Creating Recurrent Connections in BMTK

recurrent.py

###########################################################
# Build connections
###########################################################
#Connect CA3o->CA3e Inhibitory
dynamics_file = 'CA3o2CA3e.inh.json'
conn = net.add_edges(source={'pop_name': 'CA3o'}, target={'pop_name': 'CA3e'},
            connection_rule=hipp_dist_connector,
            connection_params={'con_pattern':syn[dynamics_file]['con_pattern']},
            syn_weight=5.0e-03,
            dynamics_params=dynamics_file,
            model_template=syn[dynamics_file]['level_of_detail'],
            distance_range=[0.0, 300.0],
            target_sections=['soma'],
            delay=0.0)
conn.add_properties(['sec_id','sec_x'],rule=(0, 0.5), dtypes=[np.int32,np.float])
conn.add_properties('delay', 
            rule=syn_dist_delay,
            rule_params={'base_delay':syn[dynamics_file]['delay']},
            dtypes=np.float)

###########################################################
# Build recurrent connection rules
###########################################################
def hipp_recurrent_connector(source,target,all_edges=[],min_syn=1, max_syn=1):
    """
    General logic:
    1. Given a *potential* source and target
    2. Look through all edges currently made
    3. If any of the current edges contains 
        a. the current source as a previous target of 
        b. the current target as a prevous source
    4. Return number of synapses per this connection, 0 otherwise (no connection)
    """
    for e in all_edges:
        if source['node_id'] == e.target_gid and target['node_id'] == e.source_gid:
            return random.randint(min_syn,max_syn)

    return 0

########################################################### 
# Build recurrent connections
###########################################################

#Connect CA3e->CA3o Excitatory
dynamics_file = 'CA3e2CA3o.exc.json'
conn = net.add_edges(source={'pop_name': 'CA3e'}, target={'pop_name': 'CA3o'},
            connection_rule=hipp_recurrent_connector,
            connection_params={'all_edges':net.edges()},
            syn_weight=5.0e-03,
            dynamics_params=dynamics_file,
            model_template=syn[dynamics_file]['level_of_detail'],
            distance_range=[0.0, 300.0],
            target_sections=['soma'],
            delay=0.0)
conn.add_properties(['sec_id','sec_x'],rule=(0, 0.5), dtypes=[np.int32,np.float])
conn.add_properties('delay', 
            rule=syn_dist_delay,
            rule_params={'base_delay':syn[dynamics_file]['delay'],'dist_delay':0.1}, #Connect.hoc:274 0.1 dist delay
            dtypes=np.float)