update to keep track of the last version of bids-matlab

Remi-Gau · Remi-Gau · commit 24539c45ee1b · 2021-06-01T17:48:15.000+02:00
diff --git a/.github/workflows/run_tests.yml b/.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)         
 
diff --git a/.gitignore b/.gitignore
@@ -20,7 +20,9 @@ envs/*
 # visual studio code stuff
 .vscode
 
-
+demos/*/*.json
+demos/*/*/*.json
+demos/*/derivatives
 
 
 
diff --git a/demos/atlas/create_roi_from_atlas.m b/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');
diff --git a/demos/roi/other_demo.m b/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', '')));
diff --git a/miss_hit.cfg b/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
diff --git a/run_tests.m b/run_tests.m
diff --git a/src/atlas/extractRoiByLabel.m b/src/atlas/extractRoiByLabel.m
@@ -11,11 +11,16 @@
   p = bids.internal.parse_filename(sourceImage);
   p.label = labelStruct.ROI;
   p.suffix = 'mask';
-  newName = createFilename(p);
+  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
diff --git a/src/atlas/extractRoiFromAtlas.m b/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')
 
@@ -23,15 +23,21 @@
   roiImage = extractRoiByLabel(sourceImage, labelStruct);
 
   entities = struct('space', 'MNI', ...
-      'hemi', hemisphere, ...
-      'desc', atlas, ...
-      'label', roiName);
-  nameStructure = struct('entities', entities, ...                         
+                    '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
diff --git a/src/atlas/getRetinoProbaAtlas.m b/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');
 
diff --git a/src/atlas/getRoiLabelLookUpTable.m b/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);
diff --git a/src/atlas/labelClusters.m b/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);
 
@@ -19,13 +19,18 @@
   % Write new image with cluster laebelled with their voxel size
   p = bids.internal.parse_filename(sourceImage);
   p.suffix = 'dseg'; % discrete segmentation
-  newName = createFilename(p);
+  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)
diff --git a/src/atlas/returnAtlasDir.m b/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');
 
diff --git a/src/atlas/unzipAtlas.m b/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();
 
diff --git a/src/roi/createRoi.m b/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)
@@ -328,6 +330,7 @@
     p.filename = '';
     p.ext = '.nii';
     p.suffix = 'mask';
+    p.use_schema = false;
 
     if ~isempty(volumeDefiningImage)
       tmp = bids.internal.parse_filename(volumeDefiningImage);
@@ -351,7 +354,8 @@
   end
 
   p.entities.label = [label ' ' mask.label];
+  p.use_schema = false;
 
-  roiName = createFilename(p);
+  roiName = bids.create_filename(p);
 
 end
diff --git a/src/roi/keepHemisphere.m b/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);
@@ -34,7 +34,8 @@
 
   p = bids.internal.parse_filename(inputImage);
   p.entities.hs = lower(hemisphere);
-  newName = createFilename(p);
+  p.use_schema = false;
+  newName = bids.create_filename(p);
 
   hdr.fname = spm_file(inputImage, 'filename', newName);
 
diff --git a/src/roi/renameNeuroSynth.m b/src/roi/renameNeuroSynth.m
@@ -1,10 +1,10 @@
-% (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.suffix = 'probseg';
@@ -15,7 +15,9 @@
   parts = strsplit(basename, '_');
   p.entities.label = ['neurosynth ' parts{1}];
 
-  newName = createFilename(p);
+  p.use_schema = false;
+
+  newName = bids.create_filename(p);
 
   outputImage = spm_file(inputImage, 'filename', newName);
 
diff --git a/src/roi/thresholdToMask.m b/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.suffix = 'mask';
-  newName = createFilename(p);
-  hdr.fname = spm_file(hdr.fname, 'filename', newName);
+  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
diff --git a/src/utils/convertToValidCamelCase.m b/src/utils/convertToValidCamelCase.m
diff --git a/src/utils/createFilename.m b/src/utils/createFilename.m
diff --git a/src/utils/renameFile.m b/src/utils/renameFile.m
@@ -1,18 +1,12 @@
-% (C) Copyright 2021 CPP ROI developers
+function newName = renameFile(inputFile, specification)
+  %
+  % (C) Copyright 2021 CPP ROI developers
 
-function newName = renameFile(file, specification)
+  specification.use_schema = false;
+  newName = bids.create_filename(specification, inputFile);
 
-  pth = spm_fileparts(file);
-  p = bids.internal.parse_filename(file);
+  outputFile = spm_file(inputFile, 'filename', newName);
 
-  entitiesToChange = fieldnames(specification);
-
-  for iEntity = 1:numel(entitiesToChange)
-    p.entities.(entitiesToChange{iEntity}) = specification.(entitiesToChange{iEntity});
-  end
-
-  newName = createFilename(p);
-
-  movefile(file, fullfile(pth, newName));
+  movefile(inputFile, outputFile);
 
 end
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
diff --git a/tests/test_unit_convertToValidCamelCase.m b/tests/test_unit_convertToValidCamelCase.m

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+% (C) Copyright 2021 CPP ROI developers`
	`2`	`+`
`1`	`3`	`opt.roi.atlas = 'wang';`
`2`	`4`	`opt.roi.name = {'V1v', 'V1d'};`
`3`	`5`	`opt.roi.dir = fullfile(pwd, 'derivatives', 'cpp_roi', 'group');`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-% (C) Copyright 2021 CPP ROI developers`
`2`		`-`
`3`	`1`	`function [maxProbaFiles, roiLabels] = getRetinoProbaAtlas()`
`4`	`2`	`%`
`5`	`3`	`% Loads the volumetric data from the`
`@@ -15,6 +13,7 @@`
`15`	`13`	`% PMID: 25452571`
`16`	`14`	`% Probabilistic Maps of Visual Topography in Human Cortex`
`17`	`15`	`%`
	`16`	`+ % (C) Copyright 2021 CPP ROI developers`
`18`	`17`
`19`	`18`	`unzipAtlas('wang');`
`20`	`19`