def test_recording():
""" tests if the shape of recording is correct """
import numpy as np
from rockpool import timeseries as ts
from rockpool.layers import FFIAFNest
# - Generic parameters
weights = np.array([[-0.1, 0.02, 0.4], [0.2, -0.3, -0.15]])
bias = 0.01
tau_mem = [0.02, 0.05, 0.1]
# - Layer generation
fl0 = FFIAFNest(
weights=weights,
dt=0.0001,
bias=bias,
tau_mem=tau_mem,
refractory=0.001,
record=True,
)
# - Input signal
tsInCont = ts.TSContinuous(times=np.arange(15) * 0.01, samples=np.ones((15, 2)))
# - Compare states before and after
vStateBefore = np.copy(fl0.state)
dFl0 = fl0.evolve(tsInCont, duration=0.1)
assert np.shape(fl0.recorded_states.samples) == (1000, 3)
fl0.terminate()
def test_ffiaf():
""" Test FFIAFBrian """
from brian2 import second
from rockpool import timeseries as ts
from rockpool.layers import FFIAFBrian
# - Generic parameters
weights = np.array([[-0.1, 0.02, 0.4], [0.2, -0.3, -0.15]])
bias = 0.01
tau_mem = [0.02, 0.05, 0.1]
# - Layer generation
fl0 = FFIAFBrian(
weights=weights,
dt=0.01,
bias=bias,
tau_mem=tau_mem,
noise_std=0.1,
refractory=0.001 * second,
)
# - Input signal
tsInCont = ts.TSContinuous(times=np.arange(15) * 0.01,
samples=np.ones((15, 2)))
# - Compare states and time before and after
vStateBefore = np.copy(fl0.state)
fl0.evolve(tsInCont, duration=0.1)
assert fl0.t == 0.1
assert (vStateBefore != fl0.state).any()
fl0.reset_all()
assert fl0.t == 0
assert (vStateBefore == fl0.state).all()
def test_chargeAndSpikeSingleNeuron():
"""
single neuron test
charge neuron exactly to threshold without crossing using the bias
add small input to make it spike
"""
from rockpool import timeseries as ts
from rockpool.layers import FFIAFNest
weights = [[1.0]]
bias = [0.375]
tau_mem = [0.01]
vReset = -0.07
vRest = -0.07
vTh = -0.055
fC = 0.25
dt = 0.001
refractory = 0.002
fl0 = FFIAFNest(
weights=weights,
dt=dt,
bias=bias,
tau_mem=tau_mem,
v_reset=vReset,
v_rest=vRest,
v_thresh=vTh,
capacity=fC,
refractory=refractory,
record=True,
name="test",
)
# - Input signal
vTime = np.arange(0, 1, dt)
vVal = np.zeros([len(vTime), 1])
vVal[500] = 0.001
tsInCont = ts.TSContinuous(vTime, vVal)
dFl0 = fl0.evolve(tsInCont, duration=1.0)
assert not dFl0.isempty()
fl0.terminate()
def test_FFNestLayer():
""" Test FFIAFNest"""
from rockpool import timeseries as ts
from rockpool.layers import FFIAFNest
# - Generic parameters
weights = np.array([[-0.1, 0.02, 0.4], [0.2, -0.3, -0.15]])
bias = 0.01
tau_mem = [0.02, 0.05, 0.1]
# - Layer generation
fl0 = FFIAFNest(
weights=weights,
dt=0.001,
bias=bias,
tau_mem=tau_mem,
refractory=0.001,
record=True,
)
# - Input signal
tsInCont = ts.TSContinuous(times=np.arange(15) * 0.01, samples=np.ones((15, 2)))
# - Compare states before and after
vStateBefore = np.copy(fl0.state)
dFl0 = fl0.evolve(tsInCont, duration=0.1)
dFl0 = fl0.evolve(tsInCont, duration=0.1)
assert fl0.t == 0.2
assert (vStateBefore != fl0.state).any()
fl0.reset_all()
assert fl0.t == 0
assert (vStateBefore == fl0.state).all()
fl0.terminate()
def test_reciaf():
""" Test RecIAFBrian """
from brian2 import second
from rockpool import timeseries as ts
from rockpool.layers import RecIAFBrian
# - Generic parameters
np.random.seed(1)
weights = 2 * np.random.rand(3, 3) - 1
bias = 2 * np.random.rand(3) - 1
tau_mem, tau_syn_r = np.clip(np.random.rand(2, 3), 0.01, None)
# - Layer generation
rl0 = RecIAFBrian(
weights=weights,
bias=bias,
tau_mem=tau_mem,
tau_syn_r=tau_syn_r,
dt=0.01,
noise_std=0.1,
refractory=0.001 * second,
)
# - Input signal
tsInCont = ts.TSContinuous(times=np.arange(15) * 0.01,
samples=np.ones((15, 3)))
# - Compare states and time before and after
vStateBefore = np.copy(rl0.state)
rl0.evolve(tsInCont, duration=0.1)
assert rl0.t == 0.1
assert (vStateBefore != rl0.state).any()
rl0.reset_all()
assert rl0.t == 0
assert (vStateBefore == rl0.state).all()
def test_delays():
""" test delays """
from rockpool import timeseries as ts
from rockpool.layers import FFIAFNest, RecIAFSpkInNest
from rockpool.networks import network as nw
import numpy as np
weights = [[0.001, 0.0, 0.0, 0.0]]
bias = 0.375
tau_mem = 0.01
vReset = -0.07
vRest = -0.07
vTh = -0.055
fC = 0.25
dt = 0.001
refractory = 0.002
fl0 = FFIAFNest(
weights=weights,
dt=dt,
bias=bias,
tau_mem=tau_mem,
v_reset=vReset,
v_rest=vRest,
v_thresh=vTh,
capacity=fC,
refractory=refractory,
record=True,
name="FF",
)
weights_in = [
[0.015, 0.015, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
]
weights_rec = [
[0.0, 0.0, 0.015, 0.015],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0014],
]
delay_in = [
[0.001, 0.011, 0.001, 0.001],
[0.001, 0.001, 0.001, 0.001],
[0.001, 0.001, 0.001, 0.001],
[0.001, 0.001, 0.001, 0.001],
]
delay_rec = [
[0.001, 0.001, 0.001, 0.011],
[0.001, 0.001, 0.001, 0.001],
[0.001, 0.001, 0.001, 0.001],
[0.001, 0.001, 0.001, 0.001],
]
vfBiasRec = 0.0
vtTauNRec = [0.2, 0.2, 0.2, 0.2]
tau_syn_exc_rec = [0.2, 0.2, 0.2, 0.2]
tau_syn_inh_rec = tau_syn_exc_rec
# - Layer generation
fl1 = RecIAFSpkInNest(
weights_in=weights_in,
weights_rec=weights_rec,
delay_in=delay_in,
delay_rec=delay_rec,
dt=0.001,
bias=vfBiasRec,
tau_mem=vtTauNRec,
capacity=0.1,
tau_syn_exc=tau_syn_exc_rec,
tau_syn_inh=tau_syn_inh_rec,
refractory=0.001,
record=True,
name="Rec",
)
net = nw.Network(fl0, fl1)
# - Input signal
vTime = np.arange(0, 1, dt)
vVal = np.zeros([len(vTime), 1])
vVal[500] = 0.01
tsInCont = ts.TSContinuous(vTime, vVal)
dAct = net.evolve(tsInCont, duration=1.0)
times = dAct["Rec"].times
eps = 0.000001
assert times[1] - times[0] - 0.01 < eps
assert times[3] - times[2] - 0.01 < eps
fl0.terminate()
fl1.terminate()
def test_timeconstants():
""" test delays """
from rockpool import timeseries as ts
from rockpool.layers import FFIAFNest, RecIAFSpkInNest
from rockpool.networks import network as nw
import numpy as np
weights = [[0.001]]
bias = 0.375
tau_mem = 0.01
vReset = -0.07
vRest = -0.07
vTh = -0.055
fC = 0.25
dt = 0.001
refractory = 0.002
fl0 = FFIAFNest(
weights=weights,
dt=dt,
bias=bias,
tau_mem=tau_mem,
v_reset=vReset,
v_rest=vRest,
v_thresh=vTh,
capacity=fC,
refractory=refractory,
record=True,
name="FF",
)
weights_in = [[0.001, -0.001]]
weights_rec = [[0, 0], [0, 0]]
vfBiasRec = 0.0
vtTauNRec = [0.2, 0.2]
tau_syn_exc_rec = [0.1, 0.1]
tau_syn_inh_rec = [0.01, 0.01]
# - Layer generation
fl1 = RecIAFSpkInNest(
weights_in=weights_in,
weights_rec=weights_rec,
dt=0.001,
bias=vfBiasRec,
tau_mem=vtTauNRec,
tau_syn_exc=tau_syn_exc_rec,
tau_syn_inh=tau_syn_inh_rec,
refractory=0.001,
v_reset=vReset,
v_rest=vRest,
v_thresh=vTh,
record=True,
name="Rec",
)
net = nw.Network(fl0, fl1)
# - Input signal
vTime = np.arange(0, 1, dt)
vVal = np.zeros([len(vTime), 1])
vVal[500] = 0.01
tsInCont = ts.TSContinuous(vTime, vVal)
dAct = net.evolve(tsInCont, duration=1.0)
exc_input = np.abs(fl1.recorded_states.samples[:, 0] - vRest)
inh_input = np.abs(fl1.recorded_states.samples[:, 1] - vRest)
# excitatory input peak should be later than inhibitory as the synaptic TC is longer
assert np.argmax(exc_input) > np.argmax(inh_input)
fl0.terminate()
fl1.terminate()
def test_DefaultParams():
""" Test RecIAFNest"""
from rockpool.layers import RecIAFSpkInNest, FFIAFNest
from rockpool import timeseries as ts
from rockpool.networks import network as nw
import numpy as np
# - Generic parameters
weights = np.ones([1, 2]) * 0.01
weights_in = np.array([[-0.1, 0.02, 0.4], [0.2, -0.3, -0.15]])
weights_rec = np.random.rand(3, 3) * 0.01
bias = 0.0
dt = 0.0001
tau_mem = 0.02
tau_syn_exc = 0.05
tau_syn_inh = 0.05
v_thresh = -0.055
v_reset = -0.065
v_rest = -0.065
capacity = tau_mem
refractory = 0.001
fl0 = FFIAFNest(
weights=weights,
dt=dt,
bias=bias,
tau_mem=tau_mem,
v_reset=v_reset,
v_rest=v_rest,
v_thresh=v_thresh,
capacity=capacity,
refractory=refractory,
record=True,
name="FF",
)
fl1 = RecIAFSpkInNest(
weights_in=weights_in,
weights_rec=weights_rec,
dt=dt,
bias=bias,
tau_mem=tau_mem,
tau_syn_exc=tau_syn_exc,
tau_syn_inh=tau_syn_inh,
v_thresh=v_thresh,
v_reset=v_reset,
v_rest=v_rest,
capacity=capacity,
refractory=refractory,
record=True,
name="Rec",
)
net0 = nw.Network(fl0, fl1)
fl2 = FFIAFNest(weights=weights, record=True, name="FF")
fl3 = RecIAFSpkInNest(
weights_in=weights_in, weights_rec=weights_rec, record=True, name="Rec"
)
net1 = nw.Network(fl2, fl3)
# - Input signal
vTime = np.arange(0, 1, dt)
vVal = np.zeros([len(vTime), 1])
vVal[2000:7000] = 0.01
tsInCont = ts.TSContinuous(vTime, vVal)
eps = 1e-6
assert (np.abs(fl0.state - fl2.state) < eps).all()
assert (np.abs(fl1.state - fl3.state) < eps).all()
# - Compare states before and after
dAct0 = net0.evolve(tsInCont, duration=1.0)
dAct1 = net1.evolve(tsInCont, duration=1.0)
assert (np.abs(fl0.state - fl2.state) < eps).all()
assert (np.abs(fl1.state - fl3.state) < eps).all()
fl0.terminate()
fl1.terminate()
def test_FFToRecLayerRepeat():
""" Test FFToRecNest"""
from rockpool import timeseries as ts
from rockpool.layers import FFIAFNest, RecIAFSpkInNest
from rockpool.networks import network as nw
import numpy as np
weights = [[0.0, 0.001, 0.0]]
bias = 0.375
tau_mem = 0.01
vReset = -0.07
vRest = -0.07
vTh = -0.055
fC = 0.25
dt = 0.001
refractory = 0.002
fl0 = FFIAFNest(
weights=weights,
dt=dt,
bias=bias,
tau_mem=tau_mem,
v_reset=vReset,
v_rest=vRest,
v_thresh=vTh,
capacity=fC,
refractory=refractory,
record=True,
name="FF",
)
weights_in = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.6], [0.0, 0.0, 0.0]]
weights_rec = np.random.rand(3, 3) * 0.001
vfBiasRec = 0.0
vtTauNRec = [0.02, 0.05, 0.1]
tau_syn_exc_rec = [0.2, 0.01, 0.01]
tau_syn_inh_rec = tau_syn_exc_rec
# - Layer generation
fl1 = RecIAFSpkInNest(
weights_in=weights_in,
weights_rec=weights_rec,
dt=0.001,
bias=vfBiasRec,
tau_mem=vtTauNRec,
tau_syn_exc=tau_syn_exc_rec,
tau_syn_inh=tau_syn_inh_rec,
refractory=0.001,
record=True,
name="Rec",
)
net = nw.Network(fl0, fl1)
# - Input signal
vTime = np.arange(0, 1, dt)
vVal = np.zeros([len(vTime), 1])
vVal[500] = 0.01
tsInCont = ts.TSContinuous(vTime, vVal)
# - Compare states before and after
vStateBefore = np.copy(fl1.state)
for _ in range(10):
dAct = net.evolve(tsInCont, duration=1.0 / 10)
assert fl0.t == 1.0
assert fl1.t == 1.0
assert (vStateBefore != fl1.state).any()
net.reset_all()
assert fl0.t == 0
assert fl1.t == 0
assert (vStateBefore == fl1.state).all()
fl0.terminate()
def test_save_load():
""" Test RecIAFNest"""
from rockpool.layers import RecIAFSpkInNest, FFIAFNest, FFExpSynTorch
from rockpool import timeseries as ts
from rockpool.networks import network as nw
from rockpool.networks import Network as nws
import numpy as np
import pylab as plt
# - Generic parameters
weights = np.ones([1, 1]) * 0.01
weights_in = [[0.1, 0, 0]]
weights_rec = [[0, 0.1, 0], [0, 0, 0.1], [0.0, 0, 0]]
mfWOut = [[1], [1], [1]]
bias = 0.0
dt = 0.001
tau_mem = 0.02
tau_syn = 0.05
v_thresh = -0.055
v_reset = -0.065
v_rest = -0.065
capacity = 100.0
refractory = 0.001
np.random.seed(0)
fl0 = FFIAFNest(
weights=weights,
dt=dt,
bias=bias,
tau_mem=tau_mem,
v_reset=v_reset,
v_rest=v_rest,
v_thresh=v_thresh,
capacity=capacity,
refractory=refractory,
num_cores=1,
record=True,
name="FF",
)
fl1 = RecIAFSpkInNest(
weights_in=weights_in,
weights_rec=weights_rec,
dt=dt,
bias=bias,
tau_mem=tau_mem,
tau_syn_exc=tau_syn,
tau_syn_inh=tau_syn,
v_thresh=v_thresh,
v_reset=v_reset,
v_rest=v_rest,
capacity=capacity,
refractory=refractory,
num_cores=1,
record=True,
name="Rec",
)
net0 = nw.Network(fl0, fl1)
net0.save("test_nw.json")
net1 = nws.load("test_nw.json")
fl2 = net1.FF
fl3 = net1.Rec
np.random.seed(0)
# - Input signal
vTime = np.arange(0, 1, dt)
vVal = np.zeros([len(vTime), 1])
vVal[200:201] = 0.25
tsInCont = ts.TSContinuous(vTime, vVal)
epsilon = 0.0000001
# - Compare states before and after
np.random.seed(0)
dAct0 = net0.evolve(tsInCont, duration=1.0)
np.random.seed(0)
dAct1 = net1.evolve(tsInCont, duration=1.0)
assert (
np.abs(fl0.recorded_states.samples - fl2.recorded_states.samples) < epsilon
).all()
assert (
np.abs(fl1.recorded_states.samples - fl3.recorded_states.samples) < epsilon
).all()