def cell_location_distance_from_soma(cell_location):
morph = cell_location.cell.morphology
sect_dist_dict = SectionVistorFactory.dict_section_proximal_dist_from_soma(morph, soma_centre=False)()
section_dist = sect_dist_dict[cell_location.morphlocation.section]
celllocdist = (
section_dist + cell_location.morphlocation.section.get_length() * cell_location.morphlocation.sectionpos
)
return celllocdist
def cell_location_distance_from_soma(cell_location):
morph = cell_location.cell.morphology
sect_dist_dict = SectionVistorFactory.dict_section_proximal_dist_from_soma(
morph, soma_centre=False)()
section_dist = sect_dist_dict[cell_location.morphlocation.section]
celllocdist = section_dist + cell_location.morphlocation.section.get_length(
) * cell_location.morphlocation.sectionpos
return celllocdist
def trim_axon_from_morphology(cls, morphology, max_dist_to_parent):
dist_to_parent = SectionVistorFactory.dict_section_proximal_dist_from_soma(
morph=morphology, soma_centre=False)()
print sorted(dist_to_parent.values())
section_mapping_table = {}
region_mapping_table = {}
# Create New Regions:
region_mapping_table[None] = None
for rOld in morphology.get_regions():
r_new = Region(name=rOld.name)
region_mapping_table[rOld] = r_new
# Create New Sections:
dummy_root_old = morphology.get_dummy_section()
dummy_root_new = Section(
region=region_mapping_table[dummy_root_old.region],
x=dummy_root_old.d_x,
y=dummy_root_old.d_y,
z=dummy_root_old.d_z,
r=dummy_root_old.d_r)
section_mapping_table[dummy_root_old] = dummy_root_new
for sectionOld in morphology:
print 'DistToParent', dist_to_parent[sectionOld]
if dist_to_parent[sectionOld] > max_dist_to_parent:
continue
print 'Extruding Section'
old_parent = sectionOld.parent
new_parent = section_mapping_table[old_parent]
section_new = new_parent.create_distal_section(
region=region_mapping_table[sectionOld.region],
x=sectionOld.d_x,
y=sectionOld.d_y,
z=sectionOld.d_z,
r=sectionOld.d_r,
idtag=sectionOld.idtag,
)
section_mapping_table[sectionOld] = section_new
m = MorphologyTree('TrimmedNeuron',
dummysection=dummy_root_new,
metadata={})
return m
def trim_axon_from_morphology(cls, morphology, max_dist_to_parent):
dist_to_parent = SectionVistorFactory.dict_section_proximal_dist_from_soma(morph=morphology, soma_centre=False)()
print sorted(dist_to_parent.values())
section_mapping_table = {}
region_mapping_table = {}
# Create New Regions:
region_mapping_table[None] = None
for rOld in morphology.get_regions():
r_new = Region(name=rOld.name)
region_mapping_table[rOld] = r_new
# Create New Sections:
dummy_root_old = morphology.get_dummy_section()
dummy_root_new = Section(
region=region_mapping_table[dummy_root_old.region],
x=dummy_root_old.d_x,
y=dummy_root_old.d_y,
z=dummy_root_old.d_z,
r=dummy_root_old.d_r)
section_mapping_table[dummy_root_old] = dummy_root_new
for sectionOld in morphology:
print 'DistToParent', dist_to_parent[sectionOld]
if dist_to_parent[sectionOld] > max_dist_to_parent:
continue
print 'Extruding Section'
old_parent = sectionOld.parent
new_parent = section_mapping_table[old_parent]
section_new = new_parent.create_distal_section(
region=region_mapping_table[sectionOld.region],
x=sectionOld.d_x,
y=sectionOld.d_y,
z=sectionOld.d_z,
r=sectionOld.d_r,
idtag=sectionOld.idtag,
)
section_mapping_table[sectionOld] = section_new
m = MorphologyTree('TrimmedNeuron',
dummysection=dummy_root_new, metadata={})
return m
