def _branch_connectivity(self, original_conn, new_weights, interest_areas,
new_tracts=None):
# type: (Connectivity, numpy.array, numpy.array, numpy.array) -> Connectivity
"""
Generate new Connectivity based on a previous one, by changing weights (e.g. simulate lesion).
The returned connectivity has the same number of nodes. The edges of unselected nodes will have weight 0.
:param original_conn: Original Connectivity, to copy from
:param new_weights: weights matrix for the new connectivity
:param interest_areas: ndarray of the selected node id's
:param new_tracts: tracts matrix for the new connectivity
"""
new_weights, interest_areas, new_tracts = self._reorder_arrays(original_conn, new_weights,
interest_areas, new_tracts)
if new_tracts is None:
new_tracts = original_conn.tract_lengths
for i in range(len(original_conn.weights)):
for j in range(len(original_conn.weights)):
if i not in interest_areas or j not in interest_areas:
new_weights[i][j] = 0
final_conn = Connectivity()
final_conn.parent_connectivity = original_conn.gid.hex
final_conn.saved_selection = interest_areas.tolist()
final_conn.weights = new_weights
final_conn.centres = original_conn.centres
final_conn.region_labels = original_conn.region_labels
final_conn.orientations = original_conn.orientations
final_conn.cortical = original_conn.cortical
final_conn.hemispheres = original_conn.hemispheres
final_conn.areas = original_conn.areas
final_conn.tract_lengths = new_tracts
final_conn.configure()
return final_conn
def _cut_connectivity(self,
original_conn,
new_weights,
interest_areas,
new_tracts=None):
# type: (Connectivity, numpy.array, numpy.array, numpy.array) -> Connectivity
"""
Generate new Connectivity object based on current one, by removing nodes (e.g. simulate lesion).
Only the selected nodes will get used in the result. The order of the indices in interest_areas matters.
If indices are not sorted then the nodes will be permuted accordingly.
:param original_conn: Original Connectivity(HasTraits), to cut nodes from
:param new_weights: weights matrix for the new connectivity
:param interest_areas: ndarray with the selected node id's.
:param new_tracts: tracts matrix for the new connectivity
"""
new_weights, interest_areas, new_tracts = self._reorder_arrays(
original_conn, new_weights, interest_areas, new_tracts)
if new_tracts is None:
new_tracts = original_conn.tract_lengths[
interest_areas, :][:, interest_areas]
else:
new_tracts = new_tracts[interest_areas, :][:, interest_areas]
new_weights = new_weights[interest_areas, :][:, interest_areas]
final_conn = Connectivity()
final_conn.parent_connectivity = None
final_conn.weights = new_weights
final_conn.centres = original_conn.centres[interest_areas, :]
final_conn.region_labels = original_conn.region_labels[interest_areas]
if original_conn.orientations is not None and len(
original_conn.orientations):
final_conn.orientations = original_conn.orientations[
interest_areas, :]
if original_conn.cortical is not None and len(original_conn.cortical):
final_conn.cortical = original_conn.cortical[interest_areas]
if original_conn.hemispheres is not None and len(
original_conn.hemispheres):
final_conn.hemispheres = original_conn.hemispheres[interest_areas]
if original_conn.areas is not None and len(original_conn.areas):
final_conn.areas = original_conn.areas[interest_areas]
final_conn.tract_lengths = new_tracts
final_conn.saved_selection = []
final_conn.configure()
return final_conn