%GET_FILENAMES_CSAXS compile filenames of raw data files % receives % 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 [p] = get_filenames_cSAXS(p) import utils.* % get detector paramters det = p.detectors(p.scanID).params; read_path = p.raw_data_path_full{p.scanID}; detStorage = p.detectors(p.scanID).detStorage; if isfield(det, 'filename_pattern') if iscell(det.filename_pattern) %% if filename patterns exist, use them to restrict the file search det.filename_pattern_full = [p.detector.data_prefix]; fill = []; for ii=1:size(det.filename_pattern,2) fill = [fill det.filename_pattern{ii}.str det.filename_pattern{ii}.del]; det.filename_pattern_full = [det.filename_pattern_full det.filename_pattern{ii}.str det.filename_pattern{ii}.del]; del{ii} = det.filename_pattern{ii}.del; switch det.filename_pattern{ii}.content case 'burst' burst = ii; case 'scan' scan = ii; case 'pos' pos = ii; end end det.filename_pattern_full = [det.filename_pattern_full det.file_extension]; if exist('burst', 'var') det.filename_pattern_burst = [p.detector.data_prefix]; parts = strsplit(fill, del); parts{burst} = '*'; det.filename_pattern_burst = [det.filename_pattern_burst strjoin(parts, del) det.file_extension]; end if exist('pos', 'var') det.filename_pattern_pos = [p.detector.data_prefix]; parts = strsplit(fill, del); parts{pos} = '*'; det.filename_pattern_pos = [det.filename_pattern_pos strjoin(parts, del) det.file_extension]; end if exist('scan', 'var') det.filename_pattern_scan = [p.detector.data_prefix]; parts = strsplit(fill, del); if exist('burst', 'var') parts{burst} = '*'; end if exist('pos', 'var') parts{pos} = '*'; end det.filename_pattern_scan = [det.filename_pattern_scan strjoin(parts, del) det.file_extension]; end input_vars = {}; if isfield(det, 'filename_pattern_pos') k = 1; for jj=1:length(det.filename_pattern) switch det.filename_pattern{jj}.content case 'pos' continue case 'burst' input_vars{k} = det.filename_pattern{jj}.start; case 'scan' input_vars{k} = p.scan_number(p.scanID); end k = k+1; end filename_pattern_pos = fullfile(read_path, det.filename_pattern_pos); filename_pos = sprintf(filename_pattern_pos, input_vars{:}); [~, pos_files] = find_files(filename_pos); numpos = size(pos_files,2); % apply natural sorting order i.e. sort 1,2,3,10,200 and not 1 10 100 2 20 200 % important if the file makes are not defined as S%05i but rather S%i [~,idx] = natsort({pos_files.name}); pos_files = pos_files(idx); end if isfield(det, 'filename_pattern_burst') k = 1; for jj=1:length(det.filename_pattern) switch det.filename_pattern{jj}.content case 'pos' input_vars{k} = det.filename_pattern{jj}.start; case 'burst' continue case 'scan' input_vars{k} = p.scan_number(p.scanID); end k = k+1; end filename_pattern_burst = fullfile(read_path, det.filename_pattern_burst); filename_burst = sprintf(filename_pattern_burst, input_vars{:}); [~, burst_files] = find_files(filename_burst); numburst = size(burst_files,2); else numburst = 1; end if numburst > 1 % if burst frames exist, we need to make sure that the file order is correct file_args = '['; for ii=1:length(det.filename_pattern) switch ii case burst file_args = [file_args ' det.filename_pattern{ii}.start + burstID-1']; case pos file_args = [file_args ' det.filename_pattern{ii}.start + posID-1']; case scan file_args = [file_args ' p.scan_number(p.scanID)']; end end file_args = [file_args ']']; for posID=1:numpos for burstID=1:numburst files(burstID+(posID-1)*numburst).name = sprintf(det.filename_pattern_full, eval(file_args)); end end datadir = read_path; else % if there are no burst frames, use the pos files datadir = read_path; files = pos_files; end if numel(files)==0 error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%'))) end else % use wildcards files = find_files(fullfile(read_path, [det.filename_pattern det.file_extension])); if numel(files)==0 error('Could not find any files using the filename pattern %s. \n ', fullfile(read_path, strrep(det.filename_pattern_full, '%', '%%'))) end end else % if no filename pattern was specified, just load everything containing the specified file extension [datadir, files] = find_files([read_path '*.' det.file_extension]); if numel(files)==0 error('Could not find any files using the filename pattern %s.\n ', fullfile(read_path, ['*.' det.file_extension])) end end detStorage.files = []; for ii=1:length(files) detStorage.files{ii} = fullfile(datadir, files(ii).name); end for ii=1:length(det.image_read_extraargs) if strcmpi(det.image_read_extraargs{ii}, 'H5Location') detStorage.h5_group{1} = det.image_read_extraargs{ii+1}; break; end end end