def compile(self, dt=1.0, batch_size=1, rng_seed=0, reuse_genn_model=False,
kernel_profiling=False, **genn_kwargs):
"""Compile this ML GeNN model into a GeNN model
Keyword args:
dt -- model integration time step (default: 1.0)
batch_size -- number of models to run concurrently (default: 1)
rng_seed -- GeNN RNG seed (default: 0, meaning seed will be randomised at runtime)
reuse_genn_model -- Reuse existing compiled GeNN model (default: False)
kernel_profiling -- Build model with kernel profiling code (default: False)
"""
# Define GeNN model
self.g_model = GeNNModel('float', self.name, **genn_kwargs)
self.g_model.dT = dt
self.g_model.batch_size = batch_size
self.g_model._model.set_seed(rng_seed)
self.g_model.timing_enabled = kernel_profiling
# Prepare each layer
for layer in self.layers:
layer.compile_neurons(self)
for layer in self.layers:
layer.compile_synapses(self)
# Build and load GeNN model
if os.name == 'nt':
model_exists = os.path.isfile("./runner_Release.dll")
else:
model_exists = os.path.isfile('./' + self.name + '_CODE/librunner.so')
if not reuse_genn_model or not model_exists:
self.g_model.build()
self.g_model.load()
else {
if ((dt > 2) && (dt <= 20)) {
newG = $(g) - 0.0117 * $(inSyn)*dt + 0.223 * $(inSyn);}
else {if ((dt > -200) && (dt <= 2)) {
newG = $(g) - 0.0025 * $(inSyn);}
else {newG = 0;}}
}
$(g) = fmin($(gMax), fmax($(gMin), newG));
""",
is_pre_spike_time_required=True,
is_post_spike_time_required=True)
# ----------------------------------------------------------------------------
# Build model
# ----------------------------------------------------------------------------
# Create GeNN model
model = GeNNModel("float", "simp_mnist")
model.dT = TIMESTEP
# Load weights
weights = []
while True:
filename = "weights_%u_%u.npy" % (len(weights), len(weights) + 1)
if path.exists(filename):
weights.append(np.load(filename))
else:
break
# weights[1] = np.random.uniform(G_MAX/2, G_MAX, (128,10))
# Initial values to initialise all neurons to
if_init = {"V": 0.0, "SpikeCount": 0}
import matplotlib.pyplot as plt
import numpy as np
from pygenn.genn_model import (GeNNModel, init_connectivity, create_cmlf_class,
create_custom_sparse_connect_init_snippet_class)
from pygenn.genn_wrapper import NO_DELAY
ring_model = create_custom_sparse_connect_init_snippet_class(
"ring",
row_build_code="""
$(addSynapse, ($(id_pre) + 1) % $(num_post));
$(endRow);
""",
calc_max_row_len_func=create_cmlf_class(
lambda num_pre, num_post, pars: 1)())
model = GeNNModel("float", "tennHHRing")
model.dT = 0.1
p = {
"gNa": 7.15, # Na conductance in [muS]
"ENa": 50.0, # Na equi potential [mV]
"gK": 1.43, # K conductance in [muS]
"EK": -95.0, # K equi potential [mV]
"gl": 0.02672, # leak conductance [muS]
"El": -63.563, # El: leak equi potential in mV,
"C": 0.143
} # membr. capacity density in nF
ini = {
"V": -60.0, # membrane potential
"m": 0.0529324, # prob. for Na channel activation
const scalar dt = $(t) - $(sT_post);
const scalar timing = exp(-dt / $(tau)) - $(rho);
const scalar newWeight = $(g) + ($(eta) * timing);
$(g) = fmin($(wMax), fmax($(wMin), newWeight));
""",
learn_post_code="""
const scalar dt = $(t) - $(sT_pre);
const scalar timing = exp(-dt / $(tau));
const scalar newWeight = $(g) + ($(eta) * timing);
$(g) = fmin($(wMax), fmax($(wMin), newWeight));
""",
is_pre_spike_time_required=True,
is_post_spike_time_required=True)
# Create model
model = GeNNModel("float", "mnist_mb")
model.dT = DT
model._model.set_seed(1337)
# Create neuron populations
lif_init = {"V": -60.0, "RefracTime": 0.0}
pn = model.add_neuron_population("pn", NUM_PN, "LIF", PN_PARAMS, lif_init)
kc = model.add_neuron_population("kc", NUM_KC, "LIF", KC_PARAMS, lif_init)
ggn = model.add_neuron_population("ggn", 1, "LIF", GGN_PARAMS, lif_init)
mbon = model.add_neuron_population("mbon", NUM_MBON, "LIF", MBON_PARAMS,
lif_init)
# Create current source to deliver input to network
pn_input = model.add_current_source("pn_input", cs_model, "pn", {},
{"magnitude": 0.0})
X, y = loadlocal_mnist(images_path=os.path.join(data_dir,
't10k-images-idx3-ubyte'),
labels_path=os.path.join(data_dir,
't10k-labels-idx1-ubyte'))
X = X[:20, :]
y = y[:20]
print("Loading testing images of size: " + str(X.shape))
print("Loading testing labels of size: " + str(y.shape))
# ----------------------------------------------------------------------------
# Build model
# ----------------------------------------------------------------------------
# Create GeNN model
model = GeNNModel("float", "tutorial_1")
model.dT = TIMESTEP
# Initial values for initialisation
if_init = {"V": 0.0, "SpikeCount": 0.0}
poisson_init = {"rate": 1.0}
NUM_INPUT = X.shape[1]
NUM_CLASSES = 10
OUTPUT_NEURON_NUM = 15
neurons_count = {
"inp": NUM_INPUT,
"inh": NUM_INPUT / 4,
"out": NUM_CLASSES * OUTPUT_NEURON_NUM
}
$(V) = 0.0;
$(SpikeCount)++;
""",
threshold_condition_code="$(V) >= $(Vthr)")
# Current source model which injects current with a magnitude specified by a state variable
cs_model = create_custom_current_source_class(
"cs_model",
var_name_types=[("magnitude", "scalar")],
injection_code="$(injectCurrent, $(magnitude));")
# ----------------------------------------------------------------------------
# Build model
# ----------------------------------------------------------------------------
# Create GeNN model
model = GeNNModel("float", "tutorial_2")
model.dT = TIMESTEP
# Load weights
weights = []
while True:
filename = "weights_%u_%u.npy" % (len(weights), len(weights) + 1)
if path.exists(filename):
weights.append(np.load(filename))
else:
break
# Initial values to initialise all neurons to
if_init = {"V": 0.0, "SpikeCount": 0}
# Create first neuron layer
if_init = {"V": 0.0}
fusi_params = {"tauC": 60.0, "a": 0.1, "b": 0.1, "thetaV": 0.8, "thetaLUp": 3.0,
"thetaLDown": 3.0, "thetaHUp": 13.0, "thetaHDown": 4.0, "thetaX": 0.5,
"alpha": 0.0035, "beta": 0.0035, "Xmax": 1.0, "Xmin": 0.0, "JC": 1.0,
"Jplus": 1.0, "Jminus": 0.0}
fusi_init = {"X": 0.0}
fusi_post_init = {"C": 2.0}
presyn_params = {"rate" : 50.0}
extra_poisson_params = {"rate" : 100.0}
poisson_init = {"timeStepToSpike" : 0.0}
model = GeNNModel("float", "fusi")
model.dT = TIMESTEP
presyn = model.add_neuron_population("presyn", 1, "PoissonNew", presyn_params, poisson_init)
postsyn = model.add_neuron_population("postsyn", 1, if_model, if_params, if_init)
extra_poisson = model.add_neuron_population("extra_poisson", 10, "PoissonNew",
extra_poisson_params, poisson_init)
pre2post = model.add_synapse_population(
"pre2post", "DENSE_INDIVIDUALG", NO_DELAY,
presyn, postsyn,
fusi_model, fusi_params, fusi_init, {}, fusi_post_init,
"DeltaCurr", {}, {})
import numpy as np
import matplotlib.pyplot as plt
from pygenn.genn_model import GeNNModel
model = GeNNModel("float", "pygenn")
model.dT = 0.1
# Initialise IzhikevichVariable parameters - arrays will be automatically uploaded
izk_init = {
"V": -65.0,
"U": -20.0,
"a": [0.02, 0.1, 0.02, 0.02],
"b": [0.2, 0.2, 0.2, 0.2],
"c": [-65.0, -65.0, -50.0, -55.0],
"d": [8.0, 2.0, 2.0, 4.0]
}
# Add neuron populations and current source to model
pop = model.add_neuron_population("Neurons", 4, "IzhikevichVariable", {},
izk_init)
model.add_current_source("CurrentSource", "DC", "Neurons", {"amp": 10.0}, {})
# Build and load model
model.build()
model.load()
# Create a numpy view to efficiently access the membrane voltage from Python
voltage_view = pop.vars["V"].view
}
""",
is_pre_spike_time_required=True,
is_post_spike_time_required=True)
# Current source model which injects current with a magnitude specified by a state variable
cs_model = create_custom_current_source_class(
"cs_model",
var_name_types=[("magnitude", "scalar")],
injection_code="$(injectCurrent, $(magnitude));")
# ----------------------------------------------------------------------------
# Build model
# ----------------------------------------------------------------------------
# Create GeNN model
model = GeNNModel("float", "tutorial_1")
model.dT = TIMESTEP
# Initial values for initialisation
if_init = {"V": 0.0, "SpikeCount": 0}
stdp_init = {
"g":
init_var("Uniform", {
"min": STDP_PARAMS["gmin"],
"max": STDP_PARAMS["gmax"]
})
}
neurons_count = [784, 128, NUM_CLASSES]
neuron_layers = []
poisson_model = create_custom_neuron_class(
"poisson_model",
var_name_types=[("rate", "scalar"), ("spikeCount", "scalar")],
sim_code="""
""",
reset_code="""
$(spikeCount) += 1;
""",
threshold_condition_code="$(gennrand_uniform) >= exp(-$(rate) * 0.001 * DT)"
)
TIMESTEP = 1.0
PRESENT_TIMESTEPS = 1000
model = GeNNModel("float", "tutorial_1")
model.dT = TIMESTEP
poisson_init = {"rate": 30.0, "spikeCount": 0.0}
p = model.add_neuron_population("p", 1, poisson_model, {}, poisson_init)
model.build()
model.load()
while model.timestep < PRESENT_TIMESTEPS:
model.step_time()
model.pull_var_from_device("p", "spikeCount")
spikeNum = p.vars["spikeCount"].view
params = list(parameters._asdict().values())
shared_list = shared.ShareableList(params)
run(["python3", __file__, shared_list.shm.name], stderr=STDOUT)
duration = shared_list[0]
shared_list.shm.close()
shared.shutdown()
return duration
if __name__ == "__main__":
# Assume we're running the genn benchmark and draw configs from the shared memory
parameter_list = ShareableList(sequence=None, name=sys.argv[1])
parameters = BenchmarkParameters(*parameter_list)
model = GeNNModel("float", "pygenn")
model.dT = parameters.dt
np.random.seed(0)
layers = []
for i in range(parameters.batch_size):
ones = np.ones(parameters.features)
# Note: weights, parameters and poisson rate are magic numbers that seem to generate reasonable spike activity
weights = np.random.rand(parameters.features,
parameters.features).flatten() * 8
model.add_neuron_population(
f"PoissonNew{i}",
parameters.features,
"PoissonNew",
{"rate": 100},
{"timeStepToSpike": 1},
pre_spike_code="""
const scalar dt = $(t) - $(sT_pre);
$(preTrace) = $(preTrace) * exp(-dt / $(tauPlus)) + 1.0;
""",
post_spike_code="""
const scalar dt = $(t) - $(sT_post);
$(postTrace) = $(postTrace) * exp(-dt / $(tauMinus)) + 1.0;
""",
is_pre_spike_time_required=True,
is_post_spike_time_required=True)
# ----------------------------------------------------------------------------
# Build model
# ----------------------------------------------------------------------------
# Create GeNN model
model = GeNNModel("float", "tutorial_1")
model.dT = TIMESTEP
post_syn_params = {"tau": 5.0}
stdp_init = {"g": init_var("Uniform", {"min": 0.0, "max": G_MAX})}
stdp_params = {
"tauPlus": 5.0,
"tauMinus": 20.0,
"aPlus": A_PLUS,
"aMinus": A_MINUS,
"wMin": 0.0,
"wMax": G_MAX
}
stdp_pre_init = {"preTrace": 0.0}
stdp_post_init = {"postTrace": 0.0}
class Model(object):
"""ML GeNN model class
This class enables the creation of deep learning SNN models, and
provides an interface for manipulating the underlying GeNN models.
"""
def __init__(self, inputs, outputs, name='mlg_model'):
"""Initialise an ML GeNN model
Args:
inputs -- list of network input layers
outputs -- list of network output layers
Keyword args:
name -- name of the network (default: 'mlg_model')
"""
self.set_network(inputs, outputs, name)
def set_network(self, inputs, outputs, name='mlg_model'):
"""Construct an ML GeNN Model from a graph of Layers
Args:
inputs -- list of network input layers
outputs -- list of network output layers
Keyword args:
name -- name of the network (default: 'mlg_model')
"""
self.name = name
self.layers = []
self.inputs = inputs
self.outputs = outputs
self.g_model = None
# Construct topologically sorted list of layers (Kahn's algorithm as described here: https://en.wikipedia.org/wiki/Topological_sorting)
new_layers = set(inputs)
seen_synapses = set()
while new_layers:
layer = new_layers.pop()
self.layers.append(layer)
# Explore downstream layers whose upstream synapses have all been seen
for downstream_synapse in layer.downstream_synapses:
seen_synapses.add(downstream_synapse)
if seen_synapses.issuperset(downstream_synapse.target().upstream_synapses):
new_layers.add(downstream_synapse.target())
# Check that output layers are reachable from input layers
if not all(output in self.layers for output in self.outputs):
raise ValueError('output layers unreachable from input layers')
def compile(self, dt=1.0, batch_size=1, rng_seed=0, reuse_genn_model=False,
kernel_profiling=False, **genn_kwargs):
"""Compile this ML GeNN model into a GeNN model
Keyword args:
dt -- model integration time step (default: 1.0)
batch_size -- number of models to run concurrently (default: 1)
rng_seed -- GeNN RNG seed (default: 0, meaning seed will be randomised at runtime)
reuse_genn_model -- Reuse existing compiled GeNN model (default: False)
kernel_profiling -- Build model with kernel profiling code (default: False)
"""
# Define GeNN model
self.g_model = GeNNModel('float', self.name, **genn_kwargs)
self.g_model.dT = dt
self.g_model.batch_size = batch_size
self.g_model._model.set_seed(rng_seed)
self.g_model.timing_enabled = kernel_profiling
# Prepare each layer
for layer in self.layers:
layer.compile_neurons(self)
for layer in self.layers:
layer.compile_synapses(self)
# Build and load GeNN model
if os.name == 'nt':
model_exists = os.path.isfile("./runner_Release.dll")
else:
model_exists = os.path.isfile('./' + self.name + '_CODE/librunner.so')
if not reuse_genn_model or not model_exists:
self.g_model.build()
self.g_model.load()
def set_input_batch(self, data_batch):
"""Set model input with a new batch of data
Args:
data_batch -- list of data batches for each input layer
"""
# Input sanity check
if len(data_batch) != len(self.inputs):
raise ValueError('data batch list length and input layer list length mismatch')
for i in range(len(self.inputs)):
self.inputs[i].set_input_batch(data_batch[i])
def step_time(self, iterations=1):
"""Iterate the GeNN model a given number of steps
Keyword args:
iterations -- number of iterations (default: 1)
"""
for i in range(iterations):
self.g_model.step_time()
def reset(self):
"""Reset the GeNN model"""
self.g_model.timestep = 0
self.g_model.t = 0.0
def evaluate_batched(self, data, time, save_samples=[]):
"""Evaluate the accuracy of a GeNN model
Args:
data -- an [[x_1, ..., x_m], [y_1, ..., y_n]] batch dataset
time -- sample presentation time (msec)
Keyword args:
save_samples -- list of sample indices to save spikes for (default: [])
Returns:
accuracy -- percentage of correctly classified results
spike_i -- list of spike indices for each sample index in save_samples
spike_t -- list of spike times for each sample index in save_samples
"""
n_complete = [0] * len(self.outputs)
n_correct = [0] * len(self.outputs)
accuracy = [0] * len(self.outputs)
save_samples = list(set(save_samples))
all_spikes = [[[] for i,_ in enumerate(self.layers)] for s in save_samples]
# Pipeline queues (for each output layer)
pipeline_depth = [l.pipeline_depth if hasattr(l, 'pipeline_depth') else 0 for l in self.outputs]
pipeline_y_queue = [deque(maxlen=depth + 1) for depth in pipeline_depth]
# Get batch iterator
data_remaining = True
data_iter = iter(data)
batch_x, batch_y = next(data_iter)
if not isinstance(batch_x, tuple):
batch_x = (batch_x, )
if not isinstance(batch_y, tuple):
batch_y = (batch_y, )
batch_i = 0
# Check number of x and y elements match number of inputs and outputs
if len(batch_x) != len(self.inputs):
raise ValueError('input layer and x count mismatch')
if len(batch_y) != len(self.outputs):
raise ValueError('output layer and y count mismatch')
# Process batches
progress = tqdm()
while data_remaining or any(len(q) > 0 for q in pipeline_y_queue):
if data_remaining:
batch_x = [np.asarray(d) for d in batch_x]
batch_size = batch_x[0].shape[0]
batch_start = batch_i * self.g_model.batch_size
batch_end = batch_start + batch_size
save_samples_in_batch = [i for i in save_samples if batch_start <= i < batch_end]
# Queue labels for pipelining
batch_y = [np.asarray(l) for l in batch_y]
for output_i in range(len(self.outputs)):
pipeline_y_queue[output_i].append(batch_y[output_i])
# Set new input
self.set_input_batch(batch_x)
# Reset timesteps etc
self.reset()
# Main simulation loop
while self.g_model.t < time:
# Step time
self.step_time()
# Save spikes
for i in save_samples_in_batch:
k = save_samples.index(i)
batch_i = i - batch_start
for l, layer in enumerate(self.layers):
nrn = layer.neurons.nrn
nrn.pull_current_spikes_from_device()
all_spikes[k][l].append(np.copy(
nrn.current_spikes[batch_i] if self.g_model.batch_size > 1
else nrn.current_spikes))
for output_i in range(len(self.outputs)):
# If input has passed through pipeline to this output
if batch_i >= pipeline_depth[output_i] and len(pipeline_y_queue[output_i]) > 0:
pipe_batch_i = batch_i - pipeline_depth[output_i]
pipe_batch_y = pipeline_y_queue[output_i].popleft()
pipe_batch_size = pipe_batch_y.shape[0]
pipe_batch_start = pipe_batch_i * self.g_model.batch_size
pipe_batch_end = pipe_batch_start + pipe_batch_size
# Compute accuracy
predictions = self.outputs[output_i].neurons.get_predictions(pipe_batch_size)
if pipe_batch_y.shape != predictions.shape:
pipe_batch_y = [np.argmax(i) for i in pipe_batch_y]
n_complete[output_i] += pipe_batch_size
n_correct[output_i] += np.sum(predictions == pipe_batch_y)
accuracy[output_i] = (n_correct[output_i] / pipe_batch_end) * 100
progress.set_postfix_str('accuracy: {:2.2f}'.format(np.mean(accuracy)))
if data_remaining:
progress.update(batch_size)
try:
batch_x, batch_y = next(data_iter)
if not isinstance(batch_x, tuple):
batch_x = (batch_x, )
if not isinstance(batch_y, tuple):
batch_y = (batch_y, )
except StopIteration:
data_remaining = False
batch_i += 1
progress.close()
assert all(len(q) == 0 for q in pipeline_y_queue)
# Create spike index and time lists
spike_i = [[None for i,_ in enumerate(self.layers)] for s in save_samples]
spike_t = [[None for i,_ in enumerate(self.layers)] for s in save_samples]
for i in range(len(save_samples)):
for j in range(len(self.layers)):
spikes = all_spikes[i][j]
spike_i[i][j] = np.concatenate(spikes)
spike_t[i][j] = np.concatenate([np.ones_like(s) * i * self.g_model.dT for i, s in enumerate(spikes)])
return accuracy, spike_i, spike_t
def evaluate(self, x, y, time, save_samples=[]):
"""Evaluate the accuracy of a GeNN model
Args:
x -- tuple of data for each input layer
y -- tuple of labels for each output layer
time -- sample presentation time (msec)
Keyword args:
save_samples -- list of sample indices to save spikes for (default: [])
Returns:
accuracy -- percentage of correctly classified results
spike_i -- list of spike indices for each sample index in save_samples
spike_t -- list of spike times for each sample index in save_samples
"""
# Wrap singular x or y in tuples
if not isinstance(x, tuple):
x = (x, )
if not isinstance(y, tuple):
y = (y, )
# Batch all x and y
batch_size = self.g_model.batch_size
x = tuple(np.split(xx, np.arange(batch_size, len(xx), batch_size)) for xx in x)
y = tuple(np.split(yy, np.arange(batch_size, len(yy), batch_size)) for yy in y)
data = zip(zip(*x), zip(*y))
# Pass to evaluate_batched
accuracy, spike_i, spike_t = self.evaluate_batched(data, time, save_samples)
return accuracy, spike_i, spike_t
def get_kernel_times(self):
"""Get total kernel run times"""
return {
'init_time': self.g_model.init_time,
'init_sparse_time': self.g_model.init_sparse_time,
'neuron_update_time': self.g_model.neuron_update_time,
'presynaptic_update_time': self.g_model.presynaptic_update_time,
'postsynaptic_update_time': self.g_model.postsynaptic_update_time,
'synapse_dynamics_time': self.g_model.synapse_dynamics_time,
}
def summary(self):
"""Print a summary of this model"""
# layers should already be topologically sorted
print('===== Summary of {} ====='.format(self.name))
for l in self.layers:
print('\nname: {}, shape: {}, type: {},'.format(
l.name, l.shape, l.__class__.__name__))
if isinstance(l, Layer):
print('incoming: {}'.format(
{s.source().name: s.__class__.__name__ for s in l.upstream_synapses}))
@staticmethod
def convert_tf_model(tf_model, converter=Simple(),
connectivity_type='procedural', **compile_kwargs):
"""Create a ML GeNN model from a TensorFlow model
Args:
tf_model -- TensorFlow model to be converted
Keyword args:
input_type -- type of input neurons (default: 'poisson')
connectivity_type -- type of synapses in GeNN (default: 'procedural')
compile_kwargs -- additional arguments to pass through to Model.compile
"""
tf_activation_layers = (
tf.keras.layers.Activation,
tf.keras.layers.ReLU,
tf.keras.layers.Softmax)
tf_ignored_layers = (
tf.keras.layers.Flatten,
tf.keras.layers.Dropout)
# only traverse nodes belonging to this model
tf_model_nodes = set()
for n in tf_model._nodes_by_depth.values():
tf_model_nodes.update(n)
# get inbound and outbound layers
tf_in_layers_all = {}
tf_out_layers_all = {}
for tf_layer in tf_model.layers:
# find inbound layers
tf_in_layers = []
for n in tf_layer.inbound_nodes:
if n not in tf_model_nodes:
continue
if isinstance(n.inbound_layers, list):
tf_in_layers += n.inbound_layers
else:
tf_in_layers.append(n.inbound_layers)
tf_in_layers_all[tf_layer] = tf_in_layers
# find outbound layers
tf_out_layers = [n.outbound_layer for n in tf_layer.outbound_nodes
if n in tf_model_nodes]
tf_out_layers_all[tf_layer] = tf_out_layers
# Perform any pre-conversion tasks
pre_convert_output = converter.pre_convert(tf_model)
# configure model build process
class LayerConfig(object):
def __init__(self, name, shape, is_input=False, is_output=False,
has_activation=False, neurons=None):
self.name = name
self.shape = shape
self.is_input = is_input
self.is_output = is_output
self.has_activation = has_activation
self.neurons = neurons
self.synapses = []
InSynConfig = namedtuple('InSynconfig', ['type', 'params', 'source', 'weights'])
config_steps = []
configs_lookups = {}
new_tf_layers = set()
traversed_tf_layers = set()
# get and check input layers
if isinstance(tf_model, tf.keras.models.Sequential):
# In TF Sequential models, the InputLayer is not stored in the model object,
# so we must traverse back through nodes to find the input layer's outputs.
tf_in_layers = tf_in_layers_all[tf_model.layers[0]]
assert(len(tf_in_layers) == 1)
tf_out_layers = [n.outbound_layer for n in tf_in_layers[0].outbound_nodes
if n in tf_model_nodes]
tf_in_layers_all[tf_in_layers[0]] = []
tf_out_layers_all[tf_in_layers[0]] = tf_out_layers
else:
# TF Functional models store all their InputLayers, so no trickery needed.
tf_in_layers = [tf_model.get_layer(name) for name in tf_model.input_names]
for tf_in_layer in tf_in_layers:
assert(len(tf_in_layer.output_shape) == 1)
# input layers cannot be output layers
if len(tf_out_layers_all[tf_in_layer]) == 0:
raise NotImplementedError(
'input layers as output layers not supported')
# === Input Layers ===
for tf_layer in tf_in_layers:
new_tf_layers.add(tf_layer)
print('configuring Input layer <{}>'.format(tf_layer.name))
# configure layer
config = LayerConfig(
tf_layer.name, tf_layer.output_shape[0][1:],
is_input=True, has_activation=True,
neurons=converter.create_input_neurons(pre_convert_output))
config_steps.append(config)
configs_lookups[tf_layer] = [config]
# while there are still layers to traverse
while new_tf_layers:
new_tf_layer = new_tf_layers.pop()
new_tf_out_layers = tf_out_layers_all[new_tf_layer]
traversed_tf_layers.add(new_tf_layer)
# get next TF layer to configure
for tf_layer in new_tf_out_layers:
tf_in_layers = tf_in_layers_all[tf_layer]
tf_out_layers = tf_out_layers_all[tf_layer]
# skip if we still need to configure inbound layers
if not traversed_tf_layers.issuperset(tf_in_layers):
continue
new_tf_layers.add(tf_layer)
print('configuring {} layer <{}>'.format(
tf_layer.__class__.__name__, tf_layer.name))
# === Add Layers ===
if isinstance(tf_layer, tf.keras.layers.Add):
config = []
# concatenate incoming layer configs
for tf_in_layer in tf_in_layers:
config += configs_lookups[tf_in_layer]
# do not allow output Add layers
if len(tf_out_layers) == 0:
raise NotImplementedError(
'output Add layers not supported')
configs_lookups[tf_layer] = config
# === Dense Layers ===
elif isinstance(tf_layer, tf.keras.layers.Dense):
assert(len(tf_in_layers) == 1)
tf_in_layer = tf_in_layers[0]
in_configs = configs_lookups[tf_in_layer]
# configure layer
config = LayerConfig(
tf_layer.name, tf_layer.output_shape[1:],
is_output=len(tf_out_layers) == 0,
has_activation=not tf_layer.activation is tf.keras.activations.linear,
neurons=converter.create_neurons(tf_layer, pre_convert_output))
converter.validate_tf_layer(tf_layer, config)
# configure synapses
for in_config in in_configs:
if in_config.has_activation:
# configure Dense synapses
config.synapses.append(InSynConfig(
type=DenseSynapses,
params={'units': tf_layer.units},
source=in_config,
weights=tf_layer.get_weights()[0]))
else:
for i in range(len(in_config.synapses)):
if in_config.synapses[i].type is AvePool2DSynapses:
# configure AvePool2D -> Dense synapses
config.synapses.append(InSynConfig(
type=AvePool2DDenseSynapses,
params=in_config.synapses[i].params.copy(),
source=in_config.synapses[i].source,
weights=tf_layer.get_weights()[0]))
config.synapses[-1].params.update({
'units': tf_layer.units})
else:
# fail if incoming (weighted) layer does not have activation
if not in_config.has_activation:
raise NotImplementedError(
'weighted layers without activation not supported')
if config.has_activation or config.is_output:
config_steps.append(config)
configs_lookups[tf_layer] = [config]
# === Conv2D Layers ===
elif isinstance(tf_layer, tf.keras.layers.Conv2D):
assert(len(tf_in_layers) == 1)
tf_in_layer = tf_in_layers[0]
in_configs = configs_lookups[tf_in_layer]
# configure layer
config = LayerConfig(
tf_layer.name, tf_layer.output_shape[1:],
is_output=len(tf_out_layers) == 0,
has_activation=not tf_layer.activation is tf.keras.activations.linear,
neurons=converter.create_neurons(tf_layer, pre_convert_output))
converter.validate_tf_layer(tf_layer, config)
# configure synapses
for in_config in in_configs:
if in_config.has_activation:
# configure Conv2D synapses
config.synapses.append(InSynConfig(
type=Conv2DSynapses,
params={
'filters': tf_layer.filters,
'conv_size': tf_layer.kernel_size,
'conv_strides': tf_layer.strides,
'conv_padding': tf_layer.padding,
'connectivity_type': connectivity_type},
source=in_config,
weights=tf_layer.get_weights()[0]))
else:
for i in range(len(in_config.synapses)):
if in_config.synapses[i].type is AvePool2DSynapses:
# configure AvePool2D -> Conv2D synapses
config.synapses.append(InSynConfig(
type=AvePool2DConv2DSynapses,
params=in_config.synapses[i].params.copy(),
source=in_config.synapses[i].source,
weights=tf_layer.get_weights()[0]))
config.synapses[-1].params.update({
'filters': tf_layer.filters,
'conv_size': tf_layer.kernel_size,
'conv_strides': tf_layer.strides,
'conv_padding': tf_layer.padding,
'connectivity_type': connectivity_type})
else:
# fail if incoming (weighted) layer does not have activation
if not in_config.has_activation:
raise NotImplementedError(
'weighted layers without activation not supported')
if config.has_activation or config.is_output:
config_steps.append(config)
configs_lookups[tf_layer] = [config]
# === [Global]AveragePooling2D Layers ===
elif isinstance(tf_layer, (
tf.keras.layers.AveragePooling2D,
tf.keras.layers.GlobalAveragePooling2D)):
assert(len(tf_in_layers) == 1)
tf_in_layer = tf_in_layers[0]
in_configs = configs_lookups[tf_in_layer]
# configure layer
config = LayerConfig(
tf_layer.name, tf_layer.output_shape[1:],
is_output=len(tf_out_layers) == 0)
converter.validate_tf_layer(tf_layer, config)
# do not allow output pooling layers
if config.is_output:
raise NotImplementedError(
'output pooling layers not supported')
# configure synapses
for in_config in in_configs:
if in_config.has_activation:
# configure AvePool2D synapses
if isinstance(tf_layer, tf.keras.layers.AveragePooling2D):
config.synapses.append(InSynConfig(
type=AvePool2DSynapses,
params={
'pool_size': tf_layer.pool_size,
'pool_strides': tf_layer.strides,
'connectivity_type': connectivity_type},
source=in_config,
weights=None))
elif isinstance(tf_layer, tf.keras.layers.GlobalAveragePooling2D):
config.synapses.append(InSynConfig(
type=AvePool2DSynapses,
params={
'pool_size': tf_layer.input_shape[1:3],
'pool_strides': None,
'connectivity_type': connectivity_type},
source=in_config,
weights=None))
else:
# fail if incoming (weighted) layer does not have activation
if not in_config.has_activation:
raise NotImplementedError(
'weighted layers without activation not supported')
configs_lookups[tf_layer] = [config]
# === Activation Layers ===
elif isinstance(tf_layer, tf_activation_layers):
assert(len(tf_in_layers) == 1)
tf_in_layer = tf_in_layers[0]
in_configs = configs_lookups[tf_in_layer]
# configure layer
config = LayerConfig(
tf_layer.name, tf_layer.output_shape[1:],
is_output=len(tf_out_layers) == 0,
has_activation=True,
neurons=converter.create_neurons(tf_layer, pre_convert_output))
converter.validate_tf_layer(tf_layer, config)
# configure synapses
for in_config in in_configs:
if in_config.has_activation:
# configure Identity synapses
config.synapses.append(InSynConfig(
type=IdentitySynapses,
params={'connectivity_type': connectivity_type},
source=in_config,
weights=None))
else:
for i in range(len(in_config.synapses)):
# copy incoming synapses
config.synapses.append(InSynConfig(
type=in_config.synapses[i].type,
params=in_config.synapses[i].params,
source=in_config.synapses[i].source,
weights=in_config.synapses[i].weights))
config_steps.append(config)
configs_lookups[tf_layer] = [config]
# === Ignored Layers ===
elif isinstance(tf_layer, tf_ignored_layers):
assert(len(tf_in_layers) == 1)
tf_in_layer = tf_in_layers[0]
in_configs = configs_lookups[tf_in_layer]
configs_lookups[tf_layer] = in_configs
# === Unsupported Layers ===
else:
raise NotImplementedError('{} layers not supported'.format(
tf_layer.__class__.__name__))
# execute model build process
mlg_layer_lookup = {}
mlg_model_inputs = []
mlg_model_outputs = []
# for each build step
for config in config_steps:
if config.is_input:
# build layer
mlg_layer = InputLayer(config.name, config.shape, config.neurons)
mlg_model_inputs.append(mlg_layer)
else:
# build layer
mlg_layer = Layer(config.name, config.neurons)
# build synapses
sources = [mlg_layer_lookup[s.source] for s in config.synapses]
synapses = [s.type(**s.params) for s in config.synapses]
mlg_layer.connect(sources, synapses)
weights = [s.weights for s in config.synapses]
mlg_layer.set_weights(weights)
if config.is_output:
mlg_model_outputs.append(mlg_layer)
mlg_layer_lookup[config] = mlg_layer
# create model
mlg_model = Model(mlg_model_inputs, mlg_model_outputs, name=tf_model.name)
# Perform any pre-compilation tasks
converter.pre_compile(mlg_model)
# Compile model
mlg_model.compile(**compile_kwargs)
# Perform any post-compilation tasks
converter.post_compile(mlg_model)
return mlg_model
from pygenn.genn_model import GeNNModel
import matplotlib.pyplot as plt
import numpy as np
model = GeNNModel("float", "tennHH")
model.dT = 0.1
p = {"gNa": 7.15, # Na conductance in [muS]
"ENa": 50.0, # Na equi potential [mV]
"gK": 1.43, # K conductance in [muS]
"EK": -95.0, # K equi potential [mV]
"gl": 0.02672, # leak conductance [muS]
"El": -63.563, # El: leak equi potential in mV,
"C": 0.143} # membr. capacity density in nF
ini = {"V": -60.0, # membrane potential
"m": 0.0529324, # prob. for Na channel activation
"h": 0.3176767, # prob. for not Na channel blocking
"n": 0.5961207} # prob. for K channel activation
pop1 = model.add_neuron_population("Pop1", 10, "TraubMiles", p, ini)
model.build()
model.load()
v = np.empty((10000, 10))
v_view = pop1.vars["V"].view
while model.t < 1000.0:
model.step_time()
pop1.pull_var_from_device("V")
$(V) = 0.0;
$(SpikeCount)++;
""",
threshold_condition_code="$(V) >= $(Vthr)")
# Current source model which injects current with a magnitude specified by a state variable
cs_model = create_custom_current_source_class(
"cs_model",
var_name_types=[("magnitude", "scalar")],
injection_code="$(injectCurrent, $(magnitude));")
# ----------------------------------------------------------------------------
# Build model
# ----------------------------------------------------------------------------
# Create GeNN model
model = GeNNModel("float", "tutorial_2")
model.dT = TIMESTEP
print("loading weights.")
load_weights_path = "/home/manvi/Documents/pygenn_ml_tutorial"
# Load weights
weights = []
while True:
filename = "vogelsw1_%u_%u.npy" % (len(weights), len(weights) + 1)
filename = path.join(load_weights_path, filename)
if path.exists(filename):
print("Loading weights from: " + str(filename))
weights.append(np.load(filename))
else: