gtConvertRawImages2Blobs: added basic help and formatted

Signed-off-by: preischig <preischig@gmail.com>

2_difspot/gtConvertRawImages2Blobs.m

 function gtConvertRawImages2Blobs(first, last, workingdirectory, varargin)
+% GTCONVERTRAWIMAGES2BLOBS Loads diff blobs from database and saves them as
+% hdf5 files. 
+%
+% gtConvertRawImages2Blobs(first, last, workingdirectory, varargin)
+%
+% To speed up, run it in parallel using OAR (OAR_make).
+
+
+if (isdeployed)
+    global GT_DB
+    global GT_MATLAB_HOME
+    load('workspaceGlobal.mat')
+end
 
-    if (isdeployed)
-        global GT_DB
-        global GT_MATLAB_HOME
-        load('workspaceGlobal.mat')
-    end
+cd(workingdirectory);
+gtDBConnect();
+parameters = [];
+load('parameters.mat');
 
-    cd(workingdirectory);
-    gtDBConnect();
-    parameters = [];
-    load('parameters.mat');
+if (~exist('first', 'var') || isempty(first))
+    first = 1;
+end
+difblob_num = mym(['select count(*) from ' parameters.acq.name 'difblob']);
+if (~exist('last', 'var') || isempty(last))
+    last = difblob_num;
+end
 
-    if (~exist('first', 'var') || isempty(first))
-        first = 1;
-    end
-    difblob_num = mym(['select count(*) from ' parameters.acq.name 'difblob']);
-    if (~exist('last', 'var') || isempty(last))
-        last = difblob_num;
-    end
+if (isdeployed)
+    first   = str2double(first);
+    last    = str2double(last);
+end
 
-    if (isdeployed)
-        first   = str2double(first);
-        last    = str2double(last);
-    end
+conf = struct('list', first:last, 'dilate', 5);
+conf = parse_pv_pairs(conf, varargin);
+
+info = edf_info(fullfile('1_preprocessing', 'full', 'full0000.edf'));
+totproj = parameters.acq.nproj *2;
+stats = GtTasksStatistics();
+stats.add_task('load_blob', 'Time to load from DB');
+stats.add_task('load_mask', 'Time to load mask');
+stats.add_task('save_blob', 'Time to save to HDF5');
+stats.add_task('convert_blob', 'Time for converting from DB to HDF5')
+
+fprintf('Progress: ')
+c = tic();
+for ii = conf.list
+    num_chars = fprintf('%06d/%06d (%s)', ii, numel(conf.list), ...
+        stats.get_formatted_total('convert_blob'));
+    stats.tic('convert_blob')
+    stats.tic('load_mask')
+    [mask, bb] = get_mask('2_difspot', ii, parameters, conf);
+    mask(mask < 0) = 0;
+    stats.toc('load_mask')
+    
+    stats.tic('load_blob')
+    blob = get_blob(bb, info, totproj);
+    blob(blob < 0) = 0;
+    stats.toc('load_blob')
+    
+    stats.tic('save_blob')
+    gtWriteBlobToHDF5('2_difblob', ii, blob, bb, mask);
+    stats.toc('save_blob')
+    stats.toc('convert_blob')
+    
+    fprintf(repmat('\b', [1 num_chars]))
+end
+fprintf('%06d Done in %f seconds.\n', numel(conf.list), toc(c));
+stats.printStats()
 
-    conf = struct('list', first:last, 'dilate', 5);
-    conf = parse_pv_pairs(conf, varargin);
-
-    info = edf_info(fullfile('1_preprocessing', 'full', 'full0000.edf'));
-    totproj = parameters.acq.nproj *2;
-    stats = GtTasksStatistics();
-    stats.add_task('load_blob', 'Time to load from DB');
-    stats.add_task('load_mask', 'Time to load mask');
-    stats.add_task('save_blob', 'Time to save to HDF5');
-    stats.add_task('convert_blob', 'Time for converting from DB to HDF5')
-
-    fprintf('Progress: ')
-    c = tic();
-    for ii = conf.list
-        num_chars = fprintf('%06d/%06d (%s)', ii, numel(conf.list), ...
-            stats.get_formatted_total('convert_blob'));
-        stats.tic('convert_blob')
-        stats.tic('load_mask')
-        [mask, bb] = get_mask('2_difspot', ii, parameters, conf);
-        mask(mask < 0) = 0;
-        stats.toc('load_mask')
-
-        stats.tic('load_blob')
-        blob = get_blob(bb, info, totproj);
-        blob(blob < 0) = 0;
-        stats.toc('load_blob')
-
-        stats.tic('save_blob')
-        gtWriteBlobToHDF5('2_difblob', ii, blob, bb, mask);
-        stats.toc('save_blob')
-        stats.toc('convert_blob')
-
-        fprintf(repmat('\b', [1 num_chars]))
-    end
-    fprintf('%06d Done in %f seconds.\n', numel(conf.list), toc(c));
-    stats.printStats()
 end
 
 function blob = get_blob(bb, info, totproj)