[ENH] update from bids-matlab

.github/workflows/run_tests.yml

@@ -71,7 +71,7 @@ jobs:
 
     - name: Run tests
       run: |
-        octave $OCTFLAGS --eval "runTests"
+        octave $OCTFLAGS --eval "run_tests"
         cat test_report.log | grep 0
         bash <(curl -s https://codecov.io/bash)         
 

.gitignore

@@ -20,7 +20,9 @@ envs/*
 # visual studio code stuff
 .vscode
 
-
+demos/*/*.json
+demos/*/*/*.json
+demos/*/derivatives
 
 
 

demos/atlas/create_roi_from_atlas.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2021 CPP ROI developers
+
 opt.roi.atlas = 'wang';
 opt.roi.name = {'V1v', 'V1d'};
 opt.roi.dir = fullfile(pwd, 'derivatives', 'cpp_roi', 'group');

demos/roi/other_demo.m

@@ -14,8 +14,10 @@
 
 % change the label entity and remove the hs one
 leftRoiImage = renameFile(leftRoiImage, ...
-                          struct('label', 'ns left motion', ...
-                                 'hs', ''));
+                          struct('entities', struct( ...
+                                                    'label', 'ns left motion', ...
+                                                    'hs', '')));
 rightRoiImage = renameFile(rightRoiImage, ...
-                           struct('label', 'ns right motion', ...
-                                  'hs', ''));
+                           struct('entities', struct( ...
+                                                     'label', 'ns right motion', ...
+                                                     'hs', '')));

miss_hit.cfg

@@ -1,7 +1,11 @@
 # styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
+
 regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
+regex_script_name: "[a-z0-9]+(_[a-z0-9]+)*"
+
 exclude_dir: "lib"
+
 copyright_entity: "CPP ROI developers"
 
 tab_width: 2

src/atlas/extractRoiByLabel.m

@@ -10,12 +10,17 @@
 
   p = bids.internal.parse_filename(sourceImage);
   p.label = labelStruct.ROI;
-  p.type = 'mask';
-  newName = createFilename(p);
+  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;
 
+  json = bids.derivatives_json(outputImage);
+  bids.util.jsonencode(json.filename, json.content);
+
 end

src/atlas/extractRoiFromAtlas.m

@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function roiImage = extractRoiFromAtlas(roiDir, atlas, roiName, hemisphere)
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   if strcmp(atlas, 'wang')
 
@@ -22,16 +22,22 @@
 
   roiImage = extractRoiByLabel(sourceImage, labelStruct);
 
-  nameStructure = struct( ...
-                         'space', 'MNI', ...
-                         'hemi', hemisphere, ...
-                         'desc', atlas, ...
-                         'label', roiName, ...
-                         'type', 'mask', ...
+  entities = struct('space', 'MNI', ...
+                    'hemi', hemisphere, ...
+                    'desc', atlas, ...
+                    'label', roiName);
+  nameStructure = struct('entities', entities, ...
+                         'suffix', 'mask', ...
                          'ext', '.nii');
-  newName = createFilename(nameStructure);
+
+  nameStructure.use_schema = false;
+
+  newName = bids.create_filename(nameStructure);
 
   movefile(roiImage, fullfile(roiDir, newName));
 
   roiImage = fullfile(roiDir, newName);
+
+  json = bids.derivatives_json(roiImage);
+  bids.util.jsonencode(json.filename, json.content);
 end

src/atlas/getRetinoProbaAtlas.m

@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function [maxProbaFiles, roiLabels] = getRetinoProbaAtlas()
   %
   % Loads the volumetric data from the
@@ -15,6 +13,7 @@
   %   PMID: 25452571
   %   Probabilistic Maps of Visual Topography in Human Cortex
   %
+  % (C) Copyright 2021 CPP ROI developers
 
   unzipAtlas('wang');
 

src/atlas/getRoiLabelLookUpTable.m

@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function roiLabelLUT = getRoiLabelLookUpTable(atlas)
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   if exist(atlas, 'file')
     roiLabelLUT = spm_load(atlas);

src/atlas/labelClusters.m

@@ -1,9 +1,9 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function outputImage = labelClusters(sourceImage, peakThreshold, extendThreshold)
-
+  %
   % Adapted from:
   % https://en.wikibooks.org/wiki/SPM/How-to#How_to_remove_clusters_under_a_certain_size_in_a_binary_mask?
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   hdr = spm_vol(sourceImage);
 
@@ -18,14 +18,19 @@
 
   % Write new image with cluster laebelled with their voxel size
   p = bids.internal.parse_filename(sourceImage);
-  p.type = 'dseg'; % discrete segmentation
-  newName = createFilename(p);
+  p.suffix = 'dseg'; % discrete segmentation
+  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, vol);
   outputImage = hdr.fname;
 
+  json = bids.derivatives_json(outputImage);
+  bids.util.jsonencode(json.filename, json.content);
+
 end
 
 function [l2, num] = getClusters(hdr, peakThreshold)

src/atlas/returnAtlasDir.m

@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function atlasDir = returnAtlasDir(atlas)
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   atlasDir = fullfile(fileparts(mfilename('fullpath')), '..', '..', 'atlas');
 

src/atlas/unzipAtlas.m

@@ -1,6 +1,6 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function unzipAtlas(atlas)
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   atlasDir = returnAtlasDir();
 

src/roi/createRoi.m

@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function [mask, outputFile] = createRoi(type, specification, volumeDefiningImage, outputDir, saveImg)
   %
   % Returns a mask to be used as a ROI by ``spm_summarize``.
@@ -66,6 +64,7 @@
   %      mask.global.XYZmm
   %
   %
+  % (C) Copyright 2021 CPP ROI developers
 
   if nargin < 5
     saveImg = false;
@@ -319,6 +318,9 @@
   % delete label files
   delete(fullfile(outputDir, '*_mask_labels.mat'));
 
+  json = bids.derivatives_json(outputFile);
+  bids.util.jsonencode(json.filename, json.content);
+
 end
 
 function roiName = createRoiName(mask, volumeDefiningImage)
@@ -327,14 +329,15 @@
 
     p.filename = '';
     p.ext = '.nii';
-    p.type = 'mask';
+    p.suffix = 'mask';
+    p.use_schema = false;
 
     if ~isempty(volumeDefiningImage)
       tmp = bids.internal.parse_filename(volumeDefiningImage);
 
       % if the volume defining image has a space entity we reuse it
       if isfield(p, 'space')
-        p.space = tmp.space;
+        p.entities.space = tmp.space;
       end
 
     end
@@ -347,11 +350,12 @@
 
   label = '';
   if isfield(p, 'label')
-    label = p.label;
+    label = p.entities.label;
   end
 
-  p.label = [label ' ' mask.label];
+  p.entities.label = [label ' ' mask.label];
+  p.use_schema = false;
 
-  roiName = createFilename(p);
+  roiName = bids.create_filename(p);
 
 end

src/roi/keepHemisphere.m

@@ -1,5 +1,3 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function outputImage = keepHemisphere(inputImage, hemisphere)
   %
   % Only keep the values from one hemisphere. Sets the other half to NaN.
@@ -14,6 +12,8 @@
   % :param hemisphere: ``'lh'`` or ``'rh'``
   % :type hemisphere: string
   %
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   hdr = spm_vol(inputImage);
   vol = spm_read_vols(hdr);
@@ -33,8 +33,9 @@
   vol(discard, :, :) = NaN;
 
   p = bids.internal.parse_filename(inputImage);
-  p.hs = lower(hemisphere);
-  newName = createFilename(p);
+  p.entities.hs = lower(hemisphere);
+  p.use_schema = false;
+  newName = bids.create_filename(p);
 
   hdr.fname = spm_file(inputImage, 'filename', newName);
 

src/roi/renameNeuroSynth.m

@@ -1,21 +1,23 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function outputImage = renameNeuroSynth(inputImage)
   % give the neurosynth map a name that is more bids friendly
   %
   % space-MNI_label-neurosynthKeyWordsUsed_probseg.nii
   %
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   p.filename = spm_file(inputImage, 'filename');
-  p.type = 'probseg';
+  p.suffix = 'probseg';
   p.ext = '.nii';
-  p.space = 'MNI';
+  p.entities.space = 'MNI';
 
   basename = spm_file(inputImage, 'basename');
   parts = strsplit(basename, '_');
-  p.label = ['neurosynth ' parts{1}];
+  p.entities.label = ['neurosynth ' parts{1}];
+
+  p.use_schema = false;
 
-  newName = createFilename(p);
+  newName = bids.create_filename(p);
 
   outputImage = spm_file(inputImage, 'filename', newName);
 

src/roi/thresholdToMask.m

@@ -1,22 +1,27 @@
-% (C) Copyright 2021 CPP ROI developers
-
 function outputImage = thresholdToMask(inputImage, threshold)
-
+  %
   % TODO
   % allow threshold to be inferior than, greater than or both
+  %
+  %
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
   hdr = spm_vol(inputImage);
   img = spm_read_vols(hdr);
 
   p = bids.internal.parse_filename(inputImage);
-  p.type = 'mask';
-  newName = createFilename(p);
-  hdr.fname = spm_file(hdr.fname, 'filename', newName);
+  p.suffix = 'mask';
+  p.use_schema = false;
+  newName = bids.create_filename(p);
 
+  hdr.fname = spm_file(hdr.fname, 'filename', newName);
   img = img > threshold;
-
   spm_write_vol(hdr, img);
 
   outputImage = hdr.fname;
 
+  json = bids.derivatives_json(outputImage);
+  bids.util.jsonencode(json.filename, json.content);
+
 end