def array_to_tree(cls, array, region_number_to_name_bidict=None):
if region_number_to_name_bidict is None:
if array.region_number_to_name_bidict is not None:
region_number_to_name_bidict = copy.deepcopy( array.region_number_to_name_bidict )
else:
region_number_to_name_bidict = AutoRegionToIntMapTable()
name_to_region_map= {}
dummy_vertex_index = array._dummy_vertex_index
index_to_section_map = {}
# Create the root section:
x,y,z,r = array._vertices[dummy_vertex_index]
dummySection = Section( region=None,x=x,y=y,z=z,r=r )
index_to_section_map[dummy_vertex_index] = dummySection
indices_to_visit = collections.deque([dummy_vertex_index])
while indices_to_visit:
index = indices_to_visit.pop()
section = index_to_section_map[index]
connections_to_index = array.connections_to_index(index)
for conn in connections_to_index:
# Have we made this connection already?:
if conn in index_to_section_map:
continue
# No? Lets make a connection:
else:
x,y,z,r = array._vertices[conn]
index_of_connection = array.index_of_connection(index,conn)
# Create the region, if it doesn't already exist:
rgnInt = array._section_types[index_of_connection]
rgn_name = region_number_to_name_bidict.intToRegionName(int=rgnInt)
if rgn_name is None:
rgn=None
else:
if not rgn_name in name_to_region_map:
name_to_region_map[rgn_name] = Region(rgn_name)
rgn = name_to_region_map[rgn_name]
newsection = section.extrudeChildSection(region=rgn, x=x,y=y,z=z,r=r )
index_to_section_map[conn] = newsection
indices_to_visit.append( conn )
from morphforge.morphology.core.morphologytree import MorphologyTree
tree = MorphologyTree("SimpleSomaMorph", dummysection=dummySection, )
# A sanity check:
assert len(tree) == len(array), 'The tree and array are not the same size! %d vs %d'%(len(tree), len(array))
return tree
