coord = (X.flatten(), Y.flatten())
tauConv = tauDim * timeScaleConversion
postfix = "%s_tau%03d" % (gridPostfix, tauDim * 1000)
print 'Readig spectrum...'
EigValForwardFile = '%s/eigval/eigValForward_nev%d%s.txt' % (cfg.general.specDir, nev, postfix)
EigVecForwardFile = '%s/eigvec/eigVecForward_nev%d%s.txt' % (cfg.general.specDir, nev, postfix)
EigValBackwardFile = '%s/eigval/eigValBackward_nev%d%s.txt' \
% (cfg.general.specDir, nev, postfix)
EigVecBackwardFile = '%s/eigvec/eigVecBackward_nev%d%s.txt' \
% (cfg.general.specDir, nev, postfix)
statDist = np.loadtxt('%s/transfer/initDist/initDist%s.txt' % (cfg.general.resDir, gridPostfix))
(eigValForward, eigVecForward, eigValBackward, eigVecBackward) \
= ergoPlot.readSpectrum(EigValForwardFile, EigVecForwardFile,
EigValBackwardFile, EigVecBackwardFile,
statDist, makeBiorthonormal=False)
print 'Getting conditionning of eigenvectors...'
eigenCondition = ergoPlot.getEigenCondition(eigVecForward, eigVecBackward, statDist)
# Get generator eigenvalues
eigValGen = (np.log(np.abs(eigValForward)) + np.angle(eigValForward)*1j) / tauConv
# Plot eigenvectors
alpha = 0.01
for ev in np.arange(nevPlot):
print 'Plotting real part of eigenvector %d...' % (ev+1,)
ergoPlot.plot2D(X, Y, eigVecForward[:, ev].real, ev_xlabel, ev_ylabel, alpha)
plt.savefig('%s/spectrum/eigvec/eigVecForwardReal_nev%d_ev%03d%s.%s' \
% (cfg.general.plotDir, nev, ev+1, postfix, ergoPlot.figFormat),
coord = (X.flatten(), Y.flatten())
tauConv = tauDim * timeScaleConversion
postfix = "%s_tau%03d" % (gridPostfix, tauDim * 1000)
print 'Readig spectrum...'
EigValForwardFile = '%s/eigval/eigValForward_nev%d%s.txt' % (cfg.general.specDir, nev, postfix)
EigVecForwardFile = '%s/eigvec/eigVecForward_nev%d%s.txt' % (cfg.general.specDir, nev, postfix)
EigValBackwardFile = '%s/eigval/eigValBackward_nev%d%s.txt' \
% (cfg.general.specDir, nev, postfix)
EigVecBackwardFile = '%s/eigvec/eigVecBackward_nev%d%s.txt' \
% (cfg.general.specDir, nev, postfix)
statDist = np.loadtxt('%s/transitionMatrix/initDist%s.txt' % (cfg.general.resDir, postfix))
(eigValForward, eigVecForward, eigValBackward, eigVecBackward) \
= ergoPlot.readSpectrum(nev, EigValForwardFile, EigVecForwardFile,
EigValBackwardFile, EigVecBackwardFile, statDist,
makeBiorthonormal=False)
print 'Getting conditionning of eigenvectors...'
eigenCondition = ergoPlot.getEigenCondition(eigVecForward, eigVecBackward, statDist)
# Get generator eigenvalues
eigValGen = (np.log(np.abs(eigValForward)) + np.angle(eigValForward)*1j) / tauConv
# Plot eigenvectors
alpha = 0.01
for ev in np.arange(nevPlot):
print 'Plotting real part of eigenvector %d...' % (ev+1,)
ergoPlot.plot2D(X, Y, eigVecForward[:, ev].real, ev_xlabel, ev_ylabel, alpha)
plt.savefig('%s/spectrum/eigvec/eigVecForwardReal_nev%d_ev%03d%s.%s' \
% (cfg.general.plotDir, nev, ev+1, postfix, ergoPlot.figFormat),
EigVecForwardFile = '%s/eigvec/eigVecForward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
EigValBackwardFile = '%s/eigval/eigValBackward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
EigVecBackwardFile = '%s/eigvec/eigVecBackward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
# Read stationary distribution
statDist = np.loadtxt('%s/transfer/initDist/initDist%s.txt' \
% (cfg.general.resDir, postfix))
# Read transfer operator spectrum from file and create a bi-orthonormal basis
# of eigenvectors and adjoint eigenvectors:
print 'Readig spectrum of tau = ', tau
(eigValForward, eigVecForward, eigValBackward, eigVecBackward) \
= ergoPlot.readSpectrum(cfg.spectrum.nev, EigValForwardFile, EigVecForwardFile,
EigValBackwardFile, EigVecBackwardFile, statDist)
# Save eigenvalues
eigVal[lag] = eigValForward.copy()
# Get generator eigenvalues
eigValGen[lag] = (np.log(np.abs(eigValForward)) + np.angle(eigValForward)*1j) / tauConv
# Get condition number
eigenCondition[lag] = ergoPlot.getEigenCondition(eigVecForward, eigVecBackward,
statDist)
print 'lag ', lag
print eigVal[lag]
print eigValGen[lag]
print eigenCondition[lag]
# Smoothen
# if lag > 0:
# Read mask
if maskFile is not None:
if fileFormat == 'bin':
mask = np.fromfile(maskFile, np.int32)
else:
mask = np.loadtxt(maskFile, np.int32)
else:
mask = np.arange(N)
NFilled = np.max(mask[mask < N]) + 1
# Read transfer operator spectrum from file and create a bi-orthonormal basis
# of eigenvectors and backward eigenvectors:
print 'Readig spectrum for tauDim = %.3f...' % tauDim
(eigValForward, eigValBackward, eigVecForward, eigVecBackward) \
= ergoPlot.readSpectrum(eigValForwardFile, eigValBackwardFile,
eigVecForwardFile, eigVecBackwardFile,
makeBiorthonormal=~cfg.spectrum.makeBiorthonormal,
fileFormat=fileFormat)
# Plot eigenvectors of transfer operator
alpha = 0.05
os.system('mkdir %s/spectrum/eigvec 2> /dev/null' % cfg.general.plotDir)
coordCut = 1
coordPlot = (coordCut + 1) % dimObs
cutVal = (coord[coordCut][mask < N] * statDist).sum()
idCut0 = np.argmin(np.abs(coord[coordCut] - cutVal))
idCut = np.abs(coord[1] - coord[1][idCut0]) < 1.e-6
xx = coord[coordPlot][idCut]
# Figure for the phase
figPhase = plt.figure()
EigVecForwardFile = '%s/eigvec/eigVecForward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
EigValBackwardFile = '%s/eigval/eigValBackward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
EigVecBackwardFile = '%s/eigvec/eigVecBackward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
# Read stationary distribution
statDist = np.loadtxt('%s/transfer/initDist/initDist%s.txt' \
% (cfg.general.resDir, postfix))
# Read transfer operator spectrum from file and create a bi-orthonormal basis
# of eigenvectors and adjoint eigenvectors:
print 'Readig spectrum of tau = ', tau
(eigValForward, eigVecForward, eigValBackward, eigVecBackward) \
= ergoPlot.readSpectrum(cfg.spectrum.nev, EigValForwardFile, EigVecForwardFile,
EigValBackwardFile, EigVecBackwardFile, statDist)
# Save eigenvalues
eigVal[lag] = eigValForward.copy()
# Get generator eigenvalues
eigValGen[lag] = (np.log(np.abs(eigValForward)) + np.angle(eigValForward)*1j) / tauConv
# Get condition number
eigenCondition[lag] = ergoPlot.getEigenCondition(eigVecForward, eigVecBackward,
statDist)
print 'lag ', lag
print eigVal[lag]
print eigValGen[lag]
print eigenCondition[lag]
# Smoothen
# if lag > 0:
% (cfg.general.resDir, gridPostfix)
if unfold:
tauUnfold = tauDimUnfold * timeScaleConversion
postfixUnfold = "%s_tau%03d" % (gridPostfix, tauDimUnfold * 1000)
eigValForwardFileUnfold = '%s/eigval/eigvalForward_nev%d%s.txt' \
% (cfg.general.specDir, nev, postfixUnfold)
eigVecForwardFileUnfold = '%s/eigvec/eigvecForward_nev%d%s.txt' \
% (cfg.general.specDir, nev, postfixUnfold)
tauMax = np.max([tau, tauUnfold])
# Read transfer operator spectrum from file and create a bi-orthonormal basis
# of eigenvectors and backward eigenvectors:
print 'Readig spectrum for tauDim = %.3f...' % tauDim
(eigValForward, eigValBackward, statDist, eigVecForward, eigVecBackward) \
= ergoPlot.readSpectrum(eigValForwardFile, eigValBackwardFile, statDistFile,
eigVecForwardFile, eigVecBackwardFile,
makeBiorthonormal=~cfg.spectrum.makeBiorthonormal)
print 'Getting conditionning of eigenvectors...'
eigenCondition = ergoPlot.getEigenCondition(eigVecForward, eigVecBackward,
statDist)
eigValGenOrig = ergoPlot.eig2Generator(eigValForward, tau)
# Read unfolding eigenvalues
#eigValForwardUnfold = None
st = statDist.copy()
st2 = np.concatenate((st, st))
if unfold:
print 'Readig spectrum for tauDimUnfold = %.3f to unfold...' % tauDimUnfold
(eigValForwardUnfold,) \
eigValForwardFile = '%s/eigval/eigvalForward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
eigVecForwardFile = '%s/eigvec/eigvecForward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
eigValBackwardFile = '%s/eigval/eigvalBackward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
eigVecBackwardFile = '%s/eigvec/eigvecBackward_nev%d%s.txt' \
% (cfg.general.specDir, cfg.spectrum.nev, postfix)
statDistFile = '%s/transfer/initDist/initDist%s.txt' % (cfg.general.resDir, gridPostfix)
# Read transfer operator spectrum from file and create a bi-orthonormal basis
# of eigenvectors and backward eigenvectors:
print 'Readig spectrum for tau = %.3f...' % tau
(eigValForward, eigValBackward, statDist, eigVecForward, eigVecBackward) \
= ergoPlot.readSpectrum(eigValForwardFile, eigValBackwardFile, statDistFile,
eigVecForwardFile, eigVecBackwardFile,
makeBiorthonormal=~cfg.spectrum.makeBiorthonormal)
print 'Getting conditionning of eigenvectors...'
eigenCondition = ergoPlot.getEigenCondition(eigVecForward, eigVecBackward, statDist)
# Get generator eigenvalues
eigValGen = (np.log(np.abs(eigValForward)) + np.angle(eigValForward)*1j) / tau
# Plot eigenvectors of transfer operator
alpha = 0.01
for ev in np.arange(nevPlot):
print 'Plotting real part of eigenvector %d...' % (ev + 1,)
#ergoPlot.plot2D(X, Y, eigVecForward[:, ev].real, ev_xlabel, ev_ylabel, alpha)
ergoPlot.plot2D(X, Y, eigVecForward[:, ev].real, ev_xlabel, ev_ylabel, alpha)
