mirror of
https://github.com/c-sooyoung/fold_slice.git
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151 lines
9.1 KiB
Matlab
151 lines
9.1 KiB
Matlab
% function convert(scan, raw_data_path)
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% convert .raw files to .hdf5
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% Inputs
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% scan scan number
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% raw_data_path path to the raw data (optional)
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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 convert2hdf5(scan, raw_data_path)
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convertor_path = '/sls/X12SA/data/x12saop/EigerPackage/slsDetectorsPackage/bin/hdf5MakerOMNY';
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load_dir = utils.compile_x12sa_dirname(scan);
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if exist('raw_data_path','var')&&exist(fullfile(raw_data_path,load_dir),'dir')
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load_dir = fullfile(raw_data_path,load_dir);
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elseif exist(['~/Data10/eiger_4/'],'dir')
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load_dir = ['~/Data10/eiger_4/' load_dir];
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elseif exist([raw_data_path,'eiger_4/'])
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load_dir = [raw_data_path,'/eiger_4/' load_dir];
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elseif exist([raw_data_path,'/eigeromny/'])
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load_dir = [raw_data_path,'/eigeromny/' load_dir];
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end
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if ~exist(load_dir, 'dir')
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warning('Raw data path %s not found', load_dir)
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return
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end
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testDir = [load_dir, '/deleteMe'];
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% test for write permissions by creating a folder and then deleting it
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isWritable = mkdir(testDir);
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% check if directory creation was successful
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if isWritable == 1
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rmdir(fullfile(testDir));
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end
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list_h5 = dir([load_dir, '/run_*.h5']);
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file_sizes = [list_h5.bytes];
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if any(file_sizes < 1e6) % find files < 1MB
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warning('H5 files in scan %i seem damaged, generate again ... ', scan)
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list_raw = dir([load_dir, '/run_d0_f0000000*.raw']);
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if isempty(list_raw)
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error('RAW data are missing, data cannot be converted')
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else
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delete(sprintf('%s/*.h5',load_dir))
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end
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list_h5 = dir([load_dir, '/run_*.h5']);
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end
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if isempty(list_h5)
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if ~isWritable
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warning('Conversion failed because folder %s is not writable', load_dir)
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return
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end
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list_raw = dir(fullfile(load_dir, 'run_d0_f0000000*.raw'));
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Nscans = length(list_raw);
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for ii = 1:Nscans
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ind_scans(ii) = str2num(list_raw(ii).name(16:17));
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end
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for ii = 1:Nscans
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% [~,out] = system([cbf_maker_path ' ' fullfile(load_dir,sprintf('run_d0_f00000000%02i000_%i.raw',ind_scans(ii) ,scan))]);
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systemcall = [convertor_path ' ' fullfile(list_raw(1).folder,list_raw(1).name)];
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fprintf('%s\n',systemcall);
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[~,out] = system(systemcall);
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out
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end
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list_h5 = dir([load_dir, '/*.h5']);
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if isempty(list_h5)
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error(sprintf('After conversion did not find any h5 in %s\n',load_dir))
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return
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end
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if numel(list_h5)>1
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error(sprintf('After conversion I found more than one h5 in %s\n',load_dir))
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return
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end
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h5fileinfo = h5info(fullfile(list_h5.folder,list_h5.name));
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nframes_converted = h5fileinfo.Groups.Groups(1).Datasets.Dataspace.Size(3);
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out = splitlines(out);
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nframes_expected = str2num(out{end-2}(14:end));
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fprintf('Frames expected: %i, frames converted %i \n', nframes_expected, nframes_converted)
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if nframes_converted == nframes_expected
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fprintf('Scan %i succefully converted to H5\n', scan);
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delete(sprintf('%s/*.raw',load_dir))
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else
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error('Scan %i WAS NOT CONVERTED to H5\n', scan)
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delete(sprintf('%s/*.h5',load_dir))
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end
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end
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end
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