[ENH] add gzip scripts for raw folder

demos/sourceDataProcessing/batchSource.m

@@ -16,3 +16,9 @@
 
 % Single volumes to 4D volumes conversion + remove n dummies
 convert3Dto4D(optSource);
+
+% Deface anatomical volumes in a raw folder
+% defaceAnat(optSource); COMING SOON
+
+% GZip the volumes in a raw folder
+bidsGZipRawFolder(optSource, 0)

demos/sourceDataProcessing/getOptionSource.m

@@ -17,6 +17,8 @@
 
   % Set the folder where sequences folders exist
   optSource.sourceDir = '/Users/barilari/Desktop/DICOM_UCL_leuven/renamed/sub-pilot001/ses-002/MRI';
+
+  optSource.dataDir = '/Users/barilari/Desktop/DICOM_UCL_leuven/raw';
 
   % List of the sequences that you want to skip (folder name pattern)
   optSource.sequenceToIgnore = {'AAHead_Scout', ...

src/batches/setBatch3Dto4D.m

@@ -4,7 +4,7 @@
   %
   % Set the batch for 3D to 4D conversion
   %
-  % USAGE:: matlabbatch = setBatch3Dto4D(volumesList, outputName, dataType, RT)
+  % USAGE:: 
   %
   %   matlabbatch = setBatch3Dto4D(volumesList, outputName, dataType, RT)
   %

src/batches/setBatchGZip.m

@@ -0,0 +1,22 @@
+% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+
+function matlabbatch = setBatchGZip(unzippedNiifiles, keepUnzippedNii)
+  %
+  % Set the batch for GZip the 4D volumes
+  %
+  % USAGE:: 
+  %
+  %   matlabbatch = setBatchGZip(unzippedNiifiles, keepUnzippedNii)
+  %
+  % :param unzippedNiifiles: List of volumes to be gzipped
+  % :type unzippedNiifiles: array
+  % :param keepUnzippedNii: Boolean to decide to delete the unzipped files
+  % :type keepUnzippedNii: boolean
+  %
+  % :returns: - :matlabbatch: (struct) The matlabbath ready to run the spm job
+
+  matlabbatch{1}.cfg_basicio.file_dir.file_ops.cfg_gzip_files.files = unzippedNiifiles;
+  matlabbatch{1}.cfg_basicio.file_dir.file_ops.cfg_gzip_files.outdir = {''};
+  matlabbatch{1}.cfg_basicio.file_dir.file_ops.cfg_gzip_files.keep = keepUnzippedNii;
+
+end

src/defaults/checkOptionsSource.m

@@ -12,20 +12,36 @@
   %                   to run the batch workflow for source processing
   %
   % :returns: - :optSource: (struc) The structure with any unset fields with the deaufalt values
+  %   
+  % OPTIONS (with their defaults):
+  %   - ``optSource.sourceDir = ''`` - The directory where the source data are located.
+  %   - ``optSource.dataDir = ''`` - The directory where the raw data to apply changes are located.
+  %   - ``optSource.sequenceToIgnore  = {}`` - The list of sequence(s) to ignore.
+  %   - ``optSource.dataType = 0`` - Data format conversion (0 is reccomended).
+  %   - ``optSource.zip = 0`` - Boolean to enable gzip of the new 4D file in ``convert3Dto4D``.
+  %   - ``optSource.nbDummies = 0`` - Number of volumes to discard ad dummies in ``convert3Dto4D``.
+  %   - ``optSource.sequenceRmDummies = {}`` - The list of sequence(s) where to discarding the 
+  %     dummies.
 
   fieldsToSet = setDefaultOptionSource();
 
   optSource = setDefaultFields(optSource, fieldsToSet);
 
   if isempty(optSource.sourceDir) || ~isdir(optSource.sourceDir)
 
-    error('The source folder does not exist, try again.');
+    warning('The source folder is not provided or does not exist.');
+
+  end
+
+  if isempty(optSource.dataDir) || ~isdir(optSource.dataDir)
+
+    warning('The raw folder is not provided or does not exist.');
 
   end
 
   if isempty(optSource.sequenceToIgnore)
 
-    warning('No sequence to ignore provided, I will convert all the images that I can found');
+    warning('No sequence-to-ignore provided, I will convert all the images that I can found');
 
   end
 
@@ -36,6 +52,9 @@
 
   % The directory where the source data are located
   fieldsToSet.sourceDir = '';
+
+  % The directory where the raw data to apply changes are located
+  fieldsToSet.dataDir = '';
 
   % The list of sequence(s) to ignore
   fieldsToSet.sequenceToIgnore = {};

src/workflows/bidsGZipRawFolder.m

@@ -0,0 +1,39 @@
+% (C) Copyright 2020 CPP BIDS SPM-pipeline developers
+
+function bidsGZipRawFolder(optSource, keepUnzippedNii)
+
+  %
+  % GZip the nii files in a ``raw`` bids folders from the. It will do it independently of the task.
+  %
+  % USAGE::
+  %
+  %   bidsGZipRawFolder(optSource ...
+  %                     [, keepUnzippedNii = false])
+  %
+  % :param optSource: The structure that contains the options set by the user to run the batch
+  %                   workflow for source processing
+  % :type opt: structure
+  % :param keepUnzippedNii: will keep the original ``.nii`` if set to ``true``. Default is false
+  % :type keepUnzippedNii: boolean
+
+  %% input variables default values
+
+
+  if nargin < 2 || isempty(keepUnzippedNii)
+    % delete the original unzipped .nii
+    keepUnzippedNii = false;
+  end
+
+  tic;
+
+  printWorklowName('GZip data');
+
+  rawDir = optSource.dataDir;
+
+  unzippedNiifiles = cellstr(spm_select('FPListRec', rawDir, '^.*.nii$'));
+
+  matlabbatch = setBatchGZip(unzippedNiifiles, keepUnzippedNii);
+
+  spm_jobman('run', matlabbatch);
+
+  toc;

tests/test_checkOptionsSource.m

@@ -0,0 +1,51 @@
+function test_suite = test_checkOptionsSource %#ok<*STOUT>
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_checkOptionsSourceBasic()
+
+  optSource.nbDummies = 0;
+  optSource = checkOptionsSource(optSource);
+
+  expectedOptionsSource = defaultOptionsSource();
+  expectedOptionsSource.nbDummies = 0;
+
+  assertEqual(optSource, expectedOptionsSource);
+
+end
+
+function test_checkOptionsSourceDoNotOverwrite()
+
+  optSource.dataType = 666;
+  optSource.someExtraField = 'test';
+  optSource.nbDummies = 42;
+
+  optSource = checkOptionsSource(optSource);
+
+  assertEqual(optSource.dataType, 666);
+  assertEqual(optSource.someExtraField, 'test');
+  assertEqual(optSource.nbDummies, 42);
+
+end
+
+function expectedOptionsSource = defaultOptionsSource()
+
+  expectedOptionsSource.sourceDir = '';
+
+  expectedOptionsSource.dataDir = '';
+
+  expectedOptionsSource.sequenceToIgnore = {};
+
+  expectedOptionsSource.dataType = 0;
+
+  expectedOptionsSource.zip = 0;
+
+  expectedOptionsSource.nbDummies = 0;
+
+  expectedOptionsSource.sequenceRmDummies = {};
+
+end