[ENH] Bump bids matlab

.github/workflows/miss_hit_quality.yml

@@ -30,8 +30,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
-        cd tests
-        make data
 
     - name: MISS_HIT Metrics
       run: |

.github/workflows/miss_hit_style.yml

@@ -7,7 +7,7 @@ on:
       - master
       - dev
   pull_request:
-    branches: '*'
+    branches: ['*']
 
 jobs:
   build:
@@ -30,8 +30,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
-        cd tests
-        make data
 
     - name: MISS_HIT Code style
       run: |

src/roi/get_ROI_Coordinates.m → demos/WIP/get_ROI_Coordinates.m

@@ -1,9 +1,14 @@
 function mni = get_ROI_Coordinates
   % This function gets the individual subject coordniates of the highest peak
-  % within a specified Region of interest (usually coming from the group level univariate analysis)
-
+  % within a specified Region of interest (usually coming
+  % from the group level univariate analysis)
+  %
   % Critical t-value for each experimental condition or mask file
-  CriticalTs = 1;               % Critical t-value for visual condition in L-V5 and R-V5 and bilateral PT
+  % Critical t-value for visual condition in L-V5 and R-V5 and bilateral PT
+  %
+  % (C) Copyright 2021 CPP ROI developers
+
+  CriticalTs = 1;
 
   %% load the data structure
   WD = pwd;
@@ -52,9 +57,17 @@
         %% the first 4 masks are for the FACE condition, the other 4
         % are from the SCENE condition
         if iMask <= 2
-          result_file = [data_path, '/', SubName, '/stats/ffx_visMotion/ffx_', smoothing, '/spmT_0013.nii']; % HUMAN > BIG_ENV
+          result_file = [data_path, '/', ...
+                         SubName, ...
+                         '/stats/ffx_visMotion/ffx_', ...
+                         smoothing, ...
+                         '/spmT_0013.nii']; % HUMAN > BIG_ENV
         else
-          result_file = [data_path, '/', SubName, '/stats/ffx_audMotion/ffx_', smoothing, '/spmT_0014.nii']; % BIG_ENV > HUMAN
+          result_file = [data_path, '/', ...
+                         SubName, ...
+                         '/stats/ffx_audMotion/ffx_', ...
+                         smoothing, ...
+                         '/spmT_0014.nii']; % BIG_ENV > HUMAN
         end
 
         %%
@@ -78,8 +91,11 @@
 
           % convert space from slice number to mni
           mni{1, iMask}(subCounter, :) = cor2mni([x y z], mask_path);
-          %               mni{1,iMask}(iSub,1) = mni{1,iMask}(iSub,1)* -1;   % If  masks created from AFNI or FSL,
-          %               the x coordinate could be flipped (multiplied x -1). If this is the case, multiply x with -1.
+
+          %               mni{1,iMask}(iSub,1) = mni{1,iMask}(iSub,1)* -1;
+          % If  masks created from AFNI or FSL,
+          % the x coordinate could be flipped (multiplied x -1).
+          % If this is the case, multiply x with -1.
 
           mni{1, iMask}(subCounter, :);
 

docs/Makefile

@@ -18,7 +18,3 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-
-doc:
-	@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)"

docs/source/conf.py

@@ -23,18 +23,15 @@
 author = "the CPP ROI dev team"
 
 # The full version, including alpha/beta/rc tags
-release = "v0.1.0"
+release = "v0.1.0dev"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinxcontrib.matlab',
-    'sphinx.ext.autodoc',
-    'sphinx_copybutton']
+extensions = ["sphinxcontrib.matlab", "sphinx.ext.autodoc", "sphinx_copybutton"]
 matlab_src_dir = os.path.dirname(os.path.abspath("../../src"))
 primary_domain = "mat"
 

tests/run_tests.m → run_tests.m

@@ -6,7 +6,7 @@
 
 spm('defaults', 'fMRI');
 
-testFolder = fullfile(fileparts(mfilename('fullpath')));
+testFolder = fullfile(fileparts(mfilename('fullpath')), 'tests');
 
 folderToCover = fullfile(testFolder, '..', 'src');
 

src/atlas/extractRoiByLabel.m

@@ -23,7 +23,7 @@
   outputVol(vol == labelStruct.label) = true;
 
   p = bids.internal.parse_filename(sourceImage);
-  p.entities.label = labelStruct.ROI;
+  p.entities.label = bids.internal.camel_case(labelStruct.ROI);
   p.suffix = 'mask';
 
   bidsFile = bids.File(p);

src/roi/renameNeuroSynth.m

@@ -29,7 +29,7 @@
 
   basename = spm_file(inputImage, 'basename');
   parts = strsplit(basename, '_');
-  p.entities.label = ['neurosynth ' parts{1}];
+  p.entities.label = bids.internal.camel_case(['neurosynth ' parts{1}]);
 
   bidsFile = bids.File(p);
 

src/roi/thresholdToMask.m

@@ -45,7 +45,7 @@
   p = bids.internal.parse_filename(inputImage);
 
   p.suffix = 'mask';
-  
+
   % add peakThreshold and clusterSizeInfo to desc
   if ~isfield(p.entities, 'desc')
     p.entities.desc = '';

src/utils/renameFile.m

@@ -1,24 +1,43 @@
 function newName = renameFile(inputFile, specification)
   %
   % Renames a BIDS valid file into another BIDS valid file given some
-  % specification.
+  % specificationification.
   %
   % USAGE::
   %
-  %   newName = renameFile(inputFile, specification)
+  %   newName = renameFile(inputFile, specificationification)
   %
   % :param inputFile: better if fullfile path
   % :type inputFile: string
-  % :param specification: structure specifying the details of the new name
+  % :param specificationification: structure specificationifying the details of the new name
   %                       The structure content must resemble that of the
   %                       output of bids.internal.parse_filename
-  % :type specification: structure
+  % :type specificationification: structure
   %
   % (C) Copyright 2021 CPP ROI developers
 
-  bidsFile = bids.File(inputFile, false, specification);
-  newName = bidsFile.filename;
+  bf = bids.File(inputFile, 'use_schema', false);
 
+  if isfield(specification, 'prefix')
+    bf.suffix = specification.prefix;
+  end
+  if isfield(specification, 'suffix')
+    bf.suffix = specification.suffix;
+  end
+  if isfield(specification, 'ext')
+    bf.extension = specification.ext;
+  end
+  if isfield(specification, 'entities')
+    entities = fieldnames(specification.entities);
+    for i = 1:numel(entities)
+      bf = bf.set_entity(entities{i}, ...
+                         bids.internal.camel_case(specification.entities.(entities{i})));
+    end
+  end
+
+  bf = bf.update;
+
+  newName = bf.filename;
   outputFile = spm_file(inputFile, 'filename', newName);
 
   movefile(inputFile, outputFile);

tests/test_extractRoiFromAtlas.m

@@ -12,7 +12,7 @@ function test_extractRoiFromAtlas_wang()
 
   roiImage = extractRoiFromAtlas(pwd, 'wang', 'V1v', 'L');
 
-  assertEqual(exist(fullfile(pwd, 'space-MNI_hemi-L_label-V1v_desc-wang_mask.nii'), ...
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_label-V1v_desc-wang_mask.nii'), ...
                     'file'), ...
               2);
 
@@ -29,7 +29,7 @@ function test_extractRoiFromAtlas_neuromorphometrics()
   roiImage = extractRoiFromAtlas(pwd, 'neuromorphometrics', 'Amygdala', 'L');
 
   assertEqual(exist(fullfile(pwd, ...
-                             'space-MNI_hemi-L_label-Amygdala_desc-neuromorphometrics_mask.nii'), ...
+                             'hemi-L_space-MNI_label-Amygdala_desc-neuromorphometrics_mask.nii'), ...
                     'file'), ...
               2);