Merge pull request #44 from cpp-lln-lab/simplify

[REF] refactor the way the ROIs are saved

Author: Remi-Gau

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "CPP ROI"
 
-version: v0.2.0dev
+version: 0.2.0dev
 
 abstract: Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to play nice with BIDS datasets.
 

Makefile

@@ -1,8 +1,8 @@
 .PHONY: clean install_dev
 
-clean:
+clean: clean_lib
 	rm -rf coverage*
-	rm version.txt
+	rm -f version.txt
 
 clean_lib:
 	rm -rf lib/bids-matlab

src/roi/createRoi.m

@@ -332,21 +332,8 @@
 
   % use Marsbar to save as a .mat and then convert that to an image
   % in the correct space
-  tempFile = spm_file(roiName, ...
-                      'ext', ...
-                      'mat');
-  saveroi(roiObject, ...
-          fullfile(outputDir, tempFile));
-
   outputFile = fullfile(outputDir, roiName);
-
-  mars_rois2img(fullfile(outputDir, tempFile), ...
-                outputFile, ...
-                spm_vol(volumeDefiningImage));
-  delete(fullfile(outputDir, tempFile));
-
-  % delete label files
-  delete(fullfile(outputDir, '*_mask_labels.mat'));
+  save_as_image(roiObject, outputFile);
 
   json = bids.derivatives_json(outputFile);
   bids.util.jsonencode(json.filename, json.content);

src/roi/plotDataInRoi.m

@@ -153,7 +153,7 @@
     nbBins = max(nbBinsList);
   end
 
-  maxVox = getMaxVox(args, data);
+  maxVox = getMaxVox(args, data, nbBins);
 
   %% plot histogram and mode
 
@@ -247,7 +247,7 @@ function labelAxis(roiAs, rows, cols, subplotList, roiImages, dataLabel)
 
 end
 
-function maxVox = getMaxVox(args, data)
+function maxVox = getMaxVox(args, data, nbBins)
 
   maxVox = args.Results.maxVox;