def test_adjoint_functions():
observed = Trace(data=np.ones(25))
synthetic = Trace(data=np.ones(25))
synthetic.data[0:13] *= 2.0
synthetic.stats.sac = {}
synthetic.stats.sac['dist'] = 6000.
observed.stats = synthetic.stats.copy()
window_params = {}
window_params['hw'] = 2.0
window_params['sep_noise'] = 1.0
window_params['win_overlap'] = False
window_params['wtype'] = "hann"
window_params['plot'] = False
g_speed = 2000.
adj, success = am.log_en_ratio_adj(observed, synthetic, g_speed,
window_params)
assert (success)
assert (len(adj) == 25)
assert (pytest.approx(adj[10]) == -0.16666666666666663)
adj, success = am.windowed_waveform(observed, synthetic, g_speed,
window_params)
assert (success)
assert (len(adj) == 25)
assert (pytest.approx(adj[9]) == 1.)
func = am.get_adj_func('energy_diff')
adj, success = func(observed, synthetic, g_speed, window_params)
assert (success)
assert (len(adj) == 2)
assert (type(adj) == list)
assert (pytest.approx(adj[1].sum()) == 6.)
def measurement(source_config, mtype, step, ignore_net, ix_bandpass, bandpass,
step_test, taper_perc, **options):
"""
Get measurements on noise correlation data and synthetics.
options: g_speed,window_params (only needed if
mtype is ln_energy_ratio or enery_diff)
"""
verbose = yaml.safe_load(
open(os.path.join(source_config['project_path'],
'config.yml')))['verbose']
step_n = 'iteration_{}'.format(int(step))
step_dir = os.path.join(source_config['source_path'], step_n)
if step_test:
corr_dir = os.path.join(step_dir, 'obs_slt')
else:
corr_dir = os.path.join(source_config['source_path'],
'observed_correlations')
files = [f for f in os.listdir(corr_dir)]
files = [os.path.join(corr_dir, f) for f in files]
synth_dir = os.path.join(step_dir, 'corr')
columns = [
'sta1', 'sta2', 'lat1', 'lon1', 'lat2', 'lon2', 'dist', 'az', 'baz',
'syn', 'syn_a', 'obs', 'obs_a', 'l2_norm', 'snr', 'snr_a', 'nstack'
]
measurements = pd.DataFrame(columns=columns)
options['window_params']['causal_side'] = True # relic for signal to noise
_options_ac = copy.deepcopy(options)
_options_ac['window_params']['causal_side'] = (
not (options['window_params']['causal_side']))
if files == []:
msg = 'No input found!'
raise ValueError(msg)
for i, f in enumerate(files):
# Read data
try:
tr_o = read(f)[0]
except IOError:
if verbose:
print('\nCould not read data: ' + os.path.basename(f))
continue
# Read synthetics
synth_filename = get_synthetics_filename(os.path.basename(f),
synth_dir,
ignore_network=ignore_net)
if synth_filename is None:
continue
try:
tr_s = read(synth_filename)[0]
except IOError:
if verbose:
print('\nCould not read synthetics: ' + synth_filename)
continue
# Assigning stats to synthetics, cutting them to right length
tr_s.stats.sac = tr_o.stats.sac.copy()
tr_s.data = my_centered(tr_s.data, tr_o.stats.npts)
# Get all the necessary information
info = get_station_info(tr_o.stats)
# Collect the adjoint source
adjoint_source = Stream()
adjoint_source += Trace()
adjoint_source[0].stats.sampling_rate = tr_s.stats.sampling_rate
adjoint_source[0].stats.sac = tr_s.stats.sac.copy()
# Filter
if bandpass is not None:
tr_o.taper(taper_perc / 100.)
tr_o.filter('bandpass',
freqmin=bandpass[0],
freqmax=bandpass[1],
corners=bandpass[2],
zerophase=True)
tr_s.taper(taper_perc / 100.)
tr_s.filter('bandpass',
freqmin=bandpass[0],
freqmax=bandpass[1],
corners=bandpass[2],
zerophase=True)
# Weight observed stack by nstack
tr_o.data /= tr_o.stats.sac.user0
# Take the measurement
func = rm.get_measure_func(mtype)
msr_o = func(tr_o, **options)
msr_s = func(tr_s, **options)
# Get the adjoint source
adjt_func = am.get_adj_func(mtype)
adjt, success = adjt_func(tr_o, tr_s, **options)
if not success:
continue
# timeseries-like measurements:
if mtype in ['square_envelope', 'full_waveform', 'windowed_waveform']:
l2_so = 0.5 * np.sum(np.power((msr_s - msr_o), 2))
snr = snratio(tr_o, **options)
snr_a = snratio(tr_o, **_options_ac)
info.extend([
np.nan, np.nan, np.nan, np.nan, l2_so, snr, snr_a,
tr_o.stats.sac.user0
])
adjoint_source[0].data = adjt
# single value measurements:
else:
if mtype == 'energy_diff':
l2_so = 0.5 * (msr_s - msr_o)**2 / (msr_o)**2
msr = msr_o[0]
msr_a = msr_o[1]
snr = snratio(tr_o, **options)
snr_a = snratio(tr_o, **_options_ac)
l2 = l2_so.sum()
info.extend([
msr_s[0], msr_s[1], msr, msr_a, l2, snr, snr_a,
tr_o.stats.sac.user0
])
adjoint_source += adjoint_source[0].copy()
for ix_branch in range(2):
adjoint_source[ix_branch].data = adjt[ix_branch]
adjoint_source[ix_branch].data *= (
msr_s[ix_branch] -
msr_o[ix_branch]) / msr_o[ix_branch]**2
elif mtype == 'ln_energy_ratio':
l2_so = 0.5 * (msr_s - msr_o)**2
msr = msr_o
snr = snratio(tr_o, **options)
snr_a = snratio(tr_o, **_options_ac)
info.extend([
msr_s, np.nan, msr, np.nan, l2_so, snr, snr_a,
tr_o.stats.sac.user0
])
adjt *= (msr_s - msr_o)
adjoint_source[0].data = adjt
measurements.loc[i] = info
# save the adjoint source
if len(adjoint_source) == 1:
adjt_filename = os.path.basename(synth_filename).rstrip('sac') +\
'{}.sac'.format(ix_bandpass)
adjoint_source[0].write(os.path.join(step_dir, 'adjt',
adjt_filename),
format='SAC')
elif len(adjoint_source) == 2:
for ix_branch, branch in enumerate(['c', 'a']):
adjt_filename = os.path.basename(synth_filename).\
rstrip('sac') + '{}.{}.sac'.format(branch, ix_bandpass)
adjoint_source[ix_branch].write(os.path.join(
step_dir, 'adjt', adjt_filename),
format='SAC')
else:
raise ValueError("Some problem with adjoint sources.")
return measurements
window_params['win_overlap'] = False
window_params['wtype'] = 'hann'
window_params['causal_side'] = False
window_params['plot'] = False
# *********************************************
# *********************************************
# only for testing the test:
# def l2_simple(tr_1,tr_2):
# mf = np.sum(0.5 * (tr_1.data - tr_2.data) **2)
# adstf = (tr_1.data - tr_2.data)
# return mf,adstf
m_a_options = {'g_speed':g_speed,'window_params':window_params}
m_func = rm.get_measure_func(mtype)
a_func = af.get_adj_func(mtype)
# create observed data, synthetics and perturbation
c_obs = 2 * (np.random.rand(2401,) - 0.5)
c_ini = 2 * (np.random.rand(2401,) - 0.5)
d_c = 2 * (np.random.rand(2401,) - 0.5)
# form traces (measurement script works with obspy trace objects, not pure arrays)
c_obs = Trace(data=c_obs)
c_obs.stats.sampling_rate = 1.0
c_obs.stats.sac = sacdict
c_syn = Trace(data=c_ini)
c_syn.stats.sampling_rate = 1.0
c_syn.stats.sac = sacdict
def adjointsrcs(source_config,mtype,step,ignore_network,bandpass,
taper_perc,**options):
"""
Get 'adjoint source' from noise correlation data and synthetics.
options: g_speed,window_params (only needed if mtype is ln_energy_ratio or enery_diff)
"""
files = [f for f in os.listdir(os.path.join(source_config['source_path'],
'observed_correlations')) ]
files = [os.path.join(source_config['source_path'],
'observed_correlations',f) for f in files]
step_n = 'step_{}'.format(int(step))
synth_dir = os.path.join(source_config['source_path'],
step_n,'corr')
adj_dir = os.path.join(source_config['source_path'],
step_n,'adjt')
if files == []:
msg = 'No input found!'
raise ValueError(msg)
#i = 0
hws = options['window_params']['hw'][:]
g_speed = options['g_speed'][:]
with click.progressbar(files,label='Determining adjoint sources...') as bar:
for f in bar:
# read data
try:
tr_o = read(f)[0]
except:
print('\nCould not read data: '+os.path.basename(f))
#i+=1
continue
# read synthetics
try:
synth_filename = get_synthetics_filename(os.path.basename(f),
synth_dir,ignore_network=ignore_network)
if synth_filename is None:
continue
#sname = glob(os.path.join(synth_dir,synth_filename))[0]
print(synth_filename)
tr_s = read(synth_filename)[0]
except:
print('\nCould not read synthetics: '+os.path.basename(f))
#i+=1
continue
# Add essential metadata
tr_s.stats.sac = get_essential_sacmeta(tr_o.stats.sac)
# Check sampling rates.
if round(tr_s.stats.sampling_rate,6) != round(tr_o.stats.
sampling_rate,6):
print("Sampling Rates (Hz):\n")
print(tr_s.stats.sampling_rate)
print(tr_o.stats.sampling_rate)
msg = 'Sampling rates of data and synthetics must match.'
raise ValueError(msg)
func = af.get_adj_func(mtype)
# ugly...sorry
# Bandpasses
for j in range(len(bandpass)):
options['window_params']['hw'] = hws[j]
options['g_speed'] = g_speed[j]
tr_o_filt = tr_o.copy()
tr_s_filt = tr_s.copy()
# Waveforms must have same nr of samples.
tr_s_filt.data = my_centered(tr_s_filt.data,tr_o.stats.npts)
bp = bandpass[j]
if bp != None:
tr_o_filt.taper(taper_perc)
tr_o_filt.filter('bandpass',freqmin=bp[0],freqmax=bp[1],
corners=bp[2],zerophase=True)
tr_s_filt.taper(taper_perc)
tr_s_filt.filter('bandpass',freqmin=bp[0],freqmax=bp[1],
corners=bp[2],zerophase=True)
#======================================================
# Weight observed stack by nstack
#======================================================
tr_o_filt.data /= tr_o_filt.stats.sac.user0
data, success = func(tr_o_filt,tr_s_filt,**options)
if not success:
continue
adj_src = Stream()
if isinstance(data,list):
adj_src += Trace(data=data[0])
adj_src += Trace(data=data[1])
brnchs = ['c','a']
for k in range(2):
adjtrc = adj_src[k]
adjtrc.stats.sampling_rate = tr_s.stats.sampling_rate
adjtrc.stats.sac = tr_s.stats.sac.copy()
# Save the adjoint source
file_adj_src = os.path.join(adj_dir,
os.path.basename(synth_filename).
rstrip('sac')+'{}.{}.sac'.format(brnchs[k],j))
adjtrc.write(file_adj_src,format='SAC')
else:
adj_src += Trace(data=data)
for adjtrc in adj_src:
adjtrc.stats.sampling_rate = tr_s.stats.sampling_rate
adjtrc.stats.sac = tr_s.stats.sac.copy()
# Save the adjoint source
file_adj_src = os.path.join(adj_dir,
os.path.basename(synth_filename).
rstrip('sac')+'{}.sac'.format(j))
adjtrc.write(file_adj_src,format='SAC')
return()
window_params['win_overlap'] = False
window_params['wtype'] = 'hann'
window_params['causal_side'] = False
window_params['plot'] = False
# *********************************************
# *********************************************
# only for testing the test:
# def l2_simple(tr_1,tr_2):
# mf = np.sum(0.5 * (tr_1.data - tr_2.data) **2)
# adstf = (tr_1.data - tr_2.data)
# return mf,adstf
m_a_options = {'g_speed': g_speed, 'window_params': window_params}
m_func = rm.get_measure_func(mtype)
a_func = af.get_adj_func(mtype)
# create observed data, synthetics and perturbation
c_obs = 2 * (np.random.rand(2401, ) - 0.5)
c_ini = 2 * (np.random.rand(2401, ) - 0.5)
d_c = 2 * (np.random.rand(2401, ) - 0.5)
# form traces (measurement script works with obspy trace objects, not pure arrays)
c_obs = Trace(data=c_obs)
c_obs.stats.sampling_rate = 1.0
c_obs.stats.sac = sacdict
c_syn = Trace(data=c_ini)
c_syn.stats.sampling_rate = 1.0
c_syn.stats.sac = sacdict
#tr_taper_filter = Trace(data=np.ones(c_obs.stats.npts))
def adjointsrcs(source_config,mtype,step,ignore_network,**options):
"""
Get 'adjoint source' from noise correlation data and synthetics.
options: g_speed,window_params (only needed if mtype is ln_energy_ratio or enery_diff)
"""
files = [f for f in os.listdir(os.path.join(source_config['source_path'],
'observed_correlations')) ]
files = [os.path.join(source_config['source_path'],
'observed_correlations',f) for f in files]
step_n = 'step_{}'.format(int(step))
synth_dir = os.path.join(source_config['source_path'],
step_n,'corr')
adj_dir = os.path.join(source_config['source_path'],
step_n,'adjt')
if files == []:
msg = 'No input found!'
raise ValueError(msg)
#i = 0
with click.progressbar(files,label='Determining adjoint sources...') as bar:
for f in bar:
try:
tr_o = read(f)[0]
except:
print('\nCould not read data: '+os.path.basename(f))
#i+=1
continue
try:
synth_filename = get_synthetics_filename(os.path.basename(f),synth_dir,
ignore_network=ignore_network)
if synth_filename is None:
continue
#sname = glob(os.path.join(synth_dir,synth_filename))[0]
print(synth_filename)
tr_s = read(synth_filename)[0]
except:
print('\nCould not read synthetics: '+os.path.basename(f))
#i+=1
continue
# Add essential metadata
tr_s.stats.sac = get_essential_sacmeta(tr_o.stats.sac)
# Check sampling rates.
if round(tr_s.stats.sampling_rate,6) != round(tr_o.stats.sampling_rate,6):
print("Sampling Rates (Hz)")
print(tr_s.stats.sampling_rate)
print(tr_o.stats.sampling_rate)
msg = 'Sampling rates of data and synthetics must match.'
raise ValueError(msg)
# Waveforms must have same nr of samples.
tr_s.data = my_centered(tr_s.data,tr_o.stats.npts)
# Get the adjoint source
func = af.get_adj_func(mtype)
data, success = func(tr_o,tr_s,**options)
if not success:
continue
adj_src = Stream()
if isinstance(data,list):
adj_src += Trace(data=data[0])
adj_src += Trace(data=data[1])
# TODO: super ugly
brnch = 'c'
for adjtrc in adj_src:
adjtrc.stats.sampling_rate = tr_s.stats.sampling_rate
adjtrc.stats.sac = tr_s.stats.sac.copy()
# Save the adjoint source
file_adj_src = os.path.join(adj_dir,
os.path.basename(synth_filename).
rstrip('sac')+'{}.sac'.format(brnch))
print(file_adj_src)
adjtrc.write(file_adj_src,format='SAC')
brnch = 'a'
else:
adj_src += Trace(data=data)
for adjtrc in adj_src:
adjtrc.stats.sampling_rate = tr_s.stats.sampling_rate
adjtrc.stats.sac = tr_s.stats.sac.copy()
# Save the adjoint source
file_adj_src = os.path.join(adj_dir,
os.path.basename(synth_filename))
adjtrc.write(file_adj_src,format='SAC')
def adjointsrcs(source_config, mtype, step, ignore_network, bandpass,
taper_perc, **options):
"""
Get 'adjoint source' from noise correlation data and synthetics.
options: g_speed,window_params (only needed if mtype is ln_energy_ratio or enery_diff)
"""
files = [
f for f in os.listdir(
os.path.join(source_config['source_path'],
'observed_correlations'))
]
files = [
os.path.join(source_config['source_path'], 'observed_correlations', f)
for f in files
]
step_n = 'step_{}'.format(int(step))
synth_dir = os.path.join(source_config['source_path'], step_n, 'corr')
adj_dir = os.path.join(source_config['source_path'], step_n, 'adjt')
if files == []:
msg = 'No input found!'
raise ValueError(msg)
#i = 0
hws = options['window_params']['hw'][:]
g_speed = options['g_speed'][:]
with click.progressbar(files,
label='Determining adjoint sources...') as bar:
for f in bar:
# read data
try:
tr_o = read(f)[0]
except:
print('\nCould not read data: ' + os.path.basename(f))
#i+=1
continue
# read synthetics
try:
synth_filename = get_synthetics_filename(
os.path.basename(f),
synth_dir,
ignore_network=ignore_network)
if synth_filename is None:
continue
#sname = glob(os.path.join(synth_dir,synth_filename))[0]
print(synth_filename)
tr_s = read(synth_filename)[0]
except:
print('\nCould not read synthetics: ' + os.path.basename(f))
#i+=1
continue
# Add essential metadata
tr_s.stats.sac = get_essential_sacmeta(tr_o.stats.sac)
# Check sampling rates.
if round(tr_s.stats.sampling_rate, 6) != round(
tr_o.stats.sampling_rate, 6):
print("Sampling Rates (Hz):\n")
print(tr_s.stats.sampling_rate)
print(tr_o.stats.sampling_rate)
msg = 'Sampling rates of data and synthetics must match.'
raise ValueError(msg)
func = af.get_adj_func(mtype)
# ugly...sorry
# Bandpasses
for j in range(len(bandpass)):
options['window_params']['hw'] = hws[j]
options['g_speed'] = g_speed[j]
tr_o_filt = tr_o.copy()
tr_s_filt = tr_s.copy()
# Waveforms must have same nr of samples.
tr_s_filt.data = my_centered(tr_s_filt.data, tr_o.stats.npts)
bp = bandpass[j]
if bp != None:
tr_o_filt.taper(taper_perc)
tr_o_filt.filter('bandpass',
freqmin=bp[0],
freqmax=bp[1],
corners=bp[2],
zerophase=True)
tr_s_filt.taper(taper_perc)
tr_s_filt.filter('bandpass',
freqmin=bp[0],
freqmax=bp[1],
corners=bp[2],
zerophase=True)
#======================================================
# Weight observed stack by nstack
#======================================================
tr_o_filt.data /= tr_o_filt.stats.sac.user0
data, success = func(tr_o_filt, tr_s_filt, **options)
if not success:
continue
adj_src = Stream()
if isinstance(data, list):
adj_src += Trace(data=data[0])
adj_src += Trace(data=data[1])
brnchs = ['c', 'a']
for k in range(2):
adjtrc = adj_src[k]
adjtrc.stats.sampling_rate = tr_s.stats.sampling_rate
adjtrc.stats.sac = tr_s.stats.sac.copy()
# Save the adjoint source
file_adj_src = os.path.join(
adj_dir,
os.path.basename(synth_filename).rstrip('sac') +
'{}.{}.sac'.format(brnchs[k], j))
adjtrc.write(file_adj_src, format='SAC')
else:
adj_src += Trace(data=data)
for adjtrc in adj_src:
adjtrc.stats.sampling_rate = tr_s.stats.sampling_rate
adjtrc.stats.sac = tr_s.stats.sac.copy()
# Save the adjoint source
file_adj_src = os.path.join(
adj_dir,
os.path.basename(synth_filename).rstrip('sac') +
'{}.sac'.format(j))
adjtrc.write(file_adj_src, format='SAC')
return ()