def make_morphologies(self):
"""Creating a Morphology object for each biophysical model"""
for node in self._local_nodes:
if node.cell_type == CellTypes.Biophysical:
node_type_id = node.node_type_id
morphology_file = node.morphology_file
if node_type_id in self.__morphologies_cache:
# create a single morphology object for each model_group which share that morphology
morph = self.__morphologies_cache[node_type_id]
# associate morphology with a cell
self._cells[node.node_id].set_morphology(morph)
else:
hobj = self._cells[
node.
node_id].hobj # get hoc object (hobj) from the first cell with a new morphologys
morph = Morphology(hobj)
# associate morphology with a cell
self._cells[node.node_id].set_morphology(morph)
# create a single morphology object for each model_group which share that morphology
self.__morphologies_cache[node_type_id] = morph
io.print2log0(" Created morphologies")
self._morphologies_built = True
def make_morphologies(self):
"""Creating a Morphology object for each biophysical model"""
# TODO: Let Morphology take care of the cache
# TODO: Let other types have morphologies
# TODO: Get all available morphologies from TypesTable or group
for gid, cell in self._rank_node_gids.items():
if not isinstance(cell, BioCell):
continue
morphology_file = cell.morphology_file
if morphology_file in self._morphologies_cache:
# create a single morphology object for each model_group which share that morphology
morph = self._morphologies_cache[morphology_file]
# associate morphology with a cell
cell.set_morphology(morph)
self._morphology_lookup[morphology_file].append(cell.gid)
else:
hobj = cell.hobj # get hoc object (hobj) from the first cell with a new morphologys
morph = Morphology(hobj)
# associate morphology with a cell
cell.set_morphology(morph)
# create a single morphology object for each model_group which share that morphology
self._morphologies_cache[morphology_file] = morph
self._morphology_lookup[morphology_file] = [cell.gid]
self.io.barrier()
def __init__(self, swc_file, random_seed=10):
nrn.load_neuron_modules(None, None)
self._hobj = h.Biophys1(swc_file)
self._morphology = Morphology(self._hobj)
self._morphology.set_seg_props()
self._morphology.calc_seg_coords()
self._prng = np.random.RandomState(random_seed)
self._secs = []
self._save_sections()