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Commit 43a31b1e authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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TEST: expand gifti.relatedFiles test

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with 112 additions and 71 deletions
tests/test_gifti.py
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......@@ -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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