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96 lines
3.4 KiB
Matlab
96 lines
3.4 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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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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