def act(activation, idx):
activation = activation.clip(0, 1)
l_idx = b.arange(len(idx), step=2)
r_idx = l_idx + 1
a_avg = (activation[l_idx] + activation[r_idx]) / 2
l_idx = b.arange(len(a_avg), step=2)
r_idx = l_idx + 1
theta = (a_avg[l_idx] - a_avg[r_idx]) * theta_max
e.step(theta)
e.render()
return activation
def inp_rates(idx):
la, ra = e.test_inp()
la = la.repeat(2)
ra = ra.repeat(2)
l_idx = b.arange(len(idx), step=2)
r_idx = l_idx + 1
r = np.zeros(len(idx))
r[l_idx] = la
r[r_idx] = ra
return r * b.Hz
def visualise_connectivity(S):
Ns = len(S.source)
Nt = len(S.target)
b.figure(figsize=(10, 4))
b.subplot(121)
b.plot(b.zeros(Ns), b.arange(Ns), 'ok', ms=10)
b.plot(b.ones(Nt), b.arange(Nt), 'ok', ms=10)
for i, j in zip(S.i, S.j):
b.plot([0, 1], [i, j], '-k')
b.xticks([0, 1], ['Source', 'Target'])
b.ylabel('Neuron index')
b.xlim(-0.1, 1.1)
b.ylim(-1, max(Ns, Nt))
b.subplot(122)
b.plot(S.i, S.j, 'ok')
b.xlim(-1, Ns)
b.ylim(-1, Nt)
b.xlabel('Source neuron index')
b.ylabel('Target neuron index')
def autocor(PSTH,N=None,T=20*br.ms,bin=None):
if bin is None:
bin = br.defaultclock.dt
p = int(T/ bin)
SAC = br.zeros(p)
if N is None:
SAC[0] = br.mean(PSTH * PSTH)
else: # correction to exclude self-coincidences
PSTHnoself = br.clip(PSTH - 1. / (bin * N), 0*br.kHz, br.Inf*br.kHz)
SAC[0] = br.mean(PSTH * PSTHnoself) * N / (N - 1.)
SAC[1:] = [br.mean(PSTH[:-i] * PSTH[i:]) for i in range(1,p)]
SAC = br.hstack((SAC[::-1], SAC[1:]))
out = (br.arange(len(SAC)) - len(SAC) / 2) * bin
return out, SAC
def test_arange_linspace():
# For dimensionless values, the unit-safe functions should give the same results
assert_equal(brian2.arange(5), np.arange(5))
assert_equal(brian2.arange(1, 5), np.arange(1, 5))
assert_equal(brian2.arange(10, step=2), np.arange(10, step=2))
assert_equal(brian2.arange(0, 5, 0.5), np.arange(0, 5, 0.5))
assert_equal(brian2.linspace(0, 1), np.linspace(0, 1))
assert_equal(brian2.linspace(0, 1, 10), np.linspace(0, 1, 10))
# Make sure units are checked
with pytest.raises(DimensionMismatchError):
brian2.arange(1 * mV, 5)
with pytest.raises(DimensionMismatchError):
brian2.arange(1 * mV, 5 * mV)
with pytest.raises(DimensionMismatchError):
brian2.arange(1, 5 * mV)
with pytest.raises(DimensionMismatchError):
brian2.arange(1 * mV, 5 * ms)
with pytest.raises(DimensionMismatchError):
brian2.arange(1 * mV, 5 * mV, step=1 * ms)
with pytest.raises(DimensionMismatchError):
brian2.arange(1 * ms, 5 * mV)
# Check correct functioning with units
assert_quantity(brian2.arange(5 * mV, step=1 * mV),
float(mV) * np.arange(5, step=1), mV)
assert_quantity(brian2.arange(1 * mV, 5 * mV, 1 * mV),
float(mV) * np.arange(1, 5, 1), mV)
assert_quantity(brian2.linspace(1 * mV, 2 * mV),
float(mV) * np.linspace(1, 2), mV)
# Check errors for arange with incorrect numbers of arguments/duplicate arguments
with pytest.raises(TypeError):
brian2.arange()
with pytest.raises(TypeError):
brian2.arange(0, 5, 1, 0)
with pytest.raises(TypeError):
brian2.arange(0, stop=1)
with pytest.raises(TypeError):
brian2.arange(0, 5, stop=1)
with pytest.raises(TypeError):
brian2.arange(0, 5, start=1)
with pytest.raises(TypeError):
brian2.arange(0, 5, 1, start=1)
with pytest.raises(TypeError):
brian2.arange(0, 5, 1, stop=2)
with pytest.raises(TypeError):
brian2.arange(0, 5, 1, step=2)
def test_arange_linspace():
# For dimensionless values, the unit-safe functions should give the same results
assert_equal(brian2.arange(5), np.arange(5))
assert_equal(brian2.arange(1, 5), np.arange(1, 5))
assert_equal(brian2.arange(10, step=2), np.arange(10, step=2))
assert_equal(brian2.arange(0, 5, 0.5), np.arange(0, 5, 0.5))
assert_equal(brian2.linspace(0, 1), np.linspace(0, 1))
assert_equal(brian2.linspace(0, 1, 10), np.linspace(0, 1, 10))
# Make sure units are checked
assert_raises(DimensionMismatchError, lambda: brian2.arange(1*mV, 5))
assert_raises(DimensionMismatchError, lambda: brian2.arange(1*mV, 5*mV))
assert_raises(DimensionMismatchError, lambda: brian2.arange(1, 5*mV))
assert_raises(DimensionMismatchError, lambda: brian2.arange(1*mV, 5*ms))
assert_raises(DimensionMismatchError, lambda: brian2.arange(1*mV, 5*mV, step=1*ms))
assert_raises(DimensionMismatchError, lambda: brian2.arange(1*ms, 5*mV))
# Check correct functioning with units
assert_quantity(brian2.arange(5*mV, step=1*mV), float(mV)*np.arange(5, step=1), mV)
assert_quantity(brian2.arange(1*mV, 5*mV, 1*mV), float(mV)*np.arange(1, 5, 1), mV)
assert_quantity(brian2.linspace(1*mV, 2*mV), float(mV)*np.linspace(1, 2), mV)
# Check errors for arange with incorrect numbers of arguments/duplicate arguments
assert_raises(TypeError, lambda: brian2.arange())
assert_raises(TypeError, lambda: brian2.arange(0, 5, 1, 0))
assert_raises(TypeError, lambda: brian2.arange(0, stop=1))
assert_raises(TypeError, lambda: brian2.arange(0, 5, stop=1))
assert_raises(TypeError, lambda: brian2.arange(0, 5, start=1))
assert_raises(TypeError, lambda: brian2.arange(0, 5, 1, start=1))
assert_raises(TypeError, lambda: brian2.arange(0, 5, 1, stop=2))
assert_raises(TypeError, lambda: brian2.arange(0, 5, 1, step=2))
