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https://github.com/c-sooyoung/fold_slice.git
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111 lines
8.4 KiB
Matlab
111 lines
8.4 KiB
Matlab
%% INITIALIZE TEST TEMPLATE
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% check / set default parameters for the test scripts
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%% check initial paths
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if ~exist('ptycho_path','var')
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ptycho_path = fileparts(mfilename('fullpath'));
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ptycho_path = replace(ptycho_path, 'tests', '');
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end
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if ~exist('temporal_data_path', 'var'); temporal_data_path = './temp/'; end
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if ~exist('base_path', 'var'); base_path = './'; end
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if ~exist('plot_results', 'var'); plot_results = false; end
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if ~exist('plot_save_results', 'var'); plot_save_results = false; end
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if ~exist('verbose_level', 'var'); verbose_level = -2; end
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addpath(ptycho_path)
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%% run common template for initalization
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addpath(ptycho_path)
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run(fullfile( ptycho_path, 'template_ptycho.m'))
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%% autoestimate the location of base package
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p.cSAXS_matlab_path = core.find_base_package();
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if ~exist('+math/argmax.m','file') % test existence of some function from the package
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addpath(p.cSAXS_matlab_path)
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end
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% make sure that it will be correct even when the current working folder is changed
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p.cSAXS_matlab_path = utils.abspath(p.cSAXS_matlab_path);
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%% general settings
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p = rmfield(p, 'engines');
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p. base_path = base_path; % the basic working path
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p. scan_number = []; % leave empty for artificial data
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p. src_metadata = 'artificial'; % load meta data from file; currently only 'spec' is supported;
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p. prepare.data_preparator = 'matlab'; % data preparator; 'python' or 'matlab'
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p. verbose_level = verbose_level;
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%% plotting
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p. save.external = false; % Use a new Matlab session to run save final figures (saves ~6s per reconstruction). Please be aware that this might lead to an accumulation of Matlab sessions if your single reconstruction is very fast.
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p. plot.prepared_data = false; % plot prepared data
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p. save.store_images = 1; % Write nice jpegs in [p.base_path,'analysis/online/ptycho/'] if p.use_display = 0 then the figures are opened invisible in order to create the nice layout. It writes images in analysis/online/ptycho
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p. plot.fov_box = 1; % Plot the scanning FOV box on the object (both phase and amplitude)
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p. plot.log_scale = [1 1]; % Plot on log scale for x and y
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p. plot.positions = 1; % Plot the scanning positions
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if plot_results
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p. plot.interval = 100;
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else
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p. plot.interval = inf;
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end
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%% io
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p. ptycho_matlab_path = ''; % cSAXS ptycho package path
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p. prepare_data_path = temporal_data_path;
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clear eng eng0
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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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