"""
Part of the EQcorrscan module to read nordic format s-files and write them
EQcorrscan is a python module designed to run match filter routines for
seismology, within it are routines for integration to seisan and obspy.
With obspy integration (which is necessary) all main waveform formats can be
read in and output.
Note that these functions do not provide full functionality between quakeML
and seisan s-files. Currently (as of version 0.0.9) these only convert pick
times and phase information, along with amplitude information for local
magnitudes between seisan and quakeML. Location information including
hypocentre, origin time and magnitudes are also handled.
A series of wrappers and conversions is included between the legacy PICK
and EVENTINFO classes, however these will be depreciated along with these
classes for version 0.1.0. Users should transition to using obspy.core.event
classes as these have more support and functionality.
We have not implimented any handling of focal mechanism solutions between
the two formats.
Code written by Calum John Chamberlain and Chet Hopp both of
Victoria University of Wellington, 2015 & 2016.
Copyright 2015, 2016 the authors.
This file is part of EQcorrscan.
EQcorrscan is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
EQcorrscan is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with EQcorrscan. If not, see <http://www.gnu.org/licenses/>.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from obspy import UTCDateTime
import numpy as np
import warnings
[docs]class PICK:
"""
Pick information for seisan implimentation, note all fields can be left\
blank to obtain a default pick: picks have a print function which will\
print them as they would be seen in an S-file.
Attributes:
:type station: str
:param station: Station name, less than five charectars required as\
standard
:type channel: str
:param channel: Two or three charactar channel name, stored as two\
charactars in S-file
:type impulsivity: str
:param impulsivity: either 'C' or 'D' for compressive and dilatational
:type phase: str
:param phase: Any allowable phase name in two characters
:type weight: int
:param weight: 0-4 with 0=100%, 4=0%, use weight=9 for unknown timing
:type polarity: str
:type time: obspy.UTCDateTime()
:param time: Pick time as an obspy.UTCDateTime object
:type coda: int
:param coda: Length of coda in seconds
:type amplitude: float
:param amplitude: Amplitude (zero-peak), type is given in phase
:type peri: float
:param peri: Period of amplitude
:type azimuth: float
:param azimuth: Direction of approach in degrees
:type velocity: float
:param velocity: Phase velocity (km/s)
:type AIN: int
:param AIN: Angle of incidence.
:type SNR: float
:param SNR: Signal to noise ratio
:type azimuthres: int
:param azimuthres: Residual azimuth
:type timeres: float
:param timeres: Time residual in seconds
:type finalweight: int
:param finalweight: Final weight used in location
:type distance: float
:param distance: Source-reciever distance in km
:type CAZ: int
:param CAZ: Azimuth at source.
.. rubric:: Note: Depreciated legacy function, use the obspy.core.event \
classes. This will be removed in future releases.
"""
pickcount = 0
def __init__(self, station=' ', channel=' ', impulsivity=' ', phase=' ',
weight=999, polarity=' ', time=UTCDateTime(0),
coda=999, amplitude=float('NaN'),
peri=float('NaN'), azimuth=float('NaN'),
velocity=float('NaN'), AIN=999, SNR=float('NaN'),
azimuthres=999, timeres=float('NaN'),
finalweight=999, distance=float('NaN'),
CAZ=999):
self.station = station
self.channel = channel
self.impulsivity = impulsivity
self.phase = phase
self.weight = weight
self.polarity = polarity
self.time = time
self.coda = coda
self.amplitude = amplitude
self.peri = peri
self.azimuth = azimuth
self.velocity = velocity
self.AIN = AIN
self.SNR = SNR
self.azimuthres = azimuthres
self.timeres = timeres
self.finalweight = finalweight
self.distance = distance
self.CAZ = CAZ
self.pickcount += 1
def __repr__(self):
return "PICK()"
def __str__(self):
if self.distance >= 100.0:
self.distance = _int_conv(self.distance)
elif 10.0 < self.distance < 100.0:
self.distance = round(self.distance, 1)
round_len = 1
elif self.distance < 10.0:
self.distance = round(self.distance, 2)
round_len = 2
else:
round_len = False
if self.peri < 10.0:
peri_round = 2
elif self.peri >= 10.0:
peri_round = 1
else:
peri_round = False
if not self.AIN == '':
if not np.isnan(self.AIN):
dummy = int(self.AIN)
else:
dummy = self.AIN
else:
dummy = self.SNR
print(_str_conv(self.weight).rjust(1))
print_str = ' ' + self.station.ljust(5) +\
self.channel[0]+self.channel[len(self.channel)-1] +\
' ' + self.impulsivity +\
self.phase.ljust(4) +\
_str_conv(self.weight).rjust(1) + ' ' +\
self.polarity.rjust(1) + ' ' +\
str(self.time.hour).rjust(2) +\
str(self.time.minute).rjust(2) +\
str(self.time.second).rjust(3) + '.' +\
str(float(self.time.microsecond) /
(10 ** 4)).split('.')[0].zfill(2) +\
_str_conv(int(self.coda)).rjust(5)[0:5] +\
_str_conv(round(self.amplitude, 1)).rjust(7)[0:7] +\
_str_conv(self.peri, rounded=peri_round).rjust(5) +\
_str_conv(self.azimuth).rjust(6) +\
_str_conv(self.velocity).rjust(5) +\
_str_conv(dummy).rjust(4) +\
_str_conv(int(self.azimuthres)).rjust(3) +\
_str_conv(self.timeres, rounded=2).rjust(5) +\
_str_conv(int(self.finalweight)).rjust(2) +\
_str_conv(self.distance, rounded=round_len).rjust(5) +\
_str_conv(int(self.CAZ)).rjust(4)+' '
return print_str
[docs] def write(self, filename):
"""
Public function to write the pick to a file
:type filename: str
:param filename: Path to file to write to - will append to file
"""
import os
import warnings
if os.path.isfile(filename):
open_as = 'a'
else:
warnings.warn('File does not exist, no header')
open_as = 'w'
with open(filename, open_as) as f:
pickstr = self.__str__()
f.write(pickstr+'\n')
return
[docs]class EVENTINFO:
"""
Header information for seisan events, again all fields can be left blank \
for a default empty header. The print function for header will print \
important information, but not as seen in an S-file.
For more information on parameters see the seisan manual.
Attributes:
:type time: obspy.UTCDateTime
:param time: Event origin time
:type loc_mod_ind: str
:param loc_mod_ind:
:type dist_ind: str
:param dist_ind: Distance flag, usually 'L' for local, 'R' for \
regional and 'D' for distant
:type ev_id: str
:param ev_id: Often blank, 'E' denotes explosion and fixes depth to 0km
:type latitude: float
:param latitude: Hypocentre latitude in decimal degrees
:type longitude: float
:param lognitude: Hypocentre longitude in decimal degrees
:type depth: float
:param depth: hypocentre depth in km
:type depth_ind: str
:param depth_ind:
:type loc_ind: str
:param loc_ind:
:type agency: str
:param agency: Reporting agency, three letters
:type nsta: int
:param nsta: Number of stations recording
:type t_RMS: float
:param t_RMS: Root-mean-squared time residual
:type Mag_1: float
:param Mag_1: first magnitude
:type Mag_1_type: str
:param Mag_1_type: Type of magnitude for Mag_1 ('L', 'C', 'W')
:type Mag_1_agency: str
:param Mag_1_agency: Reporting agency for Mag_1
:type Mag_2: float
:param Mag_2: second magnitude
:type Mag_2_type: str
:param Mag_2_type: Type of magnitude for Mag_2 ('L', 'C', 'W')
:type Mag_2_agency: str
:param Mag_2_agency: Reporting agency for Mag_2
:type Mag_3: float
:param Mag_3: third magnitude
:type Mag_3_type: str
:param Mag_3_type: Type of magnitude for Mag_3 ('L', 'C', 'W')
:type Mag_3_agency: str
:param Mag_3_agency: Reporting agency for Mag_3
.. rubric:: Note: Depreciated legacy function, use the obspy.core.event \
classes. This will be removed in future releases.
"""
def __init__(self, time=UTCDateTime(0), loc_mod_ind=' ', dist_ind=' ',
ev_id=' ', latitude=float('NaN'), longitude=float('NaN'),
depth=float('NaN'), depth_ind=' ', loc_ind=' ', agency=' ',
nsta=0, t_RMS=float('NaN'), Mag_1=float('NaN'),
Mag_1_type=' ', Mag_1_agency=' ', Mag_2=float('NaN'),
Mag_2_type=' ', Mag_2_agency=' ', Mag_3=float('NaN'),
Mag_3_type=' ', Mag_3_agency=' '):
self.time = time
self.loc_mod_ind = loc_mod_ind
self.dist_ind = dist_ind
self.ev_id = ev_id
self.latitude = latitude
self.longitude = longitude
self.depth = depth
self.depth_ind = depth_ind
self.loc_ind = loc_ind
self.agency = agency
self.nsta = nsta
self.t_RMS = t_RMS
self.Mag_1 = Mag_1
self.Mag_1_type = Mag_1_type
self.Mag_1_agency = Mag_1_agency
self.Mag_2 = Mag_2
self.Mag_2_type = Mag_2_type
self.Mag_2_agency = Mag_2_agency
self.Mag_3 = Mag_3
self.Mag_3_type = Mag_3_type
self.Mag_3_agency = Mag_3_agency
def __repr__(self):
return "HEADER()"
def __str__(self):
print_str = str(self.time) + ' ' + str(self.latitude) + ',' +\
str(self.longitude) + ' ' + str(self.depth) + ' ' +\
self.Mag_1_type + ':' + str(self.Mag_1) + self.Mag_2_type + ':' +\
str(self.Mag_2) + self.Mag_3_type + ':' + str(self.Mag_3) + ' '\
+ self.agency
return print_str
[docs]def _int_conv(string):
"""
Convenience tool to convert from string to integer, if empty string \
return a 999 rather than an error.
"""
try:
intstring = int(string)
except:
intstring = 999
return intstring
[docs]def _float_conv(string):
"""
Convenience tool to convert from string to float, if empty string return \
NaN rather than an error
"""
try:
floatstring = float(string)
except:
# cjh Changed this to deal with QuakeML validation issues with 'NaN'
floatstring = float('999')
return floatstring
[docs]def _str_conv(number, rounded=False):
"""
Convenience tool to convert a number, either float or into into a string, \
if the int is 999, or the float is NaN, returns empty string.
"""
if (isinstance(number, float) and np.isnan(number)) or number == 999:
string = ' '
elif isinstance(number, str):
return number
elif isinstance(number, unicode):
return str(number)
elif not rounded:
if number < 100000:
string = str(number)
else:
exponant = int('{0:.2E}'.format(number).split('E+')[-1]) - 1
divisor = 10 ** exponant
string = '{0:.1f}'.format(number / divisor) + 'e' + str(exponant)
elif rounded == 2:
string = '{0:.2f}'.format(number)
elif rounded == 1:
string = '{0:.1f}'.format(number)
return string
[docs]def _evmagtonor(mag_type):
"""
Convenience tool to switch from obspy event magnitude types to seisan \
syntax
"""
if mag_type in ['ML', 'MLv']:
# MLv is local magnitude on vertical component
mag = 'L'
elif mag_type == 'mB':
mag = 'b'
elif mag_type == 'Ms':
mag = 's'
elif mag_type == 'MS':
mag = 'S'
elif mag_type in ['MW', 'Mw']:
mag = 'W'
elif mag_type == 'MbLg':
mag = 'G'
elif mag_type in ['Mc', 'MC']:
mag = 'C'
elif mag_type == 'M':
mag = 'W' # Convert generic magnitude to moment magnitude
msg = ('Converting generic magnitude to being stored as moment mag')
warnings.warn(msg)
else:
warnings.warn(mag_type + ' is not convertable')
return ''
return mag
[docs]def _nortoevmag(mag_type):
"""
Convenience tool to switch from nordic type magnitude notation to obspy \
event magnitudes.
"""
if mag_type == 'L':
mag = 'ML'
elif mag_type == 'b':
mag = 'mB'
elif mag_type == 's':
mag = 'Ms'
elif mag_type == 'S':
mag = 'MS'
elif mag_type == 'W':
mag = 'MW'
elif mag_type == 'G':
mag = 'MbLg'
elif mag_type == 'C':
mag = 'Mc'
else:
warnings.warn(mag_type + ' is not convertable')
return ''
return mag
[docs]def readpicks(sfile):
"""
Function to read pick information from the s-file and store this in an \
obspy.event.Catalog type. This was changed for version 0.1.0 from using \
the inbuilt PICK class.
:type sfile: String
:param sfile: Path to sfile
:return: obspy.core.event.Event
.. warning:: Currently finalweight is unsupported, nor is velocity, \
or angle of incidence. This is because obspy.event stores slowness \
in s/deg and takeoff angle, which would require computation from the \
values stored in seisan. Multiple weights are also not supported in \
Obspy.event.
"""
from obspy.core.event import Pick, WaveformStreamID, Arrival, Amplitude
# Get wavefile name for use in resource_ids
wav_names = readwavename(sfile)
# First we need to read the header to get the timing info
new_event = readheader(sfile)
evtime = new_event.origins[0].time
f = open(sfile, 'r')
pickline = []
# Set a default, ignored later unless overwritten
SNR = 999
if 'headerend' in locals():
del headerend
for lineno, line in enumerate(f):
if 'headerend' in locals():
if len(line.rstrip('\n').rstrip('\r')) in [80, 79] and \
(line[79] == ' ' or line[79] == '4' or line[79] == '\n'):
pickline += [line]
elif line[79] == '7':
header = line
headerend = lineno
amplitude_index = 0
for pick_index, line in enumerate(pickline):
if line[18:28].strip() == '': # If line is empty miss it
continue
station = line[1:6].strip()
channel = line[6:8].strip()
network = 'NA' # No network information provided in Sfile.
weight = line[14]
if weight == '_':
phase = line[10:17]
weight = 0
polarity = ''
else:
phase = line[10:14].strip()
polarity = line[16]
if weight == ' ':
weight = 0
if polarity == '':
polarity = "undecidable"
elif polarity == 'C':
polarity = "positive"
elif polarity == 'D':
polarity = 'negative'
else:
polarity = "undecidable"
try:
time = UTCDateTime(evtime.year, evtime.month, evtime.day,
int(line[18:20]), int(line[20:22]),
int(line[23:28].split('.')[0]),
int(line[23:28].split('.')[1])*10000)
except (ValueError):
time = UTCDateTime(evtime.year, evtime.month, evtime.day,
int(line[18:20]), int(line[20:22]), 0, 0)
time += 60 # Add 60 seconds on to the time, this copes with s-file
# preference to write seconds in 1-60 rather than 0-59 which
# datetime objects accept
coda = _int_conv(line[28:33])
amplitude = _float_conv(line[33:40])
peri = _float_conv(line[41:45])
azimuth = _float_conv(line[46:51])
velocity = _float_conv(line[52:56])
if header[57:60] == 'AIN':
AIN = _float_conv(line[57:60])
elif header[57:60] == 'SNR':
SNR = _float_conv(line[57:60])
azimuthres = _int_conv(line[60:63])
timeres = _float_conv(line[63:68])
finalweight = _int_conv(line[68:70])
distance = _float_conv(line[70:75])
CAZ = _int_conv(line[76:79])
# Create a new obspy.event.Pick class for this pick
_waveform_id = WaveformStreamID(station_code=station,
channel_code=channel,
network_code=network)
new_event.picks.append(Pick(waveform_id=_waveform_id,
phase_hint=phase,
polarity=polarity, time=time))
if line[9] == 'I':
new_event.picks[pick_index].onset = 'impulsive'
elif line[9] == 'E':
new_event.picks[pick_index].onset = 'emergent'
if line[15] == 'A':
new_event.picks[pick_index].evaluation_mode = 'automatic'
else:
new_event.picks[pick_index].evaluation_mode = 'manual'
# Note these two are not always filled - velocity conversion not yet
# implimented, needs to be converted from km/s to s/deg
# if not velocity == 999.0:
# new_event.picks[pick_index].horizontal_slowness = 1.0 / velocity
if not azimuth == 999:
new_event.picks[pick_index].backazimuth = azimuth
del _waveform_id
# Create new obspy.event.Amplitude class which references above Pick
# only if there is an amplitude picked.
if not amplitude == 999.0:
new_event.amplitudes.append(Amplitude(generic_amplitude=amplitude,
period=peri,
pick_id=new_event.
picks[pick_index].
resource_id,
waveform_id=new_event.
picks[pick_index].
waveform_id))
if new_event.picks[pick_index].phase_hint == 'IAML':
# Amplitude for local magnitude
new_event.amplitudes[amplitude_index].type = 'AML'
# Set to be evaluating a point in the trace
new_event.amplitudes[amplitude_index].category = 'point'
# Default AML unit in seisan is nm (Page 139 of seisan
# documentation, version 10.0)
new_event.amplitudes[amplitude_index].generic_amplitude /=\
10**9
new_event.amplitudes[amplitude_index].unit = 'm'
new_event.amplitudes[amplitude_index].magnitude_hint = 'ML'
else:
# Generic amplitude type
new_event.amplitudes[amplitude_index].type = 'A'
if not SNR == 999.0:
new_event.amplitudes[amplitude_index].snr = SNR
amplitude_index += 1
elif not coda == 999:
# Create an amplitude instance for code duration also
new_event.amplitudes.append(Amplitude(generic_amplitude=coda,
pick_id=new_event.
picks[pick_index].
resource_id,
waveform_id=new_event.
picks[pick_index].
waveform_id))
# Amplitude for coda magnitude
new_event.amplitudes[amplitude_index].type = 'END'
# Set to be evaluating a point in the trace
new_event.amplitudes[amplitude_index].category = 'duration'
new_event.amplitudes[amplitude_index].unit = 's'
new_event.amplitudes[amplitude_index].magnitude_hint = 'Mc'
if SNR and not SNR == 999.0:
new_event.amplitudes[amplitude_index].snr = SNR
amplitude_index += 1
# Create new obspy.event.Arrival class referencing above Pick
new_event.origins[0].arrivals.append(Arrival(phase=new_event.
picks[pick_index].
phase_hint,
pick_id=new_event.
picks[pick_index].
resource_id))
if weight != 999:
new_event.origins[0].arrivals[pick_index].time_weight =\
weight
if azimuthres != 999:
new_event.origins[0].arrivals[pick_index].backazimuth_residual =\
azimuthres
if timeres != 999:
new_event.origins[0].arrivals[pick_index].time_residual =\
timeres
if distance != 999:
new_event.origins[0].arrivals[pick_index].distance =\
distance
if CAZ != 999:
new_event.origins[0].arrivals[pick_index].azimuth =\
CAZ
f.close()
# Write event to catalog object for ease of .write() method
return new_event
[docs]def readwavename(sfile):
"""
Convenience function to extract the waveform filename from the s-file, \
returns a list of waveform names found in the s-file as multiples can \
be present.
:type sfile: str
:param sfile: Path to the sfile
:returns: List of str
"""
f = open(sfile)
wavename = []
for line in f:
if len(line) == 81 and line[79] == '6':
wavename.append(line[1:79].strip())
f.close()
return wavename
[docs]def blanksfile(wavefile, evtype, userID, outdir, overwrite=False,
evtime=False):
"""
Module to generate an empty s-file with a populated header for a given \
waveform.
:type wavefile: String
:param wavefile: Wavefile to associate with this S-file, the timing of \
the S-file will be taken from this file if evtime is not set.
:type evtype: String
:param evtype: L,R,D
:type userID: String
:param userID: 4-charectar SEISAN USER ID
:type outdir: String
:param outdir: Location to write S-file
:type overwrite: Bool
:param overwrite: Overwrite an existing S-file, default=False
:type evtime: UTCDateTime
:param evtime: If given this will set the timing of the S-file
:returns: String, S-file name
"""
from obspy import read as obsread
import sys
import os
import datetime
if not evtime:
try:
st = obsread(wavefile)
evtime = st[0].stats.starttime
except:
print('Wavefile: '+wavefile +
' is invalid, try again with real data.')
sys.exit()
# Check that user ID is the correct length
if len(userID) != 4:
raise IOError('User ID must be 4 characters long')
# Check that outdir exists
if not os.path.isdir(outdir):
raise IOError('Out path does not exist, I will not create this: ' +
outdir)
# Check that evtype is one of L,R,D
if evtype not in ['L', 'R', 'D']:
raise IOError('Event type must be either L, R or D')
# Generate s-file name in the format dd-hhmm-ss[L,R,D].Syyyymm
sfile = outdir + '/' + str(evtime.day).zfill(2) + '-' +\
str(evtime.hour).zfill(2) +\
str(evtime.minute).zfill(2) + '-' +\
str(evtime.second).zfill(2) + evtype + '.S' +\
str(evtime.year) +\
str(evtime.month).zfill(2)
# Check is sfile exists
if os.path.isfile(sfile) and not overwrite:
print('Desired sfile: ' + sfile + ' exists, will not overwrite')
for i in range(1, 10):
sfile = outdir + '/' + str(evtime.day).zfill(2) + '-' +\
str(evtime.hour).zfill(2) +\
str(evtime.minute).zfill(2) + '-' +\
str(evtime.second+i).zfill(2) + evtype + '.S' +\
str(evtime.year) +\
str(evtime.month).zfill(2)
if not os.path.isfile(sfile):
break
else:
msg = 'Tried generated files up to 20s in advance and found ' +\
'all exist, you need to clean your stuff up!'
raise IOError(msg)
# sys.exit()
f = open(sfile, 'w')
# Write line 1 of s-file
f.write(' ' + str(evtime.year) + ' ' +
str(evtime.month).rjust(2) +
str(evtime.day).rjust(2) + ' ' +
str(evtime.hour).rjust(2) +
str(evtime.minute).rjust(2) + ' ' +
str(float(evtime.second)).rjust(4) + ' ' +
evtype + '1'.rjust(58) + '\n')
# Write line 2 of s-file
f.write(' ACTION:ARG ' + str(datetime.datetime.now().year)[2:4] + '-' +
str(datetime.datetime.now().month).zfill(2) + '-' +
str(datetime.datetime.now().day).zfill(2) + ' ' +
str(datetime.datetime.now().hour).zfill(2) + ':' +
str(datetime.datetime.now().minute).zfill(2) + ' OP:' +
userID.ljust(4) + ' STATUS:'+'ID:'.rjust(18) +
str(evtime.year) +
str(evtime.month).zfill(2) +
str(evtime.day).zfill(2) +
str(evtime.hour).zfill(2) +
str(evtime.minute).zfill(2) +
str(evtime.second).zfill(2) +
'I'.rjust(6) + '\n')
# Write line 3 of s-file
f.write(' ' + wavefile + '6'.rjust(79-len(wavefile)) + '\n')
# Write final line of s-file
f.write(' STAT SP IPHASW D HRMM SECON CODA AMPLIT PERI AZIMU' +
' VELO AIN AR TRES W DIS CAZ7\n')
f.close()
print('Written s-file: ' + sfile)
return sfile
[docs]def eventtoSfile(event, userID, evtype, outdir, wavefiles, explosion=False,
overwrite=False):
"""
Function to take an obspy.event and write the relevant information to a \
nordic formatted s-file
:type event: obspy.event.core.Catalog
:param event: A single obspy event
:type userID: str
:param userID: Up to 4 character user ID
:type evtype: str
:param evtype: Single character string to describe the event, either L, R \
or D.
:type outdir: str
:param outdir: Path to directory to write to
:type wavefiles: list of str
:param wavefiles: Waveforms to associate the sfile with
:type explosion: bool
:param explosion: Note if the event is an explosion, will be marked by an \
E.
:type overwrite: bool
:param overwrite: force to overwrite old files, defaults to False
:returns: str: name of sfile written
"""
import datetime
import os
from obspy.core.event import Catalog, Event
# First we need to work out what to call the s-file and open it
# Check that user ID is the correct length
if len(userID) != 4:
raise IOError('User ID must be 4 characters long')
# Check that outdir exists
if not os.path.isdir(outdir):
raise IOError('Out path does not exist, I will not create this: ' +
outdir)
# Check that evtype is one of L,R,D
if evtype not in ['L', 'R', 'D']:
raise IOError('Event type must be either L, R or D')
if explosion:
evtype += 'E'
# Check that there is one event
if isinstance(event, Catalog) and len(event) == 1:
event = event[0]
elif isinstance(event, Event):
event = event
else:
raise IOError('Needs a single event')
if isinstance(wavefiles, str):
wavefiles = [wavefiles]
if isinstance(wavefiles, unicode):
wavefiles = [str(wavefiles)]
elif isinstance(wavefiles, list):
wavefiles = wavefiles
else:
print(type(wavefiles))
raise IOError(wavefiles + ' is neither string or list')
# Determine name from origin time
sfilename = event.origins[0].time.datetime.strftime('%d-%H%M-%S') +\
evtype + '.S' + event.origins[0].time.datetime.strftime('%Y%m')
evtime = event.origins[0].time
# Check that the file doesn't exist
if not overwrite and os.path.isfile(outdir+'/'+sfilename):
raise IOError(outdir+'/'+sfilename +
' already exists, will not overwrite')
sfile = open(outdir + '/' + sfilename, 'w')
# Write the header info.
lat = '{0:.3f}'.format(event.origins[0].get('latitude')) or ''
lon = '{0:.3f}'.format(event.origins[0].get('longitude')) or ''
depth = '{0:.1f}'.format(event.origins[0].get('depth')/1000) or ''
agency = event.creation_info.get('agency_id') or ''
if len(agency) > 3:
agency = agency[0:3]
# Cope with differences in event uncertainty naming
if event.origins[0].time_errors:
try:
timerms = '{0:.1f}'.format(event.origins[0].
time_errors.Time_Residual_RMS)
except AttributeError:
timerms = '0.0'
else:
timerms = '0.0'
mag_1 = '{0:.1f}'.format(event.magnitudes[0].mag) or ''
mag_1_type = _evmagtonor(event.magnitudes[0].magnitude_type) or ''
mag_1_agency = event.magnitudes[0].creation_info.agency_id or ''
try:
mag_2 = '{0:.1f}'.format(event.magnitudes[1].mag) or ''
mag_2_type = _evmagtonor(event.magnitudes[1].magnitude_type) or ''
mag_2_agency = event.magnitudes[1].creation_info.agency_id or ''
except IndexError:
mag_2 = ''
mag_2_type = ''
mag_2_agency = ''
try:
mag_3 = '{0:.1f}'.format(event.magnitudes[2].mag) or ''
mag_3_type = _evmagtonor(event.magnitudes[2].magnitude_type) or ''
mag_3_agency = event.magnitudes[2].creation_info.agency_id or ''
except IndexError:
mag_3 = ''
mag_3_type = ''
mag_3_agency = ''
# Work out how many stations were used
if len(event.picks) > 0:
stations = [pick.waveform_id.station_code for pick in event.picks]
ksta = str(len(list(set(stations))))
else:
ksta = ''
sfile.write(' ' + str(evtime.year) + ' ' +
str(evtime.month).rjust(2) +
str(evtime.day).rjust(2) + ' ' +
str(evtime.hour).rjust(2) +
str(evtime.minute).rjust(2) + ' ' +
str(float(evtime.second)).rjust(4) + ' ' +
evtype.ljust(2) + lat.rjust(7) + ' ' + lon.rjust(7) +
depth.rjust(5) + agency.rjust(5) + ksta.rjust(3) +
timerms.rjust(4) +
mag_1.rjust(4) + mag_1_type.rjust(1) +
mag_1_agency[0:3].rjust(3) +
mag_2.rjust(4) + mag_2_type.rjust(1) +
mag_2_agency[0:3].rjust(3) +
mag_3.rjust(4) + mag_3_type.rjust(1) +
mag_3_agency[0:3].rjust(3) + '1' + '\n')
# Write line 2 of s-file
sfile.write(' ACTION:ARG ' + str(datetime.datetime.now().year)[2:4] + '-' +
str(datetime.datetime.now().month).zfill(2) + '-' +
str(datetime.datetime.now().day).zfill(2) + ' ' +
str(datetime.datetime.now().hour).zfill(2) + ':' +
str(datetime.datetime.now().minute).zfill(2) + ' OP:' +
userID.ljust(4) + ' STATUS:'+'ID:'.rjust(18) +
str(evtime.year) +
str(evtime.month).zfill(2) +
str(evtime.day).zfill(2) +
str(evtime.hour).zfill(2) +
str(evtime.minute).zfill(2) +
str(evtime.second).zfill(2) +
'I'.rjust(6) + '\n')
# Write line 3 of s-file
for wavefile in wavefiles:
sfile.write(' ' + wavefile + '6'.rjust(79-len(wavefile)) + '\n')
# Write final line of s-file
sfile.write(' STAT SP IPHASW D HRMM SECON CODA AMPLIT PERI AZIMU' +
' VELO AIN AR TRES W DIS CAZ7\n')
sfile.close()
# Now call the populateSfile function
if len(event.picks) > 0:
populateSfile(sfilename, event)
return sfilename
[docs]def populateSfile(sfile, event):
"""
Module to populate a blank nordic format S-file with pick information, \
arguments required are the filename of the blank s-file and the picks \
where picks is a dictionary of picks including station, channel, \
impulsivity, phase, weight, polarity, time, coda, amplitude, peri, \
azimuth, velocity, SNR, azimuth residual, Time-residual, final weight, \
epicentral distance & azimuth from event to station.
This is a full pick line information from the seisan manual, P. 341
:type sfile: str
:param sfile: Path to S-file to populate, must have a header already
:type event: :class: obspy.event.core.Catalog
:param picks: A single event to be written to a single S-file.
"""
from obspy.core.event import Catalog, Event
# first check that the event is only one event
if isinstance(event, Catalog) and len(event) == 1:
event = event[0]
elif isinstance(event, Event):
event = event
else:
raise AttributeError('More than one event in the catalog, use a ' +
' different method')
f = open(sfile, 'r')
# Find type 7 line, under which picks should be - if there are already
# picks there we should preserve them
body = ''
header = ''
if 'headerend' in locals():
del headerend
for lineno, line in enumerate(f):
identifier = line[79]
if 'headerend' in locals():
body += line
else:
header += line
if identifier == '7':
headerend = lineno
f.close()
#
# Now generate lines for the new picks
newpicks = '\n'.join(nordpick(event))
# Write all new and old info back in
f = open(sfile, 'w')
f.write(header)
f.write(body)
f.write(newpicks + '\n')
f.write('\n'.rjust(81))
# f.write('\n')
f.close()
return
[docs]def eventtopick(event):
"""
Wrapper function to convert from obspy.core.event to legacy PICK and \
EVENT classes.
:type event: obspy.core.event.Event
:param event: A single obspy event
:returns: List of PICK(), and a single EVENTINFO()
.. note:: This is a wrapper to simplify transition from PICK and \
EVENT classes to obspy.core.event classes. This will not be maintained \
beyond v 0.1.0.
.. versionadded:: 0.1.0
"""
# Check that the event is a single event
from obspy.core.event import Catalog, Event
# first check that the event is only one event
if isinstance(event, Catalog) and len(event) == 1:
event = event[0]
elif isinstance(event, Event):
event = event
else:
raise AttributeError('More than one event in the catalog, use a ' +
' different method')
stations = [pick.waveform_id.station_code for pick in event.picks]
nsta = len(list(set(stations)))
# Generate the EVENTINFO object
event_descriptions = event.event_descriptions[0].text or ' '
if len(event_descriptions) == 2:
event_descriptions = event_descriptions.rjust(3)
evinfo = EVENTINFO(time=event.origins[0].time,
loc_mod_ind=event_descriptions[0],
dist_ind=event_descriptions[1],
ev_id=event_descriptions[2],
latitude=event.origins[0].latitude,
longitude=event.origins[0].longitude,
depth=event.origins[0].depth / 1000,
depth_ind=' ',
loc_ind=' ',
agency=event.creation_info.get('agency_id') or ' ',
nsta=nsta,
t_RMS=event.origins[0].time_errors.Time_Residual_RMS or
float('NaN'),
Mag_1=event.magnitudes[0].mag or float('NaN'),
Mag_1_type=_evmagtonor(event.magnitudes[0].
magnitude_type) or ' ',
Mag_1_agency=event.magnitudes[0].creation_info.agency_id
or ' ',
Mag_2=event.magnitudes[1].mag or float('NaN'),
Mag_2_type=_evmagtonor(event.magnitudes[1].
magnitude_type) or ' ',
Mag_2_agency=event.magnitudes[1].creation_info.agency_id
or ' ',
Mag_3=event.magnitudes[2].mag or float('NaN'),
Mag_3_type=_evmagtonor(event.magnitudes[2].
magnitude_type) or ' ',
Mag_3_agency=event.magnitudes[2].creation_info.agency_id
or ' ')
# Can make use of nordpick, which will remain in place for many versions?
pick_strings = nordpick(event)
# Then convert from pick-strings to PICK class
picks = []
evtime = event.origins[0].time
for line in pick_strings:
# Copied from old readpicks function
station = line[1:6].strip()
channel = line[6:8].strip()
impulsivity = line[9]
weight = line[14]
if weight == '_':
phase = line[10:17]
weight = ''
polarity = ''
else:
phase = line[10:14].strip()
polarity = line[16]
try:
time = UTCDateTime(evtime.year, evtime.month, evtime.day,
int(line[18:20]), int(line[20:22]),
int(line[23:28].split('.')[0]),
int(line[23:28].split('.')[1]) * 10000)
# Includes possible bug with seconds not being alligned.
# Shouldn't happen in this case, but best to include for possible
# copy/paste later!
except (ValueError):
time = UTCDateTime(evtime.year, evtime.month, evtime.day,
int(line[18:20]), int(line[20:22]), 0, 0)
time += 60 # Add 60 seconds on to the time, this copes with s-file
weight = _int_conv(weight)
coda = _int_conv(line[28:33])
amplitude = _float_conv(line[33:40])
peri = _float_conv(line[41:45])
azimuth = _float_conv(line[46:51])
velocity = _float_conv(line[52:56])
azimuthres = _int_conv(line[60:63])
timeres = _float_conv(line[63:68])
finalweight = _int_conv(line[68:70])
distance = _float_conv(line[70:75])
CAZ = _int_conv(line[76:79])
AIN = 999
SNR = float('NaN')
picks += [PICK(station, channel, impulsivity, phase, weight, polarity,
time, coda, amplitude, peri, azimuth, velocity, AIN,
SNR, azimuthres, timeres, finalweight, distance, CAZ)]
return picks, evinfo
[docs]def picktoevent(evinfo, picks):
"""
Wrapper function to convert from EVENTINFO and PICK classes to \
obspy.core.event.Event.
:type evinfo: EVENTINFO
:param evinfo: Event header info for a single event
:type picks: List of PICK
:param picks: List of picks associated with the event
:returns: obspy.core.event.Event
.. note:: This is a legacy support function, users should avoid \
this as it will be removed for version 0.1.1. Written to aid transition \
from in-built classes to obspy.core.event classes.
.. versionadded:: 0.1.0
"""
from obspy.core.event import Event, Origin, Magnitude, Comment
from obspy.core.event import EventDescription, CreationInfo
from obspy.core.event import Pick, WaveformStreamID, Arrival, Amplitude
# Cope with possible single pick case
if not isinstance(picks, list):
picks = [picks]
# Convert the relevant evinfo fields to an Event instance
event = Event()
event.origins.append(Origin())
event.origins[0].time = evinfo.time
event.event_descriptions.append(EventDescription())
event.event_descriptions[0].text = ''.join([evinfo.loc_mod_ind,
evinfo.dist_ind,
evinfo.ev_id]).strip()
event.origins[0].latitude = evinfo.latitude
event.origins[0].longitude = evinfo.longitude
event.origins[0].depth = evinfo.depth * 1000
event.creation_info = CreationInfo(agency_id=evinfo.agency)
event.origins[0].comments.append(Comment(text='Number of stations=' +
str(evinfo.nsta)))
event.origins[0].time_errors['Time_Residual_RMS'] = \
evinfo.t_RMS
event.magnitudes.append(Magnitude())
event.magnitudes[0].mag = evinfo.Mag_1
event.magnitudes[0].magnitude_type = _nortoevmag(evinfo.Mag_1_type)
event.magnitudes[0].creation_info = CreationInfo(agency_id=evinfo.
Mag_1_agency)
event.magnitudes[0].origin_id = event.origins[0].resource_id
event.magnitudes.append(Magnitude())
event.magnitudes[1].mag = evinfo.Mag_2
event.magnitudes[1].magnitude_type = _nortoevmag(evinfo.Mag_2_type)
event.magnitudes[1].creation_info = CreationInfo(agency_id=evinfo.
Mag_2_agency)
event.magnitudes[1].origin_id = event.origins[0].resource_id
event.magnitudes.append(Magnitude())
event.magnitudes[2].mag = evinfo.Mag_3
event.magnitudes[2].magnitude_type = _nortoevmag(evinfo.Mag_3_type)
event.magnitudes[2].creation_info = CreationInfo(agency_id=evinfo.
Mag_3_agency)
event.magnitudes[2].origin_id = event.origins[0].resource_id
# We now have all the header info converted that we can hold in EVENT class
# Move on to the picks.
amplitude_index = 0
for pick_index, pick in enumerate(picks):
_waveform_id = WaveformStreamID(station_code=pick.station,
channel_code=pick.channel,
network_code='NA')
if pick.polarity == '':
polarity = "undecidable"
elif pick.polarity == 'C':
polarity = "positive"
elif pick.polarity == 'D':
polarity = 'negative'
else:
polarity = "undecidable"
event.picks.append(Pick(waveform_id=_waveform_id,
phase_hint=pick.phase,
polarity=polarity,
time=pick.time))
if pick.impulsivity == 'I':
event.picks[pick_index].onset = 'impulsive'
elif pick.impulsivity == 'E':
event.picks[pick_index].onset = 'emergent'
if not np.isnan(pick.azimuth):
event.picks[pick_index].backazimuth = pick.azimuth
del _waveform_id
if not np.isnan(pick.amplitude):
event.amplitudes.append(Amplitude(generic_amplitude=pick.amplitude,
period=pick.peri,
pick_id=event.picks[pick_index].
resource_id,
waveform_id=event.
picks[pick_index].waveform_id))
if event.picks[pick_index].phase_hint == 'IAML':
event.amplitudes[amplitude_index].type = 'AML'
# Set to be evaluating a point in the trace
event.amplitudes[amplitude_index].category = 'point'
# Default AML unit in seisan is nm (Page 139 of seisan
# documentation, version 10.0)
event.amplitudes[amplitude_index].generic_amplitude /=\
10**9
event.amplitudes[amplitude_index].unit = 'm'
event.amplitudes[amplitude_index].magnitude_hint = 'ML'
else:
# Generic amplitude type
event.amplitudes[amplitude_index].type = 'A'
if not np.isnan(pick.SNR):
event.amplitudes[amplitude_index].snr = pick.SNR
amplitude_index += 1
elif not pick.coda == 999:
# Create an amplitude instance for code duration also
event.amplitudes.append(Amplitude(generic_amplitude=pick.coda,
pick_id=event.
picks[pick_index].resource_id,
waveform_id=event.
picks[pick_index].waveform_id))
# Amplitude for coda magnitude
event.amplitudes[amplitude_index].type = 'END'
# Set to be evaluating a point in the trace
event.amplitudes[amplitude_index].category = 'duration'
event.amplitudes[amplitude_index].unit = 's'
event.amplitudes[amplitude_index].magnitude_hint = 'Mc'
if pick.SNR and not np.isnan(pick.SNR):
event.amplitudes[amplitude_index].snr = pick.SNR
amplitude_index += 1
# Generate Arrival objects for the pick
event.origins[0].arrivals.append(Arrival(phase=event.picks[pick_index].
phase_hint,
pick_id=event.
picks[pick_index].
resource_id))
if pick.weight != 999:
event.origins[0].arrivals[pick_index].time_weight =\
pick.weight
if pick.azimuthres != 999:
event.origins[0].arrivals[pick_index].backazimuth_residual =\
pick.azimuthres
if not np.isnan(pick.timeres):
event.origins[0].arrivals[pick_index].time_residual =\
pick.timeres
if not np.isnan(pick.distance):
event.origins[0].arrivals[pick_index].distance =\
pick.distance
if pick.CAZ != 999:
event.origins[0].arrivals[pick_index].azimuth =\
pick.CAZ
return event
[docs]def nordpick(event):
"""
Function to print information from an obspy.event class to nordic format.
:type event: :class: obspy.core.event.Event
:param event: A single obspy event.
:returns: List of String
.. note:: Currently finalweight is unsupported, nor is velocity, or \
angle of incidence. This is because obspy.event stores slowness in \
s/deg and takeoff angle, which would require computation from the \
values stored in seisan. Multiple weights are also not supported in \
Obspy.event.
.. versionadded:: 0.1.0
"""
pick_strings = []
for pick in event.picks:
# Convert string to short sting
if pick.onset == 'impulsive':
impulsivity = 'I'
elif pick.onset == 'emergent':
impulsivity = 'E'
else:
impulsivity = ' '
# Convert string to short string
if pick.polarity == 'positive':
polarity = 'C'
elif pick.polarity == 'negative':
polarity = 'D'
else:
polarity = ' '
# Extract velocity: Note that horizontal slowness in quakeML is stored
# as s/deg
if pick.horizontal_slowness:
# velocity = 1.0 / pick.horizontal_slowness
velocity = ' ' # Currently this conversion is unsupported.
else:
velocity = ' '
# Extract azimuth
if pick.backazimuth:
azimuth = pick.backazimuth
else:
azimuth = ' '
# Extract the correct arrival info for this pick - assuming only one
# arrival per pick...
arrival = [arrival for arrival in event.origins[0].arrivals
if arrival.pick_id == pick.resource_id]
if len(arrival) > 0:
arrival = arrival[0]
# Extract weight - should be stored as 0-4, or 9 for seisan.
if arrival.time_weight:
weight = int(arrival.time_weight)
else:
weight = '0'
# Extract azimuth residual
if arrival.backazimuth_residual:
azimuthres = int(arrival.backazimuth_residual)
else:
azimuthres = ' '
# Extract time residual
if arrival.time_residual:
timeres = arrival.time_residual
else:
timeres = ' '
# Extract distance
if arrival.distance:
distance = arrival.distance
if distance >= 100.0:
distance = _int_conv(distance)
elif 10.0 < distance < 100.0:
distance = round(distance, 1)
round_len = 1
elif distance < 10.0:
distance = round(distance, 2)
round_len = 2
else:
round_len = False
else:
distance = ' '
round_len = False
# Extract CAZ
if arrival.azimuth:
CAZ = int(arrival.azimuth)
else:
CAZ = ' '
else:
CAZ = ' '
round_len = False
distance = ' '
timeres = ' '
azimuthres = ' '
azimuth = ' '
weight = 0
# Extract amplitude: note there can be multiple amplitudes, but they
# should be associated with different picks.
amplitude = [amplitude for amplitude in event.amplitudes
if amplitude.pick_id == pick.resource_id]
if len(amplitude) > 0:
amplitude = amplitude[0]
# Determine type of amplitude
if amplitude.type != 'END':
# Extract period
if amplitude.period:
peri = amplitude.period
if peri < 10.0:
peri_round = 2
elif peri >= 10.0:
peri_round = 1
else:
peri_round = False
else:
peri = ' '
peri_round = False
# Extract amplitude and convert units
if amplitude.generic_amplitude:
amp = amplitude.generic_amplitude
if amplitude.unit in ['m', 'm/s', 'm/(s*s)', 'm*s']:
amp *= 10**9
# Otherwise we will assume that the amplitude is in counts
else:
amp = np.nan
coda = ' '
else:
coda = int(amplitude.generic_amplitude)
peri = ' '
peri_round = False
amp = np.nan
else:
peri = ' '
peri_round = False
amp = np.nan
coda = ' '
# If the weight is 0 then we don't need to print it
if weight == 0 or weight == '0':
weight = 999 # this will return an empty string using _str_conv
# Generate a print string and attach it to the list
if not pick.phase_hint:
# Cope with some authorities not providing phase hints :(
phase_hint = ' '
else:
phase_hint = pick.phase_hint
pick_strings.append(' ' + pick.waveform_id.station_code.ljust(5) +
pick.waveform_id.channel_code[0] +
pick.waveform_id.channel_code[len(pick.waveform_id.
channel_code)
- 1] +
' ' + impulsivity + phase_hint.ljust(4) +
_str_conv(int(weight)).rjust(1) + ' ' +
polarity.rjust(1) + ' ' +
str(pick.time.hour).rjust(2) +
str(pick.time.minute).rjust(2) +
str(pick.time.second).rjust(3) + '.' +
str(float(pick.time.microsecond) /
(10 ** 4)).split('.')[0].zfill(2) +
_str_conv(coda).rjust(5)[0:5] +
_str_conv(round(amp, 1)).rjust(7)[0:7] +
_str_conv(peri, rounded=peri_round).rjust(5) +
_str_conv(azimuth).rjust(6) +
_str_conv(velocity).rjust(5) +
_str_conv(' ').rjust(4) +
_str_conv(azimuthres).rjust(3) +
_str_conv(timeres, rounded=2).rjust(5) +
_str_conv(' ').rjust(2) +
_str_conv(distance, rounded=round_len).rjust(5) +
_str_conv(CAZ).rjust(4)+' ')
# Note that currently finalweight is unsupported, nor is velocity, or
# angle of incidence. This is because obspy.event stores slowness in
# s/deg and takeoff angle, which would require computation from the
# values stored in seisan. Multiple weights are also not supported in
# Obspy.event
return pick_strings
[docs]def stationtoseisan(station):
"""
Convert obspy station inventory to simple string to copy in to \
STATION0.HYP file for seisan locations.
:type station: obspy.core.inventory.station.Station
:param station: Inventory containing a single station.
:returns: str
.. note:: Only works to the low-precision level at the moment (see seisan \
manual for explanation).
"""
import LatLon
if station.latitude < 0:
lat_str = 'S'
else:
lat_str = 'N'
if station.longitude < 0: # Stored in =/- 180, not 0-360
lon_str = 'W'
else:
lon_str = 'E'
if len(station.code) > 4:
sta_str = station.code[0:4]
else:
sta_str = station.code.ljust(4)
if len(station.channels) > 0:
depth = station.channels[0].depth
else:
msg = 'No depth found in station.channels, have you set the level ' +\
'of stationXML download to channel if using obspy.get_stations?'
raise IOError(msg)
elev = str(int(round(station.elevation - depth))).rjust(4)
# lat and long are written in STATION0.HYP in deg,decimal mins
lat = LatLon.Latitude(station.latitude)
lon = LatLon.Longitude(station.longitude)
lat = ''.join([str(int(abs(lat.degree))),
'{0:.2f}'.format(lat.decimal_minute).rjust(5)])
lon = ''.join([str(int(abs(lon.degree))),
'{0:.2f}'.format(lon.decimal_minute).rjust(5)])
station_str = ''.join([' ', sta_str, lat, lat_str, lon, lon_str, elev])
return station_str
if __name__ == "__main__":
import doctest
doctest.testmod()
# if __name__ == '__main__':
# # Read arguments
# import sys
# if len(sys.argv) != 6:
# print('Requires 5 arguments: wavefile, evtype, userID, outdir,'
# ' overwrite')
# sys.exit()
# else:
# wavefile = str(sys.argv[1])
# evtype = str(sys.argv[2])
# userID = str(sys.argv[3])
# outdir = str(sys.argv[4])
# overwrite = str(sys.argv[5])
# sfile = blanksfile(wavefile, evtype, userID, outdir, overwrite)
# print sfile