Merge pull request #31 from cpp-lln-lab/atlas

Remi-Gau · web-flow · commit ba39937138cb · 2022-05-11T20:38:58.000+02:00
[REF &amp; ENH] remove renameFile and deal with atlas entities
diff --git a/demos/roi/label_and_extract_clusters.m b/demos/roi/label_and_extract_clusters.m
@@ -10,7 +10,7 @@
 
 gunzip(fullfile('inputs', '*.gz'));
 
-zMap = fullfile(pwd, 'inputs', 'visual_motion_association-test_z_FDR_0.01.nii');
+zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
 zMap = renameNeuroSynth(zMap);
 
 peakThreshold = 5;
diff --git a/demos/roi/neurosynth_left_right_rois.m b/demos/roi/neurosynth_left_right_rois.m
@@ -6,7 +6,7 @@
 run ../../initCppRoi;
 
 gunzip(fullfile('inputs', '*.gz'));
-zMap = fullfile(pwd, 'inputs', 'visual_motion_association-test_z_FDR_0.01.nii');
+zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
 
 zMap = renameNeuroSynth(zMap);
 roiImage = thresholdToMask(zMap, 5);
@@ -16,11 +16,13 @@
 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', '')));
+specification = struct('entities', struct('label', 'ns left motion', ...
+                                          'hemi', ''));
+bf = bids.File(leftRoiImage);
+bf = bf.rename('spec', specification, 'dry_run', false, 'verbose', true);
+leftRoiImage =  fullfile(bf.path, bf.filename);
+
+specification.entities.label = 'ns right motion';
+bf = bids.File(rightRoiImage);
+bf = bf.rename('spec', specification, 'dry_run', false, 'verbose', true);
+rightRoiImage =  fullfile(bf.path, bf.filename);
diff --git a/demos/roi/roi_script.m b/demos/roi/roi_script.m
@@ -29,7 +29,7 @@
 % You can use the resliceRoiImages for that.
 
 %%
-zMap = fullfile(pwd, 'inputs', 'visual_motion_association-test_z_FDR_0.01.nii');
+zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
 dataImage = fullfile(pwd, 'inputs', 'TStatistic.nii');
 
 opt.unzip.do = true;
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,7 +23,7 @@
 author = "the CPP ROI dev team"
 
 # The full version, including alpha/beta/rc tags
-release = "v0.2.0"
+release = "v0.2.0dev"
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
@@ -14,10 +14,3 @@ Atlas
 .. automodule:: src.atlas
 
 .. autofunction:: returnAtlasDir
-
-Utilities
-=========
-
-.. automodule:: src.utils
-
-.. autofunction:: renameFile
diff --git a/run_tests.m b/run_tests.m
@@ -9,6 +9,7 @@
 testFolder = fullfile(fileparts(mfilename('fullpath')), 'tests');
 
 addpath(fullfile(testFolder, 'utils'));
+addpath(fullfile(fileparts(mfilename('fullpath')), 'atlas'));
 
 folderToCover = fullfile(testFolder, '..', 'src');
 
diff --git a/src/atlas/extractRoiFromAtlas.m b/src/atlas/extractRoiFromAtlas.m
@@ -61,8 +61,8 @@
   % rename file
   entities = struct('hemi', hemisphere, ...
                     'space', 'MNI', ...
-                    'label', roiName, ...
-                    'desc', atlasName);
+                    'atlas', atlasName, ...
+                    'label', roiName);
   nameStructure = struct('entities', entities, ...
                          'suffix', 'mask', ...
                          'ext', '.nii');
diff --git a/src/roi/keepHemisphere.m b/src/roi/keepHemisphere.m
@@ -38,11 +38,12 @@
 
   vol(discard, :, :) = NaN;
 
-  p = bids.internal.parse_filename(inputImage);
-  p.entities.hemi = hemisphere;
-  bidsFile = bids.File(p);
+  bf = bids.File(inputImage);
+  bf.entity_order = cat(1, 'hemi', fieldnames(bf.entities));
+  bf.entities.hemi = hemisphere;
+  bf = bf.reorder_entities;
 
-  hdr.fname = spm_file(inputImage, 'filename', bidsFile.filename);
+  hdr.fname = spm_file(inputImage, 'filename', bf.filename);
 
   spm_write_vol(hdr, vol);
 
diff --git a/src/roi/renameNeuroSynth.m b/src/roi/renameNeuroSynth.m
@@ -29,7 +29,8 @@
 
   basename = spm_file(inputImage, 'basename');
   parts = strsplit(basename, '_');
-  p.entities.label = bids.internal.camel_case(['neurosynth ' parts{1}]);
+  p.entities.atlas = 'neurosynth';
+  p.entities.label = bids.internal.camel_case(parts{1});
 
   bidsFile = bids.File(p);
 
diff --git a/src/utils/renameFile.m b/src/utils/renameFile.m
diff --git a/tests/test_extractRoiFromAtlas.m b/tests/test_extractRoiFromAtlas.m
@@ -12,7 +12,7 @@ function test_extractRoiFromAtlas_wang()
 
   roiImage = extractRoiFromAtlas(pwd, 'wang', 'V1v', 'L');
 
-  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_label-V1v_desc-wang_mask.nii'), ...
+  assertEqual(exist(fullfile(pwd, 'hemi-L_space-MNI_atlas-wang_label-V1v_mask.nii'), ...
                     'file'), ...
               2);
 
@@ -29,7 +29,7 @@ function test_extractRoiFromAtlas_neuromorphometrics()
   roiImage = extractRoiFromAtlas(pwd, 'neuromorphometrics', 'Amygdala', 'L');
 
   assertEqual(exist(fullfile(pwd, ...
-                             'hemi-L_space-MNI_label-Amygdala_desc-neuromorphometrics_mask.nii'), ...
+                             'hemi-L_space-MNI_atlas-neuromorphometrics_label-Amygdala_mask.nii'), ...
                     'file'), ...
               2);
 
diff --git a/tests/test_keepHemisphere.m b/tests/test_keepHemisphere.m
@@ -8,7 +8,7 @@
   initTestSuite;
 end
 
-function test_renameFile()
+function test_keepHemisphere_basic()
 
   inputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'demos', 'roi');
 
@@ -17,14 +17,20 @@ function test_renameFile()
 
   zMap = renameNeuroSynth(zMap);
 
-  % keep only one hemisphere and appends a 'hemi-[hemisphere label]'
+  % keep only one hemisphere and add a 'hemi-[hemisphere label]' entity
   leftRoiImage = keepHemisphere(zMap, 'L');
   rightRoiImage = keepHemisphere(zMap, 'R');
 
+  basename = 'space-MNI_atlas-neurosynth_label-visualMotion_probseg.nii';
+
   assertEqual(exist(fullfile(inputDir, 'inputs', ...
-                             'space-MNI_label-neurosynthVisualMotion_hemi-L_probseg.nii'), 'file'), 2);
+                             ['hemi-L_' basename]), ...
+                    'file'), ...
+              2);
   assertEqual(exist(fullfile(inputDir, 'inputs', ...
-                             'space-MNI_label-neurosynthVisualMotion_hemi-R_probseg.nii'), 'file'), 2);
+                             ['hemi-R_' basename]), ...
+                    'file'), ...
+              2);
 
   % TODO check the data content
 
diff --git a/tests/test_unit_renameFile.m b/tests/test_unit_renameFile.m
diff --git a/tests/test_unit_renameNeuroSynth.m b/tests/test_unit_renameNeuroSynth.m
@@ -15,7 +15,7 @@ function test_renameNeuroSynth()
 
   outputImage = renameNeuroSynth(inputImage);
 
-  expected = fullfile(pwd, 'space-MNI_label-neurosynthMotion_probseg.nii.gz');
+  expected = fullfile(pwd, 'space-MNI_atlas-neurosynth_label-motion_probseg.nii.gz');
   assertEqual(exist(outputImage, 'file'), 2);
 
   assertEqual(outputImage, expected);
@@ -31,7 +31,7 @@ function test_renameNeuroSynth_unzipped()
 
   outputImage = renameNeuroSynth(inputImage);
 
-  expected = fullfile(pwd, 'space-MNI_label-neurosynthMotion_probseg.nii');
+  expected = fullfile(pwd, 'space-MNI_atlas-neurosynth_label-motion_probseg.nii');
   assertEqual(exist(outputImage, 'file'), 2);
 
   assertEqual(outputImage, expected);
diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-v0.2.0
+v0.2.0dev
