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ptycho/utils/show_recons.m
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% 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. 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.