def voxel_model_cache(fn_temp_dir, mcc):
manifest_path = os.path.join(fn_temp_dir, 'voxel_model_manifest.json')
cache = VoxelModelCache(manifest_file=manifest_path)
cache.get_reference_space = mock.Mock()
cache.get_reference_space.return_value = mcc.get_reference_space()
return cache
def main():
# initialize cache object
cache = VoxelModelCache(manifest_file=MANIFEST_FILE)
rs = cache.get_reference_space()
rs.remove_unassigned(update_self=True)
# major id children only
structures = []
for s in rs.structure_tree.get_structures_by_set_id([MAJOR_BRAIN_SET_ID]):
structures.extend(rs.structure_tree.descendants([s['id']])[0])
# load in voxel model
print('loading array')
voxel_array, source_mask, target_mask = cache.get_voxel_connectivity_array(
)
print('getting keys')
source_keys, target_keys = [], []
source_counts, target_counts = [], []
for s in structures:
s_mask = source_mask.reference_space.make_structure_mask(
[s['id']], direct_only=False)
t_mask = target_mask.reference_space.make_structure_mask(
[s['id']], direct_only=False)
# NOTE: ipsi
t_mask[..., :t_mask.shape[-1] // 2] = 0
# keys
s_key = source_mask.mask_volume(s_mask).nonzero()[0]
t_key = target_mask.mask_volume(t_mask).nonzero()[0]
source_keys.append(s_key)
target_keys.append(t_key)
source_counts.append(s_key.size)
target_counts.append(t_key.size)
del source_mask
del target_mask
# arrays
source_counts = np.asarray(source_counts)
target_counts = np.asarray(target_counts)
# compute
print('computing regional')
connection_strength = np.empty(2 * [len(structures)])
for i, j in itertools.product(range(len(structures)), repeat=2):
print(i, j)
connection_strength[i, j] = voxel_array[source_keys[i],
target_keys[j]].sum()
del voxel_array
del source_keys
del target_keys
structure_acronyms = [s['acronym'] for s in structures]
connection_strength = pd.DataFrame(connection_strength,
index=structure_acronyms,
columns=structure_acronyms)
# other metrics
connection_density = np.divide(connection_strength,
source_counts[:, np.newaxis])
normalized_connection_strength = np.divide(connection_strength,
target_counts[:, np.newaxis])
normalized_connection_density = np.divide(
connection_strength, np.outer(source_counts, target_counts))
# save
connection_strength.to_csv(
os.path.join(OUTPUT_DIR, 'connection_strength.csv'))
connection_density.to_csv(
os.path.join(OUTPUT_DIR, 'connection_density.csv'))
normalized_connection_strength.to_csv(
os.path.join(OUTPUT_DIR, 'normalized_connection_strength.csv'))
normalized_connection_density.to_csv(
os.path.join(OUTPUT_DIR, 'normalized_connection_density.csv'))
