# Copyright 2017. Allen Institute. All rights reserved
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import types
import numpy as np
from bmtk.simulator.core.sonata_reader import NodeAdaptor, SonataBaseNode, EdgeAdaptor, SonataBaseEdge
from bmtk.simulator.bionet import nrn
[docs]class BioNode(SonataBaseNode):
@property
def position(self):
return self._prop_adaptor.position(self._node)
@property
def morphology_file(self):
return self._node['morphology']
@property
def rotation_angle_xaxis(self):
return self._prop_adaptor.rotation_angle_xaxis(self._node)
@property
def rotation_angle_yaxis(self):
# TODO: Combine rotation alnges into a single property
return self._prop_adaptor.rotation_angle_yaxis(self._node)
@property
def rotation_angle_zaxis(self):
return self._prop_adaptor.rotation_angle_zaxis(self._node)
@property
def rotations(self):
return self._prop_adaptor.rotations(self._node)
@property
def rotations_quaternion(self):
return self._prop_adaptor.rotations(self._node)
[docs] def load_cell(self):
model_template = self.model_template
template_name = model_template[1]
model_type = self.model_type
if nrn.py_modules.has_cell_model(self['model_template'], model_type):
cell_fnc = nrn.py_modules.cell_model(self['model_template'], model_type)
else:
cell_fnc = nrn.py_modules.cell_model(model_template[0], model_type)
dynamics_params = self.dynamics_params
hobj = cell_fnc(self, template_name, dynamics_params)
for model_processing_str in self.model_processing:
processing_fnc = nrn.py_modules.cell_processor(model_processing_str)
hobj = processing_fnc(hobj, self, dynamics_params)
return hobj
[docs]class BioNodeAdaptor(NodeAdaptor):
[docs] def get_node(self, sonata_node):
return BioNode(sonata_node, self)
[docs] @classmethod
def patch_adaptor(cls, adaptor, node_group, network):
node_adaptor = NodeAdaptor.patch_adaptor(adaptor, node_group, network)
# Position
if 'positions' in node_group.all_columns:
node_adaptor.position = types.MethodType(positions, adaptor)
elif 'position' in node_group.all_columns:
node_adaptor.position = types.MethodType(position, adaptor)
elif 'x' in node_group.all_columns:
if 'z' in node_group.all_columns and 'y' in node_group.all_columns:
node_adaptor.position = types.MethodType(position_xyz, adaptor)
elif 'y' in node_group.all_columns:
node_adaptor.position = types.MethodType(position_xy, adaptor)
else:
node_adaptor.position = types.MethodType(position_x, adaptor)
else:
node_adaptor.position = types.MethodType(positions_default, adaptor)
# Rotation angles
if 'rotation_angle_xaxis' in node_group.all_columns:
node_adaptor.rotation_angle_xaxis = types.MethodType(rotation_angle_x, node_adaptor)
else:
node_adaptor.rotation_angle_xaxis = types.MethodType(rotation_angle_default, node_adaptor)
if 'rotation_angle_yaxis' in node_group.all_columns:
node_adaptor.rotation_angle_yaxis = types.MethodType(rotation_angle_y, node_adaptor)
else:
node_adaptor.rotation_angle_yaxis = types.MethodType(rotation_angle_default, node_adaptor)
if 'rotation_angle_zaxis' in node_group.all_columns:
node_adaptor.rotation_angle_zaxis = types.MethodType(rotation_angle_z, node_adaptor)
else:
node_adaptor.rotation_angle_zaxis = types.MethodType(rotation_angle_default, node_adaptor)
if 'rotations' in node_group.all_columns:
node_adaptor.rotations = types.MethodType(rotations, node_adaptor)
else:
node_adaptor.rotations = types.MethodType(value_none, node_adaptor)
return node_adaptor
[docs]def rotations(self, node):
return node['rotations']
[docs]def value_none(self, node):
return None
[docs]def positions_default(self, node):
return np.array([0.0, 0.0, 0.0])
[docs]def positions(self, node):
return node['positions']
[docs]def position(self, node):
return node['position']
[docs]def rotation_angle_default(self, node):
return 0.0
[docs]def rotation_angle_x(self, node):
return node['rotation_angle_xaxis']
[docs]def rotation_angle_y(self, node):
return node['rotation_angle_yaxis']
[docs]def rotation_angle_z(self, node):
return node['rotation_angle_zaxis']
[docs]def position_xyz(self, node):
return np.array([node['x'], node['y'], node['z']])
[docs]def position_xy(self, node):
return np.array([node['x'], node['y'], 0.0])
[docs]def position_x(self, node):
return np.array([node['x'], 0.0, 0.0])
[docs]class BioEdge(SonataBaseEdge):
[docs] def load_synapses(self, section_x, section_id):
synapse_fnc = nrn.py_modules.synapse_model(self.model_template)
return synapse_fnc(self.dynamics_params, section_x, section_id)
@property
def afferent_section_id(self):
return self._prop_adaptor.aff_sec_id(self._edge)
@property
def afferent_section_pos(self):
return self._prop_adaptor.aff_sec_pos(self._edge)
[docs]class BioEdgeAdaptor(EdgeAdaptor):
[docs] def get_edge(self, sonata_edge):
return BioEdge(sonata_edge, self)
[docs] @classmethod
def patch_adaptor(cls, adaptor, edge_group):
edge_adaptor = EdgeAdaptor.patch_adaptor(adaptor, edge_group)
if 'sec_id' in edge_group.all_columns:
edge_adaptor.aff_sec_id = types.MethodType(aff_sec_id_old, adaptor)
elif 'afferent_section_id' in edge_group.all_columns:
edge_adaptor.aff_sec_id = types.MethodType(aff_sec_id, adaptor)
else:
edge_adaptor.aff_sec_id = types.MethodType(ret_none_function, adaptor)
if 'sec_x' in edge_group.all_columns:
edge_adaptor.aff_sec_pos = types.MethodType(aff_sec_pos_old, adaptor)
elif 'afferent_section_pos' in edge_group.all_columns:
edge_adaptor.aff_sec_pos = types.MethodType(aff_sec_pos, adaptor)
else:
edge_adaptor.aff_sec_pos = types.MethodType(ret_none_function, adaptor)
return edge_adaptor
[docs]def ret_none_function(self, edge):
return None
[docs]def aff_sec_id(self, edge):
return edge['afferent_section_id']
[docs]def aff_sec_id_old(self, edge):
return edge['sec_id']
[docs]def aff_sec_pos(self, edge):
return edge['afferent_section_pos']
[docs]def aff_sec_pos_old(self, edge):
return edge['sec_x']
