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% CREATE_FILE_QUEUE create directories and .dat files for a file queue
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% only needed if OMNY/flOMNI is not available
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% ** start start scan number
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% ** stop stop scan number
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% ** step reconstruction bundle size
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%
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% *optional* given as name/value pair
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% ** dirpath path to the .dat files directory; default: '../reconstruction'
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% ** prop structure with parameters that need to be saved to the .dat file
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% ** prop_name structure name; default: 'p'
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% ** spec path to spec file; needed for check2detpos
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% ** check2detpos check detector positions to avoid repeated scans
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% ** det_motor detector motor; default 'dettrx'
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% ** verbose set verbose level; default 0
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%
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% EXAMPLE:
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% s.lockfile = false;
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% s.energy = 6.2015;
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% s.check_nextscan_started = 1;
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%
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% create_file_queue(646, 650, 2, 'prop', s)
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%
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%
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% create_file_queue(287, 2553, 2, 'prop', s, 'spec', '/das/work/p16/p16812/data/pilatus/e16403/', 'check2detpos', true, 'det_motor', 'dettrx')
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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 create_file_queue(start, stop, step, varargin)
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import utils.*
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par = inputParser;
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par.addParameter('dirpath', '../reconstruction', @ischar)
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par.addParameter('prop', [], @isstruct)
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par.addParameter('prop_name', 'p', @ischar)
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par.addParameter('spec', [], @ischar)
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par.addParameter('check2detpos', false, @logical)
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par.addParameter('det_motor', 'dettrx', @ischar)
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par.addParameter('verbose', 0, @isnumeric)
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par.parse(varargin{:})
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var = par.Results;
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% reduce verbose level
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vbl = utils.verbose;
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utils.verbose(var.verbose);
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% prepare directories
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if ~exist(fullfile(var.dirpath), 'dir')
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mkdir(fullfile(var.dirpath))
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end
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if ~exist(fullfile(var.dirpath, 'in_progress'), 'dir')
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mkdir(fullfile(var.dirpath, 'in_progress'))
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mkdir(fullfile(var.dirpath, 'done'))
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mkdir(fullfile(var.dirpath, 'failed'))
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end
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% filename pattern
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fname_pattern = repmat('scan%05d_',1,step);
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fname_pattern = [fname_pattern(1:end-1) '.dat'];
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scan_number_pattern = repmat('%d ',1,step);
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scan_number_pattern = scan_number_pattern(1:end-1);
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% get value for p.detector.check_2_detpos
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if var.check2detpos
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S = io.spec_read(var.spec, 'ScanNr', start);
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detpos1 = S.(var.det_motor);
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for ii=start+1:stop
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S = io.spec_read(var.spec, 'ScanNr', ii);
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if S.(var.det_motor)~=detpos1
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detpos2=S.(var.det_motor);
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break
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end
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end
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var.prop.detector.check_2_detpos = abs(detpos1-detpos2)/2+detpos2;
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end
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% if needed, prepare structure
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if ~isempty(var.prop)
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prop_fnames = utils.struc2cell(var.prop);
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else
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prop_fnames = [];
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end
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utils.verbose(0, 'Creating file queue.');
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ii = start;
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if utils.verbose < 2
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utils.progressbar(1, round((stop-start)/step))
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end
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while ii<=stop
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% check if detector positions are repeated
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if var.check2detpos
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detpos = [];
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kk= 1;
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for jj=ii:ii+step-1
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S = io.spec_read(var.spec, 'ScanNr', jj);
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detpos(kk) = S.(var.det_motor);
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kk = kk+1;
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end
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if all(detpos == detpos(1))
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utils.verbose(2,'Found repeated detector positions.')
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ii = ii+1;
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continue
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end
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end
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% write file
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fname = sprintf(fname_pattern, ii:ii+step-1);
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fid = fopen(fullfile(var.dirpath, fname), 'w');
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fprintf(fid, ['p.scan_number \t ' scan_number_pattern '\n'], ii:ii+step-1);
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if ~isempty(prop_fnames)
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for jj=1:numel(prop_fnames)
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cval = eval(['var.prop.' prop_fnames{jj}]);
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if islogical(cval) || isnumeric(cval)
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%eval(['var.prop.' prop_fnames{jj} '= double(var.prop.' prop_fnames{jj} ')']);
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prop_val = num2str(cval);
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else
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prop_val = cval;
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end
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prop_val = replace(prop_val, '%', '%%'); % avoid interpretation of special characters in strings
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fprintf(fid, [var.prop_name '.' prop_fnames{jj} '\t ' prop_val '\n']);
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end
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end
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fclose(fid);
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ii = ii+step;
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if utils.verbose < 2
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utils.progressbar(ii-start, round((stop-start)/step))
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end
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end
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utils.verbose(0, '\nDone.');
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% revert changes to verbose level
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utils.verbose(vbl);
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end
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