[ENH] overwrite files when renaming by default (#1051)

* overwrite files when renaming by default

* fix tests

docs/source/default_options.m

@@ -46,7 +46,7 @@
 opt.query.modality{1} = 'anat'  ;
 opt.query.modality{2} = 'func'  ;
 opt.realign.useUnwarp = 1, ;
-opt.rename = 1, ;
+opt.rename.do = 1, ;
 opt.results.MC = 'FWE'  ;
 opt.results.atlas = 'Neuromorphometrics'  ;
 opt.results.binary = 0, ;

src/defaults/checkOptions.m

@@ -94,9 +94,11 @@
   %     - ``opt.zeropad = 2`` - number of zeros used for padding subject numbers, in case
   %       subjects should be fetched by their number ``1`` and not their label ``O1'``.
   %
-  %     - ``opt.rename = true`` - to skip renaming files with ``bidsRename()``.
+  %     - ``opt.rename.do = true`` - to skip renaming files with ``bidsRename()``.
   %       Mostly for debugging as the output files won't be usable by any of the stats
   %       workflows.
+  %     - ``opt.rename.overwrite = true`` - To overwrite any eventual previous output of
+  %       ``bidsRename()``.
   %
   %     - ``opt.msg.color = blue`` - default font color of the prompt messages.
   %
@@ -262,7 +264,8 @@
   fieldsToSet.subjects = {[]};
   fieldsToSet.zeropad = 2;
 
-  fieldsToSet.rename = true;
+  fieldsToSet.rename.do = true;
+  fieldsToSet.rename.overwrite = true;
 
   fieldsToSet.query.modality = {'anat', 'func'};
 

src/workflows/bidsRename.m

@@ -19,13 +19,13 @@
 
   % (C) Copyright 2019 bidspm developers
 
-  if ~opt.rename
+  if ~opt.rename.do
     return
   end
 
   createdFiles = {};
 
-  if not(isfield(opt, 'spm_2_bids'))
+  if ~(isfield(opt, 'spm_2_bids'))
     opt = set_spm_2_bids_defaults(opt);
   end
 
@@ -82,7 +82,8 @@ function renameFileAndUpdateMetadata(opt, data, newFilename, json, createdFiles)
   end
 
   % TODO write test for this
-  if exist(outputFile, 'file') || ismember(newFilename, createdFiles)
+  if ~opt.rename.overwrite && exist(outputFile, 'file') || ...
+      ismember(newFilename, createdFiles)
 
     msg = sprintf('This file already exists. Will not overwrite.\n\t%s\n', ...
                   newFilename);

src/workflows/preproc/bidsCreateVDM.m

@@ -30,7 +30,7 @@ function bidsCreateVDM(opt)
   [BIDS, opt] = setUpWorkflow(opt, 'create voxel displacement map');
 
   % why?
-  opt.rename = false;
+  opt.rename.do = false;
 
   opt.query.desc = '';
 
@@ -43,7 +43,7 @@ function bidsCreateVDM(opt)
 
     if any(ismember(suffixes, {'phase12', 'phasediff', 'fieldmap', 'epi'}))
 
-      opt.rename = true;
+      opt.rename.do = true;
 
       printProcessingSubject(iSub, subLabel, opt);
 

src/workflows/preproc/bidsRealignReslice.m

@@ -42,7 +42,7 @@ function bidsRealignReslice(opt)
 
     saveAndRunWorkflow(matlabbatch, 'realign_reslice', opt, subLabel);
 
-    if ~opt.dryRun && opt.rename
+    if ~opt.dryRun && opt.rename.do
 
       copyFigures(BIDS, opt, subLabel);
 

src/workflows/preproc/bidsRealignUnwarp.m

@@ -52,7 +52,7 @@ function bidsRealignUnwarp(opt)
 
   cleanUpWorkflow(opt);
 
-  if ~opt.dryRun && opt.rename
+  if ~opt.dryRun && opt.rename.do
     opt = set_spm_2_bids_defaults(opt);
     prefix = get_spm_prefix_list();
     opt.query.prefix = prefix.unwarp;

src/workflows/preproc/bidsSegmentSkullStrip.m

@@ -71,15 +71,15 @@
 
     saveAndRunWorkflow(matlabbatch, 'segment_skullstrip', opt, subLabel);
 
-    if ~opt.dryRun && opt.rename
+    if ~opt.dryRun && opt.rename.do
       renameSegmentParameter(BIDS, subLabel, opt);
     end
 
   end
 
   cleanUpWorkflow(opt);
 
-  if opt.dryRun || ~opt.rename
+  if opt.dryRun || ~opt.rename.do
     return
   end
 

src/workflows/preproc/bidsSpatialPrepro.m

@@ -141,7 +141,7 @@
 
 function renameFiles(BIDS, opt)
 
-  if ~opt.rename || opt.dryRun
+  if ~opt.rename.do || opt.dryRun
     return
   end
 

tests/utils/defaultOptions.m

@@ -74,7 +74,8 @@
 
   expectedOptions.zeropad = 2;
 
-  expectedOptions.rename = true;
+  expectedOptions.rename.do = true;
+  expectedOptions.rename.overwrite = true;
 
   expectedOptions.QA.glm.do = false;