add tests and update CI and rename demos

Author: Remi-Gau

.github/workflows/miss_hit.yml renamed to .github/workflows/miss_hit_quality.yml

@@ -1,4 +1,4 @@
-name: miss_hit
+name: miss_hit_quality
 
 on:
   push:
@@ -28,10 +28,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
-
-    - name: MISS_HIT Code style
-      run: |
-        mh_style --process-slx
+        cd tests
+        make data
 
     - name: MISS_HIT Metrics
       run: |

.github/workflows/miss_hit_style.yml

@@ -0,0 +1,36 @@
+name: miss_hit_style
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+        cd tests
+        make data
+
+    - name: MISS_HIT Code style
+      run: |
+        mh_style

demos/roi/neurosynth_left_right_rois.m

@@ -0,0 +1,26 @@
+% (C) Copyright 2021 CPP ROI developers
+
+% small demo to show how to create and rename ROIs that come from neurosynth
+% and how to only keep the data from one hemisphere of an image.
+
+run ../../initCppRoi;
+
+gunzip(fullfile('inputs', '*.gz'));
+zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
+
+zMap = renameNeuroSynth(zMap);
+roiImage = thresholdToMask(zMap, 5);
+
+% keep only one hemisphere and appends a 'hs--[hemisphere label]'
+leftRoiImage = keepHemisphere(roiImage, 'L');
+rightRoiImage = keepHemisphere(roiImage, 'R');
+
+% change the label entity and remove the hs one
+leftRoiImage = renameFile(leftRoiImage, ...
+                          struct('entities', struct( ...
+                                                    'label', 'ns left motion', ...
+                                                    'hemi', '')));
+rightRoiImage = renameFile(rightRoiImage, ...
+                           struct('entities', struct( ...
+                                                     'label', 'ns right motion', ...
+                                                     'hemi', '')));

src/atlas/extractRoiByLabel.m

@@ -1,6 +1,20 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function outputImage = extractRoiByLabel(sourceImage, labelStruct)
+  %
+  % Given a discrete segmentation source image fullpath and a look up table
+  % label structure this creates a mask for that ROI and returns the fullpath to its BIDS name.
+  % This will also create a JSON side car file for that image.
+  %
+  % USAGE::
+  %
+  %   outputImage = extractRoiByLabel(sourceImage, labelStruct)
+  %
+  % :param sourceImage: discrete segmentation source image fullpath
+  % :type sourceImage: string
+  % :param labelStruct: 1x1 structure with fields ``ROI`` for the ROI name
+  %                     and ``label`` for the corresponding label
+  % :type labelStruct: structure
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   hdr = spm_vol(sourceImage);
   vol = spm_read_vols(hdr);
@@ -9,14 +23,13 @@
   outputVol(vol == labelStruct.label) = true;
 
   p = bids.internal.parse_filename(sourceImage);
-  p.label = labelStruct.ROI;
+  p.entities.label = labelStruct.ROI;
   p.suffix = 'mask';
   p.use_schema = false;
 
   newName = bids.create_filename(p);
   hdr.fname = spm_file(hdr.fname, 'filename', newName);
 
-  % Cluster labels as their size.
   spm_write_vol(hdr, outputVol);
   outputImage = hdr.fname;
 

src/roi/keepHemisphere.m

@@ -9,7 +9,7 @@
   %
   % :param image:
   % :type image: string
-  % :param hemisphere: ``'lh'`` or ``'rh'``
+  % :param hemisphere: ``'L'`` or ``'R'``
   % :type hemisphere: string
   %
   %
@@ -23,19 +23,23 @@
   xDim = hdr.dim(1);
   xMid = round(xDim / 2);
 
-  switch lower(hemisphere)
+  switch hemisphere
 
-    case 'lh'
+    case 'L'
       discard = 1:xMid;
 
-    case 'rh'
+    case 'R'
       discard = xMid:xDim;
+
+    otherwise
+      error('hemisphere must be L or R.');
+
   end
 
   vol(discard, :, :) = NaN;
 
   p = bids.internal.parse_filename(inputImage);
-  p.entities.hs = lower(hemisphere);
+  p.entities.hemi = hemisphere;
   p.use_schema = false;
   newName = bids.create_filename(p);
 

tests/test_extractRoiByLabel.m

@@ -0,0 +1,28 @@
+% (C) Copyright 2020 CPP ROI developers
+
+function test_suite = test_extractRoiByLabel() %#ok<*STOUT>
+  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_lut_wang()
+
+  [atlasFile, lut] = getAtlasAndLut('neuromorphometrics');
+
+  labelStruct = struct('ROI', lut.ROI{1}, ...
+                       'label', lut.label(1));
+
+  outputImage = extractRoiByLabel(atlasFile, labelStruct);
+
+  assertEqual(exist(outputImage, 'file'), 2);
+
+  vol =  spm_read_vols(spm_vol(outputImage));
+  assertEqual(sum(vol(:) == 1), 291); % check the ROI has the right number of voxel
+
+  delete(fullfile(returnAtlasDir(), '*.nii'));
+  delete(fullfile(returnAtlasDir(), '*.json'));
+
+end

tests/test_keepHemisphere.m

@@ -0,0 +1,33 @@
+% (C) Copyright 2020 CPP ROI developers
+
+function test_suite = test_keepHemisphere %#ok<*STOUT>
+  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_renameFile()
+
+  inputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'demos', 'roi');
+
+  gunzip(fullfile(inputDir, 'inputs', '*.gz'));
+  zMap = fullfile(inputDir, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
+
+  zMap = renameNeuroSynth(zMap);
+
+  % keep only one hemisphere and appends a 'hemi-[hemisphere label]'
+  leftRoiImage = keepHemisphere(zMap, 'L');
+  rightRoiImage = keepHemisphere(zMap, 'R');
+
+  assertEqual(exist(fullfile(inputDir, 'inputs', ...
+                             'space-MNI_label-neurosynthVisualMotion_hemi-L_probseg.nii'), 'file'), 2);
+  assertEqual(exist(fullfile(inputDir, 'inputs', ...
+                             'space-MNI_label-neurosynthVisualMotion_hemi-R_probseg.nii'), 'file'), 2);
+
+  % TODO check the data content
+
+  delete(fullfile(inputDir, 'inputs', '*.nii'));
+
+end