def test_read_wavename(self):
from eqcorrscan.utils.sfile_util import readwavename
import os
testing_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
'test_data', 'REA', 'TEST_',
'19-0926-59L.S201309')
wavefiles = readwavename(testing_path)
self.assertEqual(len(wavefiles), 1)
def test_read_wavename(self):
from eqcorrscan.utils.sfile_util import readwavename
import os
testing_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
'test_data', 'REA', 'TEST_',
'19-0926-59L.S201309')
wavefiles = readwavename(testing_path)
self.assertEqual(len(wavefiles), 1)
def setUpClass(cls):
cls.testing_path = os.path.join(
os.path.abspath(os.path.dirname(__file__)), 'test_data')
sfile = os.path.join(cls.testing_path, 'REA', 'TEST_',
'01-0411-15L.S201309')
cls.event = read_event(sfile)
cls.wavfiles = readwavename(sfile)
cls.datapath = os.path.join(cls.testing_path, 'WAV', 'TEST_')
cls.st = read(os.path.join(cls.datapath, cls.wavfiles[0]))
cls.respdir = cls.testing_path
def test_read_write(self):
"""
Function to test the read and write capabilities of sfile_util.
"""
import os
from obspy.core.event import Catalog
import obspy
if int(obspy.__version__.split('.')[0]) >= 1:
from obspy.core.event import read_events
else:
from obspy.core.event import readEvents as read_events
# Set-up a test event
test_event = basic_test_event()
# Add the event to a catalogue which can be used for QuakeML testing
test_cat = Catalog()
test_cat += test_event
# Write the catalog
test_cat.write("Test_catalog.xml", format='QUAKEML')
# Read and check
read_cat = read_events("Test_catalog.xml")
os.remove("Test_catalog.xml")
self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
self.assertEqual(read_cat[0].picks, test_cat[0].picks)
self.assertEqual(read_cat[0].origins[0].resource_id,
test_cat[0].origins[0].resource_id)
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residuel_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
self.assertEqual(read_cat[0].amplitudes[0].resource_id,
test_cat[0].amplitudes[0].resource_id)
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].unit,
test_cat[0].amplitudes[0].unit)
self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
test_cat[0].amplitudes[0].generic_amplitude)
self.assertEqual(read_cat[0].amplitudes[0].pick_id,
test_cat[0].amplitudes[0].pick_id)
self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
test_cat[0].amplitudes[0].waveform_id)
# Check the read-write s-file functionality
sfile = eventtosfile(test_cat[0],
userID='TEST',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
del read_cat
self.assertEqual(readwavename(sfile), ['test'])
read_cat = Catalog()
read_cat += readpicks(sfile)
os.remove(sfile)
self.assertEqual(read_cat[0].picks[0].time, test_cat[0].picks[0].time)
self.assertEqual(read_cat[0].picks[0].backazimuth,
test_cat[0].picks[0].backazimuth)
self.assertEqual(read_cat[0].picks[0].onset,
test_cat[0].picks[0].onset)
self.assertEqual(read_cat[0].picks[0].phase_hint,
test_cat[0].picks[0].phase_hint)
self.assertEqual(read_cat[0].picks[0].polarity,
test_cat[0].picks[0].polarity)
self.assertEqual(read_cat[0].picks[0].waveform_id.station_code,
test_cat[0].picks[0].waveform_id.station_code)
self.assertEqual(read_cat[0].picks[0].waveform_id.channel_code[-1],
test_cat[0].picks[0].waveform_id.channel_code[-1])
# assert read_cat[0].origins[0].resource_id ==\
# test_cat[0].origins[0].resource_id
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residuel_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(read_cat[0].magnitudes[0].mag,
test_cat[0].magnitudes[0].mag)
self.assertEqual(read_cat[0].magnitudes[1].mag,
test_cat[0].magnitudes[1].mag)
self.assertEqual(read_cat[0].magnitudes[2].mag,
test_cat[0].magnitudes[2].mag)
self.assertEqual(read_cat[0].magnitudes[0].creation_info,
test_cat[0].magnitudes[0].creation_info)
self.assertEqual(read_cat[0].magnitudes[1].creation_info,
test_cat[0].magnitudes[1].creation_info)
self.assertEqual(read_cat[0].magnitudes[2].creation_info,
test_cat[0].magnitudes[2].creation_info)
self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
test_cat[0].magnitudes[0].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
test_cat[0].magnitudes[1].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
test_cat[0].magnitudes[2].magnitude_type)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# assert read_cat[0].amplitudes[0].resource_id ==\
# test_cat[0].amplitudes[0].resource_id
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].snr,
test_cat[0].amplitudes[0].snr)
del read_cat
# assert read_cat[0].amplitudes[0].pick_id ==\
# test_cat[0].amplitudes[0].pick_id
# assert read_cat[0].amplitudes[0].waveform_id ==\
# test_cat[0].amplitudes[0].waveform_id
# Test the wrappers for PICK and EVENTINFO classes
picks, evinfo = eventtopick(test_cat)
# Test the conversion back
conv_cat = Catalog()
conv_cat.append(picktoevent(evinfo, picks))
self.assertEqual(conv_cat[0].picks[0].time, test_cat[0].picks[0].time)
self.assertEqual(conv_cat[0].picks[0].backazimuth,
test_cat[0].picks[0].backazimuth)
self.assertEqual(conv_cat[0].picks[0].onset,
test_cat[0].picks[0].onset)
self.assertEqual(conv_cat[0].picks[0].phase_hint,
test_cat[0].picks[0].phase_hint)
self.assertEqual(conv_cat[0].picks[0].polarity,
test_cat[0].picks[0].polarity)
self.assertEqual(conv_cat[0].picks[0].waveform_id.station_code,
test_cat[0].picks[0].waveform_id.station_code)
self.assertEqual(conv_cat[0].picks[0].waveform_id.channel_code[-1],
test_cat[0].picks[0].waveform_id.channel_code[-1])
# self.assertEqual(read_cat[0].origins[0].resource_id,
# test_cat[0].origins[0].resource_id)
self.assertEqual(conv_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residuel_RMS is not a quakeML format
self.assertEqual(conv_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(conv_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(conv_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(conv_cat[0].magnitudes[0].mag,
test_cat[0].magnitudes[0].mag)
self.assertEqual(conv_cat[0].magnitudes[1].mag,
test_cat[0].magnitudes[1].mag)
self.assertEqual(conv_cat[0].magnitudes[2].mag,
test_cat[0].magnitudes[2].mag)
self.assertEqual(conv_cat[0].magnitudes[0].creation_info,
test_cat[0].magnitudes[0].creation_info)
self.assertEqual(conv_cat[0].magnitudes[1].creation_info,
test_cat[0].magnitudes[1].creation_info)
self.assertEqual(conv_cat[0].magnitudes[2].creation_info,
test_cat[0].magnitudes[2].creation_info)
self.assertEqual(conv_cat[0].magnitudes[0].magnitude_type,
test_cat[0].magnitudes[0].magnitude_type)
self.assertEqual(conv_cat[0].magnitudes[1].magnitude_type,
test_cat[0].magnitudes[1].magnitude_type)
self.assertEqual(conv_cat[0].magnitudes[2].magnitude_type,
test_cat[0].magnitudes[2].magnitude_type)
self.assertEqual(conv_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# self.assertEqual(read_cat[0].amplitudes[0].resource_id,
# test_cat[0].amplitudes[0].resource_id)
self.assertEqual(conv_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(conv_cat[0].amplitudes[0].snr,
test_cat[0].amplitudes[0].snr)
def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin,
prepick=0.05, debug=0, plot=False):
r"""Function to read in picks from sfile then generate the template from \
the picks within this and the wavefile found in the pick file.
:type sfile: string
:param sfile: sfilename must be the \
path to a seisan nordic type s-file containing waveform and pick \
information.
:type lowcut: float
:param lowcut: Low cut (Hz), if set to None will look in template \
defaults file
:type highcut: float
:param highcut: High cut (Hz), if set to None will look in template \
defaults file
:type samp_rate: float
:param samp_rate: New sampling rate in Hz, if set to None will look in \
template defaults file
:type filt_order: int
:param filt_order: Filter level, if set to None will look in \
template defaults file
:type swin: str
:param swin: Either 'all', 'P' or 'S', to select which phases to output.
:type length: float
:param length: Extract length in seconds, if None will look in template \
defaults file.
:type prepick: float
:param prepick: Length to extract prior to the pick in seconds.
:type debug: int
:param debug: Debug level, higher number=more output.
:type plot: bool
:param plot: Turns template plotting on or off.
:returns: obspy.Stream Newly cut template
.. warning:: This will use whatever data is pointed to in the s-file, if \
this is not the coninuous data, we recommend using other functions. \
Differences in processing between short files and day-long files \
(inherent to resampling) will produce lower cross-correlations.
"""
# Perform some checks first
import os
if not os.path.isfile(sfile):
raise IOError('sfile does not exist')
from eqcorrscan.utils import pre_processing
from eqcorrscan.utils import sfile_util
from obspy import read as obsread
# Read in the header of the sfile
wavefiles = sfile_util.readwavename(sfile)
pathparts = sfile.split('/')[0:-1]
new_path_parts = []
for part in pathparts:
if part == 'REA':
part = 'WAV'
new_path_parts.append(part)
# * argument to allow .join() to accept a list
wavpath = os.path.join(*new_path_parts) + '/'
# In case of absolute paths (not handled with .split() --> .join())
if sfile[0] == '/':
wavpath = '/' + wavpath
# Read in waveform file
for wavefile in wavefiles:
print(''.join(["I am going to read waveform data from: ", wavpath,
wavefile]))
if 'st' not in locals():
st = obsread(wavpath + wavefile)
else:
st += obsread(wavpath + wavefile)
for tr in st:
if tr.stats.sampling_rate < samp_rate:
print('Sampling rate of data is lower than sampling rate asked ' +
'for')
print('Not good practice for correlations: I will not do this')
raise ValueError("Trace: " + tr.stats.station +
" sampling rate: " + str(tr.stats.sampling_rate))
# Read in pick info
catalog = sfile_util.readpicks(sfile)
# Read the list of Picks for this event
picks = catalog[0].picks
print("I have found the following picks")
for pick in picks:
print(' '.join([pick.waveform_id.station_code,
pick.waveform_id.channel_code, pick.phase_hint,
str(pick.time)]))
# Process waveform data
st.merge(fill_value='interpolate')
st = pre_processing.shortproc(st, lowcut, highcut, filt_order,
samp_rate, debug)
st1 = _template_gen(picks=picks, st=st, length=length, swin=swin,
prepick=prepick, plot=plot)
return st1
def test_read_write(self):
"""
Function to test the read and write capabilities of sfile_util.
"""
import os
from obspy.core.event import Catalog
import obspy
if int(obspy.__version__.split('.')[0]) >= 1:
from obspy.core.event import read_events
else:
from obspy.core.event import readEvents as read_events
# Set-up a test event
test_event = full_test_event()
# Add the event to a catalogue which can be used for QuakeML testing
test_cat = Catalog()
test_cat += test_event
# Write the catalog
test_cat.write("Test_catalog.xml", format='QUAKEML')
# Read and check
read_cat = read_events("Test_catalog.xml")
os.remove("Test_catalog.xml")
self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
for i in range(len(read_cat[0].picks)):
for key in read_cat[0].picks[i].keys():
# Ignore backazimuth errors and horizontal_slowness_errors
if key in ['backazimuth_errors', 'horizontal_slowness_errors']:
continue
self.assertEqual(read_cat[0].picks[i][key],
test_cat[0].picks[i][key])
self.assertEqual(read_cat[0].origins[0].resource_id,
test_cat[0].origins[0].resource_id)
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residual_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
# Check magnitudes
self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# Check local magnitude amplitude
self.assertEqual(read_cat[0].amplitudes[0].resource_id,
test_cat[0].amplitudes[0].resource_id)
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].unit,
test_cat[0].amplitudes[0].unit)
self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
test_cat[0].amplitudes[0].generic_amplitude)
self.assertEqual(read_cat[0].amplitudes[0].pick_id,
test_cat[0].amplitudes[0].pick_id)
self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
test_cat[0].amplitudes[0].waveform_id)
# Check coda magnitude pick
self.assertEqual(read_cat[0].amplitudes[1].resource_id,
test_cat[0].amplitudes[1].resource_id)
self.assertEqual(read_cat[0].amplitudes[1].type,
test_cat[0].amplitudes[1].type)
self.assertEqual(read_cat[0].amplitudes[1].unit,
test_cat[0].amplitudes[1].unit)
self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
test_cat[0].amplitudes[1].generic_amplitude)
self.assertEqual(read_cat[0].amplitudes[1].pick_id,
test_cat[0].amplitudes[1].pick_id)
self.assertEqual(read_cat[0].amplitudes[1].waveform_id,
test_cat[0].amplitudes[1].waveform_id)
self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
test_cat[0].amplitudes[1].magnitude_hint)
self.assertEqual(read_cat[0].amplitudes[1].snr,
test_cat[0].amplitudes[1].snr)
self.assertEqual(read_cat[0].amplitudes[1].category,
test_cat[0].amplitudes[1].category)
# Check the read-write s-file functionality
sfile = eventtosfile(test_cat[0],
userID='TEST',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
del read_cat
self.assertEqual(readwavename(sfile), ['test'])
read_cat = Catalog()
read_cat += readpicks(sfile)
os.remove(sfile)
for i in range(len(read_cat[0].picks)):
self.assertEqual(read_cat[0].picks[i].time,
test_cat[0].picks[i].time)
self.assertEqual(read_cat[0].picks[i].backazimuth,
test_cat[0].picks[i].backazimuth)
self.assertEqual(read_cat[0].picks[i].onset,
test_cat[0].picks[i].onset)
self.assertEqual(read_cat[0].picks[i].phase_hint,
test_cat[0].picks[i].phase_hint)
self.assertEqual(read_cat[0].picks[i].polarity,
test_cat[0].picks[i].polarity)
self.assertEqual(read_cat[0].picks[i].waveform_id.station_code,
test_cat[0].picks[i].waveform_id.station_code)
self.assertEqual(read_cat[0].picks[i].waveform_id.channel_code[-1],
test_cat[0].picks[i].waveform_id.channel_code[-1])
# assert read_cat[0].origins[0].resource_id ==\
# test_cat[0].origins[0].resource_id
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residual_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(read_cat[0].magnitudes[0].mag,
test_cat[0].magnitudes[0].mag)
self.assertEqual(read_cat[0].magnitudes[1].mag,
test_cat[0].magnitudes[1].mag)
self.assertEqual(read_cat[0].magnitudes[2].mag,
test_cat[0].magnitudes[2].mag)
self.assertEqual(read_cat[0].magnitudes[0].creation_info,
test_cat[0].magnitudes[0].creation_info)
self.assertEqual(read_cat[0].magnitudes[1].creation_info,
test_cat[0].magnitudes[1].creation_info)
self.assertEqual(read_cat[0].magnitudes[2].creation_info,
test_cat[0].magnitudes[2].creation_info)
self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
test_cat[0].magnitudes[0].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
test_cat[0].magnitudes[1].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
test_cat[0].magnitudes[2].magnitude_type)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# assert read_cat[0].amplitudes[0].resource_id ==\
# test_cat[0].amplitudes[0].resource_id
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].snr,
test_cat[0].amplitudes[0].snr)
# Check coda magnitude pick
# Resource ids get overwritten because you can't have two the same in
# memory
# self.assertEqual(read_cat[0].amplitudes[1].resource_id,
# test_cat[0].amplitudes[1].resource_id)
self.assertEqual(read_cat[0].amplitudes[1].type,
test_cat[0].amplitudes[1].type)
self.assertEqual(read_cat[0].amplitudes[1].unit,
test_cat[0].amplitudes[1].unit)
self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
test_cat[0].amplitudes[1].generic_amplitude)
# Resource ids get overwritten because you can't have two the same in
# memory
# self.assertEqual(read_cat[0].amplitudes[1].pick_id,
# test_cat[0].amplitudes[1].pick_id)
self.assertEqual(read_cat[0].amplitudes[1].waveform_id.station_code,
test_cat[0].amplitudes[1].waveform_id.station_code)
self.assertEqual(
read_cat[0].amplitudes[1].waveform_id.channel_code,
test_cat[0].amplitudes[1].waveform_id.channel_code[0] +
test_cat[0].amplitudes[1].waveform_id.channel_code[-1])
self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
test_cat[0].amplitudes[1].magnitude_hint)
# snr is not supported in s-file
# self.assertEqual(read_cat[0].amplitudes[1].snr,
# test_cat[0].amplitudes[1].snr)
self.assertEqual(read_cat[0].amplitudes[1].category,
test_cat[0].amplitudes[1].category)
del read_cat
# Test a deliberate fail
test_cat.append(full_test_event())
with self.assertRaises(IOError):
# Raises error due to multiple events in catalog
sfile = eventtosfile(test_cat,
userID='TEST',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
# Raises error due to too long userID
sfile = eventtosfile(test_cat[0],
userID='TESTICLE',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
# Raises error due to unrecognised event type
sfile = eventtosfile(test_cat[0],
userID='TEST',
evtype='U',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
# Raises error due to no output directory
sfile = eventtosfile(test_cat[0],
userID='TEST',
evtype='L',
outdir='albatross',
wavefiles='test',
explosion=True,
overwrite=True)
# Raises error due to incorrect wavefil formatting
sfile = eventtosfile(test_cat[0],
userID='TEST',
evtype='L',
outdir='.',
wavefiles=1234,
explosion=True,
overwrite=True)
with self.assertRaises(IndexError):
invalid_origin = test_cat[0].copy()
invalid_origin.origins = []
sfile = eventtosfile(invalid_origin,
userID='TEST',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
with self.assertRaises(ValueError):
invalid_origin = test_cat[0].copy()
invalid_origin.origins[0].time = None
sfile = eventtosfile(invalid_origin,
userID='TEST',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
# Write a near empty origin
valid_origin = test_cat[0].copy()
valid_origin.origins[0].latitude = None
valid_origin.origins[0].longitude = None
valid_origin.origins[0].depth = None
sfile = eventtosfile(valid_origin,
userID='TEST',
evtype='L',
outdir='.',
wavefiles='test',
explosion=True,
overwrite=True)
self.assertTrue(os.path.isfile(sfile))
os.remove(sfile)
def test_read_write(self):
"""
Function to test the read and write capabilities of sfile_util.
"""
import os
from obspy.core.event import Catalog
import obspy
if int(obspy.__version__.split('.')[0]) >= 1:
from obspy.core.event import read_events
else:
from obspy.core.event import readEvents as read_events
# Set-up a test event
test_event = full_test_event()
# Add the event to a catalogue which can be used for QuakeML testing
test_cat = Catalog()
test_cat += test_event
# Write the catalog
test_cat.write("Test_catalog.xml", format='QUAKEML')
# Read and check
read_cat = read_events("Test_catalog.xml")
os.remove("Test_catalog.xml")
self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
for i in range(len(read_cat[0].picks)):
for key in read_cat[0].picks[i].keys():
# Ignore backazimuth errors and horizontal_slowness_errors
if key in ['backazimuth_errors', 'horizontal_slowness_errors']:
continue
self.assertEqual(read_cat[0].picks[i][key],
test_cat[0].picks[i][key])
self.assertEqual(read_cat[0].origins[0].resource_id,
test_cat[0].origins[0].resource_id)
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residual_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
# Check magnitudes
self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# Check local magnitude amplitude
self.assertEqual(read_cat[0].amplitudes[0].resource_id,
test_cat[0].amplitudes[0].resource_id)
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].unit,
test_cat[0].amplitudes[0].unit)
self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
test_cat[0].amplitudes[0].generic_amplitude)
self.assertEqual(read_cat[0].amplitudes[0].pick_id,
test_cat[0].amplitudes[0].pick_id)
self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
test_cat[0].amplitudes[0].waveform_id)
# Check coda magnitude pick
self.assertEqual(read_cat[0].amplitudes[1].resource_id,
test_cat[0].amplitudes[1].resource_id)
self.assertEqual(read_cat[0].amplitudes[1].type,
test_cat[0].amplitudes[1].type)
self.assertEqual(read_cat[0].amplitudes[1].unit,
test_cat[0].amplitudes[1].unit)
self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
test_cat[0].amplitudes[1].generic_amplitude)
self.assertEqual(read_cat[0].amplitudes[1].pick_id,
test_cat[0].amplitudes[1].pick_id)
self.assertEqual(read_cat[0].amplitudes[1].waveform_id,
test_cat[0].amplitudes[1].waveform_id)
self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
test_cat[0].amplitudes[1].magnitude_hint)
self.assertEqual(read_cat[0].amplitudes[1].snr,
test_cat[0].amplitudes[1].snr)
self.assertEqual(read_cat[0].amplitudes[1].category,
test_cat[0].amplitudes[1].category)
# Check the read-write s-file functionality
sfile = eventtosfile(test_cat[0], userID='TEST',
evtype='L', outdir='.',
wavefiles='test', explosion=True, overwrite=True)
del read_cat
self.assertEqual(readwavename(sfile), ['test'])
read_cat = Catalog()
read_cat += readpicks(sfile)
os.remove(sfile)
for i in range(len(read_cat[0].picks)):
self.assertEqual(read_cat[0].picks[i].time,
test_cat[0].picks[i].time)
self.assertEqual(read_cat[0].picks[i].backazimuth,
test_cat[0].picks[i].backazimuth)
self.assertEqual(read_cat[0].picks[i].onset,
test_cat[0].picks[i].onset)
self.assertEqual(read_cat[0].picks[i].phase_hint,
test_cat[0].picks[i].phase_hint)
self.assertEqual(read_cat[0].picks[i].polarity,
test_cat[0].picks[i].polarity)
self.assertEqual(read_cat[0].picks[i].waveform_id.station_code,
test_cat[0].picks[i].waveform_id.station_code)
self.assertEqual(read_cat[0].picks[i].waveform_id.channel_code[-1],
test_cat[0].picks[i].waveform_id.channel_code[-1])
# assert read_cat[0].origins[0].resource_id ==\
# test_cat[0].origins[0].resource_id
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residual_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(read_cat[0].magnitudes[0].mag,
test_cat[0].magnitudes[0].mag)
self.assertEqual(read_cat[0].magnitudes[1].mag,
test_cat[0].magnitudes[1].mag)
self.assertEqual(read_cat[0].magnitudes[2].mag,
test_cat[0].magnitudes[2].mag)
self.assertEqual(read_cat[0].magnitudes[0].creation_info,
test_cat[0].magnitudes[0].creation_info)
self.assertEqual(read_cat[0].magnitudes[1].creation_info,
test_cat[0].magnitudes[1].creation_info)
self.assertEqual(read_cat[0].magnitudes[2].creation_info,
test_cat[0].magnitudes[2].creation_info)
self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
test_cat[0].magnitudes[0].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
test_cat[0].magnitudes[1].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
test_cat[0].magnitudes[2].magnitude_type)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# assert read_cat[0].amplitudes[0].resource_id ==\
# test_cat[0].amplitudes[0].resource_id
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].snr,
test_cat[0].amplitudes[0].snr)
# Check coda magnitude pick
# Resource ids get overwritten because you can't have two the same in
# memory
# self.assertEqual(read_cat[0].amplitudes[1].resource_id,
# test_cat[0].amplitudes[1].resource_id)
self.assertEqual(read_cat[0].amplitudes[1].type,
test_cat[0].amplitudes[1].type)
self.assertEqual(read_cat[0].amplitudes[1].unit,
test_cat[0].amplitudes[1].unit)
self.assertEqual(read_cat[0].amplitudes[1].generic_amplitude,
test_cat[0].amplitudes[1].generic_amplitude)
# Resource ids get overwritten because you can't have two the same in
# memory
# self.assertEqual(read_cat[0].amplitudes[1].pick_id,
# test_cat[0].amplitudes[1].pick_id)
self.assertEqual(read_cat[0].amplitudes[1].waveform_id.station_code,
test_cat[0].amplitudes[1].waveform_id.station_code)
self.assertEqual(read_cat[0].amplitudes[1].waveform_id.channel_code,
test_cat[0].amplitudes[1].
waveform_id.channel_code[0] +
test_cat[0].amplitudes[1].
waveform_id.channel_code[-1])
self.assertEqual(read_cat[0].amplitudes[1].magnitude_hint,
test_cat[0].amplitudes[1].magnitude_hint)
# snr is not supported in s-file
# self.assertEqual(read_cat[0].amplitudes[1].snr,
# test_cat[0].amplitudes[1].snr)
self.assertEqual(read_cat[0].amplitudes[1].category,
test_cat[0].amplitudes[1].category)
del read_cat
# Test a deliberate fail
test_cat.append(full_test_event())
with self.assertRaises(IOError):
# Raises error due to multiple events in catalog
sfile = eventtosfile(test_cat, userID='TEST',
evtype='L', outdir='.',
wavefiles='test', explosion=True,
overwrite=True)
# Raises error due to too long userID
sfile = eventtosfile(test_cat[0], userID='TESTICLE',
evtype='L', outdir='.',
wavefiles='test', explosion=True,
overwrite=True)
# Raises error due to unrecognised event type
sfile = eventtosfile(test_cat[0], userID='TEST',
evtype='U', outdir='.',
wavefiles='test', explosion=True,
overwrite=True)
# Raises error due to no output directory
sfile = eventtosfile(test_cat[0], userID='TEST',
evtype='L', outdir='albatross',
wavefiles='test', explosion=True,
overwrite=True)
# Raises error due to incorrect wavefil formatting
sfile = eventtosfile(test_cat[0], userID='TEST',
evtype='L', outdir='.',
wavefiles=1234, explosion=True,
overwrite=True)
with self.assertRaises(IndexError):
invalid_origin = test_cat[0].copy()
invalid_origin.origins = []
sfile = eventtosfile(invalid_origin, userID='TEST',
evtype='L', outdir='.',
wavefiles='test', explosion=True,
overwrite=True)
with self.assertRaises(ValueError):
invalid_origin = test_cat[0].copy()
invalid_origin.origins[0].time = None
sfile = eventtosfile(invalid_origin, userID='TEST',
evtype='L', outdir='.',
wavefiles='test', explosion=True,
overwrite=True)
# Write a near empty origin
valid_origin = test_cat[0].copy()
valid_origin.origins[0].latitude = None
valid_origin.origins[0].longitude = None
valid_origin.origins[0].depth = None
sfile = eventtosfile(valid_origin, userID='TEST',
evtype='L', outdir='.',
wavefiles='test', explosion=True,
overwrite=True)
self.assertTrue(os.path.isfile(sfile))
os.remove(sfile)
def write_correlations(event_list, wavbase, extract_len, pre_pick, shift_len,
lowcut=1.0, highcut=10.0, max_sep=4, min_link=8,
coh_thresh=0.0, coherence_weight=True, plotvar=False):
"""
Function to write a dt.cc file for hypoDD input - takes an input list of
events and computes pick refienements by correlation.
:type event_list: list of tuple
:param event_list: List of tuples of event_id (int) and sfile (String)
:type wavbase: str
:param wavbase: Path to the seisan wave directory that the wavefiles in the
S-files are stored
:type extract_len: float
:param extract_len: Length in seconds to extract around the pick
:type pre_pick: float
:param pre_pick: Time before the pick to start the correlation window
:type shift_len: float
:param shift_len: Time to allow pick to vary
:type lowcut: float
:param lowcut: Lowcut in Hz - default=1.0
:type highcut: float
:param highcut: Highcut in Hz - deafult=10.0
:type max_sep: float
:param max_sep: Maximum seperation between event pairs in km
:type min_link: int
:param min_link: Minimum links for an event to be paired
:type coherence_weight: bool
:param coherence_weight: Use coherence to weight the dt.cc file, or the \
raw cross-correlation value, defaults to false which uses the cross-\
correlation value.
:type plotvar: bool
:param plotvar: To show the pick-correction plots, defualts to False.
.. warning:: This is not a fast routine!
.. warning:: In contrast to seisan's \
corr routine, but in accordance with the hypoDD manual, this outputs \
corrected differential time.
.. note:: Currently we have not implemented a method for taking \
unassociated event objects and wavefiles. As such if you have events \
with associated wavefiles you are advised to generate Sfiles for each \
event using the sfile_util module prior to this step.
"""
import obspy
if int(obspy.__version__.split('.')[0]) > 0:
from obspy.signal.cross_correlation import xcorr_pick_correction
else:
from obspy.signal.cross_correlation import xcorrPickCorrection \
as xcorr_pick_correction
import matplotlib.pyplot as plt
from obspy import read
from eqcorrscan.utils.mag_calc import dist_calc
import glob
import warnings
corr_list = []
f = open('dt.cc', 'w')
f2 = open('dt.cc2', 'w')
for i, master in enumerate(event_list):
master_sfile = master[1]
master_event_id = master[0]
master_picks = sfile_util.readpicks(master_sfile).picks
master_event = sfile_util.readheader(master_sfile)
master_ori_time = master_event.origins[0].time
master_location = (master_event.origins[0].latitude,
master_event.origins[0].longitude,
master_event.origins[0].depth)
master_wavefiles = sfile_util.readwavename(master_sfile)
masterpath = glob.glob(wavbase + os.sep + master_wavefiles[0])
if masterpath:
masterstream = read(masterpath[0])
if len(master_wavefiles) > 1:
for wavefile in master_wavefiles:
try:
masterstream += read(os.join(wavbase, wavefile))
except:
continue
raise IOError("Couldn't find wavefile")
for j in range(i+1, len(event_list)):
# Use this tactic to only output unique event pairings
slave_sfile = event_list[j][1]
slave_event_id = event_list[j][0]
slave_wavefiles = sfile_util.readwavename(slave_sfile)
try:
# slavestream=read(wavbase+'/*/*/'+slave_wavefiles[0])
slavestream = read(wavbase + os.sep + slave_wavefiles[0])
except:
# print(slavestream)
raise IOError('No wavefile found: '+slave_wavefiles[0]+' ' +
slave_sfile)
if len(slave_wavefiles) > 1:
for wavefile in slave_wavefiles:
# slavestream+=read(wavbase+'/*/*/'+wavefile)
try:
slavestream += read(wavbase+'/'+wavefile)
except:
continue
# Write out the header line
event_text = '#'+str(master_event_id).rjust(10) +\
str(slave_event_id).rjust(10)+' 0.0 \n'
event_text2 = '#'+str(master_event_id).rjust(10) +\
str(slave_event_id).rjust(10)+' 0.0 \n'
slave_picks = sfile_util.readpicks(slave_sfile).picks
slave_event = sfile_util.readheader(slave_sfile)
slave_ori_time = slave_event.origins[0].time
slave_location = (slave_event.origins[0].latitude,
slave_event.origins[0].longitude,
slave_event.origins[0].depth)
if dist_calc(master_location, slave_location) > max_sep:
continue
links = 0
phases = 0
for pick in master_picks:
if pick.phase_hint[0].upper() not in ['P', 'S']:
continue
# Only use P and S picks, not amplitude or 'other'
# Find station, phase pairs
# Added by Carolin
slave_matches = [p for p in slave_picks
if p.phase_hint == pick.phase_hint
and p.waveform_id.station_code ==
pick.waveform_id.station_code]
if masterstream.select(station=pick.waveform_id.station_code,
channel='*' +
pick.waveform_id.channel_code[-1]):
mastertr = masterstream.\
select(station=pick.waveform_id.station_code,
channel='*' +
pick.waveform_id.channel_code[-1])[0]
else:
print('No waveform data for ' +
pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code)
print(pick.waveform_id.station_code +
'.' + pick.waveform_id.channel_code +
' ' + slave_sfile+' ' + master_sfile)
break
# Loop through the matches
for slave_pick in slave_matches:
if slavestream.select(station=slave_pick.waveform_id.
station_code,
channel='*'+slave_pick.waveform_id.
channel_code[-1]):
slavetr = slavestream.\
select(station=slave_pick.waveform_id.station_code,
channel='*'+slave_pick.waveform_id.
channel_code[-1])[0]
else:
print('No slave data for ' +
slave_pick.waveform_id.station_code + '.' +
slave_pick.waveform_id.channel_code)
print(pick.waveform_id.station_code +
'.' + pick.waveform_id.channel_code +
' ' + slave_sfile + ' ' + master_sfile)
break
# Correct the picks
try:
correction, cc =\
xcorr_pick_correction(pick.time, mastertr,
slave_pick.time,
slavetr, pre_pick,
extract_len - pre_pick,
shift_len, filter="bandpass",
filter_options={'freqmin':
lowcut,
'freqmax':
highcut},
plot=plotvar)
# Get the differntial travel time using the
# corrected time.
# Check that the correction is within the allowed shift
# This can occur in the obspy routine when the
# correlation function is increasing at the end of the
# window.
if abs(correction) > shift_len:
warnings.warn('Shift correction too large, ' +
'will not use')
continue
correction = (pick.time - master_ori_time) -\
(slave_pick.time + correction - slave_ori_time)
links += 1
if cc * cc >= coh_thresh:
if coherence_weight:
weight = cc * cc
else:
weight = cc
phases += 1
# added by Caro
event_text += pick.waveform_id.station_code.\
ljust(5) + _cc_round(correction, 3).\
rjust(11) + _cc_round(weight, 3).rjust(8) +\
' '+pick.phase_hint+'\n'
event_text2 += pick.waveform_id.station_code\
.ljust(5).upper() +\
_cc_round(correction, 3).rjust(11) +\
_cc_round(weight, 3).rjust(8) +\
' '+pick.phase_hint+'\n'
# links+=1
corr_list.append(cc*cc)
except:
# Should warn here
msg = "Couldn't compute correlation correction"
warnings.warn(msg)
continue
if links >= min_link and phases > 0:
f.write(event_text)
f2.write(event_text2)
if plotvar:
plt.hist(corr_list, 150)
plt.show()
# f.write('\n')
f.close()
f2.close()
return
def Amp_pick_sfile(sfile, datapath, respdir, chans=['Z'], var_wintype=True,
winlen=0.9, pre_pick=0.2, pre_filt=True, lowcut=1.0,
highcut=20.0, corners=4):
"""
Function to read information from a SEISAN s-file, load the data and the \
picks, cut the data for the channels given around the S-window, simulate \
a Wood Anderson seismometer, then pick the maximum peak-to-trough \
amplitude.
Output will be put into a mag_calc.out file which will be in full S-file \
format and can be copied to a REA database.
:type sfile: string
:type datapath: string
:param datapath: Path to the waveform files - usually the path to the WAV \
directory
:type respdir: string
:param respdir: Path to the response information directory
:type chans: List of strings
:param chans: List of the channels to pick on, defaults to ['Z'] - should \
just be the orientations, e.g. Z,1,2,N,E
:type var_wintype: bool
:param var_wintype: If True, the winlen will be \
multiplied by the P-S time if both P and S picks are \
available, otherwise it will be multiplied by the \
hypocentral distance*0.34 - dervided using a p-s ratio of \
1.68 and S-velocity of 1.5km/s to give a large window, \
defaults to True
:type winlen: float
:param winlen: Length of window, see above parameter, if var_wintype is \
False then this will be in seconds, otherwise it is the \
multiplier to the p-s time, defaults to 0.5.
:type pre_pick: float
:param pre_pick: Time before the s-pick to start the cut window, defaults \
to 0.2
:type pre_filt: bool
:param pre_filt: To apply a pre-filter or not, defaults to True
:type lowcut: float
:param lowcut: Lowcut in Hz for the pre-filter, defaults to 1.0
:type highcut: float
:param highcut: Highcut in Hz for the pre-filter, defaults to 20.0
:type corners: int
:param corners: Number of corners to use in the pre-filter
"""
# Hardwire a p-s multiplier of hypocentral distance based on p-s ratio of
# 1.68 and an S-velocity 0f 1.5km/s, deliberately chosen to be quite slow
ps_multiplier = 0.34
from eqcorrscan.utils import sfile_util
from obspy import read
from scipy.signal import iirfilter
from obspy.signal.invsim import paz2AmpValueOfFreqResp
import warnings
# First we need to work out what stations have what picks
event = sfile_util.readpicks(sfile)[0]
# Convert these picks into a lists
stations = [] # List of stations
channels = [] # List of channels
picktimes = [] # List of pick times
picktypes = [] # List of pick types
distances = [] # List of hypocentral distances
picks_out = []
for pick in event.picks:
if pick.phase_hint in ['P', 'S']:
picks_out.append(pick) # Need to be able to remove this if there
# isn't data for a station!
stations.append(pick.waveform_id.station_code)
channels.append(pick.waveform_id.channel_code)
picktimes.append(pick.time)
picktypes.append(pick.phase_hint)
arrival = [arrival for arrival in event.origins[0].arrivals
if arrival.pick_id == pick.resource_id]
distances.append(arrival.distance)
# Read in waveforms
stream = read(datapath+'/'+sfile_util.readwavename(sfile)[0])
if len(sfile_util.readwavename(sfile)) > 1:
for wavfile in sfile_util.readwavename(sfile):
stream += read(datapath+'/'+wavfile)
stream.merge() # merge the data, just in case!
# For each station cut the window
uniq_stas = list(set(stations))
del arrival
for sta in uniq_stas:
for chan in chans:
print('Working on '+sta+' '+chan)
tr = stream.select(station=sta, channel='*'+chan)
if not tr:
# Remove picks from file
# picks_out=[picks_out[i] for i in xrange(len(picks))\
# if picks_out[i].station+picks_out[i].channel != \
# sta+chan]
warnings.warn('There is no station and channel match in the ' +
'wavefile!')
break
else:
tr = tr[0]
# Apply the pre-filter
if pre_filt:
try:
tr.detrend('simple')
except:
dummy = tr.split()
dummy.detrend('simple')
tr = dummy.merge()[0]
tr.filter('bandpass', freqmin=lowcut, freqmax=highcut,
corners=corners)
sta_picks = [i for i in xrange(len(stations))
if stations[i] == sta]
pick_id = event.picks[sta_picks[0]].resource_id
arrival = [arrival for arrival in event.origins[0].arrivals
if arrival.pick_id == pick_id]
hypo_dist = arrival.distance
CAZ = arrival.azimuth
if var_wintype:
if 'S' in [picktypes[i] for i in sta_picks] and\
'P' in [picktypes[i] for i in sta_picks]:
# If there is an S-pick we can use this :D
S_pick = [picktimes[i] for i in sta_picks
if picktypes[i] == 'S']
S_pick = min(S_pick)
P_pick = [picktimes[i] for i in sta_picks
if picktypes[i] == 'P']
P_pick = min(P_pick)
try:
tr.trim(starttime=S_pick-pre_pick,
endtime=S_pick+(S_pick-P_pick)*winlen)
except:
break
elif 'S' in [picktypes[i] for i in sta_picks]:
S_pick = [picktimes[i] for i in sta_picks
if picktypes[i] == 'S']
S_pick = min(S_pick)
P_modelled = S_pick - hypo_dist * ps_multiplier
try:
tr.trim(starttime=S_pick-pre_pick,
endtime=S_pick + (S_pick - P_modelled) *
winlen)
except:
break
else:
# In this case we only have a P pick
P_pick = [picktimes[i] for i in sta_picks
if picktypes[i] == 'P']
P_pick = min(P_pick)
S_modelled = P_pick + hypo_dist * ps_multiplier
try:
tr.trim(starttime=S_modelled - pre_pick,
endtime=S_modelled + (S_modelled - P_pick) *
winlen)
except:
break
# Work out the window length based on p-s time or distance
elif 'S' in [picktypes[i] for i in sta_picks]:
# If the window is fixed we still need to find the start time,
# which can be based either on the S-pick (this elif), or
# on the hypocentral distance and the P-pick
# Take the minimum S-pick time if more than one S-pick is
# available
S_pick = [picktimes[i] for i in sta_picks
if picktypes[i] == 'S']
S_pick = min(S_pick)
try:
tr.trim(starttime=S_pick - pre_pick,
endtime=S_pick + winlen)
except:
break
else:
# In this case, there is no S-pick and the window length is
# fixed we need to calculate an expected S_pick based on the
# hypocentral distance, this will be quite hand-wavey as we
# are not using any kind of velocity model.
P_pick = [picktimes[i] for i in sta_picks
if picktypes[i] == 'P']
P_pick = min(P_pick)
hypo_dist = [distances[i] for i in sta_picks
if picktypes[i] == 'P'][0]
S_modelled = P_pick + hypo_dist * ps_multiplier
try:
tr.trim(starttime=S_modelled - pre_pick,
endtime=S_modelled + winlen)
except:
break
# Find the response information
resp_info = _find_resp(tr.stats.station, tr.stats.channel,
tr.stats.network, tr.stats.starttime,
tr.stats.delta, respdir)
PAZ = []
seedresp = []
if resp_info and 'gain' in resp_info:
PAZ = resp_info
elif resp_info:
seedresp = resp_info
# Simulate a Wood Anderson Seismograph
if PAZ and len(tr.data) > 10:
# Set ten data points to be the minimum to pass
tr = _sim_WA(tr, PAZ, None, 10)
elif seedresp and len(tr.data) > 10:
tr = _sim_WA(tr, None, seedresp, 10)
elif len(tr.data) > 10:
warnings.warn('No PAZ for '+tr.stats.station+' ' +
tr.stats.channel+' at time: ' +
str(tr.stats.starttime))
continue
if len(tr.data) <= 10:
# Should remove the P and S picks if len(tr.data)==0
warnings.warn('No data found for: '+tr.stats.station)
# print 'No data in miniseed file for '+tr.stats.station+\
# ' removing picks'
# picks_out=[picks_out[i] for i in xrange(len(picks_out))\
# if i not in sta_picks]
break
# Get the amplitude
amplitude, period, delay = _max_p2t(tr.data, tr.stats.delta)
if amplitude == 0.0:
break
print('Amplitude picked: ' + str(amplitude))
# Note, amplitude should be in meters at the moment!
# Remove the pre-filter response
if pre_filt:
# Generate poles and zeros for the filter we used earlier: this
# is how the filter is designed in the convenience methods of
# filtering in obspy.
z, p, k = iirfilter(corners, [lowcut / (0.5 *
tr.stats.
sampling_rate),
highcut / (0.5 *
tr.stats.
sampling_rate)],
btype='band', ftype='butter', output='zpk')
filt_paz = {'poles': list(p),
'zeros': list(z),
'gain': k,
'sensitivity': 1.0}
amplitude /= (paz2AmpValueOfFreqResp(filt_paz, 1 / period) *
filt_paz['sensitivity'])
# Convert amplitude to mm
if PAZ: # Divide by Gain to get to nm (returns pm? 10^-12)
# amplitude *=PAZ['gain']
amplitude /= 1000
if seedresp: # Seedresp method returns mm
amplitude *= 1000000
# Write out the half amplitude, approximately the peak amplitude as
# used directly in magnitude calculations
# Page 343 of Seisan manual:
# Amplitude (Zero-Peak) in units of nm, nm/s, nm/s^2 or counts
amplitude *= 0.5
# Generate a PICK type object for this pick
picks_out.append(sfile_util.PICK(station=tr.stats.station,
channel=tr.stats.channel,
impulsivity=' ',
phase='IAML',
weight='', polarity=' ',
time=tr.stats.starttime+delay,
coda=999, amplitude=amplitude,
peri=period, azimuth=float('NaN'),
velocity=float('NaN'), AIN=999,
SNR='',
azimuthres=999,
timeres=float('NaN'),
finalweight=999,
distance=hypo_dist,
CAZ=CAZ))
# Copy the header from the sfile to a new local S-file
fin = open(sfile, 'r')
fout = open('mag_calc.out', 'w')
for line in fin:
if not line[79] == '7':
fout.write(line)
else:
fout.write(line)
break
fin.close()
for pick in picks_out:
fout.write(pick)
# Note this uses the legacy pick class
fout.close()
# Write picks out to new s-file
for pick in picks_out:
print(pick)
# sfile_util.populatesfile('mag_calc.out', picks_out)
return picks_out
def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin,
prepick=0.05, debug=0, plot=False):
r"""Function to read in picks from sfile then generate the template from \
the picks within this and the wavefile found in the pick file.
:type sfile: string
:param sfile: sfilename must be the \
path to a seisan nordic type s-file containing waveform and pick \
information.
:type lowcut: float
:param lowcut: Low cut (Hz), if set to None will look in template \
defaults file
:type highcut: float
:param highcut: High cut (Hz), if set to None will look in template \
defaults file
:type samp_rate: float
:param samp_rate: New sampling rate in Hz, if set to None will look in \
template defaults file
:type filt_order: int
:param filt_order: Filter level, if set to None will look in \
template defaults file
:type swin: str
:param swin: Either 'all', 'P' or 'S', to select which phases to output.
:type length: float
:param length: Extract length in seconds, if None will look in template \
defaults file.
:type prepick: float
:param prepick: Length to extract prior to the pick in seconds.
:type debug: int
:param debug: Debug level, higher number=more output.
:type plot: bool
:param plot: Turns template plotting on or off.
:returns: obspy.Stream Newly cut template
.. warning:: This will use whatever data is pointed to in the s-file, if \
this is not the coninuous data, we recommend using other functions. \
Differences in processing between short files and day-long files \
(inherent to resampling) will produce lower cross-correlations.
"""
# Perform some checks first
import os
if not os.path.isfile(sfile):
raise IOError('sfile does not exist')
from eqcorrscan.utils import pre_processing
from eqcorrscan.utils import sfile_util
from obspy import read as obsread
# Read in the header of the sfile
wavefiles = sfile_util.readwavename(sfile)
pathparts = sfile.split('/')[0:-1]
new_path_parts = []
for part in pathparts:
if part == 'REA':
part = 'WAV'
new_path_parts.append(part)
# * argument to allow .join() to accept a list
wavpath = os.path.join(*new_path_parts) + '/'
# In case of absolute paths (not handled with .split() --> .join())
if sfile[0] == '/':
wavpath = '/' + wavpath
# Read in waveform file
for wavefile in wavefiles:
print(''.join(["I am going to read waveform data from: ", wavpath,
wavefile]))
if 'st' not in locals():
st = obsread(wavpath + wavefile)
else:
st += obsread(wavpath + wavefile)
for tr in st:
if tr.stats.sampling_rate < samp_rate:
print('Sampling rate of data is lower than sampling rate asked ' +
'for')
print('Not good practice for correlations: I will not do this')
raise ValueError("Trace: " + tr.stats.station +
" sampling rate: " + str(tr.stats.sampling_rate))
# Read in pick info
catalog = sfile_util.readpicks(sfile)
# Read the list of Picks for this event
picks = catalog[0].picks
print("I have found the following picks")
for pick in picks:
print(' '.join([pick.waveform_id.station_code,
pick.waveform_id.channel_code, pick.phase_hint,
str(pick.time)]))
# Process waveform data
st.merge(fill_value='interpolate')
st = pre_processing.shortproc(st, lowcut, highcut, filt_order,
samp_rate, debug)
st1 = _template_gen(picks=picks, st=st, length=length, swin=swin,
prepick=prepick, plot=plot, debug=debug)
return st1
def write_correlations(event_list,
wavbase,
extract_len,
pre_pick,
shift_len,
lowcut=1.0,
highcut=10.0,
max_sep=8,
min_link=8,
cc_thresh=0.0,
plotvar=False,
debug=0):
"""
Write a dt.cc file for hypoDD input for a given list of events.
Takes an input list of events and computes pick refinements by correlation.
Outputs two files, dt.cc and dt.cc2, each provides a different weight,
dt.cc uses weights of the cross-correlation, and dt.cc2 provides weights
as the square of the cross-correlation.
:type event_list: list
:param event_list: List of tuples of event_id (int) and sfile (String)
:type wavbase: str
:param wavbase: Path to the seisan wave directory that the wavefiles in the
S-files are stored
:type extract_len: float
:param extract_len: Length in seconds to extract around the pick
:type pre_pick: float
:param pre_pick: Time before the pick to start the correlation window
:type shift_len: float
:param shift_len: Time to allow pick to vary
:type lowcut: float
:param lowcut: Lowcut in Hz - default=1.0
:type highcut: float
:param highcut: Highcut in Hz - default=10.0
:type max_sep: float
:param max_sep: Maximum separation between event pairs in km
:type min_link: int
:param min_link: Minimum links for an event to be paired
:type cc_thresh: float
:param cc_thresh: Threshold to include cross-correlation results.
:type plotvar: bool
:param plotvar: To show the pick-correction plots, defualts to False.
:type debug: int
:param debug: Variable debug levels from 0-5, higher=more output.
.. warning:: This is not a fast routine!
.. warning::
In contrast to seisan's corr routine, but in accordance with the
hypoDD manual, this outputs corrected differential time.
.. note::
Currently we have not implemented a method for taking
unassociated event objects and wavefiles. As such if you have events \
with associated wavefiles you are advised to generate Sfiles for each \
event using the sfile_util module prior to this step.
.. note::
There is no provision to taper waveforms within these functions, if you
desire this functionality, you should apply the taper before calling
this. Note the :func:`obspy.Trace.taper` functions.
"""
from obspy.signal.cross_correlation import xcorr_pick_correction
warnings.filterwarnings(action="ignore",
message="Maximum of cross correlation " +
"lower than 0.8: *")
corr_list = []
f = open('dt.cc', 'w')
f2 = open('dt.cc2', 'w')
k_events = len(list(event_list))
for i, master in enumerate(event_list):
master_sfile = master[1]
if debug > 1:
print('Computing correlations for master: %s' % master_sfile)
master_event_id = master[0]
master_picks = sfile_util.readpicks(master_sfile).picks
master_event = sfile_util.readheader(master_sfile)
master_ori_time = master_event.origins[0].time
master_location = (master_event.origins[0].latitude,
master_event.origins[0].longitude,
master_event.origins[0].depth / 1000.0)
master_wavefiles = sfile_util.readwavename(master_sfile)
masterpath = glob.glob(wavbase + os.sep + master_wavefiles[0])
if masterpath:
masterstream = read(masterpath[0])
if len(master_wavefiles) > 1:
for wavefile in master_wavefiles:
try:
masterstream += read(os.join(wavbase, wavefile))
except:
raise IOError("Couldn't find wavefile")
continue
for j in range(i + 1, k_events):
# Use this tactic to only output unique event pairings
slave_sfile = event_list[j][1]
if debug > 2:
print('Comparing to event: %s' % slave_sfile)
slave_event_id = event_list[j][0]
slave_wavefiles = sfile_util.readwavename(slave_sfile)
try:
slavestream = read(wavbase + os.sep + slave_wavefiles[0])
except:
raise IOError('No wavefile found: ' + slave_wavefiles[0] +
' ' + slave_sfile)
if len(slave_wavefiles) > 1:
for wavefile in slave_wavefiles:
try:
slavestream += read(wavbase + os.sep + wavefile)
except IOError:
print('No waveform found: %s' %
(wavbase + os.sep + wavefile))
continue
# Write out the header line
event_text = '#' + str(master_event_id).rjust(10) +\
str(slave_event_id).rjust(10) + ' 0.0 \n'
event_text2 = '#' + str(master_event_id).rjust(10) +\
str(slave_event_id).rjust(10) + ' 0.0 \n'
slave_picks = sfile_util.readpicks(slave_sfile).picks
slave_event = sfile_util.readheader(slave_sfile)
slave_ori_time = slave_event.origins[0].time
slave_location = (slave_event.origins[0].latitude,
slave_event.origins[0].longitude,
slave_event.origins[0].depth / 1000.0)
if dist_calc(master_location, slave_location) > max_sep:
if debug > 0:
print('Seperation exceeds max_sep: %s' %
(dist_calc(master_location, slave_location)))
continue
links = 0
phases = 0
for pick in master_picks:
if not hasattr(pick, 'phase_hint') or \
len(pick.phase_hint) == 0:
warnings.warn('No phase-hint for pick:')
print(pick)
continue
if pick.phase_hint[0].upper() not in ['P', 'S']:
warnings.warn('Will only use P or S phase picks')
print(pick)
continue
# Only use P and S picks, not amplitude or 'other'
# Find station, phase pairs
# Added by Carolin
slave_matches = [
p for p in slave_picks if hasattr(p, 'phase_hint')
and p.phase_hint == pick.phase_hint and
p.waveform_id.station_code == pick.waveform_id.station_code
]
if masterstream.select(station=pick.waveform_id.station_code,
channel='*' +
pick.waveform_id.channel_code[-1]):
mastertr = masterstream.\
select(station=pick.waveform_id.station_code,
channel='*' +
pick.waveform_id.channel_code[-1])[0]
elif debug > 1:
print('No waveform data for ' +
pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code)
print(pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code + ' ' + slave_sfile +
' ' + master_sfile)
break
# Loop through the matches
for slave_pick in slave_matches:
if slavestream.select(
station=slave_pick.waveform_id.station_code,
channel='*' +
slave_pick.waveform_id.channel_code[-1]):
slavetr = slavestream.\
select(station=slave_pick.waveform_id.station_code,
channel='*' + slave_pick.waveform_id.
channel_code[-1])[0]
else:
print('No slave data for ' +
slave_pick.waveform_id.station_code + '.' +
slave_pick.waveform_id.channel_code)
print(pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code + ' ' +
slave_sfile + ' ' + master_sfile)
break
# Correct the picks
try:
correction, cc =\
xcorr_pick_correction(
pick.time, mastertr, slave_pick.time,
slavetr, pre_pick, extract_len - pre_pick,
shift_len, filter="bandpass",
filter_options={'freqmin': lowcut,
'freqmax': highcut},
plot=plotvar)
# Get the differential travel time using the
# corrected time.
# Check that the correction is within the allowed shift
# This can occur in the obspy routine when the
# correlation function is increasing at the end of the
# window.
if abs(correction) > shift_len:
warnings.warn('Shift correction too large, ' +
'will not use')
continue
correction = (pick.time - master_ori_time) -\
(slave_pick.time + correction - slave_ori_time)
links += 1
if cc >= cc_thresh:
weight = cc
phases += 1
# added by Caro
event_text += pick.waveform_id.station_code.\
ljust(5) + _cc_round(correction, 3).\
rjust(11) + _cc_round(weight, 3).rjust(8) +\
' ' + pick.phase_hint + '\n'
event_text2 += pick.waveform_id.station_code\
.ljust(5) + _cc_round(correction, 3).\
rjust(11) +\
_cc_round(weight * weight, 3).rjust(8) +\
' ' + pick.phase_hint + '\n'
if debug > 3:
print(event_text)
else:
print('cc too low: %s' % cc)
corr_list.append(cc * cc)
except:
msg = "Couldn't compute correlation correction"
warnings.warn(msg)
continue
if links >= min_link and phases > 0:
f.write(event_text)
f2.write(event_text2)
if plotvar:
plt.hist(corr_list, 150)
plt.show()
# f.write('\n')
f.close()
f2.close()
return
def test_read_write(self):
"""
Function to test the read and write capabilities of sfile_util.
"""
import os
from obspy.core.event import Catalog
import obspy
if int(obspy.__version__.split('.')[0]) >= 1:
from obspy.core.event import read_events
else:
from obspy.core.event import readEvents as read_events
# Set-up a test event
test_event = basic_test_event()
# Add the event to a catalogue which can be used for QuakeML testing
test_cat = Catalog()
test_cat += test_event
# Write the catalog
test_cat.write("Test_catalog.xml", format='QUAKEML')
# Read and check
read_cat = read_events("Test_catalog.xml")
os.remove("Test_catalog.xml")
self.assertEqual(read_cat[0].resource_id, test_cat[0].resource_id)
self.assertEqual(read_cat[0].picks, test_cat[0].picks)
self.assertEqual(read_cat[0].origins[0].resource_id,
test_cat[0].origins[0].resource_id)
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residuel_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(read_cat[0].magnitudes, test_cat[0].magnitudes)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
self.assertEqual(read_cat[0].amplitudes[0].resource_id,
test_cat[0].amplitudes[0].resource_id)
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].unit,
test_cat[0].amplitudes[0].unit)
self.assertEqual(read_cat[0].amplitudes[0].generic_amplitude,
test_cat[0].amplitudes[0].generic_amplitude)
self.assertEqual(read_cat[0].amplitudes[0].pick_id,
test_cat[0].amplitudes[0].pick_id)
self.assertEqual(read_cat[0].amplitudes[0].waveform_id,
test_cat[0].amplitudes[0].waveform_id)
# Check the read-write s-file functionality
sfile = eventtosfile(test_cat[0], userID='TEST',
evtype='L', outdir='.',
wavefiles='test', explosion=True, overwrite=True)
del read_cat
self.assertEqual(readwavename(sfile), ['test'])
read_cat = Catalog()
read_cat += readpicks(sfile)
os.remove(sfile)
self.assertEqual(read_cat[0].picks[0].time,
test_cat[0].picks[0].time)
self.assertEqual(read_cat[0].picks[0].backazimuth,
test_cat[0].picks[0].backazimuth)
self.assertEqual(read_cat[0].picks[0].onset,
test_cat[0].picks[0].onset)
self.assertEqual(read_cat[0].picks[0].phase_hint,
test_cat[0].picks[0].phase_hint)
self.assertEqual(read_cat[0].picks[0].polarity,
test_cat[0].picks[0].polarity)
self.assertEqual(read_cat[0].picks[0].waveform_id.station_code,
test_cat[0].picks[0].waveform_id.station_code)
self.assertEqual(read_cat[0].picks[0].waveform_id.channel_code[-1],
test_cat[0].picks[0].waveform_id.channel_code[-1])
# assert read_cat[0].origins[0].resource_id ==\
# test_cat[0].origins[0].resource_id
self.assertEqual(read_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residuel_RMS is not a quakeML format
self.assertEqual(read_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(read_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(read_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(read_cat[0].magnitudes[0].mag,
test_cat[0].magnitudes[0].mag)
self.assertEqual(read_cat[0].magnitudes[1].mag,
test_cat[0].magnitudes[1].mag)
self.assertEqual(read_cat[0].magnitudes[2].mag,
test_cat[0].magnitudes[2].mag)
self.assertEqual(read_cat[0].magnitudes[0].creation_info,
test_cat[0].magnitudes[0].creation_info)
self.assertEqual(read_cat[0].magnitudes[1].creation_info,
test_cat[0].magnitudes[1].creation_info)
self.assertEqual(read_cat[0].magnitudes[2].creation_info,
test_cat[0].magnitudes[2].creation_info)
self.assertEqual(read_cat[0].magnitudes[0].magnitude_type,
test_cat[0].magnitudes[0].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[1].magnitude_type,
test_cat[0].magnitudes[1].magnitude_type)
self.assertEqual(read_cat[0].magnitudes[2].magnitude_type,
test_cat[0].magnitudes[2].magnitude_type)
self.assertEqual(read_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# assert read_cat[0].amplitudes[0].resource_id ==\
# test_cat[0].amplitudes[0].resource_id
self.assertEqual(read_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(read_cat[0].amplitudes[0].snr,
test_cat[0].amplitudes[0].snr)
del read_cat
# assert read_cat[0].amplitudes[0].pick_id ==\
# test_cat[0].amplitudes[0].pick_id
# assert read_cat[0].amplitudes[0].waveform_id ==\
# test_cat[0].amplitudes[0].waveform_id
# Test the wrappers for PICK and EVENTINFO classes
picks, evinfo = eventtopick(test_cat)
# Test the conversion back
conv_cat = Catalog()
conv_cat.append(picktoevent(evinfo, picks))
self.assertEqual(conv_cat[0].picks[0].time, test_cat[0].picks[0].time)
self.assertEqual(conv_cat[0].picks[0].backazimuth,
test_cat[0].picks[0].backazimuth)
self.assertEqual(conv_cat[0].picks[0].onset,
test_cat[0].picks[0].onset)
self.assertEqual(conv_cat[0].picks[0].phase_hint,
test_cat[0].picks[0].phase_hint)
self.assertEqual(conv_cat[0].picks[0].polarity,
test_cat[0].picks[0].polarity)
self.assertEqual(conv_cat[0].picks[0].waveform_id.station_code,
test_cat[0].picks[0].waveform_id.station_code)
self.assertEqual(conv_cat[0].picks[0].waveform_id.channel_code[-1],
test_cat[0].picks[0].waveform_id.channel_code[-1])
# self.assertEqual(read_cat[0].origins[0].resource_id,
# test_cat[0].origins[0].resource_id)
self.assertEqual(conv_cat[0].origins[0].time,
test_cat[0].origins[0].time)
# Note that time_residuel_RMS is not a quakeML format
self.assertEqual(conv_cat[0].origins[0].longitude,
test_cat[0].origins[0].longitude)
self.assertEqual(conv_cat[0].origins[0].latitude,
test_cat[0].origins[0].latitude)
self.assertEqual(conv_cat[0].origins[0].depth,
test_cat[0].origins[0].depth)
self.assertEqual(conv_cat[0].magnitudes[0].mag,
test_cat[0].magnitudes[0].mag)
self.assertEqual(conv_cat[0].magnitudes[1].mag,
test_cat[0].magnitudes[1].mag)
self.assertEqual(conv_cat[0].magnitudes[2].mag,
test_cat[0].magnitudes[2].mag)
self.assertEqual(conv_cat[0].magnitudes[0].creation_info,
test_cat[0].magnitudes[0].creation_info)
self.assertEqual(conv_cat[0].magnitudes[1].creation_info,
test_cat[0].magnitudes[1].creation_info)
self.assertEqual(conv_cat[0].magnitudes[2].creation_info,
test_cat[0].magnitudes[2].creation_info)
self.assertEqual(conv_cat[0].magnitudes[0].magnitude_type,
test_cat[0].magnitudes[0].magnitude_type)
self.assertEqual(conv_cat[0].magnitudes[1].magnitude_type,
test_cat[0].magnitudes[1].magnitude_type)
self.assertEqual(conv_cat[0].magnitudes[2].magnitude_type,
test_cat[0].magnitudes[2].magnitude_type)
self.assertEqual(conv_cat[0].event_descriptions,
test_cat[0].event_descriptions)
# self.assertEqual(read_cat[0].amplitudes[0].resource_id,
# test_cat[0].amplitudes[0].resource_id)
self.assertEqual(conv_cat[0].amplitudes[0].period,
test_cat[0].amplitudes[0].period)
self.assertEqual(conv_cat[0].amplitudes[0].snr,
test_cat[0].amplitudes[0].snr)
def from_sfile(sfile, lowcut, highcut, samp_rate, filt_order, length, swin,
prepick=0.05, debug=0, plot=False):
"""
Generate multiplexed template from a Nordic (Seisan) s-file.
Function to read in picks from sfile then generate the template from \
the picks within this and the wavefile found in the pick file.
:type sfile: str
:param sfile: sfilename must be the \
path to a seisan nordic type s-file containing waveform and pick \
information.
:type lowcut: float
:param lowcut: Low cut (Hz), if set to None will look in template \
defaults file
:type highcut: float
:param highcut: High cut (Hz), if set to None will look in template \
defaults file
:type samp_rate: float
:param samp_rate: New sampling rate in Hz, if set to None will look in \
template defaults file
:type filt_order: int
:param filt_order: Filter level, if set to None will look in \
template defaults file
:type swin: str
:param swin: Either 'all', 'P' or 'S', to select which phases to output.
:type length: float
:param length: Extract length in seconds, if None will look in template \
defaults file.
:type prepick: float
:param prepick: Length to extract prior to the pick in seconds.
:type debug: int
:param debug: Debug level, higher number=more output.
:type plot: bool
:param plot: Turns template plotting on or off.
:returns: obspy.core.stream.Stream Newly cut template
.. warning:: This will use whatever data is pointed to in the s-file, if \
this is not the coninuous data, we recommend using other functions. \
Differences in processing between short files and day-long files \
(inherent to resampling) will produce lower cross-correlations.
.. rubric:: Example
>>> from eqcorrscan.core.template_gen import from_sfile
>>> sfile = 'eqcorrscan/tests/test_data/REA/TEST_/01-0411-15L.S201309'
>>> template = from_sfile(sfile=sfile, lowcut=5.0, highcut=15.0,
... samp_rate=50.0, filt_order=4, swin='P',
... prepick=0.2, length=6)
>>> print(len(template))
15
>>> print(template[0].stats.sampling_rate)
50.0
>>> template.plot(equal_scale=False, size=(800,600)) # doctest: +SKIP
.. plot::
from eqcorrscan.core.template_gen import from_sfile
import os
sfile = os.path.realpath('../../..') + \
'/tests/test_data/REA/TEST_/01-0411-15L.S201309'
template = from_sfile(sfile=sfile, lowcut=5.0, highcut=15.0,
samp_rate=50.0, filt_order=4, swin='P',
prepick=0.2, length=6)
template.plot(equal_scale=False, size=(800, 600))
"""
# Perform some checks first
import os
if not os.path.isfile(sfile):
raise IOError('sfile does not exist')
from eqcorrscan.utils import pre_processing
from eqcorrscan.utils import sfile_util
from obspy import read as obsread
# Read in the header of the sfile
wavefiles = sfile_util.readwavename(sfile)
pathparts = sfile.split('/')[0:-1]
new_path_parts = []
for part in pathparts:
if part == 'REA':
part = 'WAV'
new_path_parts.append(part)
main_wav_parts = []
for part in new_path_parts:
main_wav_parts.append(part)
if part == 'WAV':
break
mainwav = os.path.join(*main_wav_parts) + os.path.sep
# * argument to allow .join() to accept a list
wavpath = os.path.join(*new_path_parts) + os.path.sep
# In case of absolute paths (not handled with .split() --> .join())
if sfile[0] == os.path.sep:
wavpath = os.path.sep + wavpath
mainwav = os.path.sep + mainwav
# Read in waveform file
for wavefile in wavefiles:
if debug > 0:
print(''.join(["I am going to read waveform data from: ", wavpath,
wavefile]))
if 'st' not in locals():
if os.path.isfile(wavpath + wavefile):
st = obsread(wavpath + wavefile)
elif os.path.isfile(wavefile):
st = obsread(wavefile)
else:
# Read from the main WAV directory
st = obsread(mainwav + wavefile)
else:
if os.path.isfile(wavpath + wavefile):
st += obsread(wavpath + wavefile)
elif os.path.isfile(wavefile):
st += obsread(wavefile)
else:
st += obsread(mainwav + wavefile)
for tr in st:
if tr.stats.sampling_rate < samp_rate:
print('Sampling rate of data is lower than sampling rate asked ' +
'for')
print('Not good practice for correlations: I will not do this')
raise ValueError("Trace: " + tr.stats.station +
" sampling rate: " + str(tr.stats.sampling_rate))
# Read in pick info
event = sfile_util.readpicks(sfile)
# Read the list of Picks for this event
picks = event.picks
if debug > 0:
print("I have found the following picks")
for pick in picks:
print(' '.join([pick.waveform_id.station_code,
pick.waveform_id.channel_code, pick.phase_hint,
str(pick.time)]))
# Process waveform data
st.merge(fill_value='interpolate')
st = pre_processing.shortproc(st, lowcut, highcut, filt_order,
samp_rate, debug)
st1 = _template_gen(picks=picks, st=st, length=length, swin=swin,
prepick=prepick, plot=plot, debug=debug)
return st1
def amp_pick_sfile(sfile, datapath, respdir, chans=['Z'], var_wintype=True,
winlen=0.9, pre_pick=0.2, pre_filt=True, lowcut=1.0,
highcut=20.0, corners=4):
"""
Function to pick amplitudes for local magnitudes from NORDIC s-files.
Reads information from a SEISAN s-file, load the data and the \
picks, cut the data for the channels given around the S-window, simulate \
a Wood Anderson seismometer, then pick the maximum peak-to-trough \
amplitude.
Output will be put into a mag_calc.out file which will be in full S-file \
format and can be copied to a REA database.
:type sfile: str
:param sfile: Path to NORDIC format s-file
:type datapath: str
:param datapath: Path to the waveform files - usually the path to the WAV \
directory
:type respdir: str
:param respdir: Path to the response information directory
:type chans: list
:param chans: List of the channels to pick on, defaults to ['Z'] - should \
just be the orientations, e.g. Z,1,2,N,E
:type var_wintype: bool
:param var_wintype: If True, the winlen will be \
multiplied by the P-S time if both P and S picks are \
available, otherwise it will be multiplied by the \
hypocentral distance*0.34 - derived using a p-s ratio of \
1.68 and S-velocity of 1.5km/s to give a large window, \
defaults to True
:type winlen: float
:param winlen: Length of window, see above parameter, if var_wintype is \
False then this will be in seconds, otherwise it is the \
multiplier to the p-s time, defaults to 0.5.
:type pre_pick: float
:param pre_pick: Time before the s-pick to start the cut window, defaults \
to 0.2
:type pre_filt: bool
:param pre_filt: To apply a pre-filter or not, defaults to True
:type lowcut: float
:param lowcut: Lowcut in Hz for the pre-filter, defaults to 1.0
:type highcut: float
:param highcut: Highcut in Hz for the pre-filter, defaults to 20.0
:type corners: int
:param corners: Number of corners to use in the pre-filter
:returns: obspy.core.event
"""
from eqcorrscan.utils import sfile_util
from obspy import read
import shutil
# First we need to work out what stations have what picks
event = sfile_util.readpicks(sfile)
# Read in waveforms
stream = read(datapath+'/'+sfile_util.readwavename(sfile)[0])
if len(sfile_util.readwavename(sfile)) > 1:
for wavfile in sfile_util.readwavename(sfile):
stream += read(datapath+'/'+wavfile)
stream.merge() # merge the data, just in case!
event_picked = amp_pick_event(event=event, st=stream, respdir=respdir,
chans=chans, var_wintype=var_wintype,
winlen=winlen, pre_pick=pre_pick,
pre_filt=pre_filt, lowcut=lowcut,
highcut=highcut, corners=corners)
new_sfile = sfile_util.eventtosfile(event=event, userID=str('EQCO'),
evtype=str('L'), outdir=str('.'),
wavefiles=sfile_util.
readwavename(sfile))
shutil.move(new_sfile, 'mag_calc.out')
return event
def amp_pick_sfile(sfile,
datapath,
respdir,
chans=['Z'],
var_wintype=True,
winlen=0.9,
pre_pick=0.2,
pre_filt=True,
lowcut=1.0,
highcut=20.0,
corners=4):
"""
Function to pick amplitudes for local magnitudes from NORDIC s-files.
Reads information from a SEISAN s-file, load the data and the \
picks, cut the data for the channels given around the S-window, simulate \
a Wood Anderson seismometer, then pick the maximum peak-to-trough \
amplitude.
Output will be put into a mag_calc.out file which will be in full S-file \
format and can be copied to a REA database.
:type sfile: str
:param sfile: Path to NORDIC format s-file
:type datapath: str
:param datapath: Path to the waveform files - usually the path to the WAV \
directory
:type respdir: str
:param respdir: Path to the response information directory
:type chans: list
:param chans: List of the channels to pick on, defaults to ['Z'] - should \
just be the orientations, e.g. Z,1,2,N,E
:type var_wintype: bool
:param var_wintype: If True, the winlen will be \
multiplied by the P-S time if both P and S picks are \
available, otherwise it will be multiplied by the \
hypocentral distance*0.34 - derived using a p-s ratio of \
1.68 and S-velocity of 1.5km/s to give a large window, \
defaults to True
:type winlen: float
:param winlen: Length of window, see above parameter, if var_wintype is \
False then this will be in seconds, otherwise it is the \
multiplier to the p-s time, defaults to 0.5.
:type pre_pick: float
:param pre_pick: Time before the s-pick to start the cut window, defaults \
to 0.2
:type pre_filt: bool
:param pre_filt: To apply a pre-filter or not, defaults to True
:type lowcut: float
:param lowcut: Lowcut in Hz for the pre-filter, defaults to 1.0
:type highcut: float
:param highcut: Highcut in Hz for the pre-filter, defaults to 20.0
:type corners: int
:param corners: Number of corners to use in the pre-filter
:returns: obspy.core.event
"""
from eqcorrscan.utils import sfile_util
from obspy import read
import shutil
# First we need to work out what stations have what picks
event = sfile_util.readpicks(sfile)
# Read in waveforms
stream = read(datapath + '/' + sfile_util.readwavename(sfile)[0])
if len(sfile_util.readwavename(sfile)) > 1:
for wavfile in sfile_util.readwavename(sfile):
stream += read(datapath + '/' + wavfile)
stream.merge() # merge the data, just in case!
event_picked = amp_pick_event(event=event,
st=stream,
respdir=respdir,
chans=chans,
var_wintype=var_wintype,
winlen=winlen,
pre_pick=pre_pick,
pre_filt=pre_filt,
lowcut=lowcut,
highcut=highcut,
corners=corners)
new_sfile = sfile_util.eventtosfile(
event=event,
userID=str('EQCO'),
evtype=str('L'),
outdir=str('.'),
wavefiles=sfile_util.readwavename(sfile))
shutil.move(new_sfile, 'mag_calc.out')
return event
def write_correlations(event_list,
wavbase,
extract_len,
pre_pick,
shift_len,
lowcut=1.0,
highcut=10.0,
max_sep=4,
min_link=8,
coh_thresh=0.0,
coherence_weight=True,
plotvar=False):
"""
Function to write a dt.cc file for hypoDD input - takes an input list of
events and computes pick refienements by correlation.
:type event_list: list of tuple
:param event_list: List of tuples of event_id (int) and sfile (String)
:type wavbase: str
:param wavbase: Path to the seisan wave directory that the wavefiles in the
S-files are stored
:type extract_len: float
:param extract_len: Length in seconds to extract around the pick
:type pre_pick: float
:param pre_pick: Time before the pick to start the correlation window
:type shift_len: float
:param shift_len: Time to allow pick to vary
:type lowcut: float
:param lowcut: Lowcut in Hz - default=1.0
:type highcut: float
:param highcut: Highcut in Hz - deafult=10.0
:type max_sep: float
:param max_sep: Maximum seperation between event pairs in km
:type min_link: int
:param min_link: Minimum links for an event to be paired
:type coherence_weight: bool
:param coherence_weight: Use coherence to weight the dt.cc file, or the \
raw cross-correlation value, defaults to false which uses the cross-\
correlation value.
:type plotvar: bool
:param plotvar: To show the pick-correction plots, defualts to False.
.. warning:: This is not a fast routine!
.. warning:: In contrast to seisan's \
corr routine, but in accordance with the hypoDD manual, this outputs \
corrected differential time.
.. note:: Currently we have not implemented a method for taking \
unassociated event objects and wavefiles. As such if you have events \
with associated wavefiles you are advised to generate Sfiles for each \
event using the sfile_util module prior to this step.
"""
import obspy
if int(obspy.__version__.split('.')[0]) > 0:
from obspy.signal.cross_correlation import xcorr_pick_correction
else:
from obspy.signal.cross_correlation import xcorrPickCorrection \
as xcorr_pick_correction
import matplotlib.pyplot as plt
from obspy import read
from eqcorrscan.utils.mag_calc import dist_calc
import glob
import warnings
corr_list = []
f = open('dt.cc', 'w')
f2 = open('dt.cc2', 'w')
for i, master in enumerate(event_list):
master_sfile = master[1]
master_event_id = master[0]
master_picks = sfile_util.readpicks(master_sfile).picks
master_event = sfile_util.readheader(master_sfile)
master_ori_time = master_event.origins[0].time
master_location = (master_event.origins[0].latitude,
master_event.origins[0].longitude,
master_event.origins[0].depth)
master_wavefiles = sfile_util.readwavename(master_sfile)
masterpath = glob.glob(wavbase + os.sep + master_wavefiles[0])
if masterpath:
masterstream = read(masterpath[0])
if len(master_wavefiles) > 1:
for wavefile in master_wavefiles:
try:
masterstream += read(os.join(wavbase, wavefile))
except:
continue
raise IOError("Couldn't find wavefile")
for j in range(i + 1, len(event_list)):
# Use this tactic to only output unique event pairings
slave_sfile = event_list[j][1]
slave_event_id = event_list[j][0]
slave_wavefiles = sfile_util.readwavename(slave_sfile)
try:
# slavestream=read(wavbase+'/*/*/'+slave_wavefiles[0])
slavestream = read(wavbase + os.sep + slave_wavefiles[0])
except:
# print(slavestream)
raise IOError('No wavefile found: ' + slave_wavefiles[0] +
' ' + slave_sfile)
if len(slave_wavefiles) > 1:
for wavefile in slave_wavefiles:
# slavestream+=read(wavbase+'/*/*/'+wavefile)
try:
slavestream += read(wavbase + '/' + wavefile)
except:
continue
# Write out the header line
event_text = '#'+str(master_event_id).rjust(10) +\
str(slave_event_id).rjust(10)+' 0.0 \n'
event_text2 = '#'+str(master_event_id).rjust(10) +\
str(slave_event_id).rjust(10)+' 0.0 \n'
slave_picks = sfile_util.readpicks(slave_sfile).picks
slave_event = sfile_util.readheader(slave_sfile)
slave_ori_time = slave_event.origins[0].time
slave_location = (slave_event.origins[0].latitude,
slave_event.origins[0].longitude,
slave_event.origins[0].depth)
if dist_calc(master_location, slave_location) > max_sep:
continue
links = 0
phases = 0
for pick in master_picks:
if pick.phase_hint[0].upper() not in ['P', 'S']:
continue
# Only use P and S picks, not amplitude or 'other'
# Find station, phase pairs
# Added by Carolin
slave_matches = [
p for p in slave_picks
if p.phase_hint == pick.phase_hint and
p.waveform_id.station_code == pick.waveform_id.station_code
]
if masterstream.select(station=pick.waveform_id.station_code,
channel='*' +
pick.waveform_id.channel_code[-1]):
mastertr = masterstream.\
select(station=pick.waveform_id.station_code,
channel='*' +
pick.waveform_id.channel_code[-1])[0]
else:
print('No waveform data for ' +
pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code)
print(pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code + ' ' + slave_sfile +
' ' + master_sfile)
break
# Loop through the matches
for slave_pick in slave_matches:
if slavestream.select(
station=slave_pick.waveform_id.station_code,
channel='*' +
slave_pick.waveform_id.channel_code[-1]):
slavetr = slavestream.\
select(station=slave_pick.waveform_id.station_code,
channel='*'+slave_pick.waveform_id.
channel_code[-1])[0]
else:
print('No slave data for ' +
slave_pick.waveform_id.station_code + '.' +
slave_pick.waveform_id.channel_code)
print(pick.waveform_id.station_code + '.' +
pick.waveform_id.channel_code + ' ' +
slave_sfile + ' ' + master_sfile)
break
# Correct the picks
try:
correction, cc =\
xcorr_pick_correction(pick.time, mastertr,
slave_pick.time,
slavetr, pre_pick,
extract_len - pre_pick,
shift_len, filter="bandpass",
filter_options={'freqmin':
lowcut,
'freqmax':
highcut},
plot=plotvar)
# Get the differntial travel time using the
# corrected time.
# Check that the correction is within the allowed shift
# This can occur in the obspy routine when the
# correlation function is increasing at the end of the
# window.
if abs(correction) > shift_len:
warnings.warn('Shift correction too large, ' +
'will not use')
continue
correction = (pick.time - master_ori_time) -\
(slave_pick.time + correction - slave_ori_time)
links += 1
if cc * cc >= coh_thresh:
if coherence_weight:
weight = cc * cc
else:
weight = cc
phases += 1
# added by Caro
event_text += pick.waveform_id.station_code.\
ljust(5) + _cc_round(correction, 3).\
rjust(11) + _cc_round(weight, 3).rjust(8) +\
' '+pick.phase_hint+'\n'
event_text2 += pick.waveform_id.station_code\
.ljust(5).upper() +\
_cc_round(correction, 3).rjust(11) +\
_cc_round(weight, 3).rjust(8) +\
' '+pick.phase_hint+'\n'
# links+=1
corr_list.append(cc * cc)
except:
# Should warn here
msg = "Couldn't compute correlation correction"
warnings.warn(msg)
continue
if links >= min_link and phases > 0:
f.write(event_text)
f2.write(event_text2)
if plotvar:
plt.hist(corr_list, 150)
plt.show()
# f.write('\n')
f.close()
f2.close()
return