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Commit 6ebae621 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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TEST: more query tests

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tests/test_filetree/test_query.py
+ 153
− 41
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...@@ -84,32 +84,36 @@ def _expected_matches(short_name, **kwargs): ...@@ -84,32 +84,36 @@ def _expected_matches(short_name, **kwargs):
return matches return matches
def _run_and_check_query(query, short_name, **vars): def _run_and_check_query(query, short_name, asarray=False, **vars):
gotmatches = query.query( short_name, **vars) gotmatches = query.query( short_name, asarray=asarray, **vars)
expmatches = _expected_matches(short_name, **{k : [v] expmatches = _expected_matches(short_name, **{k : [v]
for k, v for k, v
in vars.items()}) in vars.items()})
snvars = query.variables(short_name)
assert len(snvars) == len(gotmatches.shape) if not asarray:
assert len(gotmatches) == len(expmatches)
for got, exp in zip(sorted(gotmatches), sorted(expmatches)):
assert got == exp
else:
snvars = query.variables(short_name)
for i, var in enumerate(sorted(snvars.keys())): assert len(snvars) == len(gotmatches.shape)
if var not in vars or vars[var] == '*':
assert len(snvars[var]) == gotmatches.shape[i]
else:
assert gotmatches.shape[i] == 1
for expmatch in expmatches: for i, var in enumerate(sorted(snvars.keys())):
slc = []
for var in query.axes(short_name):
if var not in vars or vars[var] == '*': if var not in vars or vars[var] == '*':
vidx = snvars[var].index(expmatch.variables[var]) assert len(snvars[var]) == gotmatches.shape[i]
slc.append(vidx)
else: else:
slc.append(0) assert gotmatches.shape[i] == 1
assert expmatch == gotmatches[tuple(slc)] for expmatch in expmatches:
slc = []
for var in query.axes(short_name):
if var not in vars or vars[var] == '*':
vidx = snvars[var].index(expmatch.variables[var])
slc.append(vidx)
else:
slc.append(0)
def test_query_properties(): def test_query_properties():
...@@ -180,7 +184,6 @@ def test_query_optional_var_folder(): ...@@ -180,7 +184,6 @@ def test_query_optional_var_folder():
assert query.variables()['session'] == [None, '1', '2'] assert query.variables()['session'] == [None, '1', '2']
m = query.query('T1w', participant='01') m = query.query('T1w', participant='01')
m = [ma for ma in m.flatten() if isinstance(ma, ftquery.Match)]
assert len(m) == 1 assert len(m) == 1
assert m[0].filename == op.join('subj-01', 'T1w.nii.gz') assert m[0].filename == op.join('subj-01', 'T1w.nii.gz')
...@@ -212,22 +215,19 @@ def test_query_optional_var_filename(): ...@@ -212,22 +215,19 @@ def test_query_optional_var_filename():
assert qvars['subject'] == ['01', '02', '03', '04'] assert qvars['subject'] == ['01', '02', '03', '04']
assert qvars['modality'] == [None, 't1', 't2'] assert qvars['modality'] == [None, 't1', 't2']
m = query.query('image', modality=None) got = query.query('image', modality=None)
m = [ma.filename for ma in m.flatten() assert [m.filename for m in sorted(got)] == [
if isinstance(ma, ftquery.Match)] op.join('sub-01', 'img.nii.gz'),
assert m == [op.join('sub-01', 'img.nii.gz'), op.join('sub-04', 'img.nii.gz')]
op.join('sub-04', 'img.nii.gz')]
m = query.query('image', modality='t1') got = query.query('image', modality='t1')
m = [ma.filename for ma in m.flatten() assert [m.filename for m in sorted(got)] == [
if isinstance(ma, ftquery.Match)] op.join('sub-02', 'img-t1.nii.gz'),
assert m == [op.join('sub-02', 'img-t1.nii.gz'), op.join('sub-03', 'img-t1.nii.gz')]
op.join('sub-03', 'img-t1.nii.gz')]
m = query.query('image', modality='t2') got = query.query('image', modality='t2')
m = [ma.filename for ma in m.flatten() assert len(got) == 1
if isinstance(ma, ftquery.Match)] assert got[0].filename == op.join('sub-02', 'img-t2.nii.gz')
assert m == [op.join('sub-02', 'img-t2.nii.gz')]
def test_query_missing_files(): def test_query_missing_files():
...@@ -242,21 +242,18 @@ def test_query_missing_files(): ...@@ -242,21 +242,18 @@ def test_query_missing_files():
tree = filetree.FileTree.read('_test_tree.tree', '.') tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree) query = filetree.FileTreeQuery(tree)
m = query.query('T1w', session='1') got = query.query('T1w', session='1')
m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)] assert [m.filename for m in sorted(got)] == [
assert sorted(m) == [
op.join('subj-02', 'ses-1', 'T1w.nii.gz'), op.join('subj-02', 'ses-1', 'T1w.nii.gz'),
op.join('subj-03', 'ses-1', 'T1w.nii.gz')] op.join('subj-03', 'ses-1', 'T1w.nii.gz')]
m = query.query('T2w', session='2') got = query.query('T2w', session='2')
m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)] assert [m.filename for m in sorted(got)] == [
assert sorted(m) == [
op.join('subj-01', 'ses-2', 'T2w.nii.gz'), op.join('subj-01', 'ses-2', 'T2w.nii.gz'),
op.join('subj-03', 'ses-2', 'T2w.nii.gz')] op.join('subj-03', 'ses-2', 'T2w.nii.gz')]
m = query.query('surface', session='1', hemi='L') got = query.query('surface', session='1', hemi='L')
m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)] assert [m.filename for m in sorted(got)] == [
assert sorted(m) == [
op.join('subj-01', 'ses-1', 'L.midthickness.gii'), 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.pial.gii'),
op.join('subj-01', 'ses-1', 'L.white.gii'), op.join('subj-01', 'ses-1', 'L.white.gii'),
...@@ -265,7 +262,122 @@ def test_query_missing_files(): ...@@ -265,7 +262,122 @@ def test_query_missing_files():
op.join('subj-02', 'ses-1', 'L.white.gii')] op.join('subj-02', 'ses-1', 'L.white.gii')]
pass def test_query_asarray():
with _test_data():
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
_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_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.short_names) == ['T1w', '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('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('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('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('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')]
def test_scan(): def test_scan():
......
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