initial commit

ptycho/tests/run_test.m

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+%% Prepare the reconstruction
+
+if ~exist('eng', 'var')
+   return  % return if no engine is provided 
+end
+
+fprintf('Creating dataset   .... ')
+
+[p, status] = core.ptycho_recons(p, true);
+
+if status && all(isfinite(p.fmag(:))) && all(isfinite(p.object{1}(:))) && all(isfinite(p.probes(:)))
+    fprintf('OK\n')
+else
+    error('Data creator failed, quitting ... ')
+end
+
+p.  plot.windowautopos = true;                                % distribute the plotted windows
+p.  plot.remove_phase_ramp = true; 
+
+p_0  = p; % store the initial p-structure 
+
+
+%% get all engines
+utils.verbose(struct('prefix', {'ptycho'}))
+for ieng=1:length(p.engines)
+    if ~check_option(p, 'preserve_previous_results')
+        p = p_0; 
+    end
+    p.current_engine_id = ieng;
+
+    % engine call
+    if ~isfield(p.engines{ieng}, 'method');  p.engines{ieng}.method = '' ;end
+    fprintf('Testing engine "%s" using method "%s"  .... ', p.engines{ieng}.name, p.engines{ieng}.method)
+    utils.verbose(struct('prefix', {p.engines{ieng}.name}))
+
+    try
+        t_start = tic; 
+        [p, fdb] = core.run_engine(p, ieng);
+         if p.ortho_probes && size(p.probes,4)>1
+            % orthogonalize probes
+            p.probes = core.probe_modes_ortho(p.probes);
+         end
+                
+        warning on 
+        warning off backtrace
+        if fdb.status.status ~= 0
+            fprintf('failed\n')
+            warning('Engine %s returned with exit status %d from %s [%d].\n', p.engines{ieng}.name, fdb.status.status, fdb.status.ln(1).name, fdb.status.ln(1).line);
+        elseif any(~isfinite(p.object{1}(:))) || any(~isfinite(p.probes(:)))
+            warning('Engine %s returned non finite values in reconstrutions',p.engines{ieng}.name)
+        else
+            fprintf('OK  \tTime: %3.2gs\n', (toc(t_start)))
+            p.plot.extratitlestring = sprintf('engine "%s" using method "%s"', p.engines{ieng}.name, p.engines{ieng}.method);
+            if plot_save_results && plot_results
+                p.use_display = true;
+                p.save.save_reconstructions  = false; % prevent writting to disk 
+                [p] = core.save.save_results(p, true);
+            elseif plot_results && ~plot_save_results
+                core.analysis.plot_results(p)
+            elseif plot_save_results
+                p.use_display = false; 
+                p.save.save_reconstructions  = false; % prevent writting to disk 
+                [p] = core.save.save_results(p, true);
+                p.use_display = true; 
+            end
+
+        end
+    catch err 
+        fprintf(1, 'failed\n')
+        warning(err.getReport)
+    end
+end
+
+% delete temporal data 
+for path = p.save_path
+    rmdir(path{1}, 's')
+end
+
+
+
+
+
+
+
+% 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.