file_name = None
screen = False
if args.log.lower() in ['file', 'both']:
file_name = 'neurokernel.log'
if args.log.lower() in ['screen', 'both']:
screen = True
logger = base.setup_logger(file_name, screen)
if args.port_data is None and args.port_ctrl is None:
port_data = get_random_port()
port_ctrl = get_random_port()
else:
port_data = args.port_data
port_ctrl = args.port_ctrl
man = core.Manager(port_data, port_ctrl)
man.add_brok()
# Load configurations for lamina, medulla and antennal lobe models:
(n_dict_al, s_dict_al) = LPU.lpu_parser('./data/antennallobe.gexf.gz')
lpu_al = LPU(dt,
n_dict_al,
s_dict_al,
input_file='./data/olfactory_input.h5',
output_file='antennallobe_output.h5',
port_ctrl=man.port_ctrl,
port_data=man.port_data,
device=args.al_dev,
id='antennallobe')
man.add_mod(lpu_al)
def run(connected):
if args.port_data is None and args.port_ctrl is None:
port_data = get_random_port()
port_ctrl = get_random_port()
else:
port_data = args.port_data
port_ctrl = args.port_ctrl
out_name = 'un' if not connected else 'co'
man = core.Manager(port_data, port_ctrl)
man.add_brok()
lpu_file_0 = './data/generic_lpu_0.gexf.gz'
lpu_file_1 = './data/generic_lpu_1.gexf.gz'
(n_dict_0, s_dict_0) = LPU.lpu_parser(lpu_file_0)
(n_dict_1, s_dict_1) = LPU.lpu_parser(lpu_file_1)
ge_0_id = 'ge_0'
ge_0 = LPU(dt,
n_dict_0,
s_dict_0,
input_file='./data/generic_input_0.h5',
output_file='generic_output_0_%s.h5' % out_name,
port_ctrl=port_ctrl,
port_data=port_data,
device=args.gpu_dev[0],
id=ge_0_id,
debug=args.debug)
man.add_mod(ge_0)
ge_1_id = 'ge_1'
ge_1 = LPU(dt,
n_dict_1,
s_dict_1,
input_file='./data/generic_input_1.h5',
output_file='generic_output_1_%s.h5' % out_name,
port_ctrl=port_ctrl,
port_data=port_data,
device=args.gpu_dev[1],
id=ge_1_id,
debug=args.debug)
man.add_mod(ge_1)
# Connect the public neurons in the two LPUs:
df_neu_0, df_syn_0 = neurokernel.tools.graph.graph_to_df(
nx.read_gexf(lpu_file_0))
df_neu_1, df_syn_1 = neurokernel.tools.graph.graph_to_df(
nx.read_gexf(lpu_file_1))
# Number of public neurons in each LPU:
N_spike_0 = len(df_neu_0[(df_neu_0['spiking'] == True)
& (df_neu_0['public'] == True)])
N_gpot_0 = len(df_neu_0[(df_neu_0['spiking'] == False)
& (df_neu_0['public'] == True)])
N_spike_1 = len(df_neu_1[(df_neu_1['spiking'] == True)
& (df_neu_1['public'] == True)])
N_gpot_1 = len(df_neu_1[(df_neu_1['spiking'] == False)
& (df_neu_1['public'] == True)])
# Alpha function synaptic parameters:
alphasynapse_type_params = {
'AlphaSynapse':
['ad', 'ar', 'gmax', 'id', 'class', 'conductance', 'reverse']
}
if connected:
conn = core.Connectivity(N_gpot_0, N_spike_0, N_gpot_1, N_spike_1, 1,
ge_0.id, ge_1.id, alphasynapse_type_params)
for id, (i, j) in enumerate(
itertools.product(xrange(N_spike_0), xrange(N_spike_1))):
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j] = 1
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0,
'name'] = 'int_0to1_%s_%s' % (i, j)
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0,
'model'] = 'AlphaSynapse'
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0,
'ad'] = 0.19 * 1000
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0, 'ar'] = 1.1 * 100
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0, 'class'] = 0
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0,
'conductance'] = True
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0, 'gmax'] = 0.003
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0, 'id'] = id
conn[ge_0_id, 'spike', i, ge_1_id, 'spike', j, 0,
'reverse'] = 0.065
man.connect(ge_0, ge_1, conn)
man.start(steps=args.steps)
man.stop()
port_data = args.port_data
if args.port_ctrl is None:
port_ctrl = get_random_port()
else:
port_ctrl = args.port_ctrl
if args.port_time is None:
port_time = get_random_port()
else:
port_time = args.port_time
if args.timeit:
ptime = lambda t, s: print_time(t, s)
else:
ptime = lambda t, s: print_time(t)
man = core.Manager(port_data, port_ctrl, port_time)
man.add_brok()
tic = time()
# Load configurations for lamina, medulla and antennal lobe models:
(n_dict_al, s_dict_al) = LPU.lpu_parser( './data/antennallobe.gexf.gz')
lpu_al = LPU(dt, n_dict_al, s_dict_al,
input_file='./data/olfactory_input.h5',
output_file='antennallobe_output.h5',
port_ctrl=port_ctrl, port_data=port_data, port_time=port_time,
device=args.al_dev, id='antennallobe', time_sync=args.time_sync)
man.add_mod(lpu_al)
tic = ptime(tic, 'Load AL LPU time')
(n_dict_lam, s_dict_lam) = LPU.lpu_parser('./data/lamina.gexf.gz')
def run(connected):
if args.port_data is None:
port_data = get_random_port()
else:
port_data = args.port_data
if args.port_ctrl is None:
port_ctrl = get_random_port()
else:
port_ctrl = args.port_ctrl
if args.port_time is None:
port_time = get_random_port()
else:
port_time = args.port_time
out_name = 'un' if not connected else 'co'
man = core.Manager(port_data, port_ctrl, port_time)
man.add_brok()
lpu_file_0 = './data/generic_lpu_0.gexf.gz'
lpu_file_1 = './data/generic_lpu_1.gexf.gz'
(n_dict_0, s_dict_0) = LPU.lpu_parser(lpu_file_0)
(n_dict_1, s_dict_1) = LPU.lpu_parser(lpu_file_1)
lpu_0_id = 'lpu_0'
lpu_0 = LPU(dt, n_dict_0, s_dict_0,
input_file='./data/generic_lpu_0_input.h5',
output_file='generic_lpu_0_%s_output.h5' % out_name,
port_ctrl=port_ctrl, port_data=port_data,
port_time=port_time,
device=args.gpu_dev[0], id=lpu_0_id,
debug=args.debug, time_sync=args.time_sync)
man.add_mod(lpu_0)
lpu_1_id = 'lpu_1'
lpu_1 = LPU(dt, n_dict_1, s_dict_1,
input_file='./data/generic_lpu_1_input.h5',
output_file='generic_lpu_1_%s_output.h5' % out_name,
port_ctrl=port_ctrl, port_data=port_data,
port_time=port_time,
device=args.gpu_dev[1], id=lpu_1_id,
debug=args.debug, time_sync=args.time_sync)
man.add_mod(lpu_1)
# Create random connections between the input and output ports if the LPUs
# are to be connected:
if connected:
# Find all output and input port selectors in each LPU:
out_ports_0 = lpu_0.interface.out_ports().to_selectors()
out_ports_1 = lpu_1.interface.out_ports().to_selectors()
in_ports_0 = lpu_0.interface.in_ports().to_selectors()
in_ports_1 = lpu_1.interface.in_ports().to_selectors()
out_ports_spk_0 = lpu_0.interface.out_ports().spike_ports().to_selectors()
out_ports_gpot_0 = lpu_0.interface.out_ports().gpot_ports().to_selectors()
out_ports_spk_1 = lpu_1.interface.out_ports().spike_ports().to_selectors()
out_ports_gpot_1 = lpu_1.interface.out_ports().gpot_ports().to_selectors()
in_ports_spk_0 = lpu_0.interface.in_ports().spike_ports().to_selectors()
in_ports_gpot_0 = lpu_0.interface.in_ports().gpot_ports().to_selectors()
in_ports_spk_1 = lpu_1.interface.in_ports().spike_ports().to_selectors()
in_ports_gpot_1 = lpu_1.interface.in_ports().gpot_ports().to_selectors()
# Initialize a connectivity pattern between the two sets of port
# selectors:
pat = pattern.Pattern(','.join(out_ports_0+in_ports_0),
','.join(out_ports_1+in_ports_1))
# Create connections from the ports with identifiers matching the output
# ports of one LPU to the ports with identifiers matching the input
# ports of the other LPU:
N_conn_spk_0_1 = min(len(out_ports_spk_0), len(in_ports_spk_1))
N_conn_gpot_0_1 = min(len(out_ports_gpot_0), len(in_ports_gpot_1))
for src, dest in zip(random.sample(out_ports_spk_0, N_conn_spk_0_1),
random.sample(in_ports_spk_1, N_conn_spk_0_1)):
pat[src, dest] = 1
pat.interface[src, 'type'] = 'spike'
pat.interface[dest, 'type'] = 'spike'
for src, dest in zip(random.sample(out_ports_gpot_0, N_conn_gpot_0_1),
random.sample(in_ports_gpot_1, N_conn_gpot_0_1)):
pat[src, dest] = 1
pat.interface[src, 'type'] = 'gpot'
pat.interface[dest, 'type'] = 'gpot'
man.connect(lpu_0, lpu_1, pat, 0, 1)
man.start(steps=args.steps)
man.stop()