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Remi-GauRemi-Gau
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[FIX] fix octave create roi (#130)
* test with octave * change name * fix * tweak * fix several tests * reset submod * refactor set up * update tests * fix for matlab * reuse set up
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‎.github/workflows/run_tests_octave.yml‎

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---
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name: tests and coverage with octave
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env:
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OCTFLAGS: --no-gui --no-window-system --silent
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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on:
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push:
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branches:
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- main
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pull_request:
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branches: ['*']
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schedule:
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- cron: 0 0 1 * *
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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tests_octave:
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runs-on: ubuntu-latest
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steps:
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- name: Install CPP_ROI
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uses: actions/checkout@v4
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with:
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submodules: true
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fetch-depth: 0
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- name: Install SPM
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run: |
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git clone https://github.com/spm/spm12.git --depth 1
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- name: Install Moxunit and MOcov
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run: |
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git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
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git clone https://github.com/MOcov/MOcov.git --depth 1
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- name: Install octave
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install \
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octave \
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liboctave-dev\
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octave-common \
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octave-io \
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octave-image \
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octave-signal \
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octave-statistics
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make -C MOxUnit install
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make -C MOcov install
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- name: Compile SPM
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run: |
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make -C spm12/src PLATFORM=octave distclean
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make -C spm12/src PLATFORM=octave
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make -C spm12/src PLATFORM=octave install
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
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- name: Add bids-matlab
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run: make install_dev
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- name: Run tests
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run: |
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octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"
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octave $OCTFLAGS --eval "cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_octave;"
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- name: Code coverage
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uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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flags: octave
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name: codecov-umbrella
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fail_ci_if_error: false

‎.github/workflows/tests_octave.m‎

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function tests_octave()
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%
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% (C) Copyright 2024 CPP ROI developers
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root_dir = getenv('GITHUB_WORKSPACE');
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addpath(fullfile(root_dir, 'spm12'));
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addpath(fullfile(root_dir, 'lib', 'bids-matlab'));
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addpath(fullfile(root_dir, 'MOcov', 'MOcov'));
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cd(fullfile(root_dir, 'MOxUnit', 'MOxUnit'));
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moxunit_set_path();
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cd(fullfile(root_dir));
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initCppRoi();
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run_tests();
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end

‎src/atlas/copyAtlasToSpmDir.m‎

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Original file line numberDiff line numberDiff line change
@@ -17,11 +17,6 @@ function copyAtlasToSpmDir(varargin)
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% (C) Copyright 2022 CPP ROI developers
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if bids.internal.is_octave
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% the atlas in the spm dir are only useful in matlab with the GUI
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return
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end
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args = inputParser;
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addOptional(args, 'atlas', 'AAL', @ischar);

‎src/atlas/extractRoiFromAtlas.m‎

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@@ -39,9 +39,9 @@
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args = inputParser;
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addRequired(args, 'outputDir', isChar);
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addRequired(args, 'atlasName', @(x) isAKnownAtlas(x));
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addRequired(args, 'atlasName');
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addRequired(args, 'roiName', isChar);
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addRequired(args, 'hemisphere', @(x) ismember(x, {'L', 'R'}));
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addRequired(args, 'hemisphere');
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parse(args, varargin{:});
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@@ -50,6 +50,15 @@
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roiName = args.Results.roiName;
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hemisphere = args.Results.hemisphere;
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53+
if ~ismember(hemisphere, {'L', 'R'})
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msg = sprintf('"hemisphere must be "L" or "R"": %s\nGot: "%s"', ...
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hemisphere);
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bids.internal.error_handling(mfilename(), ...
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'invalidHemisphere', msg, false);
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end
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isAKnownAtlas(atlasName);
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5362
[atlasFile, lut] = getAtlasAndLut(atlasName);
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switch lower(atlasName)

‎src/atlas/unzipAtlas.m‎

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@@ -59,7 +59,13 @@ function gunzipAtlasIfNecessary(file)
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end
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function gunzipWithOctave(file)
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copyfile(file, [file '.bak']);
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gunzip(file);
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copyfile([file '.bak'], file);
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if iscellstr(file)
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for i = 1:numel(file)
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gunzipWithOctave(file{i});
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end
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else
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copyfile(file, [file '.bak']);
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gunzip(file);
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copyfile([file '.bak'], file);
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end
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end

‎src/roi/thresholdToMask.m‎

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@@ -48,7 +48,7 @@
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% add peakThreshold and clusterSizeInfo to desc
5050
if ~isfield(bf.entities, 'desc')
51-
bf.entities.desc = '';
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bf.entities(1).desc = '';
5252
end
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descSuffix = sprintf('p%05.2f', peakThreshold);
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if clusterSize > 0
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descSuffix = strrep(descSuffix, '.', 'pt');
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bf.entities.desc = [bf.entities.desc descSuffix];
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60+
if isempty(bf.extension)
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bf.extension = '.nii';
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end
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bf = bf.update();
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hdr = spm_vol(inputImage);

‎tests/test_createRoi.m‎

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@@ -9,7 +9,8 @@
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function test_createRoi_sphere()
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volumeDefiningImage = fullfile(demoDir(), 'TStatistic.nii');
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inputDir = setUpDemoData();
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volumeDefiningImage = fullfile(inputDir, 'inputs', 'TStatistic.nii');
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sphere.location = [44 -67 0];
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sphere.radius = 5;
@@ -91,38 +92,20 @@ function test_createRoi_intersection_mask_sphere()
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value = fileparts(mfilename('fullpath'));
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end
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94-
function value = demoDir()
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96-
value = fullfile(thisDir(), '..', 'demos', 'roi', 'inputs');
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98-
if exist(fullfile(value, 'TStatistic.nii'), 'file') == 0 || ...
99-
exist(fullfile(value, 'visual motion_association-test_z_FDR_0.01.nii'), 'file') == 0
100-
gunzip(fullfile(value, '*.gz'));
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end
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end
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10595
function [roiFilename, volumeDefiningImage] = prepareRoiAndVolumeDefiningImage()
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107-
volumeDefiningImage = fullfile(demoDir(), 'TStatistic.nii');
108-
109-
roiFilename = fullfile(demoDir(), ...
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'space-MNI_atlas-neurosynth_label-visualMotion_desc-p10pt00_mask.nii');
111-
112-
if exist(roiFilename, 'file') == 2
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inputDir = setUpDemoData();
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114-
else
99+
volumeDefiningImage = fullfile(inputDir, 'inputs', 'TStatistic.nii');
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116-
zMap = fullfile(demoDir(), 'visual motion_association-test_z_FDR_0.01.nii');
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zMap = fullfile(inputDir, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
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118-
zMap = renameNeuroSynth(zMap);
119-
zMap = resliceRoiImages(volumeDefiningImage, zMap);
103+
zMap = renameNeuroSynth(zMap);
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zMap = resliceRoiImages(volumeDefiningImage, zMap);
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121-
zMap = removePrefix(zMap, 'r');
106+
zMap = removePrefix(zMap, 'r');
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123-
threshold = 10;
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roiFilename = thresholdToMask(zMap, threshold);
125-
126-
end
108+
threshold = 10;
109+
roiFilename = thresholdToMask(zMap, threshold);
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128111
end

‎tests/test_getPeakCoordinates.m‎

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Original file line numberDiff line numberDiff line change
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function test_getPeakCoordinates_basic()
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13-
roiImage = extractRoiFromAtlas(pwd, 'wang', 'V1v', 'L');
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inputDir = setUpDemoData();
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dataImage = fullfile(inputDir, 'inputs', 'TStatistic.nii');
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15-
dataImage = fullfile(demoDir(), 'TStatistic.nii');
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roiImage = extractRoiFromAtlas(pwd, 'wang', 'V1v', 'L');
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1718
reslicedImages = resliceRoiImages(dataImage, roiImage);
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assertEqual(voxelCoord, [28 8 24]);
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assertElementsAlmostEqual(maxVal, 1.6212, 'absolute', 1e-3);
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25-
delete('*hemi-L_space-MNI_atlas-wang_label-V1v_mask.*');
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end
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function value = thisDir()
30-
value = fileparts(mfilename('fullpath'));
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end
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33-
function value = demoDir()
34-
35-
value = fullfile(thisDir(), '..', 'demos', 'roi', 'inputs');
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37-
if exist(fullfile(value, 'TStatistic.nii'), 'file') == 0
38-
gunzip(fullfile(value, '*.gz'));
39-
end
40-
4126
end

‎tests/test_isBinaryMask.m‎

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1010
function test_isBinaryMask_true()
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12-
roiFilename = prepareRoiAndVolumeDefiningImage();
12+
[roiFilename, zMap] = prepareRoiAndVolumeDefiningImage();
1313
isBinaryMask(roiFilename);
14-
15-
end
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17-
function test_isBinaryMask_false()
18-
19-
[~, zMap] = prepareRoiAndVolumeDefiningImage();
2014
assertExceptionThrown(@()isBinaryMask(zMap), 'isBinaryMask:notBinaryImage');
2115

2216
end
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24-
function value = thisDir()
25-
value = fileparts(mfilename('fullpath'));
26-
end
27-
28-
function value = demoDir()
29-
30-
value = fullfile(thisDir(), '..', 'demos', 'roi', 'inputs');
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32-
if exist(fullfile(value, 'visual motion_association-test_z_FDR_0.01.nii'), 'file') == 0
33-
gunzip(fullfile(value, '*.gz'));
34-
end
35-
36-
end
37-
3818
function [roiFilename, zMap] = prepareRoiAndVolumeDefiningImage()
3919

40-
zMap = fullfile(demoDir(), 'space-MNI_atlas-neurosynth_label-visualMotion_probseg.nii');
41-
42-
roiFilename = fullfile(demoDir(), ...
43-
'space-MNI_atlas-neurosynth_label-visualMotion_desc-p10pt00_mask.nii');
44-
45-
if exist(roiFilename, 'file') == 2
20+
inputDir = setUpDemoData();
4621

47-
else
22+
zMap = fullfile(inputDir, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
4823

49-
zMap = fullfile(demoDir(), 'visual motion_association-test_z_FDR_0.01.nii');
50-
51-
zMap = renameNeuroSynth(zMap);
52-
53-
threshold = 10;
54-
roiFilename = thresholdToMask(zMap, threshold);
55-
56-
end
24+
zMap = renameNeuroSynth(zMap);
25+
threshold = 10;
26+
roiFilename = thresholdToMask(zMap, threshold);
5727

5828
end

‎tests/test_keepHemisphere.m‎

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1111
function test_keepHemisphere_basic()
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13-
inputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'demos', 'roi');
14-
15-
gunzip(fullfile(inputDir, 'inputs', '*.gz'));
13+
inputDir = setUpDemoData();
1614
zMap = fullfile(inputDir, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
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1816
zMap = renameNeuroSynth(zMap);
@@ -32,8 +30,4 @@ function test_keepHemisphere_basic()
3230
'file'), ...
3331
2);
3432

35-
% TODO check the data content
36-
37-
delete(fullfile(inputDir, 'inputs', '*.nii'));
38-
3933
end

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