.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "content/examples/20-published/plot_booky_1D_time_freq_inv.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_content_examples_20-published_plot_booky_1D_time_freq_inv.py: Heagy et al., 2017 1D RESOLVE and SkyTEM Bookpurnong Inversions =============================================================== In this example, show 1D inversions of a single sounding from each of the RESOLVE and SkyTEM data sets. The original data can be downloaded from: `https://storage.googleapis.com/simpeg/bookpurnong/bookpurnong.tar.gz `_ The forward simulation is performed on the cylindrically symmetric mesh using :code:`simpeg.electromagnetics.frequency_domain`, and :code:`simpeg.electromagnetics.time_domain` The RESOLVE data are inverted first. This recovered model is then used as a reference model for the SkyTEM inversion This example is published in Lindsey J. Heagy, Rowan Cockett, Seogi Kang, Gudni K. Rosenkjaer, Douglas W. Oldenburg, A framework for simulation and inversion in electromagnetics, Computers & Geosciences, Volume 107, 2017, Pages 1-19, ISSN 0098-3004, http://dx.doi.org/10.1016/j.cageo.2017.06.018. The script and figures are also on figshare: https://doi.org/10.6084/m9.figshare.5107711 This example was updated for SimPEG 0.14.0 on January 31st, 2020 by Joseph Capriotti .. GENERATED FROM PYTHON SOURCE LINES 27-499 .. rst-class:: sphx-glr-horizontal * .. image-sg:: /content/examples/20-published/images/sphx_glr_plot_booky_1D_time_freq_inv_001.png :alt: RESOLVE In-phase 400 Hz, SkyTEM High moment 156 $\mu$s :srcset: /content/examples/20-published/images/sphx_glr_plot_booky_1D_time_freq_inv_001.png :class: sphx-glr-multi-img * .. image-sg:: /content/examples/20-published/images/sphx_glr_plot_booky_1D_time_freq_inv_002.png :alt: plot booky 1D time freq inv :srcset: /content/examples/20-published/images/sphx_glr_plot_booky_1D_time_freq_inv_002.png :class: sphx-glr-multi-img * .. image-sg:: /content/examples/20-published/images/sphx_glr_plot_booky_1D_time_freq_inv_003.png :alt: (a) Recovered Models, (b) RESOLVE, (c) SkyTEM High-moment, (d) Waveform :srcset: /content/examples/20-published/images/sphx_glr_plot_booky_1D_time_freq_inv_003.png :class: sphx-glr-multi-img .. rst-class:: sphx-glr-script-out .. code-block:: none Downloading https://storage.googleapis.com/simpeg/bookpurnong/bookpurnong_inversion.tar.gz saved to: /home/vsts/work/1/s/examples/20-published/bookpurnong_inversion.tar.gz Download completed! Running inversion with SimPEG v0.22.0 simpeg.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv. ***Done using same Solver, and solver_opts as the Simulation3DMagneticFluxDensity problem*** model has any nan: 0 ============================ Inexact Gauss Newton ============================ # beta phi_d phi_m f |proj(x-g)-x| LS Comment ----------------------------------------------------------------------------- x0 has any nan: 0 0 2.00e+00 2.48e+02 0.00e+00 2.48e+02 5.67e+01 0 1 2.00e+00 3.66e+01 5.83e+00 4.83e+01 2.26e+01 0 2 2.00e+00 1.22e+01 3.36e+00 1.89e+01 8.93e+00 0 ------------------------- STOP! ------------------------- 1 : |fc-fOld| = 0.0000e+00 <= tolF*(1+|f0|) = 2.4920e+01 0 : |xc-x_last| = 2.1957e+00 <= tolX*(1+|x0|) = 1.3820e+00 0 : |proj(x-g)-x| = 8.9330e+00 <= tolG = 1.0000e-01 0 : |proj(x-g)-x| = 8.9330e+00 <= 1e3*eps = 1.0000e-02 0 : maxIter = 5 <= iter = 3 ------------------------- DONE! ------------------------- Running inversion with SimPEG v0.22.0 simpeg.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv. ***Done using same Solver, and solver_opts as the Simulation3DElectricField problem*** model has any nan: 0 ============================ Inexact Gauss Newton ============================ # beta phi_d phi_m f |proj(x-g)-x| LS Comment ----------------------------------------------------------------------------- x0 has any nan: 0 /usr/share/miniconda/envs/simpeg-test/lib/python3.8/site-packages/pymatsolver/direct.py:23: PardisoTypeConversionWarning: Converting csc_matrix matrix to CSR format. /usr/share/miniconda/envs/simpeg-test/lib/python3.8/site-packages/pymatsolver/direct.py:73: PardisoTypeConversionWarning: Converting csc_matrix matrix to CSR format. 0 2.00e+01 4.57e+02 4.25e+01 1.31e+03 2.64e+02 0 1 2.00e+01 9.57e+01 4.04e+00 1.77e+02 9.18e+01 0 2 2.00e+01 3.77e+01 2.39e+00 8.54e+01 2.54e+01 0 3 2.00e+01 2.26e+01 2.77e+00 7.80e+01 8.16e+00 0 4 2.00e+01 2.11e+01 2.81e+00 7.74e+01 3.48e+00 0 ------------------------- STOP! ------------------------- 1 : |fc-fOld| = 0.0000e+00 <= tolF*(1+|f0|) = 1.3070e+02 1 : |xc-x_last| = 1.0883e-01 <= tolX*(1+|x0|) = 1.3820e+00 0 : |proj(x-g)-x| = 3.4774e+00 <= tolG = 1.0000e-01 0 : |proj(x-g)-x| = 3.4774e+00 <= 1e3*eps = 1.0000e-02 1 : maxIter = 5 <= iter = 5 ------------------------- DONE! ------------------------- /home/vsts/work/1/s/examples/20-published/plot_booky_1D_time_freq_inv.py:478: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect. ('/home/vsts/work/1/s/examples/20-published',) | .. code-block:: Python import numpy as np import h5py import tarfile import os import shutil import matplotlib import matplotlib.pyplot as plt from scipy.constants import mu_0 from pymatsolver import Pardiso as Solver import discretize from simpeg import ( maps, utils, data_misfit, regularization, optimization, inversion, inverse_problem, directives, data, ) from simpeg.electromagnetics import frequency_domain as FDEM, time_domain as TDEM def download_and_unzip_data( url="https://storage.googleapis.com/simpeg/bookpurnong/bookpurnong_inversion.tar.gz", ): """ Download the data from the storage bucket, unzip the tar file, return the directory where the data are """ # download the data downloads = utils.download(url) # directory where the downloaded files are directory = downloads.split(".")[0] # unzip the tarfile tar = tarfile.open(downloads, "r") tar.extractall() tar.close() return downloads, directory def run(plotIt=True, saveFig=False, cleanup=True): """ Run 1D inversions for a single sounding of the RESOLVE and SkyTEM bookpurnong data :param bool plotIt: show the plots? :param bool saveFig: save the figure :param bool cleanup: remove the downloaded results """ downloads, directory = download_and_unzip_data() resolve = h5py.File(os.path.sep.join([directory, "booky_resolve.hdf5"]), "r") skytem = h5py.File(os.path.sep.join([directory, "booky_skytem.hdf5"]), "r") river_path = resolve["river_path"][()] # Choose a sounding location to invert xloc, yloc = 462100.0, 6196500.0 rxind_skytem = np.argmin( abs(skytem["xy"][:, 0] - xloc) + abs(skytem["xy"][:, 1] - yloc) ) rxind_resolve = np.argmin( abs(resolve["xy"][:, 0] - xloc) + abs(resolve["xy"][:, 1] - yloc) ) # Plot both resolve and skytem data on 2D plane fig = plt.figure(figsize=(13, 6)) title = ["RESOLVE In-phase 400 Hz", r"SkyTEM High moment 156 $\mu$s"] ax1 = plt.subplot(121) ax2 = plt.subplot(122) axs = [ax1, ax2] out_re = utils.plot2Ddata( resolve["xy"], resolve["data"][:, 0], ncontour=100, contourOpts={"cmap": "viridis"}, ax=ax1, ) vmin, vmax = out_re[0].get_clim() cb_re = plt.colorbar( out_re[0], ticks=np.linspace(vmin, vmax, 3), ax=ax1, fraction=0.046, pad=0.04 ) temp_skytem = skytem["data"][:, 5].copy() temp_skytem[skytem["data"][:, 5] > 7e-10] = 7e-10 out_sky = utils.plot2Ddata( skytem["xy"][:, :2], temp_skytem, ncontour=100, contourOpts={"cmap": "viridis", "vmax": 7e-10}, ax=ax2, ) vmin, vmax = out_sky[0].get_clim() cb_sky = plt.colorbar( out_sky[0], ticks=np.linspace(vmin, vmax * 0.99, 3), ax=ax2, format="%.1e", fraction=0.046, pad=0.04, ) cb_re.set_label("Bz (ppm)") cb_sky.set_label("dB$_z$ / dt (V/A-m$^4$)") for i, ax in enumerate(axs): xticks = [460000, 463000] yticks = [6195000, 6198000, 6201000] ax.set_xticks(xticks) ax.set_yticks(yticks) ax.plot(xloc, yloc, "wo") ax.plot(river_path[:, 0], river_path[:, 1], "k", lw=0.5) ax.set_aspect("equal") if i == 1: ax.plot(skytem["xy"][:, 0], skytem["xy"][:, 1], "k.", alpha=0.02, ms=1) ax.set_yticklabels([str(" ") for f in yticks]) else: ax.plot(resolve["xy"][:, 0], resolve["xy"][:, 1], "k.", alpha=0.02, ms=1) ax.set_yticklabels([str(f) for f in yticks]) ax.set_ylabel("Northing (m)") ax.set_xlabel("Easting (m)") ax.set_title(title[i]) ax.axis("equal") # plt.tight_layout() if saveFig is True: fig.savefig("resolve_skytem_data.png", dpi=600) # ------------------ Mesh ------------------ # # Step1: Set 2D cylindrical mesh cs, ncx, npad = 1.0, 10.0, 20 hx = [(cs, ncx), (cs, npad, 1.3)] npad = 12 temp = np.logspace(np.log10(1.0), np.log10(12.0), 19) temp_pad = temp[-1] * 1.3 ** np.arange(npad) hz = np.r_[temp_pad[::-1], temp[::-1], temp, temp_pad] mesh = discretize.CylindricalMesh([hx, 1, hz], "00C") active = mesh.cell_centers_z < 0.0 # Step2: Set a SurjectVertical1D mapping # Note: this sets our inversion model as 1D log conductivity # below subsurface active = mesh.cell_centers_z < 0.0 actMap = maps.InjectActiveCells(mesh, active, np.log(1e-8), nC=mesh.shape_cells[2]) mapping = maps.ExpMap(mesh) * maps.SurjectVertical1D(mesh) * actMap sig_half = 1e-1 sig_air = 1e-8 sigma = np.ones(mesh.shape_cells[2]) * sig_air sigma[active] = sig_half # Initial and reference model m0 = np.log(sigma[active]) # ------------------ RESOLVE Forward Simulation ------------------ # # Step3: Invert Resolve data # Bird height from the surface b_height_resolve = resolve["src_elevation"][()] src_height_resolve = b_height_resolve[rxind_resolve] # Set Rx (In-phase and Quadrature) rxOffset = 7.86 bzr = FDEM.Rx.PointMagneticFluxDensitySecondary( np.array([[rxOffset, 0.0, src_height_resolve]]), orientation="z", component="real", ) bzi = FDEM.Rx.PointMagneticFluxDensity( np.array([[rxOffset, 0.0, src_height_resolve]]), orientation="z", component="imag", ) # Set Source (In-phase and Quadrature) frequency_cp = resolve["frequency_cp"][()] freqs = frequency_cp.copy() srcLoc = np.array([0.0, 0.0, src_height_resolve]) source_list = [ FDEM.Src.MagDipole([bzr, bzi], freq, srcLoc, orientation="Z") for freq in freqs ] # Set FDEM survey (In-phase and Quadrature) survey = FDEM.Survey(source_list) prb = FDEM.Simulation3DMagneticFluxDensity(mesh, sigmaMap=mapping, solver=Solver) prb.survey = survey # ------------------ RESOLVE Inversion ------------------ # # Primary field bp = -mu_0 / (4 * np.pi * rxOffset**3) # Observed data cpi_inds = [0, 2, 6, 8, 10] cpq_inds = [1, 3, 7, 9, 11] dobs_re = ( np.c_[ resolve["data"][rxind_resolve, :][cpi_inds], resolve["data"][rxind_resolve, :][cpq_inds], ].flatten() * bp * 1e-6 ) # Uncertainty relative = np.repeat(np.r_[np.ones(3) * 0.1, np.ones(2) * 0.15], 2) floor = 20 * abs(bp) * 1e-6 std = abs(dobs_re) * relative + floor # Data Misfit data_resolve = data.Data(dobs=dobs_re, survey=survey, standard_deviation=std) dmisfit = data_misfit.L2DataMisfit(simulation=prb, data=data_resolve) # Regularization regMesh = discretize.TensorMesh([mesh.h[2][mapping.maps[-1].indActive]]) reg = regularization.WeightedLeastSquares( regMesh, mapping=maps.IdentityMap(regMesh) ) # Optimization opt = optimization.InexactGaussNewton(maxIter=5) # statement of the inverse problem invProb = inverse_problem.BaseInvProblem(dmisfit, reg, opt) # Inversion directives and parameters target = directives.TargetMisfit() # stop when we hit target misfit invProb.beta = 2.0 inv = inversion.BaseInversion(invProb, directiveList=[target]) reg.alpha_s = 1e-3 reg.alpha_x = 1.0 reg.reference_model = m0.copy() opt.LSshorten = 0.5 opt.remember("xc") # run the inversion mopt_re = inv.run(m0) dpred_re = invProb.dpred # ------------------ SkyTEM Forward Simulation ------------------ # # Step4: Invert SkyTEM data # Bird height from the surface b_height_skytem = skytem["src_elevation"][()] src_height = b_height_skytem[rxind_skytem] srcLoc = np.array([0.0, 0.0, src_height]) # Radius of the source loop area = skytem["area"][()] radius = np.sqrt(area / np.pi) rxLoc = np.array([[radius, 0.0, src_height]]) # Parameters for current waveform t0 = skytem["t0"][()] times = skytem["times"][()] waveform_skytem = skytem["waveform"][()] off_time = t0 times_off = times - t0 # Note: we are Using theoretical VTEM waveform, # but effectively fits SkyTEM waveform peak_time = 1.0000000e-02 dbdt_z = TDEM.Rx.PointMagneticFluxTimeDerivative( locations=rxLoc, times=times_off[:-3] + off_time, orientation="z" ) # vertical db_dt receiver_list = [dbdt_z] # list of receivers source_list = [ TDEM.Src.CircularLoop( receiver_list, location=srcLoc, radius=radius, orientation="z", waveform=TDEM.Src.VTEMWaveform( off_time=off_time, peak_time=peak_time, ramp_on_rate=3.0 ), ) ] # solve the problem at these times timeSteps = [ (peak_time / 5, 5), ((off_time - peak_time) / 5, 5), (1e-5, 5), (5e-5, 5), (1e-4, 10), (5e-4, 15), ] prob = TDEM.Simulation3DElectricField( mesh, time_steps=timeSteps, sigmaMap=mapping, solver=Solver ) survey = TDEM.Survey(source_list) prob.survey = survey src = source_list[0] rx = src.receiver_list[0] wave = [] for time in prob.times: wave.append(src.waveform.eval(time)) wave = np.hstack(wave) # plot the waveform fig = plt.figure(figsize=(5, 3)) times_off = times - t0 plt.plot(waveform_skytem[:, 0], waveform_skytem[:, 1], "k.") plt.plot(prob.times, wave, "k-", lw=2) plt.legend(("SkyTEM waveform", "Waveform (fit)"), fontsize=10) for t in rx.times: plt.plot(np.ones(2) * t, np.r_[-0.03, 0.03], "k-") plt.ylim(-0.1, 1.1) plt.grid(True) plt.xlabel("Time (s)") plt.ylabel("Normalized current") if saveFig: fig.savefig("skytem_waveform", dpi=200) # Observed data dobs_sky = skytem["data"][rxind_skytem, :-3] * area # ------------------ SkyTEM Inversion ------------------ # # Uncertainty relative = 0.12 floor = 7.5e-12 std = abs(dobs_sky) * relative + floor # Data Misfit data_sky = data.Data(dobs=-dobs_sky, survey=survey, standard_deviation=std) dmisfit = data_misfit.L2DataMisfit(simulation=prob, data=data_sky) # Regularization regMesh = discretize.TensorMesh([mesh.h[2][mapping.maps[-1].indActive]]) reg = regularization.WeightedLeastSquares( regMesh, mapping=maps.IdentityMap(regMesh) ) # Optimization opt = optimization.InexactGaussNewton(maxIter=5) # statement of the inverse problem invProb = inverse_problem.BaseInvProblem(dmisfit, reg, opt) # Directives and Inversion Parameters target = directives.TargetMisfit() invProb.beta = 20.0 inv = inversion.BaseInversion(invProb, directiveList=[target]) reg.alpha_s = 1e-1 reg.alpha_x = 1.0 opt.LSshorten = 0.5 opt.remember("xc") reg.reference_model = mopt_re # Use RESOLVE model as a reference model # run the inversion mopt_sky = inv.run(m0) dpred_sky = invProb.dpred # Plot the figure from the paper plt.figure(figsize=(12, 8)) fs = 13 # fontsize matplotlib.rcParams["font.size"] = fs ax0 = plt.subplot2grid((2, 2), (0, 0), rowspan=2) ax1 = plt.subplot2grid((2, 2), (0, 1)) ax2 = plt.subplot2grid((2, 2), (1, 1)) # Recovered Models sigma_re = np.repeat(np.exp(mopt_re), 2, axis=0) sigma_sky = np.repeat(np.exp(mopt_sky), 2, axis=0) z = np.repeat(mesh.cell_centers_z[active][1:], 2, axis=0) z = np.r_[mesh.cell_centers_z[active][0], z, mesh.cell_centers_z[active][-1]] ax0.semilogx(sigma_re, z, "k", lw=2, label="RESOLVE") ax0.semilogx(sigma_sky, z, "b", lw=2, label="SkyTEM") ax0.set_ylim(-50, 0) # ax0.set_xlim(5e-4, 1e2) ax0.grid(True) ax0.set_ylabel("Depth (m)") ax0.set_xlabel("Conducivity (S/m)") ax0.legend(loc=3) ax0.set_title("(a) Recovered Models") # RESOLVE Data ax1.loglog( frequency_cp, dobs_re.reshape((5, 2))[:, 0] / bp * 1e6, "k-", label="Obs (real)" ) ax1.loglog( frequency_cp, dobs_re.reshape((5, 2))[:, 1] / bp * 1e6, "k--", label="Obs (imag)", ) ax1.loglog( frequency_cp, dpred_re.reshape((5, 2))[:, 0] / bp * 1e6, "k+", ms=10, markeredgewidth=2.0, label="Pred (real)", ) ax1.loglog( frequency_cp, dpred_re.reshape((5, 2))[:, 1] / bp * 1e6, "ko", ms=6, markeredgecolor="k", markeredgewidth=0.5, label="Pred (imag)", ) ax1.set_title("(b) RESOLVE") ax1.set_xlabel("Frequency (Hz)") ax1.set_ylabel("Bz (ppm)") ax1.grid(True) ax1.legend(loc=3, fontsize=11) # SkyTEM data ax2.loglog(times_off[3:] * 1e6, dobs_sky / area, "b-", label="Obs") ax2.loglog( times_off[3:] * 1e6, -dpred_sky / area, "bo", ms=4, markeredgecolor="k", markeredgewidth=0.5, label="Pred", ) ax2.set_xlim(times_off.min() * 1e6 * 1.2, times_off.max() * 1e6 * 1.1) ax2.set_xlabel(r"Time ($\mu s$)") ax2.set_ylabel("dBz / dt (V/A-m$^4$)") ax2.set_title("(c) SkyTEM High-moment") ax2.grid(True) ax2.legend(loc=3) a3 = plt.axes([0.86, 0.33, 0.1, 0.09], facecolor=[0.8, 0.8, 0.8, 0.6]) a3.plot(prob.times * 1e6, wave, "k-") a3.plot( rx.times * 1e6, np.zeros_like(rx.times), "k|", markeredgewidth=1, markersize=12 ) a3.set_xlim([prob.times.min() * 1e6 * 0.75, prob.times.max() * 1e6 * 1.1]) a3.set_title("(d) Waveform", fontsize=11) a3.set_xticks([prob.times.min() * 1e6, t0 * 1e6, prob.times.max() * 1e6]) a3.set_yticks([]) # a3.set_xticklabels(['0', '2e4']) a3.set_xticklabels(["-1e4", "0", "1e4"]) plt.tight_layout() if saveFig: plt.savefig("booky1D_time_freq.png", dpi=600) if plotIt: plt.show() resolve.close() skytem.close() if cleanup: print(os.path.split(directory)[:-1]) os.remove( os.path.sep.join(directory.split()[:-1] + ["._bookpurnong_inversion"]) ) os.remove(downloads) shutil.rmtree(directory) if __name__ == "__main__": run(plotIt=True, saveFig=False, cleanup=True) .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 25.324 seconds) **Estimated memory usage:** 20 MB .. _sphx_glr_download_content_examples_20-published_plot_booky_1D_time_freq_inv.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_booky_1D_time_freq_inv.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_booky_1D_time_freq_inv.py ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_