def test_do_convolve( self ):
# Make a spike dataset [samp, trace, theta]
data = np.zeros( (1000,100,10) )
data[500,50,:] = 1.0
dt = 0.001
duration = .2
f = (20,40,60)
wavelets = ricker( duration, dt, f )
con = do_convolve( wavelets, data )
truth = np.zeros( (1000,100,10,3) )
for i in range(10):
truth[:wavelets.shape[0], 50, i, :] += wavelets
truth = np.roll( truth, 401, axis=0 )
self.assertTrue( np.allclose( truth, con ) )
def run_script(earth_model, seismic_model, theta=None,
traces=None):
if earth_model.reflectivity() is None:
if earth_model.units == "depth":
earth_model.depth2time(seismic_model.dt,
samples=seismic_model.n_sensors)
else:
earth_model.resample(seismic_model.dt)
earth_model.update_reflectivity(seismic_model.offset_angles(),
seismic_model.n_sensors)
wavelets = seismic_model.wavelets()
ref = earth_model.reflectivity(theta=theta)
#noise = np.random.randn(ref.shape[0], ref.shape[1],
# ref.shape[2]) * seismic_model.noise
seismic = do_convolve(wavelets,
ref,
traces=traces,
theta=theta)
return seismic
def run_script(earth_model, seismic_model, theta=None,
traces=None, snr=50):
if earth_model.reflectivity() is None:
if earth_model.units == "depth":
earth_model.depth2time(seismic_model.dt,
samples=seismic_model.n_sensors)
else:
earth_model.resample(seismic_model.dt)
earth_model.update_reflectivity(seismic_model.offset_angles(),
seismic_model.n_sensors)
snr_scale = np.linspace(-50,50,1000)
wavelets = seismic_model.wavelets()
ref = earth_model.reflectivity(theta=theta)
noise = noise_db(ref, snr_scale[snr])
ref += noise
seismic = do_convolve(wavelets,
ref,
traces=traces,
theta=theta)
return seismic
def test_do_convolve(self):
# Make a spike dataset [samp, trace, theta]
data = np.zeros((1000, 100, 10))
data[500, 50, :] = 1.0
dt = 0.001
duration = .2
f = (20, 40, 60)
wavelets = ricker(duration, dt, f)
con = do_convolve(wavelets, data)
truth = np.zeros((1000, 100, 10, 3))
for i in range(10):
truth[:wavelets.shape[0], 50, i, :] += wavelets
truth = np.roll(truth, 401, axis=0)
self.assertTrue(np.allclose(truth, con))
def run_script(json_payload):
"""
Calculates synthetic seismic data from a convolution model.
Creates data for a cross section, angle gather, and wavelet gather.
Inputs
json_payload = {"earth_model": See ImageModel in modelr.api,
"seismic": See SeismicModel in modelr.api,
"trace": The trace number to use for the angle and
wavelet gathers.
"offset": The offset index to use for the wavelet
and seismic cross section.}
"""
try:
seismic = Seismic.from_json(json_payload["seismic"])
# parse json
earth_model = ImageModelPersist.from_json(json_payload["earth_model"])
if earth_model.domain == 'time':
earth_model.resample(seismic.dt)
trace = json_payload["trace"]
offset = json_payload["offset"]
# seismic
data = do_convolve(
seismic.src,
earth_model.rpp_t(seismic.dt)[..., offset][...,
np.newaxis]).squeeze()
# Hard coded, could be changed to be part of the seismic object
f0 = 4.0
f1 = 100.0
f = np.logspace(max(np.log2(f0), np.log2(7)),
np.log2(f1),
50,
endpoint=True,
base=2.0)
duration = .3
wavelets = rotate_phase(seismic.wavelet(duration, seismic.dt, f),
seismic.phase)
wavelet_gather = do_convolve(
wavelets,
earth_model.rpp_t(seismic.dt)[..., trace,
offset][..., np.newaxis,
np.newaxis]).squeeze()
offset_gather = do_convolve(
seismic.src,
earth_model.rpp_t(seismic.dt)[..., trace, :][..., np.newaxis,
...]).squeeze()
if seismic.snr:
wavelet_gather += noise_db(wavelet_gather, seismic.snr)
offset_gather += noise_db(offset_gather, seismic.snr)
data += noise_db(data, seismic.snr)
# METADATA
metadata = {}
metadata["moduli"] = {}
for rock in earth_model.get_rocks():
if rock.name not in metadata["moduli"]:
metadata["moduli"][rock.name] = rock.moduli
if earth_model.domain == "time":
dt = earth_model.zrange / float(data.shape[0])
else:
dt = seismic.dt * 1000.0
payload = {
"seismic": data.T.tolist(),
"dt": dt,
"min": float(np.amin(data)),
"max": float(np.amax(data)),
"dx": earth_model.dx,
"wavelet_gather": wavelet_gather.T.tolist(),
"offset_gather": offset_gather.T.tolist(),
"f": f.tolist(),
"theta": earth_model.theta,
"metadata": metadata
}
return payload
except Exception as e:
traceback.print_exc(file=sys.stdout)
def run_script(json_payload):
"""
Calculates synthetic seismic data from a convolution model.
Creates data for a cross section, angle gather, and wavelet gather.
Inputs
json_payload = {"earth_model": See ImageModel in modelr.api,
"seismic": See SeismicModel in modelr.api,
"trace": The trace number to use for the angle and
wavelet gathers.
"offset": The offset index to use for the wavelet
and seismic cross section.}
"""
try:
seismic = Seismic.from_json(json_payload["seismic"])
# parse json
earth_model = ImageModelPersist.from_json(json_payload["earth_model"])
if earth_model.domain == 'time':
earth_model.resample(seismic.dt)
trace = json_payload["trace"]
offset = json_payload["offset"]
ph = seismic.phase
src = seismic.src
# seismic
data = do_convolve(src,
earth_model.rpp_t(seismic.dt)[..., offset]
[..., np.newaxis]).squeeze()
# angle gather
offset_gather = do_convolve(src,
earth_model.rpp_t(seismic.dt)[..., trace, :]
[..., np.newaxis, ...]).squeeze()
# frequency gather
f0 = 4.0
f1 = 100.0
f = np.logspace(max(np.log2(f0), np.log2(7)),
np.log2(f1), 50,
endpoint=True, base=2.0)
wavelets = rotate_phase(seismic.wavelet(seismic.wavelet_duration, seismic.dt, f),
ph,
degrees=True)
wavelet_gather = do_convolve(wavelets,
earth_model.rpp_t(seismic.dt)
[..., trace, offset]
[..., np.newaxis, np.newaxis]).squeeze()
# add noise if required
if seismic.snr:
data += noise_db(data, seismic.snr)
offset_gather += noise_db(offset_gather, seismic.snr)
wavelet_gather += noise_db(wavelet_gather, seismic.snr)
# METADATA
metadata = {}
metadata["moduli"] = {}
for rock in earth_model.get_rocks():
if rock.name not in metadata["moduli"]:
metadata["moduli"][rock.name] = rock.moduli
if earth_model.domain == "time":
dt = earth_model.zrange / float(data.shape[0])
else:
dt = seismic.dt * 1000.0
payload = {"seismic": data.T.tolist(),
"dt": dt,
"min": float(np.amin(data)),
"max": float(np.amax(data)),
"dx": earth_model.dx,
"wavelet_gather": wavelet_gather.T.tolist(),
"offset_gather": offset_gather.T.tolist(),
"f": f.tolist(),
"theta": earth_model.theta,
"metadata": metadata}
return payload
except Exception as e:
traceback.print_exc(file=sys.stdout)
def run_script(json_payload):
# parse json
fs_model = FluidSub1D.from_json(json_payload["earth_model"])
seismic = Seismic.from_json(json_payload["seismic"])
# extract rock properties
vp, vs, rho = (fs_model.vp, fs_model.vs, fs_model.rho)
vp_sub, vs_sub, rho_sub = fs_model.smith_sub()
# convert to time
dt = seismic.dt
dz = fs_model.dz
z = fs_model.z
# use indices so we only run the algorithm once
index = np.arange(vp.size, dtype=int)
t_index = depth_to_time(index, vp, dz, dt).astype(int)
sub_t_index = depth_to_time(index, vp_sub, dz, dt).astype(int)
vp_t, vs_t, rho_t = (vp[t_index], vs[t_index], rho[t_index])
vp_sub_t, vs_sub_t, rho_sub_t = (vp_sub[sub_t_index], vs_sub[sub_t_index],
rho_sub[sub_t_index])
# calculate reflectivities
rpp = np.nan_to_num(
np.array([
zoep(vp_t[:-1], vs_t[:-1], rho_t[:-1], vp_t[1:], vs_t[1:],
rho_t[1:], float(theta)) for theta in seismic.theta[::-1]
]).T)
rpp_sub = np.nan_to_num(
np.array([
zoep(vp_sub_t[:-1], vs_sub_t[:-1],
rho_sub_t[:-1], vp_sub_t[1:], vs_sub_t[1:], rho_sub_t[1:],
float(theta)) for theta in seismic.theta[::-1]
]).T)
# trim to be the same size
n = min(rpp.shape[0], rpp_sub.shape[0])
rpp = rpp[:n, :]
rpp_sub = rpp_sub[:n, :]
t = np.arange(n) * dt
# create synthetic seismic
traces = np.squeeze(do_convolve(seismic.src, rpp[:, np.newaxis, :]))
sub_traces = np.squeeze(do_convolve(seismic.src, rpp_sub[:,
np.newaxis, :]))
output = {
"vp":
vp.tolist(),
"vs":
vs.tolist(),
"rho":
rho.tolist(),
"vp_sub":
vp_sub.tolist(),
"vs_sub":
vs_sub.tolist(),
"rho_sub":
rho_sub.tolist(),
"synth":
np.nan_to_num(traces).T.tolist(),
"synth_sub":
np.nan_to_num(sub_traces).T.tolist(),
"theta":
seismic.theta,
"rpp":
rpp[:, 0].tolist(),
"rpp_sub":
rpp_sub[:, 0].tolist(),
"t_lim": [float(np.amin(t)), float(np.amax(t))],
"z_lim": [float(np.amin(z)), float(np.amax(z))],
"vp_lim": [float(np.amin((vp, vp_sub))),
float(np.amax((vp, vp_sub)))],
"vs_lim": [float(np.amin((vs, vs_sub))),
float(np.amax((vs, vs_sub)))],
"rho_lim":
[float(np.amin((rho, rho_sub))),
float(np.amax((rho, rho_sub)))],
"rpp_lim":
[float(np.amin((rpp, rpp_sub))),
float(np.amax((rpp, rpp_sub)))],
"synth_lim": [
float(np.amin((traces, sub_traces))),
float(np.amax((traces, sub_traces)))
],
"dt":
dt,
"dz":
dz
}
return output
def modelr_plot(model, colourmap, args):
"""
Calculates reflectivities from the earth model then convolves
against a bank of wavelets. Figures of various slices are created
based on the args structure.
:param model: The earth model image to use for forward modeling.
:param colourmap: A Dict that maps colour values in the earth
model to physical rock properties.
:param args: Structure of parsed arguments.
:returns: a png graphic of the forward model results.
"""
from modelr.constants import dt, wavelet_duration as duration
model_aspect = float(model.shape[1]) / model.shape[0]
if not hasattr(args, 'xscale'):
args.xscale = 0
if not hasattr(args, "twt_range"):
args.twt_range = (0, model.shape[0] * dt * 1000.0)
if not hasattr(args, 'fs'):
args.fs = 10
if args.slice == 'spatial':
traces = range( args.ntraces )
else:
traces = args.trace - 1
if traces >= args.ntraces:
traces = args.ntraces -1
if args.slice == 'angle':
theta0 = args.theta[0]
theta1 = args.theta[1]
try:
theta_step = args.theta[2]
except:
theta_step = 1
theta = np.linspace(theta0, theta1,
int((theta1-theta0) / theta_step))
else:
try:
theta = args.theta[0]
except:
theta = args.theta
if args.slice == 'frequency':
f0 = args.f[0]
f1 = args.f[1]
try:
f_step = args.f[2]
except:
f_step = 1
if (args.xscale) == 0:
f = np.linspace(f0, f1, (int((f1-f0)/f_step)) )
else:
f = np.logspace(max(np.log2(f0),np.log2(7)),np.log2(f1),300,endpoint=True, base=2.0)
else:
f = args.f
tstart = args.twt_range[0]
fs = int(args.fs)
model = model[:, traces, :]
model = np.reshape(model, (model.shape[0], np.size(traces),3))
############################
# Get reflectivities
reflectivity = get_reflectivity( data=model,
colourmap=colourmap,
theta=theta,
reflectivity_method = \
args.reflectivity_method
)
# Do convolution
if ( ( duration / dt ) > ( reflectivity.shape[0] ) ):
duration = reflectivity.shape[0] * dt
wavelet = args.wavelet( duration, dt, f )
if( wavelet.ndim == 1 ): wavelet = \
wavelet.reshape( ( wavelet.size, 1 ) )
warray_amp = do_convolve( wavelet, reflectivity )
nsamps, ntraces, ntheta, n_wavelets = warray_amp.shape
dx = 10 #trace offset (in metres)
#################################
# Build the plot(s)
# Simplify the plot request a bit
# This will need to be a loop if we want to cope with
# an arbitrary number of base plots; or allow up to 6 (say)
base1 = args.base1
if args.overlay1 == 'none':
overlay1 = None
else:
overlay1 = args.overlay1
if args.overlay2 == 'none':
overlay2 = None
else:
overlay2 = args.overlay2
if args.base2 == 'none':
base2 = None
plots = [(base1, overlay1)]
else:
base2 = args.base2
plots = [(base1, overlay1), (base2, overlay2)]
if( args.slice == 'spatial' ):
plot_data = warray_amp[ :, :, 0,:]
reflectivity = reflectivity[:,:,0]
xax = traces
xlabel = 'trace'
elif( args.slice == 'angle' ):
plot_data = warray_amp[ :, 0, :, 0 ]
reflectivity = reflectivity[ :, 0, : ]
xax = theta
xlabel = 'angle'
elif( args.slice == 'frequency' ):
plot_data = warray_amp[ :, 0, 0, : ]
reflectivity = np.reshape( np.repeat( reflectivity[:,0,0],
warray_amp.shape[1] ),
( reflectivity.shape[0],
warray_amp.shape[1] ) )
xax = f
xlabel = 'frequency [Hz]'
else:
# Default to spatial
plot_data = warray_amp[ :, :, 0, 0 ]
# Calculate some basic stuff
plot_data = np.nan_to_num(plot_data)
# This doesn't work well for non-spatial slices
#aspect = float(warray_amp.shape[1]) / warray_amp.shape[0]
# This is *better* for non-spatial slices, but can't have
# overlays
stretch = args.aspect_ratio
pad = np.ceil((plot_data.shape[0] - model.shape[0]) / 2)
# First, set up the matplotlib figure
#fig = plt.figure(figsize=(width, 2*height))
fig, axarr = plt.subplots(2, len(plots)) #, sharex='col', sharey='row')
if len(plots) == 1:
axarr = np.transpose(np.array([axarr]))
# Work out the size of the figure
each_width = 6
fig.set_figwidth(each_width*len(plots))
fig.set_figheight(each_width*stretch*2)
# Start a loop for the figures...
for plot in plots:
# If there's no base plot for this plot,
# then there are no more plots and we're done
if not plot[0]:
break
# Establish what sort of subplot grid we need
p = plots.index(plot)
if args.xscale:
axarr[0, p].set_xscale('log', basex = int(args.xscale) )
# Each plot can have two layers (maybe more later?)
# Display the two layers by looping over the non-blank
# elements
# of the tuple
for layer in filter(None, plot):
# for starters, find out if this is a base or an overlay
if plot.index(layer) == 1:
# then we're in an overlay so...
alpha = args.opacity
else:
alpha = 1.0
# Now find out what sort of plot we're making on this
# loop...
if layer == 'earth-model':
axarr[0, p].imshow(model.astype('uint8'),
cmap = plt.get_cmap('gist_earth'),
vmin = np.amin(model)-np.amax(model)/2,
vmax = np.amax(model)+np.amax(model)/2,
alpha = alpha,
aspect='auto',
extent=[min(xax),max(xax),
args.twt_range[1],
args.twt_range[0]
],
origin = 'upper'
)
elif layer == 'variable-density':
vddata=plot_data
if vddata.ndim == 3:
vddata = np.sum(plot_data,axis=-1)
extreme = np.percentile(vddata,99)
axarr[0, p].imshow( vddata,
cmap = args.colourmap,
vmin = -extreme,
vmax = extreme,
alpha = alpha,
aspect='auto',
extent=[min(xax),max(xax),
args.twt_range[1],
args.twt_range[0]
],
origin = 'upper'
)
elif layer == 'reflectivity':
# Show unconvolved reflectivities
#
#TO DO:put transparent when null / zero
#
masked_refl = np.ma.masked_where(reflectivity == 0.0,
reflectivity)
axarr[0,p].imshow(masked_refl,
cmap = plt.get_cmap('Greys'),
aspect='auto',
extent=[min(xax),max(xax),
args.twt_range[1], args.twt_range[0]
],
origin = 'upper' ,
vmin = np.amin( masked_refl ),
vmax = np.amax( masked_refl )
)
elif layer == 'wiggle':
wigdata=plot_data
if wigdata.ndim == 3:
wigdata= np.sum(plot_data,axis=-1)
wiggle(wigdata,
tstart = int(args.twt_range[0]),
dt = dt,
skipt = args.wiggle_skips,
gain = args.wiggle_skips + 1,
line_colour = 'black',
fill_colour = 'black',
opacity = args.opacity,
xax = xax,
quadrant = axarr[0, p]
)
if plot.index(layer) == 0:
# then we're in an base layer so...
axarr[0, p].set_ylim(max(axarr[0, p].set_ylim()),min(axarr[0, p].set_ylim()))
elif layer == 'RGB':
exponent = 2
envelope = abs(hilbert(plot_data))
envelope = envelope**exponent
envelope[:,:,0]= envelope[:,:,0]/np.amax(envelope[:,:,0])
envelope[:,:,1]= envelope[:,:,1]/np.amax(envelope[:,:,1])
envelope[:,:,2]= envelope[:,:,2]/np.amax(envelope[:,:,2])
extreme = np.amax(abs(envelope))
axarr[0, p].imshow(envelope,
cmap = args.colourmap,
vmin = -extreme,
vmax = extreme,
alpha = alpha,
aspect='auto',
extent=[min(xax),max(xax),
args.twt_range[1], args.twt_range[0]
],
origin = 'upper'
)
else:
# We should never get here
continue
axarr[0, p].set_xlabel(xlabel, fontsize=fs)
axarr[0, p].set_ylabel('time [ms]', fontsize=fs)
axarr[0, p].set_title(args.title % locals(), fontsize=fs )
for tick in axarr[0,p].xaxis.get_major_ticks():
tick.label.set_fontsize(fs)
for tick in axarr[0,p].yaxis.get_major_ticks():
tick.label.set_fontsize(fs)
#plot inst. amplitude at 150 ms (every 6 samples, we should parameterize)
t = args.tslice
t_index = int(np.amin([t, plot_data.shape[0]-1]))
y = plot_data[t_index,:].flatten()
# compute lines for instantaneous chart
amax_tune = np.amax(y)
amin_tune = np.amin(y)
aun_tuned = plot_data[t_index,-1]
# instantaneous charts
axarr[1,p].plot(xax[:],y,'ko-',lw=3,alpha=0.2, color = 'g')
if args.xscale: #check for log plot on graphs too
axarr[1, p].set_xscale('log', basex = int(args.xscale) )
axarr[1,p].set_xlabel(xlabel, fontsize=fs)
# horizontal line, plot min, plot max
axarr[1, p].axhline(y=amin_tune, alpha=0.15, lw=3, color = 'g')
axarr[1, p].axhline(y=amax_tune, alpha=0.15, lw=3, color = 'g' )
#plot ave
axarr[1, p].axhline(y=aun_tuned, alpha=0.15, lw=3, color = 'g')
# vertical line
axarr[1, p].axvline(x=xax[np.argmax(y)], alpha=0.15, lw=3, color='b' )
axarr[1, p].axvline(x=xax[np.argmin(y)], alpha=0.15, lw=3, color='b' )
axarr[0, p].axvline(x=xax[np.argmax(y)], alpha=0.15, lw=3, color='b' )
axarr[0, p].axvline(x=xax[np.argmin(y)], alpha=0.15, lw=3, color='b' )
# draw vertical line at onset of steady state
y_r = np.array(y[::-1])
try:
steady_state = np.where(abs(np.gradient(y_r)) >= (0.001*np.ptp(y)))[0][0]
axarr[1, p].axvline(x=xax[-steady_state], alpha=0.15, lw=3, color='r' )
axarr[0, p].axvline(x=xax[-steady_state], alpha=0.15, lw=3, color='r' )
except:
pass
#labels
axarr[1, p].set_title('instantaneous attribute at %s ms' % int(t),
fontsize=fs
)
axarr[1, p].set_ylabel('amplitude', fontsize=fs)
axarr[1,p].grid()
for tick in axarr[1,p].xaxis.get_major_ticks():
tick.label.set_fontsize(fs)
for tick in axarr[1,p].yaxis.get_major_ticks():
tick.label.set_fontsize(fs)
plt.xlim((xax[0], xax[-1]))
#plot horizontal green line on model image, and steady state
axarr[0,p].axhline(y=t, alpha=0.5, lw=2, color = 'g')
fig.tight_layout()
return get_figure_data()
def modelr_plot(model, colourmap, args):
"""
Calculates reflectivities from the earth model then convolves
against a bank of wavelets. Figures of various slices are created
based on the args structure.
:param model: The earth model image to use for forward modeling.
:param colourmap: A Dict that maps colour values in the earth
model to physical rock properties.
:param args: Structure of parsed arguments.
:returns: a png graphic of the forward model results.
"""
from modelr.constants import dt, wavelet_duration as duration
model_aspect = float(model.shape[1]) / model.shape[0]
if not hasattr(args, 'xscale'):
args.xscale = 0
if not hasattr(args, "twt_range"):
args.twt_range = (0, model.shape[0] * dt * 1000.0)
if not hasattr(args, 'fs'):
args.fs = 10
if args.slice == 'spatial':
traces = range(args.ntraces)
else:
traces = args.trace - 1
if traces >= args.ntraces:
traces = args.ntraces - 1
if args.slice == 'angle':
theta0 = args.theta[0]
theta1 = args.theta[1]
try:
theta_step = args.theta[2]
except:
theta_step = 1
theta = np.linspace(theta0, theta1, int(
(theta1 - theta0) / theta_step))
else:
try:
theta = args.theta[0]
except:
theta = args.theta
if args.slice == 'frequency':
f0 = args.f[0]
f1 = args.f[1]
try:
f_step = args.f[2]
except:
f_step = 1
if (args.xscale) == 0:
f = np.linspace(f0, f1, (int((f1 - f0) / f_step)))
else:
f = np.logspace(max(np.log2(f0), np.log2(7)),
np.log2(f1),
300,
endpoint=True,
base=2.0)
else:
f = args.f
tstart = args.twt_range[0]
fs = int(args.fs)
model = model[:, traces, :]
model = np.reshape(model, (model.shape[0], np.size(traces), 3))
############################
# Get reflectivities
reflectivity = get_reflectivity( data=model,
colourmap=colourmap,
theta=theta,
reflectivity_method = \
args.reflectivity_method
)
# Do convolution
if ((duration / dt) > (reflectivity.shape[0])):
duration = reflectivity.shape[0] * dt
wavelet = args.wavelet(duration, dt, f)
if( wavelet.ndim == 1 ): wavelet = \
wavelet.reshape( ( wavelet.size, 1 ) )
warray_amp = do_convolve(wavelet, reflectivity)
nsamps, ntraces, ntheta, n_wavelets = warray_amp.shape
dx = 10 #trace offset (in metres)
#################################
# Build the plot(s)
# Simplify the plot request a bit
# This will need to be a loop if we want to cope with
# an arbitrary number of base plots; or allow up to 6 (say)
base1 = args.base1
if args.overlay1 == 'none':
overlay1 = None
else:
overlay1 = args.overlay1
if args.overlay2 == 'none':
overlay2 = None
else:
overlay2 = args.overlay2
if args.base2 == 'none':
base2 = None
plots = [(base1, overlay1)]
else:
base2 = args.base2
plots = [(base1, overlay1), (base2, overlay2)]
if (args.slice == 'spatial'):
plot_data = warray_amp[:, :, 0, :]
reflectivity = reflectivity[:, :, 0]
xax = traces
xlabel = 'trace'
elif (args.slice == 'angle'):
plot_data = warray_amp[:, 0, :, 0]
reflectivity = reflectivity[:, 0, :]
xax = theta
xlabel = 'angle'
elif (args.slice == 'frequency'):
plot_data = warray_amp[:, 0, 0, :]
reflectivity = np.reshape(
np.repeat(reflectivity[:, 0, 0], warray_amp.shape[1]),
(reflectivity.shape[0], warray_amp.shape[1]))
xax = f
xlabel = 'frequency [Hz]'
else:
# Default to spatial
plot_data = warray_amp[:, :, 0, 0]
# Calculate some basic stuff
plot_data = np.nan_to_num(plot_data)
# This doesn't work well for non-spatial slices
#aspect = float(warray_amp.shape[1]) / warray_amp.shape[0]
# This is *better* for non-spatial slices, but can't have
# overlays
stretch = args.aspect_ratio
pad = np.ceil((plot_data.shape[0] - model.shape[0]) / 2)
# First, set up the matplotlib figure
#fig = plt.figure(figsize=(width, 2*height))
fig, axarr = plt.subplots(2, len(plots)) #, sharex='col', sharey='row')
if len(plots) == 1:
axarr = np.transpose(np.array([axarr]))
# Work out the size of the figure
each_width = 6
fig.set_figwidth(each_width * len(plots))
fig.set_figheight(each_width * stretch * 2)
# Start a loop for the figures...
for plot in plots:
# If there's no base plot for this plot,
# then there are no more plots and we're done
if not plot[0]:
break
# Establish what sort of subplot grid we need
p = plots.index(plot)
if args.xscale:
axarr[0, p].set_xscale('log', basex=int(args.xscale))
# Each plot can have two layers (maybe more later?)
# Display the two layers by looping over the non-blank
# elements
# of the tuple
for layer in filter(None, plot):
# for starters, find out if this is a base or an overlay
if plot.index(layer) == 1:
# then we're in an overlay so...
alpha = args.opacity
else:
alpha = 1.0
# Now find out what sort of plot we're making on this
# loop...
if layer == 'earth-model':
axarr[0, p].imshow(model.astype('uint8'),
cmap=plt.get_cmap('gist_earth'),
vmin=np.amin(model) - np.amax(model) / 2,
vmax=np.amax(model) + np.amax(model) / 2,
alpha=alpha,
aspect='auto',
extent=[
min(xax),
max(xax), args.twt_range[1],
args.twt_range[0]
],
origin='upper')
elif layer == 'variable-density':
vddata = plot_data
if vddata.ndim == 3:
vddata = np.sum(plot_data, axis=-1)
extreme = np.percentile(vddata, 99)
axarr[0, p].imshow(vddata,
cmap=args.colourmap,
vmin=-extreme,
vmax=extreme,
alpha=alpha,
aspect='auto',
extent=[
min(xax),
max(xax), args.twt_range[1],
args.twt_range[0]
],
origin='upper')
elif layer == 'reflectivity':
# Show unconvolved reflectivities
#
#TO DO:put transparent when null / zero
#
masked_refl = np.ma.masked_where(reflectivity == 0.0,
reflectivity)
axarr[0, p].imshow(masked_refl,
cmap=plt.get_cmap('Greys'),
aspect='auto',
extent=[
min(xax),
max(xax), args.twt_range[1],
args.twt_range[0]
],
origin='upper',
vmin=np.amin(masked_refl),
vmax=np.amax(masked_refl))
elif layer == 'wiggle':
wigdata = plot_data
if wigdata.ndim == 3:
wigdata = np.sum(plot_data, axis=-1)
wiggle(wigdata,
tstart=int(args.twt_range[0]),
dt=dt,
skipt=args.wiggle_skips,
gain=args.wiggle_skips + 1,
line_colour='black',
fill_colour='black',
opacity=args.opacity,
xax=xax,
quadrant=axarr[0, p])
if plot.index(layer) == 0:
# then we're in an base layer so...
axarr[0, p].set_ylim(max(axarr[0, p].set_ylim()),
min(axarr[0, p].set_ylim()))
elif layer == 'RGB':
exponent = 2
envelope = abs(hilbert(plot_data))
envelope = envelope**exponent
envelope[:, :,
0] = envelope[:, :, 0] / np.amax(envelope[:, :, 0])
envelope[:, :,
1] = envelope[:, :, 1] / np.amax(envelope[:, :, 1])
envelope[:, :,
2] = envelope[:, :, 2] / np.amax(envelope[:, :, 2])
extreme = np.amax(abs(envelope))
axarr[0, p].imshow(envelope,
cmap=args.colourmap,
vmin=-extreme,
vmax=extreme,
alpha=alpha,
aspect='auto',
extent=[
min(xax),
max(xax), args.twt_range[1],
args.twt_range[0]
],
origin='upper')
else:
# We should never get here
continue
axarr[0, p].set_xlabel(xlabel, fontsize=fs)
axarr[0, p].set_ylabel('time [ms]', fontsize=fs)
axarr[0, p].set_title(args.title % locals(), fontsize=fs)
for tick in axarr[0, p].xaxis.get_major_ticks():
tick.label.set_fontsize(fs)
for tick in axarr[0, p].yaxis.get_major_ticks():
tick.label.set_fontsize(fs)
#plot inst. amplitude at 150 ms (every 6 samples, we should parameterize)
t = args.tslice
t_index = int(np.amin([t, plot_data.shape[0] - 1]))
y = plot_data[t_index, :].flatten()
# compute lines for instantaneous chart
amax_tune = np.amax(y)
amin_tune = np.amin(y)
aun_tuned = plot_data[t_index, -1]
# instantaneous charts
axarr[1, p].plot(xax[:], y, 'ko-', lw=3, alpha=0.2, color='g')
if args.xscale: #check for log plot on graphs too
axarr[1, p].set_xscale('log', basex=int(args.xscale))
axarr[1, p].set_xlabel(xlabel, fontsize=fs)
# horizontal line, plot min, plot max
axarr[1, p].axhline(y=amin_tune, alpha=0.15, lw=3, color='g')
axarr[1, p].axhline(y=amax_tune, alpha=0.15, lw=3, color='g')
#plot ave
axarr[1, p].axhline(y=aun_tuned, alpha=0.15, lw=3, color='g')
# vertical line
max_loc = xax[np.argmax(y)]
min_loc = xax[np.argmin(y)]
axarr[1, p].axvline(x=max_loc, alpha=0.15, lw=3, color='b')
axarr[1, p].axvline(x=min_loc, alpha=0.15, lw=3, color='b')
axarr[0, p].axvline(x=max_loc, alpha=0.15, lw=3, color='b')
axarr[0, p].axvline(x=min_loc, alpha=0.15, lw=3, color='b')
# draw vertical line at onset of steady state
y_r = np.array(y[::-1])
try:
steady_state = np.where(
abs(np.gradient(y_r)) >= (0.001 * np.ptp(y)))[0][0]
axarr[1, p].axvline(x=xax[-steady_state],
alpha=0.15,
lw=3,
color='r')
axarr[0, p].axvline(x=xax[-steady_state],
alpha=0.15,
lw=3,
color='r')
except:
pass
#labels
axarr[1, p].set_title('instantaneous attribute at %s ms' % int(t),
fontsize=fs)
axarr[1, p].set_ylabel('amplitude', fontsize=fs)
axarr[1, p].grid()
for tick in axarr[1, p].xaxis.get_major_ticks():
tick.label.set_fontsize(fs)
for tick in axarr[1, p].yaxis.get_major_ticks():
tick.label.set_fontsize(fs)
plt.xlim((xax[0], xax[-1]))
#plot horizontal green line on model image, and steady state
axarr[0, p].axhline(y=t, alpha=0.5, lw=2, color='g')
fig.tight_layout()
metadata = {
"steady state": np_float(xax[-steady_state]),
"tuning max. loc.": np.float(max_loc),
"tuning min. loc.": np.float(min_loc),
"tuning max. amp.": np_float(amax_tune),
"tuning min. amp.": np_float(amin_tune),
"tuning avg. amp.": np_float(aun_tuned)
}
return get_figure_data(), metadata
def run_script(json_payload):
# parse json
fs_model = FluidSub1D.from_json(json_payload["earth_model"])
seismic = Seismic.from_json(json_payload["seismic"])
# extract rock properties
vp, vs, rho = (fs_model.vp, fs_model.vs, fs_model.rho)
vp_sub, vs_sub, rho_sub = fs_model.smith_sub()
# convert to time
dt = seismic.dt
dz = fs_model.dz
z = fs_model.z
# use indices so we only run the algorithm once
index = np.arange(vp.size, dtype=int)
t_index = depth_to_time(index, vp, dz, dt).astype(int)
sub_t_index = depth_to_time(index, vp_sub, dz, dt).astype(int)
vp_t, vs_t, rho_t = (vp[t_index], vs[t_index], rho[t_index])
vp_sub_t, vs_sub_t, rho_sub_t = (vp_sub[sub_t_index],
vs_sub[sub_t_index],
rho_sub[sub_t_index])
# calculate reflectivities
rpp = np.nan_to_num(np.array([zoep(vp_t[:-1], vs_t[:-1], rho_t[:-1],
vp_t[1:], vs_t[1:], rho_t[1:],
float(theta))
for theta in seismic.theta[::-1]]).T)
rpp_sub = np.nan_to_num(np.array([zoep(vp_sub_t[:-1], vs_sub_t[:-1],
rho_sub_t[:-1],
vp_sub_t[1:], vs_sub_t[1:],
rho_sub_t[1:], float(theta))
for theta in seismic.theta[::-1]]).T)
# trim to be the same size
n = min(rpp.shape[0], rpp_sub.shape[0])
rpp = rpp[:n, :]
rpp_sub = rpp_sub[:n, :]
t = np.arange(n) * dt
# create synthetic seismic
traces = np.squeeze(do_convolve(seismic.src, rpp[:, np.newaxis, :]))
sub_traces = np.squeeze(do_convolve(seismic.src,
rpp_sub[:, np.newaxis, :]))
output = {"vp": vp.tolist(), "vs": vs.tolist(),
"rho": rho.tolist(), "vp_sub": vp_sub.tolist(),
"vs_sub": vs_sub.tolist(), "rho_sub": rho_sub.tolist(),
"synth": np.nan_to_num(traces).T.tolist(),
"synth_sub": np.nan_to_num(sub_traces).T.tolist(),
"theta": seismic.theta,
"rpp": rpp[:, 0].tolist(),
"rpp_sub": rpp_sub[:, 0].tolist(),
"t_lim": [float(np.amin(t)), float(np.amax(t))],
"z_lim": [float(np.amin(z)), float(np.amax(z))],
"vp_lim": [float(np.amin((vp, vp_sub))),
float(np.amax((vp, vp_sub)))],
"vs_lim": [float(np.amin((vs, vs_sub))),
float(np.amax((vs, vs_sub)))],
"rho_lim": [float(np.amin((rho, rho_sub))),
float(np.amax((rho, rho_sub)))],
"rpp_lim": [float(np.amin((rpp, rpp_sub))),
float(np.amax((rpp, rpp_sub)))],
"synth_lim": [float(np.amin((traces, sub_traces))),
float(np.amax((traces, sub_traces)))],
"dt": dt,
"dz": dz}
return output