def __init__(self,
cell,
morphlocation=None,
section=None,
sectionpos=None):
self._cell = cell
if morphlocation:
assert not section and not sectionpos
self.morphlocation = morphlocation
else:
assert not morphlocation
self.morphlocation = MorphLocation(section=section,
sectionpos=sectionpos)
assert not self.morphlocation.section.is_dummy_section()
def get_locations_at_distance_away_from_dummy(cls, morphology,
distance, section_predicate=None):
dist_to_section_distal = SectionVistorFactory.dict_section_distal_dist_from_soma(morph=morphology)()
# Section predicates: allows us to generate only on a path, region, etc
section_predicate = section_predicate if section_predicate else lambda s:True
locations = []
for section in morphology:
if not section_predicate(section):
continue
if section.is_a_root_section():
if distance < dist_to_section_distal[section]:
#assert False, 'Not implemented'
locations.append(MorphLocation(section=section, sectionpos=distance/dist_to_section_distal[section]) )
else:
pass
else:
proximal_dist = dist_to_section_distal[section.parent]
distal_dist = dist_to_section_distal[section]
# Does a distance fall on this section:
if proximal_dist < distance < distal_dist:
prop = (distance - proximal_dist) / (distal_dist - proximal_dist)
assert 0.0 <= prop <= 1.0
locations.append(MorphLocation(section=section, sectionpos=prop))
else:
pass
dummy = MorphLocation(morphology.get_dummy_section().children[0], 0.0)
# Some sanity checking:
for loc in locations:
p = MorphPath(loc, dummy)
assert np.fabs(p.get_length() - distance) < 0.01
return locations
def __init__(self, cell, morphlocation=None, section=None, sectionpos=None):
self._cell = cell
if morphlocation:
assert not section and not sectionpos
self.morphlocation = morphlocation
else:
assert not morphlocation
self.morphlocation = MorphLocation(section=section, sectionpos=sectionpos)
assert not self.morphlocation.section.is_dummy_section()
class CellLocation(object):
def __init__(self,
cell,
morphlocation=None,
section=None,
sectionpos=None):
self._cell = cell
if morphlocation:
assert not section and not sectionpos
self.morphlocation = morphlocation
else:
assert not morphlocation
self.morphlocation = MorphLocation(section=section,
sectionpos=sectionpos)
assert not self.morphlocation.section.is_dummy_section()
def get_cell(self):
return self._cell
cell = property(get_cell, None, None)
# We want to be able to treat CellLocations as locations,
# so that we can measure between them for example:
@property
def section(self):
return self.morphlocation.section
@property
def sectionpos(self):
return self.morphlocation.sectionpos
def get_3d_position(self):
return self.morphlocation.get_3d_position()
def get_location_description_str(self):
desc = self.cell.name
t = ''
if self.morphlocation.section.idtag:
t = self.morphlocation.section.idtag
return desc + t
class CellLocation(object):
def __init__(self, cell, morphlocation=None, section=None, sectionpos=None):
self._cell = cell
if morphlocation:
assert not section and not sectionpos
self.morphlocation = morphlocation
else:
assert not morphlocation
self.morphlocation = MorphLocation(section=section,
sectionpos=sectionpos)
assert not self.morphlocation.section.is_dummy_section()
def get_cell(self):
return self._cell
cell = property(get_cell, None, None)
# We want to be able to treat CellLocations as locations,
# so that we can measure between them for example:
@property
def section(self):
return self.morphlocation.section
@property
def sectionpos(self):
return self.morphlocation.sectionpos
def get_3d_position(self):
return self.morphlocation.get_3d_position()
def get_location_description_str(self):
desc = self.cell.name
t = ''
if self.morphlocation.section.idtag:
t = '@' + self.morphlocation.section.idtag
return desc + t
