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.getDummySection()] = 0
for seg in tree._every_section():
index = section_index[seg]
# Store the vertices:
vertices[ index ] = seg.getDistalNPA4()
# Store the link to the parent:
if not seg.isDummySection():
connectivity.append( (index,section_index[seg.parent] ) )
# Store the type:
if not seg.isDummySection():
region = seg.region
if region:
section_types.append( region_number_to_name_bidict.regionNameToInt(region.name) )
else:
section_types.append( 0 )
m = MorphologyArray(vertices=vertices, connectivity=connectivity, dummy_vertex_index=0, section_types=section_types, )
return m
