def interev_mag_sfiles(sfiles):
r"""Function to plot interevent-time versus magnitude for series of events.
**thin** Wrapper for interev_mag.
:type sfiles: list
:param sfiles: List of sfiles to read from
"""
from eqcorrscan.utils import sfile_util
times = [sfile_util.readheader(sfile)[0].origins[0].time
for sfile in sfiles]
mags = [sfile_util.readheader(sfile)[0].magnitudes[0].mag
for sfile in sfiles]
interev_mag(times, mags)
def sfiles_to_event(sfile_list):
"""
Write an event.dat file from a list of Seisan events
:type sfile_list: list
:param sfile_list: List of s-files to sort and put into the database
:returns: List of tuples of event ID (int) and Sfile name
"""
event_list = []
sort_list = [(sfile_util.readheader(sfile).origins[0].time, sfile)
for sfile in sfile_list]
sort_list.sort(key=lambda tup: tup[0])
sfile_list = [sfile[1] for sfile in sort_list]
catalog = Catalog()
for i, sfile in enumerate(sfile_list):
event_list.append((i, sfile))
catalog.append(sfile_util.readheader(sfile))
# Hand off to sister function
write_event(catalog)
return event_list
def interev_mag_sfiles(sfiles, save=False, savefile=None):
r"""Function to plot interevent-time versus magnitude for series of events.
**thin** Wrapper for interev_mag.
:type sfiles: list
:param sfiles: List of sfiles to read from
:type save: bool
:param save: False will plot to screen, true will save plot and not show \
to screen.
:type savefile: str
:param savefile: Filename to save to, required for save=True
"""
_check_save_args(save, savefile)
from eqcorrscan.utils import sfile_util
times = [
sfile_util.readheader(sfile)[0].origins[0].time for sfile in sfiles
]
mags = [
sfile_util.readheader(sfile)[0].magnitudes[0].mag for sfile in sfiles
]
interev_mag(times, mags, save, savefile)
def sfiles_to_event(sfile_list):
"""
Function to write out an event.dat file of the events
:type sfile_list: list
:param sfile_list: List of s-files to sort and put into the database
:returns: List of tuples of event ID (int) and Sfile name
"""
from obspy.core.event import Catalog
event_list = []
sort_list = [(sfile_util.readheader(sfile).origins[0].time, sfile)
for sfile in sfile_list]
sort_list.sort(key=lambda tup: tup[0])
sfile_list = [sfile[1] for sfile in sort_list]
catalog = Catalog()
for i, sfile in enumerate(sfile_list):
event_list.append((i, sfile))
catalog.append(sfile_util.readheader(sfile))
# Hand off to sister function
write_event(catalog)
return event_list
def test_write_event(self):
"""Simple test function to test the writing of events.
"""
from eqcorrscan.utils.catalog_to_dd import sfiles_to_event
from eqcorrscan.utils import sfile_util
import os
import glob
testing_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
'test_data', 'REA', 'TEST_')
sfile_list = glob.glob(os.path.join(testing_path, '*L.S??????'))
event_list = sfiles_to_event(sfile_list)
# Check that we have written a file
self.assertTrue(os.path.isfile('event.dat'))
f = open('event.dat', 'r')
for line, event in zip(f, event_list):
header = sfile_util.readheader(event[1])
event_id_input = event[0]
output_event_info = line.strip().split()
# Check that the event id's match
self.assertEqual(event_id_input, int(output_event_info[-1]))
time_string = str(header.origins[0].time.year) +\
str(header.origins[0].time.month).zfill(2) +\
str(header.origins[0].time.day).zfill(2)+' ' +\
str(header.origins[0].time.hour).rjust(2) +\
str(header.origins[0].time.minute).zfill(2) +\
str(header.origins[0].time.second).zfill(2) +\
str(header.origins[0].time.microsecond)[0:2].zfill(2)
self.assertEqual(output_event_info[0:2], time_string.split())
self.assertEqual(header.origins[0].latitude,
float(output_event_info[2]))
self.assertEqual(header.origins[0].longitude,
float(output_event_info[3]))
self.assertEqual(header.origins[0].depth / 1000,
float(output_event_info[4]))
if header.magnitudes[0]:
self.assertEqual(header.magnitudes[0].mag,
float(output_event_info[5]))
if header.origins[0].time_errors.Time_Residual_RMS:
self.assertEqual(header.origins[0].time_errors.
Time_Residual_RMS,
float(output_event_info[-2]))
f.close()
os.remove('event.dat')
def test_write_catalog(self):
"""
Simple testing function for the write_catalogue function in \
catalog_to_dd.
"""
from eqcorrscan.utils.catalog_to_dd import write_catalog
from eqcorrscan.utils.mag_calc import dist_calc
from eqcorrscan.utils import sfile_util
import glob
import os
# Set forced variables
maximum_seperation = 1 # Maximum inter-event seperation in km
minimum_links = 8 # Minimum inter-event links to generate a pair
# We have to make an event list first
testing_path = os.path.join(os.path.abspath(os.path.dirname(__file__)),
'test_data', 'REA', 'TEST_')
sfile_list = glob.glob(os.path.join(testing_path, '*L.S??????'))
event_ids = list(range(len(sfile_list)))
event_list = zip(event_ids, sfile_list)
write_catalog(event_list=event_list,
max_sep=maximum_seperation,
min_link=minimum_links)
self.assertTrue(os.path.isfile('dt.ct'))
# Check dt.ct file, should contain only a few linked events
dt_file_out = open('dt.ct', 'r')
event_pairs = []
for i, line in enumerate(dt_file_out):
if line[0] == '#':
if i != 0:
# Check the number of links
self.assertTrue(len(event_links) >= minimum_links)
# Check the distance between events
event_1_name = [event[1] for event in event_list
if event[0] ==
int(event_pair.split()[1])][0]
event_2_name = [event[1] for event in event_list
if event[0] ==
int(event_pair.split()[2])][0]
event_1 = sfile_util.readheader(event_1_name)
event_2 = sfile_util.readheader(event_2_name)
event_1_location = (event_1.origins[0].latitude,
event_1.origins[0].longitude,
event_1.origins[0].depth / 1000)
event_2_location = (event_2.origins[0].latitude,
event_2.origins[0].longitude,
event_2.origins[0].depth / 1000)
hypocentral_seperation = dist_calc(event_1_location,
event_2_location)
self.assertTrue(hypocentral_seperation <
maximum_seperation)
# Check that the differential times are accurate
event_1_picks = sfile_util.readpicks(event_1_name).picks
event_2_picks = sfile_util.readpicks(event_2_name).picks
for pick_pair in event_links:
station = pick_pair.split()[0]
event_1_travel_time_output = pick_pair.split()[1]
event_2_travel_time_output = pick_pair.split()[2]
weight = pick_pair.split()[3]
phase = pick_pair.split()[4]
# Extract the relevant pick information from the
# two sfiles
for pick in event_1_picks:
if pick.waveform_id.station_code == station:
if pick.phase_hint[0].upper() == phase:
event_1_pick = pick
for pick in event_2_picks:
if pick.waveform_id.station_code == station:
if pick.phase_hint[0].upper() == phase:
event_2_pick = pick
# Calculate the travel-time
event_1_travel_time_input = event_1_pick.time -\
event_1.origins[0].time
event_2_travel_time_input = event_2_pick.time -\
event_2.origins[0].time
self.assertEqual(event_1_travel_time_input,
float(event_1_travel_time_output))
self.assertEqual(event_2_travel_time_input,
float(event_2_travel_time_output))
event_pair = line
event_pairs.append(line)
event_links = []
else:
event_links.append(line)
self.assertTrue(os.path.isfile('phase.dat'))
dt_file_out.close()
os.remove('phase.dat')
os.remove('dt.ct')
if os.path.isfile('dt.ct2'):
os.remove('dt.ct2')
def from_contbase(sfile, contbase_list, lowcut, highcut, samp_rate, filt_order,
length, prepick, swin, debug=0, plot=False):
r"""Function to read in picks from sfile then generate the template from \
the picks within this and the wavefiles from the continous database of \
day-long files. Included is a section to sanity check that the files are \
daylong and that they start at the start of the day. You should ensure \
this is the case otherwise this may alter your data if your data are \
daylong but the headers are incorrectly set.
:type sfile: string
:param sfile: sfilename must be the path to a seisan nordic type s-file \
containing waveform and pick information, all other arguments can \
be numbers save for swin which must be either P, S or all \
(case-sensitive).
:type contbase_list: List of tuple of string
:param contbase_list: List of tuples of the form \
['path', 'type', 'network']. Where path is the path to the \
continuous database, type is the directory structure, which can be \
either Yyyyy/Rjjj.01, which is the standard IRIS Year, julian day \
structure, or, yyyymmdd which is a single directory for every day.
:type lowcut: float
:param lowcut: Low cut (Hz), if set to None will look in template \
defaults file
:type highcut: float
:param lowcut: 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 length: float
:param length: Extract length in seconds, if None will look in template \
defaults file.
:type prepick: float
:param prepick: Pre-pick time in seconds
:type swin: str
:param swin: Either 'all', 'P' or 'S', to select which phases to output.
:type debug: int
:param debug: Level of debugging output, higher=more
:type plot: bool
:param plot: Turns template plotting on or off.
:returns: obspy.Stream Newly cut template
"""
# Perform some checks first
import os
if not os.path.isfile(sfile):
raise IOError('sfile does not exist')
# import some things
from eqcorrscan.utils import pre_processing
from eqcorrscan.utils import sfile_util
import glob
from obspy import read as obsread
# Read in the header of the sfile
event = sfile_util.readheader(sfile)
day = event.origins[0].time
# Read in pick info
catalog = sfile_util.readpicks(sfile)
picks = catalog[0].picks
print("I have found the following picks")
pick_chans = []
used_picks = []
for pick in picks:
station = pick.waveform_id.station_code
channel = pick.waveform_id.channel_code
phase = pick.phase_hint
pcktime = pick.time
if station + channel not in pick_chans and phase in ['P', 'S']:
pick_chans.append(station + channel)
used_picks.append(pick)
print(pick)
# #########Left off here
for contbase in contbase_list:
if contbase[1] == 'yyyy/mm/dd':
daydir = os.path.join([str(day.year),
str(day.month).zfill(2),
str(day.day).zfill(2)])
elif contbase[1] == 'Yyyyy/Rjjj.01':
daydir = os.path.join(['Y' + str(day.year),
'R' + str(day.julday).zfill(3) +
'.01'])
elif contbase[1] == 'yyyymmdd':
daydir = day.datetime.strftime('%Y%m%d')
if 'wavefiles' not in locals():
wavefiles = (glob.glob(os.path.join([contbase[0], daydir,
'*' + station +
'.*'])))
else:
wavefiles += glob.glob(os.path.join([contbase[0], daydir,
'*' + station +
'.*']))
elif phase in ['P', 'S']:
print(' '.join(['Duplicate pick', station, channel,
phase, str(pcktime)]))
elif phase == 'IAML':
print(' '.join(['Amplitude pick', station, channel,
phase, str(pcktime)]))
picks = used_picks
wavefiles = list(set(wavefiles))
# Read in waveform file
wavefiles.sort()
for wavefile in wavefiles:
print("I am going to read waveform data from: " + wavefile)
if 'st' not in locals():
st = obsread(wavefile)
else:
st += obsread(wavefile)
# Process waveform data
st.merge(fill_value='interpolate')
for tr in st:
tr = pre_processing.dayproc(tr, lowcut, highcut, filt_order,
samp_rate, debug, day)
# Cut and extract the templates
st1 = _template_gen(picks, st, length, swin, prepick=prepick, plot=plot)
return st1
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 test_write_catalog(self):
"""
Simple testing function for the write_catalogue function in \
catalog_to_dd.
"""
self.assertTrue(os.path.isfile('dt.ct'))
# Check dt.ct file, should contain only a few linked events
dt_file_out = open('dt.ct', 'r')
event_pairs = []
event_links = []
event_pair = ''
for i, line in enumerate(dt_file_out):
if line[0] == '#':
if i != 0:
# Check the number of links
self.assertTrue(len(event_links) >= self.minimum_links)
# Check the distance between events
event_1_name = [
event[1] for event in self.event_list
if event[0] == int(event_pair.split()[1])
][0]
event_2_name = [
event[1] for event in self.event_list
if event[0] == int(event_pair.split()[2])
][0]
event_1 = sfile_util.readheader(event_1_name)
event_2 = sfile_util.readheader(event_2_name)
event_1_location = (event_1.origins[0].latitude,
event_1.origins[0].longitude,
event_1.origins[0].depth / 1000)
event_2_location = (event_2.origins[0].latitude,
event_2.origins[0].longitude,
event_2.origins[0].depth / 1000)
hypocentral_seperation = dist_calc(event_1_location,
event_2_location)
self.assertTrue(
hypocentral_seperation < self.maximum_separation)
# Check that the differential times are accurate
event_1_picks = sfile_util.readpicks(event_1_name).picks
event_2_picks = sfile_util.readpicks(event_2_name).picks
for pick_pair in event_links:
station = pick_pair.split()[0]
event_1_travel_time_output = pick_pair.split()[1]
event_2_travel_time_output = pick_pair.split()[2]
# weight = pick_pair.split()[3]
phase = pick_pair.split()[4]
# Extract the relevant pick information from the
# two sfiles
for pick in event_1_picks:
if pick.waveform_id.station_code == station:
if pick.phase_hint[0].upper() == phase:
event_1_pick = pick
for pick in event_2_picks:
if pick.waveform_id.station_code == station:
if pick.phase_hint[0].upper() == phase:
event_2_pick = pick
# Calculate the travel-time
event_1_travel_time_input = event_1_pick.time -\
event_1.origins[0].time
event_2_travel_time_input = event_2_pick.time -\
event_2.origins[0].time
self.assertEqual(event_1_travel_time_input,
float(event_1_travel_time_output))
self.assertEqual(event_2_travel_time_input,
float(event_2_travel_time_output))
event_pair = line
event_pairs.append(line)
event_links = []
else:
event_links.append(line)
self.assertTrue(os.path.isfile('phase.dat'))
dt_file_out.close()
def from_contbase(sfile, contbase_list, lowcut, highcut, samp_rate, filt_order,
length, prepick, swin, debug=0, plot=False):
r"""Function to read in picks from sfile then generate the template from \
the picks within this and the wavefiles from the continous database of \
day-long files. Included is a section to sanity check that the files are \
daylong and that they start at the start of the day. You should ensure \
this is the case otherwise this may alter your data if your data are \
daylong but the headers are incorrectly set.
:type sfile: string
:param sfile: sfilename must be the path to a seisan nordic type s-file \
containing waveform and pick information, all other arguments can \
be numbers save for swin which must be either P, S or all \
(case-sensitive).
:type contbase_list: List of tuple of string
:param contbase_list: List of tuples of the form \
['path', 'type', 'network']. Where path is the path to the \
continuous database, type is the directory structure, which can be \
either Yyyyy/Rjjj.01, which is the standard IRIS Year, julian day \
structure, or, yyyymmdd which is a single directory for every day.
:type lowcut: float
:param lowcut: Low cut (Hz), if set to None will look in template \
defaults file
:type highcut: float
:param lowcut: 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 length: float
:param length: Extract length in seconds, if None will look in template \
defaults file.
:type prepick: float
:param prepick: Pre-pick time in seconds
:type swin: str
:param swin: Either 'all', 'P' or 'S', to select which phases to output.
:type debug: int
:param debug: Level of debugging output, higher=more
:type plot: bool
:param plot: Turns template plotting on or off.
:returns: obspy.Stream Newly cut template
"""
# Perform some checks first
import os
if not os.path.isfile(sfile):
raise IOError('sfile does not exist')
# import some things
from eqcorrscan.utils import pre_processing
from eqcorrscan.utils import sfile_util
import glob
from obspy import read as obsread
# Read in the header of the sfile
event = sfile_util.readheader(sfile)
day = event.origins[0].time
# Read in pick info
catalog = sfile_util.readpicks(sfile)
picks = catalog[0].picks
print("I have found the following picks")
pick_chans = []
used_picks = []
for pick in picks:
station = pick.waveform_id.station_code
channel = pick.waveform_id.channel_code
phase = pick.phase_hint
pcktime = pick.time
if station + channel not in pick_chans and phase in ['P', 'S']:
pick_chans.append(station + channel)
used_picks.append(pick)
print(pick)
# #########Left off here
for contbase in contbase_list:
if contbase[1] == 'yyyy/mm/dd':
daydir = os.path.join([str(day.year),
str(day.month).zfill(2),
str(day.day).zfill(2)])
elif contbase[1] == 'Yyyyy/Rjjj.01':
daydir = os.path.join(['Y' + str(day.year),
'R' + str(day.julday).zfill(3) +
'.01'])
elif contbase[1] == 'yyyymmdd':
daydir = day.datetime.strftime('%Y%m%d')
if 'wavefiles' not in locals():
wavefiles = (glob.glob(os.path.join([contbase[0], daydir,
'*' + station +
'.*'])))
else:
wavefiles += glob.glob(os.path.join([contbase[0], daydir,
'*' + station +
'.*']))
elif phase in ['P', 'S']:
print(' '.join(['Duplicate pick', station, channel,
phase, str(pcktime)]))
elif phase == 'IAML':
print(' '.join(['Amplitude pick', station, channel,
phase, str(pcktime)]))
picks = used_picks
wavefiles = list(set(wavefiles))
# Read in waveform file
wavefiles.sort()
for wavefile in wavefiles:
print("I am going to read waveform data from: " + wavefile)
if 'st' not in locals():
st = obsread(wavefile)
else:
st += obsread(wavefile)
# Process waveform data
st.merge(fill_value='interpolate')
for tr in st:
tr = pre_processing.dayproc(tr, lowcut, highcut, filt_order,
samp_rate, debug, day)
# Cut and extract the templates
st1 = _template_gen(picks, st, length, 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 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
