from __future__ import print_function, division
import collections
import datetime
import logging
import os
import sys
import tempfile
import time
import warnings
from nengo import Process, Ensemble, Connection, Probe, Network
from nengo import version as nengo_version
from nengo.builder import Model
from nengo.builder.connection import BuiltConnection
from nengo.builder.ensemble import BuiltEnsemble
from nengo.ensemble import Neurons
from nengo.exceptions import (
ReadonlyError, SimulatorClosed, NengoWarning, SimulationError,
ValidationError, ConfigError)
from nengo.solvers import NoSolver
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import gradient_checker
from nengo_dl import utils, DATA_DIR
from nengo_dl.builder import NengoBuilder
from nengo_dl.tensor_graph import TensorGraph
logger = logging.getLogger(__name__)
if sys.version_info < (3, 4):
import backports.tempfile as tempfile # noqa: F811
[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 : str, optional
If not None, save network output in the TensorFlow summary format to
the given directory, which can be loaded into TensorBoard
progress_bar : bool, optional
If True (default), display progress information when building a model
"""
# 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_simulator.py:test_simulator_progress_bars",
"nengo_dl uses a different progress bar system (see "
"tests/test_utils.py:test_progress_bar"),
("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=None, progress_bar=True):
self.closed = False
self.unroll = unroll_simulation
self.minibatch_size = 1 if minibatch_size is None else minibatch_size
self.data = SimulationData(self, minibatch_size is not None)
self.seed = (np.random.randint(np.iinfo(np.int32).max) if seed is None
else seed)
# TODO: multi-GPU support
ProgressBar = (utils.ProgressBar if progress_bar else
utils.NullProgressBar)
# build model (uses default nengo builder)
if model is None:
self.model = Model(dt=float(dt), label="%s, dt=%f" % (network, dt),
builder=NengoBuilder())
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:
if nengo_version.version_info < (2, 7, 1):
print("Building network")
start = time.time()
self.model.build(network, progress_bar=None)
print("\rBuild finished in %s " %
datetime.timedelta(seconds=int(time.time() - start)))
else:
p = ProgressBar("Building network", "Build")
self.model.build(network, progress=p)
# set up tensorflow graph plan
with ProgressBar("Optimizing graph", "Optimization",
max_value=None) as progress:
self.tensor_graph = TensorGraph(
self.model, self.dt, unroll_simulation, dtype,
self.minibatch_size, device, progress)
# construct graph
with ProgressBar("Constructing graph", "Construction",
max_value=None) as progress:
self.tensor_graph.build(progress)
# output simulation data for viewing via TensorBoard
if tensorboard is not None:
if not os.path.exists(tensorboard):
os.makedirs(tensorboard)
run_number = max(
[int(x[4:]) for x in os.listdir(tensorboard)
if x.startswith("run")] or [-1]) + 1
self.summary = tf.summary.FileWriter(
os.path.join(tensorboard, "run_%d" % run_number),
graph=self.tensor_graph.graph)
else:
self.summary = None
# start session
config = tf.ConfigProto(
allow_soft_placement=False,
log_device_placement=False,
)
# set any config options specified by user
try:
config_settings = network.config[Network].session_config
except (ConfigError, AttributeError):
config_settings = {}
for c, v in config_settings.items():
attrs = c.split(".")
x = config
for a in attrs[:-1]:
x = getattr(x, a)
setattr(x, attrs[-1], v)
# 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.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.")
self.input_funcs = {}
self.n_steps = 0
self.time = 0.0
# initialize variables
self.sess.run(self.tensor_graph.constant_init_op,
feed_dict=self.tensor_graph.signals.constant_phs)
self.soft_reset(include_trainable=True, include_probes=True)
# execute post-build processes (we do this here because
# seed can change each call to reset)
if seed is not None:
self.seed = seed
self.rng = np.random.RandomState(self.seed)
tf.set_random_seed(self.seed)
self.tensor_graph.build_post(self.sess, self.rng)
[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, feed_dict={
ph: v for _, ph, v in self.tensor_graph.base_vars.values()})
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`
Notes
-----
Progress bar is disabled by default when running via this method.
"""
kwargs.setdefault("progress_bar", False)
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
Run the simulator for the given number of simulated seconds
kwargs : dict
See :meth:`.run_steps`
"""
if time_in_seconds < 0:
raise ValidationError(
"Must be positive (got %g)" % (time_in_seconds,),
attr="time_in_seconds")
steps = int(np.round(float(time_in_seconds) / self.dt))
if steps == 0:
warnings.warn("%g results in running for 0 timesteps. Simulator "
"still at time %g." % (time_in_seconds, self.time))
else:
self.run_steps(steps, **kwargs)
[docs] def run_steps(self, n_steps, input_feeds=None, profile=False,
progress_bar=True, extra_feeds=None):
"""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).
Can also pass a dict of `config options for the profiler
<https://github.com/tensorflow/tensorflow/blob/master/tensorflow/core/profiler/g3doc/options.md>`__.
progress_bar : bool, optional
If True, print information about the simulation status to standard
output.
extra_feeds : dict of {``tf.Tensor``: :class:`~numpy:numpy.ndarray`}
Can be used to feed a value for arbitrary Tensors in the simulation
(will be passed directly to the TensorFlow session)
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)
feed = self._fill_feed(actual_steps, input_feeds,
start=self.n_steps)
if extra_feeds is not None:
feed.update(extra_feeds)
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("Simulating", "Simulation", max_value=None)
if progress_bar else utils.NullProgressBar())
# execute the simulation loop
with progress:
try:
steps_run, probe_data = self.sess.run(
[self.tensor_graph.steps_run,
list(self.tensor_graph.probe_arrays.values())],
feed_dict=feed, 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
if profile:
filename = os.path.join(DATA_DIR, "nengo_dl_profile.json")
options = tf.profiler.ProfileOptionBuilder.time_and_memory()
options["output"] = "timeline:outfile=%s" % filename
options["min_bytes"] = 0
if isinstance(profile, dict):
options.update(profile)
tf.profiler.profile(
self.tensor_graph.graph, run_meta=run_metadata,
cmd="scope", options=options)
[docs] def train(self, inputs, targets, optimizer, n_epochs=1, objective="mse",
shuffle=True, truncation=None, summaries=None, profile=False,
extra_feeds=None):
"""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). Note that by
default the same objective will be used for all probes in
``targets``; a dictionary of ``{probe: obj, ...}`` can be passed
for ``objective`` to specify a different objective for each probe.
shuffle : bool, optional
If True, randomize the data into different minibatches each epoch
truncation: int, optional
If not None, use truncated backpropagation when training the
network, with the given truncation length.
summaries : list of :class:`~nengo:nengo.Connection` or \
:class:`~nengo:nengo.Ensemble` or \
:class:`~nengo:nengo.ensemble.Neurons` or \
``"loss"`` or \
``tf.Tensor``}
If not None, collect data during the training process using
TensorFlow's ``tf.summary`` format. The summary objects can be a
Connection (in which case data on the corresponding weights will be
collected), Ensemble (encoders), Neurons (biases), or ``"loss"``
(the loss value for ``objective``). The user can also create their
own summaries and pass in the Tensors representing the summary ops.
profile : bool, optional
If True, collect TensorFlow profiling information while training
(this will slow down the training). Can also pass a dict of
`config options for the profiler
<https://github.com/tensorflow/tensorflow/blob/master/tensorflow/core/profiler/g3doc/options.md>`__.
extra_feeds : dict of {``tf.Tensor``: :class:`~numpy:numpy.ndarray`}
Can be used to feed a value for arbitrary Tensors in the simulation
(will be passed directly to the TensorFlow session)
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`)
"""
# TODO: allow error to be passed instead of objective
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 != 0:
raise ValidationError(
"The number of timesteps in training data must be evenly "
"divisible by unroll_simulation", "inputs")
if truncation is not None and truncation % self.unroll != 0:
raise ValidationError(
"Truncation length must be evenly divisible by "
"unroll_simulation", "inputs")
# check for non-differentiable elements in graph
# utils.find_non_differentiable(
# [self.tensor_graph.input_ph[n] for n in inputs],
# [self.tensor_graph.probe_arrays[self.model.probes.index(p)]
# for p in targets])
# apply objective to all probes if individual objectives weren't given
if not isinstance(objective, dict):
objective = {p: objective for p in targets}
# build optimizer op
opt_op, opt_slots_init = self.tensor_graph.build_optimizer(
optimizer, objective)
fetches = [opt_op]
# initialize any variables that were created by the optimizer
if opt_slots_init is not None:
self.sess.run(opt_slots_init)
# get loss op
loss = self.tensor_graph.build_loss(objective)
fetches.append(loss)
# add summaries
summary_op = None
if summaries is not None:
if self.summary is None:
warnings.warn("Simulator was created with tensorboard=False; "
"ignoring requested summaries")
else:
for i, v in enumerate(summaries):
if isinstance(v, str) and v == "loss":
summaries[i] = objective
summary_op = self.tensor_graph.build_summaries(summaries)
fetches.append(summary_op)
# increment training step
fetches.append(self.tensor_graph.training_step_inc)
# 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)
if profile:
run_options = tf.RunOptions(trace_level=tf.RunOptions.FULL_TRACE)
run_metadata = tf.RunMetadata()
profiler = tf.profiler.Profiler(self.tensor_graph.graph)
else:
run_options = None
run_metadata = None
progress = utils.ProgressBar(
"Training", max_value=n_epochs * batch_size // self.minibatch_size,
vars=["loss"])
# run training
with progress:
for n in range(n_epochs):
for offset, inp, tar in utils.minibatch_generator(
inputs, targets, self.minibatch_size, rng=self.rng,
shuffle=shuffle, truncation=truncation):
if offset == 0:
self.soft_reset()
steps = next(iter(inp.values())).shape[1]
feed = self._fill_feed(steps, inp, tar, start=offset)
if extra_feeds is not None:
feed.update(extra_feeds)
outputs = self.sess.run(
fetches, feed_dict=feed,
options=run_options, run_metadata=run_metadata)
if summary_op is not None:
self.summary.add_summary(outputs[2], outputs[-1])
if profile:
profiler.add_step(int(outputs[-1]), run_metadata)
if offset == 0:
progress.step(loss="%.4f" % outputs[1])
# restore internal state of simulator
self.load_params(os.path.join(tmpdir.name, "tmp"), include_local=True,
include_global=False)
tmpdir.cleanup()
if profile:
filename = os.path.join(DATA_DIR, "nengo_dl_profile.json")
options = tf.profiler.ProfileOptionBuilder.time_and_memory()
options["output"] = "timeline:outfile=%s" % filename
options["min_bytes"] = 0
if isinstance(profile, dict):
options.update(profile)
profiler.profile_name_scope(options)
[docs] def loss(self, inputs, targets, objective, extra_feeds=None):
"""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). Note that by
default the same objective will be used for all probes in
``targets``; a dictionary of ``{probe: obj, ...}`` can be passed
for ``objective`` to specify a different objective for each probe.
extra_feeds : dict of {``tf.Tensor``: :class:`~numpy:numpy.ndarray`}
Can be used to feed a value for arbitrary Tensors in the simulation
(will be passed directly to the TensorFlow session)
"""
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 != 0:
raise ValidationError(
"The number of timesteps in loss data must be evenly "
"divisible by unroll_simulation", "inputs")
# apply objective to all probes if individual objectives weren't given
if not isinstance(objective, dict):
objective = {p: objective for p in targets}
# get loss op
loss = self.tensor_graph.build_loss(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)
# 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()
feed = self._fill_feed(n_steps, inp, tar)
if extra_feeds is not None:
feed.update(extra_feeds)
loss_val += self.sess.run(loss, feed_dict=feed)
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
[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
Notes
-----
This function is useful for saving/loading entire models; for
saving/loading individual objects within a model, see
:meth:`.get_nengo_params`.
"""
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())
with tf.device("/cpu:0"):
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
Notes
-----
This function is useful for saving/loading entire models; for
saving/loading individual objects within a model, see
:meth:`.get_nengo_params`.
"""
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())
with tf.device("/cpu:0"):
tf.train.Saver(vars).restore(self.sess, path)
logger.info("Model parameters loaded from %s", path)
[docs] def get_nengo_params(self, nengo_objs, as_dict=False):
"""Extract model parameters in a form that can be used to initialize
Nengo objects in a different model.
For example:
.. code-block:: python
with nengo.Network() as net:
a = nengo.Ensemble(10, 1)
b = nengo.Ensemble(10, 1)
c = nengo.Connection(a, b)
with nengo_dl.Simulator(net) as sim:
# < do some optimization >
params = sim.get_nengo_params([a, b, c])
with nengo.Network() as new_net:
# < build some other network >
# now we want to insert two connected ensembles with the same
# parameters as our previous network:
d = nengo.Ensemble(10, 1, **params[0])
e = nengo.Ensemble(10, 1, **params[1])
f = nengo.Connection(d, e, **params[2])
Parameters
----------
nengo_objs : (list of) :class:`~nengo:nengo.Ensemble` or \
:class:`~nengo:nengo.Connection`
A single object or list of objects for which we want to get the
parameters.
as_dict : bool, optional
If True, return the values as a dictionary keyed by object label,
instead of a list (the default). Note that in this case labels
must be unique.
Returns
-------
(list or dict) of dicts
kwarg dicts corresponding to ``nengo_objs`` (passing these
dicts as kwargs when creating new Nengo objects will result in a
new object with the same parameters as the source object). A
single kwarg dict if a single object was passed in, or a list
(dict if ``as_dict=True``) of kwargs corresponding to multiple
input objects.
"""
if isinstance(nengo_objs, (list, tuple)):
scalar = False
else:
scalar = True
nengo_objs = [nengo_objs]
# convert neurons to the parent ensemble
nengo_objs = [obj.ensemble if isinstance(obj, Neurons) else obj
for obj in nengo_objs]
params = []
for obj in nengo_objs:
data = self.data[obj]
if isinstance(obj, Connection):
if isinstance(obj.pre_obj, Ensemble):
params.append({
"solver": NoSolver(data.weights.T, weights=False),
"function": lambda x, data=data: np.zeros(
data.weights.shape[0]),
"transform": 1})
else:
params.append({"transform": data.weights})
elif isinstance(obj, Ensemble):
params.append({"gain": data.gain, "bias": data.bias,
"encoders": data.encoders})
else:
raise ValueError(
"Can only get Nengo parameters for Ensembles or "
"Connections")
if scalar:
return params[0]
if as_dict:
param_dict = {}
for obj, p in zip(nengo_objs, params):
if obj.label in param_dict:
raise ValueError(
"Duplicate label ('%s') detected; cannot return "
"parameters with as_dict=True" % obj.label)
else:
param_dict[obj.label] = p
params = param_dict
return params
[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.values()]
elif isinstance(outputs, tf.Tensor):
outputs = [outputs]
else:
outputs = [self.tensor_graph.probe_arrays[p] + 0 for p in outputs]
# check gradient wrt inp
for node, inp in self.tensor_graph.input_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.input_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")
[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 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 _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 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]: t
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
Returns
-------
dict of {:class:`~nengo:nengo.Node`: :class:`~numpy:numpy.ndarray}
Simulation values for all the input Nodes in the network.
"""
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))
for _ in range(self.minibatch_size)]
elif n.size_out > 0:
self.input_funcs[(n, n.output)] = [utils.align_func(
(n.size_out,), self.tensor_graph.dtype)(n.output)]
else:
# a node with no inputs and no outputs, but it can still
# have side effects
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:
feed_val = np.zeros(
(n_steps, n.size_out, self.minibatch_size),
dtype=self.tensor_graph.dtype.as_numpy_dtype)
for i in range(n_steps):
# note: need to copy the output of func, as func
# may mutate its outputs in-place on subsequent calls
feed_val[i] = np.transpose([
func((i + self.n_steps + 1) * self.dt)
for func in self.input_funcs[(n, n.output)]])
feed_vals[self.tensor_graph.input_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
for i in range(self.n_steps + 1, self.n_steps + n_steps + 1):
for func in self.input_funcs[(n, n.output)]:
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])
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, x in data.items():
if x.ndim != 3:
raise ValidationError(
"should have rank 3 (batch_size, n_steps, dimensions), "
"found rank %d" % x.ndim,
"%s data" % mode)
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():
if x.shape[0] < self.minibatch_size:
raise ValidationError(
"Size of minibatch (%d) for %s data less than Simulation "
"`minibatch_size` (%d)" % (x.shape[0], n,
self.minibatch_size),
"%s data" % mode)
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)
@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)
@property
def training_step(self):
return self.tensor_graph.training_step
def __enter__(self):
self._graph_context = self.tensor_graph.graph.as_default()
self._device_context = self.tensor_graph.graph.device(
self.tensor_graph.device)
self._graph_context.__enter__()
self._device_context.__enter__()
return self
def __exit__(self, *args):
self._device_context.__exit__(*args)
self._graph_context.__exit__(*args)
self.close()
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]class SimulationData(collections.Mapping):
"""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=1)
if not self.minibatched:
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
if sig not in self.sim.tensor_graph.sig_map:
# 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
param = getattr(self.sim.model.params[obj], attr)
else:
param = self.sim.sess.run(self.sim.tensor_graph.get_tensor(sig))
if sig.minibatched:
if not self.minibatched:
param = param[..., 0]
else:
param = np.moveaxis(param, -1, 0)
return param
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
def __len__(self):
return len(self.sim.model.params)
def __iter__(self):
return iter(self.sim.model.params)