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.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
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
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]
dummy_section = Section(region=None, x=x, y=y, z=z, r=r)
index_to_section_map[dummy_vertex_index] = dummy_section
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:
rgn_int = array._section_types[index_of_connection]
rgn_name = region_number_to_name_bidict.int_to_region_name(
_int=rgn_int)
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.create_distal_section(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 import MorphologyTree
tree = MorphologyTree(
name=array.name,
dummysection=dummy_section,
region_number_to_name_bidict=region_number_to_name_bidict)
# 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
