def test_amplitude(self):
"""
Test calculating amplitudes
"""
plotit = True
datafile = str(self.data_path / "20190519T060917_MONA.mseed")
respfile = str(self.data_path / "SPOBS2_resp.json")
stream = obspy_read(datafile, 'MSEED')
wid = WaveformStreamID(network_code=stream[0].stats.network,
station_code=stream[0].stats.station,
channel_code=stream[0].stats.channel)
Ppick = Pick(time=UTCDateTime('2019-05-19T06:09:48.83'),
phase_hint='P',
waveform_id=wid)
Spick = Pick(time=UTCDateTime('2019-05-19T06:09:51.52'),
phase_hint='S',
waveform_id=wid)
la = LocalAmplitude(stream, [Ppick, Spick], respfile, 'JSON_PZ')
wood_calc, _ = la.get_iaml(method='wood_calc')
wood_est, _ = la.get_iaml(method='wood_est')
raw, _ = la.get_iaml(method='raw_disp')
# Values obtained when response was mis-interpreted as nm/s
# self.assertAlmostEqual(amp_wood_calc.generic_amplitude, 1097.55509106/1e9)
# self.assertAlmostEqual(amp_wood_calc.period, 0.112)
self.assertAlmostEqual(wood_calc.generic_amplitude * 1e9, 378.3697813)
self.assertAlmostEqual(wood_calc.period, 0.12)
self.assertAlmostEqual(wood_est.generic_amplitude * 1e9, 140.490154756)
self.assertAlmostEqual(wood_est.period, 0.032)
self.assertAlmostEqual(raw.generic_amplitude * 1e9, 460.35018097)
self.assertAlmostEqual(raw.period, 0.112)
def test_nordic_write(self):
"""
Test calculating amplitudes
"""
compare_file = str(self.data_path / "test.nordic")
otime = UTCDateTime('2019-05-19T06:09:48')
wid = WaveformStreamID(network_code='4G', station_code='STAT')
wid.channel_code = 'SHZ'
Ppick = Pick(time=otime + 2.2,
phase_hint='P',
waveform_id=wid,
evaluation_mode='automatic',
time_errors=QuantityError(0.01))
Parrival = Arrival(pick_id=Ppick.resource_id, time_weight=0)
wid.channel_code = 'SH1'
Spick = Pick(time=otime + 3.5,
phase_hint='S',
waveform_id=wid,
evaluation_mode='automatic',
time_errors=QuantityError(0.05))
wid.channel_code = 'SH2'
Sarrival = Arrival(pick_id=Spick.resource_id, time_weight=1)
Apick = Pick(time=otime + 4.0,
phase_hint='IAML',
waveform_id=wid,
evaluation_mode='automatic',
time_errors=QuantityError(0.1))
Amp = Amplitude(generic_amplitude=410.e-9,
type='IAML',
unit='m',
period=0.22,
magnitude_hint='ML',
category='period',
pick_id=Apick.resource_id,
waveform_id=Apick.waveform_id)
picks = [Ppick, Spick, Apick]
amps = [Amp]
arrivals = [Parrival, Sarrival]
PSPicker.save_nordic_event(picks,
otime,
'.',
'test.nordic',
amps,
arrivals=arrivals,
debug=False)
self.assertTextFilesEqual('test.nordic',
compare_file,
ignore_lines=[1])
Path("test.nordic").unlink()
for p in Path(".").glob('run_*.log'):
p.unlink()
def to_obspy(self, channel_maps, quality_thresholds=None):
"""
Return obspy Pick and Arrival
Arrival is None if there is no pick weight
:param channel_maps: {station: ChannelMap object}
:param quality_thresholds: list of 4 signal-to-noise ratio thresholds
for pick quality, from lowest [quality=3] to highest [quality=0]
:parm sampling_rate: sampling rate (used to estimate timing error)
"""
c_map = channel_maps[self.station]
if self.phase_guess == 'P':
id = WaveformStreamID(seed_string=c_map.P_write_seed_string)
phase_hint = c_map.P_write_phase
log(f'{phase_hint}: {id.get_seed_string()}', 'debug')
elif self.phase_guess == 'S':
id = WaveformStreamID(seed_string=c_map.S_write_seed_string)
phase_hint = c_map.S_write_phase
log(f'{phase_hint}: {id.get_seed_string()}', 'debug')
else:
raise ValueError("phase guess '{self.phase_guess}' not 'P' or 'S'")
self.weight = self._get_weight(quality_thresholds)
time_errors = self._time_error()
pick = Pick(time=self.time,
time_errors=time_errors,
waveform_id=id,
phase_hint=phase_hint,
evaluation_mode='automatic',
evaluation_status='preliminary')
if self.weight is not None:
return pick, Arrival(pick_id=pick.resource_id,
time_weight=self.weight)
else:
return pick, None
def make_pick(pick_str, origin_time):
""" Creates an ObsPy Pick object from a line of STP
phase output.
Sample pick_str:
CI CLC HHZ -- 35.8157 -117.5975 775.0 P c. i 1.0 6.46 1.543
"""
fields = pick_str.split()
if len(fields) != 13:
raise Exception('Invalid STP phase output')
new_pick = Pick()
(net, sta, chan, loc) = fields[:4]
new_pick.waveform_id = WaveformStreamID(network_code=net,
station_code=sta,
channel_code=chan,
location_code=loc)
# Determine polarity from first motion.
polarity = POLARITY_MAPPING[fields[8][0]]
if polarity == '':
polarity = POLARITY_MAPPING[fields[8][1]]
if polarity != '':
new_pick.polarity = polarity
# Determine signal onset.
if fields[9] == 'i':
new_pick.onset = 'impulsive'
elif fields[9] == 'e':
new_pick.onset = 'emergent'
else:
new_pick.onset = 'questionable'
# Determine time error from STP quality.
# Use Jiggle standard and assume sample rate of 100 sps.
quality = float(fields[10])
if quality == 0.0:
new_pick.time_errors = QuantityError(lower_uncertainty=0.03)
elif quality <= 0.3:
new_pick.time_errors = QuantityError(upper_uncertainty=0.03)
elif quality <= 0.5:
new_pick.time_errors = QuantityError(upper_uncertainty=0.02)
elif quality <= 0.8:
new_pick.time_errors = QuantityError(upper_uncertainty=0.01)
elif quality == 1.0:
new_pick.time_errors = QuantityError(upper_uncertainty=0.0)
# Determine pick time.
offset = float(fields[12])
new_pick.time = origin_time + offset
return new_pick
def get_picks_from_pdf(trace, height=0.5, distance=100):
start_time = trace.stats.starttime
peaks, properties = find_peaks(trace.pdf, height=height, distance=distance)
picks = []
for p in peaks:
if p:
time = start_time + p / trace.stats.sampling_rate
phase_hint = "P"
pick = Pick(time=time, phase_hint=phase_hint)
picks.append(pick)
return picks
def test_amplitude(self):
"""
Test calculating amplitudes
"""
datafile = os.path.join(self.testing_path,
"20190519T060917_MONA.mseed")
respfile = os.path.join(self.testing_path, "SPOBS2_response.json")
stream = obspy_read(datafile, 'MSEED')
wid = WaveformStreamID(network_code=stream[0].stats.network,
station_code=stream[0].stats.station,
channel_code=stream[0].stats.channel)
Ppick = Pick(time=UTCDateTime('2019-05-19T06:09:48.83'),
phase_hint='P',
waveform_id=wid)
Spick = Pick(time=UTCDateTime('2019-05-19T06:09:51.52'),
phase_hint='S',
waveform_id=wid)
obj = LocalAmplitude(stream, [Ppick, Spick], respfile, 'JSON_PZ')
amp_wood_calc, _ = obj.get_iaml(plot=False, method='wood_calc')
amp_wood_est, _ = obj.get_iaml(plot=False, method='wood_est')
amp_raw, _ = obj.get_iaml(plot=False, method='raw_disp')
self.assertAlmostEqual(amp_wood_calc.generic_amplitude,
1097.555091056036)
self.assertAlmostEqual(amp_wood_calc.period, 0.112)
def get_picks_from_pdf(trace, height=0.5, distance=100):
start_time = trace.stats.starttime
peaks, properties = find_peaks(trace.pdf, height=height, distance=distance)
picks = []
for p in peaks:
if p:
time = start_time + p / trace.stats.sampling_rate
phase_hint = "P"
pick = Pick(time=time, phase_hint=phase_hint)
pick.waveform_id = WaveformStreamID(
network_code=trace.stats.network,
station_code=trace.stats.station,
location_code=trace.stats.channel,
channel_code=trace.stats.location)
picks.append(pick)
return picks
def get_iaml(self, plot=False, method='wood_calc'):
"""
get IAML amplitude and associated pick
From IAPEI CoSOI 2013 Working Group recommentations:
"ML = log10(A) + 1.11log10(R) + 0.00189*R - 2.09
where
A = maximum *trace* amplitude in *nm* that is measured on output from
a *horizontal-component* instrument that is filtered so that the
response of the seismograph/filter system replicates that of a
*Wood-Anderson standard seismograph* but with a
static magnification of 1
R = *hypocentral distance in km*, typically less than 1000 km
the constant -2.09 is based on an experimentally determined static
magnification of the Wood-Anderson of 2080, rather than the theoretical
magnification of 2800.
The amplitudes used in the magnitude formulas ... are in most
circumstances to be measured as one-half the maximum deflection of the
seismogram trace, peak-to-adjacent- trough or trough-to-adjacent-peak,
where peak and trough are separated by one crossing of the zero-line:
the measurement is sometimes described as “one-half peak-to-peak
amplitude.” None of the magnitude formulas presented in this article
are intended to be used with the full peak-to-trough deflection as
the amplitude.
WA displacement zeros = [(0+0j), (0+0j)]
WA displacement poles = [(-5.49779 - 5.60886j), (-5.49779 + 5.60886j)]
WA seismometer free period = 0.8 s
WA damping constant = 0.7
A0 = 0.97866 @ 4 Hz
:param plot: plot the result
:param method:
"wood_calc": calculate amplitude on the signal transformed to
simulate a unity gain Wood-Anderson filter
"wood_est": calculate amplitude on the original signal and use
obspy.signal.invsim.estimate_wood_anderson_amplitude()
"raw_disp": calculate amplitude on the signal transformed to
displacement in nm
:returns: amplitude in meters (type=IAML), associated Pick
:rtype: ~class obspy.core.event.magnitude.Amplitude,
~class obspy.core.event.origin.Pick
"""
if self.ref_pick is None:
log('No ref_pick!', 'debug')
return None
assert method in ['wood_calc', 'wood_est', 'raw_disp']
signal = self.traces.copy()
# do all work in nm
paz_simulate, paz_simulate_obspy = None, None
paz_remove = self.paz.copy()
if method == 'wood_est':
paz_remove.input_units = 'm/s'
plot_units = 'Original (counts)'
else:
if method == 'wood_calc':
paz_simulate = PAZ(poles=[(-5.49779 - 5.60886j),
(-5.49779 + 5.60886j)],
zeros=[(0 + 0j), (0 + 0j)],
ref_gain=1,
ref_freq=4.0,
input_units='nm',
output_units='counts')
plot_units = 'Wood-And (nm)'
paz_simulate_obspy = paz_simulate.to_obspy()
elif method == 'raw_disp':
paz_simulate = None
paz_remove.input_units = 'nm'
plot_units = 'Disp (nm)'
for tr in signal:
tr.simulate(paz_remove=paz_remove.to_obspy(),
paz_simulate=paz_simulate_obspy,
water_level=60.0)
amp = pk2pk(signal, self.win_start, self.win_end)
if amp is None:
return None, None
if method == 'wood_est':
amp.value = estimate_wood_anderson_amplitude(
paz_remove.to_obspy(), amp.value, amp.period)
# estimate...() gives displacement amplitude ON a Wood-Anderson
# seismometer, divide by 2080 then multiply by 1e6 to get ground
# motion in nm?
amp.value /= 2080. / 1e6
if plot:
self.plot(signal, amp, plot_units)
waveform_id = self.ref_pick.waveform_id
waveform_id.channel_code = amp.channel
pick = Pick(time=amp.time,
waveform_id=waveform_id,
method_id='ps_picker',
phase_hint='IAML',
evaluation_mode='automatic',
evaluation_status='preliminary')
obspy_amp = Amplitude(generic_amplitude=amp.value / (2. * 1.e9),
type='IAML',
unit='m',
period=amp.period,
magnitude_hint='ML',
category='period',
pick_id=pick.resource_id,
waveform_id=pick.waveform_id)
return obspy_amp, pick
def get_iaml(self,
plot=False,
method='wood_calc',
pre_filt=(0.005, 0.006, 30.0, 35.),
verbose=False):
"""
get IAML amplitude and associated pick
From IAPEI CoSOI 2013 Working Group recommentations:
"ML = log10(A) + 1.11log10(R) + 0.00189*R - 2.09
where
A = maximum *trace* amplitude in *nm* that is measured on output from
a *horizontal-component* instrument that is filtered so that the
response of the seismograph/filter system replicates that of a
*Wood-Anderson standard seismograph* but with a
static magnification of 1
R = *hypocentral distance in km*, typically less than 1000 km
the constant -2.09 is based on an experimentally determined static
magnification of the Wood-Anderson of 2080, rather than the theoretical
magnification of 2800.
The amplitudes used in the magnitude formulas ... are in most
circumstances to be measured as one-half the maximum deflection of the
seismogram trace, peak-to-adjacent- trough or trough-to-adjacent-peak,
where peak and trough are separated by one crossing of the zero-line:
the measurement is sometimes described as “one-half peak-to-peak
amplitude.” None of the magnitude formulas presented in this article
are intended to be used with the full peak-to-trough deflection as
the amplitude.
WA displacement zeros = [(0+0j), (0+0j)]
WA displacement poles = [(-5.49779 - 5.60886j), (-5.49779 + 5.60886j)]
WA seismometer free period = 0.8 s
WA damping constant = 0.7
A0 = 0.97866 @ 4 Hz
Arguments:
plot (bool): plot the result
method (str): method used to calculate the amplitude. Values are:
"wood_calc": use the signal transformed to simulate a unity
gain Wood-Anderson filter
"raw_disp": use the signal transformed to displacement. For
periods > 0.25s this value can be significantly
higher than that given by wood_calc
"wood_est": use the digital signal and obspy's
estimate_wood_anderson_amplitude(). Can be
trouble if the original signal was not proportional
to displacement
pre_filt (tuple): pre_filter to apply to trace.simulate() to
prevent amplifying noise.
Returns:
tuple containing:
(obspy Amplitude): amplitude in meters, type=IAML
(obspy Pick): pick associated with the amplitude
"""
if self.ref_pick is None:
log('No ref_pick!', 'debug')
return None
assert method in ['wood_calc', 'wood_est', 'raw_disp']
signal = self.traces.copy()
# do all work in nm
paz_simulate, paz_simulate_obspy = None, None
paz_remove = self.paz.copy()
# define a filter band to prevent amplifying noise during the deconvolution
# print(f'{str(self.paz)=}')
# print(f'{str(paz_remove)=}')
if method == 'wood_est':
paz_remove.input_units = 'm/s'
plot_units = 'Original (counts)'
else:
# obspy PAZ has no units information, make displacement
# paz_remove.input_units = 'nm'
paz_remove_obspy = paz_remove.to_obspy()
if method == 'wood_calc':
# From Bormann & Dewey 2014, WA is flat w.r.t. displacement
paz_simulate = PAZ.from_refgain(1,
poles=[(-5.49779 - 5.60886j),
(-5.49779 + 5.60886j)],
zeros=[(0 + 0j), (0 + 0j)],
ref_freq=4.0,
input_units='nm',
output_units='counts')
plot_units = 'WA (nm)'
paz_simulate_obspy = paz_simulate.to_obspy()
elif method == 'raw_disp':
paz_simulate_obspy = None
plot_units = 'Disp (nm)'
for tr in signal:
tr.simulate(paz_remove=paz_remove_obspy,
paz_simulate=paz_simulate_obspy,
pre_filt=pre_filt,
water_level=60.0)
amp = pk2pk(signal, self.win_start, self.win_end)
amp.value /= 2 # Convert to zero-to-peak
# print(f'{str(self.paz)=}')
# print(f'{paz_remove_obspy=}')
# print(f'{str(paz_remove)=}')
if amp is None:
return None, None
if method == 'wood_est':
# simulated zero to peak disp amplitude on WA seismometer(mm)
amp.value = estimate_wood_anderson_amplitude(
paz_remove.to_obspy(), 2 * amp.value, amp.period)
# Divide by 2080 then multiply by 1e6 to get ground motion in nm?
# amp.value /= 2080./1e6
# Divide by 2080 then remove seismometer gain?
amp.value /= 2080. # Remove obspy's WA seismometer sensitivity
amp.value *= 1e6 # convert nm
# print(f'{plot=}')
if plot:
# print(amp)
self.plot(signal, amp, method, plot_units)
plt.show()
waveform_id = self.ref_pick.waveform_id
waveform_id.channel_code = amp.channel
pick = Pick(time=amp.time,
waveform_id=waveform_id,
method_id='ps_picker',
phase_hint='IAML',
evaluation_mode='automatic',
evaluation_status='preliminary')
obspy_amp = Amplitude(generic_amplitude=amp.value / 1.e9,
type='IAML',
unit='m',
period=amp.period,
magnitude_hint='ML',
category='period',
pick_id=pick.resource_id,
waveform_id=pick.waveform_id)
if verbose:
print('{} IAML = {:.4g} nm at {}s'.format(
waveform_id.get_seed_string(), amp.value, amp.period))
return obspy_amp, pick