from __future__ import print_function
import math
import os.path as op
import os
import logging
import time
import numpy as num
from collections import OrderedDict
from pyrocko.guts import StringChoice, Int, Float, Object, List, load_all
from pyrocko.guts_array import Array
from grond.meta import GrondError, Forbidden, has_get_plot_classes, Path
from grond import problems
from grond.problems.base import ModelHistory
from grond.optimisers.base import Optimiser, OptimiserConfig, BadProblem, \
OptimiserStatus
guts_prefix = 'grond'
logger = logging.getLogger('grond.optimisers.highscore.optimiser')
def nextpow2(i):
return 2**int(math.ceil(math.log(i)/math.log(2.)))
def excentricity_compensated_probabilities(xs, sbx, factor):
inonflat = num.where(sbx != 0.0)[0]
scale = num.zeros_like(sbx)
scale[inonflat] = 1.0 / (sbx[inonflat] * (factor if factor != 0. else 1.0))
distances_sqr_all = num.sum(
((xs[num.newaxis, :, :] - xs[:, num.newaxis, :]) *
scale[num.newaxis, num.newaxis, :])**2, axis=2)
probabilities = 1.0 / num.sum(distances_sqr_all < 1.0, axis=1)
# print(num.sort(num.sum(distances_sqr_all < 1.0, axis=1)))
probabilities /= num.sum(probabilities)
return probabilities
def excentricity_compensated_choice(xs, sbx, factor, rstate):
probabilities = excentricity_compensated_probabilities(
xs, sbx, factor)
r = rstate.random_sample()
ichoice = num.searchsorted(num.cumsum(probabilities), r)
ichoice = min(ichoice, xs.shape[0]-1)
return ichoice
def local_std(xs):
ssbx = num.sort(xs, axis=0)
dssbx = num.diff(ssbx, axis=0)
mdssbx = num.median(dssbx, axis=0)
return mdssbx * dssbx.shape[0] / 2.6
[docs]class SamplerDistributionChoice(StringChoice):
choices = ['multivariate_normal', 'normal']
[docs]class StandardDeviationEstimatorChoice(StringChoice):
choices = [
'median_density_single_chain',
'standard_deviation_all_chains',
'standard_deviation_single_chain']
class SamplerStartingPointChoice(StringChoice):
choices = ['excentricity_compensated', 'random', 'mean']
class BootstrapTypeChoice(StringChoice):
choices = ['bayesian', 'classic']
def fnone(i):
return i if i is not None else -1
class Sample(Object):
'''Sample model with context about how it was generated.'''
model = Array.T(shape=(None,), dtype=num.float, serialize_as='list')
iphase = Int.T(optional=True)
ichain_base = Int.T(optional=True)
ilink_base = Int.T(optional=True)
imodel_base = Int.T(optional=True)
def preconstrain(self, problem, optimiser=None):
self.model = problem.preconstrain(self.model, optimiser)
def pack_context(self):
i = num.zeros(4, dtype=num.int)
i[:] = (
fnone(self.iphase),
fnone(self.ichain_base),
fnone(self.ilink_base),
fnone(self.imodel_base))
return i
[docs]class SamplerPhase(Object):
niterations = Int.T(
help='Number of iteration for this phase.')
ntries_preconstrain_limit = Int.T(
default=1000,
help='Tries to find a valid preconstrained sample.')
seed = Int.T(
optional=True,
help='Random state seed.')
def __init__(self, *args, **kwargs):
Object.__init__(self, *args, **kwargs)
self._rstate = None
self.optimiser = None
def get_rstate(self, problem):
if self._rstate is None:
self._rstate = problem.get_rstate_manager().get_rstate(
self.__class__.__name__, self.seed)
return self._rstate
def get_raw_sample(self, problem, iiter, chains):
raise NotImplementedError
def get_sample(self, problem, iiter, chains):
assert 0 <= iiter < self.niterations
ntries_preconstrain = 0
for ntries_preconstrain in range(self.ntries_preconstrain_limit):
try:
sample = self.get_raw_sample(problem, iiter, chains)
sample.preconstrain(problem, self.optimiser)
return sample
except Forbidden:
pass
raise GrondError(
'could not find any suitable candidate sample within %i tries' % (
self.ntries_preconstrain_limit))
def set_optimiser(self, optimiser):
self.optimiser = optimiser
class InjectionError(Exception):
pass
[docs]class InjectionSamplerPhase(SamplerPhase):
'''Inject predefined/precomputed models into the optimisation
Injected models are given either as an array or are generated from
sources/events given in a file. Depending on the problem different sources
or events can be used:
* :py:class:`grond.problems.cmt.problem.CMTProblem` uses as input:
* :py:class:`pyrocko.model.event.Event` with
:py:class:`pyrocko.moment_tensor.MomentTensor`,
* :py:class:`pyrocko.gf.seismosizer.DCSource`,
* :py:class:`pyrocko.gf.seismosizer.MTSource`.
* :py:class:`grond.problems.double_dc.problem.DoubleDCProblem` uses as
input:
* :py:class:`pyrocko.gf.seismosizer.DoubleDCSource`.
* :py:class:`grond.problems.vlvd.problem.VLVDProblem` uses as input:
* :py:class:`pyrocko.gf.seismosizer.VLVDSource`.
* :py:class:`grond.problems.rectangular.problem.RectangularProblem` uses as
input:
* :py:class:`pyrocko.gf.seismosizer.RectangularSource`.
* :py:class:`grond.problems.dynamic_rupture.problem.DynamicRuptureProblem`
uses as input:
* :py:class:`pyrocko.gf.seismosizer.PseudoDynamicRupture`.
Only a single source or event file can be handled in one
:py:class:`grond.optimisers.highscore.optimiser.InjectionSamplerPhase`. The
number of iterations is adjusted according to the number of sources or
events found.
'''
xs_inject = Array.T(
optional=True,
dtype=num.float, shape=(None, None),
help='Array with the injected models.')
sources_path = Path.T(
optional=True,
help='File with sources to be injected as models')
events_path = Path.T(
optional=True,
help='File with events to be injected as models')
def _xs_inject_from_sources(self, problem):
sources = load_all(filename=self.sources_path)
if len(sources) == 0:
raise InjectionError('No sources found in the given sources_path.')
if num.unique([s.T.classname for s in sources]).shape[0] > 1:
raise InjectionError(
'Sources are not of same type in the given file.')
return num.array([problem.source_to_x(s) for s in sources])
def _xs_inject_from_events(self, problem):
from pyrocko import model
if not hasattr(problem, 'event_to_x'):
raise InjectionError(
'Events can only be injected using the %s. '
'Try injecting as sources defining the "sources_path" '
'attribute instead.' % (
problems.CMTProblem.T.classname))
events = model.load_events(filename=self.events_path)
if len(events) == 0:
raise InjectionError('No events found in the given events_path.')
events = [ev for ev in events if ev.moment_tensor is not None]
n_ev = len(events)
if n_ev == 0:
raise InjectionError(
'The loaded events have no moment tensor information.')
return num.array([problem.event_to_x(e) for e in events])
def xs_inject_from_file(self, problem):
if self.sources_path and self.events_path:
raise AttributeError(
'Sources_path and events_path are both given but mutually '
'exclusive.')
elif self.sources_path:
xs_inject = self._xs_inject_from_sources(problem)
elif self.events_path:
xs_inject = self._xs_inject_from_events(problem)
else:
raise IndexError(
'No event/source file found to generate xs_inject array from.')
if xs_inject.shape[0] != self.niterations:
logger.warn(
'Number of injected models (%i) not equal to the number of '
'iterations (%i) and is adjusted accordingly.' % (
xs_inject.shape[0], self.niterations))
self.niterations = xs_inject.shape[0]
self.xs_inject = xs_inject
def get_raw_sample(self, problem, iiter, chains):
if self.xs_inject is None:
self.xs_inject_from_file(problem)
return Sample(model=self.xs_inject[iiter, :])
[docs]class DirectedSamplerPhase(SamplerPhase):
scatter_scale = Float.T(
optional=True,
help='Scales search radius around the current `highscore` models')
scatter_scale_begin = Float.T(
optional=True,
help='Scaling factor at beginning of the phase.')
scatter_scale_end = Float.T(
optional=True,
help='Scaling factor at the end of the directed phase.')
starting_point = SamplerStartingPointChoice.T(
default='excentricity_compensated',
help='Tunes to the center value of the sampler distribution.'
'May increase the likelihood to draw a highscore member model'
' off-center to the mean value')
sampler_distribution = SamplerDistributionChoice.T(
default='normal',
help='Distribution new models are drawn from.')
standard_deviation_estimator = StandardDeviationEstimatorChoice.T(
default='median_density_single_chain')
ntries_sample_limit = Int.T(default=1000)
def get_scatter_scale_factor(self, iiter):
s = self.scatter_scale
sa = self.scatter_scale_begin
sb = self.scatter_scale_end
assert s is None or (sa is None and sb is None)
if sa != sb:
tb = float(self.niterations-1)
tau = tb/(math.log(sa) - math.log(sb))
t0 = math.log(sa) * tau
t = float(iiter)
return num.exp(-(t-t0) / tau)
else:
return s or 1.0
def get_raw_sample(self, problem, iiter, chains):
rstate = self.get_rstate(problem)
factor = self.get_scatter_scale_factor(iiter)
npar = problem.nparameters
pnames = problem.parameter_names
xbounds = problem.get_parameter_bounds()
ilink_choice = None
ichain_choice = num.argmin(chains.accept_sum)
if self.starting_point == 'excentricity_compensated':
models = chains.models(ichain_choice)
ilink_choice = excentricity_compensated_choice(
models,
chains.standard_deviation_models(
ichain_choice, self.standard_deviation_estimator),
2., rstate)
xchoice = chains.model(ichain_choice, ilink_choice)
elif self.starting_point == 'random':
ilink_choice = rstate.randint(0, chains.nlinks)
xchoice = chains.model(ichain_choice, ilink_choice)
elif self.starting_point == 'mean':
xchoice = chains.mean_model(ichain_choice)
else:
assert False, 'invalid starting_point choice: %s' % (
self.starting_point)
ntries_sample = 0
if self.sampler_distribution == 'normal':
x = num.zeros(npar, dtype=num.float)
sx = chains.standard_deviation_models(
ichain_choice, self.standard_deviation_estimator)
for ipar in range(npar):
ntries = 0
while True:
if sx[ipar] > 0.:
v = rstate.normal(
xchoice[ipar],
factor*sx[ipar])
else:
v = xchoice[ipar]
if xbounds[ipar, 0] <= v and \
v <= xbounds[ipar, 1]:
break
if ntries > self.ntries_sample_limit:
logger.warning(
'failed to produce a suitable '
'candidate sample from normal '
'distribution for parameter \'%s\''
'- drawing from uniform instead.' %
pnames[ipar])
v = rstate.uniform(xbounds[ipar, 0],
xbounds[ipar, 1])
break
ntries += 1
x[ipar] = v
elif self.sampler_distribution == 'multivariate_normal':
ok_mask_sum = num.zeros(npar, dtype=num.int)
while True:
ntries_sample += 1
xcandi = rstate.multivariate_normal(
xchoice, factor**2 * chains.cov(ichain_choice))
ok_mask = num.logical_and(
xbounds[:, 0] <= xcandi, xcandi <= xbounds[:, 1])
if num.all(ok_mask):
break
ok_mask_sum += ok_mask
if ntries_sample > self.ntries_sample_limit:
logger.warning(
'failed to produce a suitable candidate '
'sample from multivariate normal '
'distribution, (%s) - drawing from uniform instead' %
', '.join('%s:%i' % xx for xx in
zip(pnames, ok_mask_sum)))
xbounds = problem.get_parameter_bounds()
xcandi = problem.random_uniform(xbounds, rstate)
break
x = xcandi
imodel_base = None
if ilink_choice is not None:
imodel_base = chains.imodel(ichain_choice, ilink_choice)
return Sample(
model=x,
ichain_base=ichain_choice,
ilink_base=ilink_choice,
imodel_base=imodel_base)
def make_bayesian_weights(nbootstrap, nmisfits,
type='bayesian', rstate=None):
ws = num.zeros((nbootstrap, nmisfits))
if rstate is None:
rstate = num.random.RandomState()
for ibootstrap in range(nbootstrap):
if type == 'classic':
ii = rstate.randint(0, nmisfits, size=nmisfits)
ws[ibootstrap, :] = num.histogram(
ii, nmisfits, (-0.5, nmisfits - 0.5))[0]
elif type == 'bayesian':
f = rstate.uniform(0., 1., size=nmisfits+1)
f[0] = 0.
f[-1] = 1.
f = num.sort(f)
g = f[1:] - f[:-1]
ws[ibootstrap, :] = g * nmisfits
else:
assert False
return ws
class Chains(object):
def __init__(
self, problem, history, nchains, nlinks_cap):
self.problem = problem
self.history = history
self.nchains = nchains
self.nlinks_cap = nlinks_cap
self.chains_m = num.zeros(
(self.nchains, nlinks_cap), dtype=num.float)
self.chains_i = num.zeros(
(self.nchains, nlinks_cap), dtype=num.int)
self.nlinks = 0
self.nread = 0
self.accept_sum = num.zeros(self.nchains, dtype=num.int)
self._acceptance_history = num.zeros(
(self.nchains, 1024), dtype=num.bool)
history.add_listener(self)
def goto(self, n=None):
if n is None:
n = self.history.nmodels
n = min(self.history.nmodels, n)
assert self.nread <= n
while self.nread < n:
nread = self.nread
gbms = self.history.bootstrap_misfits[nread, :]
self.chains_m[:, self.nlinks] = gbms
self.chains_i[:, self.nlinks] = nread
nbootstrap = self.chains_m.shape[0]
self.nlinks += 1
chains_m = self.chains_m
chains_i = self.chains_i
for ichain in range(nbootstrap):
isort = num.argsort(chains_m[ichain, :self.nlinks])
chains_m[ichain, :self.nlinks] = chains_m[ichain, isort]
chains_i[ichain, :self.nlinks] = chains_i[ichain, isort]
if self.nlinks == self.nlinks_cap:
accept = (chains_i[:, self.nlinks_cap-1] != nread) \
.astype(num.bool)
self.nlinks -= 1
else:
accept = num.ones(self.nchains, dtype=num.bool)
self._append_acceptance(accept)
self.accept_sum += accept
self.nread += 1
def load(self):
return self.goto()
def extend(self, ioffset, n, models, misfits, sampler_contexts):
self.goto(ioffset + n)
def indices(self, ichain):
if ichain is not None:
return self.chains_i[ichain, :self.nlinks]
else:
return self.chains_i[:, :self.nlinks].ravel()
def models(self, ichain=None):
return self.history.models[self.indices(ichain), :]
def model(self, ichain, ilink):
return self.history.models[self.chains_i[ichain, ilink], :]
def imodel(self, ichain, ilink):
return self.chains_i[ichain, ilink]
def misfits(self, ichain=0):
return self.chains_m[ichain, :self.nlinks]
def misfit(self, ichain, ilink):
assert ilink < self.nlinks
return self.chains_m[ichain, ilink]
def mean_model(self, ichain=None):
xs = self.models(ichain)
return num.mean(xs, axis=0)
def best_model(self, ichain=0):
xs = self.models(ichain)
return xs[0]
def best_model_misfit(self, ichain=0):
return self.chains_m[ichain, 0]
def standard_deviation_models(self, ichain, estimator):
if estimator == 'median_density_single_chain':
xs = self.models(ichain)
return local_std(xs)
elif estimator == 'standard_deviation_all_chains':
bxs = self.models()
return num.std(bxs, axis=0)
elif estimator == 'standard_deviation_single_chain':
xs = self.models(ichain)
return num.std(xs, axis=0)
else:
assert False, 'invalid standard_deviation_estimator choice'
def covariance_models(self, ichain):
xs = self.models(ichain)
return num.cov(xs.T)
@property
def acceptance_history(self):
return self._acceptance_history[:, :self.nread]
def _append_acceptance(self, acceptance):
if self.nread >= self._acceptance_history.shape[1]:
new_buf = num.zeros(
(self.nchains, nextpow2(self.nread+1)), dtype=num.bool)
new_buf[:, :self._acceptance_history.shape[1]] = \
self._acceptance_history
self._acceptance_history = new_buf
self._acceptance_history[:, self.nread] = acceptance
[docs]@has_get_plot_classes
class HighScoreOptimiser(Optimiser):
'''Monte-Carlo-based directed search optimisation with bootstrap.'''
sampler_phases = List.T(SamplerPhase.T())
chain_length_factor = Float.T(default=8.)
nbootstrap = Int.T(default=100)
bootstrap_type = BootstrapTypeChoice.T(default='bayesian')
bootstrap_seed = Int.T(default=23)
SPARKS = u'\u2581\u2582\u2583\u2584\u2585\u2586\u2587\u2588'
ACCEPTANCE_AVG_LEN = 100
def __init__(self, **kwargs):
Optimiser.__init__(self, **kwargs)
self._bootstrap_weights = None
self._bootstrap_residuals = None
self._correlated_weights = None
self._status_chains = None
self._rstate_bootstrap = None
for phase in self.sampler_phases:
phase.set_optimiser(self)
def get_rstate_bootstrap(self, problem):
if self._rstate_bootstrap is None:
self._rstate_bootstrap = problem.get_rstate_manager().get_rstate(
'bootstraps', self.bootstrap_seed)
return self._rstate_bootstrap
def init_bootstraps(self, problem):
self.init_bootstrap_weights(problem)
self.init_bootstrap_residuals(problem)
def init_bootstrap_weights(self, problem):
logger.info('Initializing Bayesian bootstrap weights.')
nmisfits_w = sum(
t.nmisfits for t in problem.targets if t.can_bootstrap_weights)
ws = make_bayesian_weights(
self.nbootstrap,
nmisfits=nmisfits_w,
rstate=self.get_rstate_bootstrap(problem))
imf = 0
for t in problem.targets:
if t.can_bootstrap_weights:
t.set_bootstrap_weights(ws[:, imf:imf+t.nmisfits])
imf += t.nmisfits
else:
t.set_bootstrap_weights(
num.ones((self.nbootstrap, t.nmisfits)))
def init_bootstrap_residuals(self, problem):
logger.info('Initializing Bayesian bootstrap residuals.')
for t in problem.targets:
if t.can_bootstrap_residuals:
t.init_bootstrap_residuals(
self.nbootstrap, rstate=self.get_rstate_bootstrap(problem),
nthreads=self._nthreads)
else:
t.set_bootstrap_residuals(
num.zeros((self.nbootstrap, t.nmisfits)))
def get_bootstrap_weights(self, problem):
if self._bootstrap_weights is None:
try:
problem.targets[0].get_bootstrap_weights()
except Exception:
self.init_bootstraps(problem)
bootstrap_weights = num.hstack(
[t.get_bootstrap_weights()
for t in problem.targets])
self._bootstrap_weights = num.vstack((
num.ones((1, problem.nmisfits)),
bootstrap_weights))
return self._bootstrap_weights
def get_bootstrap_residuals(self, problem):
if self._bootstrap_residuals is None:
try:
problem.targets[0].get_bootstrap_residuals()
except Exception:
self.init_bootstraps(problem)
bootstrap_residuals = num.hstack(
[t.get_bootstrap_residuals()
for t in problem.targets])
self._bootstrap_residuals = num.vstack((
num.zeros((1, problem.nmisfits)),
bootstrap_residuals))
return self._bootstrap_residuals
def get_correlated_weights(self, problem):
if self._correlated_weights is None:
corr = dict()
misfit_idx = num.cumsum(
[0.] + [t.nmisfits for t in problem.targets], dtype=num.int)
for it, target in enumerate(problem.targets):
weights = target.get_correlated_weights(
nthreads=self._nthreads)
if weights is None:
continue
corr[misfit_idx[it]] = weights
self._correlated_weights = corr
return self._correlated_weights
@property
def nchains(self):
return self.nbootstrap + 1
def chains(self, problem, history):
nlinks_cap = int(round(
self.chain_length_factor * problem.nparameters + 1))
return Chains(
problem, history,
nchains=self.nchains, nlinks_cap=nlinks_cap)
def get_sampler_phase(self, iiter):
niter = 0
for iphase, phase in enumerate(self.sampler_phases):
if iiter < niter + phase.niterations:
return iphase, phase, iiter - niter
niter += phase.niterations
assert False, 'sample out of bounds'
def log_progress(self, problem, iiter, niter, phase, iiter_phase):
t = time.time()
if self._tlog_last < t - 10. \
or iiter_phase == 0 \
or iiter_phase == phase.niterations - 1:
logger.info(
'%s at %i/%i (%s, %i/%i)' % (
problem.name,
iiter+1, niter,
phase.__class__.__name__, iiter_phase, phase.niterations))
self._tlog_last = t
def optimise(self, problem, rundir=None, history=None):
if rundir is not None:
self.dump(filename=op.join(rundir, 'optimiser.yaml'))
if not history:
history = ModelHistory(
problem,
nchains=self.nchains,
path=rundir, mode='w')
chains = self.chains(problem, history)
if history.mode == 'r':
if history.nmodels == self.niterations:
return
logger.info('Continuing run at %d iterations...', history.nmodels)
history.mode = 'w'
chains.goto()
niter = self.niterations
isbad_mask = None
self._tlog_last = 0
for iiter in range(history.nmodels, niter):
self.iiter = iiter
iphase, phase, iiter_phase = self.get_sampler_phase(iiter)
self.log_progress(problem, iiter, niter, phase, iiter_phase)
sample = phase.get_sample(problem, iiter_phase, chains)
sample.iphase = iphase
if isbad_mask is not None and num.any(isbad_mask):
isok_mask = num.logical_not(isbad_mask)
else:
isok_mask = None
misfits = problem.misfits(
sample.model, mask=isok_mask, nthreads=self._nthreads,
raise_bad=True)
bootstrap_misfits = problem.combine_misfits(
misfits,
extra_weights=self.get_bootstrap_weights(problem),
extra_residuals=self.get_bootstrap_residuals(problem),
extra_correlated_weights=self.get_correlated_weights(problem))
isbad_mask_new = num.isnan(misfits[:, 0])
if isbad_mask is not None and num.any(
isbad_mask != isbad_mask_new):
errmess = [
'problem %s: inconsistency in data availability'
' at iteration %i' %
(problem.name, iiter)]
for target, isbad_new, isbad in zip(
problem.targets, isbad_mask_new, isbad_mask):
if isbad_new != isbad:
errmess.append(' %s, %s -> %s' % (
target.string_id(), isbad, isbad_new))
raise BadProblem('\n'.join(errmess))
isbad_mask = isbad_mask_new
if num.all(isbad_mask):
raise BadProblem(
'Problem %s: all target misfit values are NaN.'
% problem.name)
history.append(
sample.model, misfits,
bootstrap_misfits,
sample.pack_context())
@property
def niterations(self):
return sum([ph.niterations for ph in self.sampler_phases])
def get_status(self, history):
if self._status_chains is None:
self._status_chains = self.chains(history.problem, history)
self._status_chains.goto(history.nmodels)
chains = self._status_chains
problem = history.problem
row_names = [p.name_nogroups for p in problem.parameters]
row_names.append('Misfit')
def colum_array(data):
arr = num.full(len(row_names), fill_value=num.nan)
arr[:data.size] = data
return arr
phase = self.get_sampler_phase(history.nmodels-1)[1]
bs_mean = colum_array(chains.mean_model(ichain=None))
bs_std = colum_array(chains.standard_deviation_models(
ichain=None, estimator='standard_deviation_all_chains'))
glob_mean = colum_array(chains.mean_model(ichain=0))
glob_mean[-1] = num.mean(chains.misfits(ichain=0))
glob_std = colum_array(chains.standard_deviation_models(
ichain=0, estimator='standard_deviation_single_chain'))
glob_std[-1] = num.std(chains.misfits(ichain=0))
glob_best = colum_array(chains.best_model(ichain=0))
glob_best[-1] = chains.best_model_misfit()
glob_misfits = chains.misfits(ichain=0)
acceptance_latest = chains.acceptance_history[
:, -min(chains.acceptance_history.shape[1], self.ACCEPTANCE_AVG_LEN):] # noqa
acceptance_avg = acceptance_latest.mean(axis=1)
def spark_plot(data, bins):
hist, _ = num.histogram(data, bins)
hist_max = num.max(hist)
if hist_max == 0.0:
hist_max = 1.0
hist = hist / hist_max
vec = num.digitize(hist, num.linspace(0., 1., len(self.SPARKS)))
return ''.join([self.SPARKS[b-1] for b in vec])
return OptimiserStatus(
row_names=row_names,
column_data=OrderedDict(
zip(['BS mean', 'BS std',
'Glob mean', 'Glob std', 'Glob best'],
[bs_mean, bs_std, glob_mean, glob_std, glob_best])),
extra_header= # noqa
u'Optimiser phase: {phase}, exploring {nchains} BS chains\n' # noqa
u'Global chain misfit distribution: \u2080{mf_dist}\xb9\n'
u'Acceptance rate distribution: \u2080{acceptance}'
u'\u2081\u2080\u2080\ufe6a (Median {acceptance_med:.1f}%)'
.format(
phase=phase.__class__.__name__,
nchains=chains.nchains,
mf_dist=spark_plot(
glob_misfits, num.linspace(0., 1., 25)),
acceptance=spark_plot(
acceptance_avg,
num.linspace(0., 1., 25)),
acceptance_med=num.median(acceptance_avg) * 100.
))
def get_movie_maker(
self, problem, history, xpar_name, ypar_name, movie_filename):
from . import plot
return plot.HighScoreOptimiserPlot(
self, problem, history, xpar_name, ypar_name, movie_filename)
@classmethod
def get_plot_classes(cls):
from .plot import HighScoreAcceptancePlot
plots = Optimiser.get_plot_classes()
plots.append(HighScoreAcceptancePlot)
return plots
[docs]class HighScoreOptimiserConfig(OptimiserConfig):
sampler_phases = List.T(
SamplerPhase.T(),
default=[UniformSamplerPhase(niterations=1000),
DirectedSamplerPhase(niterations=5000)],
help='Stages of the sampler: Start with uniform sampling of the model'
' model space and narrow down through directed sampling.')
chain_length_factor = Float.T(
default=8.,
help='Controls the length of each chain: '
'chain_length_factor * nparameters + 1')
nbootstrap = Int.T(
default=100,
help='Number of bootstrap realisations to be tracked simultaneously in'
' the optimisation.')
def get_optimiser(self):
return HighScoreOptimiser(
sampler_phases=list(self.sampler_phases),
chain_length_factor=self.chain_length_factor,
nbootstrap=self.nbootstrap)
def load_optimiser_history(dirname, problem):
fn = op.join(dirname, 'accepted')
with open(fn, 'r') as f:
nmodels = os.fstat(f.fileno()).st_size // (problem.nbootstrap+1)
data1 = num.fromfile(
f,
dtype='<i1',
count=nmodels*(problem.nbootstrap+1)).astype(num.bool)
accepted = data1.reshape((nmodels, problem.nbootstrap+1))
fn = op.join(dirname, 'choices')
with open(fn, 'r') as f:
data2 = num.fromfile(
f,
dtype='<i8',
count=nmodels*2).astype(num.int64)
ibootstrap_choices, imodel_choices = data2.reshape((nmodels, 2)).T
return ibootstrap_choices, imodel_choices, accepted
__all__ = '''
SamplerDistributionChoice
StandardDeviationEstimatorChoice
SamplerPhase
InjectionSamplerPhase
UniformSamplerPhase
DirectedSamplerPhase
Chains
HighScoreOptimiserConfig
HighScoreOptimiser
'''.split()
