def subjects(self):
self.restLog("Returning info about subjects", 2)
projects = Navigate.getProjects(self.nidm_files)
result = {'subject': []}
if 'fields' in self.query and len(self.query['fields']) > 0:
result['fields'] = {}
for proj in projects:
subs = Navigate.getSubjects(self.nidm_files, proj)
for s in subs:
result['subject'].append([
Query.URITail(s),
Navigate.getSubjectIDfromUUID(self.nidm_files, s)
])
# print ("getting info for " + str(s))
x = self.getFieldInfoForSubject(proj, s)
if x != {}:
result['fields'][Query.URITail(s)] = x
return self.subjectFormat(result)
def subjectsList(self):
match = re.match(r"^/?projects/([^/]+)/subjects/?$", self.command)
project = match.group((1))
self.restLog(
"Returning all agents matching filter '{}' for project {}".format(
self.query['filter'], project), 2)
# result = Query.GetParticipantUUIDsForProject(self.nidm_files, project, self.query['filter'], None)
all_subjects = Navigate.getSubjects(self.nidm_files, project)
result = {}
result['uuid'] = []
result['subject id'] = []
for sub_uuid in all_subjects:
if Query.CheckSubjectMatchesFilter(self.nidm_files, project,
sub_uuid, self.query['filter']):
uuid_string = (str(sub_uuid)).split('/')[
-1] # srip off the http://whatever/whatever/
result['uuid'].append(uuid_string)
sid = Navigate.getSubjectIDfromUUID(self.nidm_files, sub_uuid)
result['subject id'].append(str(sid))
return self.format(result)
def test_navigate_get_acquisition_data_by_subject():
set_of_keys_returned = set([])
set_of_activities = set([])
subjects = Navigate.getSubjects(OPENNEURO_FILES, OPENNEURO_PROJECT_URI)
assert len(subjects) > 0
for s in subjects:
activities = Navigate.getActivities(nidm_file_tuples=OPENNEURO_FILES,
subject_id=s)
assert len(activities) > 0
for a in activities:
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)
assert 'age' in set_of_keys_returned
assert 'InversionTime' in set_of_keys_returned
assert 'hadAcquisitionModality' in set_of_keys_returned
def test_navigate_get_acquisition_data_by_subject():
set_of_keys_returned = set([])
set_of_activities = set([])
subjects = Navigate.getSubjects(BRAIN_VOL_FILES, PROJECT_URI)
assert len(subjects) > 0
for s in subjects:
activities = Navigate.getActivities(nidm_file_list=BRAIN_VOL_FILES,
subject_id=s)
assert len(activities) > 0
for a in activities:
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 'Left-Accumbens-area (voxels)' in set_of_keys_returned
assert 'hadAcquisitionModality' in set_of_keys_returned
def GetProjectsComputedMetadata(nidm_file_list):
'''
:param nidm_file_list: List of one or more NIDM files to query across for list of Projects
:return: Dictionay or projects, each project having a dictionary of project stats
including age_max, age_min, gender list, and handedness list.
'''
meta_data = {"projects": {}}
projects = Navigate.getProjects(tuple(nidm_file_list))
for p in projects:
proj_id = nidm.experiment.tools.rest.RestParser.getTailOfURI(str(p))
meta_data["projects"][proj_id] = {"age_max": 0, "age_min": sys.maxsize, "gender": [], "handedness": [] }
meta_data["projects"][proj_id].update(Navigate.GetProjectAttributes(tuple(nidm_file_list), p))
gender_set = set()
hand_set = set()
subjects = Navigate.getSubjects(tuple(nidm_file_list), p)
for s in subjects:
activities = Navigate.getActivities(tuple(nidm_file_list), s)
meta_data["projects"][proj_id]["number_of_subjects"] = len(subjects)
for a in activities:
data = Navigate.getActivityData(tuple(nidm_file_list), a)
if type(data) == nidm.experiment.Navigate.ActivityData:
for x in data.data:
if x.isAbout == Constants.NIDM_IS_ABOUT_AGE:
if float(x.value) > meta_data["projects"][proj_id]["age_max"]:
meta_data["projects"][proj_id]["age_max"] = float(x.value)
if float(x.value) < meta_data["projects"][proj_id]["age_min"]:
meta_data["projects"][proj_id]["age_min"] = float(x.value)
if x.isAbout == Constants.NIDM_IS_ABOUT_GENDER:
gender_set.add(str(x.value))
if x.isAbout == Constants.NIDM_IS_ABOUT_HANDEDNESS:
hand_set.add(str(x.value))
meta_data["projects"][proj_id]["gender"] = list(gender_set)
meta_data["projects"][proj_id]["handedness"] = list(hand_set)
return meta_data
