Note
Go to the end to download the full example code.
Tempest Datapoint Class
Credits: We would like to thank Ross Brodie at Geoscience Australia for his airborne time domain forward modeller https://github.com/GeoscienceAustralia/ga-aem
For ground-based time domain data, we are using Dieter Werthmuller’s python package Empymod https://empymod.github.io/
Thanks to Dieter for his help getting Empymod ready for incorporation into GeoBIPy
from os.path import join
import numpy as np
import h5py
import matplotlib.pyplot as plt
from geobipy import TempestData
# from geobipy import TemDataPoint
from geobipy import RectilinearMesh1D
from geobipy import Model
from geobipy import StatArray
from geobipy import Distribution
from geobipy import get_prng
dataFolder = "..//..//supplementary//data//"
# dataFolder = "source//examples//supplementary//Data"
# Obtaining a tempest datapoint from a dataset
# ++++++++++++++++++++++++++++++++++++++++++++
# More often than not, our observed data is stored in a file on disk.
# We can read in a dataset and pull datapoints from it.
#
# For more information about the time domain data set, see :ref:`Time domain dataset`
# The data file name
dataFile = dataFolder + 'tempest_saline_clay.csv'
# The EM system file name
systemFile = dataFolder + 'Tempest.stm'
# Prepare the dataset so that we can read a point at a time.
Dataset = TempestData._initialize_sequential_reading(dataFile, systemFile)
# Get a datapoint from the file.
tdp = Dataset._read_record(0)
plt.figure()
tdp.plot()
prng = get_prng(seed=146100583096709124601953385843316024947)
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
self.n_components=2, self.nTimes=array([15])
Using a tempest domain datapoint
We can define a 1D layered earth model, and use it to predict some data
par = StatArray(np.r_[0.01, 0.1, 1.], "Conductivity", "$\frac{S}{m}$")
mod = Model(mesh=RectilinearMesh1D(edges=np.r_[0.0, 50.0, 75.0, np.inf]), values=par)
par = StatArray(np.logspace(-3, 3, 30), "Conductivity", "$\frac{S}{m}$")
e = np.linspace(0, 350, 31); e[-1] = np.inf
mod = Model(mesh=RectilinearMesh1D(edges=e), values=par)
Forward model the data
tdp.forward(mod)
print('primary', tdp.primary_field)
print('sx', tdp.secondary_field[:15])
print('sz', tdp.secondary_field[15:])
# #%%
# plt.figure()
# plt.subplot(121)
# _ = mod.pcolor(transpose=True)
# plt.subplot(122)
# _ = tdp.plot()
# _ = tdp.plot_predicted()
# plt.tight_layout()
# plt.suptitle('Model and response')
# #%%
# # plt.figure()
# # tdp.plotDataResidual(xscale='log')
# # plt.title('data residual')
# #%%
# # Compute the sensitivity matrix for a given model
J = tdp.sensitivity(mod)
# plt.figure()
# _ = np.abs(J).pcolor(equalize=True, log=10, flipY=True)
print('J', J)
# print('J shape', J.shape)
# print('sx 0', J[:16, 0])
tdp.fm_dlogc(mod)
print('new primary', tdp.primary_field)
print('sx', tdp.secondary_field[:15])
print('sz', tdp.secondary_field[15:])
print('new J', tdp.sensitivity_matrix)
primary [34.27253219 17.55503397]
sx [4.46362582 2.52720951 2.10544857 1.76862398 1.52893914 1.38117676
1.19246619 1.10920301 0.94437018 0.81202664 0.67054942 0.4124596
0.34346631 0.27359586 0.19875285]
sz [6.47100177 4.53101158 3.87594468 3.43396174 3.10487058 2.80230168
2.59759025 2.34406113 2.09040444 1.83288007 1.59137993 1.34037776
1.05345525 0.79969548 0.56994112]
J [[ 1.13463137e-01 1.49920887e-01 1.76789170e-01 1.79809001e-01
1.49232157e-01 9.28385121e-02 3.82492975e-02 8.70404368e-03
7.17305034e-04 -2.13238764e-04 -3.69663472e-04 -5.69915094e-04
-8.66319388e-04 -1.29165072e-03 -1.87152454e-03 -2.59562194e-03
-3.36123923e-03 -3.90030818e-03 -3.77459399e-03 -2.64263369e-03
-8.86540172e-04 2.51618719e-04 2.30305587e-04 -6.44400641e-06
-7.48897278e-06 7.03319747e-07 -1.06012557e-08 -1.01809840e-09
1.13341751e-11 7.27489718e-13]
[ 2.09383016e-02 3.20412212e-02 4.74815387e-02 6.68394476e-02
8.66127424e-02 9.82359342e-02 9.01124001e-02 5.92842924e-02
2.34205425e-02 4.15453831e-03 -1.09167097e-04 -5.65296487e-04
-8.64759189e-04 -1.28934957e-03 -1.86840434e-03 -2.59169317e-03
-3.35694331e-03 -3.89678338e-03 -3.77361484e-03 -2.64536287e-03
-8.91147400e-04 2.49122146e-04 2.30371889e-04 -6.22013409e-06
-7.50559762e-06 7.02225318e-07 -1.04664062e-08 -1.02489023e-09
1.15994185e-11 7.25910166e-13]
[ 1.04188675e-02 1.61552555e-02 2.45575508e-02 3.61804723e-02
5.07045737e-02 6.55611414e-02 7.44548187e-02 6.86847323e-02
4.55777737e-02 1.80379279e-02 2.98696559e-03 -3.85293966e-04
-8.60809279e-04 -1.28714626e-03 -1.86528098e-03 -2.58777374e-03
-3.35265612e-03 -3.89326199e-03 -3.77262920e-03 -2.64807737e-03
-8.95745356e-04 2.46622607e-04 2.30434500e-04 -5.99618798e-06
-7.52209743e-06 7.01118939e-07 -1.03312747e-08 -1.03167228e-09
1.18645190e-11 7.24296662e-13]
[ 5.59306619e-03 8.73427922e-03 1.34567371e-02 2.03060295e-02
2.96541856e-02 4.11011150e-02 5.23902533e-02 5.84048942e-02
5.26194169e-02 3.39153269e-02 1.29270864e-02 1.84115255e-03
-7.26349266e-04 -1.28187560e-03 -1.86068331e-03 -2.58190508e-03
-3.34624172e-03 -3.88798693e-03 -3.77113807e-03 -2.65212048e-03
-9.02624129e-04 2.42867556e-04 2.30521193e-04 -5.66013350e-06
-7.54660150e-06 6.99435958e-07 -1.01280238e-08 -1.04182633e-09
1.22618909e-11 7.21872310e-13]
[ 2.90057967e-03 4.55298073e-03 7.08113868e-03 1.08624892e-02
1.63131443e-02 2.36956230e-02 3.26444333e-02 4.13290515e-02
4.57247118e-02 4.08416457e-02 2.60308912e-02 9.65207055e-03
9.85979321e-04 -1.17532082e-03 -1.85153793e-03 -2.57222629e-03
-3.33558713e-03 -3.87921268e-03 -3.76862112e-03 -2.65878596e-03
-9.14042109e-04 2.36594638e-04 2.30647153e-04 -5.09972880e-06
-7.58680811e-06 6.96570853e-07 -9.78784817e-09 -1.05870121e-09
1.29234653e-11 7.17787479e-13]
[ 1.52006455e-03 2.39426129e-03 3.74644180e-03 5.80697177e-03
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3.29616199e-02 3.61240640e-02 3.18888293e-02 1.99839155e-02
7.06087232e-03 1.66263257e-04 -1.75822596e-03 -2.55553075e-03
-3.31861213e-03 -3.86514848e-03 -3.76449138e-03 -2.66930910e-03
-9.32273995e-04 2.26471992e-04 2.30800241e-04 -4.19807425e-06
-7.64974377e-06 6.91803908e-07 -9.23713659e-09 -1.08570231e-09
1.39851809e-11 7.11116040e-13]
[ 7.95172245e-04 1.25562666e-03 1.97296556e-03 3.07922945e-03
4.75914088e-03 7.24897325e-03 1.07971005e-02 1.55309299e-02
2.11471314e-02 2.63969405e-02 2.87019743e-02 2.50612120e-02
1.53752412e-02 4.96252008e-03 -6.93865522e-04 -2.46676098e-03
-3.29044003e-03 -3.84255990e-03 -3.75760102e-03 -2.68583695e-03
-9.61436534e-04 2.10008122e-04 2.30920381e-04 -2.73869233e-06
-7.74706913e-06 6.83678713e-07 -8.33661124e-09 -1.12904183e-09
1.56973846e-11 7.00029332e-13]
[ 4.25261235e-04 6.72742356e-04 1.06013791e-03 1.66216067e-03
2.58781456e-03 3.98821239e-03 6.05390242e-03 8.97919887e-03
1.28478445e-02 1.73740944e-02 2.14865063e-02 2.30512177e-02
1.96897031e-02 1.15139729e-02 2.96683343e-03 -1.66596036e-03
-3.20516657e-03 -3.80728921e-03 -3.74651522e-03 -2.71020663e-03
-1.00569525e-03 1.84371944e-04 2.30799698e-04 -4.84184630e-07
-7.88644214e-06 6.70126101e-07 -6.92193641e-09 -1.19519648e-09
1.83301097e-11 6.82210948e-13]
[ 2.34933380e-04 3.72120311e-04 5.87563585e-04 9.24055086e-04
1.44556439e-03 2.24464388e-03 3.44801505e-03 5.21202871e-03
7.68804416e-03 1.09185107e-02 1.46108113e-02 1.77928517e-02
1.86360965e-02 1.52676336e-02 8.10520819e-03 1.04131721e-03
-2.63131518e-03 -3.73025495e-03 -3.72857047e-03 -2.74413358e-03
-1.07006043e-03 1.45642247e-04 2.29929941e-04 2.87848665e-06
-8.06931787e-06 6.47601643e-07 -4.75428545e-09 -1.29229582e-09
2.22379274e-11 6.53984309e-13]
[ 1.30756207e-04 2.07280357e-04 3.27738594e-04 5.16541357e-04
8.10756512e-04 1.26542784e-03 1.95946411e-03 2.99935495e-03
4.51300993e-03 6.61582186e-03 9.31508227e-03 1.23107970e-02
1.47115349e-02 1.49431150e-02 1.15588764e-02 5.23660250e-03
-5.73138740e-04 -3.30841709e-03 -3.68438731e-03 -2.79051701e-03
-1.16480763e-03 8.53486040e-05 2.27003150e-04 8.00168945e-06
-8.28895296e-06 6.07735187e-07 -1.30360184e-09 -1.43725413e-09
2.81764182e-11 6.06718206e-13]
[ 7.22510490e-05 1.14578847e-04 1.81325240e-04 2.86211332e-04
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1.02631180e-02 1.20097562e-02 1.17690090e-02 8.45394621e-03
2.93181526e-03 -1.70637976e-03 -3.39858476e-03 -2.84225442e-03
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3.72779086e-11 5.22736206e-13]
[ 3.95026702e-05 6.26387983e-05 9.91713508e-05 1.56690100e-04
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5.90657380e-03 1.23034377e-03 -2.18521995e-03 -2.74868554e-03
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5.08041309e-11 3.64993874e-13]
[ 2.13302188e-05 3.38065070e-05 5.35289820e-05 8.46302466e-05
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3.93975771e-03 5.38502235e-03 6.80696424e-03 7.57576392e-03
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6.77078320e-11 6.05952429e-14]
[ 1.12282264e-05 1.78635903e-05 2.83779899e-05 4.50017482e-05
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4.31681368e-04 6.67639104e-04 1.02184383e-03 1.54055267e-03
2.27116188e-03 3.23625864e-03 4.37388475e-03 5.43408279e-03
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7.45275097e-11 -4.39700593e-13]
[-1.11093671e-07 7.10535889e-06 1.35366601e-05 2.19781779e-05
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1.21409005e-03 1.78443357e-03 2.53102265e-03 3.39739027e-03
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3.51467636e-06 -6.95157016e-07 2.72069882e-08 -1.89202945e-10
2.98055790e-11 -8.12511279e-13]
[ 1.60115776e-01 2.07639005e-01 2.40739052e-01 2.40418419e-01
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9.13480086e-12 2.32731922e-12]
[ 3.99049002e-02 5.96318887e-02 8.59664978e-02 1.17218850e-01
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9.94338045e-12 2.32347000e-12]
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1.07518133e-11 2.31958355e-12]
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1.19641780e-11 2.31371842e-12]
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1.39840656e-11 2.30379831e-12]
[ 3.82116333e-03 5.94406923e-03 9.17070818e-03 1.39871419e-02
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1.72295320e-11 2.28750613e-12]
[ 2.11278271e-03 3.29974701e-03 5.12169089e-03 7.88335047e-03
1.19925627e-02 1.79371609e-02 2.61634885e-02 3.67410000e-02
4.86692847e-02 5.88706114e-02 6.17401348e-02 5.16334079e-02
2.97676770e-02 7.84982402e-03 -3.83602557e-03 -7.94329070e-03
-1.02171873e-02 -1.15879985e-02 -1.09280378e-02 -7.40844285e-03
-2.31978636e-03 8.03816816e-04 6.47519482e-04 -2.62622224e-05
-2.08268690e-05 2.06397280e-06 -3.44189048e-08 -2.78060500e-09
2.24734966e-11 2.26025209e-12]
[ 1.18787916e-03 1.86079679e-03 2.90072503e-03 4.49316096e-03
6.89992517e-03 1.04683047e-02 1.56072826e-02 2.26762962e-02
3.16873527e-02 4.17028524e-02 4.99874496e-02 5.17013957e-02
4.21733381e-02 2.28200440e-02 3.82984440e-03 -6.33720101e-03
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-2.13290962e-05 2.03378663e-06 -3.03475874e-08 -2.99444288e-09
3.05612182e-11 2.21589868e-12]
[ 6.85874915e-04 1.07682023e-03 1.68386072e-03 2.61987206e-03
4.04914185e-03 6.20161303e-03 9.37821632e-03 1.39243312e-02
2.01215828e-02 2.79102957e-02 3.63473409e-02 4.28853433e-02
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Attaching statistical descriptors to the tempest datapoint
from numpy.random import Generator
from numpy.random import PCG64DXSM
generator = PCG64DXSM(seed=0)
prng = Generator(generator)
# Set relative errors for the primary fields, and secondary fields.
tdp.relative_error = np.r_[0.001, 0.001]
# Set the additive errors for
tdp.additive_error = np.hstack([[0.011474, 0.012810, 0.008507, 0.005154, 0.004742, 0.004477, 0.004168, 0.003539, 0.003352, 0.003213, 0.003161, 0.003122, 0.002587, 0.002038, 0.002201],
[0.007383, 0.005693, 0.005178, 0.003659, 0.003426, 0.003046, 0.003095, 0.003247, 0.002775, 0.002627, 0.002460, 0.002178, 0.001754, 0.001405, 0.001283]])
# Define a multivariate log normal distribution as the prior on the predicted data.
tdp.predictedData.prior = Distribution('MvLogNormal', tdp.data[tdp.active], tdp.std[tdp.active]**2.0, prng=prng)
This allows us to evaluate the likelihood of the predicted data
print(tdp.likelihood(log=True))
# Or the misfit
print(tdp.data_misfit())
-36389.6500813217
72940.71365767403
Plot the misfits for a range of half space conductivities
plt.figure()
plt.subplot(1, 2, 1)
_ = tdp.plot_halfspace_responses(-6.0, 4.0, 200)
plt.title("Halfspace responses")
Text(0.5, 1.0, 'Halfspace responses')
We can perform a quick search for the best fitting half space
halfspace = tdp.find_best_halfspace()
print('Best half space conductivity is {} $S/m$'.format(halfspace.values))
plt.subplot(1, 2, 2)
_ = tdp.plot()
_ = tdp.plot_predicted()
plt.figure()
tdp.plot_secondary_field()
tdp.plot_predicted_secondary_field()
# #%%
# # We can attach priors to the height of the datapoint,
# # the relative error multiplier, and the additive error noise floor
# Define the distributions used as priors.
relative_prior = Distribution('Uniform', min=np.r_[0.01, 0.01], max=np.r_[0.5, 0.5], prng=prng)
receiver_x_prior = Distribution('Uniform', min=np.float64(tdp.receiver.x) - 1.0, max=np.float64(tdp.receiver.x) + 1.0, prng=prng)
receiver_z_prior = Distribution('Uniform', min=np.float64(tdp.receiver.z) - 1.0, max=np.float64(tdp.receiver.z) + 1.0, prng=prng)
receiver_pitch_prior = Distribution('Uniform', min=tdp.receiver.pitch - 5.0, max=tdp.receiver.pitch + 5.0, prng=prng)
tdp.set_priors(relative_error_prior=relative_prior, receiver_x_prior=receiver_x_prior, receiver_z_prior=receiver_z_prior, receiver_pitch_prior=receiver_pitch_prior, prng=prng)
Best half space conductivity is [0.01830738] $S/m$
/Users/nfoks/codes/repositories/geobipy/documentation_source/source/examples/Datapoints/plot_tempest_datapoint.py:156: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
receiver_x_prior = Distribution('Uniform', min=np.float64(tdp.receiver.x) - 1.0, max=np.float64(tdp.receiver.x) + 1.0, prng=prng)
/Users/nfoks/codes/repositories/geobipy/documentation_source/source/examples/Datapoints/plot_tempest_datapoint.py:157: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
receiver_z_prior = Distribution('Uniform', min=np.float64(tdp.receiver.z) - 1.0, max=np.float64(tdp.receiver.z) + 1.0, prng=prng)
In order to perturb our solvable parameters, we need to attach proposal distributions
relative_proposal = Distribution('MvNormal', mean=tdp.relative_error, variance=2.5e-4, prng=prng)
receiver_x_proposal = Distribution('Normal', mean=tdp.receiver.x, variance = 0.01, prng=prng)
receiver_z_proposal = Distribution('Normal', mean=tdp.receiver.z, variance = 0.01, prng=prng)
receiver_pitch_proposal = Distribution('Normal', mean=tdp.receiver.pitch, variance = 0.01, prng=prng)
tdp.set_proposals(relative_error_proposal=relative_proposal,
receiver_x_proposal=receiver_x_proposal,
receiver_z_proposal=receiver_z_proposal,
receiver_pitch_proposal=receiver_pitch_proposal,
solve_additive_error=True, additive_error_proposal_variance=1e-4, prng=prng)
With priors set we can auto generate the posteriors
tdp.set_posteriors()
Perturb the datapoint and record the perturbations Note we are not using the priors to accept or reject perturbations.
for i in range(10):
tdp.perturb()
tdp.update_posteriors()
plt.show()
Total running time of the script: (0 minutes 1.659 seconds)