from __future__ import print_function, division
import datetime
import logging
import os
import sys
import tempfile
import time
import warnings
from nengo import Process, Ensemble, Connection, Probe
from nengo.builder import Model
from nengo.builder.connection import BuiltConnection
from nengo.builder.ensemble import BuiltEnsemble
from nengo.exceptions import (ReadonlyError, SimulatorClosed, NengoWarning,
SimulationError, ValidationError)
import numpy as np
import tensorflow as tf
from tensorflow.python.client.timeline import Timeline
from tensorflow.python.ops import gradient_checker
from nengo_dl import utils, DATA_DIR
from nengo_dl.tensor_graph import TensorGraph
logger = logging.getLogger(__name__)
if sys.version_info < (3, 4):
import backports.tempfile as tempfile # noqa: F811
from backports.print_function import print_ as print
[docs]class Simulator(object):
"""Simulate network using the ``nengo_dl`` backend.
Parameters
----------
network : :class:`~nengo:nengo.Network` or None
a network object to be built and then simulated. If None,
then a built model must be passed to ``model`` instead
dt : float, optional
length of a simulator timestep, in seconds
seed : int, optional
seed for all stochastic operators used in this simulator
model : :class:`~nengo:nengo.builder.Model`, optional
pre-built model object
dtype : ``tf.DType``, optional
floating point precision to use for simulation
device : None or ``"/cpu:0"`` or ``"/gpu:[0-n]"``, optional
device on which to execute computations (if None then uses the
default device as determined by Tensorflow)
unroll_simulation : int, optional
unroll simulation loop by explicitly building the given number of
iterations into the computation graph (improves simulation speed
but increases build time)
minibatch_size : int, optional
the number of simultaneous inputs that will be passed through the
network
tensorboard : bool, optional
if True, save network output in the Tensorflow summary format,
which can be loaded into Tensorboard
"""
# unsupported unit tests
unsupported = [
("nengo/tests/test_simulator.py:test_warn_on_opensim_del",
"nengo_dl raises a different (more visible) warning (see "
"tests/test_nengo_tests.py:test_warn_on_opensim_del"),
("nengo/tests/test_simulator.py:test_signal_init_values",
"different method required to manually step simulator (see "
"tests/test_nengo_tests.py:test_signal_init_values"),
("nengo/tests/test_simulator.py:test_entry_point",
"overridden so we can pass custom test simulators (see "
"tests/test_nengo_tests.py:test_entry_point"),
("nengo/tests/test_node.py:test_args",
"time is passed as np.float32, not a float (see "
"tests/test_nengo_tests.py:test_args"),
("nengo/tests/test_node.py:test_unconnected_node",
"need to set `unroll_simulation` to ensure node runs the correct "
"number of times (see "
"tests/test_nengo_tests.py:test_unconnected_node"),
("nengo/tests/test_synapses.py:test_alpha",
"need to set looser tolerances due to float32 implementation (see "
"tests/test_processes.py:test_alpha"),
("nengo/tests/test_ensemble.py:test_gain_bias",
"use allclose instead of array_equal (see "
"tests/test_simulator.py:test_gain_bias")
]
def __init__(self, network, dt=0.001, seed=None, model=None,
dtype=tf.float32, device=None, unroll_simulation=1,
minibatch_size=None, tensorboard=False):
self.closed = None
self.sess = None
self.tensorboard = tensorboard
self.unroll = unroll_simulation
self.minibatch_size = 1 if minibatch_size is None else minibatch_size
# TODO: multi-GPU support
# build model (uses default nengo builder)
if model is None:
self.model = Model(dt=float(dt), label="%s, dt=%f" % (network, dt))
else:
if dt != model.dt:
warnings.warn("Model dt (%g) does not match Simulator "
"dt (%g)" % (model.dt, dt), NengoWarning)
self.model = model
if network is not None:
print("Building network", end="", flush=True)
start = time.time()
self.model.build(network, progress_bar=False)
print("\rBuilding completed in %s " %
datetime.timedelta(seconds=int(time.time() - start)))
# set up tensorflow graph plan
self.tensor_graph = TensorGraph(
self.model, self.dt, unroll_simulation, dtype, self.minibatch_size,
device)
self.data = SimulationData(self, minibatch_size is not None)
if seed is None:
seed = np.random.randint(np.iinfo(np.int32).max)
self.reset(seed=seed)
[docs] def reset(self, seed=None):
"""Resets the simulator to initial conditions.
Parameters
----------
seed : int, optional
if not None, overwrite the default simulator seed with this value
(note: this becomes the new default simulator seed)
"""
if self.closed:
raise SimulatorClosed("Cannot reset closed Simulator.")
# close old session
if self.sess is not None:
self.close()
if seed is not None:
self.seed = seed
self.rng = np.random.RandomState(self.seed)
tf.set_random_seed(self.seed)
self.input_funcs = {}
# (re)build graph
print("Constructing graph", end="", flush=True)
start = time.time()
self.tensor_graph.build(self.rng)
print("\rConstruction completed in %s " %
datetime.timedelta(seconds=int(time.time() - start)))
# output graph description to tensorboard summary
if self.tensorboard:
directory = "%s/%s" % (DATA_DIR, self.model.toplevel.label)
if os.path.isdir(directory):
run_number = max(
[int(x[4:]) for x in os.listdir(directory)
if x.startswith("run")]) + 1
else:
run_number = 0
self.summary = tf.summary.FileWriter(
"%s/run_%d" % (directory, run_number),
graph=self.tensor_graph.graph)
# start session
# note: we need to allow soft placement when using tf.while_loop,
# because tensorflow pins loop variables to the CPU
config = tf.ConfigProto(
allow_soft_placement=False,
log_device_placement=False,
)
# TODO: XLA compiling doesn't seem to provide any benefit at the
# moment, revisit later after tensorflow has developed it further
# config.graph_options.optimizer_options.global_jit_level = (
# tf.OptimizerOptions.ON_1)
self.sess = tf.Session(graph=self.tensor_graph.graph, config=config)
self.closed = False
# initialize variables
self.soft_reset(include_trainable=True, include_probes=True)
self.n_steps = 0
self.time = 0.0
self.final_bases = [
x[0] for x in self.tensor_graph.base_arrays_init.values()]
[docs] def soft_reset(self, include_trainable=False, include_probes=False):
"""Resets the internal state of the simulation, but doesn't
rebuild the graph.
Parameters
----------
include_trainable : bool, optional
if True, also reset any training that has been performed on
network parameters (e.g., connection weights)
include_probes : bool, optional
if True, also clear probe data
"""
init_ops = [self.tensor_graph.local_init_op,
self.tensor_graph.global_init_op]
if include_trainable:
init_ops.append(self.tensor_graph.trainable_init_op)
self.sess.run(init_ops)
if include_probes:
for p in self.model.probes:
self.model.params[p] = []
self.n_steps = 0
[docs] def step(self, **kwargs):
"""Run the simulation for one time step.
Parameters
----------
kwargs : dict
see :meth:`.run_steps`
"""
self.run_steps(1, **kwargs)
[docs] def run(self, time_in_seconds, **kwargs):
"""Simulate for the given length of time.
Parameters
----------
time_in_seconds : float
amount of time to run the simulation for
kwargs : dict
see :meth:`.run_steps`
"""
steps = int(np.round(float(time_in_seconds) / self.dt))
self.run_steps(steps, **kwargs)
[docs] def run_steps(self, n_steps, input_feeds=None, profile=False):
"""Simulate for the given number of steps.
Parameters
----------
n_steps : int
the number of simulation steps to be executed
input_feeds : dict of {:class:`~nengo:nengo.Node`: \
:class:`~numpy:numpy.ndarray`}
override the values of input Nodes with the given data. arrays
should have shape ``(sim.minibatch_size, n_steps, node.size_out)``.
profile : bool, optional
if True, collect TensorFlow profiling information while the
simulation is running (this will slow down the simulation)
Notes
-----
If ``unroll_simulation=x`` is specified, and ``n_steps > x``, this will
repeatedly execute ``x`` timesteps until the the number of steps
executed is >= ``n_steps``.
"""
if self.closed:
raise SimulatorClosed("Simulator cannot run because it is closed.")
actual_steps = self.unroll * int(np.ceil(n_steps / self.unroll))
if actual_steps != n_steps:
warnings.warn(
"Number of steps (%d) is not an even multiple of "
"`unroll_simulation` (%d). Simulation will run for %d steps, "
"which may have unintended side effects." %
(n_steps, self.unroll, actual_steps), RuntimeWarning)
if input_feeds is not None:
self._check_data(input_feeds, mode="input",
n_batch=self.minibatch_size, n_steps=n_steps)
print("Simulation started", end="", flush=True)
start = time.time()
if profile:
run_options = tf.RunOptions(trace_level=tf.RunOptions.FULL_TRACE)
run_metadata = tf.RunMetadata()
else:
run_options = None
run_metadata = None
# execute the simulation loop
try:
steps_run, probe_data = self.sess.run(
[self.tensor_graph.steps_run, self.tensor_graph.probe_arrays],
feed_dict=self._fill_feed(actual_steps, input_feeds,
start=self.n_steps),
options=run_options, run_metadata=run_metadata)
except (tf.errors.InternalError, tf.errors.UnknownError) as e:
if e.op.type == "PyFunc":
raise SimulationError(
"Function '%s' caused an error (see error log above)" %
e.op.name)
else:
raise e # pragma: no cover
# update probe data
self._update_probe_data(probe_data, self.n_steps, n_steps)
# update n_steps
# note: we update n_steps according to the number of steps that the
# user asked for, not the number of steps that were actually run (
# in the case of uneven unroll_simulation)
assert steps_run == actual_steps
self.n_steps += n_steps
self.time = self.n_steps * self.dt
print("\rSimulation completed in %s" %
datetime.timedelta(seconds=int(time.time() - start)))
if profile:
if isinstance(profile, str):
filename = profile
else:
filename = os.path.join(DATA_DIR, "nengo_dl_profile.json")
timeline = Timeline(run_metadata.step_stats)
with open(filename, "w") as f:
f.write(timeline.generate_chrome_trace_format())
[docs] def train(self, inputs, targets, optimizer, n_epochs=1, objective="mse",
shuffle=True, profile=False):
"""Optimize the trainable parameters of the network using the given
optimization method, minimizing the objective value over the given
inputs and targets.
Parameters
----------
inputs : dict of {:class:`~nengo:nengo.Node`: \
:class:`~numpy:numpy.ndarray`}
input values for Nodes in the network; arrays should have shape
``(batch_size, n_steps, node.size_out)``
targets : dict of {:class:`~nengo:nengo.Probe`: \
:class:`~numpy:numpy.ndarray`}
desired output value at Probes, corresponding to each value in
``inputs``; arrays should have shape
``(batch_size, n_steps, probe.size_in)``
optimizer : ``tf.train.Optimizer``
Tensorflow optimizer, e.g.
``tf.train.GradientDescentOptimizer(learning_rate=0.1)``
n_epochs : int, optional
run training for the given number of epochs (complete passes
through ``inputs``)
objective : ``"mse"`` or callable, optional
the objective to be minimized. passing ``"mse"`` will train with
mean squared error. a custom function
``f(output, target) -> loss`` can be passed that consumes the
actual output and target output for a probe in ``targets``
and returns a ``tf.Tensor`` representing the scalar loss value for
that Probe (loss will be averaged across Probes).
shuffle : bool, optional
if True, randomize the data into different minibatches each epoch
profile : bool, optional
if True, collect TensorFlow profiling information while training
(this will slow down the training)
Notes
-----
Most deep learning methods require the network to be differentiable,
which means that trying to train a network with non-differentiable
elements will result in an error. Examples of common
non-differentiable elements include :class:`~nengo:nengo.LIF`,
:class:`~nengo:nengo.Direct`, or processes/neurons that don't have a
custom TensorFlow implementation (see
:class:`.process_builders.SimProcessBuilder`/
:class:`.neuron_builders.SimNeuronsBuilder`)
"""
batch_size, n_steps = next(iter(inputs.values())).shape[:2]
# error checking
if self.closed:
raise SimulatorClosed("Simulator cannot be trained because it is "
"closed.")
self._check_data(inputs, mode="input")
self._check_data(targets, mode="target", n_steps=n_steps,
n_batch=batch_size)
if n_steps < self.unroll:
raise ValidationError("The number of timesteps in training data "
"must be >= unroll_simulation", "inputs")
# check for non-differentiable elements in graph
# utils.find_non_differentiable(
# [self.tensor_graph.invariant_ph[n] for n in inputs],
# [self.tensor_graph.probe_arrays[self.model.probes.index(p)]
# for p in targets])
# build optimizer op
opt_op, opt_slots_init = self.tensor_graph.build_optimizer(
optimizer, tuple(targets.keys()), objective)
# save the internal state of the simulator
tmpdir = tempfile.TemporaryDirectory()
self.save_params(os.path.join(tmpdir.name, "tmp"), include_local=True,
include_global=False)
# initialize any variables that were created by the optimizer
self.sess.run(opt_slots_init)
if profile:
run_options = tf.RunOptions(trace_level=tf.RunOptions.FULL_TRACE)
run_metadata = tf.RunMetadata()
else:
run_options = None
run_metadata = None
progress = utils.ProgressBar(
n_epochs * batch_size // self.minibatch_size, "Training")
for n in range(n_epochs):
for inp, tar in utils.minibatch_generator(
inputs, targets, self.minibatch_size, rng=self.rng,
shuffle=shuffle):
# TODO: set up queue to feed in data more efficiently
self.soft_reset()
self.sess.run(
[opt_op], feed_dict=self._fill_feed(n_steps, inp, tar),
options=run_options, run_metadata=run_metadata)
progress.step()
# restore internal state of simulator
self.load_params(os.path.join(tmpdir.name, "tmp"), include_local=True,
include_global=False)
tmpdir.cleanup()
if profile:
if isinstance(profile, str):
filename = profile
else:
filename = os.path.join(DATA_DIR, "nengo_dl_profile.json")
timeline = Timeline(run_metadata.step_stats)
with open(filename, "w") as f:
f.write(timeline.generate_chrome_trace_format())
[docs] def loss(self, inputs, targets, objective):
"""Compute the loss value for the given objective and inputs/targets.
Parameters
----------
inputs : dict of {:class:`~nengo:nengo.Node`: \
:class:`~numpy:numpy.ndarray`}
input values for Nodes in the network; arrays should have shape
``(batch_size, n_steps, node.size_out)``
targets : dict of {:class:`~nengo:nengo.Probe`: \
:class:`~numpy:numpy.ndarray`}
desired output value at Probes, corresponding to each value in
``inputs``; arrays should have shape
``(batch_size, n_steps, probe.size_in)``
objective : ``"mse"`` or callable
the objective used to compute loss. passing ``"mse"`` will use
mean squared error. a custom function
``f(output, target) -> loss`` can be passed that consumes the
actual output and target output for a probe in ``targets``
and returns a ``tf.Tensor`` representing the scalar loss value for
that Probe (loss will be averaged across Probes)
"""
batch_size, n_steps = next(iter(inputs.values())).shape[:2]
# error checking
if self.closed:
raise SimulatorClosed("Loss cannot be computed after simulator is "
"closed.")
self._check_data(inputs, mode="input")
self._check_data(targets, mode="target", n_steps=n_steps,
n_batch=batch_size)
if n_steps < self.unroll:
raise ValidationError("The number of timesteps in loss data "
"must be >= unroll_simulation", "inputs")
# get loss op
loss = self.tensor_graph.build_loss(objective, tuple(targets.keys()))
# save the internal state of the simulator
tmpdir = tempfile.TemporaryDirectory()
self.save_params(os.path.join(tmpdir.name, "tmp"), include_local=True,
include_global=False)
# compute loss on data
loss_val = 0
for i, (inp, tar) in enumerate(utils.minibatch_generator(
inputs, targets, self.minibatch_size, rng=self.rng)):
self.soft_reset()
loss_val += self.sess.run(
loss, feed_dict=self._fill_feed(n_steps, inp, tar))
loss_val /= i + 1
# restore internal state of simulator
self.load_params(os.path.join(tmpdir.name, "tmp"), include_local=True,
include_global=False)
tmpdir.cleanup()
return loss_val
def _fill_feed(self, n_steps, inputs, targets=None, start=0):
"""Create a feed dictionary containing values for all the placeholder
inputs in the network, which will be passed to ``tf.Session.run``.
Parameters
----------
n_steps : int
the number of execution steps
input_feeds : dict of {:class:`~nengo:nengo.Node`: \
:class:`~numpy:numpy.ndarray`}
override the values of input Nodes with the given data. arrays
should have shape ``(sim.minibatch_size, n_steps, node.size_out)``.
targets : dict of {:class:`~nengo:nengo.Probe`: \
:class:`~numpy:numpy.ndarray`}, optional
values for target placeholders (only necessary if loss is being
computed, e.g. when training the network)
start : int, optional
initial value of simulator timestep
Returns
-------
dict of {``tf.Tensor``: :class:`~numpy:numpy.ndarray`}
feed values for placeholder tensors in the network
"""
# fill in loop variables
feed_dict = {
self.tensor_graph.step_var: start,
self.tensor_graph.stop_var: start + n_steps
}
# fill in values for base variables from previous run
# TODO: remove this if we're sure we're not going back to the tensor
# approach
feed_dict.update(
{k: v for k, v in zip(
self.tensor_graph.base_vars,
self.final_bases) if k.op.type == "Placeholder"})
# fill in input values
tmp = self._generate_inputs(inputs, n_steps)
feed_dict.update(tmp)
# fill in target values
if targets is not None:
feed_dict.update(
{self.tensor_graph.target_phs[p]: np.moveaxis(t, 0, -1)
for p, t in targets.items()})
return feed_dict
def _generate_inputs(self, input_feeds, n_steps):
"""Generate inputs for the network (the output values of each Node with
no incoming connections).
Parameters
----------
input_feeds : dict of {:class:`~nengo:nengo.Node`: \
:class:`~numpy:numpy.ndarray`}
override the values of input Nodes with the given data. arrays
should have shape ``(sim.minibatch_size, n_steps, node.size_out)``.
n_steps : int
number of simulation timesteps for which to generate input data
"""
if input_feeds is None:
input_feeds = {}
feed_vals = {}
for n in self.tensor_graph.invariant_inputs:
# if the output signal is not in sig map, that means no operators
# use the output of this node. similarly, if node.size_out is 0,
# the node isn't producing any output values.
using_output = (
self.model.sig[n]["out"] in self.tensor_graph.sig_map and
n.size_out > 0)
if (not isinstance(n.output, np.ndarray) and
(n, n.output) not in self.input_funcs):
# note: we include n.output in the input_funcs hash to handle
# the case where the node output is changed after the model
# is constructed. this isn't technically supported behaviour
# in nengo, but the gui does it.
if isinstance(n.output, Process):
self.input_funcs[(n, n.output)] = n.output.make_step(
(n.size_in,), (n.size_out,), self.dt,
n.output.get_rng(self.rng))
elif n.size_out > 0:
self.input_funcs[(n, n.output)] = utils.align_func(
(n.size_out,), self.tensor_graph.dtype)(n.output)
else:
self.input_funcs[(n, n.output)] = n.output
if using_output:
if n in input_feeds:
# move minibatch dimension to the end
feed_val = np.moveaxis(input_feeds[n], 0, -1)
elif isinstance(n.output, np.ndarray):
feed_val = np.tile(n.output[None, :, None],
(n_steps, 1, self.minibatch_size))
else:
func = self.input_funcs[(n, n.output)]
feed_val = []
for i in range(self.n_steps + 1,
self.n_steps + n_steps + 1):
# note: need to copy the output of func, as func
# may mutate its outputs in-place on subsequent calls
feed_val += [np.array(func(i * self.dt))]
feed_val = np.stack(feed_val, axis=0)
feed_val = np.tile(feed_val[..., None],
(1, 1, self.minibatch_size))
feed_vals[self.tensor_graph.invariant_ph[n]] = feed_val
elif not isinstance(n.output, np.ndarray):
# note: we still call the function even if the output
# is not being used, because it may have side-effects
func = self.input_funcs[(n, n.output)]
for i in range(self.n_steps + 1, self.n_steps + n_steps + 1):
func(i * self.dt)
return feed_vals
def _update_probe_data(self, probe_data, start, n_steps):
"""Updates the stored probe data (since the last reset) with the data
from the latest run.
Downsamples the probe data returned from tensorflow (from every
simulation timestep) according to probe `sample_every` and the number
of steps run.
Parameters
----------
probe_data : list of `np.ndarray`
probe data from every timestep
start : int
the simulation timestep at which probe data starts
n_steps : int
the number of timesteps over which we want to collect data
"""
# remove any extra timesteps (due to `unroll_simulation` mismatch)
probe_data = [p[:n_steps] for p in probe_data]
for i, p in enumerate(self.model.probes):
if p.sample_every is not None:
# downsample probe according to `sample_every`
period = p.sample_every / self.dt
steps = np.arange(start, start + n_steps)
probe_data[i] = probe_data[i][(steps + 1) % period < 1]
# update stored probe data
self.model.params[p].append(probe_data[i])
[docs] def save_params(self, path, include_global=True, include_local=False):
"""Save network parameters to the given ``path``.
Parameters
----------
path : str
filepath of parameter output file
include_global : bool, optional
if True (default True), save global (trainable) network variables
include_local : bool, optional
if True (default False), save local (non-trainable) network
variables
"""
if self.closed:
raise SimulationError("Simulation has been closed, cannot save "
"parameters")
with self.tensor_graph.graph.as_default():
vars = []
if include_global:
vars.extend(tf.global_variables())
if include_local:
vars.extend(tf.local_variables())
path = tf.train.Saver(vars).save(self.sess, path)
logger.info("Model parameters saved to %s", path)
[docs] def load_params(self, path, include_global=True, include_local=False):
"""Load network parameters from the given ``path``.
Parameters
----------
path : str
filepath of parameter input file
include_global : bool, optional
if True (default True), load global (trainable) network variables
include_local : bool, optional
if True (default False), load local (non-trainable) network
variables
"""
if self.closed:
raise SimulationError("Simulation has been closed, cannot load "
"parameters")
with self.tensor_graph.graph.as_default():
vars = []
if include_global:
vars.extend(tf.global_variables())
if include_local:
vars.extend(tf.local_variables())
tf.train.Saver(vars).restore(self.sess, path)
logger.info("Model parameters loaded from %s", path)
[docs] def close(self):
"""Close the simulation, freeing resources.
Notes
-----
The simulation cannot be restarted after it is closed. This is not a
technical limitation, just a design decision made for all Nengo
simulators.
"""
if not self.closed:
# note: we use getattr in case it crashes before the object is
# created
if getattr(self, "sess", None) is not None:
self.sess.close()
self.sess = None
if getattr(self, "summary", None) is not None:
self.summary.close()
self.closed = True
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
self.close()
@property
def dt(self):
"""(float) The time step of the simulator."""
return self.model.dt
@dt.setter
def dt(self, dummy):
raise ReadonlyError(attr='dt', obj=self)
def __del__(self):
"""Raise a RuntimeWarning if the Simulator is deallocated while open.
"""
if self.closed is not None and not self.closed:
warnings.warn(
"Simulator with model=%s was deallocated while open. "
"Simulators should be closed manually to ensure resources "
"are properly freed." % self.model, RuntimeWarning)
self.close()
[docs] def trange(self, dt=None):
"""Create a vector of times matching probed data.
Note that the range does not start at 0 as one might expect, but at
the first timestep (i.e., ``dt``).
Parameters
----------
dt : float, optional
the sampling period of the probe to create a range for;
if None, the simulator's ``dt`` will be used.
"""
dt = self.dt if dt is None else dt
n_steps = int(self.n_steps * (self.dt / dt))
return dt * np.arange(1, n_steps + 1)
[docs] def check_gradients(self, outputs=None, atol=1e-5, rtol=1e-3):
"""Perform gradient checks for the network (used to verify that the
analytic gradients are correct).
Raises a simulation error if the difference between analytic and
numeric gradient is greater than ``atol + rtol * numeric_grad``
(elementwise).
Parameters
----------
outputs : ``tf.Tensor`` or list of ``tf.Tensor`` or \
list of :class:`~nengo:nengo.Probe`
compute gradients wrt this output (if None, computes wrt each
output probe)
atol : float, optional
absolute error tolerance
rtol : float, optional
relative (to numeric grad) error tolerance
Notes
-----
Calling this function will reset all values in the network, so it
should not be intermixed with calls to :meth:`.Simulator.run`.
"""
delta = 1e-3
n_steps = self.unroll * 2
feed = self._fill_feed(
n_steps, {n: np.zeros((self.minibatch_size, n_steps, n.size_out))
for n in self.tensor_graph.invariant_inputs},
{p: np.zeros((self.minibatch_size, n_steps, p.size_in))
for p in self.tensor_graph.target_phs})
if outputs is None:
# note: the x + 0 is necessary because `gradient_checker`
# doesn't work properly if the output variable is a tensorarray
outputs = [x + 0 for x in self.tensor_graph.probe_arrays]
elif isinstance(outputs, tf.Tensor):
outputs = [outputs]
else:
outputs = [
self.tensor_graph.probe_arrays[self.model.probes.index(p)] + 0
for p in outputs]
# check gradient wrt inp
for node, inp in self.tensor_graph.invariant_ph.items():
inp_shape = inp.get_shape().as_list()
inp_shape = [n_steps if x is None else x for x in inp_shape]
inp_tens = self.tensor_graph.invariant_ph[node]
feed[inp_tens] = np.ascontiguousarray(feed[inp_tens])
inp_val = np.ravel(feed[inp_tens])
for out in outputs:
out_shape = out.get_shape().as_list()
out_shape = [n_steps if x is None else x for x in out_shape]
# we need to compute the numeric jacobian manually, to
# correctly handle variables (tensorflow doesn't expect
# state ops in `compute_gradient`, because it doesn't define
# gradients for them)
numeric = np.zeros((np.prod(inp_shape, dtype=np.int32),
np.prod(out_shape, dtype=np.int32)))
for i in range(numeric.shape[0]):
self.soft_reset()
inp_val[i] = delta
plus = self.sess.run(out, feed_dict=feed)
self.soft_reset()
inp_val[i] = -delta
minus = self.sess.run(out, feed_dict=feed)
numeric[i] = np.ravel((plus - minus) / (2 * delta))
inp_val[i] = 0
self.soft_reset()
dx, dy = gradient_checker._compute_dx_and_dy(
inp, out, out_shape)
with self.sess.as_default():
analytic = gradient_checker._compute_theoretical_jacobian(
inp, inp_shape, np.zeros(inp_shape), dy, out_shape, dx,
extra_feed_dict=feed)
if np.any(np.isnan(analytic)) or np.any(np.isnan(numeric)):
raise SimulationError("NaNs detected in gradient")
fail = abs(analytic - numeric) >= atol + rtol * abs(numeric)
if np.any(fail):
raise SimulationError(
"Gradient check failed for input %s and output %s\n"
"numeric values:\n%s\n"
"analytic values:\n%s\n" % (node, out, numeric[fail],
analytic[fail]))
self.soft_reset()
logger.info("Gradient check passed")
def _check_data(self, data, mode="input", n_batch=None, n_steps=None):
"""Performs error checking on simulation data.
Parameters
----------
data : dict of {:class:`~nengo:nengo.Node` or \
:class:`~nengo:nengo.Probe`: \
:class:`~numpy:numpy.ndarray`}
array of data associated with given objects in model (Nodes if
mode=="input" or Probes if mode=="target")
mode : "input" or "target", optional
whether this data corresponds to an input or target value
n_batch : int, optional
number of elements in batch (if None, will just verify that all
data items have same batch size)
n_steps : int, optional
number of simulation steps (if None, will just verify that all
data items have same number of steps)
"""
for d in data:
if mode == "input":
if d not in self.tensor_graph.invariant_inputs:
raise ValidationError(
"%s is not an input Node (a nengo.Node with "
"size_in==0), or is from a different network." % d,
"%s data" % mode)
else:
if d not in self.model.probes:
raise ValidationError(
"%s is not a Probe, or is from a different "
"network" % d, "%s data" % mode)
args = [n_batch, n_steps]
labels = ["batch size", "number of timesteps"]
for i in range(2):
if args[i] is None:
val = next(iter(data.values())).shape[i]
for n, x in data.items():
if x.shape[i] != val:
raise ValidationError(
"Elements have different %s: %s vs %s" %
(labels[i], val, x.shape[0]), "%s data" % mode)
else:
for n, x in data.items():
if x.shape[i] != args[i]:
raise ValidationError(
"Data for %s has %s=%s, which does not match "
"expected size %s" % (n, labels[i], x.shape[i],
args[i]),
"%s data" % mode)
for n, x in data.items():
d = n.size_out if mode == "input" else n.size_in
if x.shape[2] != d:
raise ValidationError(
"Dimensionality of data (%s) does not match "
"dimensionality of %s (%s)" % (x.shape[2], n, d),
"%s data" % mode)
[docs]class SimulationData(object):
"""Data structure used to access simulation data from the model.
The main use case for this is to access Probe data; for example,
``probe_data = sim.data[my_probe]``. However, it is also
used to access the parameters of objects in the model; for example, after
the model has been optimized via :meth:`.Simulator.train`, the updated
encoder values for an ensemble can be accessed via
``trained_encoders = sim.data[my_ens].encoders``.
Parameters
----------
sim : :class:`.Simulator`
the simulator from which data will be drawn
minibatched : bool
if False, discard the minibatch dimension on probe data
Notes
-----
SimulationData shouldn't be created/accessed directly by the user, but
rather via ``sim.data`` (which is an instance of SimulationData).
"""
[docs] def __init__(self, sim, minibatched):
self.sim = sim
self.minibatched = minibatched
[docs] def __getitem__(self, obj):
"""Return the data associated with ``obj``.
Parameters
----------
obj : :class:`~nengo:nengo.Probe` or :class:`~nengo:nengo.Ensemble` \
or :class:`~nengo:nengo.Connection`
object whose simulation data is being accessed
Returns
-------
:class:`~numpy:numpy.ndarray` or \
:class:`~nengo:nengo.builder.ensemble.BuiltEnsemble` or \
:class:`~nengo:nengo.builder.connection.BuiltConnection`
array containing probed data if ``obj`` is a
:class:`~nengo:nengo.Probe`, otherwise the corresponding
parameter object
"""
if obj not in self.sim.model.params:
raise ValidationError("Object is not in parameters of model %s" %
self.sim.model, str(obj))
data = self.sim.model.params[obj]
if isinstance(obj, Probe):
if len(data) == 0:
return []
data = np.concatenate(data, axis=0)
if self.sim.model.sig[obj]["in"].minibatched:
if self.minibatched:
# move batch dimension to front
data = np.moveaxis(data, -1, 0)
else:
# get rid of batch dimension
data = data[..., 0]
data.setflags(write=False)
elif isinstance(obj, Ensemble):
# get the live simulation values
scaled_encoders = self.get_param(obj, "scaled_encoders")
bias = self.get_param(obj, "bias")
# infer the related values (rolled into scaled_encoders)
gain = (obj.radius * np.linalg.norm(scaled_encoders, axis=1) /
np.linalg.norm(data.encoders, axis=1))
encoders = obj.radius * scaled_encoders / gain[:, None]
# figure out max_rates/intercepts from neuron model
max_rates, intercepts = (
obj.neuron_type.max_rates_intercepts(gain, bias))
data = BuiltEnsemble(data.eval_points, encoders, intercepts,
max_rates, scaled_encoders, gain, bias)
elif isinstance(obj, Connection):
# get the live simulation values
weights = self.get_param(obj, "weights")
# impossible to recover transform
transform = None
data = BuiltConnection(data.eval_points, data.solver_info, weights,
transform)
return data
[docs] def get_param(self, obj, attr):
"""Returns the current parameter value for the given object.
Parameters
----------
obj : ``NengoObject``
the nengo object for which we want to know the parameters
attr : str
the parameter of ``obj`` to be returned
Returns
-------
:class:`~numpy:numpy.ndarray`
current value of the parameters associated with the given object
Notes
-----
Parameter values should be accessed through ``sim.data``
(which will call this function if necessary), rather than directly
through this function.
"""
if self.sim.closed:
warnings.warn("Checking %s.%s after simulator is closed; cannot "
"fetch live value, so the initial value will be "
"returned." % (obj, attr))
return getattr(self.sim.model.params[obj], attr)
sig_obj, sig_attr = self._attr_map(obj, attr)
try:
sig = self.sim.model.sig[sig_obj][sig_attr]
except KeyError:
# sig_attr doesn't exist for this attribute
return None
try:
tensor_sig = self.sim.tensor_graph.sig_map[sig]
except KeyError:
# if sig isn't in sig_map then that means it isn't used anywhere
# in the simulation (and therefore never changes), so we can
# safely return the static build value
return getattr(self.sim.model.params[obj], attr)
keys = list(self.sim.tensor_graph.signals.bases.keys())
param = self.sim.tensor_graph.base_vars[keys.index(tensor_sig.key)]
val = self.sim.sess.run(param)
return val[tensor_sig.indices]
def _attr_map(self, obj, attr):
"""Maps from ``sim.data[obj].attr`` to the equivalent
``model.sig[obj][attr]``.
Parameters
----------
obj : ``NengoObject``
the nengo object for which we want to know the parameters
attr : str
the parameter of ``obj`` to be returned
Returns
-------
obj : ``NengoObject``
the nengo object to key into model.sig
attr : str
the name of the signal corresponding to input attr
"""
if isinstance(obj, Ensemble) and attr == "bias":
return obj.neurons, attr
elif isinstance(obj, Ensemble) and attr == "scaled_encoders":
return obj, "encoders"
return obj, attr