def transform_to(self, other, keys=None):
"""Create a linear transform from one Vocabulary to another.
This is simply the sum of the outer products of the corresponding
terms in each Vocabulary.
Parameters
----------
other : Vocabulary
The other vocabulary to translate into
keys : list of strings
If None, any term that exists in just one of the Vocabularies
will be created in the other Vocabulary and included. Otherwise,
the transformation will only consider terms in this list. Any
terms in this list that do not exist in the Vocabularies will
be created.
"""
if keys is None:
keys = list(self.keys)
for k in other.keys:
if k not in keys:
keys.append(k)
t = np.zeros((other.dimensions, self.dimensions),
dtype=rc.get('precision', 'dtype'))
for k in keys:
a = self[k].v
b = other[k].v
t += np.outer(b, a)
return t
def validate(self, instance, ndarray):
ndim = len(self.shape)
try:
ndarray = np.asarray(ndarray, dtype=rc.get('precision', 'dtype'))
except TypeError:
raise
raise ValueError("Must be a float NumPy array (got type '%s')" %
ndarray.__class__.__name__)
if ndarray.ndim != ndim:
raise ValueError("ndarray must be %dD (got %dD)" %
(ndim, ndarray.ndim))
for i, attr in enumerate(self.shape):
assert is_integer(attr) or is_string(attr), (
"shape can only be an int or str representing an attribute")
if attr == '*':
continue
desired = attr if is_integer(attr) else getattr(instance, attr)
if not is_integer(desired):
raise ValueError("%s not yet initialized; cannot determine "
"if shape is correct. Consider using a "
"distribution instead." % attr)
if ndarray.shape[i] != desired:
raise ValueError("shape[%d] should be %d (got %d)" %
(i, desired, ndarray.shape[i]))
return ndarray
def shrink(self, limit=None):
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if limit is None:
limit = rc.get('decoder_cache', 'size')
if is_string(limit):
limit = human2bytes(limit)
fileinfo = []
excess = -limit
for path in self.get_files():
stat = safe_stat(path)
if stat is not None:
aligned_size = byte_align(stat.st_size, self._fragment_size)
excess += aligned_size
fileinfo.append((stat.st_atime, aligned_size, path))
# Remove the least recently accessed first
fileinfo.sort()
for _, size, path in fileinfo:
if excess <= 0:
break
excess -= size
safe_remove(path)
def shrink(self, limit=None):
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if limit is None:
limit = rc.get('decoder_cache', 'size')
if is_string(limit):
limit = human2bytes(limit)
fileinfo = []
for filename in self.get_files():
path = os.path.join(self.cache_dir, filename)
stat = safe_stat(path)
if stat is not None:
fileinfo.append((stat.st_atime, stat.st_size, path))
# Remove the least recently accessed first
fileinfo.sort()
excess = self.get_size_in_bytes() - limit
for _, size, path in fileinfo:
if excess <= 0:
break
excess -= size
safe_remove(path)
# We may have removed a decoder file but not solver_info file
# or vice versa, so we'll remove all orphans
self.remove_orphans()
def shrink(self, limit=None):
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if limit is None:
limit = rc.get('decoder_cache', 'size')
if is_string(limit):
limit = human2bytes(limit)
fileinfo = []
excess = -limit
for path in self.get_files():
stat = safe_stat(path)
if stat is not None:
aligned_size = byte_align(stat.st_size, self._fragment_size)
excess += aligned_size
fileinfo.append((stat.st_atime, aligned_size, path))
# Remove the least recently accessed first
fileinfo.sort()
for _, size, path in fileinfo:
if excess <= 0:
break
excess -= size
safe_remove(path)
def validate(self, conn, transform):
transform = np.asarray(transform, dtype=rc.get('precision', 'dtype'))
if transform.ndim == 0:
self.shape = ()
elif transform.ndim == 1:
self.shape = ('size_out', )
elif transform.ndim == 2:
# Actually (size_out, size_mid) but Function handles size_mid
self.shape = ('size_out', '*')
else:
raise ValueError("Cannot handle transforms with dimensions > 2")
# Checks the shapes
super(TransformParam, self).validate(conn, transform)
if transform.ndim == 2:
# check for repeated dimensions in lists, as these don't work
# for two-dimensional transforms
repeated_inds = lambda x: (not isinstance(x, slice) and np.unique(
x).size != len(x))
if repeated_inds(conn.pre_slice):
raise ValueError("Input object selection has repeated indices")
if repeated_inds(conn.post_slice):
raise ValueError(
"Output object selection has repeated indices")
return transform
def get_default_dir():
"""Returns the default location of the cache.
Returns
-------
str
"""
return rc.get("decoder_cache", "path")
def get_default_dir():
"""Returns the default location of the cache.
Returns
-------
str
"""
return rc.get('decoder_cache', 'path')
def get_default_dir():
"""Returns the default location of the cache.
Returns
-------
str
"""
return rc.get('decoder_cache', 'path')
def __init__(self, value, name=None, dtype=rc.get('precision', 'dtype')):
# Make sure we use a C-contiguous array
self._value = np.array(npext.castDecimal(value),
copy=False,
order='C',
dtype=dtype)
if name is not None:
self._name = name
if Signal.assert_named_signals:
assert name
def load_ipython_extension(ipython):
if IPython.version_info[0] >= 5:
warnings.warn(
"Loading the nengo.ipynb notebook extension is no longer "
"required. Progress bars are automatically activated for IPython "
"version 5 and later.")
elif has_ipynb_widgets() and rc.get('progress', 'progress_bar') == 'auto':
warnings.warn(
"The nengo.ipynb notebook extension is deprecated. Please upgrade "
"to IPython version 5 or later.")
IPythonProgressWidget.load_frontend(ipython)
rc.set('progress', 'progress_bar', '.'.join(
(__name__, IPython2ProgressBar.__name__)))
def load_ipython_extension(ipython):
if IPython.version_info[0] >= 5:
warnings.warn(
"Loading the nengo.ipynb notebook extension is no longer "
"required. Progress bars are automatically activated for IPython "
"version 5 and later.")
elif has_ipynb_widgets() and rc.get('progress', 'progress_bar') == 'auto':
warnings.warn(
"The nengo.ipynb notebook extension is deprecated. Please upgrade "
"to IPython version 5 or later.")
IPythonProgressWidget.load_frontend(ipython)
rc.set('progress', 'progress_bar', '.'.join((
__name__, IPython2ProgressBar.__name__)))
def __init__(self,
dimensions,
vocab=None,
neurons_per_multiply=200,
output_scaling=1.0,
radius=1.0,
direct=False,
label=None,
seed=None,
add_to_container=None):
super(Compare, self).__init__(label, seed, add_to_container)
if vocab is None:
# use the default vocab for this number of dimensions
vocab = dimensions
self.output_scaling = output_scaling
with self:
self.compare = nengo.networks.EnsembleArray(
neurons_per_multiply,
dimensions,
ens_dimensions=2,
neuron_type=nengo.Direct() if direct else nengo.LIF(),
encoders=Choice([[1, 1], [1, -1], [-1, 1], [-1, -1]]),
radius=radius * np.sqrt(2),
label='compare')
self.inputA = nengo.Node(size_in=dimensions, label='inputA')
self.inputB = nengo.Node(size_in=dimensions, label='inputB')
self.output = nengo.Node(size_in=dimensions, label='output')
self.inputs = dict(A=(self.inputA, vocab), B=(self.inputB, vocab))
self.outputs = dict(default=(self.output, vocab))
dtype = rc.get('precision', 'dtype')
t1 = np.zeros((dimensions * 2, dimensions), dtype=dtype)
t2 = np.zeros((dimensions * 2, dimensions), dtype=dtype)
for i in range(dimensions):
t1[i * 2, i] = 1
t2[i * 2 + 1, i] = 1
with self:
nengo.Connection(self.inputA, self.compare.input, transform=t1)
nengo.Connection(self.inputB, self.compare.input, transform=t2)
def multiply(x):
return [x[0] * x[1]]
self.compare.add_output('product', function=multiply)
def gen_eval_points(ens, eval_points, rng, scale_eval_points=True):
if isinstance(eval_points, Distribution):
n_points = ens.n_eval_points
if n_points is None:
n_points = default_n_eval_points(ens.n_neurons, ens.dimensions)
eval_points = eval_points.sample(n_points, ens.dimensions, rng)
else:
if (ens.n_eval_points is not None
and eval_points.shape[0] != ens.n_eval_points):
warnings.warn("Number of eval_points doesn't match "
"n_eval_points. Ignoring n_eval_points.")
eval_points = np.array(eval_points, dtype=rc.get('precision', 'dtype'))
if scale_eval_points:
eval_points *= ens.radius # scale by ensemble radius
return eval_points
def shrink(self, limit=None): # noqa: C901
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if self.readonly:
logger.info("Tried to shrink a readonly cache.")
return
if self._index is None:
warnings.warn("Cannot shrink outside of a `with cache` block.")
return
if limit is None:
limit = rc.get('decoder_cache', 'size')
if is_string(limit):
limit = human2bytes(limit)
self._close_fd()
fileinfo = []
excess = -limit
for path in self.get_files():
stat = safe_stat(path)
if stat is not None:
aligned_size = byte_align(stat.st_size, self._fragment_size)
excess += aligned_size
fileinfo.append((stat.st_atime, aligned_size, path))
# Remove the least recently accessed first
fileinfo.sort()
for _, size, path in fileinfo:
if excess <= 0:
break
excess -= size
self._index.remove_file_entry(path)
safe_remove(path)
self._index.sync()
def shrink(self, limit=None): # noqa: C901
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if self.readonly:
logger.info("Tried to shrink a readonly cache.")
return
if limit is None:
limit = rc.get('decoder_cache', 'size')
if isinstance(limit, str):
limit = human2bytes(limit)
self._close_fd()
fileinfo = []
excess = -limit
for path in self.get_files():
stat = safe_stat(path)
if stat is not None:
aligned_size = byte_align(stat.st_size, self._fragment_size)
excess += aligned_size
fileinfo.append((stat.st_atime, aligned_size, path))
# Remove the least recently accessed first
fileinfo.sort()
try:
with self._index:
for _, size, path in fileinfo:
if excess <= 0:
break
excess -= size
self.remove_file(path)
except TimeoutError:
logger.debug("Not shrinking cache. Lock could not be acquired.")
def shrink(self, limit=None): # noqa: C901
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if self.readonly:
logger.info("Tried to shrink a readonly cache.")
return
if limit is None:
limit = rc.get('decoder_cache', 'size')
if is_string(limit):
limit = human2bytes(limit)
self._close_fd()
fileinfo = []
excess = -limit
for path in self.get_files():
stat = safe_stat(path)
if stat is not None:
aligned_size = byte_align(stat.st_size, self._fragment_size)
excess += aligned_size
fileinfo.append((stat.st_atime, aligned_size, path))
# Remove the least recently accessed first
fileinfo.sort()
try:
with self._index:
for _, size, path in fileinfo:
if excess <= 0:
break
excess -= size
self.remove_file(path)
except TimeoutError:
logger.debug("Not shrinking cache. Lock could not be acquired.")
def __init__(self, dimensions, randomize=True, unitary=False,
max_similarity=0.1, include_pairs=False, rng=None):
if not is_integer(dimensions):
raise TypeError('dimensions must be an integer')
if dimensions < 1:
raise ValueError('dimensions must be positive')
self.dimensions = dimensions
self.randomize = randomize
self.unitary = unitary
self.max_similarity = max_similarity
self.pointers = {}
self.keys = []
self.key_pairs = None
self.vectors = np.zeros((0, dimensions),
dtype=rc.get('precision', 'dtype'))
self.vector_pairs = None
self._include_pairs = None
self.include_pairs = include_pairs
self._identity = None
self.rng = rng
def __init__(self,
dt=0.001,
label=None,
decoder_cache=NoDecoderCache(),
dtype=rc.get('precision', 'dtype')):
self.dt = dt
self.label = label
self.decoder_cache = decoder_cache
self.dtype = dtype
# We want to keep track of the toplevel network
self.toplevel = None
# Builders can set a config object to affect sub-builders
self.config = None
# Resources used by the build process.
self.operators = []
self.params = {}
self.seeds = {}
self.probes = []
self.sig = collections.defaultdict(dict)
def include_pairs(self, value):
"""Adjusts whether key pairs are kept track of by the Vocabulary.
If this is turned on, we need to compute all the pairs of terms
already existing.
"""
if value == self._include_pairs:
return
self._include_pairs = value
if self._include_pairs:
self.key_pairs = []
self.vector_pairs = np.zeros((0, self.dimensions),
dtype=rc.get('precision', 'dtype'))
for i in range(1, len(self.keys)):
for k in self.keys[:i]:
key = self.keys[i]
self.key_pairs.append('%s*%s' % (k, key))
v = (self.pointers[k] * self.pointers[key]).v
self.vector_pairs = np.vstack((self.vector_pairs, v))
else:
self.key_pairs = None
self.vector_pairs = None
def shrink(self, limit=None):
"""Reduces the size of the cache to meet a limit.
Parameters
----------
limit : int, optional
Maximum size of the cache in bytes.
"""
if limit is None:
limit = rc.get('decoder_cache', 'size')
if is_string(limit):
limit = human2bytes(limit)
filelist = []
for filename in os.listdir(self.cache_dir):
key, ext = os.path.splitext(filename)
if ext == self._SOLVER_INFO_EXT:
continue
path = os.path.join(self.cache_dir, filename)
stat = os.stat(path)
filelist.append((stat.st_atime, key))
filelist.sort()
excess = self.get_size_in_bytes() - limit
for _, key in filelist:
if excess <= 0:
break
decoder_path = os.path.join(
self.cache_dir, key + self._DECODER_EXT)
solver_info_path = os.path.join(
self.cache_dir, key + self._SOLVER_INFO_EXT)
excess -= os.stat(decoder_path).st_size
os.remove(decoder_path)
if os.path.exists(solver_info_path):
excess -= os.stat(solver_info_path).st_size
os.remove(solver_info_path)
def build_connection(model, conn):
# Create random number generator
rng = np.random.RandomState(model.seeds[conn])
# Get input and output connections from pre and post
def get_prepost_signal(is_pre):
target = conn.pre_obj if is_pre else conn.post_obj
print('pre', conn.pre_obj, 'post', conn.post_obj)
key = 'out' if is_pre else 'in'
if target not in model.sig:
raise ValueError("Building %s: the '%s' object %s "
"is not in the model, or has a size of zero." %
(conn, 'pre' if is_pre else 'post', target))
if key not in model.sig[target]:
raise ValueError("Error building %s: the '%s' object %s "
"has a '%s' size of zero." %
(conn, 'pre' if is_pre else 'post', target, key))
return model.sig[target][key]
model.sig[conn]['in'] = get_prepost_signal(is_pre=True)
model.sig[conn]['out'] = get_prepost_signal(is_pre=False)
decoders = None
eval_points = None
solver_info = None
transform = full_transform(conn, slice_pre=False)
# Figure out the signal going across this connection
if (isinstance(conn.pre_obj, Node)
or (isinstance(conn.pre_obj, Ensemble)
and isinstance(conn.pre_obj.neuron_type, Direct))):
# Node or Decoded connection in directmode
if (conn.function is None and isinstance(conn.pre_slice, slice)
and (conn.pre_slice.step is None or conn.pre_slice.step == 1)):
signal = model.sig[conn]['in'][conn.pre_slice]
else:
sig_in, signal = build_pyfunc(
fn=(lambda x: x[conn.pre_slice]) if conn.function is None else
(lambda x: conn.function(x[conn.pre_slice])),
t_in=False,
n_in=model.sig[conn]['in'].size,
n_out=conn.size_mid,
label=str(conn),
model=model)
model.add_op(
DotInc(model.sig[conn]['in'],
model.sig['common'][1],
sig_in,
tag="%s input" % conn))
elif isinstance(conn.pre_obj, Ensemble):
# Normal decoded connection
eval_points, activities, targets = build_linear_system(
model, conn, rng)
# Use cached solver, if configured
solver = model.decoder_cache.wrap_solver(conn.solver)
if conn.solver.weights:
# account for transform
targets = np.dot(targets, transform.T)
transform = np.array(1, dtype=rc.get('precision', 'dtype'))
decoders, solver_info = solver(
activities,
targets,
rng=rng,
E=model.params[conn.post_obj].scaled_encoders.T)
model.sig[conn]['out'] = model.sig[conn.post_obj.neurons]['in']
signal_size = model.sig[conn]['out'].size
else:
decoders, solver_info = solver(activities, targets, rng=rng)
signal_size = conn.size_mid
# Add operator for decoders
decoders = decoders.T
model.sig[conn]['decoders'] = model.Signal(decoders,
name="%s.decoders" % conn)
signal = model.Signal(npext.castDecimal(np.zeros(signal_size)),
name=str(conn))
model.add_op(Reset(signal))
model.add_op(
DotInc(model.sig[conn]['decoders'],
model.sig[conn]['in'],
signal,
tag="%s decoding" % conn))
else:
# Direct connection
signal = model.sig[conn]['in']
# Add operator for filtering
if conn.synapse is not None:
signal = filtered_signal(model, conn, signal, conn.synapse)
if conn.modulatory:
# Make a new signal, effectively detaching from post
model.sig[conn]['out'] = model.Signal(npext.castDecimal(
np.zeros(model.sig[conn]['out'].size)),
name="%s.mod_output" % conn)
model.add_op(Reset(model.sig[conn]['out']))
# Add operator for transform
if isinstance(conn.post_obj, Neurons):
if not model.has_built(conn.post_obj.ensemble):
# Since it hasn't been built, it wasn't added to the Network,
# which is most likely because the Neurons weren't associated
# with an Ensemble.
raise RuntimeError("Connection '%s' refers to Neurons '%s' "
"that are not a part of any Ensemble." %
(conn, conn.post_obj))
if conn.post_slice != slice(None):
raise NotImplementedError(
"Post-slices on connections to neurons are not implemented")
gain = model.params[conn.post_obj.ensemble].gain[conn.post_slice]
if transform.ndim < 2:
transform = transform * gain
else:
transform *= gain[:, np.newaxis]
model.sig[conn]['transform'] = model.Signal(transform,
name="%s.transform" % conn)
print('abcd', model.sig[conn]['out'].value, signal.value)
if transform.ndim < 2:
print('line 174', model.sig[conn]['transform'].value)
model.add_op(
ElementwiseInc(model.sig[conn]['transform'],
signal,
model.sig[conn]['out'],
tag=str(conn)))
else:
model.add_op(
DotInc(model.sig[conn]['transform'],
signal,
model.sig[conn]['out'],
tag=str(conn)))
if conn.learning_rule_type:
# Forcing update of signal that is modified by learning rules.
# Learning rules themselves apply DotIncs.
if isinstance(conn.pre_obj, Neurons):
modified_signal = model.sig[conn]['transform']
elif isinstance(conn.pre_obj, Ensemble):
if conn.solver.weights:
# TODO: make less hacky.
# Have to do this because when a weight_solver
# is provided, then learning rules should operators on
# "decoders" which is really the weight matrix.
model.sig[conn]['transform'] = model.sig[conn]['decoders']
modified_signal = model.sig[conn]['transform']
else:
modified_signal = model.sig[conn]['decoders']
else:
raise TypeError(
"Can't apply learning rules to connections of "
"this type. pre type: %s, post type: %s" %
(type(conn.pre_obj).__name__, type(conn.post_obj).__name__))
model.add_op(PreserveValue(modified_signal))
model.params[conn] = BuiltConnection(decoders=decoders,
eval_points=eval_points,
transform=transform,
solver_info=solver_info)
def text(self, v, minimum_count=1, maximum_count=None, # noqa: C901
threshold=0.1, join=';', terms=None, normalize=False):
"""Return a human-readable text version of the provided vector.
This is meant to give a quick text version of a vector for display
purposes. To do this, compute the dot product between the vector
and all the terms in the vocabulary. The top few vectors are
chosen for inclusion in the text. It will try to only return
terms with a match above the threshold, but will always return
at least minimum_count and at most maximum_count terms. Terms
are sorted from most to least similar.
Parameters
----------
v : SemanticPointer or array
The vector to convert into text
minimum_count : int, optional
Always return at least this many terms in the text
maximum_count : int, optional
Never return more than this many terms in the text
threshold : float, optional
How small a similarity for a term to be ignored
join : string, optional
The text separator to use between terms
terms : list of strings, optional
Only consider terms in this list
normalize : bool, optional
Whether to normalize the vector before computing similarity
"""
if isinstance(v, pointer.SemanticPointer):
v = v.v
else:
v = np.array(v, dtype=rc.get('precision', 'dtype'))
if normalize:
nrm = np.linalg.norm(v)
if nrm > 0:
v /= nrm
m = np.dot(self.vectors, v)
matches = [(mm, self.keys[i]) for i, mm in enumerate(m)]
if self.include_pairs:
m2 = np.dot(self.vector_pairs, v)
matches2 = [(mm2, self.key_pairs[i]) for i, mm2 in enumerate(m2)]
matches.extend(matches2)
if terms is not None:
# TODO: handle the terms parameter more efficiently, so we don't
# compute a whole bunch of dot products and then throw them out
matches = [mm for mm in matches if mm[1] in terms]
matches.sort()
matches.reverse()
r = []
for m in matches:
if minimum_count is not None and len(r) < minimum_count:
r.append(m)
elif maximum_count is not None and len(r) == maximum_count:
break
elif threshold is None or m[0] > threshold:
r.append(m)
else:
break
return join.join(['%0.2f%s' % (sim, key) for (sim, key) in r])
def load_ipython_extension(ipython):
if has_ipynb_widgets() and rc.get('progress', 'progress_bar') == 'auto':
IPythonProgressWidget.load_frontend(ipython)
rc.set('progress', 'progress_bar', '.'.join(
(__name__, IPython2ProgressBar.__name__)))
def load_ipython_extension(ipython):
if has_ipynb_widgets() and rc.get('progress', 'progress_bar') == 'auto':
IPythonProgressWidget.load_frontend(ipython)
rc.set('progress', 'progress_bar', '.'.join((
__name__, IPython2ProgressBar.__name__)))
def build_ensemble(model, ens):
# Create random number generator
rng = np.random.RandomState(model.seeds[ens])
dtype = rc.get('precision', 'dtype')
eval_points = gen_eval_points(ens, ens.eval_points, rng=rng)
# Set up signal
model.sig[ens]['in'] = model.Signal(npext.castDecimal(
np.zeros(ens.dimensions)),
name="%s.signal" % ens)
model.add_op(Reset(model.sig[ens]['in']))
# Set up encoders
if isinstance(ens.neuron_type, Direct):
encoders = np.identity(ens.dimensions)
elif isinstance(ens.encoders, Distribution):
encoders = ens.encoders.sample(ens.n_neurons, ens.dimensions, rng=rng)
encoders = np.asarray(encoders, dtype=dtype)
else:
encoders = npext.array(ens.encoders, min_dims=2, dtype=dtype)
encoders = np.array([[dc.Decimal(p) for p in row] for row in encoders])
encoders /= npext.norm(encoders, axis=1, keepdims=True)
# Determine max_rates and intercepts
max_rates = sample(ens.max_rates, ens.n_neurons, rng=rng)
intercepts = sample(ens.intercepts, ens.n_neurons, rng=rng)
# Build the neurons
if ens.gain is not None and ens.bias is not None:
gain = sample(ens.gain, ens.n_neurons, rng=rng)
bias = sample(ens.bias, ens.n_neurons, rng=rng)
elif ens.gain is not None or ens.bias is not None:
# TODO: handle this instead of error
raise NotImplementedError("gain or bias set for %s, but not both. "
"Solving for one given the other is not "
"implemented yet." % ens)
else:
gain, bias = ens.neuron_type.gain_bias(max_rates, intercepts)
gain = np.array([dc.Decimal(p) for p in gain])
bias = np.array([dc.Decimal(p) for p in bias])
if isinstance(ens.neuron_type, Direct):
model.sig[ens.neurons]['in'] = model.Signal(npext.castDecimal(
np.zeros(ens.dimensions)),
name='%s.neuron_in' % ens)
model.sig[ens.neurons]['out'] = model.sig[ens.neurons]['in']
model.add_op(Reset(model.sig[ens.neurons]['in']))
else:
model.sig[ens.neurons]['in'] = model.Signal(npext.castDecimal(
np.zeros(ens.n_neurons)),
name="%s.neuron_in" % ens)
model.sig[ens.neurons]['out'] = model.Signal(
npext.castDecimal(np.zeros(ens.n_neurons)),
name="%s.neuron_out" % ens)
model.add_op(
Copy(src=model.Signal(bias, name="%s.bias" % ens),
dst=model.sig[ens.neurons]['in']))
# This adds the neuron's operator and sets other signals
model.build(ens.neuron_type, ens.neurons)
# Scale the encoders
if isinstance(ens.neuron_type, Direct):
scaled_encoders = encoders
else:
scaled_encoders = encoders * (gain /
dc.Decimal(ens.radius))[:, np.newaxis]
model.sig[ens]['encoders'] = model.Signal(scaled_encoders,
name="%s.scaled_encoders" % ens)
# Inject noise if specified
if ens.noise is not None:
model.add_op(SimNoise(model.sig[ens.neurons]['in'], ens.noise))
# Create output signal, using built Neurons
model.add_op(
DotInc(model.sig[ens]['encoders'],
model.sig[ens]['in'],
model.sig[ens.neurons]['in'],
tag="%s encoding" % ens))
# Output is neural output
model.sig[ens]['out'] = model.sig[ens.neurons]['out']
model.params[ens] = BuiltEnsemble(eval_points=eval_points,
encoders=encoders,
intercepts=intercepts,
max_rates=max_rates,
scaled_encoders=scaled_encoders,
gain=gain,
bias=bias)
def __init__(self,
network,
dt=0.001,
seed=None,
model=None,
dtype=rc.get('precision', 'dtype')):
"""Initialize the simulator with a network and (optionally) a model.
Most of the time, you will pass in a network and sometimes a dt::
sim1 = nengo.Simulator(my_network) # Uses default 0.001s dt
sim2 = nengo.Simulator(my_network, dt=0.01) # Uses 0.01s dt
For more advanced use cases, you can initialize the model yourself,
and also pass in a network that will be built into the same model
that you pass in::
sim = nengo.Simulator(my_network, model=my_model)
If you want full control over the build process, then you can build
your network into the model manually. If you do this, then you must
explicitly pass in ``None`` for the network::
sim = nengo.Simulator(None, model=my_model)
Parameters
----------
network : nengo.Network instance or None
A network object to the built and then simulated.
If a fully built ``model`` is passed in, then you can skip
building the network by passing in network=None.
dt : float
The length of a simulator timestep, in seconds.
seed : int
A seed for all stochastic operators used in this simulator.
Note that there are not stochastic operators implemented
currently, so this parameters does nothing.
model : nengo.builder.Model instance or None
A model object that contains build artifacts to be simulated.
Usually the simulator will build this model for you; however,
if you want to build the network manually, or to inject some
build artifacts in the Model before building the network,
then you can pass in a ``nengo.builder.Model`` instance.
"""
dt = float(dt) # make sure it's a float (for division purposes)
if model is None:
self.model = Model(dt=dt,
label="%s, dt=%f" % (network, dt),
decoder_cache=get_default_decoder_cache(),
dtype=dtype)
else:
self.model = model
#print(network)
if network is not None:
# Build the network into the model
self.model.build(network)
self.model.decoder_cache.shrink()
self.seed = np.random.randint(npext.maxint) if seed is None else seed
self.rng = np.random.RandomState(self.seed)
# -- map from Signal.base -> ndarray
self.signals = SignalDict(
__time__=np.asarray(npext.castDecimal(0), dtype=self.dtype))
#print(self.model)
#print(self.model.operators)
for op in self.model.operators:
op.init_signals(self.signals)
self.dg = operator_depencency_graph(self.model.operators)
self._step_order = [
node for node in toposort(self.dg) if hasattr(node, 'make_step')
]
self._steps = [
node.make_step(self.signals, dt, self.rng)
for node in self._step_order
]
# Add built states to the probe dictionary
self._probe_outputs = self.model.params
# Provide a nicer interface to probe outputs
self.data = ProbeDict(self._probe_outputs)
self.reset()