# Copyright 2017. Allen Institute. All rights reserved
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
# following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following
# disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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[docs]class SimNode(object):
def __init__(self, node_id, graph, network, params):
self._node_id = node_id
self._graph = graph
self._graph_params = params
self._node_type_id = params['node_type_id']
self._network = network
self._updated_params = {}
self._model_params = {}
@property
def node_id(self):
return self._node_id
@property
def node_type_id(self):
return self._node_type_id
@property
def network(self):
"""Name of network node belongs too."""
return self._network
@property
def model_params(self):
"""Parameters (json file, nml, dictionary) that describe a specific node"""
return self._model_params
@model_params.setter
def model_params(self, value):
self._model_params = value
def __contains__(self, item):
return item in self._updated_params or item in self._graph_params
def __getitem__(self, item):
if item in self._updated_params:
return self._updated_params[item]
else:
return self._graph_params[item]
[docs]class PopNode(SimNode):
def __init__(self, node_id, graph, network, params):
self._graph = graph
self._node_id = node_id
self._network = network
self._graph_params = params
self._dynamics_params = {}
self._updated_params = {'dynamics_params': self._dynamics_params}
self._gids = set()
@property
def node_id(self):
return self._node_id
@property
def pop_id(self):
return self._node_id
@property
def network(self):
return self._network
@property
def dynamics_params(self):
return self._dynamics_params
@dynamics_params.setter
def dynamics_params(self, value):
self._dynamics_params = value
@property
def is_internal(self):
return False
def __getitem__(self, item):
if item in self._updated_params:
return self._updated_params[item]
elif item in self._graph_params:
return self._graph_params[item]
elif self._model_params is not None:
return self._model_params[item]
[docs] def add_gid(self, gid):
self._gids.add(gid)
[docs] def get_gids(self):
return list(self._gids)
[docs]class InternalNode(PopNode):
@property
def tau_m(self):
return self['tau_m']
@tau_m.setter
def tau_m(self, value):
#return self['tau_m']
self._dynamics_params['tau_m'] = value
@property
def v_max(self):
return self._dynamics_params.get('v_max', None)
@v_max.setter
def v_max(self, value):
self._dynamics_params['v_max'] = value
@property
def dv(self):
return self._dynamics_params.get('dv', None)
@dv.setter
def dv(self, value):
self._dynamics_params['dv'] = value
@property
def v_min(self):
return self._dynamics_params.get('v_min', None)
@v_min.setter
def v_min(self, value):
self._dynamics_params['v_min'] = value
@property
def is_internal(self):
return True
def __repr__(self):
props = 'pop_id={}, tau_m={}, v_max={}, v_min={}, dv={}'.format(self.pop_id, self.tau_m, self.v_max, self.v_min,
self.dv)
return 'InternalPopulation({})'.format(props)
[docs]class ExternalPopulation(PopNode):
def __init__(self, node_id, graph, network, params):
super(ExternalPopulation, self).__init__(node_id, graph, network, params)
self._firing_rate = -1
if 'firing_rate' in params:
self._firing_rate = params['firing_rate']
@property
def firing_rate(self):
return self._firing_rate
@property
def is_firing_rate_set(self):
return self._firing_rate >= 0
@firing_rate.setter
def firing_rate(self, rate):
assert(isinstance(rate, float) and rate >= 0)
self._firing_rate = rate
@property
def is_internal(self):
return False
def __repr__(self):
props = 'pop_id={}, firing_rate={}'.format(self.pop_id, self.firing_rate)
return 'ExternalPopulation({})'.format(props)
