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%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