def plot_wave_coherence(wave1,
wave2,
sample_times,
min_freq=1,
max_freq=256,
sig=False,
ax=None,
title="Wavelet Coherence",
plot_arrows=True,
plot_coi=True,
plot_period=False,
resolution=12,
all_arrows=True,
quiv_x=5,
quiv_y=24,
block=None):
"""
Calculate wavelet coherence between wave1 and wave2 using pycwt.
TODO fix min_freq, max_freq and add parameters to control arrows.
TODO also test out sig on a large dataset
Parameters
----------
wave1 : np.ndarray
The values of the first waveform.
wave2 : np.ndarray
The values of the second waveform.
sample_times : np.ndarray
The times at which waveform samples occur.
min_freq : float
Supposed to be minimum frequency, but not quite working.
max_freq : float
Supposed to be max frequency, but not quite working.
sig : bool, default False
Optional Should significance of waveform coherence be calculated.
ax : plt.axe, default None
Optional ax object to plot into.
title : str, default "Wavelet Coherence"
Optional title for the graph
plot_arrows : bool, default True
Should phase arrows be plotted.
plot_coi : bool, default True
Should the cone of influence be plotted
plot_period : bool
Should the y-axis be in period or in frequency (Hz)
resolution : int
How many wavelets should be at each level of the graph
all_arrows : bool
Should phase arrows be plotted uniformly or only at high coherence
quiv_x : float
sets quiver window in time domain in seconds
quiv_y : float
sets number of quivers evenly distributed across freq limits
block : [int, int]
Plots only points between ints.
Returns
-------
tuple : (fig, result)
Where fig is a matplotlib Figure
and result is a tuple consisting of WCT, aWCT, coi, freq, sig
WCT - 2D numpy array with coherence values
aWCT - 2D numpy array with same shape as aWCT indicating phase angles
coi - 1D numpy array with a frequency value for each time
freq - 1D numpy array with the frequencies wavelets were calculated at
sig - 2D numpy array indicating where data is significant by monte carlo
"""
t = np.asarray(sample_times)
dt = np.mean(np.diff(t))
# Set up the scales to match min max input frequencies
dj = resolution
s0 = min_freq * dt
if s0 < 2 * dt:
s0 = 2 * dt
max_J = max_freq * dt
J = dj * np.int(np.round(np.log2(max_J / np.abs(s0))))
# freqs = np.geomspace(max_freq, min_freq, num=50)
freqs = None
# Do the actual calculation
print("Calculating coherence...")
start_time = time.time()
WCT, aWCT, coi, freq, sig = wavelet.wct(
wave1,
wave2,
dt, # Fixed params
dj=(1.0 / dj),
s0=s0,
J=J,
sig=sig,
normalize=True,
freqs=freqs,
)
print("Time Taken: %s s" % (time.time() - start_time))
if np.max(WCT) > 1 or np.min(WCT) < 0:
print('WCT was out of range: min {},max {}'.format(
np.min(WCT), np.max(WCT)))
WCT = np.clip(WCT, 0, 1)
# Convert frequency to period if necessary
if plot_period:
y_vals = np.log2(1 / freq)
if not plot_period:
y_vals = np.log2(freq)
# Calculates the phase between both time series. The phase arrows in the
# cross wavelet power spectrum rotate clockwise with 'north' origin.
# The relative phase relationship convention is the same as adopted
# by Torrence and Webster (1999), where in phase signals point
# upwards (N), anti-phase signals point downwards (S). If X leads Y,
# arrows point to the right (E) and if X lags Y, arrow points to the
# left (W).
angle = 0.5 * np.pi - aWCT
u, v = np.cos(angle), np.sin(angle)
if ax is None:
fig, ax = plt.subplots()
else:
fig = None
# Set the x and y axes of the plot
extent_corr = [t.min(), t.max(), 0, max(y_vals)]
# Fill the plot with the magnitude squared coherence values
# That is, MSC = abs(Pxy) ^ 2 / (Pxx * Pyy)
# TODO I think this might be the wrong way to plot this
# It assumes that the samples are linearly spaced
im = NonUniformImage(ax, interpolation='bilinear', extent=extent_corr)
if plot_period:
im.set_data(t, y_vals, WCT)
else:
im.set_data(t, y_vals[::-1], WCT[::-1, :])
ax.images.append(im)
# pcm = ax.pcolormesh(WCT)
# Plot the cone of influence - Periods greater than
# those are subject to edge effects.
if plot_coi:
# Performed by plotting a polygon
x_positions = np.zeros(shape=(len(t), ))
x_positions = t
y_positions = np.zeros(shape=(len(t), ))
if plot_period:
y_positions = np.log2(coi)
else:
y_positions = np.log2(1 / coi)
ax.plot(x_positions, y_positions, 'w--', linewidth=2, c="w")
# Plot the significance level contour plot
if sig:
ax.contour(t,
y_vals,
sig, [-99, 1],
colors='k',
linewidths=2,
extent=extent_corr)
# Add limits, titles, etc.
ax.set_ylim(min(y_vals), max(y_vals))
if block:
ax.set_xlim(t[block[0]], t[int(block[1] * 1 / dt)])
else:
ax.set_xlim(t.min(), t.max())
# TODO split graph into smaller time chunks
# Test for smaller timescale
# quiv_x = 1
# Plot the arrows on the plot
if plot_arrows:
# TODO currently this is a uniform grid, could be changed to WCT > 0.5
x_res = int(1 / dt * quiv_x)
y_res = int(np.floor(len(y_vals) / quiv_y))
if all_arrows:
ax.quiver(
t[::x_res],
y_vals[::y_res],
u[::y_res, ::x_res],
v[::y_res, ::x_res],
units='height',
angles='uv',
pivot='mid',
linewidth=1,
edgecolor='k',
scale=30,
headwidth=10,
headlength=10,
headaxislength=5,
minshaft=2,
)
else:
# t[::x_res], y_vals[::y_res],
# u[::y_res, ::x_res], v[::y_res, ::x_res]
high_points = np.nonzero(WCT[::y_res, ::x_res] > 0.5)
sub_t = t[::x_res][high_points[1]]
sub_y = y_vals[::y_res][high_points[0]]
sub_u = u[::y_res, ::x_res][np.array(high_points[0]),
np.array(high_points[1])]
sub_v = v[::y_res, ::x_res][high_points[0], high_points[1]]
res = 1
ax.quiver(
sub_t[::res],
sub_y[::res],
sub_u[::res],
sub_v[::res],
units='height',
angles='uv',
pivot='mid',
linewidth=1,
edgecolor='k',
scale=30,
headwidth=10,
headlength=10,
headaxislength=5,
minshaft=2,
)
# splits = [0, 60, 120 ...]
# Add the colorbar to the figure
if fig is not None:
fig.colorbar(im)
else:
plt.colorbar(im, ax=ax, use_gridspec=True)
if plot_period:
y_ticks = np.linspace(min(y_vals), max(y_vals), 8)
# TODO improve ticks
y_ticks = [
np.log2(x)
for x in [0.004, 0.008, 0.016, 0.032, 0.064, 0.125, 0.25, 0.5, 1]
]
y_labels = [str(x) for x in (np.round(np.exp2(y_ticks), 3))]
ax.set_ylabel("Period")
else:
y_ticks = np.linspace(min(y_vals), max(y_vals), 8)
# TODO improve ticks
# y_ticks = [np.log2(x) for x in [256, 128, 64, 32, 16, 8, 4, 2, 1]]
y_ticks = [np.log2(x) for x in [64, 32, 16, 8, 4, 2, 1]]
y_labels = [str(x) for x in (np.round(np.exp2(y_ticks), 3))]
ax.set_ylabel("Frequency (Hz)")
plt.yticks(y_ticks, y_labels)
ax.set_title(title)
ax.set_xlabel("Time (s)")
return (fig, [WCT, aWCT, coi, freq, sig])
def test_wct(lfp1, lfp2, sig=True): # python CWT
import pycwt as wavelet
dt = 1 / lfp1.get_sampling_rate()
WCT, aWCT, coi, freq, sig = wavelet.wct(
lfp1.get_samples(), lfp2.get_samples(), dt, sig=sig)
_, ax = plt.subplots()
t = lfp1.get_timestamp()
ax.contourf(t, freq, WCT, 6, extend='both', cmap="viridis")
extent = [t.min(), t.max(), 0, max(freq)]
N = lfp1.get_total_samples()
sig95 = np.ones([1, N]) * sig[:, None]
sig95 = WCT / sig95
ax.contour(t, freq, sig95, [-99, 1], colors='k', linewidths=2,
extent=extent)
ax.fill(np.concatenate([t, t[-1:] + dt, t[-1:] + dt,
t[:1] - dt, t[:1] - dt]),
np.concatenate([coi, [1e-9], freq[-1:],
freq[-1:], [1e-9]]),
'k', alpha=0.3, hatch='x')
ax.set_title('Wavelet Power Spectrum')
ax.set_ylabel('Freq (Hz)')
ax.set_xlabel('Time (s)')
plt.show()
exit(-1)
def cross_wavelet(signal_1, signal_2, period, mother='morlet'):
signal_1 = (signal_1 - signal_1.mean()) / signal_1.std() # Normalizing
signal_2 = (signal_2 - signal_2.mean()) / signal_2.std() # Normalizing
W12, cross_coi, freq, signif = wavelet.xwt(signal_1,
signal_2,
period,
dj=1 / 100,
s0=-1,
J=-1,
significance_level=0.95,
wavelet=mother,
normalize=True)
cross_power = np.abs(W12)**2
cross_sig = np.ones([1, signal_1.size]) * signif[:, None]
cross_sig = cross_power / cross_sig
cross_period = 1 / freq
WCT, aWCT, corr_coi, freq, sig = wavelet.wct(signal_1,
signal_2,
period,
dj=1 / 100,
s0=-1,
J=-1,
sig=False,
significance_level=0.95,
wavelet=mother,
normalize=True)
cor_sig = np.ones([1, signal_1.size]) * sig[:, None]
cor_sig = np.abs(WCT) / cor_sig
cor_period = 1 / freq
t1 = np.linspace(0, period * signal_1.size, signal_1.size)
idx = find_closest(cor_period, corr_coi.max())
t1 /= 60
cross_period /= 60
cor_period /= 60
cross_coi /= 60
corr_coi /= 60
return W12, WCT, aWCT, cor_period, corr_coi, cor_sig, idx, t1
wavelet='morlet',
normalize=True)
cross_power = np.abs(W12)**2
cross_sig = np.ones([1, n]) * signif[:, None]
cross_sig = cross_power / cross_sig # Power is significant where ratio > 1
cross_period = 1/freq
'''Calculate the wavelet coherence (WTC).
The WTC finds regions in time frequency space where the
two time seris co-vary, but do not necessarily have high power.'''
WCT, aWCT, corr_coi, freq, sig = wavelet.wct(s1, s2, dt,
dj=1/12, s0=-1, J=-1,
significance_level=0.8646,
wavelet='morlet', normalize=True,
cache=True)
cor_sig = np.ones([1, n]) * sig[:, None]
cor_sig = np.abs(WCT) / cor_sig # Power is significant where ratio > 1
cor_period = 1 / freq
''' Calculates the phase between both time series.
The phase arrows in the cross wavelet power spectrum rotate clockwise
with 'north' origin.
The relative phase relationship convention is the same as adopted
by Torrence and Webster (1999), where in phase signals point
upwards (N), anti-phase signals point downwards (S). If X leads Y,
################################
# basic parameters
fs = 1 / dt
dj = 1 / 12
s0 = -1
J = -1
sig = False
wvn = 'morlet'
# wavelet cross spectrm
WCT, aWCT, coi, freq, sig = pycwt.wct(ndata,
data,
1 / fs,
dj=dj,
s0=s0,
J=J,
sig=sig,
wavelet=wvn,
normalize=True)
# unwrap the phase
phase = np.unwrap(
aWCT,
axis=-1) # axis=0, upwrap along time; axis=-1, unwrap along frequency
delta_t = phase / (2 * np.pi * freq[:, None]
) # normalize phase by (2*pi*frequency)
plot_wxt = True
if plot_wxt:
plt.imshow(delta_t,
cmap='jet',
def wxs_allfreq(cur,
ref,
allfreq,
para,
dj=1 / 12,
s0=-1,
J=-1,
sig=False,
wvn='morlet',
unwrapflag=False):
"""
Compute dt or dv/v in time and frequency domain from wavelet cross spectrum (wxs).
for all frequecies in an interest range
Parameters
--------------
:type cur: :class:`~numpy.ndarray`
:param cur: 1d array. Cross-correlation measurements.
:type ref: :class:`~numpy.ndarray`
:param ref: 1d array. The reference trace.
:type t: :class:`~numpy.ndarray`
:param t: 1d array. Cross-correlation measurements.
:param twindow: 1d array. [earlist time, latest time] time window limit
:param fwindow: 1d array. [lowest frequncy, highest frequency] frequency window limit
:params, dj, s0, J, sig, wvn, refer to function 'wavelet.wct'
:unwrapflag: True - unwrap phase delays. Default is False
:nwindow: the times of current period/frequency, which will be time window if windowflag is False
:windowflag: if True, the given window 'twindow' will be used,
otherwise, the current period*nwindow will be used as time window
Originally written by Tim Clements (1 March, 2019)
Modified by Congcong Yuan (30 June, 2019) based on (Mao et al. 2019).
"""
# common variables
twin = para['twin']
freq = para['freq']
dt = para['dt']
tmin = np.min(twin)
tmax = np.max(twin)
fmin = np.min(freq)
fmax = np.max(freq)
tvec = np.arange(tmin, tmax, dt)
# perform cross coherent analysis, modified from function 'wavelet.cwt'
WCT, aWCT, coi, freq, sig = pycwt.wct(cur,
ref,
dt,
dj=dj,
s0=s0,
J=J,
sig=sig,
wavelet=wvn,
normalize=True)
if unwrapflag:
phase = np.unwrap(
aWCT, axis=-1
) # axis=0, upwrap along time; axis=-1, unwrap along frequency
else:
phase = aWCT
# convert phase delay to time delay
delta_t = phase / (2 * np.pi * freq[:, None]
) # normalize phase by (2*pi*frequency)
# zero out data outside frequency band
if (fmax > np.max(freq)) | (fmax <= fmin):
raise ValueError('Abort: input frequency out of limits!')
else:
freq_indin = np.where((freq >= fmin) & (freq <= fmax))[0]
# initialize arrays for dv/v measurements
dvv, err = np.zeros(freq_indin.shape), np.zeros(freq_indin.shape)
# loop through freq for linear regression
for ii, ifreq in enumerate(freq_indin):
if len(tvec) > 2:
if not np.any(delta_t[ifreq]):
continue
#---- use WXA as weight for regression----
# w = 1.0 / (1.0 / (WCT[ifreq,:] ** 2) - 1.0)
# w[WCT[ifreq,time_ind] >= 0.99] = 1.0 / (1.0 / 0.9801 - 1.0)
# w = np.sqrt(w * np.sqrt(WXA[ifreq,time_ind]))
# w = np.real(w)
w = 1 / WCT[ifreq]
w[~np.isfinite(w)] = 1.0
#m, a, em, ea = linear_regression(time_axis[indx], delta_t[indx], w, intercept_origin=False)
m, em = linear_regression(tvec,
delta_t[ifreq],
w,
intercept_origin=True)
dvv[ii], err[ii] = -m, em
else:
print('not enough points to estimate dv/v')
dvv[ii], err[ii] = np.nan, np.nan
del WCT, aWCT, coi, sig, phase, delta_t
del tvec, w, m, em
if not allfreq:
return np.mean(dvv) * 100, np.mean(err) * 100
else:
return freq[freq_indin], dvv * 100, err * 100
# the PPF using chi2.ppf gives Z2(95%)=5.991. To ensure similar significance
# intervals as in Grinsted et al. (2004), one has to use confidence of 86.46%.
W12, cross_coi, freq, signif = wavelet.xwt(s1, s2, dt, dj=1/12, s0=-1, J=-1,
significance_level=0.8646,
wavelet='morlet', normalize=True)
cross_power = np.abs(W12)**2
cross_sig = np.ones([1, n]) * signif[:, None]
cross_sig = cross_power / cross_sig # Power is significant where ratio > 1
cross_period = 1/freq
# Calculate the wavelet coherence (WTC). The WTC finds regions in time
# frequency space where the two time seris co-vary, but do not necessarily have
# high power.
WCT, aWCT, corr_coi, freq, sig = wavelet.wct(s1, s2, dt, dj=1/12, s0=-1, J=-1,
significance_level=0.8646,
wavelet='morlet', normalize=True,
cache=True)
cor_sig = np.ones([1, n]) * sig[:, None]
cor_sig = np.abs(WCT) / cor_sig # Power is significant where ratio > 1
cor_period = 1 / freq
# Calculates the phase between both time series. The phase arrows in the
# cross wavelet power spectrum rotate clockwise with 'north' origin.
# The relative phase relationship convention is the same as adopted
# by Torrence and Webster (1999), where in phase signals point
# upwards (N), anti-phase signals point downwards (S). If X leads Y,
# arrows point to the right (E) and if X lags Y, arrow points to the
# left (W).
angle = 0.5 * np.pi - aWCT
u, v = np.cos(angle), np.sin(angle)
def calc_wave_coherence(wave1,
wave2,
sample_times,
min_freq=1,
max_freq=128,
sig=False,
resolution=12):
"""
Calculate wavelet coherence between wave1 and wave2 using pycwt.
Parameters
----------
wave1 : np.ndarray
The values of the first waveform.
wave2 : np.ndarray
The values of the second waveform.
sample_times : np.ndarray
The times at which waveform samples occur.
min_freq : float
Supposed to be minimum frequency, but not quite working.
max_freq : float
Supposed to be max frequency, but not quite working.
sig : bool, default False
Optional Should significance of waveform coherence be calculated.
resolution : int
How many wavelets should be at each level
Returns
-------
WCT, t, freq, coi, sig, aWCT
WCT - 2D numpy array with coherence values
t - 2D numpy array with sample_times
freq - 1D numpy array with the frequencies wavelets were calculated at
coi - 1D numpy array with a frequency value for each time
sig - 2D numpy array indicating where data is significant by monte carlo
aWCT - 2D numpy array with same shape as aWCT indicating phase angles
"""
t = np.asarray(sample_times)
dt = np.mean(np.diff(t)) # dt = 0.004
dj = resolution
s0 = 1 / max_freq
if s0 < (2 * dt):
s0 = 2 * dt
max_J = 1 / min_freq
J = dj * np.int(np.round(np.log2(max_J / np.abs(s0))))
# # Original by Sean
# s0 = min_freq * dt
# if s0 < (2 * dt):
# s0 = 2 * dt
# max_J = max_freq * dt
# J = dj * np.int(np.round(np.log2(max_J / np.abs(s0))))
# Do the actual calculation
print("Calculating coherence...")
start_time = time.time()
WCT, aWCT, coi, freq, sig = wavelet.wct(
wave1,
wave2,
dt, # Fixed params
dj=(1.0 / dj),
s0=s0,
J=J,
sig=sig,
normalize=True)
print("Time Taken: %s s" % (time.time() - start_time))
if np.max(WCT) > 1 or np.min(WCT) < 0:
print('WCT was out of range: min {},max {}'.format(
np.min(WCT), np.max(WCT)))
WCT = np.clip(WCT, 0, 1)
return WCT, t, freq, coi, sig, aWCT
def cross_wavelet(self, signal_1, signal_2, mother='morlet', plot=True):
signal_1 = (signal_1 - signal_1.mean()) / signal_1.std() # Normalizing
signal_2 = (signal_2 - signal_2.mean()) / signal_2.std() # Normalizing
W12, cross_coi, freq, signif = wavelet.xwt(signal_1, signal_2, self.period, dj=1/100, s0=-1, J=-1,
significance_level=0.95, wavelet=mother,
normalize=True)
cross_power = np.abs(W12)**2
cross_sig = np.ones([1, signal_1.size]) * signif[:, None]
cross_sig = cross_power / cross_sig
cross_period = 1/freq
WCT, aWCT, corr_coi, freq, sig = wavelet.wct(signal_1, signal_2, self.period, dj=1/100, s0=-1, J=-1,
sig=False,significance_level=0.95, wavelet=mother,
normalize=True)
cor_sig = np.ones([1, signal_1.size]) * sig[:, None]
cor_sig = np.abs(WCT) / cor_sig
cor_period = 1/freq
angle = 0.5 * np.pi - aWCT
u, v = np.cos(angle), np.sin(angle)
t1 = np.linspace(0,self.period*signal_1.size,signal_1.size)
## indices for stuff
idx = self.find_closest(cor_period,corr_coi.max())
## Into minutes
t1 /= 60
cross_period /= 60
cor_period /= 60
cross_coi /= 60
corr_coi /= 60
fig1, ax1 = plt.subplots(nrows=1,ncols=1, sharex=True, sharey=True, figsize=(12,12))
extent_cross = [t1.min(),t1.max(),0,max(cross_period)]
extent_corr = [t1.min(),t1.max(),0,max(cor_period)]
im1 = NonUniformImage(ax1, interpolation='nearest', extent=extent_cross)
im1.set_cmap('cubehelix')
im1.set_data(t1, cross_period[:idx], cross_power[:idx,:])
ax1.images.append(im1)
ax1.contour(t1, cross_period[:idx], cross_sig[:idx,:], [-99, 1], colors='k', linewidths=2, extent=extent_cross)
ax1.fill(np.concatenate([t1, t1[-1:]+self.period, t1[-1:]+self.period,t1[:1]-self.period, t1[:1]-self.period]),
(np.concatenate([cross_coi,[1e-9], cross_period[-1:], cross_period[-1:], [1e-9]])),
'k', alpha=0.3,hatch='x')
ax1.set_title('Cross-Wavelet')
# ax1.quiver(t1[::3], cross_period[::3], u[::3, ::3],
# v[::3, ::3], units='width', angles='uv', pivot='mid',
# linewidth=1.5, edgecolor='k', headwidth=10, headlength=10,
# headaxislength=5, minshaft=2, minlength=5)
ax1.set_ylim(([min(cross_period), cross_period[idx]]))
ax1.set_xlim(t1.min(),t1.max())
fig2, ax2 = plt.subplots(nrows=1,ncols=1, sharex=True, sharey=True, figsize=(12,12))
fig2.subplots_adjust(right=0.8)
cbar_ax_1 = fig2.add_axes([0.85, 0.05, 0.05, 0.35])
im2 = NonUniformImage(ax2, interpolation='nearest', extent=extent_corr)
im2.set_cmap('cubehelix')
im2.set_data(t1, cor_period[:idx], np.log10(WCT[:idx,:]))
ax2.images.append(im2)
ax2.contour(t1, cor_period[:idx], cor_sig[:idx,:], [-99, 1], colors='k', linewidths=2, extent=extent_corr)
ax2.fill(np.concatenate([t1, t1[-1:]+self.period, t1[-1:]+self.period,t1[:1]-self.period, t1[:1]-self.period]),
(np.concatenate([corr_coi,[1e-9], cor_period[-1:], cor_period[-1:], [1e-9]])),
'k', alpha=0.3,hatch='x')
ax2.set_title('Cross-Correlation')
# ax2.quiver(t1[::3], cor_period[::3], u[::3,::3], v[::3,::3],
# units='height', angles='uv', pivot='mid',linewidth=1.5, edgecolor='k',
# headwidth=10, headlength=10, headaxislength=5, minshaft=2, minlength=5)
ax2.set_ylim(([min(cor_period), cor_period[idx]]))
ax2.set_xlim(t1.min(),t1.max())
fig2.colorbar(im2, cax=cbar_ax_1)
plt.show()
plt.figure(figsize=(12,12))
im3= plt.imshow(np.rad2deg(aWCT), origin='lower',interpolation='nearest', cmap='seismic', extent=extent_corr)
plt.fill(np.concatenate([t1, t1[-1:]+self.period, t1[-1:]+self.period,t1[:1]-self.period, t1[:1]-self.period]),
(np.concatenate([corr_coi,[1e-9], cor_period[-1:], cor_period[-1:], [1e-9]])),
'k', alpha=0.3,hatch='x')
plt.ylim(([min(cor_period), cor_period[idx]]))
plt.xlim(t1.min(),t1.max())
plt.colorbar(im3)
plt.show()
return