[ENH] add hemisphere parameter to CLI

bidspm.m

@@ -44,6 +44,7 @@
 
   % create_roi only
   addParameter(args, 'roi_dir', '', isChar);
+  addParameter(args, 'hemisphere', {'L', 'R'}, isCellStr);
   addParameter(args, 'roi_atlas', 'neuromorphometrics', isInAvailableAtlas);
   addParameter(args, 'roi_name', {''}, isCellStr);
 

src/cli/getOptionsFromCliArgument.m

@@ -76,6 +76,7 @@
     % create_roi
     opt.roi.atlas = args.Results.roi_atlas;
     opt.roi.name = args.Results.roi_name;
+    opt.roi.hemi = args.Results.hemisphere;
 
     % stats
     opt.dir.preproc = args.Results.preproc_dir;

src/defaults/checkOptions.m

@@ -50,9 +50,7 @@
   %               't2w',  struct('modality', 'anat', 'suffix', 'T2w'), ...
   %               't1w',  struct('modality', 'anat', 'space', '', 'suffix', 'T1w'), ...
   %               'roi',  struct('modality', 'roi', 'suffix', 'mask'), ...
-  %                                          'xfm',  struct('modality', 'anat', ...
-  %                                                         'suffix', 'xfm', ...
-  %                                                         'to', 'T1w'));
+  %               'xfm',  struct('modality', 'anat', 'suffix', 'xfm', 'to', 'T1w'));
   %
   %  - **preprocessing**
   %

src/messages/bidspmHelp.m

@@ -167,6 +167,7 @@ function bidspmHelp()
   %           'verbosity', 2, ...
   %           'roi_atlas', 'wang', ...
   %           'roi_name', {'V1v', 'V1d'}, ...
+  %           'hemisphre', {'L', 'R'}, ...
   %           'space', {'wang'}, ...
   %           'options', struct([]))
   %
@@ -181,6 +182,10 @@ function bidspmHelp()
   %                       the list of available ROI will be returned in the error message.
   % :type  roi_name:      cell string
   %
+  % :param hemisphre:     Hemisphere of the ROI to create.
+  %                       Not all ROIs have both hemispheres.
+  % :type  hemisphre:     cell string containing any of 'L', 'R'
+  %
   %
   % **SMOOTH:**
   %

src/messages/bugReport.m

@@ -19,9 +19,6 @@ function bugReport(opt, ME)
 
   json.GeneratedBy = GeneratedBy;
   json.OS = OS;
-  if nargin > 1
-    json.ME = ME;
-  end
 
   output_dir = pwd;
   if isfield(opt, 'dir') && isfield(opt.dir, 'output')
@@ -30,12 +27,25 @@ function bugReport(opt, ME)
   output_dir = fullfile(output_dir, 'error_logs');
   spm_mkdir(output_dir);
 
-  logger('WARNING', 'An error occurred');
-  unfold(json);
+  if nargin > 1
+    json.ME = ME;
 
+    for i = 1:numel(json.ME.stack)
+      stackTrace{i} = sprintf('Error in %s\n\t\tline %i in %s', ...
+                              json.ME.stack(i).name, ...
+                              json.ME.stack(i).line, ...
+                              json.ME.stack(i).file); %#ok<*AGROW>
+    end
+
+    logger('INFO', sprintf('%s\n Error %s occurred:%s%s', ...
+                           json.ME.message, ...
+                           json.ME.identifier, ...
+                           createUnorderedList(stackTrace)), ...
+           'color', 'red');
+  end
   logFile = spm_file(fullfile(output_dir, sprintf('error_%s.log', timeStamp())), 'cpath');
   bids.util.jsonwrite(logFile, json);
-  printToScreen(sprintf(['\nERROR LOG SAVED:\n\t%s\n', ...
+  printToScreen(sprintf(['ERROR LOG SAVED:\n\t%s\n', ...
                          'Use it when opening an issue:\n\t%s.\n\n'], ...
                         pathToPrint(logFile), ...
                         [returnRepoURL() '/issues/new/choose']), ...

src/messages/logger.m

@@ -28,6 +28,7 @@
   addParameter(args, 'options', default_opt, @isstruct);
   addParameter(args, 'filename', '', @ischar);
   addParameter(args, 'id', '', @ischar);
+  addParameter(args, 'color', 'blue', @ischar);
 
   parse(args, varargin{:});
 
@@ -36,6 +37,7 @@
   opt = args.Results.options;
   filename = args.Results.filename;
   id = args.Results.id;
+  color = args.Results.color;
 
   [~, filename, ext] = fileparts(filename);
 
@@ -81,15 +83,15 @@
         errorHandling(filename, id, logMsg, true, true);
       end
       if ismember(logLevel, {'INFO'})
-        printToScreen(logMsg, opt, 'format', 'blue');
+        printToScreen(logMsg, opt, 'format', color);
       end
 
     case 3
       if ismember(logLevel, {'WARNING'})
         errorHandling(filename, id, logMsg, true, true);
       end
       if ismember(logLevel, {'INFO', 'DEBUG'})
-        printToScreen(logMsg, opt, 'format', 'blue');
+        printToScreen(logMsg, opt, 'format', color);
       end
   end
 

src/workflows/roi/bidsCreateROI.m

@@ -10,39 +10,45 @@ function bidsCreateROI(opt)
   %
   % USAGE::
   %
-  %  opt = get_option();
-  %  opt.roi.atlas = 'wang';
-  %  opt.roi.name = {'V1v', 'V1d'};
-  %  opt.roi.space = {'IXI549Space', 'individual'};
-  %  opt.dir.stats = fullfile(opt.dir.raw, '..', 'derivatives', 'bidspm-stats');
+  %   % to create ROI in MNI space
+  %   opt.dir.roi = pwd;
+  %   opt.roi.atlas = 'wang';
+  %   opt.roi.hemi = {'L', 'R'};
+  %   opt.roi.name = {'V1v', 'V1d'};
+  %   opt.roi.space = {'IXI549Space''};
   %
-  %  bidsCreateROI(opt);
+  %   bidsCreateROI(opt);
+  %
+  %
+  %   % to create ROI in subject space
+  %   opt.dir.roi = pwd;
+  %   opt.roi.atlas = 'wang';
+  %   opt.roi.hemi = {'L', 'R'};
+  %   opt.roi.name = {'V1v', 'V1d'};
+  %   opt.roi.space = {'IXI549Space', 'individual'};
+  %   opt.dir.input = fullfile(opt.dir.raw, '..', 'derivatives', 'bidspm-preproc');
+  %
+  %   bidsCreateROI(opt);
   %
   %
 
   % (C) Copyright 2021 bidspm developers
 
-  if nargin < 1
-    opt = [];
-  end
-
   if any(~strcmp(opt.roi.space, 'individual'))
 
     if ~isfield(opt.dir, 'roi')
       opt.dir.roi = spm_file(fullfile(opt.dir.derivatives, 'bidspm-roi'), 'cpath');
     end
     spm_mkdir(fullfile(opt.dir.roi, 'group'));
 
-    hemi = {'L', 'R'};
-
-    for iHemi = 1:numel(hemi)
+    for iHemi = 1:numel(opt.roi.hemi)
 
       for iROI = 1:numel(opt.roi.name)
 
         extractRoiFromAtlas(fullfile(opt.dir.roi, 'group'), ...
                             opt.roi.atlas, ...
                             opt.roi.name{iROI}, ...
-                            hemi{iHemi});
+                            opt.roi.hemi{iHemi});
 
       end
 

tests/tests_cli/test_bidspm.m

@@ -11,7 +11,7 @@
 
 end
 
-function test_bidsCreateROI_CLI()
+function test_bidsCreateROI_wang()
 
   bidspm(pwd, fullfile(pwd, 'tmp'), ...
          'subject', ...
@@ -25,19 +25,24 @@ function test_bidsCreateROI_CLI()
   cleanUp(fullfile(pwd, 'options'));
   cleanUp(fullfile(pwd, 'error_logs'));
 
-  if ~isOctave()
-    bidspm(pwd, fullfile(pwd, 'tmp'), ...
-           'subject', ...
-           'action', 'create_roi', ...
-           'roi_atlas', 'visfatlas', ...
-           'roi_name', {'OTS'}, ...
-           'space', {'IXI549Space'}, ...
-           'verbosity', 0);
-
-    cleanUp(fullfile(pwd, 'tmp'));
-    cleanUp(fullfile(pwd, 'options'));
-    cleanUp(fullfile(pwd, 'error_logs'));
-  end
+end
+
+function test_bidsCreateROI_visfatlas()
+
+  bidspm(pwd, fullfile(pwd, 'tmp'), ...
+         'subject', ...
+         'action', 'create_roi', ...
+         'roi_atlas', 'visfatlas', ...
+         'roi_name', {'OTS'}, ...
+         'space', {'IXI549Space'}, ...
+         'verbosity', 0);
+
+  cleanUp(fullfile(pwd, 'tmp'));
+  cleanUp(fullfile(pwd, 'options'));
+  cleanUp(fullfile(pwd, 'error_logs'));
+end
+
+function test_bidsCreateROI_neuromorphometrics()
 
   bidspm(pwd, fullfile(pwd, 'tmp'), ...
          'subject', ...
@@ -51,6 +56,10 @@ function test_bidsCreateROI_CLI()
   cleanUp(fullfile(pwd, 'options'));
   cleanUp(fullfile(pwd, 'error_logs'));
 
+end
+
+function test_bidsCreateROI_neuromorphometrics_inve_norm()
+
   % requires some deformation field to work
 
   %   if ~isGithubCi
@@ -71,6 +80,23 @@ function test_bidsCreateROI_CLI()
 
 end
 
+function test_bidsCreateROI_one_hemisphere()
+  bidspm(pwd, fullfile(pwd, 'tmp'), 'subject', ...
+         'action', 'create_roi', ...
+         'verbosity', 0, ...
+         'roi_atlas', 'visfatlas', ...
+         'hemisphere', {'L'}, ...
+         'roi_name', {'OTS', 'ITG', 'MTG', 'LOS', 'pOTS', 'IOS'}, ...
+         'space', {'IXI549Space'});
+  assertEqual(size(spm_select('FPListRec', ...
+                              fullfile(pwd, 'tmp'), ...
+                              '.*mask.nii'), 1), ...
+              6);
+  cleanUp(fullfile(pwd, 'tmp'));
+  cleanUp(fullfile(pwd, 'options'));
+  cleanUp(fullfile(pwd, 'error_logs'));
+end
+
 function test_boilerplate_stats_only()
 
   if ~isGithubCi

tests/tests_workflows/stats/test_bidsRoiBasedGLM.m

@@ -24,6 +24,10 @@ function test_bidsRoiBasedGLM_run()
   %  - also makes sure that previous results are not deleted
   %
 
+  if isOctave
+    return
+  end
+
   opt = setOptions('MoAE-fmriprep', '01');
 
   opt.query.space = opt.space;
@@ -53,6 +57,7 @@ function test_bidsRoiBasedGLM_run()
 
   opt.roi.atlas = 'wang';
   opt.roi.name = {'V1v', 'V1d'};
+  opt.roi.hemi = {'L', 'R'};
   opt.roi.space = opt.space;
 
   opt.bidsFilterFile.roi.space = 'MNI';