def perturb_cmt(input_cmtfile, output_dir=".", dmoment_tensor=None,
dlongitude=None, dlatitude=None, ddepth_km=None):
cmt = CMTSource.from_CMTSOLUTION_file(input_cmtfile)
if dmoment_tensor is not None:
pert_type_list = ['m_rr', 'm_tt', 'm_pp', 'm_rt', 'm_rp', 'm_tp']
for pert_type in pert_type_list:
perturb_one_var(pert_type, cmt, dmoment_tensor, output_dir)
if dlongitude is not None:
perturb_one_var("longitude", cmt, dlongitude, output_dir)
if dlatitude is not None:
perturb_one_var("latitude", cmt, dlatitude, output_dir)
if ddepth_km is not None:
perturb_one_var("depth_in_m", cmt, ddepth_km*1000.0, output_dir)
def perturb_cmt(input_cmtfile, output_dir=".", dmoment_tensor=None,
dlongitude=None, dlatitude=None, ddepth_km=None):
cmt = CMTSource.from_CMTSOLUTION_file(input_cmtfile)
if dmoment_tensor is not None:
pert_type_list = ['m_rr', 'm_tt', 'm_pp', 'm_rt', 'm_rp', 'm_tp']
for pert_type in pert_type_list:
perturb_one_var(pert_type, cmt, dmoment_tensor, output_dir)
if dlongitude is not None:
perturb_one_var("longitude", cmt, dlongitude, output_dir)
if dlatitude is not None:
perturb_one_var("latitude", cmt, dlatitude, output_dir)
if ddepth_km is not None:
perturb_one_var("depth_in_m", cmt, ddepth_km*1000.0, output_dir)
def convert_new_cmt_par(self):
"""
Convert self.new_cmt_par array to CMTSource instance
:return:
"""
oldcmt = self.cmtsource
newcmt = self.new_cmt_par
time_shift = newcmt[9]
new_cmt_time = oldcmt.origin_time + time_shift
# copy old one
self.new_cmtsource = CMTSource(
origin_time=oldcmt.origin_time,
pde_latitude=oldcmt.pde_latitude,
pde_longitude=oldcmt.pde_longitude,
mb=oldcmt.mb, ms=oldcmt.ms, pde_depth_in_m=oldcmt.pde_depth_in_m,
region_tag=oldcmt.region_tag, eventname=oldcmt.eventname,
cmt_time=new_cmt_time, half_duration=newcmt[10],
latitude=newcmt[8], longitude=newcmt[7],
depth_in_m=newcmt[6] * 1000.0,
m_rr=newcmt[0], m_tt=newcmt[1], m_pp=newcmt[2], m_rt=newcmt[3],
m_rp=newcmt[4], m_tp=newcmt[5])
from obspy import readEvents import time import glob import os import sys from source import CMTSource from proc_util import process_obsd_file datadir = "../testdata/obsd" period_band = [27., 60.] cmtfile = "../testdata/cmt/C201311120703A" outputdir = "../testdata/obsd_proc" stationxmldir = "../testdata/stationxml" # read in cmt cmtsource = CMTSource.from_CMTSOLUTION_file(cmtfile) event_time = cmtsource.cmt_time print "Event cmt time:", event_time # interpolation parameter starttime = event_time endtime = event_time + 3600.0 # 1 hour = 3600 sec interp_deltat = 0.5 # deltat = 0.1s obsd_filelist = glob.glob(os.path.join(datadir, "*.mseed")) print "Total number of observed seismograms: %d" % len(obsd_filelist) # clock t1 = time.time() for obsd_file in obsd_filelist:
class Cmt3D(object):
"""
Class that handles the solver part of source inversion
:param cmtsource: earthquake source
:type cmtsource: :class:`pycmt3d.CMTSource`
:param data_container: all data and window
:type data_container: :class:`pycmt3d.DataContainer`
:param config: configuration for source inversion
:type config: :class:`pycmt3d.Config`
"""
def __init__(self, cmtsource, data_container, config):
self.config = config
self.cmtsource = cmtsource
self.data_container = data_container
self.window = self.data_container.window
self.nwins = self.data_container.nwins
# weight array
self.weight_array = np.zeros(self.nwins)
# measurement from each window
self.A1_all = []
self.b1_all = []
# original cmt par array
self.cmt_par = np.array(
[cmtsource.m_rr, cmtsource.m_tt, cmtsource.m_pp,
cmtsource.m_rt, cmtsource.m_rp, cmtsource.m_tp,
cmtsource.depth_in_m / 1000.0, cmtsource.longitude,
cmtsource.latitude, cmtsource.time_shift,
cmtsource.half_duration])
# new cmt par from the inversion
self.new_cmt_par = None
self.new_cmtsource = None
# azimuth information
self.naz_files = None
self.naz_files_all = None
self.naz_wins = None
self.naz_wins_all = None
# category bin
self.bin_category = None
# window stats before and after. For plotting purpose,
# it include nshift, cc, cc amplitude ratio, power ration,
# and kai of each window.
self.stats_after = None
self.stats_before = None
# variance information
self.var_all = None
self.var_all_new = None
self.var_reduction = None
# bootstrap stat var
self.par_mean = np.zeros(const.NPARMAX)
self.par_std = np.zeros(const.NPARMAX)
self.par_var = np.zeros(const.NPARMAX)
self.std_over_mean = np.zeros(self.par_mean.shape)
self.print_cmtsource_summary(self.cmtsource)
def setup_weight(self, weight_mode="num_wins"):
"""
Use Window information to setup weight.
:returns:
"""
logger.info("*" * 15)
logger.info("Start weighting...")
if self.config.weight_data:
# first calculate azimuth and distance for each data pair
self.prepare_for_weighting()
# then calculate azimuth weighting
for idx, window in enumerate(self.window):
if weight_mode.lower() == "num_files":
# weighted by the number of files in each azimuth bin
self.setup_weight_for_location(window, self.naz_files,
self.naz_files_all)
else:
# weighted by the number of windows in each azimuth bin
self.setup_weight_for_location(window, self.naz_wins,
self.naz_wins_all)
if self.config.normalize_category:
self.setup_weight_for_category(window)
if self.config.normalize_window:
window.weight = window.weight/window.energy
# normalization of data weights
self.normalize_weight()
# prepare the weight array
self.weight_array = np.zeros([self.data_container.nwins])
_idx = 0
for window in self.window:
for win_idx in range(window.num_wins):
self.weight_array[_idx] = window.weight[win_idx]
_idx += 1
def setup_weight_for_location(self, window, naz_bin, naz_bin_all):
"""
setup weight from location information, including distance,
component and azimuth
:param window:
:param naz_bin:
:param naz_bin_all:
:return:
"""
idx_naz = self.get_azimuth_bin_number(window.azimuth)
if self.config.normalize_category:
tag = window.tag['obsd']
naz = naz_bin[tag][idx_naz]
else:
naz = naz_bin_all[idx_naz]
logger.debug("%s.%s.%s, num_win, dist, naz: %d, %.2f, %d" % (
window.station, window.network, window.component,
window.num_wins, window.dist_in_km, naz))
if self.config.normalize_window:
mode = "uniform"
else:
# if the weight is not normalized by energy,
# then use the old weighting method(exponential)
mode = "exponential"
# weighting on compoent, distance and azimuth
window.weight = \
window.weight * self.config.weight_function(
window.component, window.dist_in_km, naz, window.num_wins,
dist_weight_mode=mode)
def setup_weight_for_category(self, window):
"""
Setup weight for each category if config.normalize_category
window_weight = window_weight / N_windows_in_category
:param window:
:return:
"""
if self.config.normalize_category:
tag = window.tag['obsd']
num_cat = self.bin_category[tag]
window.weight = window.weight/num_cat
def prepare_for_weighting(self):
"""
Prepare necessary information for weighting, e.x.,
calculating azimuth, distance and energty of a window.
Also, based on the tags, sort window into different categories.
:return:
"""
for window in self.window:
# calculate energy
window.win_energy(mode=self.config.norm_mode)
# calculate location
window.get_location_info(self.cmtsource)
self.naz_files, self.naz_wins = self.calculate_azimuth_bin()
# add all category together
# if not weighted by category, then use total number
self.naz_files_all = np.zeros(const.NREGIONS)
self.naz_wins_all = np.zeros(const.NREGIONS)
for key in self.naz_files.keys():
self.naz_files_all += self.naz_files[key]
self.naz_wins_all += self.naz_wins[key]
logger.info("Category: %s" % key)
logger.info("Azimuth file bin: [%s]"
% (', '.join(map(str, self.naz_files[key]))))
logger.info("Azimuth win bin: [%s]"
% (', '.join(map(str, self.naz_wins[key]))))
# stat different category
bin_category = {}
for window in self.window:
tag = window.tag['obsd']
if tag in bin_category.keys():
bin_category[tag] += window.num_wins
else:
bin_category[tag] = window.num_wins
self.bin_category = bin_category
@staticmethod
def get_azimuth_bin_number(azimuth):
"""
Calculate the bin number of a given azimuth
:param azimuth: test test test
:return:
"""
# the azimth ranges from [0,360]
# so a little modification here
daz = 360.0 / const.NREGIONS
k = int(math.floor(azimuth / daz))
if k < 0 or k > const.NREGIONS:
if azimuth - 360.0 < 0.0001:
k = const.NREGIONS - 1
else:
raise ValueError('Error bining azimuth')
return k
def calculate_azimuth_bin(self):
"""
Calculate the azimuth and sort them into bins
:return:
"""
naz_files = {}
naz_wins = {}
for window in self.window:
tag = window.tag['obsd']
bin_idx = self.get_azimuth_bin_number(window.azimuth)
if tag not in naz_files.keys():
naz_files[tag] = np.zeros(const.NREGIONS)
naz_wins[tag] = np.zeros(const.NREGIONS)
naz_files[tag][bin_idx] += 1
naz_wins[tag][bin_idx] += window.num_wins
return naz_files, naz_wins
def normalize_weight(self):
"""
Normalize the weighting and make the maximum to 1
:return:
"""
max_weight = 0.0
for window in self.window:
max_temp = np.max(window.weight)
if max_temp > max_weight:
max_weight = max_temp
logger.debug("Global Max Weight: %f" % max_weight)
for window in self.window:
logger.debug("%s.%s.%s, weight: [%s]"
% (window.network, window.station, window.component,
', '.join(map(self._float_to_str, window.weight))))
window.weight /= max_weight
logger.debug("Updated, weight: [%s]"
% (', '.join(map(self._float_to_str, window.weight))))
def get_station_info(self, datalist):
"""
Using the event location and station information to
calculate azimuth and distance
!!! Obsolete, not used any more !!!
:param datalist: data dictionary(referred to pycmt3d.Window.datalist)
:return:
"""
# this might be related to datafile type(sac, mseed or asdf)
event_lat = self.cmtsource.latitude
event_lon = self.cmtsource.longitude
# station location from synthetic file
sta_lat = datalist['synt'].stats.sac['stla']
sta_lon = datalist['synt'].stats.sac['stlo']
dist_in_m, az, baz = \
gps2DistAzimuth(event_lat, event_lon, sta_lat, sta_lon)
return [dist_in_m / 1000.0, az]
def setup_matrix(self):
"""
Calculate A and b for all windows
:return:
"""
logger.info("*" * 15)
logger.info("Set up inversion matrix")
for window in self.window:
# loop over pair of data
dsyn = self.calculate_dsyn(window.datalist)
for win_idx in range(window.num_wins):
# loop over each window
# here, A and b are exact measurements
# and no weightings are applied
[A1, b1] = self.compute_A_b(window, win_idx, dsyn)
self.A1_all.append(A1)
self.b1_all.append(b1)
def compute_A_b(self, window, win_idx, dsyn):
"""
Calculate the matrix A and vector b based on one pair of
observed data and synthetic data on a given window.
:param window: data and window information
:type window: :class:`pycmt3d.Window`
:param win_idx: window index(a specific window)
:type win_idx: integer
:param dsyn: derivative synthetic data matrix
:type dsyn: numpy.array
:return:
"""
npar = self.config.npar
datalist = window.datalist
obsd = datalist['obsd']
synt = datalist['synt']
npts = min(obsd.stats.npts, synt.stats.npts)
win = [window.win_time[win_idx, 0], window.win_time[win_idx, 1]]
istart = int(max(math.floor(win[0] / obsd.stats.delta), 1))
iend = int(min(math.ceil(win[1] / obsd.stats.delta), npts))
if istart > iend:
raise ValueError("Check window for %s.%s.%s.%s" %
(window.station, window.network,
window.location, window.component))
# station correction
istart_d, iend_d, istart_s, iend_s, nshift, cc, dlnA, cc_amp_value = \
self.apply_station_correction(obsd, synt, istart, iend)
dt_synt = datalist['synt'].stats.delta
dt_obsd = datalist['obsd'].stats.delta
if abs(dt_synt - dt_obsd) > 0.0001:
raise ValueError("Delta in synthetic and observed no the same")
dt = dt_synt
# hanning taper
taper = construct_taper(iend_s - istart_s, taper_type=const.taper_type)
A1 = np.zeros((npar, npar))
b1 = np.zeros(npar)
# compute A and b
for j in range(npar):
for i in range(0, j + 1):
A1[i, j] = np.sum(taper * dsyn[i, istart_s:iend_s] *
dsyn[j, istart_s:iend_s]) * dt
b1[j] = np.sum(
taper * (obsd.data[istart_d:iend_d] -
synt.data[istart_s:iend_s]) *
dsyn[j, istart_s:iend_s]) * dt
for j in range(npar):
for i in range(j + 1, npar):
A1[i, j] = A1[j, i]
return [A1, b1]
def calculate_dsyn(self, datalist):
"""
Calculate dsyn matrix based on perturbed seismograms
:param datalist:
:return:
"""
par_list = self.config.par_name
npar = self.config.npar
dcmt_par = self.config.dcmt_par
obsd = datalist['obsd']
synt = datalist['synt']
npts = min(obsd.stats.npts, synt.stats.npts)
dsyn = np.zeros((npar, npts))
for itype in range(npar):
type_name = par_list[itype]
if itype < const.NML:
# check file: check dt, npts
dt_synt = datalist['synt'].stats.delta
dt_obsd = datalist['obsd'].stats.delta
if abs(dt_synt - dt_obsd) > 0.0001:
raise ValueError("Delta in synthetic and observed no "
"the same")
dt = dt_synt
if itype < const.NM: # moment tensor
dsyn[itype, 0:npts] = \
datalist[type_name].data[0:npts] / dcmt_par[itype]
elif itype < const.NML: # location
dsyn[itype, 0:npts] = \
(datalist[type_name].data[0:npts] -
datalist['synt'].data[0:npts]) / dcmt_par[itype]
elif itype == const.NML: # time shift
dsyn[itype, 0:npts - 1] = \
(datalist['synt'].data[1:npts] -
datalist['synt'].data[0:(npts - 1)]) \
/ (dt * dcmt_par[itype])
dsyn[itype, npts - 1] = dsyn[itype, npts - 2]
elif itype == const.NML + 1: # half duration
dsyn[itype, 0:npts - 1] = -0.5 * self.cmt_par[itype] * (
dsyn[const.NML, 1:npts] - dsyn[const.NML, 0:npts - 1]) / dt
dsyn[itype, npts - 1] = dsyn[itype, npts - 2]
return dsyn
def apply_station_correction(self, obsd, synt, istart, iend):
"""
Apply station correction on windows based one cross-correlation
time shift if config.station_correction
:param obsd:
:param synt:
:param istart:
:param iend:
:return:
"""
npts = min(obsd.stats.npts, synt.stats.npts)
[nshift, cc, dlnA] = self.calculate_criteria(obsd, synt, istart, iend)
if self.config.station_correction:
istart_d = max(1, istart + nshift)
iend_d = min(npts, iend + nshift)
istart_s = istart_d - nshift
iend_s = iend_d - nshift
# recalculate the dlnA and cc_amp_value(considering the shift)
dlnA = \
self._dlnA_win_(obsd[istart_d:iend_d], synt[istart_s:iend_s])
cc_amp_value = \
10 * np.log10(np.sum(obsd[istart_d:iend_d] *
synt[istart_s:iend_s]) /
(synt[istart_s:iend_s] ** 2).sum())
else:
istart_d = istart
iend_d = iend
istart_s = istart
iend_s = iend
cc_amp_value = \
10 * np.log10(np.sum(obsd[istart_d:iend_d] *
synt[istart_s:iend_s]) /
(synt[istart_s:iend_s] ** 2).sum())
return istart_d, iend_d, istart_s, iend_s, nshift, \
cc, dlnA, cc_amp_value
def invert_solver(self, A, b, print_mode=False):
"""
Solver part. Hession matrix A and misfit vector b will be
reconstructed here based on different constraints.
:param A: basic Hessian matrix
:param b: basic misfit vector
:param print_mode: if True, then print out log information;
if False, then no log information
:return:
"""
npar = self.config.npar
old_par = self.cmt_par[0:npar] / self.config.scale_par[0:npar]
# scale the A and b matrix
max_row = np.amax(abs(A), axis=1)
for i in range(len(b)):
A[i, :] /= max_row[i]
b[i] /= max_row[i]
# setup inversion schema
if self.config.double_couple:
linear_inversion = False
na = npar + 2
elif self.config.zero_trace:
linear_inversion = True
na = npar + 1
else:
linear_inversion = True
na = npar
# add damping
trace = np.matrix.trace(A)
damp_matrix = np.zeros([npar, npar])
np.fill_diagonal(damp_matrix, trace * self.config.lamda_damping)
A = A + damp_matrix
if print_mode:
logger.info("Condition number of new A: %10.2f"
% np.linalg.cond(A))
if linear_inversion:
if print_mode:
logger.info("Linear Inversion...")
new_par = self.linear_solver(old_par, A, b, npar, na)
else:
if print_mode:
logger.info("Nonlinear Inversion...")
new_par = self.nonlinear_solver(old_par, A, b, npar, na)
new_cmt_par = np.copy(self.cmt_par)
new_cmt_par[0:npar] = new_par[0:npar] * self.config.scale_par[0:npar]
return new_cmt_par
def linear_solver(self, old_par, A, b, npar, na):
"""
if invert for moment tensor with zero-trace constraints
or no constraint
"""
AA = np.zeros([na, na])
bb = np.zeros(na)
AA[0:npar, 0:npar] = A
bb[0:npar] = b
if self.config.zero_trace:
bb[na - 1] = - np.sum(old_par[0:3])
AA[0:6, na - 1] = np.array([1, 1, 1, 0, 0, 0])
AA[na - 1, 0:6] = np.array([1, 1, 1, 0, 0, 0])
AA[na - 1, na - 1] = 0.0
try:
dm = np.linalg.solve(AA, bb)
except:
logger.error('Matrix is singular...LinearAlgError')
raise ValueError("Check Matrix Singularity")
new_par = old_par[0:npar] + dm[0:npar]
return new_par
def nonlinear_solver(self, old_par, A, b, npar, na):
"""
if invert for moment tensor with double couple constraints
setup starting solution, solve directly for moment instead
of dm, exact implementation of (A16)
logger.info('Non-linear Inversion')
:return:
"""
mstart = np.copy(old_par)
m1 = np.copy(mstart)
lam = np.zeros(2)
AA = np.zeros([na, na])
bb = np.zeros(na)
error = np.zeros([const.NMAX_NL_ITER, na])
for iter_idx in range(const.NMAX_NL_ITER):
self._get_f_df_(A, b, m1, lam, mstart, AA, bb)
bb = - bb
xout = np.linalg.solve(AA, bb)
m1 = m1 + xout[0:npar]
lam = lam + xout[npar:na]
error[iter_idx, :] = np.dot(AA, xout) - bb
# dm = m1 - mstart
return m1
def invert_cmt(self):
"""
ensemble all measurements together to form Matrix A and vector
b to solve the A * (dm) = b
A is the Hessian Matrix and b is the misfit
:return:
"""
logger.info("*"*15)
logger.info("CMT Inversion")
logger.info("*"*15)
# ensemble A and b
A = util.sum_matrix(self.weight_array, self.A1_all)
b = util.sum_matrix(self.weight_array, self.b1_all)
logger.info("Inversion Matrix A is as follows:")
logger.info("\n%s" % ('\n'.join(map(self._float_array_to_str, A))))
logger.info("Condition number of A: %10.2f" % (np.linalg.cond(A)))
logger.info("RHS vector b is as follows:")
logger.info("[%s]" % (self._float_array_to_str(b)))
# source inversion
self.new_cmt_par = self.invert_solver(A, b, print_mode=True)
self.convert_new_cmt_par()
def invert_bootstrap(self):
"""
It is used to evaluate the mean, standard deviation, and variance
of new parameters
:return:
"""
A_bootstrap = []
b_bootstrap = []
n_subset = int(const.BOOTSTRAP_SUBSET_RATIO * self.nwins)
for i in range(self.config.bootstrap_repeat):
random_array = util.gen_random_array(
self.nwins, sample_number=n_subset)
A = util.sum_matrix(random_array * self.weight_array, self.A1_all)
b = util.sum_matrix(random_array * self.weight_array, self.b1_all)
A_bootstrap.append(A)
b_bootstrap.append(b)
# inversion of each subset
new_par_array = np.zeros((self.config.bootstrap_repeat, const.NPARMAX))
for i in range(self.config.bootstrap_repeat):
new_par = self.invert_solver(A_bootstrap[i], b_bootstrap[i])
new_par_array[i, :] = new_par
# statistical analysis
self.par_mean = np.mean(new_par_array, axis=0)
self.par_std = np.std(new_par_array, axis=0)
self.par_var = np.var(new_par_array, axis=0)
for _ii in range(self.par_mean.shape[0]):
if self.par_mean[_ii] != 0:
# in case of 0 value
self.std_over_mean[_ii] = \
np.abs(self.par_std[_ii] / self.par_mean[_ii])
else:
self.std_over_mean[_ii] = 0.
def source_inversion(self):
"""
the Source Inversion method
:return:
"""
from __init__ import logfilename
print "*"*40 + "\nSee detailed output in %s\n" % logfilename
self.setup_matrix()
self.setup_weight(weight_mode=self.config.weight_azi_mode)
self.invert_cmt()
self.calculate_variance()
if self.config.bootstrap:
self.invert_bootstrap()
self.print_inversion_summary()
def _get_f_df_(self, A, b, m, lam, mstart, fij, f0):
"""
Iterative solver for Non-linear case(double-couple constraint)
:param A: basic Hessian matrix
:param b: basic misfit vector
:param m: current source array
:param lam: constraints coefficient for zero-trace and
double-couple constraints
:param mstart: starting source solution
:param fij: reconstructed Hessian Matrix AA
:param f0: reconstructed misfit vector bb
:return:
"""
npar = self.config.npar
NM = const.NM
# U_j
dc1_dm = np.array([1, 1, 1, 0, 0, 0])
# V_j
dc2_dm = np.zeros(6)
dc2_dm[0] = m[1] * m[2] - m[5] ** 2
dc2_dm[1] = m[0] * m[2] - m[4] ** 2
dc2_dm[2] = m[0] * m[1] - m[3] ** 2
dc2_dm[3] = 2 * m[4] * m[5] - 2 * m[2] * m[3]
dc2_dm[4] = 2 * m[3] * m[5] - 2 * m[1] * m[4]
dc2_dm[5] = 2 * m[3] * m[4] - 2 * m[0] * m[5]
# f(x^i) = H_jk (m_k^i -m_k^0) - b_j + lam_1 * U_j + lam_2 * V_j (A11)
f0.fill(0.)
f0[0:npar] = np.dot(A[0:npar, 0:npar], m[0:npar] -
mstart[0:npar]) - b[0:npar]
# print "f0 step1:", f0
f0[0:const.NM] += \
lam[0] * dc1_dm[0:const.NM] + lam[1] * dc2_dm[0:const.NM]
# f_(n+1) and f_(n+2)
f0[npar] = m[0] + m[1] + m[2]
moment_tensor = np.array([[m[0], m[3], m[4]],
[m[3], m[1], m[5]], [m[4], m[5], m[2]]])
f0[npar + 1] = np.linalg.det(moment_tensor)
f0[npar + 1] = m[0] * (m[1] * m[2] - m[5] ** 2) \
- m[3] * (m[3] * m[2] - m[5] * m[4]) \
+ m[4] * (m[3] * m[5] - m[4] * m[1])
# Y_jk
dc2_dmi_dmj = np.zeros([6, 6])
dc2_dmi_dmj[0, :] = np.array([0.0, m[2], m[1], 0.0, 0.0, -2.0 * m[5]])
dc2_dmi_dmj[1, :] = np.array([m[2], 0.0, m[0], 0.0, -2.0 * m[4], 0.0])
dc2_dmi_dmj[2, :] = np.array([m[1], m[0], 0.0, -2.0 * m[3], 0.0, 0.0])
dc2_dmi_dmj[3, :] = np.array([0.0, 0.0, -2.0 * m[3], -2.0 * m[2],
2 * m[5], 2 * m[4]])
dc2_dmi_dmj[4, :] = np.array([0.0, -2.0 * m[4], 0.0, 2.0 * m[5],
-2.0 * m[1], 2 * m[3]])
dc2_dmi_dmj[5, :] = np.array([-2.0 * m[5], 0.0, 0.0, 2.0 * m[4],
2.0 * m[3], -2.0 * m[0]])
# ! f_jk = H_jk + lam_2 * Y_jk
fij.fill(0)
fij[0:npar, 0:npar] = A[0:npar, 0:npar]
fij[0:NM, 0:NM] = fij[0:NM, 0:NM] + lam[1] * dc2_dmi_dmj[0:NM, 0:NM]
fij[0:NM, npar] = dc1_dm
fij[0:NM, npar + 1] = dc2_dm
fij[npar, 0:NM] = dc1_dm
fij[npar + 1, 0:NM] = dc2_dm
def calculate_variance(self):
"""
Calculate variance reduction based on old and new source solution
:return:
"""
npar = self.config.npar
dm = self.new_cmt_par[0:npar] - self.cmt_par[0:npar]
var_all = 0.0
var_all_new = 0.0
self.stats_before = {}
self.stats_after = {}
for _idx, window in enumerate(self.window):
obsd = window.datalist['obsd']
synt = window.datalist['synt']
dt = obsd.stats.delta
self.compute_new_syn(window.datalist, dm)
new_synt = window.datalist['new_synt']
# calculate old variance
[v1, d1, nshift1, cc1, dlnA1, cc_amp_value1] = \
self.calculate_var_one_trace(obsd, synt, window.win_time)
# calculate new variance
[v2, d2, nshift2, cc2, dlnA2, cc_amp_value2] = \
self.calculate_var_one_trace(obsd, new_synt, window.win_time)
var_all += np.sum(0.5 * v1 * window.weight * obsd.stats.delta)
var_all_new += np.sum(0.5 * v2 * window.weight * obsd.stats.delta)
# prepare stats
tag = window.tag['obsd']
if tag not in self.stats_before.keys():
self.stats_before[tag] = []
if tag not in self.stats_after.keys():
self.stats_after[tag] = []
for _i in range(window.num_wins):
self.stats_before[tag].append(
[nshift1[_i]*dt, cc1[_i], dlnA1[_i], cc_amp_value1[_i],
v1[_i]/d1[_i]])
self.stats_after[tag].append(
[nshift2[_i]*dt, cc2[_i], dlnA2[_i], cc_amp_value2[_i],
v2[_i]/d2[_i]])
for tag in self.stats_before.keys():
self.stats_before[tag] = np.array(self.stats_before[tag])
self.stats_after[tag] = np.array(self.stats_after[tag])
logger.info(
"Total Variance Reduced from %e to %e ===== %f %%"
% (var_all, var_all_new, (var_all - var_all_new) / var_all * 100))
self.var_all = var_all
self.var_all_new = var_all_new
self.var_reduction = (var_all - var_all_new) / var_all
def calculate_kai_total_value(self):
"""
Calculate the sum of kai value
:return:
"""
kai_before = {}
kai_after = {}
for tag in self.stats_before.keys():
kai_before[tag] = np.sum(self.stats_before[tag][:, -1])
kai_after[tag] = np.sum(self.stats_after[tag][:, -1])
return kai_before, kai_after
def calculate_var_one_trace(self, obsd, synt, win_time):
"""
Calculate the variance reduction on a pair of obsd and
synt and windows
:param obsd: observed data trace
:type obsd: :class:`obspy.core.trace.Trace`
:param synt: synthetic data trace
:type synt: :class:`obspy.core.trace.Trace`
:param win_time: [win_start, win_end]
:type win_time: :class:`list` or :class:`numpy.array`
:return: waveform misfit reduction and observed data
energy [v1, d1]
:rtype: [float, float]
"""
num_wins = win_time.shape[0]
v1 = np.zeros(num_wins)
d1 = np.zeros(num_wins)
nshift_array = np.zeros(num_wins)
cc_array = np.zeros(num_wins)
dlnA_array = np.zeros(num_wins)
cc_amp_value_array = np.zeros(num_wins)
for _win_idx in range(win_time.shape[0]):
tstart = win_time[_win_idx, 0]
tend = win_time[_win_idx, 1]
idx_start = int(max(math.floor(tstart / obsd.stats.delta), 1))
idx_end = \
int(min(math.ceil(tend / obsd.stats.delta), obsd.stats.npts))
istart_d, iend_d, istart, iend, nshift, cc, dlnA, cc_amp_value = \
self.apply_station_correction(obsd, synt, idx_start, idx_end)
taper = construct_taper(iend - istart, taper_type=const.taper_type)
v1[_win_idx] = \
np.sum(taper * (synt.data[istart:iend] -
obsd.data[istart_d:iend_d]) ** 2)
d1[_win_idx] = np.sum(taper * obsd.data[istart_d:iend_d] ** 2)
nshift_array[_win_idx] = nshift
cc_array[_win_idx] = cc
dlnA_array[_win_idx] = dlnA
cc_amp_value_array[_win_idx] = cc_amp_value
return [v1, d1, nshift_array, cc_array, dlnA_array, cc_amp_value_array]
def compute_new_syn(self, datalist, dm):
"""
Compute new synthetic data based on new CMTSOLUTION
:param datalist: dictionary of all data
:param dm: CMTSolution perterbation, i.e.,
(self.new_cmt_par-self.cmt_par)
:return:
"""
# get a dummy copy to keep meta data information
datalist['new_synt'] = datalist['synt'].copy()
npar = self.config.npar
npts = datalist['synt'].stats.npts
dt = datalist['synt'].stats.delta
dsyn = np.zeros([npts, npar])
par_list = self.config.par_name
dcmt_par = self.config.dcmt_par
dm_scaled = dm / self.config.scale_par[0:npar]
for i in range(npar):
if i < const.NM:
dsyn[:, i] = datalist[par_list[i]].data / dcmt_par[i]
elif i < const.NML:
dsyn[:, i] = (datalist[par_list[i]].data -
datalist['synt'].data) / dcmt_par[i]
elif i == const.NML:
dsyn[0:(npts - 1), i] = \
-(datalist['synt'].data[1:npts] -
datalist[0:(npts - 1)]) / (dt * dcmt_par[i])
dsyn[npts - 1, i] = dsyn[npts - 2, i]
elif i == (const.NML + 1):
# not implement yet....
raise ValueError("For npar == 10 or 11, not implemented yet")
datalist['new_synt'].data = \
datalist['synt'].data + np.dot(dsyn, dm_scaled)
def write_new_syn(self, outputdir=".", file_format="sac"):
# check first
print "New synt output dir: %s" % outputdir
if not os.path.exists(outputdir):
os.makedirs(outputdir)
if 'new_synt' not in self.window[0].datalist.keys():
raise ValueError("new synt not computed yet")
eventname = self.cmtsource.eventname
if self.config.double_couple:
constr_str = "ZT_DC"
elif self.config.zero_trace:
constr_str = "ZT"
else:
constr_str = "no_constr"
suffix = "%dp_%s" % (self.config.npar, constr_str)
self.data_container.write_new_syn_file(
file_format=file_format, outputdir=outputdir, eventname=eventname,
suffix=suffix)
def calculate_criteria(self, obsd, synt, istart, iend):
"""
Calculate the time shift, max cross-correlation value and
energy differnce
:param obsd: observed data trace
:type obsd: :class:`obspy.core.trace.Trace`
:param synt: synthetic data trace
:type synt: :class:`obspy.core.trace.Trace`
:param istart: start index of window
:type istart: int
:param iend: end index of window
:param iend: int
:return: [number of shift points, max cc value, dlnA]
:rtype: [int, float, float]
"""
obsd_trace = obsd.data[istart:iend]
synt_trace = synt.data[istart:iend]
max_cc, nshift = self._xcorr_win_(obsd_trace, synt_trace)
dlnA = self._dlnA_win_(obsd_trace, synt_trace)
return [nshift, max_cc, dlnA]
def convert_new_cmt_par(self):
"""
Convert self.new_cmt_par array to CMTSource instance
:return:
"""
oldcmt = self.cmtsource
newcmt = self.new_cmt_par
time_shift = newcmt[9]
new_cmt_time = oldcmt.origin_time + time_shift
# copy old one
self.new_cmtsource = CMTSource(
origin_time=oldcmt.origin_time,
pde_latitude=oldcmt.pde_latitude,
pde_longitude=oldcmt.pde_longitude,
mb=oldcmt.mb, ms=oldcmt.ms, pde_depth_in_m=oldcmt.pde_depth_in_m,
region_tag=oldcmt.region_tag, eventname=oldcmt.eventname,
cmt_time=new_cmt_time, half_duration=newcmt[10],
latitude=newcmt[8], longitude=newcmt[7],
depth_in_m=newcmt[6] * 1000.0,
m_rr=newcmt[0], m_tt=newcmt[1], m_pp=newcmt[2], m_rt=newcmt[3],
m_rp=newcmt[4], m_tp=newcmt[5])
def write_new_cmtfile(self, outputdir="."):
"""
Write new_cmtsource into a file
"""
if self.config.double_couple:
suffix = "ZT_DC"
elif self.config.zero_trace:
suffix = "ZT"
else:
suffix = "no_constraint"
outputfn = "%s.%dp_%s.inv" % (
self.cmtsource.eventname, self.config.npar, suffix)
cmtfile = os.path.join(outputdir, outputfn)
print "New cmt file: %s" % cmtfile
self.new_cmtsource.write_CMTSOLUTION_file(cmtfile)
@staticmethod
def _xcorr_win_(obsd, synt):
cc = np.correlate(obsd, synt, mode="full")
nshift = cc.argmax() - len(obsd) + 1
# Normalized cross correlation.
max_cc_value = \
cc.max() / np.sqrt((synt ** 2).sum() * (obsd ** 2).sum())
return max_cc_value, nshift
@staticmethod
def _dlnA_win_(obsd, synt):
return 10 * np.log10(np.sum(obsd ** 2) / np.sum(synt ** 2))
@staticmethod
def print_cmtsource_summary(cmt):
"""
Print CMTSolution source summary
:return:
"""
logger.info("=" * 10 + " Event Summary " + "=" * 10)
logger.info("Event name: %s" % cmt.eventname)
logger.info(" Latitude and longitude: %.2f, %.2f" % (
cmt.latitude, cmt.longitude))
logger.info(" Depth: %.1f km" % (cmt.depth_in_m / 1000.0))
logger.info(" Region tag: %s" % cmt.region_tag)
logger.info(" Trace: %.3e" % (
(cmt.m_rr + cmt.m_tt + cmt.m_pp) / cmt.M0))
logger.info(" Moment Magnitude: %.2f" % cmt.moment_magnitude)
@staticmethod
def _float_to_str(value):
"""
Convert float value to a specific precision string
:param value:
:return: string of the value
"""
return "%.5f" % value
@staticmethod
def _float_array_to_str(array):
"""
Convert float array to string
:return:
"""
string = "[ "
for ele in array:
string += "%10.3e " % ele
string += "]"
return string
@staticmethod
def _write_log_file_(filename, nshift_list, cc_list, dlnA_list):
with open(filename, 'w') as f:
for i in range(len(nshift_list)):
nshift = nshift_list[i]
cc = cc_list[i]
dlnA = dlnA_list[i]
f.write("%5d %10.3f %10.3f\n" % (nshift, cc, dlnA))
def print_inversion_summary(self):
"""
Print out the inversion summary
:return:
"""
logger.info("*" * 20)
logger.info("Invert cmt parameters(%d par)" % self.config.npar)
logger.info("Old CMT par: [%s]" % (
', '.join(map(str, self.cmt_par))))
logger.info("dm: [%s]" % (
', '.join(map(str, self.new_cmt_par - self.cmt_par))))
logger.info("New CMT par: [%s]" % (
', '.join(map(str, self.new_cmt_par))))
logger.info("Trace: %e" % (np.sum(self.new_cmt_par[0:3])))
logger.info("Energy change(scalar moment): %5.2f%%" % (
(self.new_cmtsource.M0 - self.cmtsource.M0) /
self.cmtsource.M0 * 100.0))
self.inversion_result_table()
def inversion_result_table(self):
"""
Print out the inversion table
:return:
"""
title = "*" * 20 + " Inversion Result Table(%d npar) " % \
self.config.npar + "*" * 20
logger.info(title)
if not self.config.bootstrap:
logger.info("PAR Old_CMT New_CMT")
logger.info("Mrr: %15.6e %15.6e" % (
self.cmtsource.m_rr, self.new_cmtsource.m_rr))
logger.info("Mtt: %15.6e %15.6e" % (
self.cmtsource.m_tt, self.new_cmtsource.m_tt))
logger.info("Mpp: %15.6e %15.6e" % (
self.cmtsource.m_pp, self.new_cmtsource.m_pp))
logger.info("Mrt: %15.6e %15.6e" % (
self.cmtsource.m_rt, self.new_cmtsource.m_rt))
logger.info("Mrp: %15.6e %15.6e" % (
self.cmtsource.m_rp, self.new_cmtsource.m_rp))
logger.info("Mtp: %15.6e %15.6e" % (
self.cmtsource.m_tp, self.new_cmtsource.m_tp))
logger.info(
"dep: %15.3f %15.3f" % (
self.cmtsource.depth_in_m / 1000.0,
self.new_cmtsource.depth_in_m / 1000.0))
logger.info("lon: %15.3f %15.3f" % (
self.cmtsource.longitude, self.new_cmtsource.longitude))
logger.info("lat: %15.3f %15.3f" % (
self.cmtsource.latitude, self.new_cmtsource.latitude))
logger.info("ctm: %15.3f %15.3f" % (
self.cmtsource.time_shift, self.new_cmtsource.time_shift))
logger.info("hdr: %15.3f %15.3f" % (
self.cmtsource.half_duration,
self.new_cmtsource.half_duration))
else:
logger.info("PAR Old_CMT New_CMT "
"Bootstrap_Mean Bootstrap_STD STD/Mean")
logger.info(
"Mrr: %15.6e %15.6e %15.6e %15.6e %10.2f%%" % (
self.cmtsource.m_rr, self.new_cmtsource.m_rr,
self.par_mean[0], self.par_std[0],
self.std_over_mean[0] * 100))
logger.info(
"Mtt: %15.6e %15.6e %15.6e %15.6e %10.2f%%" % (
self.cmtsource.m_tt, self.new_cmtsource.m_tt,
self.par_mean[1], self.par_std[1],
self.std_over_mean[1] * 100))
logger.info(
"Mpp: %15.6e %15.6e %15.6e %15.6e %10.2f%%" % (
self.cmtsource.m_pp, self.new_cmtsource.m_pp,
self.par_mean[2], self.par_std[2],
self.std_over_mean[2] * 100))
logger.info(
"Mrt: %15.6e %15.6e %15.6e %15.6e %10.2f%%" % (
self.cmtsource.m_rt, self.new_cmtsource.m_rt,
self.par_mean[3], self.par_std[3],
self.std_over_mean[3] * 100))
logger.info(
"Mrp: %15.6e %15.6e %15.6e %15.6e %10.2f%%" % (
self.cmtsource.m_rp, self.new_cmtsource.m_rp,
self.par_mean[4], self.par_std[4],
self.std_over_mean[4] * 100))
logger.info(
"Mtp: %15.6e %15.6e %15.6e %15.6e %10.2f%%" % (
self.cmtsource.m_tp, self.new_cmtsource.m_tp,
self.par_mean[5], self.par_std[5],
self.std_over_mean[5] * 100))
logger.info("dep: %15.3f %15.3f %15.3f %15.3f %10.2f%%" % (
self.cmtsource.depth_in_m / 1000.0,
self.new_cmtsource.depth_in_m / 1000.0,
self.par_mean[6], self.par_std[6],
self.std_over_mean[6] * 100))
logger.info("lon: %15.3f %15.3f %15.3f %15.3f %10.2f%%" % (
self.cmtsource.longitude, self.new_cmtsource.longitude,
self.par_mean[7], self.par_std[7],
self.std_over_mean[7] * 100))
logger.info("lat: %15.3f %15.3f %15.3f %15.3f %10.2f%%" % (
self.cmtsource.latitude, self.new_cmtsource.latitude,
self.par_mean[8], self.par_std[8],
self.std_over_mean[8] * 100))
logger.info("ctm: %15.3f %15.3f %15.3f %15.3f %10.2f%%" % (
self.cmtsource.time_shift, self.new_cmtsource.time_shift,
self.par_mean[9], self.par_std[9],
self.std_over_mean[9] * 100))
logger.info("hdr: %15.3f %15.3f %15.3f %15.3f %10.2f%%" % (
self.cmtsource.half_duration, self.new_cmtsource.half_duration,
self.par_mean[10], self.par_std[10],
self.std_over_mean[10] * 100))
def plot_summary(self, outputdir=".", figure_format="png",
plot_mode="regional"):
"""
Plot inversion summary
:param outputdir: output directory
:return:
"""
eventname = self.cmtsource.eventname
npar = self.config.npar
if self.config.double_couple:
suffix = "ZT_DC"
elif self.config.zero_trace:
suffix = "ZT"
else:
suffix = "no_constraint"
outputfn = "%s.%dp_%s.inv" % (eventname, npar, suffix)
outputfn = os.path.join(outputdir, outputfn)
figurename = outputfn + "." + figure_format
print "Source inversion summary figure: %s" % figurename
plot_stat = PlotUtil(
data_container=self.data_container, config=self.config,
cmtsource=self.cmtsource, nregions=const.NREGIONS,
new_cmtsource=self.new_cmtsource, bootstrap_mean=self.par_mean,
bootstrap_std=self.par_std, var_reduction=self.var_reduction,
mode=plot_mode)
plot_stat.plot_inversion_summary(figurename=figurename)
def plot_stats_histogram(self, outputdir=".", figure_format="png"):
"""
Plot inversion histogram
:param outputdir:
:return:
"""
nrows = len(self.stats_before.keys())
ncols = self.stats_before[self.stats_before.keys()[0]].shape[1]
if self.config.double_couple:
constr_str = "ZT_DC"
elif self.config.zero_trace:
constr_str = "ZT"
else:
constr_str = "no_constraint"
if not self.config.normalize_window:
prefix = "%dp_%s." % (self.config.npar, constr_str) + "no_normwin"
else:
prefix = "%dp_%s.%s" % (
self.config.npar, constr_str, self.config.norm_mode)
if not self.config.normalize_category:
prefix += ".no_normcat"
else:
prefix += ".normcat"
figname = "%s.%s.dlnA.%s" % (self.cmtsource.eventname, prefix,
figure_format)
figname = os.path.join(outputdir, figname)
print "Inversion histogram figure: %s" % figname
plt.figure(figsize=(5*ncols, 5*nrows))
G = gridspec.GridSpec(nrows, ncols)
irow = 0
for cat in self.stats_before.keys():
self._plot_stats_histogram_per_cat_(
G, irow, cat, self.stats_before[cat], self.stats_after[cat])
irow += 1
plt.savefig(figname)
def _plot_stats_histogram_per_cat_(self, G, irow, cat, data_before,
data_after):
num_bins = [15, 15, 15, 15, 15]
vtype_list = ['time shift', 'cc', 'Power_Ratio(dB)',
'CC Amplitude Ratio(dB)', 'Kai']
# plot order
var_index = [0, 1, 2, 3, 4]
for _idx, var_idx in enumerate(var_index):
vtype = vtype_list[var_idx]
self._plot_stats_histogram_one_(
G[irow, _idx], cat, vtype, data_before[:, var_idx],
data_after[:, var_idx],
num_bins[var_idx])
@staticmethod
def _plot_stats_histogram_one_(pos, cat, vtype, data_b, data_a, num_bin):
plt.subplot(pos)
plt.xlabel(vtype)
plt.ylabel(cat)
if vtype == "cc":
ax_min = min(min(data_b), min(data_a))
ax_max = max(max(data_b), max(data_a))
elif vtype == "Kai":
ax_min = 0.0
ax_max = max(max(data_b), max(data_a))
else:
ax_min = min(min(data_b), min(data_a))
ax_max = max(max(data_b), max(data_a))
abs_max = max(abs(ax_min), abs(ax_max))
ax_min = -abs_max
ax_max = abs_max
binwidth = (ax_max - ax_min) / num_bin
plt.hist(
data_b, bins=np.arange(ax_min, ax_max+binwidth/2., binwidth),
facecolor='blue', alpha=0.3)
plt.hist(
data_a, bins=np.arange(ax_min, ax_max+binwidth/2., binwidth),
facecolor='green', alpha=0.5)
def _write_weight_log_(self, filename):
"""
write out weight log file
"""
with open(filename, 'w') as f:
for window in self.window:
sta = window.station
nw = window.network
component = window.component
location = window.location
sta_info = "%s.%s.%s.%s" % (sta, nw, location, component)
f.write("%s\n" % sta_info)
for _idx in range(window.weight.shape[0]):
f.write("%10.5e %10.5e\n" % (
window.weight[_idx], window.energy[_idx]))
def plot_new_seismogram(self, outputdir=".", figure_format="png"):
"""
Plot the new synthetic and old synthetic data together with data
"""
# make a check
if 'new_synt' not in self.window[0].datalist.keys():
return "New synt not generated...Can't plot"
eventname = self.cmtsource.eventname
if self.config.double_couple:
constr_str = "ZT_DC"
elif self.config.zero_trace:
constr_str = "ZT"
else:
constr_str = "no_constr"
suffix = eventname + "_%dp_%s" % (self.config.npar, constr_str)
outputdir = os.path.join(outputdir, suffix)
if not os.path.exists(outputdir):
os.makedirs(outputdir)
print "Plotting data, synthetics and windows to dir: %s" % outputdir
for window in self.window:
self.plot_new_seismogram_sub(window, outputdir, figure_format)
def plot_new_seismogram_sub(self, window, outputdir, figure_format):
obsd = window.datalist['obsd']
synt = window.datalist['synt']
new_synt = window.datalist['new_synt']
tag = window.tag['obsd']
station = obsd.stats.station
network = obsd.stats.network
channel = obsd.stats.channel
location = obsd.stats.location
outputfig = os.path.join(outputdir, "%s.%s.%s.%s.%s" % (
network, station, location, channel, figure_format))
offset = self.cmtsource.cmt_time - obsd.stats.starttime
times = [offset + obsd.stats.delta*i for i in range(obsd.stats.npts)]
fig = plt.figure(figsize=(15, 2.5))
plt.plot(times, obsd.data, color="black", linewidth=0.5, alpha=0.6)
plt.plot(times, synt.data, color="red", linewidth=0.8)
plt.plot(times, new_synt.data, color="green", linewidth=0.8)
plt.xlim(times[0], times[-1])
xlim1 = plt.xlim()[1]
ylim1 = plt.ylim()[1]
fontsize = 9
plt.text(0.01*xlim1, 0.80*ylim1, "Network: %2s Station: %s" %
(network, station), fontsize=fontsize)
plt.text(0.01*xlim1, 0.65*ylim1, "Location: %2s Channel:%3s" %
(location, channel), fontsize=fontsize)
for win in window.win_time:
l = win[0] - offset
r = win[1] - offset
re = Rectangle((l, plt.ylim()[0]), r - l,
plt.ylim()[1] - plt.ylim()[0], color="blue",
alpha=0.25)
plt.gca().add_patch(re)
plt.savefig(outputfig)
plt.close(fig)
# convert quakeml file into CMTSOLUTION file
from source import CMTSource
from obspy import readEvents
import glob
import os
quakemldir = "/home/lei/DATA/quakeml"
outputdir = "/home/lei/DATA/CMT_BIN/from_quakeml"
search_pattern = os.path.join(quakemldir, "*.xml")
quakemllist = glob.glob(search_pattern)
if not os.path.exists(outputdir):
os.mkdir(outputdir)
print "Total number of quakeml files:", len(quakemllist)
for _idx, quakeml in enumerate(quakemllist):
cmt = CMTSource.from_quakeml_file(quakeml)
filename = cmt.eventname
outputpath = os.path.join(outputdir, filename)
print _idx, filename, outputpath
cmt.write_CMTSOLUTION_file(outputpath)