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%CONVERT2HDF5_WRAPPER converts Eiger 1.5M raw data files to HDF5 and
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% deletes the raw files if the conversion has finished successfully
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% convert2hdf5_wrapper(raw_data_path)
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%
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% ** raw_data_path path to the eiger directory, e.g. ~/Data10/
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%
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% *optional*
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% ** scanID start at the given scan number
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%
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% EXAMPLES:
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% % start at scan number 1:
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% convert2hdf5_wrapper('~/Data10/');
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%
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% % start at scan number 150:
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% convert2hdf5_wrapper('~/Data10/', 150);
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%
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% Pleas note that the script is designed to be used during an ongoing
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% measurement, and therefore only converts n-1 datasets, that is it waits
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% until the next measurement has started.
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%*-----------------------------------------------------------------------*
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%| |
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%| Except where otherwise noted, this work is licensed under a |
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%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
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%| International (CC BY-NC-SA 4.0) license. |
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%| |
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%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
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%| |
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%| Author: CXS group, PSI |
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%*-----------------------------------------------------------------------*
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% You may use this code with the following provisions:
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%
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% If the code is fully or partially redistributed, or rewritten in another
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% computing language this notice should be included in the redistribution.
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%
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% If this code, or subfunctions or parts of it, is used for research in a
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% publication or if it is fully or partially rewritten for another
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% computing language the authors and institution should be acknowledged
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% in written form in the publication: “Data processing was carried out
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% using the “cSAXS matlab package” developed by the CXS group,
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% Paul Scherrer Institut, Switzerland.”
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% Variations on the latter text can be incorporated upon discussion with
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% the CXS group if needed to more specifically reflect the use of the package
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% for the published work.
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%
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% A publication that focuses on describing features, or parameters, that
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% are already existing in the code should be first discussed with the
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% authors.
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%
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% This code and subroutines are part of a continuous development, they
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% are provided “as they are” without guarantees or liability on part
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% of PSI or the authors. It is the user responsibility to ensure its
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% proper use and the correctness of the results.
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function convert2hdf5_wrapper(raw_data_path, varargin)
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import utils.*
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if nargin > 1
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scanID = varargin{1};
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else
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scanID = 1;
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end
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while true
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[started, newScan, specDatFile] = beamline.next_scan_started(raw_data_path, scanID);
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if started
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convert2hdf5(scanID, raw_data_path, specDatFile);
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fprintf('Converting scan %d\n', scanID);
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scanID = newScan;
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else
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fprintf('Waiting for next scan to start.\n');
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pause(1);
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end
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end
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end
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function convert2hdf5(scan, raw_data_path, specDatFile)
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% some defaults
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convertor_path = '~/Data10/bin/eiger1p5M_converter/hdf5MakerOMNY';
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xmlLayoutFile = '~/Data10/bin/nexus/layout.xml';
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orchestraPath = '~/Data10/specES1/scan_positions/';
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specParser = '~/Data10/matlab/+io/spec_reader/spec_reader';
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% check if orchestraPath exists
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if exist(orchestraPath, 'dir')
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orchestraPath = ['--orchestra ' orchestraPath];
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else
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orchestraPath = '';
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end
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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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warning('RAW data is missing, data cannot be converted')
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return
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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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% toc
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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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systemcall = [convertor_path ' ' fullfile(list_raw(1).folder,list_raw(1).name)];
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fprintf('%s\n',systemcall);
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[stat,out] = system(systemcall);
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systemcall = sprintf('%s -s %s --scanNr %u --hdf5 --xmlLayout %s -o %s %s', specParser, specDatFile, scan, xmlLayoutFile, fullfile(load_dir, sprintf('run_%05d_000000000000.h5',scan)), orchestraPath);
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[stat, out_spec] = system(systemcall);
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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), '/entry/instrument/eiger_4/data');
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nframes_converted = h5fileinfo.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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