def _configure_cosimulation(self):
"""This method will
- set the synchronization time and number of steps,
- check the time and the variable of interest are correct
- create and initialize CosimHistory,
- configure the cosimulation monitor
- zero connectivity weights to/from nodes modelled exclusively by the other cosimulator
"""
# the synchronization time should be at least equal to integrator.dt:
self.synchronization_time = numpy.maximum(self.synchronization_time,
self.integrator.dt)
# Compute the number of synchronization time steps:
self.synchronization_n_step = iround(self.synchronization_time /
self.integrator.dt)
# Check if the synchronization time is smaller than the delay of the connectivity
# the condition is probably not correct. It will change with usage.
if self.synchronization_n_step > numpy.min(
self.connectivity.idelays[numpy.nonzero(
self.connectivity.idelays)]):
raise ValueError('the synchronization time is too long')
# Check if the couplings variables are in the cosimulation variables of interest
for cvar in self.model.cvar:
if cvar not in self.voi:
raise ValueError(
'The variables of interest need to contain the coupling variables'
)
self.good_cosim_update_values_shape = (self.synchronization_n_step,
self.voi.shape[0],
self.proxy_inds.shape[0],
self.model.number_of_modes)
# We create a CosimHistory,
# for delayed state [synchronization_step+1, n_var, n_node, n_mode],
# including, initialization of the delayed state from the simulator's history,
# which must be already configured.
self.cosim_history = CosimHistory.from_simulator(self)
# Reconfigure the connectivity for regions modelled by the other cosimulator exclusively:
if self.exclusive:
self.connectivity.weights[self.proxy_inds][:,
self.proxy_inds] = 0.0
self.connectivity.configure()
# Configure the cosimulator monitor
self.number_of_cosim_monitors = len(self.cosim_monitors)
self._cosim_monitors_noncoupling_indices = list(
range(self.number_of_cosim_monitors))
self._cosim_monitors_coupling_indices = []
for iM, monitor in enumerate(self.cosim_monitors):
monitor.configure()
monitor.config_for_sim(self)
if isinstance(monitor, CosimMonitorFromCoupling):
self._cosim_monitors_noncoupling_indices.remove(iM)
self._cosim_monitors_coupling_indices.append(iM)
def config_for_sim(self, simulator):
"""Configure monitor for given simulator.
Grab the Simulator's integration step size. Set the monitor's variables
of interest based on the Monitor's 'variables_of_interest' attribute, if
it was specified, otherwise use the 'variables_of_interest' specified
for the Model. Calculate the number of integration steps (isteps)
between returns by the record method. This method is called from within
the the Simulator's configure() method.
"""
self.dt = simulator.integrator.dt
self.istep = iround(self.period / self.dt)
self.voi = self.variables_of_interest
if self.voi is None or self.voi.size == 0:
self.voi = numpy.r_[:len(simulator.model.variables_of_interest)]
def evaluate(self):
"""
Calculate the continuous wavelet transform of time_series.
"""
cls_attr_name = self.__class__.__name__ + ".time_series"
self.time_series.trait["data"].log_debug(owner=cls_attr_name)
ts_shape = self.time_series.data.shape
if self.frequencies.step == 0:
LOG.warning(
"Frequency step can't be 0! Trying default step, 2e-3.")
self.frequencies.step = 0.002
freqs = numpy.arange(self.frequencies.lo, self.frequencies.hi,
self.frequencies.step)
if (freqs.size == 0) or any(
freqs <= 0.0
): #TODO: Maybe should limit number of freqs... ~100 is probably a reasonable upper bound.
LOG.warning("Invalid frequency range! Falling back to default.")
util.log_debug_array(LOG, freqs, "freqs")
self.frequencies = basic.Range(lo=0.008, hi=0.060, step=0.002)
freqs = numpy.arange(self.frequencies.lo, self.frequencies.hi,
self.frequencies.step)
util.log_debug_array(LOG, freqs, "freqs")
sample_rate = self.time_series.sample_rate
# Duke: code below is as given by Andreas Spiegler, I've just wrapped
# some of the original argument names
nf = len(freqs)
temporal_step = max(
(1, iround(self.sample_period / self.time_series.sample_period)))
nt = int(numpy.ceil(ts_shape[0] / temporal_step))
if not isinstance(self.q_ratio, numpy.ndarray):
Q_ratio = self.q_ratio * numpy.ones((1, nf))
if numpy.nanmin(Q_ratio) < 5:
msg = "Q_ratio must be not lower than 5 !"
LOG.error(msg)
raise Exception(msg)
if numpy.nanmax(freqs) > sample_rate / 2.0:
msg = "Sampling rate is too low for the requested frequency range !"
LOG.error(msg)
raise Exception(msg)
#TODO: This isn't used, but min frequency seems like it should be important... Check with A.S.
# fmin = 3.0 * numpy.nanmin(Q_ratio) * sample_rate / numpy.pi / nt
sigma_f = freqs / Q_ratio
sigma_t = 1.0 / (2.0 * numpy.pi * sigma_f)
if self.normalisation == 'energy':
Amp = 1.0 / numpy.sqrt(
sample_rate * numpy.sqrt(numpy.pi) * sigma_t)
elif self.normalisation == 'gabor':
Amp = numpy.sqrt(2.0 / numpy.pi) / sample_rate / sigma_t
coef_shape = (nf, nt, ts_shape[1], ts_shape[2], ts_shape[3])
coef = numpy.zeros(coef_shape, dtype=numpy.complex128)
util.log_debug_array(LOG, coef, "coef")
scales = numpy.arange(0, nf, 1)
for i in scales:
f0 = freqs[i]
SDt = sigma_t[(0, i)]
A = Amp[(0, i)]
x = numpy.arange(0, 4.0 * SDt * sample_rate, 1) / sample_rate
wvlt = A * numpy.exp(-x**2 / (2.0 * SDt**2)) * numpy.exp(
2j * numpy.pi * f0 * x)
wvlt = numpy.hstack((numpy.conjugate(wvlt[-1:0:-1]), wvlt))
#util.log_debug_array(LOG, wvlt, "wvlt")
for var in range(ts_shape[1]):
for node in range(ts_shape[2]):
for mode in range(ts_shape[3]):
data = self.time_series.data[:, var, node, mode]
wt = signal.convolve(data, wvlt, 'same')
#util.log_debug_array(LOG, wt, "wt")
res = wt[0::temporal_step]
#NOTE: this is a horrible horrible quick hack (alas, a solution) to avoid broadcasting errors
# when using dt and sample periods which are not powers of 2.
coef[i, :, var, node, mode] = res if len(
res) == nt else res[:coef.shape[1]]
util.log_debug_array(LOG, coef, "coef")
spectra = spectral.WaveletCoefficients(
source=self.time_series,
mother=self.mother,
sample_period=self.sample_period,
frequencies=self.frequencies,
normalisation=self.normalisation,
q_ratio=self.q_ratio,
array_data=coef,
use_storage=False)
return spectra
def evaluate(self):
"""
Calculate the continuous wavelet transform of time_series.
"""
cls_attr_name = self.__class__.__name__+".time_series"
self.time_series.trait["data"].log_debug(owner = cls_attr_name)
ts_shape = self.time_series.data.shape
if self.frequencies.step == 0:
LOG.warning("Frequency step can't be 0! Trying default step, 2e-3.")
self.frequencies.step = 0.002
freqs = numpy.arange(self.frequencies.lo, self.frequencies.hi,
self.frequencies.step)
if (freqs.size == 0) or any(freqs <= 0.0): #TODO: Maybe should limit number of freqs... ~100 is probably a reasonable upper bound.
LOG.warning("Invalid frequency range! Falling back to default.")
util.log_debug_array(LOG, freqs, "freqs")
self.frequencies = basic.Range(lo = 0.008, hi = 0.060, step = 0.002)
freqs = numpy.arange(self.frequencies.lo, self.frequencies.hi,
self.frequencies.step)
util.log_debug_array(LOG, freqs, "freqs")
sample_rate = self.time_series.sample_rate
# Duke: code below is as given by Andreas Spiegler, I've just wrapped
# some of the original argument names
nf = len(freqs)
temporal_step = max((1, iround(self.sample_period / self.time_series.sample_period)))
nt = int(numpy.ceil(ts_shape[0] / temporal_step))
if not isinstance(self.q_ratio, numpy.ndarray):
Q_ratio = self.q_ratio * numpy.ones((1, nf))
if numpy.nanmin(Q_ratio) < 5:
msg = "Q_ratio must be not lower than 5 !"
LOG.error(msg)
raise Exception, msg
if numpy.nanmax(freqs) > sample_rate / 2.0:
msg = "Sampling rate is too low for the requested frequency range !"
LOG.error(msg)
raise Exception, msg
#TODO: This isn't used, but min frequency seems like it should be important... Check with A.S.
# fmin = 3.0 * numpy.nanmin(Q_ratio) * sample_rate / numpy.pi / nt
sigma_f = freqs / Q_ratio
sigma_t = 1.0 / (2.0 * numpy.pi * sigma_f)
if self.normalisation == 'energy':
Amp = 1.0 / numpy.sqrt(sample_rate * numpy.sqrt(numpy.pi) * sigma_t)
elif self.normalisation == 'gabor':
Amp = numpy.sqrt(2.0 / numpy.pi) / sample_rate / sigma_t
coef_shape = (nf, nt, ts_shape[1], ts_shape[2], ts_shape[3])
coef = numpy.zeros(coef_shape, dtype = numpy.complex128)
util.log_debug_array(LOG, coef, "coef")
scales = numpy.arange(0, nf, 1)
for i in scales:
f0 = freqs[i]
SDt = sigma_t[(0, i)]
A = Amp[(0, i)]
x = numpy.arange(0, 4.0 * SDt * sample_rate, 1) / sample_rate
wvlt = A * numpy.exp(-x**2 / (2.0 * SDt**2) ) * numpy.exp(2j * numpy.pi * f0 * x )
wvlt = numpy.hstack((numpy.conjugate(wvlt[-1:0:-1]), wvlt))
#util.log_debug_array(LOG, wvlt, "wvlt")
for var in range(ts_shape[1]):
for node in range(ts_shape[2]):
for mode in range(ts_shape[3]):
data = self.time_series.data[:, var, node, mode]
wt = signal.convolve(data, wvlt, 'same')
#util.log_debug_array(LOG, wt, "wt")
res = wt[0::temporal_step]
#NOTE: this is a horrible horrible quick hack (alas, a solution) to avoid broadcasting errors
# when using dt and sample periods which are not powers of 2.
coef[i, :, var, node, mode] = res if len(res) == nt else res[:coef.shape[1]]
util.log_debug_array(LOG, coef, "coef")
spectra = spectral.WaveletCoefficients(
source = self.time_series,
mother = self.mother,
sample_period = self.sample_period,
frequencies = self.frequencies,
normalisation = self.normalisation,
q_ratio = self.q_ratio,
array_data = coef,
use_storage = False)
return spectra