[REF] add tests bids name and refactor

src/atlas/extractRoiByLabel.m

@@ -22,13 +22,11 @@
   outputVol = false(size(vol));
   outputVol(vol == labelStruct.label) = true;
 
-  p = bids.internal.parse_filename(sourceImage);
-  p.entities.label = bids.internal.camel_case(labelStruct.ROI);
-  p.suffix = 'mask';
+  bf = bids.File(sourceImage);
+  bf.entities.label = bids.internal.camel_case(labelStruct.ROI);
+  bf.suffix = 'mask';
 
-  bidsFile = bids.File(p);
-
-  hdr.fname = spm_file(hdr.fname, 'filename', bidsFile.filename);
+  hdr.fname = spm_file(hdr.fname, 'filename', bf.filename);
 
   spm_write_vol(hdr, outputVol);
   outputImage = hdr.fname;

src/atlas/labelClusters.m

@@ -28,17 +28,17 @@
   isFile = @(x) exist(x, 'file') == 2;
   isPositive = @(x) isnumeric(x) && x >= 0;
 
-  p = inputParser;
+  args = inputParser;
 
-  addRequired(p, 'inputImage', isFile);
-  addRequired(p, 'peakThreshold', @isnumeric);
-  addOptional(p, 'clusterSize', default_clusterSize, isPositive);
+  addRequired(args, 'inputImage', isFile);
+  addRequired(args, 'peakThreshold', @isnumeric);
+  addOptional(args, 'clusterSize', default_clusterSize, isPositive);
 
-  parse(p, varargin{:});
+  parse(args, varargin{:});
 
-  inputImage = p.Results.inputImage;
-  peakThreshold = p.Results.peakThreshold;
-  clusterSize = p.Results.clusterSize;
+  inputImage = args.Results.inputImage;
+  peakThreshold = args.Results.peakThreshold;
+  clusterSize = args.Results.clusterSize;
 
   [l2, num] = getClusters(inputImage, peakThreshold);
 
@@ -50,12 +50,11 @@
   vol = sortAndLabelClusters(l2, num, clusterSize);
 
   % Write new image with cluster laebelled with their voxel size
-  p = bids.internal.parse_filename(inputImage);
-  p.suffix = 'dseg'; % discrete segmentation
+  bf = bids.File(inputImage);
+  bf.suffix = 'dseg'; % discrete segmentation
 
   hdr = spm_vol(inputImage);
-  bidsFile = bids.File(p);
-  hdr.fname = spm_file(hdr.fname, 'filename', bidsFile.filename);
+  hdr.fname = spm_file(hdr.fname, 'filename', bf.filename);
 
   % Cluster labels as their size.
   spm_write_vol(hdr, vol);

src/roi/createRoiName.m

@@ -1,9 +1,26 @@
-function roiName = createRoiName(mask, volumeDefiningImage)
+function roiName = createRoiName(varargin)
   %
+  % creates BIDS like filename for ROIs
+  %
+  % USAGE::
+  %
+  %     roiName = createRoiName(mask, volumeDefiningImage)
   %
   % (C) Copyright 2022 CPP ROI developers
 
-  if strcmp(mask.def, 'sphere')
+  args = inputParser;
+
+  args.addRequired('mask', @isstruct);
+  args.addOptional('volumeDefiningImage', '', @ischar);
+
+  args.parse(varargin{:});
+
+  type = args.Results.mask.def;
+  label = args.Results.mask.label;
+  mask = args.Results.mask;
+  volumeDefiningImage = args.Results.volumeDefiningImage;
+
+  if strcmp(type, 'sphere')
 
     bf = bids.File('');
     bf.extension = '.nii';
@@ -20,28 +37,32 @@
 
     end
 
-    label = '';
+    tmp = '';
     if isfield(bf.entities, 'label')
-      label = bf.entities.label;
+      tmp = bf.entities.label;
     end
 
-    entities.label = bids.internal.camel_case([label ' ' mask.label]);
+    entities.label = bids.internal.camel_case([tmp ' ' label]);
 
     bf.entities = entities;
 
   else
 
     bf = bids.File(mask.global.hdr.fname);
 
-    label = '';
+    bf.suffix = 'mask';
+
+    tmp = '';
     if isfield(bf.entities, 'label')
-      label = bf.entities.label;
+      tmp = bf.entities.label;
     end
 
-    bf.entities.label = bids.internal.camel_case([label ' ' mask.label]);
+    bf.entities.label = bids.internal.camel_case([tmp ' ' label]);
 
   end
 
+  bf = bf.reorder_entities();
+  bf = bf.update;
   roiName = bf.filename;
 
 end

src/roi/thresholdToMask.m

@@ -26,40 +26,40 @@
   isFile = @(x) exist(x, 'file') == 2;
   isPositive = @(x) isnumeric(x) && x >= 0;
 
-  p = inputParser;
+  args = inputParser;
 
-  addRequired(p, 'inputImage', isFile);
-  addRequired(p, 'peakThreshold', @isnumeric);
-  addOptional(p, 'clusterSize', default_clusterSize, isPositive);
+  addRequired(args, 'inputImage', isFile);
+  addRequired(args, 'peakThreshold', @isnumeric);
+  addOptional(args, 'clusterSize', default_clusterSize, isPositive);
 
-  parse(p, varargin{:});
-
-  inputImage = p.Results.inputImage;
-  peakThreshold = p.Results.peakThreshold;
-  clusterSize = p.Results.clusterSize;
+  parse(args, varargin{:});
 
+  inputImage = args.Results.inputImage;
+  peakThreshold = args.Results.peakThreshold;
+  clusterSize = args.Results.clusterSize;
   [l2, num] = getClusters(inputImage, peakThreshold);
   vol = sortAndThresholdClusters(l2, num, clusterSize);
 
   % create output name
-  p = bids.internal.parse_filename(inputImage);
+  bf = bids.File(inputImage);
 
-  p.suffix = 'mask';
+  bf.suffix = 'mask';
 
   % add peakThreshold and clusterSizeInfo to desc
-  if ~isfield(p.entities, 'desc')
-    p.entities.desc = '';
+  if ~isfield(bf.entities, 'desc')
+    bf.entities.desc = '';
   end
   descSuffix = sprintf('p%05.2f', peakThreshold);
   if clusterSize > 0
     descSuffix = [descSuffix, sprintf('k%03.0f', clusterSize)];
   end
   descSuffix = strrep(descSuffix, '.', 'pt');
-  p.entities.desc = [p.entities.desc descSuffix];
+  bf.entities.desc = [bf.entities.desc descSuffix];
+
+  bf = bf.update();
 
-  bidsFile = bids.File(p);
   hdr = spm_vol(inputImage);
-  hdr.fname = spm_file(hdr.fname, 'filename', bidsFile.filename);
+  hdr.fname = spm_file(hdr.fname, 'filename', bf.filename);
   outputImage = hdr.fname;
 
   spm_write_vol(hdr, vol);

tests/test_createRoiName.m

@@ -0,0 +1,97 @@
+function test_suite = test_createRoiName %#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_createRoiName_non_sphere()
+
+  mask.def = 'expand';
+  mask.global.hdr.fname = 'suffixOnly.nii';
+
+  %%
+  mask.label = '';
+  roiName = createRoiName(mask);
+  assertEqual(roiName, 'mask.nii');
+
+  mask.label = 'foo';
+  roiName = createRoiName(mask);
+  assertEqual(roiName, 'label-foo_mask.nii');
+
+  %%
+  mask.global.hdr.fname = 'one-entity.nii';
+
+  mask.label = '';
+  roiName = createRoiName(mask);
+  assertEqual(roiName, 'one-entity_mask.nii');
+
+  % This will likely break when bids-matlab is updated and the order of entities
+  % is imposed by the schema
+  %
+  % label-foo_one-entity_mask.nii
+  %
+  mask.label = 'foo';
+  roiName = createRoiName(mask);
+  assertEqual(roiName, 'one-entity_label-foo_mask.nii');
+
+end
+
+function test_createRoiName_sphere()
+
+  mask.def = 'sphere';
+
+  %%
+  mask.label = '';
+  roiName = createRoiName(mask);
+  assertEqual(roiName, 'mask.nii');
+
+  mask.label = 'foo';
+  roiName = createRoiName(mask);
+  assertEqual(roiName, 'label-foo_mask.nii');
+
+  %%
+  volumeDefiningImage = fullfile(pwd, 'TStatistic.nii');
+
+  mask.label = '';
+  roiName = createRoiName(mask, volumeDefiningImage);
+  assertEqual(roiName, 'mask.nii');
+
+  mask.label = 'foo';
+  roiName = createRoiName(mask, volumeDefiningImage);
+  assertEqual(roiName, 'label-foo_mask.nii');
+
+  %%
+  volumeDefiningImage = fullfile(pwd, 'space-MNI_TStatistic.nii');
+
+  mask.label = '';
+  roiName = createRoiName(mask, volumeDefiningImage);
+  assertEqual(roiName, 'space-MNI_mask.nii');
+
+  mask.label = 'foo';
+  roiName = createRoiName(mask, volumeDefiningImage);
+  assertEqual(roiName, 'space-MNI_label-foo_mask.nii');
+
+end
+
+function test_createRoiName_sphere_spm()
+
+  % spm (ish) output
+
+  % https://github.com/cpp-lln-lab/CPP_ROI/issues/6
+  volumeDefiningImage = fullfile(pwd, 'task-auditory_p-0001_k-0_MC-none_label-001_spmT.nii');
+  mask.def = 'sphere';
+  mask.label = 'sphere5x44yMinus67z0';
+  roiName = createRoiName(mask, volumeDefiningImage);
+  assertEqual(roiName, 'label-sphere5x44yMinus67z0_mask.nii');
+
+  % https://github.com/cpp-lln-lab/CPP_ROI/issues/16
+  volumeDefiningImage = fullfile(pwd, 'con_0001.niii');
+  mask.def = 'sphere';
+  mask.label = 'sphere5x44yMinus67z0';
+  roiName = createRoiName(mask, volumeDefiningImage);
+  assertEqual(roiName, 'label-sphere5x44yMinus67z0_mask.nii');
+
+end

tests/test_labelClusters.m

@@ -0,0 +1,46 @@
+function test_suite = test_labelClusters %#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_labelClusters_basic
+
+  zMap = fullfile(demoDir(), 'visual motion_association-test_z_FDR_0.01.nii');
+
+  zMap = renameNeuroSynth(zMap);
+
+  peakThreshold = 5;
+  extendThreshold = 50;
+
+  labeledClusters = labelClusters(zMap, peakThreshold, extendThreshold);
+
+  expected = 'space-MNI_atlas-neurosynth_label-visualMotion_dseg.nii';
+  assertEqual(exist(fullfile(demoDir(), expected), 'file'), 2);
+
+  labelStruct = struct('ROI', 'ns left MT', ...
+                       'label', 1);
+
+  roiName = extractRoiByLabel(labeledClusters, labelStruct);
+
+  expected = 'space-MNI_atlas-neurosynth_label-nsLeftMT_mask.nii';
+  assertEqual(exist(fullfile(demoDir(), expected), 'file'), 2);
+
+end
+
+function value = thisDir()
+  value = fullfile(fileparts(mfilename('fullpath')));
+end
+
+function value = demoDir()
+
+  value = fullfile(thisDir(), '..', 'demos', 'roi', 'inputs');
+
+  if exist(fullfile(value, 'visual motion_association-test_z_FDR_0.01.nii'), 'file') == 0
+    gunzip(fullfile(value, '*.gz'));
+  end
+
+end