add test for createRoi sphere and refactor

Author: Remi-Gau

src/roi/createRoi.m

@@ -1,4 +1,4 @@
-function [mask, outputFile] = createRoi(type, specification, volumeDefiningImage, outputDir, saveImg)
+function [mask, outputFile] = createRoi(varargin)
   %
   % Returns a mask to be used as a ROI by ``spm_summarize``.
   % Can also save the ROI as binary image.
@@ -20,18 +20,23 @@
   %
   % :param type: ``'mask'``, ``'sphere'``, ``'intersection'``, ``'expand'``
   % :type type: string
+  %
   % :param volumeDefiningImage: fullpath of the image that will define the space
   %                             (resolution, ...) if the ROI is to be saved.
   % :type volumeDefiningImage: string
+  %
   % :param saveImg: Will save the resulting image as binary mask if set to
   %                 ``true``
   % :type saveImg: boolean
+  %
   % :param specification: depending on the chosen ``type`` this can be:
   %
   %   :roiImage: - :string: fullpath of the roi image for ``'mask'``
+  %
   %   :sphere: - :structure: defines the charateristic for ``'sphere'``
   %                          - ``sphere.location``: X Y Z coordinates in millimeters
   %                          - ``spehere.radius``: radius in millimeters
+  %
   %   :specification: - :structure: defines the charateristic for ``'intersection'`` and ``'expand'``
   %                                 - ``sphere.location``: X Y Z coordinates in millimeters
   %                                 - ``sphere.radius``: radius in millimeters
@@ -64,17 +69,23 @@
   %
   % (C) Copyright 2021 CPP ROI developers
 
-  if nargin < 5
-    saveImg = false;
-  end
+  args = inputParser;
 
-  if nargin < 4
-    outputDir = pwd;
-  end
+  allowedTypes = @(x) ismember(x, {'mask', 'sphere', 'intersection', 'expand'});
 
-  if nargin < 3
-    volumeDefiningImage = '';
-  end
+  args.addRequired('type', allowedTypes);
+  args.addRequired('specification');
+  args.addOptional('volumeDefiningImage', '', @ischar);
+  args.addOptional('outputDir', pwd, @isdir);
+  args.addOptional('saveImg', false, @islogical);
+
+  args.parse(varargin{:});
+
+  type = args.Results.type;
+  specification = args.Results.specification;
+  volumeDefiningImage = args.Results.volumeDefiningImage;
+  outputDir = args.Results.outputDir;
+  saveImg = args.Results.saveImg;
 
   switch type
 

tests/test_createRoi.m

@@ -0,0 +1,42 @@
+function test_suite = test_createRoi %#ok<*STOUT>
+  % (C) Copyright 2022 CPP ROI developers
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_createRoi_sphere()
+
+  volumeDefiningImage = fullfile(demoDir(), 'TStatistic.nii');
+
+  sphere.location = [44 -67 0];
+  sphere.radius = 5;
+
+  saveImg = true;
+  outputDir = thisDir();
+
+  mask = createRoi('sphere', sphere, volumeDefiningImage, outputDir, saveImg);
+
+  assertEqual(exist(fullfile(thisDir(), 'label-sphere5x44yMinus67z0_mask.nii'), 'file'), 2);
+  assertEqual(exist(fullfile(thisDir(), 'label-sphere5x44yMinus67z0_mask.json'), 'file'), 2);
+
+  delete(fullfile(thisDir(), '*.nii'));
+  delete(fullfile(thisDir(), '*.json'));
+
+  mask = createRoi('sphere', sphere, volumeDefiningImage, outputDir, false);
+
+  assertEqual(exist(fullfile(thisDir(), 'label-sphere5x44yMinus67z0_mask.nii'), 'file'), 0);
+  assertEqual(exist(fullfile(thisDir(), 'label-sphere5x44yMinus67z0_mask.json'), 'file'), 0);
+
+end
+
+function value = thisDir()
+  value = fullfile(fileparts(mfilename('fullpath')));
+end
+
+function value = demoDir()
+  value = fullfile(thisDir(), '..', 'demos', 'roi', 'inputs');
+  gunzip(fullfile(value, '*.gz'));
+end