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171 lines
9.1 KiB
Matlab
171 lines
9.1 KiB
Matlab
% filename_with_path = find_ptycho_filename(base_analysis_path,scan_number,fileprefix,filesuffix)
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% Looks for a ptychography reconstruction name inside the path given as
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% initial argument. I will look in the folder given and also try with
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% adding analysis. If the scan_number is given it will compile an analysis
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% folder and look for it. e.g. find_ptycho_filename('~/Data10',235);
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% Use verbose(2) in order to see all directories and names attempted.
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% Inputs
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% base_analysis_path % String with path to start looking
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% scan_number % (optional) Number with the scan number, used to
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% compile folder
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% fileprefix % String specifying the starting of the name
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% filesuffix % String specifying the ending of the name
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% Output
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% filename_with_path % String with the first file found that satisfies
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% the input arguments
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% 15 June 2015;
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% September 2017 Return all files matching the criteria;
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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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function [ filename_with_path ] = find_ptycho_filename( base_analysis_path, varargin)
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import utils.verbose
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% Checks and defaults
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if nargin < 5
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fileextension = 'h5';
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else
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fileextension = varargin{4};
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end
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if nargin < 4
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filesuffix = [];
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else
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filesuffix = varargin{3};
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end
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if nargin < 3
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fileprefix = [];
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else
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fileprefix = varargin{2};
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end
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if nargin < 2
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scan_number = [];
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else
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scan_number = varargin{1};
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end
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%%% Give all matching files
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trial_path = fullfile(base_analysis_path, utils.compile_x12sa_dirname(scan_number));
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if isempty(filesuffix)
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searchstring = [fileprefix '*.' fileextension];
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else
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searchstring = [fileprefix '*' filesuffix '*.' fileextension];
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end
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search_filename = fullfile(trial_path, searchstring);
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output = dir(search_filename);
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if numel(output) == 0
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verbose(2,['Did not find any file matching' search_filename]);
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% Then see if analysis folder exists here
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trial_path = fullfile(base_analysis_path,'analysis');
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if exist(trial_path,'dir')~=0
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search_filename = fullfile(trial_path,searchstring);
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output = dir(search_filename);
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else
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trial_path = base_analysis_path;
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end
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if numel(output) == 0
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verbose(2,['Did not find any file matching' search_filename]);
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if ~isempty(scan_number)
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% Then add the string for the scan folder
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trial_path = fullfile(trial_path,sprintf('S%05d',scan_number));
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search_filename = fullfile(trial_path,searchstring);
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output = dir(search_filename);
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if numel(output) == 0
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verbose(2,['Did not find any file matching' search_filename]);
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filename_with_path = [];
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% return
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end
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else
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verbose(2,['Did not find any file matching' search_filename]);
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filename_with_path = [];
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% return
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end
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end
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end
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for ii = 1:length(output)
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filename_with_path{ii} = fullfile(trial_path, output(ii).name);
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end
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if numel(filename_with_path)~=0
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if iscell(filename_with_path) && numel(filename_with_path)==1
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filename_with_path = filename_with_path{1};
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else
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verbose(1,'Found %d file matching the criteria -> providing all in cell', numel(filename_with_path))
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end
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else
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verbose(1,'Found no file matching %s', fullfile(base_analysis_path, utils.compile_x12sa_dirname(scan_number),searchstring ))
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filename_with_path = [];
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end
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end
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