% show recons.m % Warning: Currently working only for square pixels % close all % Recommended if improfile will be used (there is a bug with cursor positioning otherwise) % Mayor changes, basically rewritten, made on Oct 19, 2015 in order to accomodate waiting for clear import utils.* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% Show recons parameters %%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% base_path='~/Data10/'; addpath '~/Data10/matlab' addpath ~/Data10/matlab/ptycho/ colorbarphase = [-1 1]*pi; % Give the range, or 'auto' saveplots = 1; % Saves JPEGs of reconstruction %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% Parameters to find the file %%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% Option 1 %%% % Path + name filefixname = []; % Provide a full path and filename. Leave empty to use the next option. %%% Option 2 %%% % Range of scan numbers scans = fliplr([17000:25000]); % Specify a range of scan numbers, the code will try to be smart and find the reconstructions. Leave empty to use the next option. prefix = ''; % Define a prefix to choose one reconstruction if there are many in the folder. Leave empty to just grab the first one. suffix = '_recons'; % Alternatively you can define a suffix. %%% Option 3 %%% Specify an OMNY/flOMNI dat file path. The code will % keep looking in this folder, it finds the file and moves it to the % second folder. If the name of second folder is specified, if left % empty it will not move it queue_path = ['~/Data10/specES1/recontruct/done/']; queue_path_out = ['~/Data10/specES1/recontruct/done_shown/']; % If you leave this empty it will not move the files, but then this is pretty useless, eh? %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% continuewithloop = true; verbose(0); % Change to = 2 in order to have more output on the varargs{1} = 'PhaseColorBarAxis'; varargs{2} = colorbarphase; if saveplots varargs{3} = 'ImageSaveFolder'; varargs{4} = fullfile(base_path,'analysis/online/ptycho/show_recons/'); end scans_to_do = scans; scans_plotted = 0; while(~isempty(scans_to_do)) % while(continuewithloop) if ~isempty(filefixname) % Just use the fixed name file = filefixname; continuewithloop = false; plotting.ptycho_show_recons(file,varargs); else if isempty(scans) % Use OMNY reconstruct dat file %%% Find file with task to plot lookforafile = true; verbose(1,['queue_path is active, looking for files in the queue in ' queue_path]); while(lookforafile) files_recons = dir([queue_path 'scan*']); if ~isempty(files_recons) file_dat = fullfile(queue_path,files_recons(1).name); verbose(1,['Found file in queue ' file_dat]); lookforafile = false; else verbose(1,sprintf('Did not find files in the queue: %s, pausing 10 sec',queue_path)); pause(10) end end %%% p_out = parse_queue_file(file_dat); scanstoplot = p_out.scan_number; % Now move the file if ~exist(queue_path_out,'dir') warning(sprintf('Creating folder %s',queue_path_out)) mkdir(queue_path_out); end verbose(1,sprintf('Moving %s to %s',file_dat,queue_path_out)) movefile(file_dat,queue_path_out) else % Use the scan numbers provided continuewithloop = false; scanstoplot = scans; end % Ok, now it knows which scans to plot num_orig_args = numel(varargs); for scannum = scans_to_do%scanstoplot file = find_ptycho_filename(base_path,scannum,prefix,suffix); % Compile name % waitingforrecons = false; % while(waitingforrecons) if iscell(file) warning('More than one file found, using the 1st one. Consider specific filename.'); file = file{1}; end if exist(file,'file') verbose(1,sprintf('Found %s',file)); verbose(1,'Waiting 3 sec to make sure the file is written') pause(3) varargs{num_orig_args+1} = 'ScanNumber'; varargs{num_orig_args+2} = scannum; try JavaObj = java.lang.Runtime.getRuntime; fprintf('Free memory: %d\n', JavaObj.freeMemory/1e6) plotting.ptycho_show_recons(file,varargs); scans_plotted = scans_plotted+1; save('debug11.mat','scans_plotted','scans_to_do'); catch fprintf('failed to open file\n') end waitingforrecons = false; scans_to_do(find(scans_to_do==scannum)) = []; else verbose(1,sprintf('Reconstruction %s not found, pausing 10 sec',file)); % pause(10) end % end end end % end end return % 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. 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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. 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