Merge pull request #111 from cpp-lln-lab/bids_matlab

Remi-Gau · web-flow · commit f93daa747a45 · 2023-12-06T18:07:59.000+01:00
[MAINT] use bids matlab main (remove atlas entity), update RTD config
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -6,6 +6,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: '3.12'
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
@@ -14,6 +19,5 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: '3.8'
   install:
   - requirements: requirements.txt
diff --git a/Makefile b/Makefile
@@ -8,7 +8,7 @@ clean_lib:
 	rm -rf lib/bids-matlab
 
 install_dev:
-	git clone https://github.com/bids-standard/bids-matlab.git --branch dev --depth 1 lib/bids-matlab
+	git clone https://github.com/bids-standard/bids-matlab.git --branch main --depth 1 lib/bids-matlab
 
 version.txt: CITATION.cff
 	grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
diff --git a/atlas/Glasser/space-MNI152ICBM2009anlin_seg-glasser_dseg.nii.gz b/atlas/Glasser/space-MNI152ICBM2009anlin_seg-glasser_dseg.nii.gz
diff --git a/atlas/Glasser/space-MNI152ICBM2009anlin_seg-glasser_dseg.xml b/atlas/Glasser/space-MNI152ICBM2009anlin_seg-glasser_dseg.xml
diff --git a/atlas/space-MNI_seg-wang_dseg.xml b/atlas/space-MNI_seg-wang_dseg.xml
diff --git a/atlas/visfAtlas/space-MNI_seg-visfAtlas_dseg.nii.gz b/atlas/visfAtlas/space-MNI_seg-visfAtlas_dseg.nii.gz
diff --git a/atlas/visfAtlas/space-MNI_seg-visfAtlas_dseg.xml b/atlas/visfAtlas/space-MNI_seg-visfAtlas_dseg.xml
diff --git a/src/atlas/copyAtlasToSpmDir.m b/src/atlas/copyAtlasToSpmDir.m
@@ -94,22 +94,22 @@ function copyAtlasToSpmDir(varargin)
       sourceAtlasXml = fullfile(returnAtlasDir(), 'HCPex.xml');
 
     case 'visfatlas'
-      sourceAtlasImage = fullfile(returnAtlasDir(atlas), 'space-MNI_atlas-visfAtlas_dseg.nii');
-      sourceAtlasXml = fullfile(returnAtlasDir(atlas), 'space-MNI_atlas-visfAtlas_dseg.xml');
+      sourceAtlasImage = fullfile(returnAtlasDir(atlas), 'space-MNI_seg-visfAtlas_dseg.nii');
+      sourceAtlasXml = fullfile(returnAtlasDir(atlas), 'space-MNI_seg-visfAtlas_dseg.xml');
 
     case 'glasser'
 
       sourceAtlasImage = fullfile(returnAtlasDir(atlas), ...
-                                  'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
+                                  'space-MNI152ICBM2009anlin_seg-glasser_dseg.nii');
       sourceAtlasXml = fullfile(returnAtlasDir(atlas), ...
-                                'space-MNI152ICBM2009anlin_atlas-glasser_dseg.xml');
+                                'space-MNI152ICBM2009anlin_seg-glasser_dseg.xml');
 
     case 'wang'
       sourceAtlasImage = fullfile(returnAtlasDir(atlas), ...
                                   'subj_vol_all', ...
-                                  'space-MNI_atlas-wang_dseg.nii');
+                                  'space-MNI_seg-wang_dseg.nii');
       sourceAtlasXml = fullfile(returnAtlasDir(), ...
-                                'space-MNI_atlas-wang_dseg.xml');
+                                'space-MNI_seg-wang_dseg.xml');
 
     otherwise
       error(['Only the following atlases can be copied to SPM atlas folder:\n', ...
diff --git a/src/atlas/extractRoiFromAtlas.m b/src/atlas/extractRoiFromAtlas.m
@@ -122,7 +122,7 @@
   % rename file
   entities = struct('hemi', hemisphere, ...
                     'space', 'MNI', ...
-                    'atlas', lower(atlasName), ...
+                    'seg', lower(atlasName), ...
                     'label', roiName);
   nameStructure = struct('entities', entities, ...
                          'suffix', 'mask', ...
diff --git a/src/atlas/getAtlasFilename.m b/src/atlas/getAtlasFilename.m
@@ -39,15 +39,15 @@
 
     case 'visfatlas'
 
-      atlasFilename = fullfile(atlasDir, 'space-MNI_atlas-visfAtlas_dseg.nii');
+      atlasFilename = fullfile(atlasDir, 'space-MNI_seg-visfAtlas_dseg.nii');
 
     case 'hcpex'
 
       atlasFilename = fullfile(atlasDir, 'HCPex.nii');
 
     case 'glasser'
 
-      atlasFilename = fullfile(atlasDir, 'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
+      atlasFilename = fullfile(atlasDir, 'space-MNI152ICBM2009anlin_seg-glasser_dseg.nii');
 
   end
 
diff --git a/src/atlas/getLookUpTable.m b/src/atlas/getLookUpTable.m
@@ -41,7 +41,10 @@
       roiLabelLUT = fullfile(atlasDir, 'Anatomy_v22c_MPM.txt');
 
       if ~exist(roiLabelLUT, 'file')
-        error('Did you install the spm Anatomy toolbox?\n\nDownload it from: %s', ...
+        error(['Could not find look up table: %s.\n'...
+               'Did you install the spm Anatomy toolbox?\n\n', ...
+               'Download it from: %s'], ...
+              roiLabelLUT, ...
               anat_tb_URL);
       end
 
diff --git a/src/atlas/unzipAtlas.m b/src/atlas/unzipAtlas.m
@@ -30,11 +30,11 @@ function unzipAtlas(atlas)
       end
 
     case 'glasser'
-      file = fullfile(atlasDir, 'Glasser', 'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
+      file = fullfile(atlasDir, 'Glasser', 'space-MNI152ICBM2009anlin_seg-glasser_dseg.nii');
       gunzipAtlasIfNecessary(file);
 
     case 'visfatlas'
-      file = fullfile(atlasDir, 'visfAtlas', 'space-MNI_atlas-visfAtlas_dseg.nii');
+      file = fullfile(atlasDir, 'visfAtlas', 'space-MNI_seg-visfAtlas_dseg.nii');
       gunzipAtlasIfNecessary(file);
 
     case 'hcpex'
diff --git a/src/roi/createRoi.m b/src/roi/createRoi.m
@@ -33,11 +33,11 @@
   %
   %   :roiImage: - :string: fullpath of the roi image for ``'mask'``
   %
-  %   :sphere: - :structure: defines the charateristic for ``'sphere'``
+  %   :sphere: - :structure: defines the characteristic for ``'sphere'``
   %                          - ``sphere.location``: X Y Z coordinates in millimeters
   %                          - ``spehere.radius``: radius in millimeters
   %
-  %   :specification: - :structure: defines the charateristic for ``'intersection'`` and ``'expand'``
+  %   :specification: - :structure: defines the characteristic for ``'intersection'`` and ``'expand'``
   %                                 - ``sphere.location``: X Y Z coordinates in millimeters
   %                                 - ``sphere.radius``: radius in millimeters
   %
diff --git a/src/roi/renameNeuroSynth.m b/src/roi/renameNeuroSynth.m
@@ -40,7 +40,7 @@
 
   parts = strsplit(basename, '_');
 
-  p.entities.atlas = 'neurosynth';
+  p.entities.seg = 'neurosynth';
 
   p.entities.label = bids.internal.camel_case(parts{1});
 
diff --git a/tests/test_copyAtlasToSpmDir.m b/tests/test_copyAtlasToSpmDir.m
@@ -12,9 +12,9 @@ function test_copyAtlasToSpmDir_wang()
   copyAtlasToSpmDir('wang', 'verbose', false);
 
   targetAtlasImage = fullfile(spmAtlasDir(), ...
-                              'space-MNI_atlas-wang_dseg.nii');
+                              'space-MNI_seg-wang_dseg.nii');
   targetAtlasXml = fullfile(spmAtlasDir(), ...
-                            'space-MNI_atlas-wang_dseg.xml');
+                            'space-MNI_seg-wang_dseg.xml');
 
   assertEqual(exist(targetAtlasImage, 'file'), 2);
   assertEqual(exist(targetAtlasXml, 'file'), 2);
@@ -28,9 +28,9 @@ function test_copyAtlasToSpmDir_visfatlas()
   copyAtlasToSpmDir('visfatlas', 'verbose', false);
 
   targetAtlasImage = fullfile(spmAtlasDir(), ...
-                              'space-MNI_atlas-visfAtlas_dseg.nii');
+                              'space-MNI_seg-visfAtlas_dseg.nii');
   targetAtlasXml = fullfile(spmAtlasDir(), ...
-                            'space-MNI_atlas-visfAtlas_dseg.xml');
+                            'space-MNI_seg-visfAtlas_dseg.xml');
 
   assertEqual(exist(targetAtlasImage, 'file'), 2);
   assertEqual(exist(targetAtlasXml, 'file'), 2);
@@ -44,9 +44,9 @@ function test_copyAtlasToSpmDir_glasser()
   copyAtlasToSpmDir('Glasser', 'verbose', false);
 
   targetAtlasImage = fullfile(spmAtlasDir(), ...
-                              'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
+                              'space-MNI152ICBM2009anlin_seg-glasser_dseg.nii');
   targetAtlasXml = fullfile(spmAtlasDir(), ...
-                            'space-MNI152ICBM2009anlin_atlas-glasser_dseg.xml');
+                            'space-MNI152ICBM2009anlin_seg-glasser_dseg.xml');
 
   assertEqual(exist(targetAtlasImage, 'file'), 2);
   assertEqual(exist(targetAtlasXml, 'file'), 2);
diff --git a/tests/test_createRoi.m b/tests/test_createRoi.m
@@ -49,7 +49,7 @@ function test_createRoi_intersection_mask_sphere()
 
   mask = createRoi('intersection', specification, volumeDefiningImage, outputDir, saveImg);
 
-  basename = 'space-MNI_atlas-neurosynth_label-visualMotionIntersection_desc-p10pt00_mask';
+  basename = 'space-MNI_seg-neurosynth_label-visualMotionIntersection_desc-p10pt00_mask';
 
   assertEqual(exist(fullfile(thisDir(), [basename '.nii']), 'file'), 2);
   assertEqual(exist(fullfile(thisDir(), [basename '.json']), 'file'), 2);
@@ -75,7 +75,7 @@ function test_createRoi_intersection_mask_sphere()
 
   mask = createRoi('expand', specification, volumeDefiningImage, outputDir, saveImg);
 
-  basename = 'space-MNI_atlas-neurosynth_label-visualMotionExpandVox57_desc-p10pt00_mask';
+  basename = 'space-MNI_seg-neurosynth_label-visualMotionExpandVox57_desc-p10pt00_mask';
 
   assertEqual(mask.roi.size, 57);
 
diff --git a/tests/test_extractRoiFromAtlas.m b/tests/test_extractRoiFromAtlas.m
@@ -12,7 +12,7 @@ function test_extractRoiFromAtlas_glasser()
 
   roiImage = extractRoiFromAtlas(pwd, 'Glasser', 'FEF', 'L');
 
-  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-glasser_label-FEF_mask.nii'), ...
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_seg-glasser_label-FEF_mask.nii'), ...
                     'file'), ...
               2);
 
@@ -28,7 +28,7 @@ function test_extractRoiFromAtlas_wang()
 
   roiImage = extractRoiFromAtlas(pwd, 'wang', 'V1v', 'L');
 
-  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-wang_label-V1v_mask.nii'), ...
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_seg-wang_label-V1v_mask.nii'), ...
                     'file'), ...
               2);
 
@@ -45,7 +45,7 @@ function test_extractRoiFromAtlas_neuromorphometrics()
   roiImage = extractRoiFromAtlas(pwd, 'neuromorphometrics', 'Amygdala', 'L');
 
   assertEqual(exist(fullfile(pwd, ...
-                             'hemi-L_space-MNI_atlas-neuromorphometrics_label-Amygdala_mask.nii'), ...
+                             'hemi-L_space-MNI_seg-neuromorphometrics_label-Amygdala_mask.nii'), ...
                     'file'), ...
               2);
 
@@ -61,7 +61,7 @@ function test_extractRoiFromAtlas_visfAtlas()
 
   roiImage = extractRoiFromAtlas(pwd, 'visfatlas', 'pFus', 'L');
 
-  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-visfatlas_label-pFus_mask.nii'), ...
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_seg-visfatlas_label-pFus_mask.nii'), ...
                     'file'), ...
               2);
 
@@ -79,7 +79,7 @@ function test_extractRoiFromAtlas_hcpex()
 
   roiImage = extractRoiFromAtlas(pwd, 'hcpex', 'MT', 'L');
 
-  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-hcpex_label-MT_mask.nii'), ...
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_seg-hcpex_label-MT_mask.nii'), ...
                     'file'), ...
               2);
 
diff --git a/tests/test_keepHemisphere.m b/tests/test_keepHemisphere.m
@@ -21,7 +21,7 @@ function test_keepHemisphere_basic()
   leftRoiImage = keepHemisphere(zMap, 'L');
   rightRoiImage = keepHemisphere(zMap, 'R');
 
-  basename = 'space-MNI_atlas-neurosynth_label-visualMotion_probseg.nii';
+  basename = 'space-MNI_seg-neurosynth_label-visualMotion_probseg.nii';
 
   assertEqual(exist(fullfile(inputDir, 'inputs', ...
                              ['hemi-L_' basename]), ...
diff --git a/tests/test_labelClusters.m b/tests/test_labelClusters.m
@@ -18,15 +18,15 @@
 
   labeledClusters = labelClusters(zMap, peakThreshold, extendThreshold);
 
-  expected = 'space-MNI_atlas-neurosynth_label-visualMotion_dseg.nii';
+  expected = 'space-MNI_seg-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';
+  expected = 'space-MNI_seg-neurosynth_label-nsLeftMT_mask.nii';
   assertEqual(exist(fullfile(demoDir(), expected), 'file'), 2);
 
 end
diff --git a/tests/test_unit_renameNeuroSynth.m b/tests/test_unit_renameNeuroSynth.m
@@ -27,7 +27,7 @@ function test_renameNeuroSynth()
 
   outputImage = renameNeuroSynth(inputImage);
 
-  expected = fullfile(pwd, 'space-MNI_atlas-neurosynth_label-motion_probseg.nii.gz');
+  expected = fullfile(pwd, 'space-MNI_seg-neurosynth_label-motion_probseg.nii.gz');
   assertEqual(exist(outputImage, 'file'), 2);
 
   assertEqual(outputImage, expected);
@@ -43,7 +43,7 @@ function test_renameNeuroSynth_unzipped()
 
   outputImage = renameNeuroSynth(inputImage);
 
-  expected = fullfile(pwd, 'space-MNI_atlas-neurosynth_label-motion_probseg.nii');
+  expected = fullfile(pwd, 'space-MNI_seg-neurosynth_label-motion_probseg.nii');
   assertEqual(exist(outputImage, 'file'), 2);
 
   assertEqual(outputImage, expected);
diff --git a/tests/test_unzipAtlas.m b/tests/test_unzipAtlas.m
@@ -13,7 +13,7 @@ function test_unzipAtlas_glasser()
   unzipAtlas('Glasser');
 
   expectedFile = fullfile(returnAtlasDir('Glasser'), ...
-                          'space-MNI152ICBM2009anlin_atlas-glasser_dseg.nii');
+                          'space-MNI152ICBM2009anlin_seg-glasser_dseg.nii');
 
   assertEqual(exist(expectedFile, 'file'), 2);
 
