mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 23:39:08 +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 +1,147 @@
|
||||
% 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.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.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.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
|
||||
Reference in New Issue
Block a user