mirror of
https://github.com/c-sooyoung/fold_slice.git
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initial commit
This commit is contained in:
@@ -0,0 +1,147 @@
|
||||
% function convert(scan, raw_data_path)
|
||||
% convert .raw files to .cbf
|
||||
|
||||
% 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 convert(scan, raw_data_path)
|
||||
|
||||
cbf_maker_path = '/sls/X12SA/data/x12saop/EigerPackage/slsDetectorsPackage/bin/cbfMaker1.5MOMNY';
|
||||
load_dir = utils.compile_x12sa_dirname(scan);
|
||||
if exist(['~/Data10/eiger_4/'])
|
||||
load_dir = ['~/Data10/eiger_4/' load_dir];
|
||||
elseif exist([raw_data_path,'eiger_4/'])
|
||||
load_dir = [raw_data_path,'/eiger_4/' load_dir];
|
||||
elseif exist([raw_data_path,'/eigeromny/'])
|
||||
load_dir = [raw_data_path,'/eigeromny/' load_dir];
|
||||
end
|
||||
|
||||
if ~exist(load_dir, 'dir')
|
||||
return
|
||||
end
|
||||
|
||||
testDir = [load_dir, '/deleteMe'];
|
||||
% test for write permissions by creating a folder and then deleting it
|
||||
isWritable = mkdir(testDir);
|
||||
% check if directory creation was successful
|
||||
if isWritable == 1
|
||||
rmdir(fullfile(testDir));
|
||||
end
|
||||
|
||||
list_cbf = dir([load_dir, '/run_*.cbf']);
|
||||
|
||||
|
||||
file_sizes = [list_cbf.bytes];
|
||||
if any(file_sizes < 1e6) % find files < 1MB
|
||||
warning('CBF files in scan %i seems damaged, generate again ... ', scan)
|
||||
list_raw = dir([load_dir, '/run_d0_f0000000*.raw']);
|
||||
if isempty(list_raw)
|
||||
error('RAW data are missing, data cannot be converted')
|
||||
else
|
||||
delete(sprintf('%s/*.cbf',load_dir))
|
||||
end
|
||||
list_cbf = dir([load_dir, '/run_*.cbf']);
|
||||
end
|
||||
if isempty(list_cbf)
|
||||
|
||||
if ~isWritable
|
||||
warning('Conversion failed because folder %s is not writable', load_dir)
|
||||
return
|
||||
end
|
||||
|
||||
list_raw = dir([load_dir, '/run_d0_f0000000*.raw']);
|
||||
|
||||
Nscans = length(list_raw);
|
||||
for ii = 1:Nscans
|
||||
ind_scans(ii) = str2num(list_raw(ii).name(16:17));
|
||||
end
|
||||
|
||||
% if Nscans > 1
|
||||
% parfor (ii = 1:Nscans, Nscans)
|
||||
% [~,out] = system(sprintf('%s %s/run_d0_f00000000%02i000_%05i.cbf',cbf_maker_path, load_dir, ind_scans(ii) ,scan));
|
||||
% end
|
||||
% else
|
||||
for ii = 1:Nscans
|
||||
[~,out] = system(sprintf('%s %s/run_d0_f00000000%02i000_%05i.raw',cbf_maker_path, load_dir, ind_scans(ii) ,scan));
|
||||
end
|
||||
% end
|
||||
list_cbf = dir([load_dir, '/*.cbf']);
|
||||
nframes_converted = length(list_cbf);
|
||||
out = splitlines(out);
|
||||
nframes_expected = str2num(out{end-2}(14:end));
|
||||
fprintf('Frames expected: %i, frames converted %i \n', nframes_expected, nframes_converted)
|
||||
if nframes_converted == nframes_expected
|
||||
% for ii=1:nframes_expected
|
||||
% thisfile = fullfile(load_dir,list_cbf(ii).name);
|
||||
% dataaux = io.image_read(thisfile,'RowFrom',1,'RowTo',2,'ColumnFrom',1,'ColumnTo',2);
|
||||
% data(:,:,ii) = dataaux.data(:,:,1);
|
||||
% end
|
||||
fprintf('Scan %i succefully converted to CBF\n', scan);
|
||||
delete(sprintf('%s/*.raw',load_dir))
|
||||
|
||||
else
|
||||
error('Scan %i WAS NOT CONVERTED to CBF\n', scan)
|
||||
delete(sprintf('%s/*.cbf',load_dir))
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
end
|
||||
@@ -0,0 +1,150 @@
|
||||
% function convert(scan, raw_data_path)
|
||||
% convert .raw files to .hdf5
|
||||
% Inputs
|
||||
% scan scan number
|
||||
% raw_data_path path to the raw data (optional)
|
||||
|
||||
% 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 convert2hdf5(scan, raw_data_path)
|
||||
|
||||
convertor_path = '/sls/X12SA/data/x12saop/EigerPackage/slsDetectorsPackage/bin/hdf5MakerOMNY';
|
||||
load_dir = utils.compile_x12sa_dirname(scan);
|
||||
if exist('raw_data_path','var')&&exist(fullfile(raw_data_path,load_dir),'dir')
|
||||
load_dir = fullfile(raw_data_path,load_dir);
|
||||
elseif exist(['~/Data10/eiger_4/'],'dir')
|
||||
load_dir = ['~/Data10/eiger_4/' load_dir];
|
||||
elseif exist([raw_data_path,'eiger_4/'])
|
||||
load_dir = [raw_data_path,'/eiger_4/' load_dir];
|
||||
elseif exist([raw_data_path,'/eigeromny/'])
|
||||
load_dir = [raw_data_path,'/eigeromny/' load_dir];
|
||||
end
|
||||
|
||||
if ~exist(load_dir, 'dir')
|
||||
warning('Raw data path %s not found', load_dir)
|
||||
return
|
||||
end
|
||||
|
||||
testDir = [load_dir, '/deleteMe'];
|
||||
% test for write permissions by creating a folder and then deleting it
|
||||
isWritable = mkdir(testDir);
|
||||
% check if directory creation was successful
|
||||
if isWritable == 1
|
||||
rmdir(fullfile(testDir));
|
||||
end
|
||||
|
||||
list_h5 = dir([load_dir, '/run_*.h5']);
|
||||
|
||||
|
||||
file_sizes = [list_h5.bytes];
|
||||
if any(file_sizes < 1e6) % find files < 1MB
|
||||
warning('H5 files in scan %i seem damaged, generate again ... ', scan)
|
||||
list_raw = dir([load_dir, '/run_d0_f0000000*.raw']);
|
||||
if isempty(list_raw)
|
||||
error('RAW data are missing, data cannot be converted')
|
||||
else
|
||||
delete(sprintf('%s/*.h5',load_dir))
|
||||
end
|
||||
list_h5 = dir([load_dir, '/run_*.h5']);
|
||||
end
|
||||
|
||||
if isempty(list_h5)
|
||||
if ~isWritable
|
||||
warning('Conversion failed because folder %s is not writable', load_dir)
|
||||
return
|
||||
end
|
||||
|
||||
list_raw = dir(fullfile(load_dir, 'run_d0_f0000000*.raw'));
|
||||
|
||||
Nscans = length(list_raw);
|
||||
|
||||
for ii = 1:Nscans
|
||||
ind_scans(ii) = str2num(list_raw(ii).name(16:17));
|
||||
end
|
||||
|
||||
for ii = 1:Nscans
|
||||
% [~,out] = system([cbf_maker_path ' ' fullfile(load_dir,sprintf('run_d0_f00000000%02i000_%i.raw',ind_scans(ii) ,scan))]);
|
||||
systemcall = [convertor_path ' ' fullfile(list_raw(1).folder,list_raw(1).name)];
|
||||
fprintf('%s\n',systemcall);
|
||||
[~,out] = system(systemcall);
|
||||
out
|
||||
end
|
||||
|
||||
list_h5 = dir([load_dir, '/*.h5']);
|
||||
if isempty(list_h5)
|
||||
error(sprintf('After conversion did not find any h5 in %s\n',load_dir))
|
||||
return
|
||||
end
|
||||
if numel(list_h5)>1
|
||||
error(sprintf('After conversion I found more than one h5 in %s\n',load_dir))
|
||||
return
|
||||
end
|
||||
|
||||
h5fileinfo = h5info(fullfile(list_h5.folder,list_h5.name));
|
||||
|
||||
nframes_converted = h5fileinfo.Groups.Groups(1).Datasets.Dataspace.Size(3);
|
||||
out = splitlines(out);
|
||||
nframes_expected = str2num(out{end-2}(14:end));
|
||||
fprintf('Frames expected: %i, frames converted %i \n', nframes_expected, nframes_converted)
|
||||
if nframes_converted == nframes_expected
|
||||
fprintf('Scan %i succefully converted to H5\n', scan);
|
||||
delete(sprintf('%s/*.raw',load_dir))
|
||||
else
|
||||
error('Scan %i WAS NOT CONVERTED to H5\n', scan)
|
||||
delete(sprintf('%s/*.h5',load_dir))
|
||||
end
|
||||
end
|
||||
end
|
||||
@@ -0,0 +1,146 @@
|
||||
%EIGER1P5M settings for Eiger 1.5M detector
|
||||
% This file is called if you specify p.detector = 'eiger1p5M'
|
||||
%
|
||||
% ** p p structure
|
||||
% returns:
|
||||
% ++ det detector structure; later accessible via p.detectors(ii).params
|
||||
%
|
||||
% see also: detector.load_detector
|
||||
|
||||
|
||||
% 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 [ det ] = eiger1p5M( p )
|
||||
|
||||
local_path = fileparts(mfilename('fullpath'));
|
||||
|
||||
|
||||
%% parameter
|
||||
det.pixel_size = 75e-6; % detector pixel size
|
||||
det.file_extension = 'h5'; % raw data file extension
|
||||
det.mask = [local_path, '/eiger1p5m_mask.mat']; % detector mask
|
||||
if exist(fullfile(p.raw_data_path{1}, 'eiger_4'))
|
||||
det.basepath_dir = 'eiger_4/'; % raw data directory
|
||||
else
|
||||
det.basepath_dir = 'eigeromny/'; % raw data directory, legacy, remove in future
|
||||
end
|
||||
det.mask_saturated_value = []; % mask pixels above given value
|
||||
det.mask_below_value = []; % mask pixels below given value
|
||||
det.data_stored = true; % false == data are generated "onfly", no need to load / store
|
||||
det.detposmotor = 'dettr'; % name of spec motor used for checking detector position
|
||||
det.geometry.sz = [1030 1614]; % detector readout size
|
||||
det.geometry.mask = []; % if the mask is larger than the readout
|
||||
% geometry (det.geometry.sz), geometry.mask defines the readout for the mask
|
||||
% e.g. geometry.mask = {[50:500], [50:500]}
|
||||
|
||||
|
||||
% det.orientation = [0 0 1]; % [<Transpose> <FlipLR> <FlipUD>]
|
||||
% changed from 30/08/2018
|
||||
det.orientation = [1 0 0]; % [<Transpose> <FlipLR> <FlipUD>]
|
||||
|
||||
|
||||
% additional arguments for image_read
|
||||
if strcmpi(det.file_extension, 'h5')
|
||||
det.image_read_extraargs = {'H5Location', '/entry/instrument/eiger_4/data/'};
|
||||
else
|
||||
det.image_read_extraargs = {};
|
||||
end
|
||||
|
||||
%% define directory tree structure
|
||||
% define a function handle for compiling the scan directory tree. Input
|
||||
% should be the scan number.
|
||||
det.read_path = @utils.compile_x12sa_dirname;
|
||||
|
||||
%% filename
|
||||
% specify funcion for compiling the filename. Input and output should be p and a
|
||||
% temporary structure, containing information about the currently prepared scan.
|
||||
% Cf. '+scans/get_filenames_cSAXS.m'
|
||||
|
||||
det.get_filename = @scans.get_filenames_cSAXS;
|
||||
|
||||
% additional parameters for the filename function (det.get_filename)
|
||||
% define filename pattern
|
||||
% det.read_path_format = '%05d/';
|
||||
% det.filename_pattern{1}.str = '%05d';
|
||||
% det.filename_pattern{1}.del = '_';
|
||||
% det.filename_pattern{1}.content = 'scan';
|
||||
% det.filename_pattern{1}.start = 1;
|
||||
% det.filename_pattern{2}.str = '%05d';
|
||||
% det.filename_pattern{2}.del = '.';
|
||||
% det.filename_pattern{2}.content = 'pos';
|
||||
% det.filename_pattern{2}.start = 1;
|
||||
%
|
||||
% det.data_prefix = 'run_';
|
||||
|
||||
|
||||
% for scan = p.scan_number
|
||||
% % if ~isempty(dir(fullfile(p.raw_data_path{1}, 'eiger_4', utils.compile_x12sa_dirname(scan), '*.cbf')))
|
||||
% % det.file_extension = 'cbf';
|
||||
% % end
|
||||
% %%%% convert data from raw to cbf or hdf5
|
||||
% switch det.file_extension
|
||||
% case 'cbf'
|
||||
% detector.eiger1p5M.convert(scan, p.raw_data_path{1});
|
||||
% case 'h5'
|
||||
% detector.eiger1p5M.convert2hdf5(scan, p.raw_data_path{1});
|
||||
% otherwise
|
||||
% error('Unknown file extension for Eiger 1.5M.')
|
||||
% end
|
||||
%
|
||||
% end
|
||||
|
||||
|
||||
end
|
||||
|
||||
Reference in New Issue
Block a user