def plot_currentmodels(self, nchains):
"""Return fig.
Plots the first nchains chains, no matter of outlier status.
"""
fig, ax = plt.subplots(figsize=(4, 6.5))
base = cm.get_cmap(name='rainbow')
color_list = base(np.linspace(0, 1, nchains))
for i, modfile in enumerate(self.modfiles[1][:nchains]):
chainidx, _, _ = self._return_c_p_t(modfile)
models = np.load(modfile)
vpvs = np.load(modfile.replace('models', 'vpvs')).T
currentvpvs = vpvs[-1]
currentmodel = models[-1]
color = color_list[i]
vp, vs, h = Model.get_vp_vs_h(currentmodel, currentvpvs, self.mantle)
cvp, cvs, cdepth = Model.get_stepmodel_from_h(h=h, vs=vs, vp=vp)
label = 'c%d / %d' % (chainidx, vs.size-1)
ax.plot(cvs, cdepth, color=color, ls='-', lw=0.8,
alpha=0.7, label=label)
ax.invert_yaxis()
ax.set_xlabel('$V_S$ in km/s')
ax.set_ylabel('Depth in km')
# ax.set_xlim(self.priors['vs'])
ax.set_ylim(self.priors['z'][::-1])
ax.set_title('Current models')
ax.grid(color='gray', alpha=0.6, ls=':', lw=0.5)
ax.legend(loc='center left', bbox_to_anchor=(1, 0.5))
return fig
def update_models(self, model, vpvs):
logger.debug('### Found new chain model')
vp, vs, dep = Model.get_stepmodel(model, vpvs=vpvs, mantle=self.mantle)
self.vs_step = np.roll(self.vs_step, -1, axis=0) # rolling up models
nantmp = np.ones(self.modellength) * np.nan
nantmp[:vs.size] = vs
self.vs_step[-1] = nantmp
self.dep_step = np.roll(self.dep_step, -1, axis=0) # rolling up models
nantmp = np.ones(self.modellength) * np.nan
nantmp[:dep.size] = dep
self.dep_step[-1] = nantmp
vp, vs, h = Model.get_vp_vs_h(model, vpvs=vpvs, mantle=self.mantle)
ymod = self.compute_synth(h, vs, vp)
for i, tline in enumerate(self.targetlines):
if tline is not None:
tline.set_ydata(ymod[i])
# # create LineCollection
segments = [
np.column_stack([x, y])
for x, y in zip(self.vs_step, self.dep_step)
]
self.modelcollection.set_segments(segments)
a = np.repeat(([0, 1], ), self.capacity, axis=0)
b = np.array([[v] * 2 for v in self.vpvss])
segments = [np.column_stack([x, y]) for x, y in zip(b, a)]
self.vpvscollection.set_segments(segments)
def plot_bestdatafits(self):
"""Plot best data fits from each chain and ever best,
ignoring outliers."""
targets = Targets.JointTarget(targets=self.targets)
fig, ax = targets.plot_obsdata(mod=False)
thebestmodel = np.nan
thebestmisfit = 1e15
thebestchain = np.nan
modfiles = self.modfiles[1]
for i, modfile in enumerate(modfiles):
chainidx, _, _ = self._return_c_p_t(modfile)
if chainidx in self.outliers:
continue
models = np.load(modfile)
misfits = np.load(modfile.replace('models', 'misfits')).T[-1]
bestmodel = models[np.argmin(misfits)]
bestmisfit = misfits[np.argmin(misfits)]
if bestmisfit < thebestmisfit:
thebestmisfit = bestmisfit
thebestmodel = bestmodel
thebestchain = chainidx
vp, vs, h = Model.get_vp_vs_h(bestmodel, self.priors['vpvs'])
rho = vp * 0.32 + 0.77
for n, target in enumerate(targets.targets):
xmod, ymod = target.moddata.plugin.run_model(h=h,
vp=vp,
vs=vs,
rho=rho)
if len(targets.targets) > 1:
ax[n].plot(xmod, ymod, color='k', alpha=0.5, lw=0.7)
else:
ax.plot(xmod, ymod, color='k', alpha=0.5, lw=0.7)
if len(targets.targets) > 1:
ax[0].set_title('Best data fits from %d chains' %
(len(modfiles) - self.outliers.size))
# idx = len(targets.targets) - 1
han, lab = ax[0].get_legend_handles_labels()
handles, labels = self._unique_legend(han, lab)
ax[0].legend().set_visible(False)
else:
ax.set_title('Best data fits from %d chains' %
(len(modfiles) - self.outliers.size))
han, lab = ax.get_legend_handles_labels()
handles, labels = self._unique_legend(han, lab)
ax.legend().set_visible(False)
fig.legend(handles,
labels,
loc='center left',
bbox_to_anchor=(0.92, 0.5))
return fig
def plot_currentdatafits(self, nchains):
"""Plot the first nchains chains, no matter of outlier status.
"""
base = cm.get_cmap(name='rainbow')
color_list = base(np.linspace(0, 1, nchains))
targets = Targets.JointTarget(targets=self.targets)
fig, ax = targets.plot_obsdata(mod=False)
for i, modfile in enumerate(self.modfiles[1][:nchains]):
color = color_list[i]
chainidx, _, _ = self._return_c_p_t(modfile)
models = np.load(modfile)
vpvs = np.load(modfile.replace('models', 'vpvs')).T
currentvpvs = vpvs[-1]
currentmodel = models[-1]
vp, vs, h = Model.get_vp_vs_h(currentmodel, currentvpvs, self.mantle)
rho = vp * 0.32 + 0.77
jmisfit = 0
for n, target in enumerate(targets.targets):
xmod, ymod = target.moddata.plugin.run_model(
h=h, vp=vp, vs=vs, rho=rho)
yobs = target.obsdata.y
misfit = target.valuation.get_rms(yobs, ymod)
jmisfit += misfit
label = ''
if len(targets.targets) > 1:
if ((len(targets.targets) - 1) - n) < 1e-2:
label = 'c%d / %.3f' % (chainidx, jmisfit)
ax[n].plot(xmod, ymod, color=color, alpha=0.7, lw=0.8,
label=label)
else:
label = 'c%d / %.3f' % (chainidx, jmisfit)
ax.plot(xmod, ymod, color=color, alpha=0.5, lw=0.7,
label=label)
if len(targets.targets) > 1:
ax[0].set_title('Current data fits')
idx = len(targets.targets) - 1
han, lab = ax[idx].get_legend_handles_labels()
handles, labels = self._unique_legend(han, lab)
ax[0].legend().set_visible(False)
else:
ax.set_title('Current data fits')
han, lab = ax.get_legend_handles_labels()
handles, labels = self._unique_legend(han, lab)
ax.legend().set_visible(False)
fig.legend(handles, labels, loc='center left',
bbox_to_anchor=(0.92, 0.5))
return fig
def plot_bestmodels(self):
"""Return fig.
Plot the best (fit) models ever discovered per each chain,
ignoring outliers.
"""
fig, ax = plt.subplots(figsize=(4, 6.5))
thebestmodel = np.nan
thebestmisfit = 1e15
thebestchain = np.nan
modfiles = self.modfiles[1]
for i, modfile in enumerate(modfiles):
chainidx, _, _ = self._return_c_p_t(modfile)
if chainidx in self.outliers:
continue
models = np.load(modfile)
vpvs = np.load(modfile.replace('models', 'vpvs')).T
misfits = np.load(modfile.replace('models', 'misfits')).T[-1]
bestmodel = models[np.argmin(misfits)]
bestvpvs = vpvs[np.argmin(misfits)]
bestmisfit = misfits[np.argmin(misfits)]
if bestmisfit < thebestmisfit:
thebestmisfit = bestmisfit
thebestmodel = bestmodel
thebestvpvs = bestvpvs
thebestchain = chainidx
vp, vs, h = Model.get_vp_vs_h(bestmodel, bestvpvs, self.mantle)
cvp, cvs, cdepth = Model.get_stepmodel_from_h(h=h, vs=vs, vp=vp)
ax.plot(cvs, cdepth, color='k', ls='-', lw=0.8, alpha=0.5)
# label = 'c%d' % thebestchain
# vp, vs, h = Model.get_vp_vs_h(thebestmodel, thebestvpvs, self.mantle)
# cvp, cvs, cdepth = Model.get_stepmodel_from_h(h=h, vs=vs, vp=vp)
# ax.plot(cvs, cdepth, color='red', ls='-', lw=1,
# alpha=0.8, label=label)
ax.invert_yaxis()
ax.set_xlabel('$V_S$ in km/s')
ax.set_ylabel('Depth in km')
# ax.set_xlim(self.priors['vs'])
ax.set_ylim(self.priors['z'][::-1])
ax.set_title('Best fit models from %d chains' %
(len(modfiles)-self.outliers.size))
ax.grid(color='gray', alpha=0.6, ls=':', lw=0.5)
# ax.legend(loc=3)
return fig
def _init_model_and_currentvalues(self):
imodel = self.draw_initmodel()
inoise, corrfix = self.draw_initnoiseparams()
rcond = self.initparams['rcond']
self.set_target_covariance(corrfix[::2], inoise[::2], rcond)
vp, vs, h = Model.get_vp_vs_h(imodel, self.vpvs)
self.targets.evaluate(h=h, vp=vp, vs=vs, noise=inoise)
self.currentmodel = imodel
self.currentnoise = inoise
self.currentmisfits = self.targets.proposalmisfits
self.currentlikelihood = self.targets.proposallikelihood
logger.debug((vs, h))
self.n = 0 # accepted models counter
self.accept_as_currentmodel(imodel, inoise)
self.append_currentmodel()
def plot_rfcorr(self, rf='prf'):
from BayHunter import SynthObs
p2models, p2noise, p2misfits, p2vpvs = self._get_posterior_data(
['models', 'noise', 'misfits', 'vpvs'], final=True)
fig, axes = plt.subplots(2, sharex=True, sharey=True)
ind = self.refs.index(rf)
best = np.argmin(p2misfits.T[ind])
model = p2models[best]
vpvs = p2vpvs[best]
target = self.targets[ind]
x, y = target.obsdata.x, target.obsdata.y
vp, vs, h = Model.get_vp_vs_h(model, vpvs, self.mantle)
rho = vp * 0.32 + 0.77
_, ymod = target.moddata.plugin.run_model(
h=h, vp=vp, vs=vs, rho=rho)
yobs = target.obsdata.y
yresiduals = yobs - ymod
# axes[0].set_title('Residuals [dobs-g(m)] obtained with best fitting model m')
axes[0].plot(x, yresiduals, color='k', lw=0.7, label='residuals')
corr, sigma = p2noise[best][2*ind:2*(ind+1)]
yerr = SynthObs.compute_gaussnoise(y, corr=corr, sigma=sigma)
# axes[1].set_title('One Realization of random noise from inferred CeRF')
axes[1].plot(x, yerr, color='k', lw=0.7, label='noise realization')
axes[1].set_xlabel('Time in s')
axes[0].legend(loc=4)
axes[1].legend(loc=4)
axes[0].grid(color='gray', ls=':', lw=0.5)
axes[1].grid(color='gray', ls=':', lw=0.5)
axes[0].set_xlim([x[0], x[-1]])
return fig
def iterate(self):
if self.iiter < (-self.iter_phase1 + (self.iterations * 0.01)):
# only allow vs and z modifications the first 1 % of iterations
modify = self.rstate.choice(['vsmod', 'zvmod'] + self.noisemods +
self.vpvsmods)
else:
modify = self.rstate.choice(self.modifications)
if modify in self.modelmods:
proposalmodel = self._get_modelproposal(modify)
proposalnoise = self.currentnoise
proposalvpvs = self.currentvpvs
if not self._validmodel(proposalmodel):
proposalmodel = None
elif modify in self.noisemods:
proposalmodel = self.currentmodel
proposalnoise = self._get_hyperparameter_proposal()
proposalvpvs = self.currentvpvs
if not self._validnoise(proposalnoise):
proposalmodel = None
elif modify == 'vpvs':
proposalmodel = self.currentmodel
proposalnoise = self.currentnoise
proposalvpvs = self._get_vpvs_proposal()
if not self._validvpvs(proposalvpvs):
proposalmodel = None
if proposalmodel is None:
# If not a valid proposal model and noise params are found,
# leave self.iterate and try with another modification
# should not occur often.
logger.debug('Not able to find a proposal for %s' % modify)
self.iiter += 1
return
# compute synthetic data and likelihood, misfit
vp, vs, h = Model.get_vp_vs_h(proposalmodel, proposalvpvs, self.mantle)
self.targets.evaluate(h=h, vp=vp, vs=vs, noise=proposalnoise)
aidx = self.modifications.index(modify)
self.proposed[aidx] += 1
# Replace self.currentmodel with proposalmodel with acceptance
# probability alpha. Accept candidate sample (proposalmodel)
# with probability alpha, or reject it with probability (1 - alpha).
# these are log values ! alpha is log.
u = np.log(self.rstate.uniform(0, 1))
alpha = self.get_acceptance_probability(modify)
# #### _____________________________________________________________
if u < alpha:
# always the case if self.jointlike > self.bestlike (alpha>1)
self.accept_as_currentmodel(proposalmodel, proposalnoise,
proposalvpvs)
self.append_currentmodel()
self.accepted[aidx] += 1
# print inversion status information
if self.iiter % 5000 == 0:
runtime = time.time() - self.tnull
current_iterations = self.iiter + self.iter_phase1
if current_iterations > 0:
acceptrate = float(self.n) / current_iterations * 100.
logger.info('%6d %5d + hs %8.3f\t%9d |%6.1f s | %.1f ' %
(self.lastmoditer, self.currentmodel.size / 2 - 1,
self.currentmisfits[-1], self.currentlikelihood,
runtime, acceptrate) + r'%')
self.tnull = time.time()
# stabilize model acceptance rate
if self.iiter % 1000 == 0:
if np.all(self.proposed) != 0:
self.adjust_acceptrate()
self.iiter += 1
def _validmodel(self, model):
"""
Check model before the forward modeling.
- The model must contain all values > 0.
- The layer thicknesses must be at least thickmin km.
- if lvz: low velocity zones are allowed with the deeper layer velocity
no smaller than (1-perc) * velocity of layer above.
- ... and some other constraints. E.g. vs boundaries (prior) given.
"""
vp, vs, h = Model.get_vp_vs_h(model, self.currentvpvs, self.mantle)
# check whether nlayers lies within the prior
layermin = self.priors['layers'][0]
layermax = self.priors['layers'][1]
layermodel = (h.size - 1)
if not (layermodel >= layermin and layermodel <= layermax):
logger.debug("chain%d: model- nlayers not in prior" %
self.chainidx)
return False
# check model for layers with thicknesses of smaller thickmin
if np.any(h[:-1] < self.thickmin):
logger.debug("chain%d: thicknesses are not larger than thickmin" %
self.chainidx)
return False
# check whether vs lies within the prior
vsmin = self.priors['vs'][0]
vsmax = self.priors['vs'][1]
if np.any(vs < vsmin) or np.any(vs > vsmax):
logger.debug("chain%d: model- vs not in prior" % self.chainidx)
return False
# check whether interfaces lie within prior
zmin = self.priors['z'][0]
zmax = self.priors['z'][1]
z = np.cumsum(h)
if np.any(z < zmin) or np.any(z > zmax):
logger.debug("chain%d: model- z not in prior" % self.chainidx)
return False
if self.lowvelperc is not None:
# check model for low velocity zones. If larger than perc, then
# compvels must be positive
compvels = vs[1:] - (vs[:-1] * (1 - self.lowvelperc))
if not compvels.size == compvels[compvels > 0].size:
logger.debug("chain%d: low velocity zone issues" %
self.chainidx)
return False
if self.highvelperc is not None:
# check model for high velocity zones. If larger than perc, then
# compvels must be positive.
compvels = (vs[:-1] * (1 + self.highvelperc)) - vs[1:]
if not compvels.size == compvels[compvels > 0].size:
logger.debug("chain%d: high velocity zone issues" %
self.chainidx)
return False
return True
def plot_moho_crustvel_tradeoff(self, moho=None, mohovs=None, refmodel=None):
models, vpvs = self._get_posterior_data(['models', 'vpvs'], final=True)
if moho is None:
moho = self.priors['z']
if mohovs is None:
mohovs = 4.2 # km/s
mohos = np.zeros(len(models)) * np.nan
vscrust = np.zeros(len(models)) * np.nan
vslastlayer = np.zeros(len(models)) * np.nan
vsjumps = np.zeros(len(models)) * np.nan
for i, model in enumerate(models):
thisvpvs = vpvs[i]
vp, vs, h = Model.get_vp_vs_h(model, thisvpvs, self.mantle)
# cvp, cvs, cdepth = Model.get_stepmodel_from_h(h=h, vs=vs, vp=vp)
# ifaces, vs = cdepth[1::2], cvs[::2] # interfaces, vs
ifaces = np.cumsum(h)
vsstep = np.diff(vs) # velocity change at interfaces
mohoidxs = np.argwhere((ifaces > moho[0]) & (ifaces < moho[1]))
if len(mohoidxs) == 0:
continue
# mohoidx = mohoidxs[np.argmax(vsstep[mohoidxs])][0]
mohoidxs = mohoidxs.flatten()
mohoidxs_vs = np.where((vs > mohovs))[0]-1
if len(mohoidxs_vs) == 0:
continue
mohoidx = np.intersect1d(mohoidxs, mohoidxs_vs)
if len(mohoidx) == 0:
continue
mohoidx = mohoidx[0]
# ------
thismoho = ifaces[mohoidx]
crustmean = np.sum(vs[:(mohoidx+1)] * h[:(mohoidx+1)]) / ifaces[mohoidx]
lastvs = vs[mohoidx]
vsjump = vsstep[mohoidx]
mohos[i] = thismoho
vscrust[i] = crustmean
vslastlayer[i] = lastvs
vsjumps[i] = vsjump
# exclude nan values
mohos = mohos[~np.isnan(vsjumps)]
vscrust = vscrust[~np.isnan(vsjumps)]
vslastlayer = vslastlayer[~np.isnan(vsjumps)]
vsjumps = vsjumps[~np.isnan(vsjumps)]
fig, ax = plt.subplots(2, 4, figsize=(11, 6))
fig.subplots_adjust(hspace=0.05)
fig.subplots_adjust(wspace=0.05)
labels = ['$V_S$ last crustal layer', '$V_S$ crustal mean', '$V_S$ increase']
bins = 50
for n, xdata in enumerate([vslastlayer, vscrust, vsjumps]):
try:
histdata = ax[0][n].hist(xdata, bins=bins,
color='darkblue', alpha=0.7,
edgecolor='white', linewidth=0.4)
median = np.median(xdata)
ax[0][n].axvline(median, color='k', ls='--', lw=1.2, alpha=1)
stats = 'median:\n%.2f km/s' % median
ax[0][n].text(0.97, 0.97, stats,
fontsize=9, color='k',
horizontalalignment='right',
verticalalignment='top',
transform=ax[0][n].transAxes)
except:
pass
for n, xdata in enumerate([vslastlayer, vscrust, vsjumps]):
try:
ax[1][n].set_xlabel(labels[n])
data = ax[1][n].hist2d(xdata, mohos, bins=bins)
data2d, xedges, yedges, _ = np.array(data).T
xi, yi = np.unravel_index(data2d.argmax(), data2d.shape)
x_mode = ((xedges[:-1] + xedges[1:]) / 2.)[xi]
y_mode = ((yedges[:-1] + yedges[1:]) / 2.)[yi]
ax[1][n].axhline(y_mode, color='white', ls='--', lw=0.5, alpha=0.7)
ax[1][n].axvline(x_mode, color='white', ls='--', lw=0.5, alpha=0.7)
xmin, xmax = ax[1][n].get_xlim()
ax[0][n].set_xlim([xmin, xmax])
except:
pass
ax[0][n].set_yticks([])
ax[0][n].set_yticklabels([], visible=False)
ax[0][n].set_xticklabels([], visible=False)
ax[1][1].set_yticklabels([], visible=False)
ax[1][2].set_yticklabels([], visible=False)
ax[1][3].set_yticklabels([], visible=False)
ax[1][0].set_ylabel('Moho depth in km')
# plot moho 1d histogram
histdata = ax[1][3].hist(mohos, bins=bins, orientation='horizontal',
color='darkblue', alpha=0.7,
edgecolor='white', linewidth=0.4)
median = np.median(mohos)
std = np.std(mohos)
print 'moho: %.4f +- %.4f km' % (median, std)
ax[1][3].axhline(median, color='k', ls='--', lw=1.2, alpha=1)
stats = 'median:\n%.2f km' % median
ax[1][3].text(0.97, 0.97, stats,
fontsize=9, color='k',
horizontalalignment='right',
verticalalignment='top',
transform=ax[1][3].transAxes)
ymin, ymax = ax[1][0].get_ylim()
# ymin, ymax = median - 4*std, median + 4*std
ax[1][0].set_ylim(ymin, ymax)
ax[1][1].set_ylim(ymin, ymax)
ax[1][2].set_ylim(ymin, ymax)
ax[1][3].set_ylim(ymin, ymax)
ax[1][3].set_xticklabels([], visible=False)
ax[1][3].set_yticks([])
ax[1][3].set_yticklabels([], visible=False)
ax[0][3].axis('off')
if refmodel is not None:
dep, vs = refmodel
h = (dep[1:] - dep[:-1])[::2]
ifaces, lvs = dep[1::2], vs[::2]
vsstep = np.diff(lvs) # velocity change at interfaces
mohoidxs = np.argwhere((ifaces > moho[0]) & (ifaces < moho[1]))
mohoidx = mohoidxs[np.argmax(vsstep[mohoidxs])][0]
truemoho = ifaces[mohoidx]
truecrust = np.sum(lvs[:(mohoidx+1)] * h[:(mohoidx+1)]) / ifaces[mohoidx]
truevslast = lvs[mohoidx]
truevsjump = vsstep[mohoidx]
for n, xdata in enumerate([truevslast, truecrust, truevsjump]):
ax[1][n].axhline(truemoho, color='red', ls='--', lw=0.5, alpha=0.7)
ax[1][n].axvline(xdata, color='red', ls='--', lw=0.5, alpha=0.7)
return fig
def update_chain(self):
print('New chain index:', self.chainidx)
# if new chain is chosen
self.modelmatrix, self.likes, self.noises, self.vpvss = self.chainarrays[
self.chainidx]
nantmp = np.ones(self.modellength) * np.nan
# reset vs and dep matrix to nan
self.vs_step = np.ones((self.capacity, self.modellength)) * np.nan
self.dep_step = np.ones((self.capacity, self.modellength)) * np.nan
for i, model in enumerate(self.modelmatrix):
# if nan model, the first element is also nan !
if ~np.isnan(model[0]):
vp, vs, dep = Model.get_stepmodel(model,
vpvs=self.vpvss[i],
mantle=self.mantle)
dep[-1] = self.priors['z'][-1] * 1.5
self.vs_step = np.roll(self.vs_step, -1,
axis=0) # rolling up models
vs = nantmp[:vs.size] = vs
self.vs_step[-1][:vs.size] = vs
self.dep_step = np.roll(self.dep_step, -1,
axis=0) # rolling up models
dep = nantmp[:dep.size] = dep
self.dep_step[-1][:dep.size] = dep
# update title
self.axes[0].set_title('Chain %d' % self.chainidx)
lastmodel = model
lastvpvs = self.vpvss[-1]
# immediately update data fit lines
vp, vs, h = Model.get_vp_vs_h(lastmodel,
vpvs=lastvpvs,
mantle=self.mantle)
ymod = self.compute_synth(h, vs, vp)
for i, tline in enumerate(self.targetlines):
if tline is not None:
tline.set_ydata(ymod[i])
# # create LineCollection and update velocity models
segments = [
np.column_stack([x, y])
for x, y in zip(self.vs_step, self.dep_step)
]
self.modelcollection.set_segments(segments)
self.likeline.set_ydata(self.likes)
self.axes[3].set_ylim(
[np.nanmin(self.likes) * 0.999,
np.nanmax(self.likes) * 1.001])
# vpvs
a = np.repeat(([0, 1], ), self.capacity, axis=0)
b = np.array([[v] * 2 for v in self.vpvss])
segments = [np.column_stack([x, y]) for x, y in zip(b, a)]
self.vpvscollection.set_segments(segments)
for i, sline in enumerate(self.sigmalines):
if sline is not None:
ref = self.targetrefs[i]
idx = self.targetrefs.index(ref)
sline.set_ydata(self.noises.T[1::2][idx])
self.axes[4].set_ylim([
np.nanmin(self.noises.T[1::2]) * 0.98,
np.nanmax(self.noises.T[1::2]) * 1.02
])
self.fig.canvas.draw_idle()