def tree_to_array(cls, tree, region_number_to_name_bidict=None):
if region_number_to_name_bidict is None:
if tree.region_number_to_name_bidict is not None:
region_number_to_name_bidict = copy.deepcopy(
tree.region_number_to_name_bidict)
else:
region_number_to_name_bidict = AutoRegionToIntMapTable()
vertices = [None] * (len(tree) + 1)
connectivity = []
section_types = []
section_index = SectionIndexerDF(morph=tree, offset=1).dict
section_index[tree.get_dummy_section()] = 0
for seg in tree._every_section():
index = section_index[seg]
# Store the vertices:
vertices[index] = seg.get_distal_npa4()
# Store the link to the parent:
if not seg.is_dummy_section():
connectivity.append((index, section_index[seg.parent]))
# Store the type:
if not seg.is_dummy_section():
region = seg.region
if region:
section_types.append(
region_number_to_name_bidict.region_name_to_int(
region.name))
else:
section_types.append(0)
return MorphologyArray(vertices=vertices,
connectivity=connectivity,
dummy_vertex_index=0,
section_types=section_types)
def tree_to_array(cls, tree, region_number_to_name_bidict=None):
if region_number_to_name_bidict is None:
if tree.region_number_to_name_bidict is not None:
region_number_to_name_bidict = copy.deepcopy(tree.region_number_to_name_bidict)
else:
region_number_to_name_bidict = AutoRegionToIntMapTable()
vertices = [None] * (len(tree) + 1)
connectivity = []
section_types = []
section_index = SectionIndexerDF(morph=tree, offset=1).dict
section_index[tree.get_dummy_section()] = 0
for seg in tree._every_section():
index = section_index[seg]
# Store the vertices:
vertices[index] = seg.get_distal_npa4()
# Store the link to the parent:
if not seg.is_dummy_section():
connectivity.append((index, section_index[seg.parent]))
# Store the type:
if not seg.is_dummy_section():
region = seg.region
if region:
section_types.append(region_number_to_name_bidict.region_name_to_int(region.name))
else:
section_types.append(0)
return MorphologyArray(vertices=vertices,
connectivity=connectivity,
dummy_vertex_index=0,
section_types=section_types)
