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Commit aacba13a authored by Sebastian Heimann's avatar Sebastian Heimann
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corrected harvesting, improved plots, hudson plot added

parent 0922e8a0
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src/cmt.py
View file @ aacba13a
......@@ -20,22 +20,22 @@ as_km = dict(scale_factor=km, scale_unit='km')
class CMTProblem(core.Problem):
parameters = [
core.Parameter('time', 's'),
core.Parameter('north_shift', 'm', **as_km),
core.Parameter('east_shift', 'm', **as_km),
core.Parameter('depth', 'm', **as_km),
core.Parameter('magnitude'),
core.Parameter('rmnn'),
core.Parameter('rmee'),
core.Parameter('rmdd'),
core.Parameter('rmne'),
core.Parameter('rmnd'),
core.Parameter('rmed'),
core.Parameter('duration')]
core.Parameter('time', 's', label='Time'),
core.Parameter('north_shift', 'm', label='Northing', **as_km),
core.Parameter('east_shift', 'm', label='Easting', **as_km),
core.Parameter('depth', 'm', label='Depth', **as_km),
core.Parameter('magnitude', label='Magnitude'),
core.Parameter('rmnn', label='$m_{nn} / M_0$'),
core.Parameter('rmee', label='$m_{ee} / M_0$'),
core.Parameter('rmdd', label='$m_{dd} / M_0$'),
core.Parameter('rmne', label='$m_{ne} / M_0$'),
core.Parameter('rmnd', label='$m_{nd} / M_0$'),
core.Parameter('rmed', label='$m_{ed} / M_0$'),
core.Parameter('duration', 's', label='Duration')]
dependants = [
core.Parameter('rel_moment_iso'),
core.Parameter('rel_moment_clvd')]
core.Parameter('rel_moment_iso', label='$M_{0}^{ISO}/M_{0}$'),
core.Parameter('rel_moment_clvd', label='$M_{0}^{CLVD}/M_{0}$')]
base_source = gf.Source.T()
targets = List.T(core.MisfitTarget.T())
......@@ -43,7 +43,7 @@ class CMTProblem(core.Problem):
ranges = Dict.T(String.T(), gf.Range.T())
distance_min = Float.T(default=0.0)
nbootstrap = Int.T(default=10)
mt_type = StringChoice.T(choices=['full', 'deviatoric'])
mt_type = StringChoice.T(default='full', choices=['full', 'deviatoric'])
def unpack(self, x):
d = self.parameter_dict(x)
......@@ -114,6 +114,15 @@ class CMTProblem(core.Problem):
return x
def random_uniform(self, xbounds):
x = num.zeros(self.nparameters)
for i in [0, 1, 2, 3, 4, 11]:
x[i] = num.random.uniform(xbounds[i, 0], xbounds[i, 1])
x[5:11] = mtm.random_m6()
return x.tolist()
def preconstrain(self, x):
d = self.parameter_dict(x)
......
src/core.py
View file @ aacba13a
......@@ -33,6 +33,7 @@ class Parameter(Object):
unit = String.T(optional=True)
scale_factor = Float.T(default=1., optional=True)
scale_unit = String.T(optional=True)
label = String.T(optional=True)
def __init__(self, *args, **kwargs):
if len(args) >= 1:
......@@ -42,15 +43,35 @@ class Parameter(Object):
Object.__init__(self, **kwargs)
def get_label(self):
l = [self.name]
if self.scale_unit is not None:
l.append('[%s]' % self.scale_unit)
elif self.unit is not None:
l.append('[%s]' % self.unit)
def get_label(self, with_unit=True):
l = [self.label or self.name]
if with_unit:
unit = self.get_unit_label()
if unit:
l.append('[%s]' % unit)
return ' '.join(l)
def get_value_label(self, value, format='%(value)g%(unit)s'):
value = self.scaled(value)
unit = self.get_unit_suffix()
return format % dict(value=value, unit=unit)
def get_unit_label(self):
if self.scale_unit is not None:
return self.scale_unit
elif self.unit:
return self.unit
else:
return None
def get_unit_suffix(self):
unit = self.get_unit_label()
if not unit:
return ''
else:
return ' %s' % unit
def scaled(self, x):
if isinstance(x, tuple):
return tuple(v/self.scale_factor for v in x)
......@@ -72,7 +93,7 @@ class Problem(Object):
name = String.T()
parameters = List.T(Parameter.T())
dependants = List.T(Parameter.T())
apply_balancing_weights = Bool.T()
apply_balancing_weights = Bool.T(default=True)
def __init__(self, **kwargs):
Object.__init__(self, **kwargs)
......@@ -822,6 +843,7 @@ def solve(problem,
xhist = num.zeros((niter, npar))
isbad_mask = None
accept_sum = num.zeros(1 + problem.nbootstrap, dtype=num.int)
accept_hist = num.zeros(niter, dtype=num.int)
while iiter < niter:
......@@ -843,10 +865,7 @@ def solve(problem,
ntries_preconstrain += 1
if mbx is None or iiter < niter_inject + niter_uniform:
x = []
for i in xrange(npar):
v = num.random.uniform(xbounds[i, 0], xbounds[i, 1])
x.append(v)
x = problem.random_uniform(xbounds)
else:
# jchoice = num.random.randint(0, 1 + problem.nbootstrap)
jchoice = num.argmin(accept_sum)
......@@ -932,6 +951,7 @@ def solve(problem,
accept = num.ones(1 + problem.nbootstrap, dtype=num.int)
accept_sum += accept
accept_hist[iiter] = num.sum(accept)
lines = []
if 'state' in status:
......@@ -1105,12 +1125,11 @@ def harvest(rundir, problem=None, nbest=10, force=False, weed=0):
if gms[ibest] > mean_gm_best + std_gm_best:
ibad.add(ibootstrap)
print ibad
ibests_list = [
ibests_ for (ibootstrap, ibests_) in enumerate(ibests_list)
if ibootstrap not in ibad]
ibests = num.vstack(ibests_list)
ibests = num.concatenate(ibests_list)
if weed == 2:
ibests = ibests[gms[ibests] < mean_gm_best]
......@@ -1143,7 +1162,7 @@ def go(config, force=False, nparallel=1, status=('state',)):
g_state[id(g_data)] = g_data
for x in parimap.parimap(
process_event,
process_event,
xrange(nevents),
[id(g_data)] * nevents,
nprocs=nparallel):
......@@ -1171,6 +1190,12 @@ def process_event(ievent, g_data_id):
problem = config.get_problem(event)
# FIXME
synt = ds.synthetic_test
if synt and synt.inject_solution:
problem.base_source = problem.unpack(synt.get_x())
check(problem)
rundir = config.rundir_template % dict(
......
src/plot.py
View file @ aacba13a
import math
import random
import logging
import os.path as op
import numpy as num
from scipy import signal
from pyrocko import automap, moment_tensor as mtm, beachball, guts, trace, util
from pyrocko import hudson
from grond import core
from matplotlib import pyplot as plt
from matplotlib import cm, patches
from pyrocko.cake_plot import mpl_init, labelspace, colors, \
str_to_mpl_color as scolor, light
logger = logging.getLogger('grond.plot')
km = 1000.
......@@ -24,6 +28,21 @@ def nextpow2(i):
return 2**int(math.ceil(math.log(i)/math.log(2.)))
def get_mean_source(problem, xs):
x_mean = num.mean(xs, axis=0)
source = problem.unpack(x_mean)
return source
def get_best_source(problem, xs, misfits):
gms = problem.global_misfits(misfits)
print gms.min(), gms.mean()
ibest = num.argmin(gms)
x_best = xs[ibest, :]
source = problem.unpack(x_best)
return source
def fixlim(lo, hi):
if lo == hi:
return lo - 1.0, hi + 1.0
......@@ -311,7 +330,16 @@ def draw_sequence_figures(model, plt, misfit_cutoff=None):
def draw_jointpar_figures(
model, plt, misfit_cutoff=None, ibootstrap=None, color=None):
model, plt, misfit_cutoff=None, ibootstrap=None, color=None,
exclude=None):
color = 'magnitude'
#exclude = ['duration']
neach = 6
figsize = (8, 8)
#cmap = cm.YlOrRd
#cmap = cm.jet
cmap = cm.coolwarm
problem = model.problem
if not problem:
......@@ -340,8 +368,6 @@ def draw_jointpar_figures(
nmodels = xs.shape[0]
color = 'misfit'
if color == 'dist':
mx = num.mean(xs, axis=0)
cov = num.cov(xs.T)
......@@ -353,38 +379,47 @@ def draw_jointpar_figures(
color = iorder
elif color in problem.parameter_names:
print 'xx'
ind = problem.name_to_index(color)
color = ordersort(problem.extract(xs, ind))
# npar = problem.nparameters
ncomb = problem.ncombined
smap = {}
iselected = 0
for ipar in xrange(problem.ncombined):
par = problem.combined[ipar]
if exclude and par.name in exclude:
continue
neach = 8
cmap = cm.YlOrRd
cmap = cm.jet
#cmap = cm.coolwarm
smap[iselected] = ipar
iselected += 1
nselected = iselected
nfig = (ncomb-1) / neach + 1
if nselected == 0:
return
nfig = (nselected-2) / neach + 1
figs = []
for ifig in xrange(nfig):
figs_row = []
for jfig in xrange(nfig):
if ifig >= jfig:
figs_row.append(plt.figure())
figs_row.append(plt.figure(figsize=figsize))
else:
figs_row.append(None)
figs.append(figs_row)
for ipar in xrange(ncomb):
for iselected in xrange(nselected):
ipar = smap[iselected]
ypar = problem.combined[ipar]
for jpar in xrange(ipar):
for jselected in xrange(iselected):
jpar = smap[jselected]
xpar = problem.combined[jpar]
ixg = (ipar - 1)
iyg = jpar
ixg = (iselected - 1)
iyg = jselected
ix = ixg % neach
iy = iyg % neach
......@@ -398,15 +433,48 @@ def draw_jointpar_figures(
axes = fig.add_subplot(*aind)
axes.set_xlim(*fixlim(*xpar.scaled(bounds[jpar])))
axes.set_ylim(*fixlim(*ypar.scaled(bounds[ipar])))
axes.axvline(0., color=scolor('aluminium3'), lw=0.5)
axes.axhline(0., color=scolor('aluminium3'), lw=0.5)
for spine in axes.spines.values():
spine.set_edgecolor(scolor('aluminium5'))
spine.set_linewidth(0.5)
xmin, xmax = fixlim(*xpar.scaled(bounds[jpar]))
ymin, ymax = fixlim(*ypar.scaled(bounds[ipar]))
if ix == 0 or jselected + 1 == iselected:
for (xpos, xoff, x) in [(0.0, 10., xmin), (1.0, -10., xmax)]:
axes.annotate(
'%.2g%s' % (x, xpar.get_unit_suffix()),
xy=(xpos, 1.05),
xycoords='axes fraction',
xytext=(xoff, 5.),
textcoords='offset points',
verticalalignment='bottom',
horizontalalignment='left',
rotation=45.)
if iy == neach - 1 or jselected + 1 == iselected:
for (ypos, yoff, y) in [(0., 10., ymin), (1.0, -10., ymax)]:
axes.annotate(
'%.2g%s' % (y, ypar.get_unit_suffix()),
xy=(1.0, ypos),
xycoords='axes fraction',
xytext=(5., yoff),
textcoords='offset points',
verticalalignment='bottom',
horizontalalignment='left',
rotation=45.)
axes.set_xlim(xmin, xmax)
axes.set_ylim(ymin, ymax)
axes.get_xaxis().set_ticks([])
axes.get_yaxis().set_ticks([])
if ipar == ncomb - 1 or ix == neach - 1:
if iselected == nselected - 1 or ix == neach - 1:
axes.annotate(
xpar.get_label(),
xpar.get_label(with_unit=False),
xy=(0.5, -0.05),
xycoords='axes fraction',
verticalalignment='top',
......@@ -415,21 +483,21 @@ def draw_jointpar_figures(
if iy == 0:
axes.annotate(
ypar.get_label(),
ypar.get_label(with_unit=False),
xy=(-0.05, 0.5),
xycoords='axes fraction',
verticalalignment='center',
horizontalalignment='right')
verticalalignment='top',
horizontalalignment='right',
rotation=45.)
fx = problem.extract(xs, jpar)
fy = problem.extract(xs, ipar)
axes.scatter(
xpar.scaled(fx),
ypar.scaled(fy),
c=color,
s=3, alpha=0.5, lw=0, cmap=cmap)
s=3, alpha=0.5, cmap=cmap, edgecolors='none')
cov = num.cov((xpar.scaled(fx), ypar.scaled(fy)))
evals, evecs = eigh_sorted(cov)
......@@ -445,8 +513,17 @@ def draw_jointpar_figures(
fx = problem.extract(xref, jpar)
fy = problem.extract(xref, ipar)
axes.axvline(xpar.scaled(fx), color='black', alpha=0.3)
axes.axhline(ypar.scaled(fy), color='black', alpha=0.3)
ref_color = scolor('aluminium6')
ref_color_light = 'none'
axes.plot(
xpar.scaled(fx), ypar.scaled(fy), 's',
mew=1.5, ms=5, color=ref_color_light, mec=ref_color)
for jfig, figs_row in enumerate(figs):
for ifig, fig in enumerate(figs_row):
if fig is not None:
fig.savefig('jointpar-%i-%i.pdf' % (jfig, ifig))
def draw_solution_figure(
......@@ -640,7 +717,6 @@ def draw_bootstrap_figure(model, plt):
bms_softclip = num.where(bms > 1.0, 0.1 * num.log10(bms) + 1.0, bms)
axes.plot(imodels, bms_softclip[isort_bms], color='red', alpha=0.2)
isort = num.argsort(gms)[::-1]
iorder = num.empty(isort.size)
iorder[isort] = imodels
......@@ -654,16 +730,12 @@ def draw_bootstrap_figure(model, plt):
axes.axhline(m, color='black')
axes.axhline(m-s, color='black', alpha=0.5)
#axes.plot(imodels[ibests], gms_softclip[isort[ibests]], 'x', color='black')
#axes.plot(imodels[ibests], gms_softclip[isort][ibests], '+', color='black')
#iii = isort[-1]
#axes.plot(imodels[iii], gms_softclip[isort][iii], 'o')
axes.plot(imodels, gms_softclip[isort], color='black')
axes.set_xlim(imodels[0], imodels[-1])
axes.set_xlabel('Tested model, sorted descending by global misfit value')
def gather(l, key, sort=None, filter=None):
d = {}
for x in l:
......@@ -859,7 +931,7 @@ def draw_fits_figures(ds, model, plt):
ixx = ix/nxmax
iyy = iy/nymax
if (iyy, ixx) not in figures:
figures[iyy, ixx] = plt.figure()
figures[iyy, ixx] = plt.figure(figsize=(16, 9))
fig = figures[iyy, ixx]
......@@ -992,10 +1064,93 @@ def draw_fits_figures(ds, model, plt):
title += ' (%i/%i, %i/%i)' % (iyy+1, nyy, ixx+1, nxx)
fig.suptitle(title, fontsize=fontsize)
fig.savefig('fits-%s-%i-%i.pdf' % (
title, iyy, ixx))
plt.show()
def draw_hudson_figure(model, plt):
color = 'black'
fontsize = 12.
markersize = fontsize * 1.5
markersize_small = markersize * 0.2
beachballsize = markersize
beachballsize_small = beachballsize * 0.5
width = 7.
figsize = (width, width / (4./3.))
problem = model.problem
mean_source = get_mean_source(problem, model.xs)
best_source = get_best_source(problem, model.xs, model.misfits)
fig = plt.figure(figsize=figsize)
axes = fig.add_subplot(1, 1, 1)
data = []
for ix, x in enumerate(model.xs):
source = problem.unpack(x)
mt = source.pyrocko_moment_tensor()
u, v = hudson.project(mt)
if random.random() < 0.1:
try:
beachball.plot_beachball_mpl(
mt, axes,
beachball_type='dc',
position=(u, v),
size=beachballsize_small,
color_t=color,
alpha=0.5,
zorder=1,
linewidth=0.25)
except beachball.BeachballError, e:
logger.warn(str(e))
else:
data.append((u, v))
if data:
u, v = num.array(data).T
axes.plot(
u, v, 'o',
color=color,
ms=markersize_small,
mec='none',
mew=0,
alpha=0.25,
zorder=0)
hudson.draw_axes(axes)
mt = mean_source.pyrocko_moment_tensor()
u, v = hudson.project(mt)
beachball.plot_beachball_mpl(
mt, axes,
beachball_type='dc',
position=(u, v),
size=beachballsize,
color_t=color,
zorder=-1,
linewidth=0.5)
mt = best_source.pyrocko_moment_tensor()
u, v = hudson.project(mt)
axes.plot(
u, v, 's',
markersize=markersize,
mew=1,
mec='black',
color='none',
zorder=1)
fig.savefig('hudson.pdf')
def xpop(s, k):
try:
s.remove(k)
......@@ -1010,6 +1165,7 @@ plot_dispatch = {
'sequence': draw_sequence_figures,
'contributions': draw_contributions_figure,
'jointpar': draw_jointpar_figures,
'hudson': draw_hudson_figure,
'fits': draw_fits_figures,
'solution': draw_solution_figure}
......@@ -1037,7 +1193,7 @@ def plot_result(dirname, plotnames_want):
if plotname in plotnames_want:
plot_dispatch[plotname](model, plt)
if 3 != len({'fits', 'jointpar', 'solution'} - plotnames_want):
if 4 != len({'fits', 'jointpar', 'hudson', 'solution'} - plotnames_want):
problem, xs, misfits = core.load_problem_info_and_data(
dirname, subset='harvest')
......@@ -1052,7 +1208,7 @@ def plot_result(dirname, plotnames_want):
ds = config.get_dataset()
plot_dispatch[plotname](ds, model, plt)
for plotname in ['jointpar', 'solution']:
for plotname in ['jointpar', 'hudson', 'solution']:
if plotname in plotnames_want:
plot_dispatch[plotname](model, plt)
......
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