def check_lesion_tract_overlaps(tracts):
#cached_data = current_app.cache.get(cache_key)
cache = JobCache(current_app.cache, current_app.cache_lock)
for tract in tracts:
# average density maps for this tract based on current query
# save averaged map and cache the file path
status = cache.job_status(cache_key, tract.code)
if status == 'COMPLETE':
# get file path from cache
tract_file_path = cache.job_result(cache_key, tract.code)
else:
# recalculate density map
file_path_data = dbu.density_map_file_path_data(request_query)
if len(file_path_data) > 0:
current_app.logger.info(f'Adding job {tract.code}')
cache.add_job(cache_key, tract.code)
data_dir = current_app.config[
'DATA_FILE_PATH'] # file path to data folder
tract_file_path = du.generate_average_density_map(
data_dir, file_path_data, tract, 'MNI')
cache.job_complete(cache_key, tract.code, tract_file_path)
current_app.logger.info(f'Job {tract.code} complete')
else:
current_app.logger.info(
f'No subjects returned for query {json.dumps(request_query, indent=4)}'
)
return 'No subjects returned for the current query', 404
# # perform weighted overlap: lesion * tract
# tract_data = du.get_nifti_data(tract_file_path)
# overlap = lesion_data * tract_data
# # weighted sum of voxels occupied by overlap
# # figure out percentage of tract overlapping with lesion
# overlap_sum = np.sum(overlap)
# if overlap_sum:
# overlap_score = overlap_sum / np.sum(tract_data)
# # add dict to intersecting_tracts list
# intersecting_tracts.append({"tractCode": tract.code, "overlapScore": overlap_score})
# alternative overlap score
tract_data = du.get_nifti_data(tract_file_path)
masked_tract_data = ma.masked_where(tract_data < threshold,
tract_data)
overlap = lesion_data * masked_tract_data
over_threshold_count = masked_tract_data.count()
over_threshold_overlap_count = len(overlap.nonzero()[0])
if over_threshold_overlap_count:
overlap_percent = (over_threshold_overlap_count /
over_threshold_count) * 100.
# add dict to intersecting_tracts list
intersecting_tracts.append({
"tractName": tract.name,
"tractCode": tract.code,
"overlapScore": overlap_percent,
"description": tract.description
})
def test_add_job(self):
cache = CacheMock()
lock = LockMock()
job_cache = JobCache(cache, lock)
# test when no jobs in cache for key
job_cache.add_job(self.TEST_KEY, self.JOB1_KEY)
assert cache.get(self.TEST_KEY).get(
self.JOB1_KEY).get('status') == 'IN_PROGRESS'
# test when jobs already exist for key but job doesn't exist
job_cache.add_job(self.TEST_KEY, self.JOB2_KEY)
assert cache.get(self.TEST_KEY).get(
self.JOB2_KEY).get('status') == 'IN_PROGRESS'
# test when completed job already exists (shouldn't change cached job)
jobs = cache.get(self.TEST_KEY)
jobs[self.JOB2_KEY]['status'] = 'COMPLETE'
cache.set(self.TEST_KEY, jobs)
job_cache.add_job(self.TEST_KEY, self.JOB2_KEY)
assert cache.get(self.TEST_KEY).get(
self.JOB2_KEY).get('status') == 'COMPLETE'