def mtem(i, j, dt):
"""
multitaper estimation method
Input:
i first time series
j second time series
Output:
fki power spectral density i
fkj power spectral density j
cij cross-spectral density ij
coh coherence
ph phase spectrum between ij at input freq
"""
print 'i size', i.shape
print 'j size', j.shape
# apply multi taper cross spectral density from nitime module
f, pcsd_est = tsa.multi_taper_csd(np.vstack([i,j]), Fs=1/dt, low_bias=True, adaptive=True, sides='onesided')
# output is MxMxN matrix, extract the psd and csd
fki = pcsd_est.diagonal().T[0]
fkj = pcsd_est.diagonal().T[1]
cij = pcsd_est.diagonal(+1).T.ravel()
# using complex argument of cxy extract phase component
ph = np.angle(cij)
# calculate coherence using csd and psd
coh = np.abs(cij)**2 / (fki * fkj)
return f, fki, fkj, cij, ph, coh
def mtem(x, y):
"""
multitaper estimation method
input:
x first time series
y second time series
output:
fkx power spectral density x
fky power spectral density y
cxy cross-spectral density xy
coh coherence
ph phase between xy at input freq
"""
print ('x size', x.shape)
print ('y size', y.shape)
# apply multi taper cross spectral density from nitime module
f, pcsd_est = tsa.multi_taper_csd(np.vstack([x,y]), Fs=1., low_bias=True, adaptive=True, sides='onesided')
# output is MxMxN matrix, extract the psd and csd
fkx = pcsd_est.diagonal().T[0]
fky = pcsd_est.diagonal().T[1]
cxy = pcsd_est.diagonal(+1).T.ravel()
# using complex argument of cxy extract phase component
ph = np.angle(cxy)
# calculate coherence using csd and psd
coh = np.abs(cxy)**2 / (fkx * fky)
return f, fkx, fky, cxy, ph, coh
def mtem_unct(x_, y_, cf, mc_no=20):
"""
Uncertainty function using Monte Carlo analysis
Input:
x_ = timeseries x
y_ = timeseries y
cf = coherence function between x and y
mc_no = number of iterations default is 20, minimum is 3
Output:
phif = phase uncertainty bounded between 0 and pi
"""
print 'iteration no is', mc_no
data = np.vstack([x_, y_])
# number of iterations
# flip coherence and horizontal stack
cg = np.hstack((cf[:-1], np.flipud(cf[:-1])))
# random time series fx
mc_fx = np.random.standard_normal(size=(mc_no, len(data[0])))
mc_fx = mc_fx / np.sum(abs(mc_fx), axis=1)[None].T
# random time series fy
mc_fy = np.random.standard_normal(size=(mc_no, len(data[0])))
mc_fy = mc_fy / np.sum(abs(mc_fy), axis=1)[None].T
# create semi random timeseries based on magnitude squared coherence
# and inverse fourier transform for ys
ys = np.real(np.fft.ifft(mc_fy * np.sqrt(1 - cg**2)))
ys = ys + np.real(np.fft.ifft(mc_fx * cg))
# inverse fourier transform for xs
xs = np.real(np.fft.ifft(mc_fx))
# spectral analysis
f_s, pcsd_est = tsa.multi_taper_csd(np.vstack([xs, ys]),
Fs=1.,
low_bias=True,
adaptive=True,
sides='onesided')
cxyi = pcsd_est.diagonal(+int(xs.shape[0])).T
phi = np.angle(cxyi)
# sort and average the highest uncertianties
pl = int(round(0.975 * mc_no) + 1)
phi = np.sort(phi, axis=0)
phi = phi[((mc_no + 1) - pl):pl]
phi = np.array([phi[pl - 2, :], -phi[pl - mc_no, :]])
phi = phi.mean(axis=0) #
phi = np.convolve(phi, np.array([1, 1, 1]) / 3)
phif = phi[1:-1]
return phif
def mtem_unct(i_, j_, dt_, cf, mc_no=20):
"""
Uncertainty function using Monte Carlo analysis
Input:
i_ timeseries i
j_ timeseries j
cf coherence function between i and j
mc_no number of iterations default is 20, minimum is 3
Output:
phif phase uncertainty bounded between 0 and pi
"""
print 'iteration no is', mc_no
data = np.vstack([i_,j_])
# number of iterations
# flip coherence and horizontal stack
cg = np.hstack((cf[:-1], np.flipud(cf[:-1])))
# random time series fi
mc_fi = np.random.standard_normal(size=(mc_no,len(data[0])))
mc_fi = mc_fi / np.sum(abs(mc_fi),axis=1)[None].T
# random time series fj
mc_fj = np.random.standard_normal(size=(mc_no,len(data[0])))
mc_fj = mc_fj / np.sum(abs(mc_fj),axis=1)[None].T
# create semi random timeseries based on magnitude squared coherence
# and inverse fourier transform for js
js = np.real(np.fft.ifft(mc_fj * np.sqrt(1 - cg ** 2)))
js_ = js + np.real(np.fft.ifft(mc_fi *cg))
# inverse fourier transform for xs
is_ = np.real(np.fft.ifft(mc_fi))
# spectral analysis
f_s, pcsd_est = tsa.multi_taper_csd(np.vstack([is_,js_]), Fs=1/dt_, low_bias=True, adaptive=True, sides='onesided')
cijx = pcsd_est.diagonal(+int(is_.shape[0])).T
phi = np.angle(cijx)
# sort and average the highest uncertianties
pl = int(round(0.95*mc_no)+1)
phi = np.sort(phi,axis=0)
phi = phi[((mc_no+1)-pl):pl]
phi = np.array([phi[pl-2,:],-phi[pl-mc_no,:]])
phi = phi.mean(axis=0)#
phi = np.convolve(phi, np.array([1,1,1])/3)
phif = phi[1:-1]
return phif
def test_multi_taper_psd_csd():
"""
Test the multi taper psd and csd estimation functions.
Based on the example in
doc/examples/multi_taper_spectral_estimation.py
"""
N = 2**10
n_reps = 10
psd = []
est_psd = []
est_csd = []
for jk in [True, False]:
for k in range(n_reps):
for adaptive in [True, False]:
ar_seq, nz, alpha = utils.ar_generator(N=N, drop_transients=10)
ar_seq -= ar_seq.mean()
fgrid, hz = tsa.freq_response(1.0,
a=np.r_[1, -alpha],
n_freqs=N)
psd.append(2 * (hz * hz.conj()).real)
f, psd_mt, nu = tsa.multi_taper_psd(ar_seq,
adaptive=adaptive,
jackknife=jk)
est_psd.append(psd_mt)
f, csd_mt = tsa.multi_taper_csd(np.vstack([ar_seq, ar_seq]),
adaptive=adaptive)
# Symmetrical in this case, so take one element out:
est_csd.append(csd_mt[0][1])
fxx = np.mean(psd, axis=0)
fxx_est1 = np.mean(est_psd, axis=0)
fxx_est2 = np.mean(est_csd, axis=0)
# Tests the psd:
psd_ratio1 = np.mean(fxx_est1 / fxx)
npt.assert_array_almost_equal(psd_ratio1, 1, decimal=-1)
# Tests the csd:
psd_ratio2 = np.mean(fxx_est2 / fxx)
npt.assert_array_almost_equal(psd_ratio2, 1, decimal=-1)
def test_multi_taper_psd_csd():
"""
Test the multi taper psd and csd estimation functions.
Based on the example in
doc/examples/multi_taper_spectral_estimation.py
"""
N = 2 ** 10
n_reps = 10
psd = []
est_psd = []
est_csd = []
for jk in [True, False]:
for k in range(n_reps):
for adaptive in [True, False]:
ar_seq, nz, alpha = utils.ar_generator(N=N, drop_transients=10)
ar_seq -= ar_seq.mean()
fgrid, hz = tsa.freq_response(1.0, a=np.r_[1, -alpha],
n_freqs=N)
psd.append(2 * (hz * hz.conj()).real)
f, psd_mt, nu = tsa.multi_taper_psd(ar_seq, adaptive=adaptive,
jackknife=jk)
est_psd.append(psd_mt)
f, csd_mt = tsa.multi_taper_csd(np.vstack([ar_seq, ar_seq]),
adaptive=adaptive)
# Symmetrical in this case, so take one element out:
est_csd.append(csd_mt[0][1])
fxx = np.mean(psd, axis=0)
fxx_est1 = np.mean(est_psd, axis=0)
fxx_est2 = np.mean(est_csd, axis=0)
# Tests the psd:
psd_ratio1 = np.mean(fxx_est1 / fxx)
npt.assert_array_almost_equal(psd_ratio1, 1, decimal=-1)
# Tests the csd:
psd_ratio2 = np.mean(fxx_est2 / fxx)
npt.assert_array_almost_equal(psd_ratio2, 1, decimal=-1)
def test_hermitian_multitaper_csd():
"""
Make sure CSD matrices returned by various methods have
Hermitian symmetry.
"""
sig = np.random.randn(4, 256)
_, csd1 = tsa.multi_taper_csd(sig, adaptive=False)
for i in range(4):
for j in range(i + 1):
xc1 = csd1[i, j]
xc2 = csd1[j, i]
npt.assert_equal(xc1, xc2.conj(), err_msg='MTM CSD not Hermitian')
_, psd, _ = tsa.multi_taper_psd(sig, adaptive=False)
for i in range(4):
npt.assert_almost_equal(
psd[i],
csd1[i, i].real,
err_msg='MTM CSD diagonal inconsistent with real PSD')
def test_hermitian_multitaper_csd():
"""
Make sure CSD matrices returned by various methods have
Hermitian symmetry.
"""
sig = np.random.randn(4,256)
_, csd1 = tsa.multi_taper_csd(sig, adaptive=False)
for i in range(4):
for j in range(i+1):
xc1 = csd1[i,j]
xc2 = csd1[j,i]
npt.assert_equal(
xc1, xc2.conj(), err_msg='MTM CSD not Hermitian'
)
_, psd, _ = tsa.multi_taper_psd(sig, adaptive=False)
for i in range(4):
npt.assert_almost_equal(
psd[i], csd1[i,i].real,
err_msg='MTM CSD diagonal inconsistent with real PSD'
)
def PCA(arr,
ncomp,
verbose=True,
sample_rate=488.28125,
filename="",
**keywords):
pdf_pages = PdfPages('PCA_diag' + filename +
'.pdf') # name of the pdf produced
# do mean subration
mean_vec_arr = np.mean(arr, axis=0)
arr = arr - mean_vec_arr
# normalize by the variance
var = np.std(arr, axis=0)**2
arr = arr / var
covmat = np.dot(arr.T, arr) #/data_arr.shape[0]
#compute the eigvectors and eigenvalues
evals, evects = np.linalg.eig(covmat)
#sort the eigenvectors and values by largest to smallest
idx = evals.argsort()[::-1]
evals = evals[idx]
evects = evects[:, idx]
#make the eigenfunction array
efuncarr = np.dot(arr, evects)
# pick components to subtract
efuncarr[:, 0:ncomp] = 0
res_index_used = idx[0:ncomp]
#transform back
arr_clean = np.inner(efuncarr, evects)
if verbose:
print("the covariance matrix is")
print(covmat)
print("")
print("the eigenvalues are")
print(evals)
print("")
print("the eigenvectors are")
print(evects)
print("")
fig = plt.figure(1, figsize=(12, 6))
plt.subplot(1, 2, 1)
plt.title("Eigenvalues")
plt.plot(np.log10(np.abs(evals)), label="eigenvalues")
plt.plot(np.log10(np.abs(evals[0:ncomp])), 'o', label="components removed")
plt.xlabel("Eigenvalue index")
plt.ylabel("Eigenvalue Magnitude")
plt.legend()
plt.subplot(1, 2, 2)
plt.title("Log10(covariance matrix)")
plt.imshow(np.log10(covmat), interpolation='nearest')
plt.colorbar()
pdf_pages.savefig(fig)
plt.close()
#need to unnormalize by the varaince
arr = arr * var
arr_clean = arr_clean * var
#need to add the mean back in to get the right units
arr = arr + mean_vec_arr
arr_clean = arr_clean + mean_vec_arr
#block for plotting the correlation between the two most corrrelated detectors
fig = plt.figure(2, figsize=(12, 6))
plt.title("Cross correlation of two most correlated detectors")
# make a figure that show the correlation between the two most correlated detectors
cov_matrix_2 = covmat
for i in range(0, cov_matrix_2.shape[0]):
cov_matrix_2[
i,
i] = 0 #zeros out diagonal obviously detecotrs are correlated with them selves
max_corr_index1 = np.where(cov_matrix_2 == np.max(cov_matrix_2))[0][0]
max_corr_index2 = np.where(cov_matrix_2 == np.max(cov_matrix_2))[0][1]
# this is kind of a neat package for doing cross correlation on time streams
# see this page for explanation
# http://nbviewer.jupyter.org/github/mattijn/pynotebook/blob/master/ipynotebooks/Python2.7/2016/2016-05-25%20cross-spectral%20analysis.ipynb
#calculate the cross correlation
f, pcsd_est = tsa.multi_taper_csd(np.vstack(
(arr[:, max_corr_index1], arr[:, max_corr_index2])),
Fs=sample_rate,
low_bias=True,
adaptive=False,
sides='onesided')
fki = pcsd_est.diagonal().T[0]
fkj = pcsd_est.diagonal().T[1]
cij = pcsd_est.diagonal(+1).T.ravel()
#calculate the coherene
coh = np.abs(cij)**2 / (fki * fkj)
plt.loglog(f, fki, label="Resonator psd index = " + str(max_corr_index1))
plt.loglog(f, fkj, label="Resonator psd index = " + str(max_corr_index2))
ylim = plt.ylim()
plt.loglog(f, np.abs(cij), label="Cross psd")
plt.ylim(ylim[0], ylim[1])
plt.legend()
pdf_pages.savefig(fig)
plt.close()
fig = plt.figure(3, figsize=(12, 6))
plt.semilogx(f, np.abs(coh))
plt.title("Coherence")
plt.xlabel("Frequency Hz")
plt.ylim(0, 1)
pdf_pages.savefig(fig)
plt.close()
pdf_pages.close()
PCA_dict = {
'arr': arr,
'cleaned': arr_clean,
'ncomp': ncomp,
'res_index_used': res_index_used,
'cov_matrix': covmat
}
return PCA_dict