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https://github.com/c-sooyoung/fold_slice.git
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162 lines
9.1 KiB
Matlab
162 lines
9.1 KiB
Matlab
% Detect an interruption of the scan in the Log file
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% From spec compile post_scan.mac
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% = 1, if the scan is ready for processing
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% = 0, if the scan was interrupted and is not yet repeated, or if the scan
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% is being repeated now
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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 out = check_scan_interruption(specLogFile,scanno)
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specLogFile = find_specLogFile(specLogFile);
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cmd = sprintf('cat -n %s | grep "S %d " | cut -f 1 -d ''#''', specLogFile,scanno);
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[~,sysout] = system(cmd);
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arroutbegin = regexp(sysout,'[:\n]','split');
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cmd = sprintf('cat -n %s | grep "X %d" | cut -f 1 -d ''#''', specLogFile,scanno);
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[~,sysout] = system(cmd);
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cmd = sprintf('cat -n %s | grep "X %d" | cut -f 2 -d ''#''', specLogFile,scanno);
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[~,sysout_2] = system(cmd);
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arroutend = regexp(sysout,'[:\n]','split');
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arroutend_text = regexp(sysout_2,'[:\n]','split');
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numbegin = [];
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numend = [];
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for ii = 1:numel(arroutbegin)-1
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numbegin(ii) = str2num(arroutbegin{ii});
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end
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count = 1;
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for ii = 1:numel(arroutend)-1
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if strcmp(arroutend_text{ii}(3:end),num2str(scanno))
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numend(count) = str2num(arroutend{ii});
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count = count+1;
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end
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end
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if numel(numbegin)~=numel(numend)
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% The experiment is being repeated now
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out = 0;
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return
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else
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cmd = sprintf('head -n %d %s | tail -n %d|grep chk',numend(end) ,specLogFile,numend(end)-numbegin(end));
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[~,sysout] = system(cmd);
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errorout = regexp(sysout,'[:\n]','split');
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if isempty(errorout{1})
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out = 1;
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else
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% There was an error in this scan
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out = 0;
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end
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return
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end
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% if any(strcmp(arrout,sprintf('#X %d',scanno)))
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% out = true;
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% else
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% out = false;
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% end
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end
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%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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function specLogFile = find_specLogFile(specLogFile)
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while (exist(specLogFile,'file') ~= 2)
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% if the variable specLogFile is not a complete path to a file
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% try to guess where a spec data file can be found, by
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% - look for directories called 'spec' or 'dat-files'
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% - look for files called '*.dat'
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% - take the newest one
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compare_str = specLogFile;
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fname = dir(specLogFile);
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if (exist(specLogFile,'dir'))
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if (specLogFile(end) ~= '/')
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specLogFile = strcat(specLogFile,'/');
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end
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for ii=1:numel(fname)
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if (regexp(fname(ii).name,'.log$'))
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specLogFile = strcat(specLogFile,'*.log');
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fname = [];
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break;
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end
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end
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for ii=1:numel(fname)
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if (strcmp(fname(ii).name,'log-files'))
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specLogFile = strcat(specLogFile,fname(ii).name);
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fname = [];
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break;
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end
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end
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for ii=1:numel(fname)
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if (strcmp(fname(ii).name,'specES1'))
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specLogFile = strcat(specLogFile,fname(ii).name);
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break;
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end
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if (strcmp(fname(ii).name,'spec'))
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specLogFile = strcat(specLogFile,fname(ii).name);
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break;
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end
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end
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else
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if (numel(fname)>0)
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[~,ii] = max(cell2mat({fname.datenum}));
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specLogFile = regexprep(specLogFile,'\*\.log$',fname(ii).name);
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else
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error('''%s'' cannot be found.', specLogFile);
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break
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end
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end
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if (strcmp(specLogFile,compare_str))
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break
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end
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end
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end |