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