[REF / FIX / ENH] misc

src/batches/preproc/setBatchRenameSegmentParameter.m

@@ -0,0 +1,56 @@
+function matlabbatch = setBatchRenameSegmentParameter(varargin)
+  %
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBachRenameSegmentParameter(matlabbatch, opt)
+  %
+  % :param matlabbatch: matlabbatch to append to.
+  % :type matlabbatch: cell
+  % :param opt: structure or json filename containing the options. See
+  %             ``checkOptions()`` and ``loadAndCheckOptions()``.
+  % :type opt: structure
+  %
+  %
+  % :returns: - :matlabbatch: (cell) The matlabbatch ready to run the spm job
+  %
+  % (C) Copyright 2022 CPP_SPM developers
+
+  p = inputParser;
+
+  addRequired(p, 'matlabbatch', @iscell);
+  addRequired(p, 'opt', @isstruct);
+
+  parse(p, varargin{:});
+
+  matlabbatch = p.Results.matlabbatch;
+  opt = p.Results.opt;
+
+  printBatchName('rename segmentation parameter file', opt);
+
+  cfg_fileparts.files(1) = cfg_dep('Segment: Seg Params', ...
+                                   returnDependency(opt, 'segment'), ...
+                                   substruct('.', 'param', '()', {':'}));
+
+  matlabbatch{end + 1}.cfg_basicio.file_dir.cfg_fileparts = cfg_fileparts;
+
+  files = cfg_dep('Segment: Seg Params', ...
+                  returnDependency(opt, 'segment'), ...
+                  substruct('.', 'param', '()', {':'}));
+
+  moveTo = cfg_dep('Get Pathnames: Directories (unique)', ...
+                   substruct('.', ...
+                             'val', '{}', {numel(matlabbatch)}, '.', ...
+                             'val', '{}', {1}, '.', ...
+                             'val', '{}', {1}), ...
+                   substruct('.', 'up'));
+
+  % TODO: adapt in case suffix is not T1w
+  patternReplace(1).pattern = 'T1w';
+  patternReplace(1).repl = 'label-T1w';
+  patternReplace(2).pattern = 'seg8';
+  patternReplace(2).repl = 'segparam';
+
+  matlabbatch = setBachRename(matlabbatch, files, moveTo, patternReplace);
+
+end

src/batches/setBachRename.m

@@ -0,0 +1,41 @@
+function matlabbatch = setBachRename(varargin)
+  %
+  %
+  % USAGE::
+  %
+  %   matlabbatch = setBachRename(matlabbatch, files, moveTo, patternReplace, overwriteDuplicate)
+  %
+  %
+  % :returns: - :matlabbatch: (cell) The matlabbatch ready to run the spm job
+  %
+  % (C) Copyright 2022 CPP_SPM developers
+
+  p = inputParser;
+
+  isPatternReplaceStruct = @(x) isstruct(x) && all(ismember({'pattern', 'repl'}, fieldnames(x)));
+
+  addRequired(p, 'matlabbatch', @iscell);
+  addRequired(p, 'files', @iscell);
+  addRequired(p, 'moveTo', @iscell);
+  addRequired(p, 'patternReplace', isPatternReplaceStruct);
+  addOptional(p, 'overwriteDuplicate', false, @islogical);
+
+  parse(p, varargin{:});
+
+  matlabbatch = p.Results.matlabbatch;
+  files = p.Results.files;
+  moveTo = p.Results.moveTo;
+  patternReplace = p.Results.patternReplace;
+  overwriteDuplicate = p.Results.overwriteDuplicate;
+
+  file_move.files = files;
+
+  file_move.action.moveren.moveto = moveTo;
+
+  file_move.action.moveren.patrep = patternReplace;
+
+  file_move.action.moveren.unique = overwriteDuplicate;
+
+  matlabbatch{end + 1}.cfg_basicio.file_dir.file_ops.file_move = file_move;
+
+end

src/batches/stats/setBatchSubjectLevelGLMSpec.m

@@ -24,7 +24,7 @@
   if ~isfield(BIDS, 'raw')
     msg = sprintf(['Provide raw BIDS dataset path in opt.dir.raw .\n' ...
                    'It is needed to load events.tsv files.\n']);
-    errorHandling(mfilename(), 'missingRawDir', msg, false, opt.verbosity);
+    errorHandling(mfilename(), 'missingRawDir', msg, false);
   end
 
   getModelType(opt.model.file);

src/utils/setDirectories.m

@@ -11,16 +11,17 @@
     return
   end
 
-  fields = fieldnames(opt.dir);
-  for i = 1:numel(fields)
-    opt.dir.(fields{i}) = canonicalizeIfNonEmpty(opt.dir.(fields{i}));
-  end
-
   opt = setDerivativesDir(opt);
   opt = setDir(opt, 'preproc');
   opt = setDir(opt, 'stats');
   opt = setInputDir(opt);
   opt = setOutputDir(opt);
+  opt = setJobsDir(opt, opt.dir.output);
+
+  fields = fieldnames(opt.dir);
+  for i = 1:numel(fields)
+    opt.dir.(fields{i}) = canonicalizeIfNonEmpty(opt.dir.(fields{i}));
+  end
 
 end
 
@@ -36,7 +37,7 @@
     end
   end
 
-  opt.dir.input = spm_file(inputDir, 'cpath');
+  opt.dir.input = inputDir;
 
 end
 
@@ -75,12 +76,11 @@
   % to set preproc and stats directory
   %
 
-  opt.dir.(step) = opt.dir.(step);
-
   if ~strcmp(opt.pipeline.type, step)
     return
 
   else
+
     % check that the pth ends with the pipeline type (preproc or stats) or
     % is just derivatives
     if ~isempty(opt.dir.(step)) && ( ...
@@ -89,6 +89,7 @@
                                     ~bids.internal.ends_with(opt.dir.(step), opt.pipeline.type))
       opt.dir.(step) = '';
     end
+
     if isempty(opt.dir.(step))
       % try to avoid creating folders called "preproc-preproc"
       if strcmp(opt.pipeline.name, opt.pipeline.type)
@@ -100,9 +101,8 @@
       return
 
     end
-  end
 
-  opt.dir.(step) = spm_file(opt.dir.(step), 'cpath');
+  end
 
 end
 
@@ -119,19 +119,19 @@
     end
   end
 
-  opt.dir.output = spm_file(outputDir, 'cpath');
-  opt = setJobsDir(opt, outputDir);
+  opt.dir.output = outputDir;
+
 end
 
 function opt = setJobsDir(opt, targetDir)
 
   jobDir = fullfile(targetDir, 'jobs');
+
   if isfield(opt, 'taskName') && ~isempty(opt.taskName) && ~isempty(opt.taskName{1})
     jobDir = fullfile(targetDir, 'jobs',  strjoin(opt.taskName, ''));
   end
-  opt.dir.jobs = jobDir;
 
-  opt.dir.jobs = spm_file(jobDir, 'cpath');
+  opt.dir.jobs = jobDir;
 
 end
 

src/workflows/bidsRename.m

@@ -48,22 +48,23 @@ function bidsRename(opt)
       msg = sprintf('%s --> %s\n', spm_file(data{iFile}, 'filename'), new_filename);
       printToScreen(msg, opt);
 
-      createdFiles{end + 1, 1} = new_filename;
-
       if ~opt.dryRun && ~strcmp(new_filename, spm_file(data{iFile}, 'filename'))
 
         % TODO write test for this
         if exist(new_filename, 'file') || ismember(new_filename, createdFiles)
           msg = sprintf('This file already exists. Will not overwrite.\n\t%s\n', ...
                         new_filename);
-          error_handling(mfilename(), 'fileAlreadyExist', msg, true, opt.verbosity);
+          errorHandling(mfilename(), 'fileAlreadyExist', msg, true, opt.verbosity);
 
         else
           movefile(data{iFile}, spm_file(data{iFile}, 'filename', new_filename));
 
         end
 
       end
+
+      createdFiles{end + 1, 1} = new_filename;
+
     end
 
   end

src/workflows/stats/bidsFFX.m

@@ -1,4 +1,4 @@
-function matlabbatch = bidsFFX(action, opt)
+function [matlabbatch, opt] = bidsFFX(action, opt)
   %
   % - specify the subject level fMRI model
   % - estimates it
@@ -36,7 +36,9 @@
   % (C) Copyright 2020 CPP_SPM developers
 
   opt.pipeline.type = 'stats';
+
   opt.dir.input = opt.dir.preproc;
+  opt.dir.output = opt.dir.stats;
 
   description = 'subject level GLM';
 
@@ -164,10 +166,9 @@ function checks(opt, action)
 end
 
 function batchName = createBatchName(opt, action)
-  batchName = ...
-      [action '_ffx_task-', strjoin(opt.taskName, ''), ...
-       '_space-', char(opt.space), ...
-       '_FWHM-', num2str(opt.fwhm.func)];
+  batchName = [action '_ffx_task-', strjoin(opt.taskName, ''), ...
+               '_space-', char(opt.space), ...
+               '_FWHM-', num2str(opt.fwhm.func)];
 end
 
 function matlabbatch = setAction(action, matlabbatch, BIDS, opt, subLabel)

src/workflows/stats/bidsRFX.m

@@ -29,6 +29,8 @@
 
   description = 'group level GLM';
 
+  opt.dir.output = opt.dir.stats;
+
   [~, opt] = setUpWorkflow(opt, description);
 
   checks(opt, action);

src/workflows/stats/bidsResults.m

@@ -119,6 +119,8 @@
 
   opt.pipeline.type = 'stats';
 
+  opt.dir.output = opt.dir.stats;
+
   [~, opt] = setUpWorkflow(opt, 'computing GLM results');
 
   % loop trough the steps and more results to compute for each contrast