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228 lines
12 KiB
Matlab
228 lines
12 KiB
Matlab
%GET_FILENAMES_CSAXS compile filenames of raw data files
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% receives
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% Academic License Agreement
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%
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% Source Code
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%
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% Introduction
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% • This license agreement sets forth the terms and conditions under which the PAUL SCHERRER INSTITUT (PSI), CH-5232 Villigen-PSI, Switzerland (hereafter "LICENSOR")
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% will grant you (hereafter "LICENSEE") a royalty-free, non-exclusive license for academic, non-commercial purposes only (hereafter "LICENSE") to use the cSAXS
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% ptychography MATLAB package computer software program and associated documentation furnished hereunder (hereafter "PROGRAM").
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%
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% Terms and Conditions of the LICENSE
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% 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
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% hereinafter set out and until termination of this license as set forth below.
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% 2. LICENSEE acknowledges that the PROGRAM is a research tool still in the development stage. The PROGRAM is provided without any related services, improvements
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% 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
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% LICENSEE’s responsibility to ensure its proper use and the correctness of the results.”
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% 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
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% A PARTICULAR PURPOSE AND NONINFRINGEMENT OF ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. IN NO EVENT SHALL THE LICENSOR, THE AUTHORS OR THE COPYRIGHT
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% 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
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% OF THE PROGRAM OR OTHER DEALINGS IN THE PROGRAM.
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% 4. LICENSEE agrees that it will use the PROGRAM and any modifications, improvements, or derivatives of PROGRAM that LICENSEE may create (collectively,
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% "IMPROVEMENTS") solely for academic, non-commercial purposes and that any copy of PROGRAM or derivatives thereof shall be distributed only under the same
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% 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
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% 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
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% in the commercial use, application or exploitation of works similar to the PROGRAM.
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% 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
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% another computing language:
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% "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
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% Scherrer Institut, Switzerland."
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%
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% Additionally, any publication using the package, or any translation of the code into another computing language should cite for difference map:
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% P. Thibault, M. Dierolf, A. Menzel, O. Bunk, C. David, F. Pfeiffer, High-resolution scanning X-ray diffraction microscopy, Science 321, 379–382 (2008).
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% (doi: 10.1126/science.1158573),
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% for maximum likelihood:
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% P. Thibault and M. Guizar-Sicairos, Maximum-likelihood refinement for coherent diffractive imaging, New J. Phys. 14, 063004 (2012).
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% (doi: 10.1088/1367-2630/14/6/063004),
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% for mixed coherent modes:
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% P. Thibault and A. Menzel, Reconstructing state mixtures from diffraction measurements, Nature 494, 68–71 (2013). (doi: 10.1038/nature11806),
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% and/or for multislice:
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% 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).
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% (doi: 10.1364/OE.24.029089).
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% 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
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% 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.
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% 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
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% 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
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% 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:
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% © All rights reserved. PAUL SCHERRER INSTITUT, Switzerland, Laboratory for Macromolecules and Bioimaging, 2017.
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% 8. The LICENSE shall not be construed to confer any rights upon LICENSEE by implication or otherwise except as specifically set forth herein.
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% 9. DISCLAIMER: LICENSEE shall be aware that Phase Focus Limited of Sheffield, UK has an international portfolio of patents and pending applications which relate
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% 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,
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% in particular of patent with international application number PCT/GB2005/001464. The LICENSOR explicitly declares not to indemnify the users of the software
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% in case Phase Focus or any other third party will open a legal action against the LICENSEE due to the use of the program.
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% 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
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% the courts of Zürich, Switzerland.
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function [p] = get_filenames_cSAXS(p)
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import utils.*
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% get detector paramters
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det = p.detectors(p.scanID).params;
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read_path = p.raw_data_path_full{p.scanID};
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detStorage = p.detectors(p.scanID).detStorage;
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if isfield(det, 'filename_pattern')
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if iscell(det.filename_pattern)
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%% if filename patterns exist, use them to restrict the file search
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det.filename_pattern_full = [p.detector.data_prefix];
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fill = [];
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for ii=1:size(det.filename_pattern,2)
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fill = [fill det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
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det.filename_pattern_full = [det.filename_pattern_full det.filename_pattern{ii}.str det.filename_pattern{ii}.del];
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del{ii} = det.filename_pattern{ii}.del;
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switch det.filename_pattern{ii}.content
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case 'burst'
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burst = ii;
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case 'scan'
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scan = ii;
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case 'pos'
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pos = ii;
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end
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end
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det.filename_pattern_full = [det.filename_pattern_full det.file_extension];
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if exist('burst', 'var')
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det.filename_pattern_burst = [p.detector.data_prefix];
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parts = strsplit(fill, del);
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parts{burst} = '*';
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det.filename_pattern_burst = [det.filename_pattern_burst strjoin(parts, del) det.file_extension];
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end
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if exist('pos', 'var')
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det.filename_pattern_pos = [p.detector.data_prefix];
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parts = strsplit(fill, del);
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parts{pos} = '*';
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det.filename_pattern_pos = [det.filename_pattern_pos strjoin(parts, del) det.file_extension];
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end
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if exist('scan', 'var')
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det.filename_pattern_scan = [p.detector.data_prefix];
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parts = strsplit(fill, del);
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if exist('burst', 'var')
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parts{burst} = '*';
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end
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if exist('pos', 'var')
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parts{pos} = '*';
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end
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det.filename_pattern_scan = [det.filename_pattern_scan strjoin(parts, del) det.file_extension];
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end
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input_vars = {};
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if isfield(det, 'filename_pattern_pos')
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k = 1;
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for jj=1:length(det.filename_pattern)
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switch det.filename_pattern{jj}.content
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case 'pos'
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continue
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case 'burst'
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input_vars{k} = det.filename_pattern{jj}.start;
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case 'scan'
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input_vars{k} = p.scan_number(p.scanID);
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end
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k = k+1;
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end
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filename_pattern_pos = fullfile(read_path, det.filename_pattern_pos);
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filename_pos = sprintf(filename_pattern_pos, input_vars{:});
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[~, pos_files] = find_files(filename_pos);
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numpos = size(pos_files,2);
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% apply natural sorting order i.e. sort 1,2,3,10,200 and not 1 10 100 2 20 200
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% important if the file makes are not defined as S%05i but rather S%i
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[~,idx] = natsort({pos_files.name});
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pos_files = pos_files(idx);
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end
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if isfield(det, 'filename_pattern_burst')
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k = 1;
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for jj=1:length(det.filename_pattern)
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switch det.filename_pattern{jj}.content
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case 'pos'
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input_vars{k} = det.filename_pattern{jj}.start;
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case 'burst'
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continue
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case 'scan'
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input_vars{k} = p.scan_number(p.scanID);
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end
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k = k+1;
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end
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filename_pattern_burst = fullfile(read_path, det.filename_pattern_burst);
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filename_burst = sprintf(filename_pattern_burst, input_vars{:});
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[~, burst_files] = find_files(filename_burst);
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numburst = size(burst_files,2);
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else
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numburst = 1;
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end
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if numburst > 1
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% if burst frames exist, we need to make sure that the file order is correct
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file_args = '[';
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for ii=1:length(det.filename_pattern)
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switch ii
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case burst
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file_args = [file_args ' det.filename_pattern{ii}.start + burstID-1'];
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case pos
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file_args = [file_args ' det.filename_pattern{ii}.start + posID-1'];
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case scan
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file_args = [file_args ' p.scan_number(p.scanID)'];
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end
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end
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file_args = [file_args ']'];
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for posID=1:numpos
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for burstID=1:numburst
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files(burstID+(posID-1)*numburst).name = sprintf(det.filename_pattern_full, eval(file_args));
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end
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end
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datadir = read_path;
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else
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% if there are no burst frames, use the pos files
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datadir = read_path;
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files = pos_files;
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end
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if numel(files)==0
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error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
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end
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else
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% use wildcards
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files = find_files(fullfile(read_path, [det.filename_pattern det.file_extension]));
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if numel(files)==0
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error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%')))
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end
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end
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else
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% if no filename pattern was specified, just load everything containing the specified file extension
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[datadir, files] = find_files([read_path '*.' det.file_extension]);
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if numel(files)==0
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error('Could not find any files using the filename pattern %s.\n ', fullfile(read_path, ['*.' det.file_extension]))
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end
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end
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detStorage.files = [];
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for ii=1:length(files)
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detStorage.files{ii} = fullfile(datadir, files(ii).name);
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end
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for ii=1:length(det.image_read_extraargs)
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if strcmpi(det.image_read_extraargs{ii}, 'H5Location')
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detStorage.h5_group{1} = det.image_read_extraargs{ii+1};
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break;
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end
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end
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end
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