mirror of
https://github.com/c-sooyoung/fold_slice.git
synced 2026-09-17 23:39:08 +09:00
194 lines
9.8 KiB
Matlab
194 lines
9.8 KiB
Matlab
% CREATE_FILE_QUEUE create directories and .dat files for a file queue
|
||
% only needed if OMNY/flOMNI is not available
|
||
% ** start start scan number
|
||
% ** stop stop scan number
|
||
% ** step reconstruction bundle size
|
||
%
|
||
% *optional* given as name/value pair
|
||
% ** dirpath path to the .dat files directory; default: '../reconstruction'
|
||
% ** prop structure with parameters that need to be saved to the .dat file
|
||
% ** prop_name structure name; default: 'p'
|
||
% ** spec path to spec file; needed for check2detpos
|
||
% ** check2detpos check detector positions to avoid repeated scans
|
||
% ** det_motor detector motor; default 'dettrx'
|
||
% ** verbose set verbose level; default 0
|
||
%
|
||
% EXAMPLE:
|
||
% s.lockfile = false;
|
||
% s.energy = 6.2015;
|
||
% s.check_nextscan_started = 1;
|
||
%
|
||
% create_file_queue(646, 650, 2, 'prop', s)
|
||
%
|
||
%
|
||
% create_file_queue(287, 2553, 2, 'prop', s, 'spec', '/das/work/p16/p16812/data/pilatus/e16403/', 'check2detpos', true, 'det_motor', 'dettrx')
|
||
|
||
% 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 create_file_queue(start, stop, step, varargin)
|
||
import utils.*
|
||
|
||
par = inputParser;
|
||
par.addParameter('dirpath', '../reconstruction', @ischar)
|
||
par.addParameter('prop', [], @isstruct)
|
||
par.addParameter('prop_name', 'p', @ischar)
|
||
par.addParameter('spec', [], @ischar)
|
||
par.addParameter('check2detpos', false, @logical)
|
||
par.addParameter('det_motor', 'dettrx', @ischar)
|
||
par.addParameter('verbose', 0, @isnumeric)
|
||
|
||
par.parse(varargin{:})
|
||
|
||
var = par.Results;
|
||
|
||
% reduce verbose level
|
||
vbl = utils.verbose;
|
||
utils.verbose(var.verbose);
|
||
|
||
% prepare directories
|
||
if ~exist(fullfile(var.dirpath), 'dir')
|
||
mkdir(fullfile(var.dirpath))
|
||
end
|
||
if ~exist(fullfile(var.dirpath, 'in_progress'), 'dir')
|
||
mkdir(fullfile(var.dirpath, 'in_progress'))
|
||
mkdir(fullfile(var.dirpath, 'done'))
|
||
mkdir(fullfile(var.dirpath, 'failed'))
|
||
end
|
||
|
||
% filename pattern
|
||
fname_pattern = repmat('scan%05d_',1,step);
|
||
fname_pattern = [fname_pattern(1:end-1) '.dat'];
|
||
scan_number_pattern = repmat('%d ',1,step);
|
||
scan_number_pattern = scan_number_pattern(1:end-1);
|
||
|
||
% get value for p.detector.check_2_detpos
|
||
if var.check2detpos
|
||
|
||
S = io.spec_read(var.spec, 'ScanNr', start);
|
||
detpos1 = S.(var.det_motor);
|
||
for ii=start+1:stop
|
||
S = io.spec_read(var.spec, 'ScanNr', ii);
|
||
if S.(var.det_motor)~=detpos1
|
||
detpos2=S.(var.det_motor);
|
||
break
|
||
end
|
||
end
|
||
var.prop.detector.check_2_detpos = abs(detpos1-detpos2)/2+detpos2;
|
||
end
|
||
|
||
|
||
% if needed, prepare structure
|
||
if ~isempty(var.prop)
|
||
prop_fnames = utils.struc2cell(var.prop);
|
||
else
|
||
prop_fnames = [];
|
||
end
|
||
|
||
utils.verbose(0, 'Creating file queue.');
|
||
|
||
ii = start;
|
||
if utils.verbose < 2
|
||
utils.progressbar(1, round((stop-start)/step))
|
||
end
|
||
while ii<=stop
|
||
% check if detector positions are repeated
|
||
if var.check2detpos
|
||
detpos = [];
|
||
kk= 1;
|
||
for jj=ii:ii+step-1
|
||
S = io.spec_read(var.spec, 'ScanNr', jj);
|
||
detpos(kk) = S.(var.det_motor);
|
||
kk = kk+1;
|
||
end
|
||
if all(detpos == detpos(1))
|
||
utils.verbose(2,'Found repeated detector positions.')
|
||
ii = ii+1;
|
||
continue
|
||
end
|
||
end
|
||
|
||
% write file
|
||
fname = sprintf(fname_pattern, ii:ii+step-1);
|
||
fid = fopen(fullfile(var.dirpath, fname), 'w');
|
||
fprintf(fid, ['p.scan_number \t ' scan_number_pattern '\n'], ii:ii+step-1);
|
||
if ~isempty(prop_fnames)
|
||
for jj=1:numel(prop_fnames)
|
||
cval = eval(['var.prop.' prop_fnames{jj}]);
|
||
if islogical(cval) || isnumeric(cval)
|
||
%eval(['var.prop.' prop_fnames{jj} '= double(var.prop.' prop_fnames{jj} ')']);
|
||
prop_val = num2str(cval);
|
||
else
|
||
prop_val = cval;
|
||
end
|
||
prop_val = replace(prop_val, '%', '%%'); % avoid interpretation of special characters in strings
|
||
fprintf(fid, [var.prop_name '.' prop_fnames{jj} '\t ' prop_val '\n']);
|
||
end
|
||
end
|
||
|
||
fclose(fid);
|
||
|
||
ii = ii+step;
|
||
if utils.verbose < 2
|
||
utils.progressbar(ii-start, round((stop-start)/step))
|
||
end
|
||
end
|
||
|
||
utils.verbose(0, '\nDone.');
|
||
|
||
% revert changes to verbose level
|
||
utils.verbose(vbl);
|
||
|
||
end
|