def test_navigate_get_subjects_for_acquisition():
subjects = set([])
sessions = Navigate.getSessions(BRAIN_VOL_FILES, PROJECT_URI)
for s in sessions:
acquisitions = Navigate.getAcquisitions(BRAIN_VOL_FILES, s)
for acq in acquisitions:
sub = Navigate.getSubject(BRAIN_VOL_FILES, acq)
assert sub != None
subjects.add(sub)
assert len(subjects) > 5
def ExpandProjectMetaData(self, meta_data):
"""
Takes in the meta_data from GetProjectsMetadata() and adds
the following statistics about each project to the existing
meta_data structure:
age_max (float)
age_min (float)
handedness of subjects (list)
genders of subjects (list)
number of subjects (int)
:param meta_data:
:return:
"""
for project_id in meta_data['projects']:
project_uuid = str(project_id)[6:] if (
str(project_id).startswith("niiri:")) else project_id
project = meta_data['projects'][project_id]
ages = set()
hands = set()
genders = set()
for session in Navigate.getSessions(self.nidm_files, project_uuid):
for acq in Navigate.getAcquisitions(self.nidm_files, session):
act_data = Navigate.getActivityData(self.nidm_files, acq)
for de in act_data.data:
if de.isAbout == "http://uri.interlex.org/ilx_0100400" or de.isAbout == "http://uri.interlex.org/base/ilx_0100400":
ages.add(float(de.value))
elif de.isAbout == "http://uri.interlex.org/ilx_0101292" or de.isAbout == "http://uri.interlex.org/base/ilx_0101292"\
or de.isAbout == "http://uri.interlex.org/ilx_0738439" or de.isAbout == \
"https://ndar.nih.gov/api/datadictionary/v2/dataelement/gender":
genders.add(de.value)
elif de.isAbout == "http://purl.obolibrary.org/obo/PATO_0002201":
hands.add(de.value)
print(
Query.GetParticipantUUIDsForProject(self.nidm_files,
project_uuid))
project['age_max'] = max(ages) if len(ages) > 0 else 0
project['age_min'] = min(ages) if len(ages) > 0 else 0
project[Query.matchPrefix(str(
Constants.NIDM_NUMBER_OF_SUBJECTS))] = len(
(Query.GetParticipantUUIDsForProject(
self.nidm_files, project_uuid))['uuid'])
project[str(Constants.NIDM_GENDER)] = list(genders)
project[str(Constants.NIDM_HANDEDNESS)] = list(hands)
def test_navigate_get_acquisition_data_by_session():
set_of_keys_returned = set([])
set_of_activities = set([])
sessions = Navigate.getSessions(BRAIN_VOL_FILES, PROJECT_URI)
assert len(sessions) > 0
for s in sessions:
acquisitions = Navigate.getAcquisitions(BRAIN_VOL_FILES, s)
assert len(acquisitions) > 0
for a in acquisitions:
set_of_activities.add(str(a))
ad = Navigate.getActivityData(BRAIN_VOL_FILES, a)
assert len(ad.data) > 5
for vt in ad.data:
set_of_keys_returned.add(vt.label)
assert 'AGE_AT_SCAN' in set_of_keys_returned
assert 'hadAcquisitionModality' in set_of_keys_returned
def test_navigate_get_acquisition_data_by_session():
set_of_keys_returned = set([])
set_of_activities = set([])
sessions = Navigate.getSessions(OPENNEURO_FILES, OPENNEURO_PROJECT_URI)
assert len(sessions) > 0
for s in sessions:
acquisitions = Navigate.getAcquisitions(OPENNEURO_FILES, s)
assert len(acquisitions) > 0
for a in acquisitions:
set_of_activities.add(str(a))
ad = Navigate.getActivityData(OPENNEURO_FILES, a)
assert len(ad.data) > 5
for vt in ad.data:
set_of_keys_returned.add(vt.label)
print(set_of_keys_returned)
assert 'age' in set_of_keys_returned
assert 'hadAcquisitionModality' in set_of_keys_returned
def test_navigate_get_acquisitions_for_session():
sessions = Navigate.getSessions(BRAIN_VOL_FILES, PROJECT_URI)
for s in sessions:
acquisitions = Navigate.getAcquisitions(BRAIN_VOL_FILES, sessions[0])
assert len(acquisitions) > 0