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[FIX] run test create roi octave #1285

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Merged
merged 6 commits into from
Jul 13, 2024
Merged

[FIX] run test create roi octave #1285

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1320e1d
run test create roi octave
Remi-Gau Jul 13, 2024
9c9888c
fix several tests in cpp roi
Remi-Gau Jul 13, 2024
99b544d
reset submod
Remi-Gau Jul 13, 2024
d5f5c20
update CPP_ROI
Remi-Gau Jul 13, 2024
6671a8f
fix default path output create roi
Remi-Gau Jul 13, 2024
da0e7ae
fix typo
Remi-Gau Jul 13, 2024
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2 changes: 1 addition & 1 deletion lib/CPP_ROI
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Submodule CPP_ROI updated 16 files
+78 −0 .github/workflows/run_tests_octave.yml
+22 −0 .github/workflows/tests_octave.m
+0 −5 src/atlas/copyAtlasToSpmDir.m
+11 −2 src/atlas/extractRoiFromAtlas.m
+9 −3 src/atlas/unzipAtlas.m
+5 −1 src/roi/thresholdToMask.m
+10 −27 tests/test_createRoi.m
+3 −18 tests/test_getPeakCoordinates.m
+6 −36 tests/test_isBinaryMask.m
+1 −7 tests/test_keepHemisphere.m
+4 −17 tests/test_labelClusters.m
+5 −30 tests/test_thresholdToMask.m
+9 −0 tests/utils/demoDir.m
+1 −1 tests/utils/rmRetinoAtlas.m
+16 −0 tests/utils/setUpDemoData.m
+6 −0 tests/utils/tempDir.m
2 changes: 1 addition & 1 deletion src/bidspm/bidspm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,7 @@ def create_roi(
) -> str:
roi_name = "{ '" + "', '".join(roi_name) + "' }" if roi_name is not None else None # type: ignore
if roi_dir is None:
roi_dir = Path()
roi_dir = output_dir

cmd = generate_cmd(
bids_dir=bids_dir,
Expand Down
2 changes: 1 addition & 1 deletion src/workflows/roi/bidsCreateROI.m
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ function bidsCreateROI(opt)
% opt.roi.atlas = 'wang';
% opt.roi.hemi = {'L', 'R'};
% opt.roi.name = {'V1v', 'V1d'};
% opt.roi.space = {'IXI549Space''};
% opt.roi.space = {'IXI549Space'};
%
% bidsCreateROI(opt);
%
Expand Down
26 changes: 6 additions & 20 deletions tests/tests_slow/tests_cli/test_bidspm_create_roi.m
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,6 @@ function test_bidsCreateROI_boilerplate_only()

markTestAs('slow');

if bids.internal.is_octave
moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
end

outputPath = tempName();

bidspm(pwd, outputPath, ...
Expand All @@ -40,10 +36,6 @@ function test_bidsCreateROI_glasser()

markTestAs('slow');

if bids.internal.is_octave
moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
end

outputPath = tempName();

bidspm(pwd, outputPath, ...
Expand All @@ -54,6 +46,12 @@ function test_bidsCreateROI_glasser()
'space', {'IXI549Space'}, ...
'verbosity', 3);

assert(exist(fullfile(outputPath, ...
'derivatives', ...
'bidspm-roi', ...
'reports', ...
'create_roi_atlas-glasser_citation.md'), 'file') == 2);

rois = spm_select('FPList', fullfile(outputPath, ...
'derivatives', ...
'bidspm-roi', 'group'), '.*glasser.*_mask\.nii');
Expand All @@ -65,10 +63,6 @@ function test_bidsCreateROI_wang()

markTestAs('slow');

if bids.internal.is_octave
moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
end

outputPath = tempName();

bidspm(pwd, outputPath, ...
Expand All @@ -90,10 +84,6 @@ function test_bidsCreateROI_neuromorphometrics()

markTestAs('slow');

if bids.internal.is_octave
moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
end

outputPath = tempName();

bidspm(pwd, outputPath, ...
Expand Down Expand Up @@ -133,10 +123,6 @@ function test_bidsCreateROI_one_hemisphere()

markTestAs('slow');

if bids.internal.is_octave
moxunit_throw_test_skipped_exception('Need bug fix in CPP ROI extractRoiFromAtlas.');
end

outputPath = tempName();

bidspm(pwd, outputPath, 'subject', ...
Expand Down