def test_scan_label_quality(self):
tmp_dir = tempfile.mkdtemp()
repository = XnatRepo(
project_id=self.project,
server=SERVER, cache_dir=tmp_dir)
tree = repository.tree(
subject_ids=[self.SUBJECT],
visit_ids=[self.VISIT])
for accepted, expected in (
(None, '1unusable'),
((None, 'questionable', 'usable'), '2unlabelled'),
(('questionable', 'usable'), '3questionable'),
('usable', '4usable')):
inpt = InputFilesets('dummy', order=0, valid_formats=text_format,
acceptable_quality=accepted)
matched = inpt.match(tree).item(subject_id=self.SUBJECT,
visit_id=self.VISIT)
self.assertEqual(matched.name, expected)
def test_cache_on_path_access(self):
tmp_dir = tempfile.mkdtemp()
repository = XnatRepo(server=SERVER, cache_dir=tmp_dir)
dataset = repository.dataset(self.project,
subject_ids=[self.SUBJECT],
visit_ids=[self.VISIT])
tree = dataset.tree
# Get a fileset
fileset = list(list(list(tree.subjects)[0].sessions)[0].filesets)[0]
fileset.format = text_format
self.assertEqual(fileset._path, None)
target_path = op.join(
tmp_dir, self.project, '{}_{}'.format(self.project, self.SUBJECT),
'{}_{}_{}'.format(self.project, self.SUBJECT, self.VISIT),
'{}-{}'.format(fileset.id, fileset.basename), fileset.fname)
# This should implicitly download the fileset
self.assertEqual(fileset.path, target_path)
with open(target_path) as f:
self.assertEqual(f.read(), self.INPUT_FILESETS[fileset.basename])
def test_dicom_match(self):
analysis = test_data.TestMatchAnalysis(
name='test_dicom',
dataset=XnatRepo(server=SERVER,
cache_dir=tempfile.mkdtemp()).dataset(
self.project),
processor=SingleProc(self.work_dir),
inputs=test_data.TestDicomTagMatch.DICOM_MATCH)
phase = list(analysis.data('gre_phase', derive=True))[0]
mag = list(analysis.data('gre_mag', derive=True))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_connect_disconnect(self):
repository = XnatRepo(server=SERVER, cache_dir=tempfile.mkdtemp())
with repository:
self._test_open(repository)
self._test_closed(repository)
with repository:
self._test_open(repository)
with repository:
self._test_open(repository)
self._test_open(repository)
self._test_closed(repository)
def test_dicom_match(self):
study = test_data.TestMatchStudy(
name='test_dicom',
repository=XnatRepo(
project_id=self.project,
server=SERVER, cache_dir=tempfile.mkdtemp()),
processor=SingleProc(self.work_dir),
inputs=test_data.TestDicomTagMatch.DICOM_MATCH)
phase = list(study.data('gre_phase'))[0]
mag = list(study.data('gre_mag'))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_id_match(self):
study = test_data.TestMatchStudy(
name='test_dicom',
repository=XnatRepo(
project_id=self.project,
server=SERVER, cache_dir=tempfile.mkdtemp()),
processor=SingleProc(self.work_dir),
inputs=[
InputFilesets('gre_phase', valid_formats=dicom_format, id=7),
InputFilesets('gre_mag', valid_formats=dicom_format, id=6)])
phase = list(study.data('gre_phase'))[0]
mag = list(study.data('gre_mag'))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_id_match(self):
analysis = test_data.TestMatchAnalysis(
name='test_dicom',
dataset=XnatRepo(server=SERVER,
cache_dir=tempfile.mkdtemp()).dataset(
self.project),
processor=SingleProc(self.work_dir),
inputs=[
FilesetFilter('gre_phase', valid_formats=dicom_format, id=7),
FilesetFilter('gre_mag', valid_formats=dicom_format, id=6)
])
phase = list(analysis.data('gre_phase', derive=True))[0]
mag = list(analysis.data('gre_mag', derive=True))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')