def fwd_grav_fatiando():
"""
GravMag: 3D imaging using the migration method on synthetic gravity data
(more complex model + noisy data)
"""
# Make some synthetic gravity data from a simple prism model
za = 5000
zb = 7000
model = [mesher.Prism(-4000, 0, -4000, -2000, za, zb,
{'density': 1200})] #,
# mesher.Prism(-1000, 1000, -1000, 1000, 1000, 7000, {'density': -800}),
# mesher.Prism(2000, 4000, 3000, 4000, 0, 2000, {'density': 600})]
# Calculate on a scatter of points to show that migration doesn't need gridded
# data
# xp, yp, zp = gridder.scatter((-6000, 6000, -6000, 6000), 1000, z=0)
shape = (25, 25)
xp, yp, zp = gridder.regular((-5000, 5000, -5000, 5000), shape, z=0)
#gz = utils.contaminate(prism.gz(xp, yp, zp, model), 0.1)
gz = prism.gz(xp, yp, zp, model)
# Plot the data
shape = (50, 50)
mpl.figure()
mpl.axis('scaled')
mpl.contourf(yp, xp, gz, shape, 30, interp=True)
mpl.colorbar()
mpl.plot(yp, xp, '.k')
mpl.xlabel('East (km)')
mpl.ylabel('North (km)')
mpl.m2km()
mpl.show()
return xp, yp, zp, gz, shape, model
# Print the estimated and true dipole monents, inclinations and declinations
print 'Estimated magnetization (intensity, inclination, declination)'
for e in solver.estimate_:
print e
# Plot the fit and the normalized histogram of the residuals
mpl.figure(figsize=(14, 5))
mpl.subplot(1, 2, 1)
mpl.title("Total Field Anomaly (nT)", fontsize=14)
mpl.axis('scaled')
nlevels = mpl.contour(y, x, tf, (50, 50), 15, interp=True, color='r',
label='Observed', linewidth=2.0)
mpl.contour(y, x, solver.predicted(), (50, 50), nlevels, interp=True,
color='b', label='Predicted', style='dashed', linewidth=2.0)
mpl.legend(loc='upper left', shadow=True, prop={'size': 13})
mpl.xlabel('East y (m)', fontsize=14)
mpl.ylabel('North x (m)', fontsize=14)
mpl.subplot(1, 2, 2)
residuals_mean = numpy.mean(solver.residuals())
residuals_std = numpy.std(solver.residuals())
# Each residual is subtracted from the mean and the resulting
# difference is divided by the standard deviation
s = (solver.residuals() - residuals_mean) / residuals_std
mpl.hist(s, bins=21, range=None, normed=True, weights=None,
cumulative=False, bottom=None, histtype='bar', align='mid',
orientation='vertical', rwidth=None, log=False,
color=None, label=None)
mpl.xlim(-4, 4)
mpl.title("mean = %.3f std = %.3f" % (residuals_mean, residuals_std),
fontsize=14)
mpl.ylabel("P(z)", fontsize=14)
gxy = utils.contaminate(gm.prism.gxy(xp, yp, zp, model), noise)
gxz = utils.contaminate(gm.prism.gxz(xp, yp, zp, model), noise)
gyy = utils.contaminate(gm.prism.gyy(xp, yp, zp, model), noise)
gyz = utils.contaminate(gm.prism.gyz(xp, yp, zp, model), noise)
gzz = utils.contaminate(gm.prism.gzz(xp, yp, zp, model), noise)
tensor = [gxx, gxy, gxz, gyy, gyz, gzz]
titles = ['gxx', 'gxy', 'gxz', 'gyy', 'gyz', 'gzz']
# plot the data
mpl.figure()
for i in xrange(len(tensor)):
mpl.subplot(2, 3, i + 1)
mpl.title(titles[i])
mpl.axis('scaled')
levels = mpl.contourf(yp, xp, tensor[i], shape, 30)
mpl.colorbar()
mpl.xlabel('y (km)')
mpl.ylabel('x (km)')
mpl.m2km()
mpl.show()
# Inversion setup
# Create a mesh
mesh = PrismMesh(bounds, (30, 30, 30))
# Wrap the data so that harvester can use it
data = [gm.harvester.Gxx(xp, yp, zp, gxx),
gm.harvester.Gxy(xp, yp, zp, gxy),
gm.harvester.Gxz(xp, yp, zp, gxz),
gm.harvester.Gyy(xp, yp, zp, gyy),
gm.harvester.Gyz(xp, yp, zp, gyz),
gm.harvester.Gzz(xp, yp, zp, gzz)]
# Make the seeds
# Should be close to the data error if the inversion was able to fit the data
residuals = tomo.residuals()
print "Assumed error: %g" % (error)
print "Standard deviation of residuals: %g" % (np.std(residuals))
mpl.figure(figsize=(14, 5))
mpl.subplot(1, 2, 1)
mpl.axis('scaled')
mpl.title('Vp model')
mpl.squaremesh(model, prop='vp', cmap=mpl.cm.seismic)
cb = mpl.colorbar()
cb.set_label('Velocity')
mpl.points(src_loc, '*y', label="Sources")
mpl.points(rec_loc, '^r', label="Receivers")
mpl.legend(loc='lower left', shadow=True, numpoints=1, prop={'size': 10})
mpl.m2km()
mpl.subplot(1, 2, 2)
mpl.axis('scaled')
mpl.title('Tomography result')
mpl.squaremesh(mesh, prop='vp', vmin=4000, vmax=10000,
cmap=mpl.cm.seismic)
cb = mpl.colorbar()
cb.set_label('Velocity')
mpl.m2km()
mpl.figure()
mpl.grid()
mpl.title('Residuals (data with %.4f s error)' % (error))
mpl.hist(residuals, color='gray', bins=10)
mpl.xlabel("seconds")
mpl.show()
mesher.Prism(-1000, 1000, -1000, 1000, 1000, 7000, {'density': -800}),
mesher.Prism(2000, 4000, 3000, 4000, 0, 2000, {'density': 600})
]
# Calculate on a scatter of points to show that migration doesn't need gridded
# data
xp, yp, zp = gridder.scatter((-6000, 6000, -6000, 6000), 1000, z=-10)
gz = utils.contaminate(prism.gz(xp, yp, zp, model), 0.1)
# Plot the data
shape = (50, 50)
mpl.figure()
mpl.axis('scaled')
mpl.contourf(yp, xp, gz, shape, 30, interp=True)
mpl.colorbar()
mpl.plot(yp, xp, '.k')
mpl.xlabel('East (km)')
mpl.ylabel('North (km)')
mpl.m2km()
mpl.show()
mesh = imaging.migrate(xp, yp, zp, gz, 0, 10000, (30, 30, 30), power=0.8)
# Plot the results
myv.figure()
myv.prisms(model, 'density', style='wireframe', linewidth=2)
myv.prisms(mesh, 'density', edges=False)
axes = myv.axes(myv.outline())
myv.wall_bottom(axes.axes.bounds)
myv.wall_north(axes.axes.bounds)
myv.show()
# Create a synthetic model
model = [Prism(250, 750, 250, 750, 200, 700, {'density':1000})]
# and generate synthetic data from it
shape = (25, 25)
bounds = [0, 1000, 0, 1000, 0, 1000]
area = bounds[0:4]
xp, yp, zp = gridder.regular(area, shape, z=-1)
noise = 0.1 # 0.1 mGal noise
gz = utils.contaminate(gm.prism.gz(xp, yp, zp, model), noise)
# plot the data
mpl.figure()
mpl.title("Synthetic gravity anomaly (mGal)")
mpl.axis('scaled')
levels = mpl.contourf(yp, xp, gz, shape, 12)
mpl.colorbar()
mpl.xlabel('Horizontal coordinate y (km)')
mpl.ylabel('Horizontal coordinate x (km)')
mpl.m2km()
mpl.show()
# Inversion setup
# Create a mesh
mesh = PrismMesh(bounds, (25, 25, 25))
# Wrap the data so that harvester can use it
data = [gm.harvester.Gz(xp, yp, zp, gz)]
# Make the seed
seeds = gm.harvester.sow([[500, 500, 450, {'density':1000}]], mesh)
# Run the inversioin
estimate, predicted = gm.harvester.harvest(data, seeds, mesh,
compactness=0.5, threshold=0.0005)
temp, error = utils.contaminate(climsig.abrupt(amp, age, zp),
0.02,
percent=True,
return_stddev=True)
# Preparing for the inversion
p, residuals = climsig.iabrupt(temp, zp)
est_amp, est_age = p
mpl.figure(figsize=(12, 5))
mpl.subplot(1, 2, 1)
mpl.title("Climate signal (abrupt)")
mpl.plot(temp, zp, 'ok', label='Observed')
mpl.plot(temp - residuals, zp, '--r', linewidth=3, label='Predicted')
mpl.legend(loc='lower right', numpoints=1)
mpl.xlabel("Temperature (C)")
mpl.ylabel("Z")
mpl.ylim(100, 0)
ax = mpl.subplot(1, 2, 2)
ax2 = mpl.twinx()
mpl.title("Age and amplitude")
width = 0.3
ax.bar([1 - width], [age], width, color='b', label="True")
ax.bar([1], [est_age], width, color='r', label="Estimate")
ax2.bar([2 - width], [amp], width, color='b')
ax2.bar([2], [est_amp], width, color='r')
ax.legend(loc='upper center', numpoints=1)
ax.set_ylabel("Age (years)")
ax2.set_ylabel("Amplitude (C)")
ax.set_xticks([1, 2])
ax.set_xticklabels(['Age', 'Amplitude'])
mpl.ylim(-10**(-3), 10**(-3))
mpl.subplot(2, 2, 4)
mpl.title('z component')
zseismogram, = mpl.plot([], [], '-k')
mpl.xlim(0, duration)
mpl.ylim(-10**(-3), 10**(-3))
mpl.subplot(1, 2, 1)
# Start with everything zero and grab the plot so that it can be updated later
wavefield = mpl.imshow(np.zeros(shape),
extent=area,
vmin=-10**-6,
vmax=10**-6,
cmap=mpl.cm.gray_r)
mpl.points(stations, '^k')
mpl.ylim(area[2:][::-1])
mpl.xlabel('x (km)')
mpl.ylabel('z (km)')
mpl.m2km()
times = np.linspace(0, maxit * dt, maxit)
# This function updates the plot every few timesteps
def animate(i):
# Simulation will yield panels corresponding to P and S waves because
# xz2ps=True
t, p, s, xcomp, zcomp = simulation.next()
mpl.title('time: %0.1f s' % (times[t]))
wavefield.set_array((p + s)[::-1])
xseismogram.set_data(times[:t + 1], xcomp[0][:t + 1])
zseismogram.set_data(times[:t + 1], zcomp[0][:t + 1])
return wavefield, xseismogram, zseismogram
titles = ('gxy', 'gzz')
mpl.figure()
mpl.suptitle("True: color | Inversion: contour")
for i in xrange(len(tensor)):
mpl.subplot(2, 2, i + 1)
mpl.title(titles[i])
mpl.axis('scaled')
levels = mpl.contourf(y*0.001, x*0.001, tensor[i], shape, 12)
mpl.colorbar()
mpl.contour(y*0.001, x*0.001, predicted[i], shape, levels, color='k')
for i in xrange(len(tensor)):
mpl.subplot(2, 2, i + 3)
residuals = tensor[i] - predicted[i]
mpl.title('residuals stddev = %.2f' % (residuals.std()))
mpl.hist(residuals, bins=10)
mpl.xlabel('Residual (Eotvos)')
mpl.show()
myv.figure()
myv.prisms(model, 'density', style='wireframe')
myv.prisms([mesh[s.i] for s in seeds], 'density')
myv.axes(myv.outline(bounds), ranges=[i*0.001 for i in bounds], fmt='%.1f',
nlabels=6)
myv.wall_bottom(bounds)
myv.wall_north(bounds)
myv.figure()
myv.prisms(model, 'density', style='wireframe')
myv.prisms(density_model, 'density')
myv.axes(myv.outline(bounds), ranges=[i*0.001 for i in bounds], fmt='%.1f',
nlabels=6)
myv.wall_bottom(bounds)
myv.wall_north(bounds)
maxit = int(duration / simulation.dt)
maxt = duration
# This part makes an animation using matplotlibs animation API
background = (velocity - 6000) * 10**-3
fig = mpl.figure(figsize=(8, 6))
mpl.subplots_adjust(right=0.98, left=0.11, hspace=0.5, top=0.93)
mpl.subplot2grid((4, 3), (0, 0), colspan=3, rowspan=3)
wavefield = mpl.imshow(np.zeros_like(velocity),
extent=area,
cmap=mpl.cm.gray_r,
vmin=-0.05,
vmax=0.05)
mpl.points([75 * ds, 125 * ds], '^b', size=8) # seismometer position
mpl.ylim(area[2:][::-1])
mpl.xlabel('x (km)')
mpl.ylabel('z (km)')
mpl.m2km()
mpl.subplot2grid((4, 3), (3, 0), colspan=3)
seismogram1, = mpl.plot([], [], '-k')
mpl.xlim(0, duration)
mpl.ylim(-0.05, 0.05)
mpl.ylabel('Amplitude')
mpl.xlabel('Time (s)')
times = np.linspace(0, maxt, maxit)
# This function updates the plot every few timesteps
simulation.run(maxit)
seismogram = simulation[:, 125, 75] # (time, z and x) shape
padding=50,
taper=0.01)
# This part makes an animation using matplotlibs animation API
fig = mpl.figure(figsize=(12, 5))
# Start with everything zero and grab the plot so that it can be updated later
mpl.imshow(pvel[::-1], extent=area, alpha=0.25)
wavefield = mpl.imshow(np.zeros(shape),
extent=area,
vmin=-10**-7,
vmax=10**-7,
alpha=0.75,
cmap=mpl.cm.gray_r)
mpl.points(stations, '.k')
mpl.ylim(area[2:][::-1])
mpl.xlabel('x (km)')
mpl.ylabel('z (km)')
mpl.m2km()
times = np.linspace(0, maxit * dt, maxit)
# the only way for getting the feedback response of the seimograms
global seismograms
# This function updates the plot every few timesteps
def animate(i):
# Simulation will yield panels corresponding to P and S waves because
# xz2ps=True
t, ux, uz, xcomp, zcomp = simulation.next()
mpl.title('time: %0.3f s' % (times[t]))
# wavefield.set_array((p + s)[::-1])
wavefield.set_data(uz[::-1])
mpl.subplot(3, 1, 2)
mpl.title("Seismogram 2")
seismogram2, = mpl.plot([], [], "-k")
mpl.xlim(0, duration)
mpl.ylim(-0.1, 0.1)
mpl.ylabel("Amplitude")
ax = mpl.subplot(3, 1, 3)
mpl.title("time: 0.0 s")
wavefield = mpl.imshow(background, extent=area, cmap=mpl.cm.gray_r, vmin=-0.005, vmax=0.005)
mpl.points(stations, "^b", size=8)
mpl.text(750000, 20000, "Crust")
mpl.text(740000, 100000, "Mantle")
fig.text(0.82, 0.33, "Seismometer 2")
fig.text(0.16, 0.33, "Seismometer 1")
mpl.ylim(area[2:][::-1])
mpl.xlabel("x (km)")
mpl.ylabel("z (km)")
mpl.m2km()
times = np.linspace(0, dt * maxit, maxit)
# This function updates the plot every few timesteps
def animate(i):
t, u, seismogram = simulation.next()
mpl.title("time: %0.1f s" % (times[t]))
wavefield.set_array((background + u)[::-1])
seismogram1.set_data(times[: t + 1], seismogram[0][: t + 1])
seismogram2.set_data(times[: t + 1], seismogram[1][: t + 1])
return wavefield, seismogram1, seismogram2
"""
Gridding: Load a Surfer ASCII grid file
"""
from fatiando import datasets, gridder
from fatiando.vis import mpl
# Fetching Bouguer anomaly model data (Surfer ASCII grid file)"
# Will download the archive and save it with the default name
archive = datasets.fetch_bouguer_alps_egm()
# Load the GRD file and convert in three numpy-arrays (x, y, bouguer)
x, y, bouguer, shape = gridder.load_surfer(archive, fmt="ascii")
mpl.figure()
mpl.axis("scaled")
mpl.title("Data loaded from a Surfer ASCII grid file")
mpl.contourf(y, x, bouguer, shape, 15, cmap=mpl.cm.RdBu_r)
cb = mpl.colorbar()
cb.set_label("mGal")
mpl.xlabel("y points to East (km)")
mpl.ylabel("x points to North (km)")
mpl.m2km()
mpl.show()
# Create a synthetic model
model = [Prism(250, 750, 250, 750, 200, 700, {'density': 1000})]
# and generate synthetic data from it
shape = (25, 25)
bounds = [0, 1000, 0, 1000, 0, 1000]
area = bounds[0:4]
xp, yp, zp = gridder.regular(area, shape, z=-1)
noise = 0.1 # 0.1 mGal noise
gz = utils.contaminate(gm.prism.gz(xp, yp, zp, model), noise)
# plot the data
mpl.figure()
mpl.title("Synthetic gravity anomaly (mGal)")
mpl.axis('scaled')
levels = mpl.contourf(yp, xp, gz, shape, 12)
mpl.colorbar()
mpl.xlabel('Horizontal coordinate y (km)')
mpl.ylabel('Horizontal coordinate x (km)')
mpl.m2km()
mpl.show()
# Inversion setup
# Create a mesh
mesh = PrismMesh(bounds, (25, 25, 25))
# Wrap the data so that harvester can use it
data = [gm.harvester.Gz(xp, yp, zp, gz)]
# Make the seed
seeds = gm.harvester.sow([[500, 500, 450, {'density': 1000}]], mesh)
# Run the inversioin
estimate, predicted = gm.harvester.harvest(data,
seeds,
mesh,
mpl.points(src, '*y')
initial = mpl.pick_points(area, mpl.gca(), marker='*', color='b')
if len(initial) > 1:
print "Don't be greedy! Pick only one point"
sys.exit()
estimate = solver.config('levmarq', initial=initial[0]).fit().estimate_
mpl.figure(figsize=(10, 4))
mpl.subplot(1, 2, 1)
mpl.title('Epicenter + %d recording stations' % (len(recs)))
mpl.axis('scaled')
mpl.points(src, '*y', label="True")
mpl.points(recs, '^r', label="Stations")
mpl.points(initial, '*b', label="Initial")
mpl.points([estimate], '*g', label="Estimate")
mpl.set_area(area)
mpl.legend(loc='lower right', shadow=True, numpoints=1, prop={'size': 12})
mpl.xlabel("X")
mpl.ylabel("Y")
ax = mpl.subplot(1, 2, 2)
mpl.title('Travel-time residuals + error bars')
s = numpy.arange(len(traveltime)) + 1
width = 0.3
mpl.bar(s - width, traveltime, width, color='g', label="Observed", yerr=error)
mpl.bar(s, solver.predicted(), width, color='r', label="Predicted")
ax.set_xticks(s)
mpl.legend(loc='upper right', shadow=True, prop={'size': 12})
mpl.xlabel("Station number")
mpl.ylabel("Travel-time residual")
mpl.show()
initial = mpl.pick_points(area, mpl.gca(), marker='*', color='b')
if len(initial) > 1:
print "Don't be greedy! Pick only one point"
sys.exit()
estimate = solver.config('levmarq', initial=initial[0]).fit().estimate_
mpl.figure(figsize=(10,4))
mpl.subplot(1, 2, 1)
mpl.title('Epicenter + %d recording stations' % (len(recs)))
mpl.axis('scaled')
mpl.points(src, '*y', label="True")
mpl.points(recs, '^r', label="Stations")
mpl.points(initial, '*b', label="Initial")
mpl.points([estimate], '*g', label="Estimate")
mpl.set_area(area)
mpl.legend(loc='lower right', shadow=True, numpoints=1, prop={'size':12})
mpl.xlabel("X")
mpl.ylabel("Y")
ax = mpl.subplot(1, 2, 2)
mpl.title('Travel-time residuals + error bars')
s = numpy.arange(len(traveltime)) + 1
width = 0.3
mpl.bar(s - width, traveltime, width, color='g', label="Observed",
yerr=error)
mpl.bar(s, solver.predicted(), width, color='r', label="Predicted")
ax.set_xticks(s)
mpl.legend(loc='upper right', shadow=True, prop={'size':12})
mpl.xlabel("Station number")
mpl.ylabel("Travel-time residual")
mpl.show()
utils.contaminate(gravmag.prism.gxx(x, y, z, model), noise),
utils.contaminate(gravmag.prism.gxy(x, y, z, model), noise),
utils.contaminate(gravmag.prism.gxz(x, y, z, model), noise),
utils.contaminate(gravmag.prism.gyy(x, y, z, model), noise),
utils.contaminate(gravmag.prism.gyz(x, y, z, model), noise),
utils.contaminate(gravmag.prism.gzz(x, y, z, model), noise)
]
with open('data.txt', 'w') as f:
f.write(logger.header(comment='#'))
f.write("# Noise corrupted gz and tensor components:\n")
f.write("# noise = %g Eotvos\n" % (noise))
f.write("# noise = %g mGal\n" % (noisegz))
f.write("# coordinates are in meters\n")
f.write("# gz in mGal and tensor in Eotvos\n")
f.write("# x y z height gz gxx gxy gxz gyy gyz gzz\n")
numpy.savetxt(f, numpy.transpose(data))
# Show it
mpl.figure(figsize=(10, 9))
names = "z height gz gxx gxy gxz gyy gyz gzz".split()
for i, comp in enumerate(data[2:]):
mpl.subplot(3, 3, i + 1)
mpl.axis('scaled')
mpl.title(names[i])
levels = mpl.contourf(y * 0.001, x * 0.001, comp, shape, 8)
mpl.contour(y * 0.001, x * 0.001, comp, shape, levels)
if i == 3:
mpl.ylabel('North = x (km)')
if i == 7:
mpl.xlabel('East = y (km)')
mpl.show()
xp, yp, zp = gridder.regular(area, shape, z=-1)
noise = 0.1 # 0.1 mGal noise
gz = utils.contaminate(polyprism.gz(xp, yp, zp, model), noise)
# Create a mesh
mesh = PrismMesh(bounds, (25, 50, 50))
# Wrap the data so that harvester can read it
data = [harvester.Gz(xp, yp, zp, gz)]
# Plot the data and pick the location of the seeds
mpl.figure()
mpl.suptitle("Pick the seeds (polygon is the true source)")
mpl.axis("scaled")
levels = mpl.contourf(yp, xp, gz, shape, 12)
mpl.colorbar()
mpl.polygon(model[0], xy2ne=True)
mpl.xlabel("Horizontal coordinate y (km)")
mpl.ylabel("Horizontal coordinate x (km)")
seedx, seedy = mpl.pick_points(area, mpl.gca(), xy2ne=True).T
# Set the right density and depth
locations = [[x, y, 1500, {"density": 1000}] for x, y in zip(seedx, seedy)]
mpl.show()
# Make the seed and set the compactness regularizing parameter mu
seeds = harvester.sow(locations, mesh)
# Run the inversion
estimate, predicted = harvester.harvest(data, seeds, mesh, compactness=0.05, threshold=0.0005)
# Put the estimated density values in the mesh
mesh.addprop("density", estimate["density"])
# Plot the adjustment and the result
mpl.figure()
mpl.title("True: color | Predicted: contour")
mpl.axis("scaled")
log.info("Generating synthetic data")
verts = [(10000, 1.), (90000, 1.), (90000, 7000), (10000, 3330)]
model = mesher.Polygon(verts, {'density':-100})
xp = numpy.arange(0., 100000., 1000.)
zp = numpy.zeros_like(xp)
gz = utils.contaminate(gravmag.talwani.gz(xp, zp, [model]), 0.5)
log.info("Preparing for the inversion")
solver = inversion.gradient.levmarq(initial=(9000, 500))
estimate, residuals = gravmag.basin2d.trapezoidal(xp, zp, gz, verts[0:2], -100,
solver)
mpl.figure()
mpl.subplot(2, 1, 1)
mpl.title("Gravity anomaly")
mpl.plot(xp, gz, 'ok', label='Observed')
mpl.plot(xp, gz - residuals, '-r', linewidth=2, label='Predicted')
mpl.legend(loc='lower left', numpoints=1)
mpl.ylabel("mGal")
mpl.xlim(0, 100000)
mpl.subplot(2, 1, 2)
mpl.polygon(estimate, 'o-r', linewidth=2, fill='r', alpha=0.3,
label='Estimated')
mpl.polygon(model, '--k', linewidth=2, label='True')
mpl.legend(loc='lower left', numpoints=1)
mpl.xlabel("X")
mpl.ylabel("Z")
mpl.set_area((0, 100000, 10000, -500))
mpl.show()
stations = [[50000, 0]] # x, z coordinate of the seismometer
snapshot = int(0.5 / dt) # Plot a snapshot of the simulation every 0.5 seconds
simulation = wavefd.elastic_sh(mu, density, area, dt, maxit, sources, stations,
snapshot, padding=50, taper=0.01)
# This part makes an animation using matplotlibs animation API
fig = mpl.figure(figsize=(14, 5))
ax = mpl.subplot(1, 2, 2)
mpl.title('Wavefield')
# Start with everything zero and grab the plot so that it can be updated later
wavefield_plt = mpl.imshow(np.zeros(shape), extent=area, vmin=-10 ** (-5),
vmax=10 ** (-5), cmap=mpl.cm.gray_r)
mpl.points(stations, '^b')
mpl.xlim(area[:2])
mpl.ylim(area[2:][::-1])
mpl.xlabel('x (km)')
mpl.ylabel('z (km)')
mpl.subplot(1, 2, 1)
seismogram_plt, = mpl.plot([], [], '-k')
mpl.xlim(0, duration)
mpl.ylim(-10 ** (-4), 10 ** (-4))
mpl.xlabel('time (s)')
mpl.ylabel('Amplitude')
times = np.linspace(0, duration, maxit)
# Update the plot everytime the simulation yields
def animate(i):
"""
Grab the iteration number, displacment panel and seismograms
"""
"""
GravMag: 2D forward modeling with polygons
"""
import numpy
from fatiando import utils, mesher
from fatiando.gravmag import talwani
from fatiando.vis import mpl
# Notice that the last two number are switched.
# This way, the z axis in the plots points down.
area = (-5000, 5000, 5000, 0)
axes = mpl.figure().gca()
mpl.xlabel("X")
mpl.ylabel("Z")
mpl.axis('scaled')
polygons = [mesher.Polygon(mpl.draw_polygon(area, axes),
{'density': 500})]
xp = numpy.arange(-4500, 4500, 100)
zp = numpy.zeros_like(xp)
gz = talwani.gz(xp, zp, polygons)
mpl.figure()
mpl.axis('scaled')
mpl.subplot(2, 1, 1)
mpl.title(r"Gravity anomaly produced by the model")
mpl.plot(xp, gz, '-k', linewidth=2)
mpl.ylabel("mGal")
mpl.xlim(-5000, 5000)
mpl.subplot(2, 1, 2)
mpl.polygon(polygons[0], 'o-k', linewidth=2, fill='k', alpha=0.5)
mpl.xlabel("X")
xp, yp, zp = gridder.regular(area, shape, z=-1)
noise = 0.1 # 0.1 mGal noise
gz = utils.contaminate(gm.polyprism.gz(xp, yp, zp, model), noise)
# Create a mesh
mesh = PrismMesh(bounds, (25, 50, 50))
# Wrap the data so that harvester can read it
data = [gm.harvester.Gz(xp, yp, zp, gz)]
# Plot the data and pick the location of the seeds
mpl.figure()
mpl.suptitle("Pick the seeds (polygon is the true source)")
mpl.axis('scaled')
levels = mpl.contourf(yp, xp, gz, shape, 12)
mpl.colorbar()
mpl.polygon(model[0], xy2ne=True)
mpl.xlabel('Horizontal coordinate y (km)')
mpl.ylabel('Horizontal coordinate x (km)')
seedx, seedy = mpl.pick_points(area, mpl.gca(), xy2ne=True).T
# Set the right density and depth
locations = [[x, y, 1500, {'density': 1000}] for x, y in zip(seedx, seedy)]
mpl.show()
# Make the seed and set the compactness regularizing parameter mu
seeds = gm.harvester.sow(locations, mesh)
# Run the inversion
estimate, predicted = gm.harvester.harvest(data,
seeds,
mesh,
compactness=0.05,
threshold=0.0005)
# Put the estimated density values in the mesh
mesh.addprop('density', estimate['density'])
"""
Seismic: Invert vertical seismic profile (VSP) traveltimes for the velocity
of a layered model.
"""
import numpy
from fatiando import utils
from fatiando.seismic.profile import layered_straight_ray, LayeredStraight
from fatiando.inversion.regularization import Damping
from fatiando.vis import mpl
# The limits in velocity and depths, respectively
area = (0, 10000, 0, 100)
vmin, vmax, zmin, zmax = area
# Use the interactive functions of mpl to draw a layered model
figure = mpl.figure()
mpl.xlabel("Velocity (m/s)")
mpl.ylabel("Depth (m)")
thickness, velocity = mpl.draw_layers(area, figure.gca())
# Make some synthetic noise-corrupted travel-time data
zp = numpy.arange(zmin + 0.5, zmax, 0.5)
tts, error = utils.contaminate(layered_straight_ray(thickness, velocity, zp),
0.02,
percent=True,
return_stddev=True)
# Make the solver and run the inversion using damping regularization
# (assumes known thicknesses of the layers)
solver = (LayeredStraight(tts, zp, thickness) +
0.1 * Damping(len(thickness))).fit()
velocity_ = solver.estimate_
# Plot the results
0.02, percent=True, return_stddev=True)
# Assume that the thicknesses are unknown. In this case, use a mesh of many
# thin layers and invert for each slowness
thick = 10.
mesh = [thick]*int(sum(thickness)/thick)
solver = (LayeredStraight(tts, zp, mesh) +
5*Smoothness1D(len(mesh))).fit()
velocity_ = solver.estimate_
mpl.figure(figsize=(12,5))
mpl.subplot(1, 2, 1)
mpl.grid()
mpl.title("Vertical seismic profile")
mpl.plot(tts, zp, 'ok', label='Observed')
mpl.plot(solver.predicted(), zp, '-r', linewidth=3, label='Predicted')
mpl.legend(loc='upper right', numpoints=1)
mpl.xlabel("Travel-time (s)")
mpl.ylabel("Z (m)")
mpl.ylim(sum(mesh), 0)
mpl.subplot(1, 2, 2)
mpl.grid()
mpl.title("True velocity + smooth estimate")
mpl.layers(mesh, velocity_, '.-k', linewidth=2, label='Estimated')
mpl.layers(thickness, velocity, '--b', linewidth=2, label='True')
mpl.ylim(sum(mesh), 0)
mpl.xlim(0, 10000)
mpl.legend(loc='upper right', numpoints=1)
mpl.xlabel("Velocity (m/s)")
mpl.ylabel("Z (m)")
mpl.show()
duration = 2.5
maxit = int(duration/dt)
stations = [[75*ds, 125*ds]] # x, z coordinate of the seismometer
snapshots = 3 # every 3 iterations plots one
simulation = wavefd.scalar(velocity, area, dt, maxit, sources, stations, snapshots)
# This part makes an animation using matplotlibs animation API
background = (velocity-4000)*10**-1
fig = mpl.figure(figsize=(8, 6))
mpl.subplots_adjust(right=0.98, left=0.11, hspace=0.5, top=0.93)
mpl.subplot2grid((4, 3), (0,0), colspan=3,rowspan=3)
wavefield = mpl.imshow(np.zeros_like(velocity), extent=area, cmap=mpl.cm.gray_r,
vmin=-1000, vmax=1000)
mpl.points(stations, '^b', size=8)
mpl.ylim(area[2:][::-1])
mpl.xlabel('x (km)')
mpl.ylabel('z (km)')
mpl.m2km()
mpl.subplot2grid((4,3), (3,0), colspan=3)
seismogram1, = mpl.plot([],[],'-k')
mpl.xlim(0, duration)
mpl.ylim(-200, 200)
mpl.ylabel('Amplitude')
times = np.linspace(0, dt*maxit, maxit)
# This function updates the plot every few timesteps
def animate(i):
t, u, seismogram = simulation.next()
seismogram1.set_data(times[:t+1], seismogram[0][:t+1])
wavefield.set_array(background[::-1]+u[::-1])
return wavefield, seismogram1
anim = animation.FuncAnimation(fig, animate, frames=maxit/snapshots, interval=1)
"""
Gridding: Load a Surfer ASCII grid file
"""
from fatiando import datasets, gridder
from fatiando.vis import mpl
# Fetching Bouguer anomaly model data (Surfer ASCII grid file)"
# Will download the archive and save it with the default name
archive = datasets.fetch_bouguer_alps_egm()
# Load the GRD file and convert in three numpy-arrays (y, x, bouguer)
y, x, bouguer, shape = gridder.load_surfer(archive, fmt='ascii')
mpl.figure()
mpl.axis('scaled')
mpl.title("Data loaded from a Surfer ASCII grid file")
mpl.contourf(y, x, bouguer, shape, 15)
cb = mpl.colorbar()
cb.set_label('mGal')
mpl.xlabel('y points to East (km)')
mpl.ylabel('x points to North (km)')
mpl.m2km()
mpl.show()
stations = [[2200+i*dx, 0] for i in range(220)] # x, z coordinate of the seismometers
snapshot = int(0.004/dt) # Plot a snapshot of the simulation every 4 miliseconds
print "dt for simulation is ", dt
print "max iteration for simulation is ", maxit
print "duration for simulation is ", duration
simulation = wavefd.elastic_psv(lamb, mu, density, area, dt, maxit, sources,
stations, snapshot, padding=50, taper=0.01)
# This part makes an animation using matplotlibs animation API
fig = mpl.figure(figsize=(12, 5))
# Start with everything zero and grab the plot so that it can be updated later
mpl.imshow(pvel[::-1], extent=area, alpha=0.25)
wavefield = mpl.imshow(np.zeros(shape), extent=area, vmin=-10**-7, vmax=10**-7, alpha=0.75, cmap=mpl.cm.gray_r)
mpl.points(stations, '.k')
mpl.ylim(area[2:][::-1])
mpl.xlabel('x (km)')
mpl.ylabel('z (km)')
mpl.m2km()
times = np.linspace(0, maxit*dt, maxit)
# the only way for getting the feedback response of the seimograms
global seismograms
# This function updates the plot every few timesteps
def animate(i):
# Simulation will yield panels corresponding to P and S waves because
# xz2ps=True
t, ux, uz, xcomp, zcomp = simulation.next()
mpl.title('time: %0.3f s' % (times[t]))
# wavefield.set_array((p + s)[::-1])
wavefield.set_data(uz[::-1])
global seismograms
"""
Gridding: Load a Surfer ASCII grid file
"""
from fatiando import datasets, gridder
from fatiando.vis import mpl
# Fetching Bouguer anomaly model data (Surfer ASCII grid file)"
# Will download the archive and save it with the default name
archive = datasets.fetch_bouguer_alps_egm()
# Load the GRD file and convert in three numpy-arrays (x, y, bouguer)
x, y, bouguer, shape = gridder.load_surfer(archive, fmt='ascii')
mpl.figure()
mpl.axis('scaled')
mpl.title("Data loaded from a Surfer ASCII grid file")
mpl.contourf(y, x, bouguer, shape, 15, cmap=mpl.cm.RdBu_r)
cb = mpl.colorbar()
cb.set_label('mGal')
mpl.xlabel('y points to East (km)')
mpl.ylabel('x points to North (km)')
mpl.m2km()
mpl.show()
from fatiando import utils
from fatiando.geothermal.climsig import linear, SingleChange
from fatiando.vis import mpl
# Generating synthetic data
amp = 5.43
age = 78.2
# along a well at these depths
zp = numpy.arange(0, 100, 1)
temp, error = utils.contaminate(linear(amp, age, zp), 0.02,
percent=True, return_stddev=True)
# Preparing for the inversion
data = SingleChange(temp, zp, mode='linear').config('levmarq', initial=[1, 1])
amp_, age_ = data.fit().estimate_
print "Linear change in temperature"
print " true: amp=%.3f age=%.3f" % (amp, age)
print " estimated: amp=%.3f age=%.3f" % (amp_, age_)
mpl.figure(figsize=(4, 5))
mpl.title("Residual well temperature")
mpl.plot(temp, zp, 'ok', label='Observed')
mpl.plot(data.predicted(), zp, '--r', linewidth=3, label='Predicted')
mpl.legend(loc='lower right', numpoints=1)
mpl.xlabel("Temperature (C)")
mpl.ylabel("Z (m)")
mpl.ylim(100, 0)
mpl.show()
gxy = utils.contaminate(gm.prism.gxy(xp, yp, zp, model), noise)
gxz = utils.contaminate(gm.prism.gxz(xp, yp, zp, model), noise)
gyy = utils.contaminate(gm.prism.gyy(xp, yp, zp, model), noise)
gyz = utils.contaminate(gm.prism.gyz(xp, yp, zp, model), noise)
gzz = utils.contaminate(gm.prism.gzz(xp, yp, zp, model), noise)
tensor = [gxx, gxy, gxz, gyy, gyz, gzz]
titles = ['gxx', 'gxy', 'gxz', 'gyy', 'gyz', 'gzz']
# plot the data
mpl.figure()
for i in xrange(len(tensor)):
mpl.subplot(2, 3, i + 1)
mpl.title(titles[i])
mpl.axis('scaled')
levels = mpl.contourf(yp, xp, tensor[i], shape, 30)
mpl.colorbar()
mpl.xlabel('y (km)')
mpl.ylabel('x (km)')
mpl.m2km()
mpl.show()
# Inversion setup
# Create a mesh
mesh = PrismMesh(bounds, (30, 30, 30))
# Wrap the data so that harvester can use it
data = [
gm.harvester.Gxx(xp, yp, zp, gxx),
gm.harvester.Gxy(xp, yp, zp, gxy),
gm.harvester.Gxz(xp, yp, zp, gxz),
gm.harvester.Gyy(xp, yp, zp, gyy),
gm.harvester.Gyz(xp, yp, zp, gyz),
gm.harvester.Gzz(xp, yp, zp, gzz)
mesher.Prism(-4000, -3000, -4000, -3000, 0, 2000,
{'magnetization': 2}), # a scalar magnetization means only induced
mesher.Prism(-1000, 1000, -1000, 1000, 0, 2000,
{'magnetization': 1}),
# This prism will have magnetization in a different direction
mesher.Prism(2000, 4000, 3000, 4000, 0, 2000,
{'magnetization': utils.ang2vec(3, -10, 45)})] # induced + remanent
# Create a regular grid at 100m height
shape = (200, 200)
area = bounds[:4]
xp, yp, zp = gridder.regular(area, shape, z=-500)
# Calculate the anomaly for a given regional field
tf = prism.tf(xp, yp, zp, model, inc, dec)
# Plot
mpl.figure()
mpl.title("Total-field anomaly (nT)")
mpl.axis('scaled')
mpl.contourf(yp, xp, tf, shape, 15)
mpl.colorbar()
mpl.xlabel('East y (km)')
mpl.ylabel('North x (km)')
mpl.m2km()
mpl.show()
# Show the prisms
myv.figure()
myv.prisms(model, 'magnetization')
myv.axes(myv.outline(bounds), ranges=[i * 0.001 for i in bounds])
myv.wall_north(bounds)
myv.wall_bottom(bounds)
myv.show()
xp, yp, zp = gridder.regular(area, shape, z=-1)
noise = 0.1 # 0.1 mGal noise
gz = utils.contaminate(polyprism.gz(xp, yp, zp, model), noise)
# Create a mesh
mesh = PrismMesh(bounds, (25, 50, 50))
# Wrap the data so that harvester can read it
data = [harvester.Gz(xp, yp, zp, gz)]
# Plot the data and pick the location of the seeds
mpl.figure()
mpl.suptitle("Pick the seeds (polygon is the true source)")
mpl.axis('scaled')
levels = mpl.contourf(yp, xp, gz, shape, 12)
mpl.colorbar()
mpl.polygon(model[0], xy2ne=True)
mpl.xlabel('Horizontal coordinate y (km)')
mpl.ylabel('Horizontal coordinate x (km)')
seedx, seedy = mpl.pick_points(area, mpl.gca(), xy2ne=True).T
# Set the right density and depth
locations = [[x, y, 1500, {'density': 1000}] for x, y in zip(seedx, seedy)]
mpl.show()
# Make the seed and set the compactness regularizing parameter mu
seeds = harvester.sow(locations, mesh)
# Run the inversion
estimate, predicted = harvester.harvest(data, seeds, mesh,
compactness=0.05, threshold=0.0005)
# Put the estimated density values in the mesh
mesh.addprop('density', estimate['density'])
# Plot the adjustment and the result
mpl.figure()
mpl.title("True: color | Predicted: contour")
# Calculate and print the standard deviation of the residuals
# Should be close to the data error if the inversion was able to fit the data
residuals = tomo.residuals()
print "Assumed error: %g" % (error)
print "Standard deviation of residuals: %g" % (np.std(residuals))
mpl.figure(figsize=(14, 5))
mpl.subplot(1, 2, 1)
mpl.axis('scaled')
mpl.title('Vp model')
mpl.squaremesh(model, prop='vp', cmap=mpl.cm.seismic)
cb = mpl.colorbar()
cb.set_label('Velocity')
mpl.points(src_loc, '*y', label="Sources")
mpl.points(rec_loc, '^r', label="Receivers")
mpl.legend(loc='lower left', shadow=True, numpoints=1, prop={'size': 10})
mpl.m2km()
mpl.subplot(1, 2, 2)
mpl.axis('scaled')
mpl.title('Tomography result')
mpl.squaremesh(mesh, prop='vp', vmin=4000, vmax=10000, cmap=mpl.cm.seismic)
cb = mpl.colorbar()
cb.set_label('Velocity')
mpl.m2km()
mpl.figure()
mpl.grid()
mpl.title('Residuals (data with %.4f s error)' % (error))
mpl.hist(residuals, color='gray', bins=10)
mpl.xlabel("seconds")
mpl.show()
15,
interp=True,
color='r',
label='Observed',
linewidth=2.0)
mpl.contour(y,
x,
solver.predicted(), (50, 50),
nlevels,
interp=True,
color='b',
label='Predicted',
style='dashed',
linewidth=2.0)
mpl.legend(loc='upper left', shadow=True, prop={'size': 13})
mpl.xlabel('East y (m)', fontsize=14)
mpl.ylabel('North x (m)', fontsize=14)
mpl.subplot(1, 2, 2)
residuals_mean = numpy.mean(solver.residuals())
residuals_std = numpy.std(solver.residuals())
# Each residual is subtracted from the mean and the resulting
# difference is divided by the standard deviation
s = (solver.residuals() - residuals_mean) / residuals_std
mpl.hist(s,
bins=21,
range=None,
normed=True,
weights=None,
cumulative=False,
bottom=None,
histtype='bar',
