def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
"""
Get seismic likelihood formula for the model built. Has to be called
within a with model context.
Parameters
----------
input_rvs : list
of :class:`pymc3.distribution.Distribution`
fixed_rvs : dict
of :class:`numpy.array`
hyperparams : dict
of :class:`pymc3.distribution.Distribution`
problem_config : :class:`config.ProblemConfig`
Returns
-------
posterior_llk : :class:`theano.tensor.Tensor`
"""
hp_specific = problem_config.dataset_specific_residual_noise_estimation
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
logger.info('Seismic optimization on: \n '
' %s' % ', '.join(self.input_rvs.keys()))
t2 = time()
wlogpts = []
self.init_hierarchicals(problem_config)
if self.config.station_corrections:
logger.info('Initialized %i hierarchical parameters for '
'station corrections.' %
len(self.get_unique_stations()))
for wmap in self.wavemaps:
synths, tmins = self.synthesizers[wmap.name](self.input_rvs)
if len(self.hierarchicals) > 0:
tmins += self.hierarchicals[self.correction_name][
wmap.station_correction_idxs]
data_trcs = self.choppers[wmap.name](tmins)
residuals = data_trcs - synths
logpts = multivariate_normal_chol(wmap.datasets,
wmap.weights,
hyperparams,
residuals,
hp_specific=hp_specific)
wlogpts.append(logpts)
t3 = time()
logger.debug('Teleseismic forward model on test model takes: %f' %
(t3 - t2))
llk = Deterministic(self._like_name, tt.concatenate((wlogpts)))
return llk.sum()
def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
"""
Get geodetic likelihood formula for the model built. Has to be called
within a with model context.
Part of the pymc3 model.
Parameters
----------
input_rvs : dict
of :class:`pymc3.distribution.Distribution`
fixed_rvs : dict
of :class:`numpy.array`
hyperparams : dict
of :class:`pymc3.distribution.Distribution`
problem_config : :class:`config.ProblemConfig`
Returns
-------
posterior_llk : :class:`theano.tensor.Tensor`
"""
hp_specific = self.config.dataset_specific_residual_noise_estimation
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
logger.info('Geodetic optimization on: \n '
'%s' % ', '.join(self.input_rvs.keys()))
self.input_rvs.update(fixed_rvs)
t0 = time()
disp = self.get_synths(self.input_rvs)
t1 = time()
logger.debug('Geodetic forward model on test model takes: %f' %
(t1 - t0))
los_disp = (disp * self.slos_vectors).sum(axis=1)
residuals = self.Bij.srmap(
tt.cast((self.sdata - los_disp) * self.sodws, tconfig.floatX))
self.init_hierarchicals(problem_config)
if self.config.corrections_config.has_enabled_corrections:
logger.info('Applying corrections! ...')
residuals = self.apply_corrections(residuals, operation='-')
logpts = multivariate_normal_chol(self.datasets,
self.weights,
hyperparams,
residuals,
hp_specific=hp_specific)
llk = Deterministic(self._like_name, logpts)
return llk.sum()
def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
"""
Formulation of the distribution problem for the model built. Has to be
called within a with-model-context.
Parameters
----------
input_rvs : list
of :class:`pymc3.distribution.Distribution`
hyperparams : dict
of :class:`pymc3.distribution.Distribution`
Returns
-------
llk : :class:`theano.tensor.Tensor`
log-likelihood for the distributed slip
"""
logger.info("Loading %s Green's Functions" % self.name)
self.load_gfs(crust_inds=[self.config.gf_config.reference_model_idx],
make_shared=True)
hp_specific = self.config.dataset_specific_residual_noise_estimation
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
ref_idx = self.config.gf_config.reference_model_idx
mu = tt.zeros((self.Bij.ordering.size), tconfig.floatX)
for var in self.slip_varnames:
key = self.get_gflibrary_key(crust_ind=ref_idx,
wavename='static',
component=var)
mu += self.gfs[key].stack_all(slips=input_rvs[var])
residuals = self.Bij.srmap(
tt.cast((self.sdata - mu) * self.sodws, tconfig.floatX))
self.init_hierarchicals(problem_config)
if len(self.hierarchicals) > 0:
residuals = self.remove_ramps(residuals)
logpts = multivariate_normal_chol(self.datasets,
self.weights,
hyperparams,
residuals,
hp_specific=hp_specific)
llk = Deterministic(self._like_name, logpts)
return llk.sum()
def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
"""
Get seismic likelihood formula for the model built. Has to be called
within a with model context.
Parameters
----------
input_rvs : list
of :class:`pymc3.distribution.Distribution` of source parameters
fixed_rvs : dict
of :class:`numpy.array`
hyperparams : dict
of :class:`pymc3.distribution.Distribution`
problem_config : :class:`config.ProblemConfig`
Returns
-------
posterior_llk : :class:`theano.tensor.Tensor`
"""
chop_bounds = ['b', 'c'] # we want llk calculation only between b c
hp_specific = self.config.dataset_specific_residual_noise_estimation
tpoint = problem_config.get_test_point()
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
logger.info('Seismic optimization on: \n '
' %s' % ', '.join(self.input_rvs.keys()))
self.input_rvs.update(fixed_rvs)
t2 = time()
wlogpts = []
self.init_hierarchicals(problem_config)
self.analyse_noise(tpoint, chop_bounds=chop_bounds)
self.init_weights()
if self.config.station_corrections:
logger.info('Initialized %i hierarchical parameters for '
'station corrections.' %
len(self.get_all_station_names()))
for wmap in self.wavemaps:
if len(self.hierarchicals) > 0:
time_shifts = self.hierarchicals[wmap.time_shifts_id][
wmap.station_correction_idxs]
self.input_rvs[self.correction_name] = time_shifts
wc = wmap.config
logger.info('Preparing data of "%s" for optimization' %
wmap._mapid)
wmap.prepare_data(source=self.events[wc.event_idx],
engine=self.engine,
outmode='array',
chop_bounds=chop_bounds)
logger.info('Initializing synthesizer for "%s"' % wmap._mapid)
if self.nevents == 1:
logger.info('Using all sources for wavemap %s !' % wmap._mapid)
sources = self.sources
else:
logger.info('Using source based on event %i for wavemap %s!' %
(wc.event_idx, wmap._mapid))
sources = [self.sources[wc.event_idx]]
self.synthesizers[wmap._mapid] = theanof.SeisSynthesizer(
engine=self.engine,
sources=sources,
targets=wmap.targets,
event=self.events[wc.event_idx],
arrival_taper=wc.arrival_taper,
arrival_times=wmap._arrival_times,
wavename=wmap.name,
filterer=wc.filterer,
pre_stack_cut=self.config.pre_stack_cut,
station_corrections=self.config.station_corrections)
synths, _ = self.synthesizers[wmap._mapid](self.input_rvs)
residuals = wmap.shared_data_array - synths
logpts = multivariate_normal_chol(wmap.datasets,
wmap.weights,
hyperparams,
residuals,
hp_specific=hp_specific)
wlogpts.append(logpts)
t3 = time()
logger.debug('Teleseismic forward model on test model takes: %f' %
(t3 - t2))
llk = Deterministic(self._like_name, tt.concatenate((wlogpts)))
return llk.sum()
def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
# no a, d taper bounds as GF library saved between b c
chop_bounds = ['b', 'c']
logger.info("Loading %s Green's Functions" % self.name)
self.load_gfs(crust_inds=[self.config.gf_config.reference_model_idx],
make_shared=False)
hp_specific = self.config.dataset_specific_residual_noise_estimation
tpoint = problem_config.get_test_point()
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
logger.info('Seismic optimization on: \n '
' %s' % ', '.join(self.input_rvs.keys()))
t2 = time()
wlogpts = []
self.analyse_noise(tpoint, chop_bounds=chop_bounds)
for gfs in self.gfs.values():
gfs.init_optimization()
self.init_weights()
self.init_hierarchicals(problem_config)
if self.config.station_corrections:
logger.info('Initialized %i hierarchical parameters for '
'station corrections.' %
len(self.get_all_station_names()))
self.input_rvs.update(fixed_rvs)
ref_idx = self.config.gf_config.reference_model_idx
nuc_strike = input_rvs['nucleation_strike']
nuc_dip = input_rvs['nucleation_dip']
t2 = time()
# convert velocities to rupture onset
logger.debug('Fast sweeping ...')
starttimes0 = tt.zeros((self.fault.npatches), dtype=tconfig.floatX)
for index in range(self.fault.nsubfaults):
nuc_dip_idx, nuc_strike_idx = self.fault.fault_locations2idxs(
index=index,
positions_dip=nuc_dip[index],
positions_strike=nuc_strike[index],
backend='theano')
sf_patch_indexs = self.fault.cum_subfault_npatches[index:index + 2]
starttimes_tmp = self.sweepers[index](
(1. /
self.fault.vector2subfault(index, input_rvs['velocities'])),
nuc_dip_idx, nuc_strike_idx)
starttimes_tmp += input_rvs['time'][index]
starttimes0 = tt.set_subtensor(
starttimes0[sf_patch_indexs[0]:sf_patch_indexs[1]],
starttimes_tmp)
wlogpts = []
for wmap in self.wavemaps:
wc = wmap.config
# station corrections
if len(self.hierarchicals) > 0:
logger.info('Applying station corrections ...')
starttimes = (tt.tile(starttimes0, wmap.n_t) - tt.repeat(
self.hierarchicals[wmap.time_shifts_id][
wmap.station_correction_idxs],
self.fault.npatches)).reshape(
(wmap.n_t, self.fault.npatches))
else:
logger.info('No station corrections ...')
starttimes = tt.tile(starttimes0, wmap.n_t).reshape(
(wmap.n_t, self.fault.npatches))
targetidxs = shared(num.atleast_2d(num.arange(wmap.n_t)).T,
borrow=True)
logger.debug('Stacking %s phase ...' % wc.name)
synthetics = tt.zeros(
(wmap.n_t,
wc.arrival_taper.nsamples(self.config.gf_config.sample_rate)),
dtype=tconfig.floatX)
# make sure data is init as array, if non-toeplitz above-traces!
wmap.prepare_data(source=self.events[wc.event_idx],
engine=self.engine,
outmode='array',
chop_bounds=chop_bounds)
for var in self.slip_varnames:
logger.debug('Stacking %s variable' % var)
key = self.get_gflibrary_key(crust_ind=ref_idx,
wavename=wmap.name,
component=var)
synthetics += self.gfs[key].stack_all(
targetidxs=targetidxs,
starttimes=starttimes,
durations=input_rvs['durations'],
slips=input_rvs[var],
interpolation=wc.interpolation)
residuals = wmap.shared_data_array - synthetics
logger.debug('Calculating likelihoods ...')
logpts = multivariate_normal_chol(wmap.datasets,
wmap.weights,
hyperparams,
residuals,
hp_specific=hp_specific)
wlogpts.append(logpts)
t3 = time()
logger.debug('Seismic formula on test model takes: %f' % (t3 - t2))
llk = Deterministic(self._like_name, tt.concatenate((wlogpts)))
return llk.sum()
def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
hp_specific = problem_config.dataset_specific_residual_noise_estimation
tpoint = problem_config.get_test_point()
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
logger.info(
'Seismic optimization on: \n '
' %s' % ', '.join(self.input_rvs.keys()))
t2 = time()
wlogpts = []
self.analyse_noise(tpoint)
self.init_weights()
self.init_hierarchicals(problem_config)
if self.config.station_corrections:
logger.info(
'Initialized %i hierarchical parameters for '
'station corrections.' % len(self.get_unique_stations()))
self.input_rvs.update(fixed_rvs)
ref_idx = self.config.gf_config.reference_model_idx
nuc_strike = input_rvs['nucleation_strike']
nuc_dip = input_rvs['nucleation_dip']
t2 = time()
# convert velocities to rupture onset
logger.debug('Fast sweeping ...')
nuc_dip_idx, nuc_strike_idx = self.fault.fault_locations2idxs(
positions_dip=nuc_dip,
positions_strike=nuc_strike,
backend='theano')
starttimes0 = self.sweeper(
(1. / input_rvs['velocities']), nuc_dip_idx, nuc_strike_idx)
starttimes0 += input_rvs['nucleation_time']
wlogpts = []
for wmap in self.wavemaps:
# station corrections
if len(self.hierarchicals) > 0:
raise NotImplementedError(
'Station corrections not fully implemented! for ffi!')
starttimes = (
tt.tile(starttimes0, wmap.n_t) +
tt.repeat(self.hierarchicals[self.correction_name][
wmap.station_correction_idxs],
self.fault.npatches)).reshape(
wmap.n_t, self.fault.npatches)
targetidxs = shared(
num.atleast_2d(num.arange(wmap.n_t)).T, borrow=True)
else:
starttimes = starttimes0
targetidxs = shared(num.lib.index_tricks.s_[:], borrow=True)
logger.debug('Stacking %s phase ...' % wmap.config.name)
synthetics = tt.zeros(
(wmap.n_t, wmap.config.arrival_taper.nsamples(
self.config.gf_config.sample_rate)),
dtype=tconfig.floatX)
for var in self.slip_varnames:
logger.debug('Stacking %s variable' % var)
key = self.get_gflibrary_key(
crust_ind=ref_idx, wavename=wmap.name, component=var)
synthetics += self.gfs[key].stack_all(
targetidxs=targetidxs,
starttimes=starttimes,
durations=input_rvs['durations'],
slips=input_rvs[var],
interpolation=wmap.config.interpolation)
residuals = wmap.shared_data_array - synthetics
logger.debug('Calculating likelihoods ...')
logpts = multivariate_normal_chol(
wmap.datasets, wmap.weights, hyperparams, residuals,
hp_specific=hp_specific)
wlogpts.append(logpts)
t3 = time()
logger.debug(
'Seismic formula on test model takes: %f' % (t3 - t2))
llk = Deterministic(self._like_name, tt.concatenate((wlogpts)))
return llk.sum()
def get_formula(self, input_rvs, fixed_rvs, hyperparams, problem_config):
hp_specific = problem_config.dataset_specific_residual_noise_estimation
self.input_rvs = input_rvs
self.fixed_rvs = fixed_rvs
logger.info('Seismic optimization on: \n '
' %s' % ', '.join(self.input_rvs.keys()))
t2 = time()
wlogpts = []
self.init_hierarchicals(problem_config)
if self.config.station_corrections:
logger.info('Initialized %i hierarchical parameters for '
'station corrections.' %
len(self.get_unique_stations()))
self.input_rvs.update(fixed_rvs)
ref_idx = self.config.gf_config.reference_model_idx
nuc_strike = input_rvs['nucleation_strike']
nuc_dip = input_rvs['nucleation_dip']
t2 = time()
# convert velocities to rupture onset
logger.debug('Fast sweeping ...')
nuc_dip_idx, nuc_strike_idx = self.fault.fault_locations2idxs(
positions_dip=nuc_dip,
positions_strike=nuc_strike,
backend='theano')
starttimes = self.sweeper((1. / input_rvs['velocities']), nuc_dip_idx,
nuc_strike_idx)
wlogpts = []
for wmap in self.wavemaps:
logger.debug('Stacking %s phase ...' % wmap.config.name)
synthetics = tt.zeros((wmap.n_t,
wmap.config.arrival_taper.nsamples(
self.config.gf_config.sample_rate)),
dtype=tconfig.floatX)
for var in self.slip_varnames:
logger.debug('Stacking %s variable' % var)
key = self.get_gflibrary_key(crust_ind=ref_idx,
wavename=wmap.name,
component=var)
synthetics += self.gfs[key].stack_all(
starttimes=starttimes,
durations=input_rvs['durations'],
slips=input_rvs[var],
interpolation=wmap.config.interpolation)
logger.debug('Get hypocenter location ...')
patchidx = self.fault.spatchmap(0,
dipidx=nuc_dip_idx,
strikeidx=nuc_strike_idx)
# cut data according to wavemaps
logger.debug('Cut data accordingly')
tmins = self.gfs[key].get_all_tmins(
patchidx).ravel() + input_rvs['nucleation_time']
# add station corrections
if len(self.hierarchicals) > 0:
tmins += self.hierarchicals[self.correction_name][
wmap.station_correction_idxs]
data_traces = self.choppers[wmap.name](tmins)
residuals = data_traces - synthetics
logger.debug('Calculating likelihoods ...')
logpts = multivariate_normal_chol(wmap.datasets,
wmap.weights,
hyperparams,
residuals,
hp_specific=hp_specific)
wlogpts.append(logpts)
t3 = time()
logger.debug('Seismic formula on test model takes: %f' % (t3 - t2))
llk = Deterministic(self._like_name, tt.concatenate((wlogpts)))
return llk.sum()