From d79174564cfb4099ef6c801b77f5a05ed90e1e10 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 29 Mar 2019 10:28:25 +0000
Subject: [PATCH] TEST: unit tests for filetree.query
---
tests/test_filetree/__init__.py | 0
tests/test_filetree/test_query.py | 326 ++++++++++++++++++++++++++++++
2 files changed, 326 insertions(+)
create mode 100644 tests/test_filetree/__init__.py
create mode 100644 tests/test_filetree/test_query.py
diff --git a/tests/test_filetree/__init__.py b/tests/test_filetree/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/test_filetree/test_query.py b/tests/test_filetree/test_query.py
new file mode 100644
index 000000000..094686d9e
--- /dev/null
+++ b/tests/test_filetree/test_query.py
@@ -0,0 +1,326 @@
+#!/usr/bin/env python
+#
+# test_query.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os
+import glob
+import shutil
+import os.path as op
+import contextlib
+import textwrap as tw
+import itertools as it
+
+from .. import testdir
+
+import fsl.utils.filetree as filetree
+import fsl.utils.filetree.query as ftquery
+
+
+_test_tree = """
+subj-{participant}
+ [ses-{session}]
+ T1w.nii.gz (T1w)
+ T2w.nii.gz (T2w)
+ {hemi}.{surf}.gii (surface)
+""".strip()
+
+_subjs = ['01', '02', '03']
+_sess = ['1', '2']
+_hemis = ['L', 'R']
+_surfs = ['midthickness', 'pial', 'white']
+
+
+@contextlib.contextmanager
+def _test_data():
+
+ 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):
+ files.append(op.join(sesdir, '{}.{}.gii'.format(hemi, surf)))
+
+ with testdir(files):
+ with open('_test_tree.tree', 'wt') as f:
+ f.write(_test_tree)
+ yield
+
+
+def _expected_matches(short_name, **kwargs):
+
+ matches = []
+ subjs = kwargs.get('participant', _subjs)
+ sess = kwargs.get('session', _sess)
+ surfs = kwargs.get('surf', _surfs)
+ hemis = kwargs.get('hemi', _hemis)
+
+ for subj, ses in it.product(subjs, sess):
+
+ sesdir = op.join('subj-{}'.format(subj), 'ses-{}'.format(ses))
+
+ if short_name in ('T1w', 'T2w'):
+ f = op.join(sesdir, '{}.nii.gz'.format(short_name))
+ matches.append(ftquery.Match(f,
+ short_name,
+ {'participant' : subj,
+ 'session' : ses}))
+
+ elif short_name == 'surface':
+ for hemi, surf in it.product(hemis, surfs):
+ f = op.join(sesdir, '{}.{}.gii'.format(hemi, surf))
+ matches.append(ftquery.Match(f,
+ short_name,
+ {'participant' : subj,
+ 'session' : ses,
+ 'hemi' : hemi,
+ 'surf' : surf}))
+
+ return matches
+
+
+def _run_and_check_query(query, short_name, **vars):
+
+ gotmatches = query.query( short_name, **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)
+
+ 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
+
+ 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)
+
+ assert expmatch == gotmatches[tuple(slc)]
+
+
+def test_query_properties():
+ with _test_data():
+
+ tree = filetree.FileTree.read('_test_tree.tree', '.')
+ query = filetree.FileTreeQuery(tree)
+
+ 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.short_names) == ['T1w', 'T2w', 'surface']
+
+ 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():
+ with _test_data():
+ tree = filetree.FileTree.read('_test_tree.tree', '.')
+ query = filetree.FileTreeQuery(tree)
+
+ _run_and_check_query(query, 'T1w')
+ _run_and_check_query(query, 'T1w', participant='01')
+ _run_and_check_query(query, 'T1w', session='2')
+ _run_and_check_query(query, 'T1w', participant='02', session='1')
+ _run_and_check_query(query, 'T2w')
+ _run_and_check_query(query, 'T2w', participant='01')
+ _run_and_check_query(query, 'T2w', session='2')
+ _run_and_check_query(query, 'T2w', participant='02', session='1')
+ _run_and_check_query(query, 'surface')
+ _run_and_check_query(query, 'surface', hemi='L')
+ _run_and_check_query(query, 'surface', surf='midthickness')
+ _run_and_check_query(query, 'surface', hemi='R', surf='pial')
+ _run_and_check_query(query, 'surface', participant='03', surf='pial')
+ _run_and_check_query(query, 'surface', participant='03', sssion='2')
+
+
+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')
+ 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')
+
+
+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']
+
+ 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')]
+
+ 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')]
+
+ 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')]
+
+
+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)
+
+ m = query.query('T1w', session='1')
+ m = [ma.filename for ma in m.flatten() if isinstance(ma, ftquery.Match)]
+ assert sorted(m) == [
+ 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) == [
+ 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) == [
+ 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')]
+
+
+ pass
+
+
+def test_scan():
+
+ with _test_data():
+ tree = filetree.FileTree.read('_test_tree.tree', '.')
+ gotmatches = ftquery.scan(tree)
+
+ expmatches = []
+
+ for subj, ses in it.product(_subjs, _sess):
+
+ sesdir = op.join('subj-{}'.format(subj), 'ses-{}'.format(ses))
+ t1wf = op.join(sesdir, 'T1w.nii.gz')
+ t2wf = op.join(sesdir, 'T2w.nii.gz')
+
+ expmatches.append(ftquery.Match(t1wf, 'T1w', {'participant' : subj,
+ 'session' : ses}))
+ expmatches.append(ftquery.Match(t2wf, 'T2w', {'participant' : subj,
+ 'session' : ses}))
+
+ for hemi, surf in it.product(_hemis, _surfs):
+ surff = op.join(sesdir, '{}.{}.gii'.format(hemi, surf))
+
+ expmatches.append(ftquery.Match(surff,
+ 'surface',
+ {'participant' : subj,
+ 'session' : ses,
+ 'surf' : surf,
+ 'hemi' : hemi}))
+
+
+ assert len(gotmatches) == len(expmatches)
+
+ for got, exp in zip(sorted(gotmatches), sorted(expmatches)):
+ assert got.filename == exp.filename
+ assert got.short_name == exp.short_name
+ assert got.variables == exp.variables
+
+
+def test_allVariables():
+ with _test_data():
+ tree = filetree.FileTree.read('_test_tree.tree', '.')
+ matches = ftquery.scan(tree)
+ qvars, snames = ftquery.allVariables(tree, matches)
+
+ expqvars = {
+ 'participant' : _subjs,
+ 'session' : _sess,
+ 'surf' : _surfs,
+ 'hemi' : _hemis}
+ expsnames = {
+ 'T1w' : ['participant', 'session'],
+ 'T2w' : ['participant', 'session'],
+ 'surface' : ['hemi', 'participant', 'session', 'surf']}
+
+ assert qvars == expqvars
+ assert snames == expsnames
--
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