initial commit

2026-09-17 21:49:08 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
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+% function convert(scan, raw_data_path)
+% convert .raw files to .hdf5
+%  Inputs
+%     scan              scan number
+%     raw_data_path     path to the raw data (optional)
+
+function convert2hdf5(scan, raw_data_path)
+
+    convertor_path = '/sls/X12SA/data/x12saop/EigerPackage/slsDetectorsPackage/bin/hdf5MakerOMNY'; 
+    load_dir = utils.compile_x12sa_dirname(scan);
+    if exist('raw_data_path','var')&&exist(fullfile(raw_data_path,load_dir),'dir')
+        load_dir = fullfile(raw_data_path,load_dir);
+    elseif exist(['~/Data10/eiger_4/'],'dir')
+        load_dir = ['~/Data10/eiger_4/' load_dir]; 
+    elseif exist([raw_data_path,'eiger_4/'])
+        load_dir = [raw_data_path,'/eiger_4/' load_dir]; 
+    elseif exist([raw_data_path,'/eigeromny/'])
+        load_dir = [raw_data_path,'/eigeromny/' load_dir]; 
+    end
+    
+    if ~exist(load_dir, 'dir')
+        warning('Raw data path %s not found', load_dir)
+        return
+    end
+
+    testDir = [load_dir, '/deleteMe'];
+    % test for write permissions by creating a folder and then deleting it
+    isWritable = mkdir(testDir);
+    % check if directory creation was successful
+    if isWritable == 1
+        rmdir(fullfile(testDir));
+    end
+
+    list_h5 = dir([load_dir, '/run_*.h5']); 
+        
+    
+    file_sizes = [list_h5.bytes]; 
+    if any(file_sizes < 1e6)  % find files < 1MB
+        warning('H5 files in scan %i seem damaged, generate again ... ', scan)
+        list_raw = dir([load_dir, '/run_d0_f0000000*.raw']);
+        if isempty(list_raw)
+           error('RAW data are missing, data cannot be converted')
+        else
+           delete(sprintf('%s/*.h5',load_dir))
+        end
+        list_h5 = dir([load_dir, '/run_*.h5']); 
+    end
+    
+    if isempty(list_h5)    
+        if ~isWritable
+            warning('Conversion failed because folder %s is not writable', load_dir)
+            return
+        end
+        
+        list_raw = dir(fullfile(load_dir, 'run_d0_f0000000*.raw')); 
+
+        Nscans = length(list_raw); 
+        
+        for ii = 1:Nscans
+            ind_scans(ii) = str2num(list_raw(ii).name(16:17)); 
+        end
+        
+        for ii = 1:Nscans
+%            [~,out] = system([cbf_maker_path ' ' fullfile(load_dir,sprintf('run_d0_f00000000%02i000_%i.raw',ind_scans(ii) ,scan))]);     
+            systemcall = [convertor_path ' ' fullfile(list_raw(1).folder,list_raw(1).name)];
+            fprintf('%s\n',systemcall);
+            [~,out] = system(systemcall);
+            out
+        end
+        
+        list_h5 = dir([load_dir, '/*.h5']);
+        if isempty(list_h5)
+           error(sprintf('After conversion did not find any h5 in %s\n',load_dir))
+           return
+        end
+        if numel(list_h5)>1
+           error(sprintf('After conversion I found more than one h5 in %s\n',load_dir))
+           return
+        end
+            
+        h5fileinfo = h5info(fullfile(list_h5.folder,list_h5.name));
+            
+        nframes_converted = h5fileinfo.Groups.Groups(1).Datasets.Dataspace.Size(3);
+        out = splitlines(out); 
+        nframes_expected = str2num(out{end-2}(14:end)); 
+        fprintf('Frames expected: %i, frames converted %i \n', nframes_expected, nframes_converted)
+        if nframes_converted == nframes_expected
+            fprintf('Scan %i succefully converted to H5\n', scan); 
+             delete(sprintf('%s/*.raw',load_dir))
+        else
+            error('Scan %i WAS NOT CONVERTED to H5\n', scan)    
+             delete(sprintf('%s/*.h5',load_dir))
+        end
+    end
+end