def test_log_to_console():
nengo.log(debug=False, path=None)
assert logging.root.getEffectiveLevel() == logging.WARNING
assert nengo.utils.logging.console_handler in logging.root.handlers
n_handlers = len(logging.root.handlers)
nengo.log(debug=True, path=None)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == n_handlers
logging.root.handlers.remove(nengo.utils.logging.console_handler)
def test_log_to_console():
nengo.log(path=None)
assert logging.root.getEffectiveLevel() == logging.WARNING
assert nengo.utils.logging.console_handler in logging.root.handlers
n_handlers = len(logging.root.handlers)
nengo.log('debug', path=None)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == n_handlers
logging.root.handlers.remove(nengo.utils.logging.console_handler)
def test_log_to_file(tmpdir):
tmpfile = str(tmpdir.join("log.txt"))
nengo.log(path=tmpfile)
n_handlers = len(logging.root.handlers)
handler = logging.root.handlers[-1]
assert logging.root.getEffectiveLevel() == logging.WARNING
assert isinstance(handler, logging.FileHandler)
assert handler.baseFilename == tmpfile
nengo.log('debug', path=tmpfile)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == n_handlers
logging.root.handlers.remove(handler)
def test_log_to_file(tmpdir):
tmpfile = str(tmpdir.join("log.txt"))
nengo.log(debug=False, path=tmpfile)
n_handlers = len(logging.root.handlers)
handler = logging.root.handlers[-1]
assert logging.root.getEffectiveLevel() == logging.WARNING
assert isinstance(handler, logging.FileHandler)
assert handler.baseFilename == tmpfile
nengo.log(debug=True, path=tmpfile)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == n_handlers
logging.root.handlers.remove(handler)
def test_log_to_console():
logging.shutdown()
reload(logging)
nengo.log(debug=False, path=None)
assert logging.root.getEffectiveLevel() == logging.WARNING
assert len(logging.root.handlers) == 1
handler = logging.root.handlers[0]
assert isinstance(handler, logging.StreamHandler)
assert handler.formatter == nengo.utils.logging.console_formatter
nengo.log(debug=True, path=None)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == 1
def test_log_to_file(tmpdir):
logging.shutdown()
reload(logging)
tmpfile = str(tmpdir.join("log.txt"))
nengo.log(debug=False, path=tmpfile)
assert logging.root.getEffectiveLevel() == logging.WARNING
assert len(logging.root.handlers) == 1
handler = logging.root.handlers[0]
assert isinstance(handler, logging.FileHandler)
assert handler.formatter == nengo.utils.logging.file_formatter
nengo.log(debug=True, path=tmpfile)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == 1
def test_log_to_file(tmpdir):
tmpfile = str(tmpdir.join("log.txt"))
handler = nengo.log(path=tmpfile)
try:
n_handlers = len(logging.root.handlers)
handler = logging.root.handlers[-1]
assert logging.root.getEffectiveLevel() == logging.WARNING
assert isinstance(handler, logging.FileHandler)
assert handler.baseFilename == tmpfile
nengo.log('debug', path=tmpfile)
assert logging.root.getEffectiveLevel() == logging.DEBUG
assert len(logging.root.handlers) == n_handlers
logging.root.handlers.remove(handler)
finally:
handler.close()
# returns None
def none_function(t):
pass
model2 = nengo.Network()
with model2:
nengo.Node(output=none_function)
sim = nengo.Simulator(model2)
sim.run(1)
def test_scalar(Simulator):
model = nengo.Network()
with model:
a = nengo.Node(output=1)
b = nengo.Ensemble(nengo.LIF(100), dimensions=1)
nengo.Connection(a, b)
ap = nengo.Probe(a)
bp = nengo.Probe(b)
sim = nengo.Simulator(model)
sim.run(1)
assert sim.data[ap].shape == (1000, 1)
assert sim.data[bp].shape == (1000, 1)
if __name__ == "__main__":
nengo.log(debug=True)
pytest.main([__file__, '-v'])
with product:
input_A = nengo.Node(output=func_A)
input_B = nengo.Node(output=func_B)
nengo.Connection(input_A, product.A)
nengo.Connection(input_B, product.B)
p = nengo.Probe(product.output, synapse=pstc)
sim = Simulator(product, seed=123)
sim.run(1.0)
t = sim.trange()
AB = np.asarray(list(map(func_A, t))) * np.asarray(list(map(func_B, t)))
delay = 0.011
offset = np.where(t > delay)[0]
with Plotter(Simulator) as plt:
for i in range(dim):
plt.subplot(dim+1, 1, i+1)
plt.plot(t + delay, AB[:, i], label="$A \cdot B$")
plt.plot(t, sim.data[p][:, i], label="Output")
plt.legend()
plt.savefig('test_product.test_sine_waves.pdf')
plt.close()
assert rmse(AB[:len(offset), :], sim.data[p][offset, :]) < 0.3
if __name__ == "__main__":
nengo.log(debug=True)
pytest.main([__file__, '-v'])
setattr(vocab, cfg_param, eval(cfg_value))
# ----- Check if data folder exists -----
if not (os.path.isdir(cfg.data_dir) and os.path.exists(cfg.data_dir)):
raise RuntimeError('Data directory "%s"' % (cfg.data_dir) +
' does not exist. Please ensure the correct path' +
' has been specified.')
# ----- Spaun imports -----
from _spaun.utils import get_total_n_neurons
from _spaun.probes import default_probe_config, default_anim_config
from _spaun.spaun_main import Spaun
# ----- Enable debug logging -----
if args.debug:
nengo.log('debug')
# ----- Experiment and vocabulary initialization -----
experiment.initialize(args.s, vis_data.get_image_ind,
vis_data.get_image_label,
cfg.mtr_est_digit_response_time, cfg.rng)
vocab.initialize(experiment.num_learn_actions, cfg.rng)
vocab.initialize_mtr_vocab(mtr_data.dimensions, mtr_data.sps)
vocab.initialize_vis_vocab(vis_data.dimensions, vis_data.sps)
# ----- Configure output log files -----
if cfg.use_mpi:
sys.path.append('C:\\Users\\xchoo\\GitHub\\nengo_mpi')
mpi_save = args.mpi_save.split('.')
mpi_savename = '.'.join(mpi_save[:-1])
import nengo
from nengo.tests.helpers import SimulatorTestCase, unittest
class TestBasalGanglia(SimulatorTestCase):
def test_basic(self):
model = nengo.Model('test_basalganglia_basic')
with model:
bg = nengo.networks.BasalGanglia(dimensions=5, label='BG')
input = nengo.Node([0.8, 0.4, 0.4, 0.4, 0.4], label='input')
nengo.Connection(input, bg.input)
p = nengo.Probe(bg.output, 'output')
sim = self.Simulator(model)
sim.run(0.2)
output = np.mean(sim.data(p)[50:], axis=0)
self.assertGreater(output[0], -0.15)
self.assertLess(output[1], -0.8)
self.assertLess(output[2], -0.8)
self.assertLess(output[3], -0.8)
self.assertLess(output[4], -0.8)
if __name__ == "__main__":
nengo.log(debug=True, path='log.txt')
unittest.main()
def create_spaun_model(n, args, max_probe_time):
print("\n======================== RUN %i OF %i ========================" %
(n + 1, args.n))
# ----- Seeeeeeeed -----
if args.seed < 0:
seed = int(time.time())
else:
seed = args.seed
cfg.set_seed(seed)
print "MODEL SEED: %i" % cfg.seed
# ----- Model Configurations -----
vocab.sp_dim = args.d
cfg.data_dir = args.data_dir
# Parse --config options
if args.config is not None:
print "USING CONFIGURATION OPTIONS: "
for cfg_options in args.config:
cfg_opts = cfg_options.split('=')
cfg_param = cfg_opts[0]
cfg_value = cfg_opts[1]
if hasattr(cfg, cfg_param):
print " * cfg: " + str(cfg_options)
setattr(cfg, cfg_param, eval(cfg_value))
elif hasattr(experiment, cfg_param):
print " * experiment: " + str(cfg_options)
setattr(experiment, cfg_param, eval(cfg_value))
elif hasattr(vocab, cfg_param):
print " * vocab: " + str(cfg_options)
setattr(vocab, cfg_param, eval(cfg_value))
# ----- Check if data folder exists -----
if not (os.path.isdir(cfg.data_dir) and os.path.exists(cfg.data_dir)):
raise RuntimeError('Data directory "%s"' % (cfg.data_dir) +
' does not exist. Please ensure the correct path' +
' has been specified.')
# ----- Enable debug logging -----
if args.debug:
nengo.log('debug')
# ----- Experiment and vocabulary initialization -----
experiment.initialize(args.s, vis_data.get_image_ind,
vis_data.get_image_label,
cfg.mtr_est_digit_response_time, cfg.rng)
vocab.initialize(experiment.num_learn_actions, cfg.rng)
vocab.initialize_mtr_vocab(mtr_data.dimensions, mtr_data.sps)
vocab.initialize_vis_vocab(vis_data.dimensions, vis_data.sps)
# ----- Configure output log files -----
mpi_savename = None
mpi_saveext = None
probe_cfg = None
probe_anim_cfg = None
anim_probe_data_filename = None
if cfg.use_mpi:
sys.path.append('C:\\Users\\xchoo\\GitHub\\nengo_mpi')
mpi_save = args.mpi_save.split('.')
mpi_savename = '.'.join(mpi_save[:-1])
mpi_saveext = mpi_save[-1]
cfg.probe_data_filename = get_probe_data_filename(mpi_savename,
suffix=args.tag)
else:
cfg.probe_data_filename = get_probe_data_filename(suffix=args.tag)
# ----- Initalize looger and write header data -----
logger.initialize(cfg.data_dir, cfg.probe_data_filename[:-4] + '_log.txt')
cfg.write_header()
experiment.write_header()
vocab.write_header()
logger.flush()
# ----- Raw stimulus seq -----
print "RAW STIM SEQ: %s" % (str(experiment.raw_seq_str))
# ----- Spaun proper -----
model = Spaun()
# ----- Display stimulus seq -----
print "PROCESSED RAW STIM SEQ: %s" % (str(experiment.raw_seq_list))
print "STIMULUS SEQ: %s" % (str(experiment.stim_seq_list))
# ----- Calculate runtime -----
# Note: Moved up here so that we have data to disable probes if necessary
runtime = args.t if args.t > 0 else experiment.get_est_simtime()
# ----- Set up probes -----
make_probes = not args.noprobes
if runtime > max_probe_time and make_probes:
print(">>> !!! WARNING !!! EST RUNTIME > %0.2fs - DISABLING PROBES" %
max_probe_time)
make_probes = False
if make_probes:
print "PROBE FILENAME: %s" % cfg.probe_data_filename
probe_cfg = default_probe_config(model, vocab, cfg.sim_dt,
cfg.data_dir, cfg.probe_data_filename)
# ----- Set up animation probes -----
if args.showanim or args.showiofig or args.probeio:
anim_probe_data_filename = cfg.probe_data_filename[:-4] + '_anim.npz'
print "ANIM PROBE FILENAME: %s" % anim_probe_data_filename
probe_anim_cfg = default_anim_config(model, vocab, cfg.sim_dt,
cfg.data_dir,
anim_probe_data_filename)
# ----- Neuron count debug -----
print "MODEL N_NEURONS: %i" % (get_total_n_neurons(model))
if hasattr(model, 'vis'):
print "- vis n_neurons: %i" % (get_total_n_neurons(model.vis))
if hasattr(model, 'ps'):
print "- ps n_neurons: %i" % (get_total_n_neurons(model.ps))
if hasattr(model, 'bg'):
print "- bg n_neurons: %i" % (get_total_n_neurons(model.bg))
if hasattr(model, 'thal'):
print "- thal n_neurons: %i" % (get_total_n_neurons(model.thal))
if hasattr(model, 'enc'):
print "- enc n_neurons: %i" % (get_total_n_neurons(model.enc))
if hasattr(model, 'mem'):
print "- mem n_neurons: %i" % (get_total_n_neurons(model.mem))
if hasattr(model, 'trfm'):
print "- trfm n_neurons: %i" % (get_total_n_neurons(model.trfm))
if hasattr(model, 'dec'):
print "- dec n_neurons: %i" % (get_total_n_neurons(model.dec))
if hasattr(model, 'mtr'):
print "- mtr n_neurons: %i" % (get_total_n_neurons(model.mtr))
# ----- Connections count debug -----
print "MODEL N_CONNECTIONS: %i" % (len(model.all_connections))
return (model, mpi_savename, mpi_saveext, runtime, make_probes, probe_cfg,
probe_anim_cfg, anim_probe_data_filename)
setattr(vocab, cfg_param, eval(cfg_value))
# ----- Check if data folder exists -----
if not(os.path.isdir(cfg.data_dir) and os.path.exists(cfg.data_dir)):
raise RuntimeError('Data directory "%s"' % (cfg.data_dir) +
' does not exist. Please ensure the correct path' +
' has been specified.')
# ----- Spaun imports -----
from _spaun.utils import get_total_n_neurons
from _spaun.probes import default_probe_config, default_anim_config
from _spaun.spaun_main import Spaun
# ----- Enable debug logging -----
if args.debug:
nengo.log('debug')
# ----- Experiment and vocabulary initialization -----
experiment.initialize(args.s, vis_data.get_image_ind,
vis_data.get_image_label,
cfg.mtr_est_digit_response_time, cfg.rng)
vocab.initialize(experiment.num_learn_actions, cfg.rng)
vocab.initialize_mtr_vocab(mtr_data.dimensions, mtr_data.sps)
vocab.initialize_vis_vocab(vis_data.dimensions, vis_data.sps)
# ----- Configure output log files -----
if cfg.use_mpi:
sys.path.append('C:\\Users\\xchoo\\GitHub\\nengo_mpi')
mpi_save = args.mpi_save.split('.')
mpi_savename = '.'.join(mpi_save[:-1])
from collections import OrderedDict
import matplotlib.pyplot as plt
import numpy as np
import nengo
nengo.log(level='info')
import nengo_extras
from run_core import load_network, SoftLIFRate, round_layer
def hist_dist(hist, edges):
p = np.zeros(edges.size, dtype=float)
p[1:-1] = hist[:-1] + hist[1:]
p /= p.sum()
return nengo.dists.PDF(edges, p)
def build_layer(layer, inputs, data, hist=None, pt=None):
assert isinstance(inputs, list)
assert len(layer.get('inputs', [])) == len(inputs)
name = layer['name']
if layer['type'] == 'cost.logreg':
labels, probs = inputs
return probs
# pt = params['presentation_time']
# nlabels, nprobs = layer['numInputs']
# assert nlabels == 1
with open(decoder_file) as f:
dt = 0.001
synapse = 0.01
self.decoders = np.asarray([[float(x) / (1 - np.exp(-dt / synapse)) for x in line.split()]
for line in f.readlines()])
# note: dividing by filter to undo the filter that will be applied
# when the decoders are set
def __call__(self, A, Y, rng=None):
return self.decoders, []
SEED = 1
rng = random.Random()
rng.seed(SEED)
nengo.log()
pong_game = PongGame(["computer", "computer"], seed=SEED)
l_rate = 5e-5
discount = 0.97
#d_file = os.path.join("data", "decoders_%s_%s_%s.txt" % (l_rate, discount, SEED))
d_file = os.path.join("data", "decoders_best.txt")
d_solve = decoder_setter(d_file)
#d_solve = nengo.decoders.lstsq_L2nz
with nengo.Network() as net:
p0 = DecoderPongPlayer(0, pong_game, opposite=True, noise=None)
p1 = rl_pongplayer.RLPongPlayer(1, pong_game, decoder_solver=d_solve,
l_rate=l_rate, discount=discount, rng=rng)
import logging
import argparse
import numpy as np
import time
import os
import nengo
import nengo_mpi
from nengo_mpi.partition import metis_partitioner, work_balanced_partitioner
from nengo_mpi.partition import random_partitioner, EnsembleArraySplitter
from utils import write_to_csv
logger = logging.getLogger(__name__)
nengo.log(debug=False)
parser = argparse.ArgumentParser(description="A grid network.")
parser.add_argument(
'--ns', type=int, default=1,
help='Number of streams in the network.')
parser.add_argument(
'--sl', type=int, default=1,
help='Length of each stream.')
parser.add_argument(
'-d', type=int, default=1,
help='Number of dimensions in each neural ensemble.')
parser.add_argument(
'--npd', type=int, default=50,