def setup():
global cmu_test_project_uuid, PROJECT_URI, OPENNEURO_PROJECT_URI
for f in BRAIN_VOL_FILES:
if Path(f).is_file():
os.remove(f)
if not Path('./cmu_a.nidm.ttl').is_file():
urllib.request.urlretrieve(
"https://raw.githubusercontent.com/dbkeator/simple2_NIDM_examples/master/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl",
"cmu_a.nidm.ttl")
if not Path('./caltech.nidm.ttl').is_file():
urllib.request.urlretrieve(
"https://raw.githubusercontent.com/dbkeator/simple2_NIDM_examples/master/datasets.datalad.org/abide/RawDataBIDS/Caltech/nidm.ttl",
"caltech.nidm.ttl")
projects = Navigate.getProjects(BRAIN_VOL_FILES)
PROJECT_URI = projects[0]
if not Path('./ds000168.nidm.ttl').is_file():
urllib.request.urlretrieve(
"https://raw.githubusercontent.com/dbkeator/simple2_NIDM_examples/master/datasets.datalad.org/openneuro/ds000168/nidm.ttl",
"ds000168.nidm.ttl")
projects2 = Navigate.getProjects(OPENNEURO_FILES)
OPENNEURO_PROJECT_URI = projects2[0]
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 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
def test_navigate_get_projects():
projects = Navigate.getProjects(BRAIN_VOL_FILES)
assert len(projects) == 2