ALLEN INSTITUTE

# Source code for bmtk.simulator.bionet.pointprocesscell

    # Copyright 2017. Allen Institute. All rights reserved
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    # disclaimer in the documentation and/or other materials provided with the distribution.
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    # products derived from this software without specific prior written permission.
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    # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
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    from neuron import h
    import six
    import numpy as np

    from bmtk.simulator.bionet.cell import Cell

    pc = h.ParallelContext()    # object to access MPI methods

    class ConnectionStruct(object):
        def __init__(self, edge_prop, src_node, nc, is_virtual=False):
            self._src_node = src_node
            self._edge_prop = edge_prop
            self._nc = nc
            self._is_virtual = is_virtual

        @property
        def is_virtual(self):
            return self._is_virtual

        @property
        def source_node(self):
            return self._src_node

        @property
        def syn_weight(self):
            return self._nc.weight[0]

        @syn_weight.setter
        def syn_weight(self, val):
            self._nc.weight[0] = val

    class PointProcessCell(Cell):
        """Implimentation of a Leaky Integrate-and-file neuron type cell."""
        def __init__(self, node, population_name, bionetwork):
            super(PointProcessCell, self).__init__(node, population_name=population_name, network=bionetwork)
            self.set_spike_detector()
            self._src_gids = []
            self._src_nets = []
            self._edge_type_ids = []
            self._connections = []

        def set_spike_detector(self):
            nc = h.NetCon(self.hobj, None)
            pc.cell(self.gid, nc)

        def set_im_ptr(self):
            pass

        def set_syn_connection(self, edge_prop, src_node, stim=None):
            syn_params = edge_prop.dynamics_params
            nsyns = edge_prop.nsyns
            delay = edge_prop.delay

            syn_weight = edge_prop.syn_weight(src_node, self._node)
            if not edge_prop.preselected_targets:
                # TODO: this is not very robust, need some other way
                syn_weight *= syn_params['sign'] * nsyns

            if stim is not None:
                src_gid = -1
                #src_gid = src_node.node_id
                nc = h.NetCon(stim.hobj, self.hobj)
            else:
                # src_gid = src_node.node_id
                src_gid = self._network.gid_pool.get_gid(name=src_node.population_name, node_id=src_node.node_id)
                nc = pc.gid_connect(src_gid, self.hobj)

            weight = syn_weight
            nc.weight[0] = weight
            nc.delay = delay
            self._netcons.append(nc)
            self._src_gids.append(src_gid)
            self._src_nets.append(-1)
            self._edge_type_ids.append(edge_prop.edge_type_id)
            self._edge_props.append(edge_prop)
            self._connections.append(ConnectionStruct(edge_prop, src_node, nc, stim is not None))

            return nsyns

        def connections(self):
            return self._connections

        def get_connection_info(self):
            # TODO: There should be a more effecient and robust way to return synapse information.
            return [[self.gid, self._src_gids[i], self.network_name, self._src_nets[i], 'NaN', 'NaN',
                     self.netcons[i].weight[0], self.netcons[i].delay, self._edge_type_id[i], 1]
                    for i in range(len(self._src_gids))]

        def print_synapses(self):
            rstr = ''
            for i in six.moves.range(len(self._src_gids)):
                rstr += '{}> <-- {} ({}, {})\n'.format(i, self._src_gids[i], self.netcons[i].weight[0],
                                                       self.netcons[i].delay)

            return rstr

    class PointProcessCellSpontSyns(PointProcessCell):
        """Special class that allows certain synapses to spontaneously fire (without spiking) at a specific time.
        """
        def __init__(self, node, population_name, bionetwork):
            super(PointProcessCellSpontSyns, self).__init__(node, population_name=population_name, bionetwork=bionetwork)

            self._syn_timestamps = bionetwork.spont_syns_times
            self._syn_timestamps = [self._syn_timestamps] if np.isscalar(self._syn_timestamps) else self._syn_timestamps
            self._spike_trains = h.Vector(self._syn_timestamps)
            self._vecstim = h.VecStim()
            self._vecstim.play(self._spike_trains)

            self._precell_filter = bionetwork.spont_syns_filter_pre
            self._postcell_filter = bionetwork.spont_syns_filter_post
            assert(isinstance(self._precell_filter, dict))

        def _matches_filter(self, src_node):
            for k, v in self._precell_filter.items():
                if isinstance(v, (list, tuple)):
                    if src_node[k] not in v:
                        return False
                else:
                    if src_node[k] != v:
                        return False

            trg_node = trg_node or self
            for k, v in self._postcell_filter.items():
                # Some key may not show up as node_variable
                if k == 'population' and k not in trg_node:
                    key_val = trg_node._node.population_name
                else:
                    key_val = trg_node[k]

                if isinstance(v, (list, tuple)):
                    if key_val not in v:
                        return False
                else:
                    if key_val != v:
                        return False

            return True

        def set_syn_connection(self, edge_prop, src_node, stim=None):
            syn_params = edge_prop.dynamics_params
            nsyns = edge_prop.nsyns
            delay = edge_prop.delay

            syn_weight = edge_prop.syn_weight(src_node, self._node)
            if not edge_prop.preselected_targets:
                # TODO: this is not very robust, need some other way
                syn_weight *= syn_params['sign'] * nsyns

            src_gid = src_node.node_id

            if stim is not None:
                src_gid = -1
                nc = h.NetCon(stim.hobj, self.hobj)

            elif self._matches_filter(src_node):
                nc = h.NetCon(self._vecstim, self.hobj)

            else:
                nc = pc.gid_connect(src_gid, self.hobj)
                syn_weight = 0.0

            weight = syn_weight
            nc.weight[0] = weight
            nc.delay = delay
            self._netcons.append(nc)
            self._src_gids.append(src_gid)
            self._src_nets.append(-1)
            self._edge_type_ids.append(edge_prop.edge_type_id)
            self._edge_props.append(edge_prop)
            self._connections.append(ConnectionStruct(edge_prop, src_node, nc, stim is not None))