From 6ebae621cd7f69ff73844e4019b7ad830981207c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 29 Mar 2019 11:44:29 +0000
Subject: [PATCH] TEST: more query tests
---
tests/test_filetree/test_query.py | 194 +++++++++++++++++++++++-------
1 file changed, 153 insertions(+), 41 deletions(-)
diff --git a/tests/test_filetree/test_query.py b/tests/test_filetree/test_query.py
index 094686d9e..66e50c1f8 100644
--- a/tests/test_filetree/test_query.py
+++ b/tests/test_filetree/test_query.py
@@ -84,32 +84,36 @@ def _expected_matches(short_name, **kwargs):
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]
for k, v
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())):
- if var not in vars or vars[var] == '*':
- assert len(snvars[var]) == gotmatches.shape[i]
- else:
- assert gotmatches.shape[i] == 1
+ assert len(snvars) == len(gotmatches.shape)
- for expmatch in expmatches:
- slc = []
- for var in query.axes(short_name):
+ for i, var in enumerate(sorted(snvars.keys())):
if var not in vars or vars[var] == '*':
- vidx = snvars[var].index(expmatch.variables[var])
- slc.append(vidx)
+ assert len(snvars[var]) == gotmatches.shape[i]
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():
@@ -180,7 +184,6 @@ def test_query_optional_var_folder():
assert query.variables()['session'] == [None, '1', '2']
m = query.query('T1w', participant='01')
- m = [ma for ma in m.flatten() if isinstance(ma, ftquery.Match)]
assert len(m) == 1
assert m[0].filename == op.join('subj-01', 'T1w.nii.gz')
@@ -212,22 +215,19 @@ def test_query_optional_var_filename():
assert qvars['subject'] == ['01', '02', '03', '04']
assert qvars['modality'] == [None, 't1', 't2']
- m = query.query('image', modality=None)
- m = [ma.filename for ma in m.flatten()
- if isinstance(ma, ftquery.Match)]
- assert m == [op.join('sub-01', 'img.nii.gz'),
- op.join('sub-04', 'img.nii.gz')]
+ 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')]
- m = query.query('image', modality='t1')
- m = [ma.filename for ma in m.flatten()
- if isinstance(ma, ftquery.Match)]
- assert m == [op.join('sub-02', 'img-t1.nii.gz'),
- op.join('sub-03', 'img-t1.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')]
- m = query.query('image', modality='t2')
- m = [ma.filename for ma in m.flatten()
- if isinstance(ma, ftquery.Match)]
- assert m == [op.join('sub-02', 'img-t2.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 test_query_missing_files():
@@ -242,21 +242,18 @@ def test_query_missing_files():
tree = filetree.FileTree.read('_test_tree.tree', '.')
query = filetree.FileTreeQuery(tree)
- m = query.query('T1w', session='1')
- m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)]
- assert sorted(m) == [
+ 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')]
- m = query.query('T2w', session='2')
- m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)]
- assert sorted(m) == [
+ 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')]
- m = query.query('surface', session='1', hemi='L')
- m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)]
- assert sorted(m) == [
+ 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'),
@@ -265,7 +262,122 @@ def test_query_missing_files():
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():
--
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