Merge pull request #634 from Remi-Gau/remi_fix_win_bug

[FIX] use unix format when priting path to screen

Author: Remi-Gau

lib/bids-matlab

@@ -15,7 +15,8 @@ function  createDerivativeDir(opt)
 
   if ~exist(opt.dir.derivatives, 'dir')
     spm_mkdir(opt.dir.derivatives);
-    msg = sprintf('derivatives directory created: %s \n', opt.dir.derivatives);
+    msg = sprintf('derivatives directory created: %s \n', ...
+                  pathToPrint(opt.dir.derivatives));
   end
 
   printToScreen(msg, opt);

src/IO/createDerivativeDir.m

@@ -33,7 +33,7 @@
     printToScreen(msg, opt);
   end
 
-  msg = sprintf('Getting data from:\n %s\n', bidsDir);
+  msg = sprintf('Getting data from:\n %s\n', pathToPrint(bidsDir));
   printToScreen(msg, opt);
 
   validationInputFile(bidsDir, 'dataset_description.json');

src/IO/getData.m

@@ -3,7 +3,7 @@ function overwriteDir(directory, opt)
   % (C) Copyright 2021 CPP_SPM developers
 
   if exist(directory, 'dir') == 7
-    msg = sprintf('overwriting directory: %s \n', directory);
+    msg = sprintf('overwriting directory: %s \n', pathToPrint(directory));
     errorHandling(mfilename(), 'overWritingDir', msg, true, opt.verbosity);
     rmdir(directory, 's');
   end

src/IO/overwriteDir.m

@@ -24,6 +24,7 @@ function saveOptions(opt)
   jsonFormat.indent = '    ';
   spm_jsonwrite(filename, opt, jsonFormat);
 
-  printToScreen(sprintf('Options saved in: %s\n\n', filename), opt);
+  printToScreen(sprintf('Options saved in: %s\n\n', ...
+                        pathToPrint(filename)), opt);
 
 end

src/IO/saveOptions.m

@@ -114,7 +114,7 @@
 
     runCounter = runCounter + 1;
 
-    printToScreen([files{iFile}, '\n'], opt);
+    printToScreen([pathToPrint(files{iFile}), '\n'], opt);
 
   end
 

src/batches/preproc/setBatchSTC.m

@@ -36,8 +36,7 @@
   sessions = getInfo(BIDS, subLabel, opt, 'Sessions');
   runs = getInfo(BIDS, subLabel, opt, 'Runs', sessions{1});
 
-  [fileName, subFuncDataDir] = getBoldFilename( ...
-                                               BIDS, ...
+  [fileName, subFuncDataDir] = getBoldFilename(BIDS, ...
                                                subLabel, sessions{1}, runs{1}, opt);
   bf = bids.File(fileName);
 
@@ -57,8 +56,7 @@
   matlabbatch{end}.cfg_basicio.var_ops.cfg_save_vars.vars.vname = 'transformationMatrix';
 
   matlabbatch{end}.cfg_basicio.var_ops.cfg_save_vars.vars.vcont(1) = ...
-      cfg_dep( ...
-              'Coregister: Estimate: Coregistration Matrix', ...
+      cfg_dep('Coregister: Estimate: Coregistration Matrix', ...
               returnDependency(opt, 'coregister'), ...
               substruct('.', 'M'));
 

src/batches/preproc/setBatchSaveCoregistrationMatrix.m

@@ -67,7 +67,7 @@
   % If it exists, issue a warning that it has been overwritten
   ffxDir = getFFXdir(subLabel, opt);
   overwriteDir(ffxDir, opt);
-  printToScreen(sprintf(' output dir: %s\n', ffxDir), opt);
+  printToScreen(sprintf(' output dir: %s\n', pathToPrint(ffxDir)), opt);
   fmri_spec.dir = {ffxDir};
 
   fmri_spec.fact = struct('name', {}, 'levels', {});

src/batches/stats/setBatchSubjectLevelGLMSpec.m

@@ -48,14 +48,14 @@
   % it could be required to take another one, or several and mean them...
   if numel(anat) > 1
     msg = sprintf('More than one anat file found:%s\n\nTaking the first one:\n\n %s\n', ...
-                  createUnorderedList(anat), ...
-                  anat{1});
+                  createUnorderedList(pathToPrint(anat)), ...
+                  pathToPrint(anat{1}));
     errorHandling(mfilename(), 'severalAnatFile', msg, true, opt.verbosity);
   end
   anat = anat{1};
   anatImage = unzipAndReturnsFullpathName(anat);
 
-  msg = sprintf('selecting anat file: %s\n', anat);
+  msg = sprintf('selecting anat file: %s\n', pathToPrint(anat));
   printToScreen(msg, opt);
 
   [anatDataDir, anatImage, ext] = spm_fileparts(anatImage);

src/bids/getAnatFilename.m

@@ -11,13 +11,17 @@
   %
   % :param BIDS:        returned by bids.layout when exploring a BIDS data set.
   % :type BIDS:         structure
-  % :param subLabel:       label of the subject ; in BIDS lingo that means that for a file name
+  %
+  % :param subLabel:    label of the subject ; in BIDS lingo that means that for a file name
   %                     ``sub-02_task-foo_bold.nii`` the subLabel will be the string ``02``
-  % :type subLabel:        string
+  % :type subLabel:      char
+  %
   % :param sessionID:   session label (for `ses-001`, the label will be `001`)
-  % :type sessionID:    string
+  % :type sessionID:    char
+  %
   % :param runID:       run index label (for `run-001`, the label will be `001`)
-  % :type runID:        string
+  % :type runID:        char
+  %
   % :param opt:         Mostly used to find the task name.
   % :type opt:          structure
   %
@@ -43,7 +47,7 @@
   % some part of it is in getInfo
   if isempty(boldFilename)
     msg = sprintf('No bold file found in:\n\t%s\nfor filter:%s\n', ...
-                  BIDS.pth, ...
+                  pathToPrint(BIDS.pth), ...
                   createUnorderedList(opt.query));
 
     errorHandling(mfilename(), 'emptyInput', msg, false, true);
@@ -52,7 +56,7 @@
   % in case files have been unzipped, we do it now
   fullPathBoldFilename = unzipAndReturnsFullpathName(boldFilename, opt);
 
-  printToScreen(createUnorderedList(fullPathBoldFilename), opt);
+  printToScreen(createUnorderedList(pathToPrint(fullPathBoldFilename)), opt);
 
   boldFilename = spm_file(fullPathBoldFilename, 'filename');
   subFuncDataDir = spm_file(fullPathBoldFilename, 'path');