def test_range(self):
'''Test the ranged version of ``corr``.'''
# Half the range of both signals
for a1, a2 in _data_generator(self.maxLoops, self.maxN):
if a1.size <= 1 or a2.size <= 1:
continue
lag_start = - (a1.size // 2)
lag_end = a2.size // 2
c_np_centre = a1.size - 1
c_cpp = asignal.corr(a1, a2, mode='range', lag_start=lag_start,
lag_end=lag_end)
c_np = np.correlate(a1, a2, mode='full')[::-1]
np.testing.assert_allclose(
c_cpp,
c_np[c_np_centre + lag_start:c_np_centre + lag_end + 1],
rtol=RTOL)
def extractCCStat(self, mon, out):
'''
Extract x-correlation statistics from a monitor.
For each pair of monitored neurons
Parameters
----------
mon : list of dicts
A list of (NEST) state monitors' status dictionaries
out : dictionary
Output data dictionary.
'''
out['x-corr'] = dict(correlations=[])
xcOut = out['x-corr']['correlations']
for n_id1 in range(len(mon)):
sig1, dt1 = simei.sumAllVariables(mon, n_id1, self.stateList)
xcOut.append([])
xcOut2 = xcOut[n_id1]
for n_id2 in range(len(mon)):
cc_logger.debug('n_id1, n_id2 = {0}, {1}'.format(n_id1, n_id2))
sig2, dt2 = simei.sumAllVariables(mon, n_id2, self.stateList)
if (dt1 != dt2):
raise ValueError('dt1 != dt2')
dt = dt1
startIdx = 0
lag_start = -int(self.maxLag / dt)
lag_end = -lag_start
endIdx1 = len(sig1)
endIdx2 = len(sig2)
if (self.tStart is not None):
startIdx = int(self.tStart / dt)
if (self.tEnd is not None):
endIdx1 = int(self.tEnd / dt)
endIdx2 = endIdx1
sig1 = sig1[startIdx:endIdx1]
sig2 = sig2[startIdx:endIdx2]
C = corr(sig1,
sig2,
mode='range',
lag_start=lag_start,
lag_end=lag_end)
if (self.norm):
C /= np.max(C)
xcOut2.append(C)
out['x-corr']['lags'] = np.arange(lag_start, lag_end + 1) * dt
def extractCCStat(self, mon, out):
'''Extract x-correlation statistics from a monitor.
This is done for each pair of monitored neurons
Parameters
----------
mon : list of dicts
A list of (NEST) state monitors' status dictionaries
out : dictionary
Output data dictionary.
'''
out['x-corr'] = dict(
correlations=[])
xcOut = out['x-corr']['correlations']
for n_id1 in range(len(mon)):
sig1, dt1 = simei.sumAllVariables(mon, n_id1, self.stateList)
xcOut.append([])
xcOut2 = xcOut[n_id1]
for n_id2 in range(len(mon)):
cc_logger.debug('n_id1, n_id2 = {0}, {1}'.format(n_id1, n_id2))
sig2, dt2 = simei.sumAllVariables(mon, n_id2, self.stateList)
if (dt1 != dt2):
raise ValueError('dt1 != dt2')
dt = dt1
startIdx = 0
lag_start = -int(self.maxLag/dt)
lag_end = -lag_start
endIdx1 = len(sig1)
endIdx2 = len(sig2)
if (self.tStart is not None):
startIdx = int(self.tStart / dt)
if (self.tEnd is not None):
endIdx1 = int(self.tEnd / dt)
endIdx2 = endIdx1
sig1 = sig1[startIdx:endIdx1]
sig2 = sig2[startIdx:endIdx2]
C = corr(sig1, sig2, mode='range', lag_start=lag_start,
lag_end=lag_end)
if (self.norm):
C /= np.max(C)
xcOut2.append(C)
out['x-corr']['lags'] = np.arange(lag_start, lag_end+1) * dt
def test_range(self):
'''Test the ranged version of ``corr``.'''
# Half the range of both signals
for a1, a2 in _data_generator(self.maxLoops, self.maxN):
if a1.size <= 1 or a2.size <= 1:
continue
lag_start = -(a1.size // 2)
lag_end = a2.size // 2
c_np_centre = a1.size - 1
c_cpp = asignal.corr(a1,
a2,
mode='range',
lag_start=lag_start,
lag_end=lag_end)
c_np = np.correlate(a1, a2, mode='full')[::-1]
np.testing.assert_allclose(
c_cpp,
c_np[c_np_centre + lag_start:c_np_centre + lag_end + 1],
rtol=RTOL)
def test_zero_len(self):
'''Test that an exception is raised when inputs have zero length.'''
a1 = np.array([])
a2 = np.arange(10)
# corr(a1, a2)
lag_start = 0
lag_end = 0
for mode in ("onesided", "twosided", "range"):
with pytest.raises(TypeError):
asignal.corr(a1, a2, mode, lag_start, lag_end)
with pytest.raises(TypeError):
asignal.corr(a2, a1, mode, lag_start, lag_end)
with pytest.raises(TypeError):
asignal.corr(a1, a1, mode, lag_start, lag_end)
def test_zero_len(self):
'''Test that an exception is raised when inputs have zero length.'''
a1 = np.array([])
a2 = np.arange(10)
# corr(a1, a2)
lag_start = 0
lag_end = 0
for mode in ("onesided", "twosided", "range"):
with pytest.raises(TypeError):
asignal.corr(a1, a2, mode, lag_start, lag_end)
with pytest.raises(TypeError):
asignal.corr(a2, a1, mode, lag_start, lag_end)
with pytest.raises(TypeError):
asignal.corr(a1, a1, mode, lag_start, lag_end)
def test_non_double(self):
'''Test the corr function when dtype is not double.'''
a1 = np.array([1, 2, 3], dtype=int)
asignal.corr(a1, a1, mode='twosided')
def test_twosided(self):
'''Test the two-sided version of ``corr``.'''
for a1, a2 in _data_generator(self.maxLoops, self.maxN):
c_cpp = asignal.corr(a1, a2, mode='twosided')
c_np = np.correlate(a1, a2, mode='full')[::-1]
np.testing.assert_allclose(c_cpp, c_np, rtol=RTOL)
def test_non_double(self):
'''Test the corr function when dtype is not double.'''
a1 = np.array([1, 2, 3], dtype=int)
asignal.corr(a1, a1, mode='twosided')
def test_twosided(self):
'''Test the two-sided version of ``corr``.'''
for a1, a2 in _data_generator(self.maxLoops, self.maxN):
c_cpp = asignal.corr(a1, a2, mode='twosided')
c_np = np.correlate(a1, a2, mode='full')[::-1]
np.testing.assert_allclose(c_cpp, c_np, rtol=RTOL)