threadsPerBlockEachDim;
|
||||
int const blocksPerGrid_O = 1;
|
||||
|
||||
dim3 const dimBlock(blocksPerGrid_M, blocksPerGrid_N, blocksPerGrid_O);
|
||||
dim3 const dimThread(threadsPerBlockEachDim, threadsPerBlockEachDim, 1);
|
||||
|
||||
checkLastError("after dimThread");
|
||||
|
||||
checkLastError("after cudaMemcpyToSymbol");
|
||||
|
||||
const bool isFlat = (Ndims == 2);
|
||||
const bool isComplex = mxGPUGetComplexity(m_obj_proj) == mxCOMPLEX;
|
||||
// ================== call the right kernel ===================
|
||||
if (isComplex) {
|
||||
const float2 * p_obj_proj = (float2 *)mxGPUGetDataReadOnly(m_obj_proj);
|
||||
float2 * p_object = (float2 *)mxGPUGetData(m_object);
|
||||
if (Np_pp < MAX_IND_READ)
|
||||
addToArray_c<true><<<dimBlock, dimThread>>>(p_obj_proj,p_object, p_ind_ok, p_positions_x,p_positions_y ,Np_p[0],Np_p[1],Np_p[2],Np_o[0],Np_o[1], Npos, isFlat);
|
||||
else
|
||||
addToArray_c<false><<<dimBlock, dimThread>>>(p_obj_proj,p_object, p_ind_ok, p_positions_x,p_positions_y ,Np_p[0],Np_p[1],Np_p[2],Np_o[0],Np_o[1], Npos, isFlat);
|
||||
} else {
|
||||
const float * p_obj_proj = (float *)mxGPUGetDataReadOnly(m_obj_proj);
|
||||
float * p_object = (float *)mxGPUGetData(m_object);
|
||||
if (Np_pp < MAX_IND_READ)
|
||||
addToArray_r<true><<<dimBlock, dimThread>>>(p_obj_proj,p_object, p_ind_ok, p_positions_x,p_positions_y ,Np_p[0],Np_p[1],Np_p[2],Np_o[0],Np_o[1], Npos, isFlat);
|
||||
else
|
||||
addToArray_r<false><<<dimBlock, dimThread>>>(p_obj_proj,p_object, p_ind_ok, p_positions_x,p_positions_y ,Np_p[0],Np_p[1],Np_p[2],Np_o[0],Np_o[1], Npos, isFlat);
|
||||
}
|
||||
|
||||
checkLastError("after kernel");
|
||||
|
||||
mxGPUDestroyGPUArray(m_object);
|
||||
mxGPUDestroyGPUArray(m_ind_ok);
|
||||
}
|
||||
|
||||
cudaThreadSynchronize();
|
||||
|
||||
// plhs[0] = mxGPUCreateMxArrayOnGPU(m_object);
|
||||
mxGPUDestroyGPUArray(m_obj_proj);
|
||||
mxGPUDestroyGPUArray(m_positions_x);
|
||||
mxGPUDestroyGPUArray(m_positions_y);
|
||||
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,193 @@
|
||||
% SET_VIEWS Reduce stack of projections into one shared object
|
||||
%
|
||||
% object = set_views(object, object_update, layer,object_id, indices, cache, scan_ids, skip_ind)
|
||||
%
|
||||
% ** obj_update [Nx_o, Ny_o] array or cells containing object
|
||||
% ** obj_proj [Nx_p, Ny_p, N] preallocated array for the views
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
% ** object_id id of the object, ie scan or incoherent mode
|
||||
% ** indices processed positions
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** scan_ids determines to which scan correponds each of the position
|
||||
% ** skip_ind list of indices to be skipped
|
||||
%
|
||||
% returns:
|
||||
% ++ object reduced sum of the views
|
||||
|
||||
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function object = set_views(object, object_update, layer,object_id, indices, cache, scan_ids, skip_ind)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import utils.verbose
|
||||
global use_gpu
|
||||
|
||||
if nargin < 8
|
||||
skip_ind = [];
|
||||
end
|
||||
if nargin > 6
|
||||
%% !!! call recursivelly -> wrapper for multiscan version !!!!
|
||||
|
||||
% get unique IDs of the scans
|
||||
if isempty(scan_ids)
|
||||
unq_scans = [];
|
||||
elseif all(scan_ids == scan_ids(1))
|
||||
unq_scans = scan_ids(1);
|
||||
else
|
||||
unq_scans = unique(scan_ids);
|
||||
end
|
||||
if length(unq_scans)> 1
|
||||
if ~isempty(use_gpu) && use_gpu && isa(object{1}, 'gpuArray') && isa(object_update, 'gpuArray')
|
||||
if size(object,1) == 1
|
||||
% shared object or single object
|
||||
ind_ok{1} = uint16(1:length(indices));
|
||||
else
|
||||
for kk = 1:size(object,1)
|
||||
ind_ok{kk} = uint16(find(scan_ids == kk));
|
||||
end
|
||||
end
|
||||
% feed data directly to the GPU mex without splitting
|
||||
object(:,layer) = set_views_gpu(object(:,layer),object_update,cache.oROI_s{object_id(1)},indices, ind_ok);
|
||||
else
|
||||
% ONLY if GPU not available use this "wrapper" around single
|
||||
% set_projection function
|
||||
for kk = unq_scans
|
||||
ind = scan_ids == kk;
|
||||
skip_ind = indices(~ind); % avoid going through these indices
|
||||
object{kk,layer} = set_views(object{kk,layer},object_update, object_id, indices, cache,[],skip_ind);
|
||||
end
|
||||
end
|
||||
return
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
is_cell = iscell(object);
|
||||
if is_cell
|
||||
object_0 = object;
|
||||
object = object_0{min(end,object_id), layer};
|
||||
end
|
||||
|
||||
if ~isfield(cache,'skip_ind'); cache.skip_ind = []; end
|
||||
|
||||
if ~isempty(cache.skip_ind) && ~isempty(skip_ind)
|
||||
ind_ok = uint16(find(~ismember(indices, [cache.skip_ind,skip_ind]))); % skip wrong patterns
|
||||
else
|
||||
ind_ok = uint16(1:length(indices));
|
||||
end
|
||||
if isa(object, 'gpuArray')
|
||||
%% USE CUDA MEX FOR GPU
|
||||
object = set_views_gpu(object,object_update,cache.oROI_s{min(object_id,end)},indices,ind_ok);
|
||||
else
|
||||
%% USE CPU
|
||||
positions = int32([cache.oROI_s{min(end,object_id)}{1}(indices,1), cache.oROI_s{min(end,object_id)}{2}(indices,1)]);
|
||||
object = utils.add_to_3D_projection(object_update,object, positions, ind_ok,true);
|
||||
end
|
||||
|
||||
if is_cell
|
||||
object_0{min(object_id,end), layer}= object;
|
||||
object = object_0;
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
function object = set_views_gpu(object,proj,oROI,ind, ind_ok)
|
||||
% Description: Set projections to the object function using GPU
|
||||
% mexcuda -v -output +engines/+GPU/set_views_gpu_mex +engines/+GPU/set_views_gpu_mex.cu
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.verbose
|
||||
|
||||
x = uint16(oROI{1}(ind,1));
|
||||
y = uint16(oROI{2}(ind,1));
|
||||
|
||||
return_cell = iscell(object);
|
||||
|
||||
if ~iscell(object); object = {Garray(object)}; end
|
||||
if ~iscell(ind_ok); ind_ok = {Garray(uint16(ind_ok))}; end
|
||||
for i = 1:length(object)
|
||||
assert(~isempty(object{i}), 'Input object cannot be empty')
|
||||
end
|
||||
for i = 1:length(ind_ok)
|
||||
assert(~isempty(ind_ok{i}), 'Vector ind_ok cannot be empty')
|
||||
end
|
||||
try
|
||||
set_views_gpu_mex( proj, object,x,y,ind_ok);
|
||||
catch err
|
||||
verbose(0, 'Recompilation of MEX functions ... ')
|
||||
if any(strcmp(err.identifier, { 'MATLAB:UndefinedFunction','MATLAB:mex:ErrInvalidMEXFile'}))
|
||||
path = replace(mfilename('fullpath'), mfilename, '');
|
||||
mexcuda('-output', [path,'private/set_views_gpu_mex'], [path, 'private/set_views_gpu_mex.cu'])
|
||||
set_views_gpu_mex( proj, object,x,y,ind_ok);
|
||||
else
|
||||
rethrow(err)
|
||||
end
|
||||
end
|
||||
|
||||
if ~return_cell
|
||||
object = object{1};
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,189 @@
|
||||
% SET_VIEWS_RC Reduce stack of projections into one shared object
|
||||
% ! update complex and real object at once
|
||||
%
|
||||
% [obj_update,obj_illum] = set_views_rc(obj_update,obj_illum, psi,aprobe2,layer,object_id, indices, cache, scan_ids, skip_ind, object_modes)
|
||||
%
|
||||
% ** obj_update [Nx_o, Ny_o] array or cells containing object
|
||||
% ** obj_illum [Nx_o, Ny_o] array or cells containing illumination sum
|
||||
% ** obj_proj [Nx_p, Ny_p, N] preallocated array for the views
|
||||
% ** psi complex valued exit wave (psi ~ P*O)
|
||||
% ** aprobe2 illumination intensity patch
|
||||
% ** layer_ids id of the solved layer for multilayer ptycho
|
||||
% ** object_id id of the object, ie scan or incoherent mode
|
||||
% ** indices processed positions
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** scan_ids determines to which scan correponds each of the position
|
||||
% ** skip_ind list of indices to be skipped
|
||||
% ** object_modes number of incoherent object modes
|
||||
%
|
||||
% returns:
|
||||
% ++ object reduced sum of the views
|
||||
|
||||
|
||||
|
||||
|
||||
%
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function [obj_update,obj_illum] = set_views_rc(obj_update,obj_illum, psi,aprobe2,layer,object_id, indices, cache, scan_ids, skip_ind)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import utils.verbose
|
||||
global use_gpu
|
||||
|
||||
if nargin < 10
|
||||
skip_ind = [];
|
||||
end
|
||||
if nargin > 8 && ~isempty(scan_ids)
|
||||
|
||||
%% !!! call recursivelly -> wrapper for multiscan version !!!!
|
||||
|
||||
% get unique IDs of the scans
|
||||
if isempty(scan_ids)
|
||||
unq_scans = [];
|
||||
elseif all(scan_ids == scan_ids(1))
|
||||
unq_scans = scan_ids(1);
|
||||
else
|
||||
unq_scans = unique(scan_ids);
|
||||
end
|
||||
|
||||
if length(unq_scans)> 1 || (iscell(obj_update) && length(obj_update) > 1)
|
||||
if ~isempty(use_gpu) && use_gpu && isa(obj_update{1}, 'gpuArray') && isa(psi, 'gpuArray')
|
||||
if size(obj_update,1) == 1
|
||||
% shared object or single object
|
||||
ind_ok{1} = uint16(1:length(indices));
|
||||
else
|
||||
for kk = 1:size(obj_update,1)
|
||||
ind_ok{kk} = uint16(find(scan_ids == kk));
|
||||
end
|
||||
end
|
||||
% feed data directly to the GPU mex without splitting
|
||||
[obj_update(:,layer),obj_illum(:,layer)] = set_views_gpu_rc(obj_update(:,layer),obj_illum(:,layer),psi, aprobe2,cache.oROI_s{min(object_id,end)},indices, ind_ok );
|
||||
else
|
||||
% if GPU not available use this "wrapper" around single
|
||||
% set_projection function
|
||||
for kk = unq_scans
|
||||
ind = scan_ids == kk;
|
||||
skip_ind = indices(~ind); % avoid going through these indices
|
||||
[obj_update{kk,layer},obj_illum{kk,layer}] = set_views_rc(obj_update{kk,layer},obj_illum{kk,layer},psi,aprobe2, layer, object_id, indices, cache,[],skip_ind);
|
||||
end
|
||||
end
|
||||
return
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
is_cell = iscell(obj_update);
|
||||
if is_cell
|
||||
obj_update_0 = obj_update;
|
||||
obj_illum_0 = obj_illum;
|
||||
obj_update = obj_update{object_id, min(end,layer)};
|
||||
obj_illum = obj_illum{object_id, min(end,layer)};
|
||||
end
|
||||
|
||||
if ~isempty(cache.skip_ind) && ~isempty(skip_ind)
|
||||
ind_ok = uint16(find(~ismember(indices, [cache.skip_ind,skip_ind]))); % skip wrong patterns
|
||||
else
|
||||
ind_ok = uint16(1:length(indices));
|
||||
end
|
||||
|
||||
if ~isempty(use_gpu) && use_gpu && isa(obj_update, 'gpuArray') && isa(psi, 'gpuArray')
|
||||
%% USE CUDA MEX FOR GPU
|
||||
[obj_update,obj_illum] = set_views_gpu_rc(obj_update,obj_illum, psi,aprobe2,cache.oROI_s{min(object_id,end)},indices, ind_ok);
|
||||
else
|
||||
%% USE CPU
|
||||
obj_illum = set_views(obj_illum , aprobe2, layer, object_id,indices, cache,scan_ids, skip_ind);
|
||||
obj_update = set_views(complex(obj_update),complex(psi), layer, object_id, indices, cache,scan_ids, skip_ind);
|
||||
end
|
||||
|
||||
if is_cell
|
||||
obj_update_0{object_id,min(end,layer)} = obj_update;
|
||||
obj_illum_0{object_id,min(end,layer)} = obj_illum;
|
||||
obj_update = obj_update_0;
|
||||
obj_illum = obj_illum_0;
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
function [object_c,object_r] = set_views_gpu_rc(object_c,object_r,proj_c, proj_r,oROI,ind, ind_ok )
|
||||
% Description: update complex and real object at once
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
x = uint16(oROI{1}(ind,1));
|
||||
y = uint16(oROI{2}(ind,1));
|
||||
|
||||
return_cell = iscell(object_c);
|
||||
|
||||
if ~iscell(object_c); object_c = {Garray(object_c)}; end
|
||||
if ~iscell(object_r); object_r = {Garray(object_r)}; end
|
||||
if ~iscell(ind_ok); ind_ok = {Garray(uint16(ind_ok))}; end
|
||||
proj_c = complex(proj_c);
|
||||
|
||||
set_views_gpu_mex( proj_c, object_c,x,y, ind_ok );
|
||||
set_views_gpu_mex( proj_r, object_r,x,y, ind_ok );
|
||||
|
||||
if ~return_cell
|
||||
object_c = object_c{1};
|
||||
object_r = object_r{1};
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
@@ -0,0 +1,109 @@
|
||||
% APPLY_SUBPX_SHIFT subpixel probe shifting , equivalet just a bit faster than imshift_fft
|
||||
%
|
||||
% img = apply_subpx_shift(img, shift)
|
||||
%
|
||||
% ** img stack images
|
||||
% ** shift (N,2) array of shifts
|
||||
% returns
|
||||
% ++ img shifted imaeg stack
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for maximum likelihood:
|
||||
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
|
||||
% (doi: 10.1088/1367-2630/14/6/063004),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% (doi: 10.1364/OE.24.029089).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function img = apply_subpx_shift(img, shift)
|
||||
% subpixel probe shifting
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
persistent xgrid ygrid
|
||||
if nargin == 0
|
||||
xgrid = [];
|
||||
return
|
||||
end
|
||||
if all(shift(:) == 0); return ; end
|
||||
global use_gpu
|
||||
|
||||
|
||||
shift = single(shift);
|
||||
x = reshape(shift(:,1),1,1,[]);
|
||||
y = reshape(shift(:,2),1,1,[]);
|
||||
|
||||
|
||||
Np = size(img);
|
||||
|
||||
if size(img,3) ~= size(shift,1) && use_gpu
|
||||
% ugly trick making matlab GPU FFT faster
|
||||
img = repmat(img,1,1,size(shift,1));
|
||||
end
|
||||
img = fft2_safe(img);
|
||||
|
||||
if isempty(xgrid)
|
||||
% matlab seems to need quite a lot of time to generate it -> preallocate
|
||||
xgrid = Garray(fftshift((0:Np(2)-1)'/Np(2))-0.5)';
|
||||
ygrid = Garray(fftshift((0:Np(1)-1)'/Np(1))-0.5);
|
||||
end
|
||||
|
||||
if use_gpu
|
||||
img = Gfun(@apply_shift_Gfun,img,x,y,xgrid, ygrid);
|
||||
else
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times, x,xgrid)));
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times,y,ygrid)));
|
||||
end
|
||||
img = ifft2_safe(img);
|
||||
end
|
||||
|
||||
function img = apply_shift_Gfun(img,x,y,xgrid, ygrid)
|
||||
img = img .* exp((-2i*pi)*(x*xgrid+y*ygrid));
|
||||
end
|
||||
@@ -0,0 +1,98 @@
|
||||
% SHIFT_PROBE_FFT fast shifting in fourier space (ie apply phase ramp )
|
||||
%
|
||||
% img = shift_probe_fft(img, shift)
|
||||
%
|
||||
% ** img stack images
|
||||
% ** shift (N,2) array of shifts
|
||||
% returns
|
||||
% ++ img shifted image stack
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for maximum likelihood:
|
||||
% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
|
||||
% (doi: 10.1088/1367-2630/14/6/063004),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% (doi: 10.1364/OE.24.029089).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function img = shift_probe_fft(img, shift)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
if all(shift(:) == 0); return ; end
|
||||
global use_gpu
|
||||
persistent grid
|
||||
|
||||
shift = Garray(shift);
|
||||
|
||||
x = reshape(shift(:,1),1,1,[]);
|
||||
y = reshape(shift(:,2),1,1,[]);
|
||||
|
||||
|
||||
Np = size(img);
|
||||
|
||||
if Np(1) ~= Np(2); error('Not implemented'); end
|
||||
grid = Garray((0:Np(1)-1)'/Np(1)-0.5);
|
||||
|
||||
if isempty(grid)
|
||||
grid = Garray((0:Np(1)-1)'/Np(1)-0.5);
|
||||
end
|
||||
|
||||
if use_gpu
|
||||
img = Gfun(@apply_shift_Gfun,img,x,y,grid', grid);
|
||||
else
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times,x,grid')));
|
||||
img = bsxfun(@times, img, exp((-2i*pi)*bsxfun(@times,y,grid)));
|
||||
end
|
||||
end
|
||||
|
||||
function img = apply_shift_Gfun(img,x,y,xgrid, ygrid)
|
||||
img = img .* exp((-2i*pi)*(x*xgrid+y*ygrid));
|
||||
end
|
||||
@@ -0,0 +1,298 @@
|
||||
%DM Difference-Map algorithm
|
||||
%
|
||||
% [self, cache, psi_dash, fourier_error ] = DM(self,par,cache,psi_dash,fourier_error, iter)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** psi_dash complex projection from previous iteration, or emppty in first iteration
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
% ** iter current iteration number
|
||||
%
|
||||
% returns:
|
||||
% ++ self self-like structure with final reconstruction
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ++ psi_dash complex projection from previous iteration, or emppty in first iteration
|
||||
% ++ fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
%
|
||||
% Publications most relevant to the Difference-Map implementation
|
||||
% + P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer,
|
||||
% "High-Resolution Scanning X-ray Diffraction Microscopy," Science 321, 379-382 (2008)
|
||||
% + P. Thibault, M. Dierolf, O. Bunk, A. Menzel, F. Pfeiffer,
|
||||
% "Probe retrieval in ptychographic coherent diffractive imaging,"
|
||||
% Ultramicroscopy 109, 338–343 (2009)
|
||||
|
||||
function [self, cache, psi_dash, fourier_error ] = DM(self,par,cache,psi_dash,fourier_error, iter)
|
||||
import utils.*
|
||||
import math.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
psi = cell(par.Nmodes, 1);
|
||||
Psi = cell(par.Nmodes, 1);
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%% Difference maps algorithm %%%%%%%%%%%%%%%%%%%
|
||||
beta = 1;
|
||||
gamma = 1;
|
||||
relax_mask = 1; % smoothly change relaxation of the mask
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
probe_norm = norm2(self.probe{1});
|
||||
object_modes = length(self.object);
|
||||
probe_amp_corr = [0,0];
|
||||
|
||||
for ll = 1:par.object_modes
|
||||
obj_proj{ll} = Gzeros([self.Np_p, 0], true);
|
||||
end
|
||||
for ll = 1:object_modes
|
||||
obj_illum{ll,1} = Gzeros(self.Np_o);
|
||||
obj_update{ll,1} = Gzeros(self.Np_o, true);
|
||||
end
|
||||
for ll = 1:par.probe_modes
|
||||
probe_illum{ll} = Gzeros(size(self.probe{ll}));
|
||||
probe_update{ll} = Gzeros(size(self.probe{ll}), true);
|
||||
end
|
||||
|
||||
% use precalculated blocks to be solved in parallel
|
||||
indices = cache.preloaded_indices_simple{1}.indices;
|
||||
scan_ids = cache.preloaded_indices_simple{1}.scan_ids;
|
||||
Nind = length(indices);
|
||||
|
||||
p_ind = cell(max(par.probe_modes, par.object_modes),1);
|
||||
for jj = 1:Nind
|
||||
g_ind = indices{jj};
|
||||
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
if par.share_probe || ll > 1 % share incoherent modes
|
||||
p_ind{ll} = 1;
|
||||
else
|
||||
if all(scan_ids{jj} == scan_ids{jj}(1))
|
||||
p_ind{ll} = scan_ids{jj}(1);
|
||||
else
|
||||
p_ind{ll} = scan_ids{jj};
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
% load on GPU if needed
|
||||
if ~par.keep_on_gpu
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
try; psi_dash{ll,jj} = Garray(psi_dash{ll,jj}); end
|
||||
end
|
||||
end
|
||||
|
||||
%% fourier propagation
|
||||
for ll = 1:par.object_modes
|
||||
obj_proj{ll} = get_views(self.object, obj_proj{ll},1,ll, g_ind, cache, scan_ids{jj},[]);
|
||||
end
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
probe{ll} = self.probe{min(ll,end)}(:,:,p_ind{ll});
|
||||
psi{ll} = bsxfun(@times, obj_proj{min(ll, end)}, probe{ll});
|
||||
if isempty(psi_dash{ll,jj}); psi_dash{ll,jj} = psi{ll}; end % initial guess
|
||||
% P_M (P_0(psi))
|
||||
Psi{ll} = Gfun(@DM_update_psi, gamma,psi{ll}, psi_dash{ll,jj} );
|
||||
Psi{ll} = fwd_fourier_proj(Psi{ll}, self.modes{min(ll,end)} );
|
||||
end
|
||||
|
||||
%% load data to GPU (if not loaded yet)
|
||||
modF = get_modulus(self, cache, g_ind,true,jj);
|
||||
mask = get_mask(self, cache.mask_indices, g_ind);
|
||||
|
||||
% get intensity (modulus) on detector including different corrections
|
||||
aPsi = get_reciprocal_model(self, Psi, modF, mask,iter, g_ind, par,cache);
|
||||
|
||||
if iter > 0 && (par.get_error && (mod(iter,min(20, 2^(floor(2+iter/50)))) == 0 || iter < 20) || iter == par.number_iterations )
|
||||
[fourier_error(iter,g_ind)] = get_fourier_error(modF, aPsi, [],mask);
|
||||
end
|
||||
|
||||
if ~isempty(mask)
|
||||
mask = single(1)-mask;
|
||||
mask = relax_mask + (min(relax_mask, par.pfft_relaxation) - relax_mask ) * mask;
|
||||
else
|
||||
mask = par.pfft_relaxation;
|
||||
end
|
||||
|
||||
if iter == 0
|
||||
% in the first iteration only find optimal scale for the probe
|
||||
probe_amp_corr(1) = probe_amp_corr(1) + Ggather(sum(modF(:).^2));
|
||||
probe_amp_corr(2) = probe_amp_corr(2) + Ggather(sum(aPsi(:).^2));
|
||||
for ll = 1:size(psi_dash,2); psi_dash{ll,jj} = []; end
|
||||
continue
|
||||
end
|
||||
|
||||
%% fourier (modulus) contraint
|
||||
Psi = modulus_constraint(modF,aPsi,Psi, mask, [], par, 0 );
|
||||
|
||||
|
||||
aPsi = []; modF = []; mask = [];
|
||||
|
||||
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
Psi{ll} = back_fourier_proj(Psi{ll}, self.modes{min(end,ll)});
|
||||
psi_dash{ll,jj} = Gfun(@DM_update, psi_dash{ll,jj} ,beta, Psi{ll},psi{ll});
|
||||
end
|
||||
Psi = [];
|
||||
|
||||
% get back from GPU if required
|
||||
if ~par.keep_on_gpu
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
psi_dash{ll,jj} = Ggather(psi_dash{ll,jj});
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
if iter == 0
|
||||
% apply initial correction for the probe intensity and return
|
||||
probe_amp_corr = sqrt(probe_amp_corr(1) / probe_amp_corr(2)); %% calculate ratio between modF^2 and aPsi^2
|
||||
|
||||
for ii = 1:par.probe_modes
|
||||
self.probe{ii} = self.probe{ii}*probe_amp_corr;
|
||||
end
|
||||
psi_dash = cell(size(psi_dash));
|
||||
verbose(2,'Probe amplitude corrected by %.3g',probe_amp_corr)
|
||||
return
|
||||
end
|
||||
|
||||
%% iterative solver of the overlap constraint, important for initial convergence
|
||||
for kk = 1:10
|
||||
for ll = 1:object_modes
|
||||
obj_illum{ll}(:) = 0;
|
||||
obj_update{ll}(:) = 0i;
|
||||
end
|
||||
for ll = 1:par.probe_modes
|
||||
probe_illum{ll}(:) = 0;
|
||||
probe_update{ll}(:) = 0i;
|
||||
end
|
||||
|
||||
probe_0 = self.probe;
|
||||
%% obj_update , obj_illum,probe_update,probe_illum is not reset to make it more stable
|
||||
for jj = 1:length(indices)
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
if par.share_probe || ll > 1 % share incoherent modes
|
||||
p_ind{ll} = 1;
|
||||
else
|
||||
if all(scan_ids{jj} == scan_ids{jj}(1))
|
||||
p_ind{ll} = scan_ids{jj}(1);
|
||||
else
|
||||
p_ind{ll} = scan_ids{jj};
|
||||
end
|
||||
end
|
||||
end
|
||||
for ll = 1:par.probe_modes
|
||||
probe{ll} = self.probe{ll}(:,:,p_ind{ll});
|
||||
cprobe{ll} = conj(probe{ll});
|
||||
aprobe{ll} = real(probe{ll}.*cprobe{ll});
|
||||
end
|
||||
|
||||
% move to GPU (if not there yet)
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
psi_dash{ll,jj} = Garray(psi_dash{ll,jj});
|
||||
end
|
||||
g_ind = indices{jj};
|
||||
|
||||
for ll = 1:par.object_modes
|
||||
obj_proj{ll} = get_views(self.object, obj_proj{ll},1,ll, g_ind, cache, scan_ids{jj},[]);
|
||||
end
|
||||
if iter >= par.probe_change_start
|
||||
for ll = 1:par.probe_modes
|
||||
%% update probe
|
||||
[probe_update{ll},probe_illum{ll}] = QQ_probe(psi_dash{ll,jj}, obj_proj{min(end,ll)}, probe_update{ll},probe_illum{ll}, p_ind{ll});
|
||||
end
|
||||
end
|
||||
|
||||
if iter >= par.object_change_start
|
||||
%% update object
|
||||
[obj_update,obj_illum] = QQ_object(psi_dash{ll,jj}, obj_update,obj_illum, aprobe{min(ll,end)}, cprobe{min(ll,end)}, g_ind,min(ll, object_modes),scan_ids{jj},cache);
|
||||
end
|
||||
|
||||
% get back from GPU if required
|
||||
if ~par.keep_on_gpu
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
psi_dash{ll,jj} = Ggather(psi_dash{ll,jj});
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
for ll = 1:max([par.probe_modes, object_modes])
|
||||
if iter >= par.probe_change_start && ll <= par.probe_modes
|
||||
% add some inertia to prevent oscilations
|
||||
self.probe{ll} = update_probe(self, self.probe{ll} , probe_update{ll} , probe_illum{ll} , par, ll);
|
||||
end
|
||||
if iter >= par.object_change_start && ll <= object_modes
|
||||
self.object{ll} = Gfun(@update_object, self.object{ll}, obj_update{ll}, obj_illum{ll}, cache.MAX_ILLUM(ll)*1e-4, par.probe_inertia);
|
||||
end
|
||||
end
|
||||
|
||||
if iter > par.probe_change_start
|
||||
% if both object and probe are recontructed, solve the
|
||||
% realspace constraint iterativelly
|
||||
min_iter = 1 + par.keep_on_gpu; % if par.keep_on_gpu==true, then the code is so slow that it is not worthy skip the norm calculation
|
||||
min_change = 0.01;
|
||||
if kk >= min_iter || verbose >= 2
|
||||
dprobe = max(norm2(self.probe{1} - probe_0{1}) ./ probe_norm);
|
||||
verbose(2,'Update probe difference: %3.2f%%', dprobe*100)
|
||||
end
|
||||
if kk >= min_iter && dprobe < min_change % change is below 1% and at least 2 iterations were done
|
||||
break
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
if verbose > 2
|
||||
for kk = 1:object_modes
|
||||
Nresid = sum2(utils.findresidues(self.object{kk}(cache.object_ROI{:})) > 0.1);
|
||||
if Nresid > 0
|
||||
verbose(1,'Number of residua in object %i: %i', kk, Nresid)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
function [probe_update,probe_illum] = QQ_probe(psi, obj_proj, probe_update,probe_illum, p_ind)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
%% update probe
|
||||
[upd, illum] = Gfun(@QQ_probe_Gfun, psi,obj_proj);
|
||||
if size(probe_update,3)==1 % shared probe
|
||||
probe_update = probe_update+sum(upd,3);
|
||||
probe_illum = probe_illum+sum(illum,3);
|
||||
else
|
||||
probe_update(:,:,p_ind) = probe_update(:,:,p_ind)+sum(upd,3);
|
||||
probe_illum(:,:,p_ind) = probe_illum(:,:,p_ind)+sum(illum,3);
|
||||
end
|
||||
end
|
||||
function norm = get_probe_norm_aux(P0, P1)
|
||||
norm = abs(P0-P1).^2;
|
||||
end
|
||||
|
||||
function [upd, illum] = QQ_probe_Gfun(psi,proj)
|
||||
upd = psi .* conj(proj) ;
|
||||
illum = abs(proj).^2;
|
||||
end
|
||||
function [obj_update,obj_illum] = QQ_object(psi,obj_update,obj_illum, aprobe, cprobe, g_ind,ll,scan_ids,cache)
|
||||
import engines.GPU_MS.shared.*
|
||||
%% update object
|
||||
psi = psi .* cprobe;
|
||||
[obj_update,obj_illum] = set_views_rc(obj_update,obj_illum,psi,aprobe,1,ll, g_ind, cache, scan_ids,[]);
|
||||
end
|
||||
function psi = DM_update_psi(gamma,psi, psi_dash )
|
||||
% real space update function for difference maps
|
||||
psi = (1+gamma)*psi - gamma*psi_dash;
|
||||
end
|
||||
function psi_dash = DM_update(psi_dash,beta, psi_tmp,psi )
|
||||
% update funciton for difference maps
|
||||
psi_dash = psi_dash + beta * ( psi_tmp - psi ) ;
|
||||
end
|
||||
function object = update_object(object, object_upd, object_illum, delta, inertia)
|
||||
% apply also some inertia in the object update
|
||||
object = object*inertia + (1-inertia)*object_upd./ (object_illum+delta);
|
||||
end
|
||||
function probe = update_probe(self, probe, probe_update, probe_illum, par, probe_id)
|
||||
import engines.GPU_MS.shared.*
|
||||
probe_new = probe_update ./ (probe_illum+1e-6);
|
||||
% apply probe support on the first probe mode
|
||||
if probe_id == 1
|
||||
probe_new = apply_probe_contraints(probe_new, self.modes{probe_id});
|
||||
end
|
||||
% add some inertia to prevent oscilations
|
||||
probe = par.probe_inertia*probe + (1-par.probe_inertia)*probe_new;
|
||||
end
|
||||
@@ -0,0 +1,417 @@
|
||||
%LSQML least squared maximum likelihood solver
|
||||
%
|
||||
%[self, cache, fourier_error] = LSQML(self,par,cache,fourier_error,iter)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
% ** iter current iteration number
|
||||
% returns:
|
||||
% ++ self self-like structure with final reconstruction
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ++ fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
%
|
||||
|
||||
function [self, cache, fourier_error] = LSQML(self,par,cache,fourier_error,iter)
|
||||
import engines.GPU_MS.shared.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import plotting.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.LSQML.*
|
||||
|
||||
assert( ~(par.Nscans > 1 && par.object_modes > 1), 'Multiobject + multiscan not supported')
|
||||
|
||||
% define some useful variables
|
||||
object_modes = size(self.object,1);
|
||||
object_upd_sum = cell(object_modes,par.Nlayers);
|
||||
obj_illum_sum = cell(object_modes,par.Nlayers);
|
||||
obj_proj = cell(par.object_modes,1);
|
||||
apply_subpx_shift(); % reset persistent values
|
||||
|
||||
for ll = 1:object_modes
|
||||
for layer = 1:par.Nlayers
|
||||
obj_illum_sum{ll,layer} = Gzeros(self.Np_o);
|
||||
object_upd_sum{ll,layer} = Gzeros(self.Np_o, true);
|
||||
end
|
||||
end
|
||||
|
||||
probe_update_sum = Gzeros(size(self.probe{1}));
|
||||
probe_amp_corr = [0,0];
|
||||
%%%%%%%%%%%%%%%%%% LSQ-ML algorithm %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
beta_probe = ones(self.Npos,par.Nlayers);
|
||||
beta_object = ones(self.Npos,par.Nlayers);
|
||||
|
||||
%for ML is more useful to get close/overlapping positions
|
||||
% use already precalculated indices
|
||||
if is_method(par, 'MLs')
|
||||
% load sparse indices
|
||||
rand_ind = randi(length( cache.preloaded_indices_sparse));
|
||||
indices = cache.preloaded_indices_sparse{rand_ind}.indices;
|
||||
scan_ids = cache.preloaded_indices_sparse{rand_ind}.scan_ids;
|
||||
else % load compact indices
|
||||
indices = cache.preloaded_indices_compact{1}.indices;
|
||||
scan_ids = cache.preloaded_indices_compact{1}.scan_ids;
|
||||
end
|
||||
Nind = length(indices);
|
||||
|
||||
for jj = 1:Nind
|
||||
layer_ids{jj} = 1:par.Nlayers;
|
||||
end
|
||||
|
||||
|
||||
% shuffle order but keep same over iterations
|
||||
if is_method(par, 'MLs')
|
||||
% shuffle order
|
||||
ind_range = randperm(Nind);
|
||||
else
|
||||
% MLc, call groups in given order, they are sorted by size to make
|
||||
% execution on GPU more effecient + stable convergence
|
||||
ind_range = 1:Nind;
|
||||
end
|
||||
|
||||
obj_proj_mean = 0;
|
||||
%% apply updated in parallel over sets indices{jj}
|
||||
for jj = ind_range
|
||||
% list of positions solved in current subiteration
|
||||
g_ind = indices{jj};
|
||||
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
% generate indices of the used probes
|
||||
% single probe only
|
||||
if par.share_probe % share incoherent modes
|
||||
p_ind{ll} = 1;
|
||||
else
|
||||
if all(scan_ids{jj} == scan_ids{jj}(1))
|
||||
p_ind{ll} = scan_ids{jj}(1);
|
||||
else
|
||||
% scan positions from multiple scans are processed in a single bunch
|
||||
p_ind{ll} = scan_ids{jj};
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
%% suppress large amplitude of object, quick try by ZC
|
||||
% if iter >= par.object_change_start && par.Nlayers > 1
|
||||
% for ll=1:par.Nlayers
|
||||
% temp = abs(self.object{ll});
|
||||
% if any(gather(temp(:))>10)
|
||||
% % keyboard;
|
||||
% end
|
||||
% % temp (temp> 2) =1;
|
||||
% % self.object{ll} = temp.* exp(1i* angle(self.object{ll}));
|
||||
% end
|
||||
% end
|
||||
|
||||
% estimate forward model, ie wavefront behind the sample
|
||||
[self, probe, obj_proj, psi] = get_forward_model(self, obj_proj, par,cache, g_ind, p_ind, scan_ids{jj}, layer_ids{jj});
|
||||
% obj_proj_mean = obj_proj_mean + mean(abs(temp(:)));
|
||||
%% load data to GPU
|
||||
modF = get_modulus(self, cache, g_ind,true,jj);
|
||||
mask = get_mask(self, cache.mask_indices, g_ind, par.damped_mask);
|
||||
noise = get_noise(self, par, g_ind);
|
||||
% get intensity (modulus) on detector including different corrections
|
||||
[aPsi, aPsi2, cache, self] = get_reciprocal_model(self, psi, modF, mask,iter, g_ind, par, cache);
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%% LINEAR MODEL CORRECTIONS END %%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if iter > 0 && (verbose >= -1 || par.number_iterations > par.plot_results_every) && ...
|
||||
((mod(iter,min(20, 2^(floor(2+iter/50)))) == 0 || iter < 10) ...
|
||||
|| verbose()> 2) || any(iter == max(1,[1,par.number_iterations])) % || par.accelerated_gradients_start-1 >= iter
|
||||
% calculate only sometimes to make it faster
|
||||
[fourier_error(iter,g_ind)] = get_fourier_error(modF, aPsi, noise,mask, par.likelihood);
|
||||
fourier_error(isnan(fourier_error)) = max(fourier_error(~isnan(fourier_error)));
|
||||
fourier_error(isinf(fourier_error)) = max(fourier_error(~isinf(fourier_error)));
|
||||
if any(~isfinite(fourier_error(iter,g_ind)))
|
||||
%disp(any(~isfinite(fourier_error(iter,g_ind))))
|
||||
|
||||
if par.accelerated_gradients_start < par.number_iterations || par.momentum > 0
|
||||
error('Convergence failed, error contains NaNs, quitting ... \n%s', 'If repeated, try to set eng.accelerated_gradients_start = inf or eng.momentum = 0; ')
|
||||
else
|
||||
error('Convergence failed, error contains NaNs, quitting ... \n%s', 'If repeated, try to set eng.beta_LSQ = 0.5 or less ')
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
if strcmp(par.likelihood, 'poisson') || iter == 0
|
||||
[chi,R] = modulus_constraint(modF,aPsi,psi, mask, noise, par, 1);
|
||||
if iter == 0
|
||||
% in the first iteration only find optimal scale for the probe
|
||||
probe_amp_corr(1) = probe_amp_corr(1) + Ggather(sum(modF(:).^2));
|
||||
probe_amp_corr(2) = probe_amp_corr(2) + Ggather(sum(aPsi(:).^2));
|
||||
continue
|
||||
end
|
||||
else
|
||||
chi = modulus_constraint(modF,aPsi,psi, mask, noise, par, 1);
|
||||
end
|
||||
|
||||
|
||||
if ~strcmp(par.likelihood, 'poisson') % soft memory cleanup
|
||||
mask = []; aPsi = []; noise = []; modF = []; R=[];
|
||||
end
|
||||
|
||||
if iter > par.estimate_NF_distance
|
||||
% update estimation of the nearfield propagation distance
|
||||
[self, cache] = gradient_NF_propagation_solver(self,psi(:,end),chi, cache, g_ind);
|
||||
end
|
||||
if ~strcmp(par.likelihood, 'poisson') % soft memory cleanup
|
||||
psi = [];
|
||||
end
|
||||
|
||||
if strcmp(par.likelihood, 'poisson') % calculate only for the first mode
|
||||
%ll = 1;
|
||||
%% automatically find optimal step-size, note that for Gauss it is 1 !!
|
||||
beta_xi = gradient_descent_xi_solver(self,modF, aPsi2, R,mask, g_ind, mean(cache.beta_xi(g_ind)), cache);
|
||||
R = [];
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
chi{ll} = chi{ll} .* beta_xi ;
|
||||
end
|
||||
end
|
||||
|
||||
% At this point, chi is at the far-field (detector) plane
|
||||
% Now propagate chi back to the last object layer
|
||||
% This is same as using back_fourier_proj w. distance = inf and no camera angle refinement
|
||||
for ll= 1:max(par.object_modes, par.probe_modes)
|
||||
chi{ll} = ifft2_safe(chi{ll}); % fully farfield inverse fft
|
||||
end
|
||||
|
||||
%% %%%%%%%%%% LSQ optimization code (probe & object updates)%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
for layer = par.Nlayers:-1:1
|
||||
for ll = 1:max(par.probe_modes, par.object_modes)
|
||||
object_reconstruct = iter >= par.object_change_start && (par.apply_multimodal_update || is_used(par, 'fly_scan') || ll <= par.object_modes );
|
||||
probe_reconstruct = iter >= par.probe_change_start;
|
||||
|
||||
llo = min(par.object_modes, ll);
|
||||
llp = min(par.probe_modes, ll);
|
||||
|
||||
% propagate to the previous layer
|
||||
if layer < par.Nlayers
|
||||
chi{ll} = back_fourier_proj(chi{ll}, self.modes{layer},g_ind);
|
||||
end
|
||||
|
||||
if layer ~= par.Nlayers
|
||||
% if only single layer is used, reuse obj_proj already
|
||||
% loaded, but avoid storing obj_proj for each layer, rather load it again
|
||||
obj_proj{llo} = get_views(self.object, obj_proj{llo},layer_ids{jj}(layer),llo, g_ind, cache, scan_ids{jj},[]);
|
||||
end
|
||||
|
||||
% get update directions for each scan positions
|
||||
if ( probe_reconstruct || layer > 1) && object_reconstruct
|
||||
[probe_update, object_update_proj] = Gfun(@get_update_both, chi{ll}, obj_proj{llo}, probe{llp,layer});
|
||||
elseif ( probe_reconstruct || layer > 1)
|
||||
probe_update = Gfun(@get_update, chi{ll}, obj_proj{llo});
|
||||
object_update_proj = 0;
|
||||
else
|
||||
probe_update = 0; m_probe_update = 0;
|
||||
object_update_proj = Gfun(@get_update, chi{ll}, probe{llp,layer});
|
||||
end
|
||||
|
||||
% refine single optimal probe update direction (use overlap constraint)
|
||||
if probe_reconstruct || layer > 1
|
||||
[self,m_probe_update, probe_update, cache] = refine_probe_update(self, obj_proj{llo}, probe_update, chi{ll},layer,ll,p_ind{ll},g_ind, par, cache);
|
||||
end
|
||||
if layer == 1
|
||||
probe_update = [] ; % soft memory clean
|
||||
end
|
||||
|
||||
% refine single optimal object update direction (use overlap constraint)
|
||||
if object_reconstruct
|
||||
[object_upd_sum,object_update_proj, cache] = refine_object_update(self, ...
|
||||
object_update_proj,object_upd_sum,layer_ids{jj}(layer),scan_ids{jj},g_ind, par, cache);
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%% calculate the optimal step %%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if ll == 1 % && layer == par.Nlayers
|
||||
if par.beta_LSQ > 0 && object_reconstruct && probe_reconstruct && par.Nlayers == 1 % for Nlayers > 1 seems to be better using gradient_projection_solver in order to keep behaviour the same for each layer !!
|
||||
% calculate the optimal step using LSQ method
|
||||
[beta_probe(g_ind,layer), beta_object(g_ind,layer)] = ...
|
||||
get_optimal_LSQ_step(self,chi{ll},object_update_proj,m_probe_update,obj_proj{llo},probe{llp,layer},p_ind{ll} , par);
|
||||
|
||||
elseif par.beta_LSQ > 0 && (object_reconstruct || probe_reconstruct )
|
||||
% computationally cheaper method that assumes only
|
||||
% diagonal terms of the AA matrix
|
||||
[beta_probe(g_ind,layer),beta_object(g_ind,layer)] = ...
|
||||
gradient_projection_solver(self,chi{ll},obj_proj{llo},probe{llp,layer},...
|
||||
object_update_proj, m_probe_update,p_ind{ll}, par, cache);
|
||||
elseif par.beta_LSQ == 0
|
||||
% use constant step
|
||||
beta_probe(g_ind,layer) = par.beta_probe;
|
||||
beta_object(g_ind,layer) = par.beta_object;
|
||||
end
|
||||
|
||||
beta_object(g_ind,layer) = beta_object(g_ind,layer) / par.Nlayers;
|
||||
|
||||
if (is_used(par, 'fly_scan') || par.apply_multimodal_update)
|
||||
beta_object(g_ind,layer) = beta_object(g_ind,layer) / par.probe_modes;
|
||||
end
|
||||
end
|
||||
object_update_proj = []; % soft memory clean
|
||||
beta_object = max(0.2, beta_object);
|
||||
beta_probe = max(0, beta_probe);
|
||||
|
||||
if any(jj == ind_range(end)) && ll == 1
|
||||
% show the optimal steps calculation
|
||||
% if verbose() > 2
|
||||
% if mod(iter, 5) == 0
|
||||
% plotting.smart_figure(121122)
|
||||
% plot(squeeze(real(beta_object)))
|
||||
% hold all
|
||||
% plot(squeeze(real(beta_probe)))
|
||||
% hold off
|
||||
% legend({'O', 'P'})
|
||||
% title('Update step for each scan position')
|
||||
% xlabel('Scan positions #')
|
||||
% ylabel('Step')
|
||||
% drawnow
|
||||
% end
|
||||
% end
|
||||
verbose(1,'Average step p%i: %3.3g o%i: %3.3g layer %i', llp,mean(beta_probe(g_ind,layer)),llo,mean(beta_object(g_ind,layer)), layer);
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%% apply update with the optimal LSQ step %%%%%%%%%%%%%%%%%
|
||||
if probe_reconstruct && layer == 1 && ll <= max(par.probe_modes) % multilayer extension -> update probe only from the first layer
|
||||
self.probe{ll} = update_probe(self.probe{ll}, m_probe_update, par, p_ind{ll}, g_ind, beta_probe, Nind); % finally update also the probe
|
||||
end
|
||||
|
||||
if object_reconstruct && is_method(par, 'MLs')
|
||||
|
||||
self.object = update_object(self, self.object, object_upd_sum, layer_ids{jj}(layer), llo, {g_ind}, scan_ids(jj), par, cache, beta_object);
|
||||
end
|
||||
|
||||
if ll == 1 && layer == par.layer4pos %layer == ceil(par.Nlayers/2) % assume that sample in center is best constrained . Changed to variable layer by Zhen Chen
|
||||
%%%%%%%%%%%%% update other parameters of the ptychography model
|
||||
if iter >= par.probe_position_search || iter >= par.detector_rotation_search || iter >= par.detector_scale_search
|
||||
% find optimal position shift that minimize chi{1} in current iteration
|
||||
[pos_update, pos_rotate_upd,probe_scale_upd, cache] = gradient_position_solver(self, chi{1}, obj_proj{1},probe{1,layer}, g_ind, iter, cache, par);
|
||||
self.modes{1}.probe_scale_upd(end+1)=self.modes{1}.probe_scale_upd(end)+mean(probe_scale_upd);
|
||||
self.modes{1}.probe_positions(g_ind,:)=self.modes{1}.probe_positions(g_ind,:)+pos_update;
|
||||
self.modes{1}.probe_rotation_all(g_ind)=self.modes{1}.probe_rotation_all(g_ind)+squeeze(pos_rotate_upd);
|
||||
end
|
||||
|
||||
if iter > par.probe_fourier_shift_search
|
||||
% search position corrections in the Fourier space, use
|
||||
% only informatiom from the first mode, has to be after
|
||||
% the probes updated , SEARCH ONLY FOR THE FIRST MODE
|
||||
self.modes{1} = gradient_fourier_position_solver(chi{1}, obj_proj{1},probe{1,layer},self.modes{1}, g_ind);
|
||||
end
|
||||
end
|
||||
|
||||
if par.Nlayers > 1
|
||||
% get update direction for the next layer
|
||||
chi{ll} = probe_update; % .* median(beta_probe(g_ind,layer));
|
||||
else
|
||||
chi{ll} = []; % soft memory clean
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
if iter > par.estimate_NF_distance
|
||||
%% correct propagation distance if updated
|
||||
for i = 1:par.Nlayers %par.Nmodes % layers by Zhen Chen
|
||||
ASM = exp( self.modes{i}.distances(end)* cache.ASM_difference);
|
||||
self.modes{i}.ASM_factor = ASM;
|
||||
self.modes{i}.cASM_factor = conj(ASM);
|
||||
end
|
||||
end
|
||||
% to be used for momentum calculation, use only the last layer
|
||||
if par.momentum
|
||||
uniq_p_ind = unique(p_ind{ll});
|
||||
probe_update_sum(:,:,uniq_p_ind,1) = probe_update_sum(:,:,uniq_p_ind,1) + m_probe_update / Nind;
|
||||
end
|
||||
|
||||
%% constraint periodic along propagation,Added by ZC
|
||||
% regularize_layers works better (set regularize_layers > 0), then this is unnecessary.
|
||||
% if par.Nlayers > 1 && isfield(par.p,'samelayer') && par.p.samelayer && (iter >= par.p.Nst_samelayer && iter <= par.p.Nend_samelayer)
|
||||
% object_avg=0;
|
||||
% for layer=1:par.Nlayers-1 % last layer is fixed to 1s.
|
||||
% object_avg = object_avg + self.object{layer};
|
||||
% end
|
||||
% object_avg = object_avg ./(par.Nlayers-1);
|
||||
% % object_avg = (object_avg .* exp(1i*angle(self.object{par.Nlayers})))./(par.Nlayers-1);
|
||||
% for layer=1:par.Nlayers-1
|
||||
% self.object{layer} = object_avg ;
|
||||
% end
|
||||
% end
|
||||
% % self.object{par.Nlayers}(:)=1;
|
||||
%
|
||||
|
||||
end
|
||||
if iter == 0
|
||||
% apply initial correction for the probe intensity and return
|
||||
probe_amp_corr = sqrt(probe_amp_corr(1) / probe_amp_corr(2)); %% calculate ratio between modF^2 and aPsi^2
|
||||
for ii = 1:par.probe_modes
|
||||
self.probe{ii} = self.probe{ii}*probe_amp_corr;
|
||||
end
|
||||
verbose(2,'Probe amplitude corrected by %.3g',probe_amp_corr)
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
% applying single update emulates behaviour of the original ML method ->
|
||||
% provides better noise robustness
|
||||
% advantage is that less memory is needed and no linesearch is required
|
||||
|
||||
object_reconstruct = iter >= par.object_change_start; % && (par.apply_multimodal_update || is_used(par, 'fly_scan') || ll <= par.object_modes );
|
||||
probe_reconstruct = iter >= par.probe_change_start;
|
||||
% if true, caclulate momentum and use is for acceleration
|
||||
momentum_acceleration = isfield(par, 'momentum') && par.momentum && par.number_iterations < par.accelerated_gradients_start;
|
||||
if object_reconstruct && is_method(par, 'MLc')
|
||||
for ll = 1:par.object_modes
|
||||
for layer = 1:par.Nlayers
|
||||
[self.object, object_upd_sum] = update_object(self, self.object, object_upd_sum, layer, ll, indices, scan_ids, par, cache, beta_object(:,layer));
|
||||
end
|
||||
end
|
||||
%% apply momentum update on the object
|
||||
if momentum_acceleration
|
||||
[self, cache] = add_momentum_object(self, cache, par, object_upd_sum, iter, fourier_error, beta_object);
|
||||
end
|
||||
end
|
||||
|
||||
if probe_reconstruct && momentum_acceleration
|
||||
%% apply momentum update on the probe
|
||||
[self, cache] = add_momentum_probe(self, cache, par, {probe_update_sum}, iter, fourier_error, beta_probe);
|
||||
end
|
||||
%if iter>0
|
||||
% disp(any(~isfinite(fourier_error(iter,:))))
|
||||
%end
|
||||
%% FLY-SCAN: join all subprobes
|
||||
if iter >= par.probe_change_start
|
||||
if is_used(par,'fly_scan')
|
||||
probe_new = 0;
|
||||
for ll = 1:par.Nmodes
|
||||
probe_new = probe_new + self.probe{ll}/par.Nmodes;
|
||||
end
|
||||
for ll = 1:par.Nmodes
|
||||
% allow variation of the modes intensity
|
||||
proj(ll,1,:) = real(sum2( self.probe{ll} .* conj( probe_new)) ./ sum2(abs(probe_new).^2)) ;
|
||||
self.probe{ll} = proj(ll,1,:) .* probe_new;
|
||||
% assume constant intensity
|
||||
% self.probe{ll} = probe_new;
|
||||
end
|
||||
end
|
||||
end
|
||||
% if iter >= par.probe_change_start
|
||||
% for ll = 1:par.probe_modes
|
||||
% self.probe{ll} = apply_probe_contraints(self.probe{ll}, self.modes{min(ll,end)});
|
||||
% end
|
||||
% end
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
%% merged CUDA kernels for faster calculations
|
||||
function update = get_update(chi, proj)
|
||||
update = chi .* conj(proj);
|
||||
end
|
||||
|
||||
function [update_1, update_2] = get_update_both(chi, proj_1, proj_2)
|
||||
update_1 = chi .* conj(proj_1);
|
||||
update_2 = chi .* conj(proj_2);
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,400 @@
|
||||
% PIE - generalized version of the ptychographic iterative engine
|
||||
%
|
||||
%[self, cache, fourier_error] = PIE(self,par,cache,fourier_error,iter)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
% ** iter current iteration number
|
||||
% returns:
|
||||
% ++ self self-like structure with final reconstruction
|
||||
% ++ cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ++ fourier_error array [Npos,1] containing evolution of reconstruction error
|
||||
%
|
||||
|
||||
function [self, cache, fourier_error] = PIE(self,par,cache,fourier_error,iter)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import engines.GPU_MS.PIE.*
|
||||
|
||||
%% MULTILAYER EXTENSION fix or remove in future
|
||||
par.probe_modes = max(par.Nlayers, par.probe_modes);
|
||||
par.object_modes = max(par.Nlayers, par.object_modes);
|
||||
|
||||
|
||||
if par.variable_probe
|
||||
% expand the probe to the full size
|
||||
probe_0 = self.probe{1};
|
||||
self.probe{1} = reshape(self.probe{1},prod(self.Np_p),[]);
|
||||
self.probe{1} = reshape(self.probe{1} * self.probe_evolution', self.Np_p(1), self.Np_p(2), []);
|
||||
end
|
||||
par.multilayer_object = par.Nlayers > 1;
|
||||
par.multilayer_probe = false; % not supported anymore
|
||||
probe_amp_corr = [0,0];
|
||||
|
||||
psi = cell(par.Nmodes, 1);
|
||||
Psi = cell(par.Nmodes, 1);
|
||||
probe_max = cell(par.probe_modes,1);
|
||||
object_max = cell(par.object_modes,1);
|
||||
aprobe2 = abs(mean(self.probe{1},3)).^2; % update only once per iteration
|
||||
|
||||
if (is_method(par, 'ePIE') && ...
|
||||
... % empirical estimation when the hybrid PIE method should be used
|
||||
par.grouping > self.Npos/sqrt( pi^2 * mean(Ggather(cache.MAX_ILLUM)) / max(aprobe2(:)))) % || ...% use hybrid ePIE in case of large grouping
|
||||
% (~isempty(self.modes{end}.ASM_factor) && par.grouping > 1) || ...
|
||||
% (is_method(par, 'ePIE')&& par.multilayer_object)
|
||||
par.method = 'hPIE'; % hybrid ePIE
|
||||
if iter == 1;verbose(1,'Switching to hybrid PIE method '); end
|
||||
end
|
||||
if is_method(par, {'hPIE'})
|
||||
for ll = 1:(par.object_modes*par.Nscans)
|
||||
for layer = 1:par.Nlayers
|
||||
obj_illum_sum{ll,layer} = Gzeros(self.Np_o);
|
||||
object_upd_sum{ll,layer} = Gzeros(self.Np_o, true);
|
||||
end
|
||||
end
|
||||
for ll = 1:par.probe_modes
|
||||
probe_upd_sum{ll}= (1+1i)*1e-8;
|
||||
probe_illum_sum{ll} = 1e-8;
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
for ll = 1:par.Nlayers
|
||||
obj_proj{ll} = Gzeros([self.Np_p, par.grouping], true);
|
||||
end
|
||||
if par.delta_p
|
||||
grad = @get_grad_lsq; % dumped least squares gradient (preconditioner)
|
||||
else
|
||||
grad = @get_grad_flat; % common PIE gradient
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%%%% ePIE algorithm %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if par.grouping > 1
|
||||
for ll = 1:par.probe_modes
|
||||
if ~par.multilayer_object || ll == 1 % update only first layer probe
|
||||
probe_max{ll} = Ggather(max2(abs(self.probe{ll}))).^2;
|
||||
end
|
||||
end
|
||||
for ll = 1:par.object_modes
|
||||
if ~par.multilayer_probe || ll == 1 % update only first layer object
|
||||
object_max{ll} = Ggather(max2(abs(self.object{ll}(cache.object_ROI{:})))).^2;
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
if any(isnan(object_max{1})) || any(isnan(probe_max{1}))
|
||||
error('Object or probe is nan, try smaller grouping')
|
||||
end
|
||||
|
||||
|
||||
|
||||
% use already precalculated indices
|
||||
rand_ind = randi(length( cache.preloaded_indices_sparse));
|
||||
indices = cache.preloaded_indices_sparse{rand_ind}.indices;
|
||||
scan_ids = cache.preloaded_indices_sparse{rand_ind}.scan_ids;
|
||||
|
||||
for ind_ii = randperm(length(indices))
|
||||
g_ind = indices{ind_ii};
|
||||
for ll = 1:max([par.probe_modes, par.object_modes,par.Nlayers])
|
||||
% generate indices of the used probes
|
||||
if par.variable_probe && ll == 1
|
||||
p_ind{ll} = g_ind;
|
||||
% elseif par.multilayer_object && ll > 1
|
||||
% p_ind{ll} = 1:length(ii);
|
||||
else % single probe only
|
||||
if par.share_probe %|| ll > 1 % share incoherent modes
|
||||
p_ind{ll} = 1;
|
||||
else
|
||||
if all(scan_ids{ind_ii} == scan_ids{ind_ii}(1))
|
||||
p_ind{ll} = scan_ids{ind_ii}(1);
|
||||
else
|
||||
p_ind{ll} = scan_ids{ind_ii};
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
%% load data to GPU (if not loaded yet)
|
||||
modF = get_modulus(self, cache, g_ind);
|
||||
mask = get_mask(self, cache.mask_indices, g_ind);
|
||||
noise = get_noise(self, par, g_ind);
|
||||
|
||||
|
||||
% get objects projections
|
||||
|
||||
|
||||
|
||||
for layer = 1:par.Nlayers
|
||||
ll = 1;
|
||||
obj_proj{layer} = get_views(self.object, obj_proj{layer},layer,ll,g_ind, cache, scan_ids{ind_ii},[]);
|
||||
end
|
||||
% get illumination probe
|
||||
for ll = 1:par.probe_modes
|
||||
if ~par.multilayer_object || ismember(ll, [1,par.Nlayers:par.probe_modes])
|
||||
probe{ll} = self.probe{min(ll,end)}(:,:,min(end,p_ind{ll}));
|
||||
end
|
||||
end
|
||||
|
||||
for ll = 1:max([par.probe_modes, par.object_modes, par.Nlayers]) % Nlayers
|
||||
%% fourier propagation
|
||||
|
||||
if (ll == 1 && (par.multilayer_object || par.multilayer_probe) )
|
||||
probe{ll} = self.probe{min(ll,end)}(:,:,min(end,p_ind{ll}));
|
||||
end
|
||||
if ll > 1 && par.multilayer_object || par.grouping == 1 % raw ePIE
|
||||
probe_max{ll} = max(Ggather(max2(abs(probe{ll})))).^2;
|
||||
end
|
||||
if ll > 1 && par.multilayer_probe || par.grouping == 1 % raw ePIE
|
||||
object_max{ll} = max(Ggather(max2(abs(obj_proj{ll})))).^2;
|
||||
end
|
||||
if (ll == 1 && par.apply_subpix_shift)
|
||||
probe{ll} = apply_subpx_shift(probe{ll}, self.modes{min(end,ll)}.sub_px_shift(g_ind,:) );
|
||||
end
|
||||
|
||||
probe{ll} = apply_subpx_shift_fft(probe{ll}, self.modes{1}.probe_fourier_shift(g_ind,:));
|
||||
|
||||
|
||||
% get projection of the object and probe
|
||||
psi{ll} = bsxfun(@times, obj_proj{min(ll,end)}, probe{min(ll,end)});
|
||||
Psi{ll} = fwd_fourier_proj(psi{ll} , self.modes{min(end, ll)});
|
||||
|
||||
if ll < par.Nlayers && par.multilayer_object
|
||||
probe{ll+1} = Psi{ll};
|
||||
end
|
||||
|
||||
if ll < par.Nlayers && par.multilayer_probe
|
||||
obj_proj{ll+1} = Psi{ll};
|
||||
end
|
||||
end
|
||||
|
||||
% get intensity (modulus) on detector including different corrections
|
||||
aPsi = get_reciprocal_model(self, Psi, modF, mask,iter, g_ind, par, cache);
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%% LINEAR MODEL CORRECTIONS END %%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if iter > 0 && par.get_error && (mod(iter,min(20, 2^(floor(2+iter/50)))) == 0 || (iter < 20)) || iter == par.number_iterations % calculate only sometimes to make it faster
|
||||
[fourier_error(iter,g_ind)] = get_fourier_error(modF, aPsi, noise,mask, par.likelihood);
|
||||
end
|
||||
|
||||
|
||||
|
||||
if (par.multilayer_object || par.multilayer_probe)
|
||||
[Psi(end),R] = modulus_constraint(modF,aPsi,Psi(end), mask, noise, par, 1); % apply only on the last layer !!!
|
||||
else
|
||||
[Psi,R] = modulus_constraint(modF,aPsi,Psi, mask, noise, par,1);
|
||||
end
|
||||
if iter == 0
|
||||
% in the first iteration only find optimal scale for the probe
|
||||
probe_amp_corr(1) = probe_amp_corr(1) + Ggather(sum(modF(:).^2));
|
||||
probe_amp_corr(2) = probe_amp_corr(2) + Ggather(sum(aPsi(:).^2));
|
||||
continue
|
||||
end
|
||||
if strcmp(par.likelihood, 'poisson') % calculate only for the first mode
|
||||
%% automatically find optimal step-size, note that for Gauss it is 1 !!
|
||||
cache.beta_xi(g_ind) = gradient_descent_chi_solver(self,modF, aPsi2, R,mask, g_ind, mean(cache.beta_xi), cache);
|
||||
end
|
||||
|
||||
if(par.multilayer_object || par.multilayer_probe)
|
||||
ind_modes = par.Nlayers:-1:1;
|
||||
else
|
||||
ind_modes = 1:max(par.probe_modes, par.object_modes);
|
||||
end
|
||||
|
||||
|
||||
for ll = ind_modes
|
||||
layer = ll;
|
||||
chi = back_fourier_proj(Psi{min(end,ll)}, self.modes{min(end,ll)})-psi{min(end,ll)};
|
||||
|
||||
|
||||
%% get optimal gradient lenghts
|
||||
object_update=0; probe_update=0;m_probe_update= 0;
|
||||
|
||||
if iter >= par.object_change_start && (ll <= max(par.Nlayers, par.object_modes) || par.apply_multimodal_update)
|
||||
object_update = Gfun(grad,chi, probe{min(ll,end)},...
|
||||
probe_max{min(end,ll)}(1,1,min(end,p_ind{ll})),par.delta_p);
|
||||
end
|
||||
|
||||
|
||||
if iter >= par.probe_change_start && ll <= max(par.probe_modes, par.Nlayers)
|
||||
%% find optimal probe update !!!
|
||||
probe_update = Gfun(grad,chi,obj_proj{min(end,ll)},...
|
||||
object_max{min(ll,end)}, par.delta_p);
|
||||
m_probe_update = mean(probe_update,3);
|
||||
end
|
||||
|
||||
if ((ll == 1 && ~(par.multilayer_object || par.multilayer_probe)) || ...
|
||||
(ll == par.Nlayers && (par.multilayer_object || par.multilayer_probe))) && ...
|
||||
(par.beta_LSQ || iter >= par.probe_position_search)
|
||||
%% variable step extension, apply only the first mode except the 3PIE case
|
||||
%% it will use the same alpha for the higher modes !!!!
|
||||
|
||||
[cache.beta_probe(g_ind),cache.beta_object(g_ind)] = gradient_projection_solver(self,chi,obj_proj{min(end,ll)},probe{ll},...
|
||||
object_update, m_probe_update,p_ind{ll}, par, cache);
|
||||
if any(g_ind ==1)
|
||||
verbose(1,'Average alpha p:%3.3g o:%3.3g ', mean(cache.beta_probe),mean(cache.beta_object));
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%% PROBE UPDATE %%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%
|
||||
%% update probe first
|
||||
if ((iter >= par.probe_change_start) && ll <= max(par.probe_modes,par.Nlayers) ...
|
||||
&& is_method(par, 'PIE')) || ...
|
||||
(par.multilayer_object && ll > 1 && ll <= par.probe_modes)
|
||||
% only in case of first layer probe, otherwise update interprobes
|
||||
|
||||
beta_probe = get_vals(cache.beta_probe,g_ind) .* get_vals(cache.beta_xi,g_ind);
|
||||
|
||||
if is_method(par, {'ePIE', 'hPIE'})
|
||||
%%%%%%%%%%% update probe %%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
probe{ll} = Gfun(@upd_probe_Gfun,probe{ll},probe_update, beta_probe);
|
||||
|
||||
if (ll == 1 && par.apply_subpix_shift)
|
||||
probe{ll} = apply_subpx_shift(probe{ll} , -self.modes{min(end,ll)}.sub_px_shift(g_ind,:));
|
||||
end
|
||||
|
||||
|
||||
if iter >= par.probe_change_start
|
||||
if (par.variable_probe && ll == 1)
|
||||
self.probe{ll}(:,:,p_ind{ll}) = probe{ll}; % slowest line for large datasets !!!!!
|
||||
elseif (~par.multilayer_object || ll == 1) && ll <= par.probe_modes
|
||||
self.probe{ll} = mean(probe{ll},3); % merge information from all the shifted probes if needed
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
if iter > par.probe_fourier_shift_search && ll == 1
|
||||
% search position corrections in the Fourier space, use
|
||||
% only informatiom from the first mode, has to be after
|
||||
% the probes updated
|
||||
self.modes{1} = gradient_fourier_position_solver(chi, obj_proj{1},probe{1},self.modes{1}, g_ind);
|
||||
end
|
||||
if iter >= par.probe_position_search
|
||||
% find optimal position shift that minimize chi{1} in current iteration
|
||||
[pos_update, cache] = gradient_position_solver(self, chi, obj_proj{1},probe{1,layer}, g_ind, iter, cache);
|
||||
self.modes{1}.probe_positions(g_ind,:)=self.modes{1}.probe_positions(g_ind,:)+pos_update;
|
||||
end
|
||||
%%%%%%%%%%%%%%%%%%%%% OBJECT UPDATE %%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%
|
||||
if iter >= min([par.object_change_start]) && ....
|
||||
( ll <= max(par.Nlayers, par.object_modes) || par.apply_multimodal_update )
|
||||
if ll ~= 1 && ~(par.multilayer_object || par.multilayer_probe) ; continue; end
|
||||
|
||||
if iter >= par.object_change_start % && ~(par.multilayer_probe && ll > 1) % the objects are just empty
|
||||
|
||||
beta_object = get_vals(cache.beta_object,g_ind) .* get_vals(cache.beta_xi,g_ind);
|
||||
if par.share_object
|
||||
obj_ids = 1; % update only the first object
|
||||
else
|
||||
obj_ids = unique(scan_ids{ind_ii}); % update only the objects processed in this block
|
||||
end
|
||||
|
||||
if any(beta_object ~= 1)
|
||||
object_update = bsxfun(@times, object_update, beta_object);
|
||||
end
|
||||
|
||||
|
||||
if is_method(par, 'ePIE') % use always in nearfield
|
||||
% classical ePIE, faster constraint application, but it will fail with too high grouping
|
||||
self.object = set_views(self.object, object_update,layer, obj_ids, g_ind, cache, scan_ids{ind_ii},[]);
|
||||
elseif is_method(par, 'hPIE') %% hybrid PIE
|
||||
if par.Nscans == 1 || par.share_object
|
||||
ind_tmp = 1;
|
||||
else
|
||||
ind_tmp = 1+par.object_modes* ((1:par.Nscans)-1);
|
||||
end
|
||||
for kk = ind_tmp
|
||||
obj_illum_sum{kk,layer}(:) = 0;
|
||||
object_upd_sum{kk,layer}(:) = 0;
|
||||
end
|
||||
object_update = bsxfun(@times, object_update, aprobe2); % make is more like dumped LSQ solution
|
||||
[object_upd_sum,obj_illum_sum] = set_views_rc(object_upd_sum,obj_illum_sum, object_update,aprobe2,layer,obj_ids, g_ind, cache, scan_ids{ind_ii},[]);
|
||||
for kk = ind_tmp
|
||||
self.object{kk,layer} = Gfun(@object_update_Gfun, self.object{kk,layer},object_upd_sum{kk,layer}, obj_illum_sum{kk,layer}, cache.MAX_ILLUM(min(kk,end)));
|
||||
end
|
||||
else
|
||||
error('Unimplemented method %s ', par.method)
|
||||
end
|
||||
end
|
||||
end
|
||||
if ll > 1 && par.multilayer_object
|
||||
% % apply rescaling to make scaling correction
|
||||
Psi{ll-1} = probe{ll};
|
||||
end
|
||||
if ll > 1 && par.multilayer_probe
|
||||
Psi{ll-1} = obj_proj{ll} + object_update;
|
||||
end
|
||||
end
|
||||
|
||||
if check_avail_memory < 0.2 || ~par.keep_on_gpu
|
||||
% slow step that is not needed if there is enough memory ,
|
||||
% it can slow down almost twice !!!
|
||||
clear Psi R aPsi2 psi probe_update object_update chi
|
||||
if par.keep_on_gpu
|
||||
warning('Low GPU memory')
|
||||
end
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
if par.multilayer_object
|
||||
self.probe = self.probe(1);
|
||||
end
|
||||
|
||||
if par.variable_probe && iter >= par.probe_change_start
|
||||
[self.probe{1}, self.probe_evolution] = apply_SVD_filter(self.probe{1}, par.variable_probe_modes+1, self.modes{1});
|
||||
elseif par.variable_probe && iter < par.probe_change_start
|
||||
self.probe{1} = probe_0;
|
||||
elseif ( ~isempty(self.probe_support)) && iter >= par.probe_change_start
|
||||
self.probe{1} = apply_probe_contraints(self.probe{1}, self.modes{1});
|
||||
end
|
||||
|
||||
if iter == 0
|
||||
% apply initial correction for the probe intensity and return
|
||||
% it seems to be safer to underestimate the probe amplitude for variable probe method
|
||||
probe_amp_corr = 0.5*sqrt(probe_amp_corr(1) / probe_amp_corr(2)); %% calculate ratio between modF^2 and aPsi^2
|
||||
|
||||
for ii = 1:par.probe_modes
|
||||
self.probe{ii} = self.probe{ii}*probe_amp_corr;
|
||||
end
|
||||
verbose(2,'Probe amplitude corrected by %.3g',probe_amp_corr)
|
||||
return
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
function probe = upd_probe_Gfun(probe,probe_update, alpha_p)
|
||||
probe = probe + alpha_p.*probe_update;
|
||||
end
|
||||
|
||||
function grad = get_grad_flat(chi,proj,max2, delta )
|
||||
% ePIE method
|
||||
grad = (1/max2) * chi .* conj(proj) ;
|
||||
end
|
||||
|
||||
function grad = get_grad_lsq(chi,proj,max2, delta )
|
||||
% dumped LSQ method
|
||||
aproj = abs(proj) ;
|
||||
grad = chi .* conj(proj) .* aproj ./ (aproj.^2 + delta*max2)./sqrt(max2);
|
||||
end
|
||||
|
||||
function object = object_update_Gfun(object,object_upd_sum, obj_illum_sum, max)
|
||||
object = object + object_upd_sum ./ (obj_illum_sum+1e-9* max);
|
||||
end
|
||||
|
||||
function array = get_vals(array, ind)
|
||||
if isscalar(array)
|
||||
return
|
||||
else
|
||||
array = reshape(array(ind),1,1,[]);
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,117 @@
|
||||
% ACCELERATE_GRADIENTS use the Nesterov's Accelerated Gradient method
|
||||
%
|
||||
% cache = accelerate_gradients(self, par, cache, iter)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
% ** iter number of the current iteration
|
||||
%
|
||||
% returns:
|
||||
% ** self updated structure containing inputs
|
||||
% ** cache structure with precalculated values - stores the previous accelerated gradients updates
|
||||
%
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
|
||||
|
||||
function [self,cache] = accelerate_gradients(self, par, cache, iter)
|
||||
%% accelerated gradients extension, tries to look ahead in direction of the last update
|
||||
if iter == par.accelerated_gradients_start
|
||||
cache.object_prev = {self.object, self.object};
|
||||
cache.probe_prev = {self.probe, self.probe};
|
||||
for ii = 1:length(cache.illum_sum_0)
|
||||
cache.update_weights{ii} = cache.illum_sum_0{ii}.^2 ./ (cache.illum_sum_0{ii}.^2 + 0.1*cache.MAX_ILLUM(ii)^2);
|
||||
end
|
||||
elseif iter > par.accelerated_gradients_start
|
||||
object_start = max(par.object_change_start, par.accelerated_gradients_start);
|
||||
probe_start = max(par.probe_change_start, par.accelerated_gradients_start);
|
||||
cache.object_prev{1} = cache.object_prev{2};
|
||||
cache.object_prev{2} = self.object;
|
||||
|
||||
cache.probe_prev{1} = cache.probe_prev{2};
|
||||
cache.probe_prev{2} = self.probe;
|
||||
% accelerate the object reconstructions
|
||||
if iter > par.object_change_start
|
||||
beta = (iter-object_start+1)/(iter-object_start+3);
|
||||
for ii = 1:size(self.object,1)
|
||||
for layer = 1:size(self.object,2)
|
||||
if ii == 1 && utils.verbose() > 3
|
||||
plotting.smart_figure(555)
|
||||
update = cache.update_weights{ii}.* (self.object{ii,layer} - cache.object_prev{1}{ii,layer});
|
||||
plotting.imagesc3D(update)
|
||||
title('Acceleration step in the Nesterov method')
|
||||
axis xy off
|
||||
utils.verbose(0, 'Norm of accelerated gradient = %g', math.norm2(update) )
|
||||
drawnow
|
||||
end
|
||||
self.object{ii,layer} = self.object{ii,layer} + ...
|
||||
beta*cache.update_weights{ii}.*(self.object{ii,layer} - cache.object_prev{1}{ii,layer});
|
||||
end
|
||||
end
|
||||
end
|
||||
% accelerate only the first OPR mode of the probe
|
||||
if iter > par.probe_change_start
|
||||
beta = (iter-probe_start+1)/(iter-probe_start+3);
|
||||
for ii = 1:numel(self.probe)
|
||||
self.probe{ii}(:,:,:,1) = self.probe{ii}(:,:,:,1) + ...
|
||||
beta.*(self.probe{ii}(:,:,:,1) - cache.probe_prev{1}{ii}(:,:,:,1));
|
||||
end
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,78 @@
|
||||
% APPLY_SMOOTHNESS_CONSTRAINT simple weak smoothness constaint by convolution
|
||||
%
|
||||
% x = apply_smoothness_constraint(x, alpha)
|
||||
%
|
||||
% ** x image stack to be smoothed
|
||||
% ** alpha relaxation smoothing constant, 0 = no smoothness, 1/8 = maximal smoothness given as conv(x, ones(3)/9)
|
||||
%
|
||||
% returns:
|
||||
% ++ x smoothed array
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function x = apply_smoothness_constraint(x, alpha)
|
||||
assert(alpha < 1/8, 'Too high smoothing')
|
||||
if alpha > 0
|
||||
psf = ones(3)*alpha;
|
||||
psf(2,2) = 1-8*alpha;
|
||||
|
||||
if size(x,3) == 1
|
||||
x = conv2(x, psf, 'same');
|
||||
else
|
||||
x = convn(x, psf, 'same');
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,82 @@
|
||||
% concatenate values from list of cells contaning structures with arrays
|
||||
%
|
||||
% array = cat_struct( struct, name, ind)
|
||||
%
|
||||
% ** struct list structures
|
||||
% ** name field name to be ccntatenated
|
||||
% ** ind which index to take {'last', 'first'}
|
||||
%
|
||||
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function array = cat_struct( struct, name, ind)
|
||||
array = [];
|
||||
if nargin < 3
|
||||
ind = [];
|
||||
end
|
||||
for i = 1:length(struct)
|
||||
s = struct{i}.(name);
|
||||
if strcmp(ind, 'last')
|
||||
s = s(end);
|
||||
elseif strcmp(ind, 'first')
|
||||
s = s(1);
|
||||
end
|
||||
array = [array, s(:)];
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,126 @@
|
||||
% GET_FOURIER_ERROR fast calculation of the Fourier plane (at detector) error normalized so that for
|
||||
% gaussian noise approximation the ideal error should be close to 1
|
||||
%
|
||||
% Err = get_fourier_error(modF, aPsi, Noise,Mask, likelihood)
|
||||
%
|
||||
% ** modF pre-fftshifted and sqrt-ed data
|
||||
% ** aPsi reciprocal amplitude model
|
||||
% ** Noise estimated noise (STD) in each pixel after sqrt transform
|
||||
% ** Mask masked values, 1 = ignored, 0 = use this pixel
|
||||
% ** likelihood L1 or poisson
|
||||
%
|
||||
% returns:
|
||||
% ++ Err calculated error for provided positions
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
|
||||
function Err = get_fourier_error(modF, aPsi, Noise,Mask, likelihood)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import utils.*
|
||||
import math.*
|
||||
|
||||
if ~exist('likelihood', 'var'); likelihood = 'L1'; end
|
||||
|
||||
|
||||
likelihood = lower(likelihood);
|
||||
% USE Gfun IN ORDER TO MAKE IT FASTER ON GPU
|
||||
if isempty(Mask) && isempty(Noise)
|
||||
switch likelihood
|
||||
case 'l1', Err = Gfun(@get_err,modF, aPsi);
|
||||
case 'poisson', Err = Gfun(@get_loglik,modF, aPsi);
|
||||
end
|
||||
elseif ~isempty(Mask) && isempty(Noise)
|
||||
switch likelihood
|
||||
case 'l1', Err = Gfun(@get_err_masked,modF, aPsi, Mask);
|
||||
case 'poisson', Err = Gfun(@get_loglik_masked,modF, aPsi, Mask);
|
||||
end
|
||||
elseif isempty(Mask) && ~isempty(Noise)
|
||||
Err = Gfun(@get_err_noise,modF, aPsi, Noise);
|
||||
else
|
||||
Err = Gfun(@get_err_noise_mask, modF, aPsi, Mask, Noise);
|
||||
end
|
||||
switch likelihood
|
||||
case 'l1', Err = sqrt(squeeze(mean2(Err)))';
|
||||
case 'poisson', Err = squeeze(mean2(Err))';
|
||||
otherwise, error('Unsupported likelihood')
|
||||
end
|
||||
end
|
||||
|
||||
function L = get_loglik(modF, aPsi)
|
||||
modF2 = modF.^2;
|
||||
aPsi2 = aPsi.^2;
|
||||
L = -(modF2 .* log(aPsi2+1e-6) - aPsi2) ;
|
||||
end
|
||||
function L = get_loglik_masked(modF, aPsi,Mask)
|
||||
modF2 = modF.^2;
|
||||
aPsi2 = aPsi.^2;
|
||||
L = -(1-Mask) .* (modF2 .* log(aPsi2+1e-6) - aPsi2) ;
|
||||
end
|
||||
function E = get_err(modF, aPsi)
|
||||
E = (modF-aPsi).^2 / (0.5)^2; % 0.5 is correction for the Poisson noise (if we expect single photon precision)
|
||||
end
|
||||
function E = get_err_masked(modF, aPsi, Mask)
|
||||
E = (modF-aPsi).^2 .* (1-Mask) / (0.5)^2;
|
||||
end
|
||||
function E = get_err_noise(modF, aPsi, Noise)
|
||||
E = (modF-aPsi).^2 ./ Noise.^2;
|
||||
end
|
||||
function E = get_err_noise_mask(modF, aPsi, Mask, Noise)
|
||||
E = (modF-aPsi).^2 ./ Noise.^2 .* (1-Mask);
|
||||
end
|
||||
@@ -0,0 +1,109 @@
|
||||
% GET_IMG_GRAD get vertical and horizontal gradient of the image, it is slightly faster on GPU than
|
||||
% the version in math.get_img_grad
|
||||
%
|
||||
% [dX, dY] = get_img_grad(img)
|
||||
%
|
||||
% ** img stack of complex images
|
||||
%
|
||||
% returns:
|
||||
% ++ dX,dY - directional gradients of the image
|
||||
|
||||
%
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
|
||||
|
||||
function [dX, dY] = get_img_grad(img)
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
Np = size(img);
|
||||
|
||||
if nargout == 1
|
||||
fX = fft(img,[],2);
|
||||
X = (fftshift((0:Np(2)-1)/Np(2))-0.5);
|
||||
dX = bsxfun(@times, fX,2i*pi*X);
|
||||
dX = ifft(dX,[],2);
|
||||
return
|
||||
end
|
||||
if nargout > 1
|
||||
X = (fftshift((0:Np(2)-1)/Np(2))-0.5);
|
||||
Y = (fftshift((0:Np(1)-1)/Np(1))-0.5)';
|
||||
|
||||
% use matlab implicite GPU paralelization
|
||||
if isa(img, 'gpuArray')
|
||||
% it is much faster to use 2D fft for GPU despite higher
|
||||
% computational costs
|
||||
img = fft2(img);
|
||||
% make it slightly faster with GPU
|
||||
[dX, dY] = Gfun(@multiply_gfun, img, X, Y);
|
||||
dX = ifft2(dX);
|
||||
dY = ifft2(dY);
|
||||
else
|
||||
fX = fft(img,[],2);
|
||||
fY = fft(img,[],1);
|
||||
dX = bsxfun(@times, fX,2i*pi*X);
|
||||
dY = bsxfun(@times, fY,2i*pi*Y);
|
||||
dX = ifft(dX,[],2);
|
||||
dY = ifft(dY,[],1);
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
|
||||
function [dX, dY]=multiply_gfun(img, X,Y)
|
||||
dX = img .* (2i*pi)* X;
|
||||
dY = img .* (2i*pi)* Y;
|
||||
end
|
||||
@@ -0,0 +1,287 @@
|
||||
% GET_RECIPROCAL_MODEL get estimate of the measured intensity from given electric field Psi
|
||||
%
|
||||
% [aPsi, aPsi2, cache, self] = get_reciprocal_model(self, Psi, modF, mask,iter, g_ind, par, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** Psi where Psi is the propagated exitwave
|
||||
% ** modF pre-fftshifted and sqrt-ed data
|
||||
% ** mask masked values, 1 = ignored, 0 = use this pixel
|
||||
% ** iter current iteration number
|
||||
% ** ind processed indices
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache structure with precalculated values
|
||||
%
|
||||
% returns:
|
||||
% ++ aPsi reciprocal amplitude model
|
||||
% ++ aPsi reciprocal intensity model
|
||||
% ++ cache structure with precalculated values
|
||||
% ++ self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
function [aPsi, aPsi2, cache, self] = get_reciprocal_model(self, Psi, modF, mask,iter, g_ind, par, cache)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
aPsi2 = [];
|
||||
|
||||
if par.probe_modes == 1 && isempty(self.background) && self.diff_pattern_blur == 0 ...
|
||||
&& ~par.background_detection && strcmpi(par.likelihood, 'l1') && par.upsampling_data_factor == 0
|
||||
% or the simplest and fastest option: just get absolute value
|
||||
aPsi = abs(Psi{1});
|
||||
aPsi2 = [];
|
||||
elseif par.probe_modes == 1 && ~isempty(self.background) && self.diff_pattern_blur == 0 ...
|
||||
&& ~par.background_detection && strcmpi(par.likelihood, 'l1') && par.upsampling_data_factor == 0
|
||||
% second simplest option, abs + background
|
||||
aPsi = Gfun(@modulus_with_background,Psi{1}, self.background , cache.background_profile);
|
||||
else
|
||||
% apply corrected model and sum up all coherence modes
|
||||
aPsi2 = sumsq_cell(Psi);
|
||||
|
||||
% assume that the data were upsampled by the utils.unbinning_2D function
|
||||
if par.upsampling_data_factor
|
||||
aPsi2 = utils.binning_2D(aPsi2, 2^par.upsampling_data_factor);
|
||||
end
|
||||
|
||||
%%%%%%%%%%%%%%%% linear correction model %%%%%%%%%%%%%%%%%%%%%%%
|
||||
[aPsi2,cache, self] = get_linear_correction_model(self,par,cache,aPsi2,modF,mask,iter, g_ind );
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
aPsi = sqrt(aPsi2);
|
||||
end
|
||||
end
|
||||
|
||||
function aPsi = modulus_with_background(Psi, background_value, background_shape)
|
||||
rPsi = real(Psi);
|
||||
iPsi = imag(Psi);
|
||||
aPsi2 = rPsi.^2 + iPsi.^2;
|
||||
aPsi2 = aPsi2 + background_value .* background_shape;
|
||||
% sqrt is very slow ...
|
||||
aPsi = sqrt(aPsi2);
|
||||
% aPsi = exp(0.5*log(aPsi2)); % log identity has exactly the same calculation time
|
||||
end
|
||||
|
||||
function y = sumsq_cell(x)
|
||||
% Description: sum incoherently cells x, make it inplace and fast
|
||||
|
||||
N = length(x);
|
||||
if N <= 15 && builtin( 'isa', x{1}, 'gpuArray' )
|
||||
switch N
|
||||
case 1, fun = @sum_1;
|
||||
case 2, fun = @sum_2;
|
||||
case 3, fun = @sum_3;
|
||||
case 4, fun = @sum_4;
|
||||
case 5, fun = @sum_5;
|
||||
case 6, fun = @sum_6;
|
||||
case 7, fun = @sum_7;
|
||||
case 8, fun = @sum_8;
|
||||
case 9, fun = @sum_9;
|
||||
case 10, fun = @sum_10;
|
||||
case 11, fun = @sum_11;
|
||||
case 12, fun = @sum_12;
|
||||
case 13, fun = @sum_13;
|
||||
case 14, fun = @sum_14;
|
||||
case 15, fun = @sum_15;
|
||||
end
|
||||
y = arrayfun(fun, x{:});
|
||||
else
|
||||
y = 0;
|
||||
for i = 1:N
|
||||
y = y + abs(x{i}).^2;
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
% !! using sqrt(imag(x)^2 + real(x)^2) is much slower !!!
|
||||
|
||||
% merged GPU kernels
|
||||
function y = sum_1(x)
|
||||
y = abs(x).^2;
|
||||
end
|
||||
function y = sum_2(x1,x2)
|
||||
y = abs(x1).^2+abs(x2).^2;
|
||||
end
|
||||
function y = sum_3(x1,x2,x3)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2;
|
||||
end
|
||||
function y = sum_4(x1,x2,x3,x4)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2;
|
||||
end
|
||||
function y = sum_5(x1,x2,x3,x4,x5)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2;
|
||||
end
|
||||
function y = sum_6(x1,x2,x3,x4,x5,x6)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2;
|
||||
end
|
||||
function y = sum_7(x1,x2,x3,x4,x5,x6,x7)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2;
|
||||
end
|
||||
function y = sum_8(x1,x2,x3,x4,x5,x6,x7,x8)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2;
|
||||
end
|
||||
function y = sum_9(x1,x2,x3,x4,x5,x6,x7,x8,x9)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2;
|
||||
end
|
||||
function y = sum_10(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2+abs(x10).^2;
|
||||
end
|
||||
function y = sum_11(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2+abs(x10).^2+abs(x11).^2;
|
||||
end
|
||||
function y = sum_12(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,x12)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2+abs(x10).^2+abs(x11).^2+abs(x12).^2;
|
||||
end
|
||||
function y = sum_13(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,x12,x13)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2+abs(x10).^2+abs(x11).^2+abs(x12).^2+abs(x13).^2;
|
||||
end
|
||||
function y = sum_14(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,x12,x13,x14)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2+abs(x10).^2+abs(x11).^2+abs(x12).^2+abs(x13).^2+abs(x14).^2;
|
||||
end
|
||||
function y = sum_15(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,x12,x13,x14,x15)
|
||||
y = abs(x1).^2+abs(x2).^2+abs(x3).^2+abs(x4).^2+abs(x5).^2+abs(x6).^2+abs(x7).^2+abs(x8).^2+abs(x9).^2+abs(x10).^2+abs(x11).^2+abs(x12).^2+abs(x13).^2+abs(x14).^2+abs(x15).^2;
|
||||
end
|
||||
function [aPsi2, cache, self] = get_linear_correction_model(self,par,cache,aPsi2,modF,mask, iter, ii )
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
if isempty(self.background) && self.diff_pattern_blur == 0 && strcmp(par.background_detection, 'none')
|
||||
return % nothing to be done, return
|
||||
end
|
||||
|
||||
%% add background
|
||||
if ~isempty(self.background)
|
||||
if ~isfield(cache, 'background_profile') || isscalar(cache.background_profile)
|
||||
aPsi2 = aPsi2 + self.background;
|
||||
else
|
||||
aPsi2 = Gfun(@add_background, aPsi2, self.background, cache.background_profile,modF);
|
||||
end
|
||||
end
|
||||
|
||||
if self.diff_pattern_blur > 0
|
||||
%%%%%%%%%%%%%%%%%%%%%%% LINEAR MODEL CORRECTIONS START %%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%
|
||||
if isempty(self.modes{1}.ASM_factor) % is not nearfield
|
||||
aPsi2 = aPsi2(cache.fftshift_idx{:},:);
|
||||
end
|
||||
|
||||
% apply blur correction change to Gaussian by ZC
|
||||
if self.diff_pattern_blur > 0
|
||||
blur_kernel = fspecial('gaussian',round(self.diff_pattern_blur) *10+1,self.diff_pattern_blur);
|
||||
aPsi2 = convn(aPsi2, blur_kernel, 'same');
|
||||
end
|
||||
% apply blur correction
|
||||
% if self.diff_pattern_blur > 0
|
||||
% % generate blurring kernel
|
||||
% x = [-1, 0,-1]/self.diff_pattern_blur;
|
||||
% [X,Y] = meshgrid(x,x);
|
||||
% blur_kernel = exp( -(X.^2 + Y.^2) );
|
||||
% blur_kernel = blur_kernel / math.sum2( blur_kernel );
|
||||
% aPsi2 = convn(aPsi2, blur_kernel, 'same');
|
||||
% end
|
||||
|
||||
if isempty(self.modes{1}.ASM_factor) % is not nearfield
|
||||
aPsi2 = aPsi2(cache.fftshift_idx{:},:);
|
||||
end
|
||||
end
|
||||
|
||||
% simple estimation of background
|
||||
if par.background_detection && iter > par.background_detection
|
||||
if isempty(mask); mask = false; end
|
||||
% calculate the most optimal background update
|
||||
[nom,denom] = Gfun(@get_background_estimate,modF, aPsi2, mask, cache.background_profile_weight, cache.background_profile );
|
||||
update = sum2(nom)./sum2(denom);
|
||||
if any(ii == 1)
|
||||
fprintf('Background update: %3.3g curr value:%3.3g \n ', mean(update), self.background);
|
||||
end
|
||||
|
||||
|
||||
|
||||
self.background = posit(self.background + (par.grouping/self.Npos)*mean(update));
|
||||
|
||||
% %% Check if background is fitted well
|
||||
% X = (-self.Np_p(1)/2:self.Np_p(1)/2-1);
|
||||
% Y = (-self.Np_p(2)/2:self.Np_p(2)/2-1);
|
||||
% [X,Y] = meshgrid(X,Y);
|
||||
%
|
||||
% R = (sqrt(X.^2 + Y.^2));
|
||||
% D = fftshift(single(modF.^2) - aPsi2);
|
||||
% for i = 1:mean(self.Np_p)/2
|
||||
% progressbar(i, mean(self.Np_p)/2);
|
||||
% mask = (R==i);
|
||||
% mask = mask / sum2(mask);
|
||||
% B(i) = median(sum2(bsxfun(@times, D, mask)));
|
||||
% end
|
||||
% plot(B)
|
||||
% ylim([-5,5])
|
||||
% drawnow
|
||||
%
|
||||
|
||||
|
||||
end
|
||||
end
|
||||
|
||||
function aPsi2 = add_background(aPsi2, background,background_profile,modF)
|
||||
aPsi2 = aPsi2 + background .* background_profile .* (modF > 0); % leave empty pixels empty
|
||||
end
|
||||
|
||||
function [nom, denom] = get_background_estimate(modF, aPsi2, mask, distribution, background )
|
||||
W = ~mask .* distribution;
|
||||
nom = W.* (modF.^2 - aPsi2).*background;
|
||||
denom = W.*background.^2;
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -0,0 +1,149 @@
|
||||
% GRADIENT_NF_PROPAGATION_SOLVER update estimate of the nearfield propagation distance based on the
|
||||
% current update of the wavefront
|
||||
%
|
||||
% self = gradient_NF_propagation_solver(self,psi,chi, cache, ind)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** psi exitwave (psi = P*O)
|
||||
% ** chi [Nx,Ny,N] array, difference between original and updated exit-wave
|
||||
% ** cache precalculated values
|
||||
% ** ind indices containg corresponding probe id for each processed position
|
||||
%
|
||||
% returns:
|
||||
% ++ self updated self structure with optimized propagation distance
|
||||
% ++ cache precalculated values with updated velocity for momentum method
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
|
||||
function [self, cache] = gradient_NF_propagation_solver(self,psi,chi, cache, ind, layer_id)
|
||||
% update estimate of the nearfield propagation distance based on the
|
||||
% current update of the wavefront
|
||||
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import engines.GPU_MS.shared.*
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
dH = cache.ASM_difference;
|
||||
|
||||
% propagate to farfield
|
||||
Psi_0 = fft2_safe(psi{1});
|
||||
Psi_1 = fft2_safe(psi{1}+chi{1});
|
||||
% get phase diffence
|
||||
Psi_diff = sum(Psi_0 .* conj(Psi_1),3);
|
||||
aPsi = abs(Psi_diff);
|
||||
Psi_diff = Psi_diff ./ (aPsi+mean2(aPsi).*1e-6);
|
||||
|
||||
% calculate distance that best explains the differences
|
||||
dz = -Ggather(sum2(real(conj(dH) .* Psi_diff)) ./ sum2(abs(dH).^2));
|
||||
|
||||
|
||||
% %% USE MOMENTUM ACCELERATION TO MAKE THE CONVERGENCE FASTER
|
||||
% try
|
||||
% momentum_memory = 10; % compare 10 iterations
|
||||
% if length(self.modes{1}.distances) > momentum_memory
|
||||
% if ~isfield(cache, 'velocity_NF_propagation')
|
||||
% cache.velocity_NF_propagation = 0;
|
||||
% end
|
||||
%
|
||||
% updates = diff(self.modes{1}.distances(end-momentum_memory:end));
|
||||
% corr_level = corr(updates(1:end-1)', updates(2:end)');
|
||||
%
|
||||
% corr_level
|
||||
%
|
||||
%
|
||||
% if all(corr_level > 0 )
|
||||
% %%%%%%%%%%%% very empritical model %%%
|
||||
% gain = 1; % smaller -> lower relative speed (less momentum)
|
||||
% friction = 0.1*max(0, 0.5-corr_level); % smaller -> longer memory, more momentum
|
||||
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% else
|
||||
% gain = 0; friction = 0.5;
|
||||
% end
|
||||
%
|
||||
% cache.velocity_NF_propagation = cache.velocity_NF_propagation*(1-friction) + dz;
|
||||
% %% apply the velocity to the refined positions , if the postition updated are sufficiently small
|
||||
%
|
||||
% cache.velocity_NF_propagation
|
||||
%
|
||||
% dz = dz + gain*cache.velocity_NF_propagation;
|
||||
%
|
||||
%
|
||||
% end
|
||||
% catch
|
||||
% keyboard
|
||||
% end
|
||||
|
||||
|
||||
% update propagation values
|
||||
if any(ind==1)
|
||||
% add new field only when new iteration is started
|
||||
self.modes{1}.distances = [self.modes{1}.distances,self.modes{1}.distances(end) + dz];
|
||||
verbose(1, 'Propagation distance: %3.5gum ', self.modes{1}.distances(end)*1e6)
|
||||
else
|
||||
self.modes{1}.distances = self.modes{1}.distances + dz;
|
||||
end
|
||||
|
||||
% use the same distance for all positions
|
||||
for i = 1:length(self.modes)
|
||||
self.modes{i}.distances = self.modes{1}.distances;
|
||||
end
|
||||
|
||||
end
|
||||
@@ -0,0 +1,117 @@
|
||||
% GRADIENT_DESCENT_XI_SOLVER solve optimal update step for the Poisson noise method
|
||||
%
|
||||
% [beta_chi, find_xi_step] = gradient_descent_xi_solver(self,modF, aPsi2, R,mask, ind, beta_xi, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** modF pre-fftshifted and sqrt-ed data
|
||||
% ** aPsi2 reciprocal intensity model
|
||||
% ** R 1- modF / aPsi
|
||||
% ** mask masked values on detector
|
||||
% ** ind processed indices
|
||||
% ** beta_xi previous steps, needed for calculation as initial guess
|
||||
% ** cache precalculated values
|
||||
%
|
||||
% returns:
|
||||
% ++ beta_xi optimal probe step
|
||||
% ++ find_xi_step optimal object step
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML, engines.GPU_MS.PIE
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
function [beta_xi, find_xi_step] = gradient_descent_xi_solver(self,modF, aPsi2, R,mask, ind, beta_xi, cache)
|
||||
|
||||
import utils.*
|
||||
import math.*
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
find_xi_step = true;
|
||||
|
||||
%% !! use precached values if the change is small
|
||||
if ~find_xi_step
|
||||
beta_xi = cache.beta_xi_all(ind,end);
|
||||
else
|
||||
if isempty(mask)
|
||||
mask = 0;
|
||||
end
|
||||
for i = 1:2
|
||||
[nom, denom] = Gfun(@get_coefs, aPsi2,modF,R,mask,beta_xi);
|
||||
% avoid oscilations of the solution
|
||||
beta_xi = beta_xi*0.5 + 0.5* Ggather(sum2(nom) ./ sum2(denom));
|
||||
|
||||
beta_xi = abs(max(min(beta_xi,1),0));
|
||||
end
|
||||
beta_xi = beta_xi + randn(size(beta_xi)) * 1e-2;
|
||||
end
|
||||
|
||||
if any(ind ==1)
|
||||
verbose(1,'Average xi_alpha %3.2g find_step %i ', mean(beta_xi(:)), find_xi_step)
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
function [nom, denom,W] = get_coefs(aPsi2,modF,R,mask,alpha)
|
||||
modF2 = modF.^2;
|
||||
chi = 1-R;
|
||||
W = 1-mask;
|
||||
nom = -W.*chi.* (modF2./ (1-alpha.*chi) - aPsi2);
|
||||
denom = W.*aPsi2.*chi.^2;
|
||||
end
|
||||
@@ -0,0 +1,110 @@
|
||||
% FUNCTION mode = gradient_fourier_position_solver(chi,O,P,mode, ind)
|
||||
% Description: solve position errors in the Fourier space
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** chi [Nx,Ny,N] array, difference between original and updated exit-wave
|
||||
% ** O [Nx,Ny,N] array, object views
|
||||
% ** P [Nx,Ny,1] or [Nx,Ny,N] array, single or variable probe
|
||||
% ** mode structure with information about each incoherent mode
|
||||
% ** ind processed indices
|
||||
%
|
||||
% returns:
|
||||
% ++ mode updated mode structure
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML, engines.GPU_MS.PIE
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
function mode = gradient_fourier_position_solver(chi,O,P,mode, ind)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
|
||||
% use gradinent solver for position correction in fourier space
|
||||
|
||||
Np = size(P);
|
||||
|
||||
X = linspace(-0.5, 0.5,Np(2)) ;
|
||||
Y = linspace(-0.5, 0.5,Np(1))' ;
|
||||
|
||||
|
||||
[nom_dx, denom_dx, nom_dy, denom_dy] = Gfun(@get_coefs,chi, P,O,X, Y);
|
||||
dx = - sum2(nom_dx)./ sum2(denom_dx);
|
||||
dy = - sum2(nom_dy)./ sum2(denom_dy);
|
||||
|
||||
shift = squeeze(Ggather(cat(4,dx, dy)));
|
||||
shift = min(abs(shift), 0.2) .* sign(shift); % avoid too fast jumps, <0.5px/iter is enough
|
||||
if any(ind==1)
|
||||
verbose(1,'Grad fourier pos correction -- AVG step %3.2g px', mean(abs(shift(:))))
|
||||
end
|
||||
mode.probe_fourier_shift(ind,:)=mode.probe_fourier_shift(ind,:)+reshape(shift,[],2);
|
||||
end
|
||||
|
||||
function [nom1, denom1, nom2, denom2] = get_coefs(chi, P, O, dX, dY)
|
||||
|
||||
dPx = 2i*pi.*dX.*P.*O;
|
||||
dPy = 2i*pi.*dY.*P.*O;
|
||||
nom1 = real(conj(dPx) .* chi);
|
||||
denom1 = abs(dPx).^2;
|
||||
|
||||
nom2 = real(conj(dPy) .* chi);
|
||||
denom2 = abs(dPy).^2;
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,196 @@
|
||||
% GRADIENT_POSITION_SOLVER solve position errors in the real space
|
||||
%
|
||||
% [pos_update, cache] = gradient_position_solver(self,xi,O,P,ind, iter, cache)
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** xi exit wave update vector
|
||||
% ** O object views
|
||||
% ** P probe or probes
|
||||
% ** ind indices of of processed position
|
||||
% ++ iter current iteration
|
||||
% ** cache structure with precalculated values to avoid unnecessary overhead
|
||||
%
|
||||
% returns:
|
||||
% ++ pos_update position updates for each of the indices
|
||||
% ++ cache updated structure with precalculated values
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML, engines.GPU_MS.PIE
|
||||
|
||||
|
||||
function [pos_update, probe_rotation,probe_scale,cache] = gradient_position_solver(self,xi,O,P,ind, iter, cache, par)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
import math.*
|
||||
import utils.*
|
||||
% use gradinent solver for position correction
|
||||
|
||||
low_mem_errs = {'id:parallel:gpu:array:OOMForOperation',...
|
||||
'id:MATLAB:LowGPUMem','MATLAB:LowGPUMem',...
|
||||
'parallel:gpu:array:OOM',...
|
||||
'parallel:gpu:device:UnknownCUDAError', ...
|
||||
'parallel:gpu:array:OOMForOperation', ...
|
||||
'parallel:gpu:array:FFTInternalError'};
|
||||
|
||||
% wrapper around get_img_grad, in case of low memory it will try to repeat
|
||||
% Ntimes before giving up
|
||||
pos_update = 0; probe_rotation = 0; probe_scale = 0;
|
||||
N = 5;
|
||||
for ii = 1:N
|
||||
try
|
||||
% reuse dx_O, dy_O to save memory !!
|
||||
[dx_O,dy_O]=get_img_grad(O);
|
||||
|
||||
if iter >= par.detector_rotation_search
|
||||
%% estimate detector rotation
|
||||
xgrid = Garray(linspace(-1,1,self.Np_p(1))');
|
||||
ygrid = Garray(-linspace(-1,1,self.Np_p(2)));
|
||||
[nom, denom] = Gfun(@get_coefs_mixed,xi, P, dx_O, dy_O, xgrid, ygrid);
|
||||
probe_rotation = gather(sum2(nom)./ sum2(denom));
|
||||
end
|
||||
|
||||
if iter >= par.detector_scale_search
|
||||
%% estimate detector scale (ie pixel scale error in farfield mode)
|
||||
xgrid = Garray(-linspace(-1,1,self.Np_p(2)) .* tukeywin(self.Np_p(2), 0.1)');
|
||||
ygrid = Garray(-linspace(-1,1,self.Np_p(1))'.* tukeywin(self.Np_p(1), 0.1));
|
||||
[nom, denom] = Gfun(@get_coefs_mixed,xi, P, dx_O, dy_O, xgrid, ygrid);
|
||||
probe_scale = gather(sum2(nom)./ sum2(denom));
|
||||
probe_scale = 0.5*mean(probe_scale) / mean(self.Np_p);
|
||||
end
|
||||
|
||||
if iter >= par.probe_position_search
|
||||
%% estimate sample shift
|
||||
[dx_O, denom_dx, dy_O, denom_dy] = Gfun(@get_coefs_shift,xi,P,dx_O, dy_O);
|
||||
dx = sum2(dx_O)./ sum2(denom_dx);
|
||||
dy = sum2(dy_O)./ sum2(denom_dy);
|
||||
end
|
||||
break
|
||||
catch ME
|
||||
warning('Low memory')
|
||||
if ~any(strcmpi(ME.identifier, low_mem_errs))
|
||||
rethrow(ME)
|
||||
end
|
||||
pause(1)
|
||||
end
|
||||
end
|
||||
if ii == 5
|
||||
rethrow(ME)
|
||||
end
|
||||
|
||||
if iter < par.probe_position_search
|
||||
return
|
||||
end
|
||||
|
||||
shift = squeeze(Ggather(cat(4,dx, dy)));
|
||||
|
||||
% modified by YJ. allow user to spcify maximum position update
|
||||
max_shift = min(par.max_pos_update_shift, 10*mad(shift)); %why a factor of 10??
|
||||
|
||||
% prevent outliers and too rapid shifts
|
||||
%max_shift = min(0.1, 10*mad(shift));
|
||||
shift = min(abs(shift), max_shift) .* sign(shift); % avoid too fast jumps, <0.5px/iter is enough
|
||||
%old code
|
||||
%shift = min(abs(shift), 0.2) .* sign(shift); % avoid too fast jumps, <0.5px/iter is enough
|
||||
|
||||
pos_update = reshape(shift,[],2);
|
||||
|
||||
if ~isfield(cache, 'velocity_map_positions')
|
||||
cache.velocity_map_positions = zeros(self.Npos,2,'single');
|
||||
end
|
||||
if ~isfield(cache, 'position_update_memory')
|
||||
cache.position_update_memory = {};
|
||||
end
|
||||
|
||||
cache.position_update_memory{iter}(ind,:) = pos_update;
|
||||
|
||||
%% USE MOMENTUM ACCELERATION TO MAKE THE CONVERGENCE FASTER
|
||||
ACC = 0;
|
||||
if par.probe_position_search_momentum >0
|
||||
momentum_memory = par.probe_position_search_momentum; %
|
||||
|
||||
% only in case far field ptychography
|
||||
if isinf(self.z_distance) && sum(cellfun(@length, cache.position_update_memory) > 0) > momentum_memory
|
||||
%corr_level = zeros(momentum_memory,1);
|
||||
for ii = 1:momentum_memory
|
||||
corr_level(ii) = mean(diag(corr(cache.position_update_memory{end}(ind,:), cache.position_update_memory{end-ii}(ind,:))));
|
||||
end
|
||||
if all(corr_level > 0 )
|
||||
%estimate optimal friction from previous steps
|
||||
poly_fit = polyfit(0:momentum_memory,log([1,corr_level]),1);
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
gain = 0.5; % smaller -> lower relative speed (less momentum)
|
||||
friction = 0.1*max(-poly_fit(1),0); % smaller -> longer memory, more momentum
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
else
|
||||
gain = 0; friction = 0.5;
|
||||
end
|
||||
|
||||
cache.velocity_map_positions(ind,:) = cache.velocity_map_positions(ind,:)*(1-friction) + pos_update;
|
||||
% apply the velocity to the refined positions , if the postition updated are sufficiently small
|
||||
|
||||
if max(abs(pos_update)) < 0.1
|
||||
ACC = norm2(pos_update + gain*cache.velocity_map_positions(ind,:)) / norm2(pos_update);
|
||||
pos_update = pos_update + gain*cache.velocity_map_positions(ind,:);
|
||||
end
|
||||
end
|
||||
end
|
||||
% try
|
||||
%ACC = 0;
|
||||
% momentum_memory = 5; % remember 5 iterations
|
||||
%
|
||||
% % only in case far field ptychography
|
||||
% if isinf(self.z_distance) && sum(cellfun(@length, cache.position_update_memory) > 0) > momentum_memory
|
||||
% for ii = 1:momentum_memory
|
||||
% corr_level(ii) = mean(diag(corr(cache.position_update_memory{end}(ind,:), cache.position_update_memory{end-ii}(ind,:))));
|
||||
% end
|
||||
% if all(corr_level > 0 )
|
||||
% %estimate optimal friction from previous steps
|
||||
% poly_fit = polyfit(0:momentum_memory,log([1,corr_level]),1);
|
||||
%
|
||||
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% gain = 0.5; % smaller -> lower relative speed (less momentum)
|
||||
% friction = 0.1*max(-poly_fit(1),0); % smaller -> longer memory, more momentum
|
||||
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% else
|
||||
% gain = 0; friction = 0.5;
|
||||
% end
|
||||
%
|
||||
% cache.velocity_map_positions(ind,:) = cache.velocity_map_positions(ind,:)*(1-friction) + pos_update;
|
||||
% % apply the velocity to the refined positions , if the postition updated are sufficiently small
|
||||
%
|
||||
% if max(abs(pos_update)) < 0.1
|
||||
% ACC = norm2(pos_update + gain*cache.velocity_map_positions(ind,:)) / norm2(pos_update);
|
||||
% pos_update = pos_update + gain*cache.velocity_map_positions(ind,:);
|
||||
% end
|
||||
%
|
||||
% end
|
||||
% catch
|
||||
% keyboard
|
||||
% end
|
||||
if any(ind==1)
|
||||
verbose(1,'Grad pos corr -- AVG step %3.3g px , acceleration = %4.1f', max(abs(pos_update(:))), ACC)
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
function [nom1, denom1, nom2, denom2] = get_coefs_shift(xi, P, dx_O, dy_O)
|
||||
|
||||
dx_OP = dx_O.*P;
|
||||
nom1 = real(conj(dx_OP) .* xi);
|
||||
denom1 = abs(dx_OP).^2;
|
||||
|
||||
dy_OP = dy_O.*P;
|
||||
nom2 = real(conj(dy_OP) .* xi);
|
||||
denom2 = abs(dy_OP).^2;
|
||||
|
||||
end
|
||||
|
||||
|
||||
function [nom, denom] = get_coefs_mixed(xi, P, dx_O, dy_O, xgrid, ygrid)
|
||||
|
||||
dm_O = dx_O .* xgrid + dy_O .* ygrid;
|
||||
|
||||
dm_OP = dm_O.*P;
|
||||
nom = real(conj(dm_OP) .* xi);
|
||||
denom = abs(dm_OP).^2;
|
||||
|
||||
end
|
||||
@@ -0,0 +1,153 @@
|
||||
% GRADIENT_PROJECTION_SOLVER: 1D search for the optimal step in the gradients descent-like methods
|
||||
% used in ML and PIE functions
|
||||
%
|
||||
% [beta_p, beta_o] = gradient_projection_solver(self,xi,O,P,dO,dP,p_ind,par, cache)
|
||||
%
|
||||
%
|
||||
% ** self structure containing inputs: e.g. current reconstruction results, data, mask, positions, pixel size, ..
|
||||
% ** chi [Nx,Ny,N] array, difference between original and updated exit-wave
|
||||
% ** dO [Nx,Ny,N] array, object update direction
|
||||
% ** dP [Nx,Ny,N] array, probe update direction
|
||||
% ** O [Nx,Ny,N] array, object views
|
||||
% ** P [Nx,Ny,1] or [Nx,Ny,N] array, single or variable probe
|
||||
% ** p_ind indices containg corresponding probe id for each processed position
|
||||
% ** par structure containing parameters for the engines
|
||||
% ** cache precalculated values
|
||||
%
|
||||
% returns:
|
||||
% ++ beta_p optimal probe step
|
||||
% ++ beta_o optimal object step
|
||||
%
|
||||
% see also: engines.GPU_MS.LSQML, engines.GPU_MS.PIE
|
||||
|
||||
|
||||
|
||||
% Academic License Agreement
|
||||
%
|
||||
% Source Code
|
||||
%
|
||||
% Introduction
|
||||
% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
|
||||
% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
|
||||
% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
|
||||
%
|
||||
% Terms and Conditions of the LICENSE
|
||||
% 1. LICENSOR grants to LICENSEE a royalty-free, non-exclusive license to use the PROGRAM for academic, non-commercial purposes, upon the terms and conditions
|
||||
% hereinafter set out and until termination of this license as set forth below.
|
||||
% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
|
||||
% or warranties from LICENSOR and that the LICENSE is entered into in order to enable others to utilize the PROGRAM in their academic activities. It is the
|
||||
% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
|
||||
% 3. THE PROGRAM IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR
|
||||
% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
|
||||
% HOLDERS BE LIABLE FOR ANY CLAIM, DIRECT, INDIRECT OR CONSEQUENTIAL DAMAGES OR OTHER LIABILITY ARISING FROM, OUT OF OR IN CONNECTION WITH THE PROGRAM OR THE USE
|
||||
% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
|
||||
% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
|
||||
% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
|
||||
% license as PROGRAM. The terms "academic, non-commercial", as used in this Agreement, mean academic or other scholarly research which (a) is not undertaken for
|
||||
% profit, or (b) is not intended to produce works, services, or data for commercial use, or (c) is neither conducted, nor funded, by a person or an entity engaged
|
||||
% in the commercial use, application or exploitation of works similar to the PROGRAM.
|
||||
% 5. LICENSEE agrees that it shall make the following acknowledgement in any publication resulting from the use of the PROGRAM or any translation of the code into
|
||||
% another computing language:
|
||||
% "Data processing was carried out using the cSAXS ptychography MATLAB package developed by the Science IT and the coherent X-ray scattering (CXS) groups, Paul
|
||||
% Scherrer Institut, Switzerland."
|
||||
%
|
||||
% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
|
||||
% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
|
||||
% (doi: 10.1126/science.1158573),
|
||||
% for mixed coherent modes:
|
||||
% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
|
||||
% for LSQ-ML method
|
||||
% M. Odstrcil, A. Menzel, M.G. Sicairos, Iterative least-squares solver for generalized maximum-likelihood ptychography, Optics Express, 2018
|
||||
% for OPRP method
|
||||
% M. Odstrcil, P. Baksh, S. A. Boden, R. Card, J. E. Chad, J. G. Frey, W. S. Brocklesby, "Ptychographic coherent diffractive imaging with orthogonal probe relaxation." Optics express 24.8 (2016): 8360-8369
|
||||
% and/or for multislice:
|
||||
% E. H. R. Tsai, I. Usov, A. Diaz, A. Menzel, and M. Guizar-Sicairos, X-ray ptychography with extended depth of field, Opt. Express 24, 29089–29108 (2016).
|
||||
% 6. Except for the above-mentioned acknowledgment, LICENSEE shall not use the PROGRAM title or the names or logos of LICENSOR, nor any adaptation thereof, nor the
|
||||
% names of any of its employees or laboratories, in any advertising, promotional or sales material without prior written consent obtained from LICENSOR in each case.
|
||||
% 7. Ownership of all rights, including copyright in the PROGRAM and in any material associated therewith, shall at all times remain with LICENSOR, and LICENSEE
|
||||
% agrees to preserve same. LICENSEE agrees not to use any portion of the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the PROGRAM, nor to
|
||||
% make any copies except for its internal use, without prior written consent of LICENSOR. LICENSEE agrees to place the following copyright notice on any such copies:
|
||||
% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
|
||||
% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
|
||||
% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
|
||||
% to ptychography and that the PROGRAM may be capable of being used in circumstances which may fall within the claims of one or more of the Phase Focus patents,
|
||||
% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
|
||||
% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
|
||||
% 10. This Agreement shall be governed by the material laws of Switzerland and any dispute arising out of this Agreement or use of the PROGRAM shall be brought before
|
||||
% the courts of Zürich, Switzerland.
|
||||
%
|
||||
%
|
||||
|
||||
|
||||
|
||||
function [beta_p, beta_o] = gradient_projection_solver(self,xi,O,P,dO,dP,p_ind,par, cache)
|
||||
import engines.GPU_MS.GPU_wrapper.*
|
||||
|
||||
import utils.*
|
||||
import math.*
|
||||
|
||||
%% initial setting
|
||||
beta_o = 0;
|
||||
beta_p = 0;
|
||||
|
||||
find_object_step = numel(dO) > 1;
|
||||
find_probe_step = numel(dP) > 1;
|
||||
|
||||
if ~( par.share_probe || length(unique(p_ind)) == 1 ) && find_probe_step
|
||||
% in case of multiple scans !!
|
||||
% replicate the update back to the original probe_update size
|
||||
dP = dP(:,:,p_ind);
|
||||
end
|
||||
|
||||
dP = mean(dP,3);
|
||||
% !! reusing dP,dO variables to same GPU memory
|
||||
if find_probe_step && find_object_step
|
||||
[dP, denom_p, dO, denom_o] = Gfun(@get_coefs,xi, P,O, dP, dO);
|
||||
elseif find_probe_step
|
||||
[dP, denom_p] = Gfun(@get_coef,xi, O, dP);
|
||||
elseif find_object_step
|
||||
[dO, denom_o] = Gfun(@get_coef,xi, P, dO);
|
||||
end
|
||||
|
||||
if find_probe_step
|
||||
beta_p = sum2(dP)./ sum2(denom_p) ; % half of the corrections goes to probe , half to object
|
||||
end
|
||||
if find_object_step
|
||||
beta_o = sum2(dO)./ sum2(denom_o) ; % half of the corrections goes to probe , half to object
|
||||
end
|
||||
|
||||
%% allow matlab GPU paralelization to process the sums while positions corrections are calculated
|
||||
beta_p = Ggather(beta_p).*par.beta_LSQ * par.beta_probe ;
|
||||
beta_o = Ggather(beta_o).*par.beta_LSQ * par.beta_object;
|
||||
|
||||
beta_o(isnan(beta_o)) = 0;
|
||||
beta_p(isnan(beta_p)) = 0;
|
||||
if any(isnan(beta_o)) || any(isnan(beta_p))
|
||||
%keyboard
|
||||
error('Convergence failed')
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
function [nom1, denom1, nom2, denom2] = get_coefs(xi, P,O, dP, dO)
|
||||
% projection of dPO in direction of xi, to avoid issues caused by
|
||||
% correlation between dPO and dOP, the step is divided by 2
|
||||
|
||||
dPO = dP.*O;
|
||||
nom1 = 0.5* real(conj(dPO) .* xi);
|
||||
denom1 = abs(dPO).^2;
|
||||
|
||||
PdO = P.*dO;
|
||||
nom2 = 0.5* real(conj(PdO) .* xi);
|
||||
denom2 = abs(PdO).^2;
|
||||
|
||||
end
|
||||
|
||||
function [nom1, denom1] = get_coef(xi, X, dX)
|
||||
|
||||
XdX = X.*dX;
|
||||
nom1 = 0.5*real(conj(XdX) .* xi);
|
||||
denom1 = abs(XdX).^2;
|
||||
|
||||
end
|
||||
|
||||
@@ -0,0 +1,67 @@
|
||||
% function f = local_TV2D_chambolle(f, lambda, niter)
|
||||
% apply local total variation usiniter matlab functions, it uses chambolle
|
||||
% solver -> faster but more memory demanding
|
||||
% Inputs: x - 2D array to be regularized
|
||||
% lambda - constant to be tuned
|
||||
% niter - number of iterations
|
||||
% Modified from PSI's tomo code. Written by Jonathan Schwartz at U. Mich
|
||||
|
||||
function x = local_TV2D_chambolle(x,lambda, niter)
|
||||
[M,N] = size(x);
|
||||
|
||||
if lambda == 0
|
||||
return
|
||||
end
|
||||
|
||||
x0 = x;
|
||||
|
||||
xi = zeros(M,N,2, class(x));
|
||||
tau=1/8;
|
||||
|
||||
%%% INNER LOOP
|
||||
for iinner = 1:niter
|
||||
% chambolle step
|
||||
gdv = grad( div(xi) - x/lambda );
|
||||
|
||||
%% isotropic
|
||||
d = sqrt(sum(gdv.^2,3));
|
||||
|
||||
xi = bsxfun(@times, xi + tau*gdv, 1 ./ ( 1+tau*d ));
|
||||
|
||||
% reconstruct
|
||||
x = x - lambda*div( xi );
|
||||
|
||||
end
|
||||
|
||||
% prevent pushing values to zero by the TV regularization
|
||||
x = sum(x0(:).* x(:)) / sum(x(:).^2) * x;
|
||||
|
||||
end
|
||||
|
||||
function fd = div(P)
|
||||
|
||||
% div - divergence (backward difference)
|
||||
%
|
||||
% fd = div(P);
|
||||
|
||||
Px = P(:,:,1);
|
||||
Py = P(:,:,2);
|
||||
|
||||
fx = Px-Px([1 1:end-1],:);
|
||||
fy = Py-Py(:,[1 1:end-1]);
|
||||
|
||||
fd = fx+fy;
|
||||
|
||||
end
|
||||
|
||||
function f = grad(M)
|
||||
|
||||
% grad - gradient, forward differences
|
||||
% g = grad(M);
|
||||
|
||||
fx = M([2:end end],:)-M;
|
||||
fy = M(:,[2:end end])-M;
|
||||
|
||||
f = cat(3,fx,fy);
|
||||
|
||||
end
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user