def test_query_missing_files():
with _test_data():
os.remove(op.join('subj-01', 'ses-1', 'T1w.nii.gz'))
os.remove(op.join('subj-02', 'ses-2', 'T2w.nii.gz'))
os.remove(op.join('subj-03', 'ses-1', 'L.white.gii'))
os.remove(op.join('subj-03', 'ses-1', 'L.midthickness.gii'))
os.remove(op.join('subj-03', 'ses-1', 'L.pial.gii'))
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
got = query.query('T1w', session='1')
assert [m.filename for m in sorted(got)] == [
op.join('subj-02', 'ses-1', 'T1w.nii.gz'),
op.join('subj-03', 'ses-1', 'T1w.nii.gz')
]
got = query.query('T2w', session='2')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'ses-2', 'T2w.nii.gz'),
op.join('subj-03', 'ses-2', 'T2w.nii.gz')
]
got = query.query('surface', session='1', hemi='L')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'ses-1', 'L.midthickness.gii'),
op.join('subj-01', 'ses-1', 'L.pial.gii'),
op.join('subj-01', 'ses-1', 'L.white.gii'),
op.join('subj-02', 'ses-1', 'L.midthickness.gii'),
op.join('subj-02', 'ses-1', 'L.pial.gii'),
op.join('subj-02', 'ses-1', 'L.white.gii')
]
def test_query_properties():
with _test_data():
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
assert sorted(query.axes('scalar')) == []
assert sorted(query.axes('T1w')) == ['participant', 'session']
assert sorted(query.axes('T2w')) == ['participant', 'session']
assert sorted(query.axes('surface')) == [
'hemi', 'participant', 'session', 'surf'
]
assert sorted(query.templates) == ['T1w', 'T2w', 'scalar', 'surface']
assert query.variables('scalar') == {}
assert query.variables('T1w') == {
'participant': ['01', '02', '03'],
'session': ['1', '2']
}
assert query.variables('T2w') == {
'participant': ['01', '02', '03'],
'session': ['1', '2']
}
assert query.variables('surface') == {
'participant': ['01', '02', '03'],
'session': ['1', '2'],
'surf': ['midthickness', 'pial', 'white'],
'hemi': ['L', 'R']
}
assert query.variables() == {
'participant': ['01', '02', '03'],
'session': ['1', '2'],
'surf': ['midthickness', 'pial', 'white'],
'hemi': ['L', 'R']
}
def test_query_optional_var_folder():
with _test_data():
# make subj-01 have no session sub-directories
for f in glob.glob(op.join('subj-01', 'ses-1', '*')):
shutil.move(f, 'subj-01')
shutil.rmtree(op.join('subj-01', 'ses-1'))
shutil.rmtree(op.join('subj-01', 'ses-2'))
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
assert query.variables()['session'] == [None, '1', '2']
m = query.query('T1w', participant='01')
assert len(m) == 1
assert m[0].filename == op.join('subj-01', 'T1w.nii.gz')
def test_query_asarray():
with _test_data():
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
_run_and_check_query(query, 'scalar', asarray=True)
_run_and_check_query(query, 'T1w', asarray=True)
_run_and_check_query(query, 'T1w', asarray=True, participant='01')
_run_and_check_query(query, 'T1w', asarray=True, session='2')
_run_and_check_query(query,
'T1w',
asarray=True,
participant='02',
session='1')
_run_and_check_query(query, 'T2w', asarray=True)
_run_and_check_query(query, 'T2w', asarray=True, participant='01')
_run_and_check_query(query, 'T2w', asarray=True, session='2')
_run_and_check_query(query,
'T2w',
asarray=True,
participant='02',
session='1')
_run_and_check_query(query, 'surface', asarray=True)
_run_and_check_query(query, 'surface', asarray=True, hemi='L')
_run_and_check_query(query,
'surface',
asarray=True,
surf='midthickness')
_run_and_check_query(query,
'surface',
asarray=True,
hemi='R',
surf='pial')
_run_and_check_query(query,
'surface',
asarray=True,
participant='03',
surf='pial')
_run_and_check_query(query,
'surface',
asarray=True,
participant='03',
sssion='2')
def test_query_optional_var_filename():
treefile = tw.dedent("""
sub-{subject}
img[-{modality}].nii.gz (image)
""").strip()
files = [
op.join('sub-01', 'img.nii.gz'),
op.join('sub-02', 'img-t1.nii.gz'),
op.join('sub-02', 'img-t2.nii.gz'),
op.join('sub-03', 'img-t1.nii.gz'),
op.join('sub-04', 'img.nii.gz')
]
with testdir(files):
with open('_test_tree.tree', 'wt') as f:
f.write(treefile)
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
qvars = query.variables()
assert sorted(qvars.keys()) == ['modality', 'subject']
assert qvars['subject'] == ['01', '02', '03', '04']
assert qvars['modality'] == [None, 't1', 't2']
got = query.query('image', modality=None)
assert [m.filename for m in sorted(got)] == [
op.join('sub-01', 'img.nii.gz'),
op.join('sub-04', 'img.nii.gz')
]
got = query.query('image', modality='t1')
assert [m.filename for m in sorted(got)] == [
op.join('sub-02', 'img-t1.nii.gz'),
op.join('sub-03', 'img-t1.nii.gz')
]
got = query.query('image', modality='t2')
assert len(got) == 1
assert got[0].filename == op.join('sub-02', 'img-t2.nii.gz')
def _query(specs=None, files=None, realdata=False):
if specs is None:
specs = {'tree': treespec}
root = list(specs.keys())[0]
volfile = op.join(datadir, '3d.nii.gz')
meshfile = op.join(datadir, 'gifti', 'white.surf.gii')
with tempdir():
for name, spec in specs.items():
with open('{}.tree'.format(name), 'wt') as f:
f.write(spec)
if files is None:
files = []
for subj, ses in it.product(subjs, sess):
sesdir = op.join('subj-{}'.format(subj), 'ses-{}'.format(ses))
files.append(op.join(sesdir, 'T1w.nii.gz'))
files.append(op.join(sesdir, 'T2w.nii.gz'))
for hemi, surf in it.product(hemis, surfs):
fname = '{}.{}.gii'.format(hemi, surf)
files.append(op.join(sesdir, fname))
for file in files:
dirname, filename = op.split(file)
os.makedirs(dirname, exist_ok=True)
if realdata:
if file.endswith('.gii'): src = meshfile
elif file.endswith('.nii.gz'): src = volfile
shutil.copy(src, file)
else:
with open(file, 'wt') as f:
pass
tree = filetree.FileTree.read('{}.tree'.format(root), '.')
query = filetree.FileTreeQuery(tree)
yield query
def _loadTree(self, treename, dirname):
"""Called when a new tree or data directory is selected. Clears
any previous file tree, and loads the new one. If either the tree
or directory are ``None``, any existing file tree is cleared.
:arg treename: File tree name or file
:arg dirname: Data directory
"""
if treename is None or dirname is None:
dirname = None
tree = None
query = None
mgr = None
allvars = None
filetypes = None
else:
tree = filetree.FileTree.read(treename, directory=dirname)
query = filetree.FileTreeQuery(tree)
mgr = ftmanager.FileTreeManager(self.overlayList, self.displayCtx,
query)
allvars = query.variables()
allvars = [(var, vals) for var, vals in allvars.items()]
allvars = collections.OrderedDict(list(sorted(allvars)))
filetypes = list(sorted(query.templates))
self.__tree = tree
self.__query = query
self.__mgr = mgr
self.__dirName.SetLabel(dirname or '')
self.__varPanel.SetVariables(allvars)
self.__fileTypes.SetFileTypes(filetypes)
self.__leftPanel.Layout()
self.UpdateFileList()
def test_query_multi_subtree():
tree1 = tw.dedent("""
subj-{participant}
T1w.nii.gz (T1w)
native
->surface space=native (surf_native)
mni
->surface space=mni (surf_mni)
""")
tree2 = tw.dedent("""
{hemi}.{space}.gii (surface)
""")
files = [
op.join('subj-01', 'T1w.nii.gz'),
op.join('subj-01', 'native', 'L.native.gii'),
op.join('subj-01', 'native', 'R.native.gii'),
op.join('subj-01', 'mni', 'L.mni.gii'),
op.join('subj-01', 'mni', 'R.mni.gii'),
op.join('subj-02', 'T1w.nii.gz'),
op.join('subj-02', 'native', 'L.native.gii'),
op.join('subj-02', 'native', 'R.native.gii'),
op.join('subj-02', 'mni', 'L.mni.gii'),
op.join('subj-02', 'mni', 'R.mni.gii'),
op.join('subj-03', 'T1w.nii.gz'),
op.join('subj-03', 'native', 'L.native.gii'),
op.join('subj-03', 'native', 'R.native.gii'),
op.join('subj-03', 'mni', 'L.mni.gii'),
op.join('subj-03', 'mni', 'R.mni.gii')
]
with testdir(files):
with open('tree1.tree', 'wt') as f:
f.write(tree1)
with open('surface.tree', 'wt') as f:
f.write(tree2)
tree = filetree.FileTree.read('tree1.tree', '.')
query = filetree.FileTreeQuery(tree)
assert sorted(query.templates) == [
'T1w', 'surf_mni/surface', 'surf_native/surface'
]
qvars = query.variables()
assert sorted(qvars.keys()) == ['hemi', 'participant']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
qvars = query.variables('T1w')
assert sorted(qvars.keys()) == ['participant']
assert qvars['participant'] == ['01', '02', '03']
qvars = query.variables('surf_mni/surface')
assert sorted(qvars.keys()) == ['hemi', 'participant']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
qvars = query.variables('surf_native/surface')
assert sorted(qvars.keys()) == ['hemi', 'participant']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
got = query.query('T1w')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'T1w.nii.gz'),
op.join('subj-02', 'T1w.nii.gz'),
op.join('subj-03', 'T1w.nii.gz')
]
got = query.query('T1w', participant='01')
assert [m.filename
for m in sorted(got)] == [op.join('subj-01', 'T1w.nii.gz')]
got = query.query('surf_mni/surface')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'mni', 'L.mni.gii'),
op.join('subj-01', 'mni', 'R.mni.gii'),
op.join('subj-02', 'mni', 'L.mni.gii'),
op.join('subj-02', 'mni', 'R.mni.gii'),
op.join('subj-03', 'mni', 'L.mni.gii'),
op.join('subj-03', 'mni', 'R.mni.gii')
]
got = query.query('surf_native/surface', hemi='L')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'native', 'L.native.gii'),
op.join('subj-02', 'native', 'L.native.gii'),
op.join('subj-03', 'native', 'L.native.gii')
]
def test_query_variable_partial_set():
tree1 = tw.dedent("""
subj-{participant}
T1w.nii.gz (T1w)
native
->surface space=native (surf_native)
standard
->surface (surf_standard)
""")
tree2 = tw.dedent("""
{hemi}.{space}.gii (surface)
""")
files = [
op.join('subj-01', 'T1w.nii.gz'),
op.join('subj-01', 'native', 'L.native.gii'),
op.join('subj-01', 'native', 'R.native.gii'),
op.join('subj-01', 'standard', 'L.mni.gii'),
op.join('subj-01', 'standard', 'R.mni.gii'),
op.join('subj-01', 'standard', 'L.freesurfer.gii'),
op.join('subj-01', 'standard', 'R.freesurfer.gii'),
op.join('subj-02', 'T1w.nii.gz'),
op.join('subj-02', 'native', 'L.native.gii'),
op.join('subj-02', 'native', 'R.native.gii'),
op.join('subj-02', 'standard', 'L.mni.gii'),
op.join('subj-02', 'standard', 'R.mni.gii'),
op.join('subj-02', 'standard', 'L.freesurfer.gii'),
op.join('subj-02', 'standard', 'R.freesurfer.gii'),
op.join('subj-03', 'T1w.nii.gz'),
op.join('subj-03', 'native', 'L.native.gii'),
op.join('subj-03', 'native', 'R.native.gii'),
op.join('subj-03', 'standard', 'L.mni.gii'),
op.join('subj-03', 'standard', 'R.mni.gii')
]
with testdir(files):
with open('tree1.tree', 'wt') as f:
f.write(tree1)
with open('surface.tree', 'wt') as f:
f.write(tree2)
tree = filetree.FileTree.read('tree1.tree', '.')
query = filetree.FileTreeQuery(tree)
assert sorted(query.templates) == [
'T1w', 'surf_native/surface', 'surf_standard/surface'
]
qvars = query.variables()
assert sorted(qvars.keys()) == ['hemi', 'participant', 'space']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
assert qvars['space'] == ['freesurfer', 'mni']
qvars = query.variables('T1w')
assert sorted(qvars.keys()) == ['participant']
assert qvars['participant'] == ['01', '02', '03']
qvars = query.variables('surf_native/surface')
assert sorted(qvars.keys()) == ['hemi', 'participant']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
qvars = query.variables('surf_standard/surface')
assert sorted(qvars.keys()) == ['hemi', 'participant', 'space']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
assert qvars['space'] == ['freesurfer', 'mni']
got = query.query('T1w')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'T1w.nii.gz'),
op.join('subj-02', 'T1w.nii.gz'),
op.join('subj-03', 'T1w.nii.gz')
]
got = query.query('T1w', participant='01')
assert [m.filename
for m in sorted(got)] == [op.join('subj-01', 'T1w.nii.gz')]
got = query.query('surf_native/surface')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'native', 'L.native.gii'),
op.join('subj-01', 'native', 'R.native.gii'),
op.join('subj-02', 'native', 'L.native.gii'),
op.join('subj-02', 'native', 'R.native.gii'),
op.join('subj-03', 'native', 'L.native.gii'),
op.join('subj-03', 'native', 'R.native.gii')
]
got = query.query('surf_native/surface', hemi='L')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'native', 'L.native.gii'),
op.join('subj-02', 'native', 'L.native.gii'),
op.join('subj-03', 'native', 'L.native.gii')
]
got = query.query('surf_standard/surface', hemi='L')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'standard', 'L.freesurfer.gii'),
op.join('subj-01', 'standard', 'L.mni.gii'),
op.join('subj-02', 'standard', 'L.freesurfer.gii'),
op.join('subj-02', 'standard', 'L.mni.gii'),
# subj03/standard/L.freesurfer.gii was skipped when creating files
op.join('subj-03', 'standard', 'L.mni.gii')
]
def test_query_subtree():
tree1 = tw.dedent("""
subj-{participant}
T1w.nii.gz (T1w)
surf
->surface (surfdir)
""")
tree2 = tw.dedent("""
{hemi}.{surf}.gii (surface)
""")
files = [
op.join('subj-01', 'T1w.nii.gz'),
op.join('subj-01', 'surf', 'L.pial.gii'),
op.join('subj-01', 'surf', 'R.pial.gii'),
op.join('subj-01', 'surf', 'L.white.gii'),
op.join('subj-01', 'surf', 'R.white.gii'),
op.join('subj-02', 'T1w.nii.gz'),
op.join('subj-02', 'surf', 'L.pial.gii'),
op.join('subj-02', 'surf', 'R.pial.gii'),
op.join('subj-02', 'surf', 'L.white.gii'),
op.join('subj-02', 'surf', 'R.white.gii'),
op.join('subj-03', 'T1w.nii.gz'),
op.join('subj-03', 'surf', 'L.pial.gii'),
op.join('subj-03', 'surf', 'R.pial.gii'),
op.join('subj-03', 'surf', 'L.white.gii'),
op.join('subj-03', 'surf', 'R.white.gii')
]
with testdir(files):
with open('tree1.tree', 'wt') as f:
f.write(tree1)
with open('surface.tree', 'wt') as f:
f.write(tree2)
tree = filetree.FileTree.read('tree1.tree', '.')
query = filetree.FileTreeQuery(tree)
assert sorted(query.templates) == ['T1w', 'surfdir/surface']
qvars = query.variables()
assert sorted(qvars.keys()) == ['hemi', 'participant', 'surf']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
assert qvars['surf'] == ['pial', 'white']
qvars = query.variables('T1w')
assert sorted(qvars.keys()) == ['participant']
assert qvars['participant'] == ['01', '02', '03']
qvars = query.variables('surfdir/surface')
assert sorted(qvars.keys()) == ['hemi', 'participant', 'surf']
assert qvars['hemi'] == ['L', 'R']
assert qvars['participant'] == ['01', '02', '03']
assert qvars['surf'] == ['pial', 'white']
got = query.query('T1w')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'T1w.nii.gz'),
op.join('subj-02', 'T1w.nii.gz'),
op.join('subj-03', 'T1w.nii.gz')
]
got = query.query('T1w', participant='01')
assert [m.filename
for m in sorted(got)] == [op.join('subj-01', 'T1w.nii.gz')]
got = query.query('surfdir/surface')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'surf', 'L.pial.gii'),
op.join('subj-01', 'surf', 'L.white.gii'),
op.join('subj-01', 'surf', 'R.pial.gii'),
op.join('subj-01', 'surf', 'R.white.gii'),
op.join('subj-02', 'surf', 'L.pial.gii'),
op.join('subj-02', 'surf', 'L.white.gii'),
op.join('subj-02', 'surf', 'R.pial.gii'),
op.join('subj-02', 'surf', 'R.white.gii'),
op.join('subj-03', 'surf', 'L.pial.gii'),
op.join('subj-03', 'surf', 'L.white.gii'),
op.join('subj-03', 'surf', 'R.pial.gii'),
op.join('subj-03', 'surf', 'R.white.gii')
]
got = query.query('surfdir/surface', hemi='L')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'surf', 'L.pial.gii'),
op.join('subj-01', 'surf', 'L.white.gii'),
op.join('subj-02', 'surf', 'L.pial.gii'),
op.join('subj-02', 'surf', 'L.white.gii'),
op.join('subj-03', 'surf', 'L.pial.gii'),
op.join('subj-03', 'surf', 'L.white.gii')
]
got = query.query('surfdir/surface', surf='white')
assert [m.filename for m in sorted(got)] == [
op.join('subj-01', 'surf', 'L.white.gii'),
op.join('subj-01', 'surf', 'R.white.gii'),
op.join('subj-02', 'surf', 'L.white.gii'),
op.join('subj-02', 'surf', 'R.white.gii'),
op.join('subj-03', 'surf', 'L.white.gii'),
op.join('subj-03', 'surf', 'R.white.gii')
]