From 43a31b1efd65f802fa5c69730bcbeec0ee0a15fd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 18 Mar 2020 15:32:12 +0000
Subject: [PATCH] TEST: expand gifti.relatedFiles test
---
tests/test_gifti.py | 183 +++++++++++++++++++++++++++-----------------
1 file changed, 112 insertions(+), 71 deletions(-)
diff --git a/tests/test_gifti.py b/tests/test_gifti.py
index 835655b1e..6d23e665e 100644
--- a/tests/test_gifti.py
+++ b/tests/test_gifti.py
@@ -47,9 +47,9 @@ def test_GiftiMesh_create_loadAll():
with tempdir() as td:
- vertSets = [op.join(td, 'prefix.L.1.surf.gii'),
- op.join(td, 'prefix.L.2.surf.gii'),
- op.join(td, 'prefix.L.3.surf.gii')]
+ vertSets = [op.join(td, 'prefix.L.1.space.surf.gii'),
+ op.join(td, 'prefix.L.2.space.surf.gii'),
+ op.join(td, 'prefix.L.3.space.surf.gii')]
for vs in vertSets:
shutil.copy(testfile, vs)
@@ -154,82 +154,122 @@ def test_loadGiftiVertexData():
assert isinstance(gimg, nib.gifti.GiftiImage)
assert tuple(data.shape) == (642, 10)
-
-def test_relatedFiles():
-
- listing = [
- 'subject.L.ArealDistortion_FS.32k_fs_LR.shape.gii',
- 'subject.L.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
- 'subject.L.BA.32k_fs_LR.label.gii',
- 'subject.L.MyelinMap.32k_fs_LR.func.gii',
- 'subject.L.MyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.L.SmoothedMyelinMap.32k_fs_LR.func.gii',
- 'subject.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.L.aparc.32k_fs_LR.label.gii',
- 'subject.L.aparc.a2009s.32k_fs_LR.label.gii',
- 'subject.L.atlasroi.32k_fs_LR.shape.gii',
- 'subject.L.corrThickness.32k_fs_LR.shape.gii',
- 'subject.L.curvature.32k_fs_LR.shape.gii',
- 'subject.L.flat.32k_fs_LR.surf.gii',
- 'subject.L.inflated.32k_fs_LR.surf.gii',
- 'subject.L.midthickness.32k_fs_LR.surf.gii',
- 'subject.L.pial.32k_fs_LR.surf.gii',
- 'subject.L.sphere.32k_fs_LR.surf.gii',
- 'subject.L.sulc.32k_fs_LR.shape.gii',
- 'subject.L.thickness.32k_fs_LR.shape.gii',
- 'subject.L.very_inflated.32k_fs_LR.surf.gii',
- 'subject.L.white.32k_fs_LR.surf.gii',
- 'subject.R.ArealDistortion_FS.32k_fs_LR.shape.gii',
- 'subject.R.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
- 'subject.R.BA.32k_fs_LR.label.gii',
- 'subject.R.MyelinMap.32k_fs_LR.func.gii',
- 'subject.R.MyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.R.SmoothedMyelinMap.32k_fs_LR.func.gii',
- 'subject.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
- 'subject.R.aparc.32k_fs_LR.label.gii',
- 'subject.R.aparc.a2009s.32k_fs_LR.label.gii',
- 'subject.R.atlasroi.32k_fs_LR.shape.gii',
- 'subject.R.corrThickness.32k_fs_LR.shape.gii',
- 'subject.R.curvature.32k_fs_LR.shape.gii',
- 'subject.R.flat.32k_fs_LR.surf.gii',
- 'subject.R.inflated.32k_fs_LR.surf.gii',
- 'subject.R.midthickness.32k_fs_LR.surf.gii',
- 'subject.R.pial.32k_fs_LR.surf.gii',
- 'subject.R.sphere.32k_fs_LR.surf.gii',
- 'subject.R.sulc.32k_fs_LR.shape.gii',
- 'subject.R.thickness.32k_fs_LR.shape.gii',
- 'subject.R.very_inflated.32k_fs_LR.surf.gii',
- 'subject.R.white.32k_fs_LR.surf.gii',
- 'badly-formed-filename.surf.gii'
- ]
-
- lsurfaces = [l for l in listing if (l.startswith('subject.L') and
- l.endswith('surf.gii'))]
- lrelated = [l for l in listing if (l.startswith('subject.L') and
- not l.endswith('surf.gii'))]
-
- rsurfaces = [l for l in listing if (l.startswith('subject.R') and
- l.endswith('surf.gii'))]
- rrelated = [l for l in listing if (l.startswith('subject.R') and
- not l.endswith('surf.gii'))]
+hcp_listing = [
+ 'subject.L.ArealDistortion_FS.32k_fs_LR.shape.gii',
+ 'subject.L.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
+ 'subject.L.BA.32k_fs_LR.label.gii',
+ 'subject.L.MyelinMap.32k_fs_LR.func.gii',
+ 'subject.L.MyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.L.SmoothedMyelinMap.32k_fs_LR.func.gii',
+ 'subject.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.L.aparc.32k_fs_LR.label.gii',
+ 'subject.L.aparc.a2009s.32k_fs_LR.label.gii',
+ 'subject.L.atlasroi.32k_fs_LR.shape.gii',
+ 'subject.L.corrThickness.32k_fs_LR.shape.gii',
+ 'subject.L.curvature.32k_fs_LR.shape.gii',
+ 'subject.L.flat.32k_fs_LR.surf.gii',
+ 'subject.L.inflated.32k_fs_LR.surf.gii',
+ 'subject.L.midthickness.32k_fs_LR.surf.gii',
+ 'subject.L.pial.32k_fs_LR.surf.gii',
+ 'subject.L.sphere.32k_fs_LR.surf.gii',
+ 'subject.L.sulc.32k_fs_LR.shape.gii',
+ 'subject.L.thickness.32k_fs_LR.shape.gii',
+ 'subject.L.very_inflated.32k_fs_LR.surf.gii',
+ 'subject.L.white.32k_fs_LR.surf.gii',
+ 'subject.R.ArealDistortion_FS.32k_fs_LR.shape.gii',
+ 'subject.R.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii',
+ 'subject.R.BA.32k_fs_LR.label.gii',
+ 'subject.R.MyelinMap.32k_fs_LR.func.gii',
+ 'subject.R.MyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.R.SmoothedMyelinMap.32k_fs_LR.func.gii',
+ 'subject.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii',
+ 'subject.R.aparc.32k_fs_LR.label.gii',
+ 'subject.R.aparc.a2009s.32k_fs_LR.label.gii',
+ 'subject.R.atlasroi.32k_fs_LR.shape.gii',
+ 'subject.R.corrThickness.32k_fs_LR.shape.gii',
+ 'subject.R.curvature.32k_fs_LR.shape.gii',
+ 'subject.R.flat.32k_fs_LR.surf.gii',
+ 'subject.R.inflated.32k_fs_LR.surf.gii',
+ 'subject.R.midthickness.32k_fs_LR.surf.gii',
+ 'subject.R.pial.32k_fs_LR.surf.gii',
+ 'subject.R.sphere.32k_fs_LR.surf.gii',
+ 'subject.R.sulc.32k_fs_LR.shape.gii',
+ 'subject.R.thickness.32k_fs_LR.shape.gii',
+ 'subject.R.very_inflated.32k_fs_LR.surf.gii',
+ 'subject.R.white.32k_fs_LR.surf.gii'
+]
+
+bids_listing = [
+ 'sub-001_ses-001_hemi-L_desc-corr_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-L_desc-drawem_space-T2w_dparc.label.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_desc-medialwall_mask.shape.gii',
+ 'sub-001_ses-001_hemi-L_desc-smoothed_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_curv.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_inflated.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_midthickness.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_pial.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_sphere.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_sulc.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_veryinflated.surf.gii',
+ 'sub-001_ses-001_hemi-L_space-T2w_wm.surf.gii',
+ 'sub-001_ses-001_hemi-R_desc-corr_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-R_desc-drawem_space-T2w_dparc.label.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_desc-medialwall_mask.shape.gii',
+ 'sub-001_ses-001_hemi-R_desc-smoothed_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_curv.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_inflated.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_midthickness.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_myelinmap.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_pial.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_sphere.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_sulc.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_thickness.shape.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_veryinflated.surf.gii',
+ 'sub-001_ses-001_hemi-R_space-T2w_wm.surf.gii'
+]
+
+
+def test_relatedFiles_hcp(): _test_relatedFiles(hcp_listing)
+def test_relatedFiles_bids(): _test_relatedFiles(bids_listing)
+def _test_relatedFiles(listing):
+
+ listing = list(listing)
+ listing.append('badly-formed-filename.surf.gii')
+
+ def ishemi(f, hemi):
+ return ('hemi-{}'.format(hemi) in f) or \
+ ('.{}.' .format(hemi) in f)
+
+ def issurf(f):
+ return f.endswith('surf.gii')
+
+ def isrelated(f):
+ return not issurf(f)
+
+ lsurfaces = [l for l in listing if issurf( l) and ishemi(l, 'L')]
+ lrelated = [l for l in listing if isrelated(l) and ishemi(l, 'L')]
+ rsurfaces = [l for l in listing if issurf( l) and ishemi(l, 'R')]
+ rrelated = [l for l in listing if isrelated(l) and ishemi(l, 'R')]
with tempdir() as td:
+ listing = [op.join(td, f) for f in listing]
+ lsurfaces = [op.join(td, f) for f in lsurfaces]
+ rsurfaces = [op.join(td, f) for f in rsurfaces]
+ lrelated = [op.join(td, f) for f in lrelated]
+ rrelated = [op.join(td, f) for f in rrelated]
+
for l in listing:
- with open(op.join(td, l), 'wt') as f:
+ with open(l, 'wt') as f:
f.write(l)
- badname = op.join(op.join(td, 'badly-formed-filename'))
+ badname = op.join(td, 'badly-formed-filename.surf.gii')
assert len(gifti.relatedFiles(badname)) == 0
assert len(gifti.relatedFiles('nonexistent')) == 0
- llisting = [op.join(td, f) for f in listing]
- lsurfaces = [op.join(td, f) for f in lsurfaces]
- rsurfaces = [op.join(td, f) for f in rsurfaces]
- lrelated = [op.join(td, f) for f in lrelated]
- rrelated = [op.join(td, f) for f in rrelated]
-
for s in lsurfaces:
result = gifti.relatedFiles(s)
assert sorted(lrelated) == sorted(result)
@@ -237,12 +277,13 @@ def test_relatedFiles():
result = gifti.relatedFiles(s)
assert sorted(rrelated) == sorted(result)
- exp = lsurfaces + lrelated
+ exp = lsurfaces
exp = [f for f in exp if f != lsurfaces[0]]
result = gifti.relatedFiles(lsurfaces[0],
- ftypes=gifti.ALLOWED_EXTENSIONS)
+ ftypes=[gifti.ALLOWED_EXTENSIONS[0]])
assert sorted(exp) == sorted(result)
+
TEST_VERTS = np.array([
[0, 0, 0],
[1, 0, 0],
--
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