#!/usr/bin/env python
# ------------------------------------------------------------------
# Filename: sacio.py
# Purpose: Read & Write Seismograms, Format SAC.
# Author: Yannik Behr, C. J. Ammon's, C. Satriano, L. Krischer
# Email: yannik.behr@vuw.ac.nz
#
# Copyright (C) 2008-2015 Yannik Behr, C. J. Ammon's, C. Satriano,
# L. Krischer
# ------------------------------------------------------------------
"""
Low-level module internally used for handling SAC files
An object-oriented version of C. J. Ammon's SAC I/O module.
:copyright:
The ObsPy Development Team (devs@obspy.org) & C. J. Ammon
:license:
GNU Lesser General Public License, Version 3
(http://www.gnu.org/copyleft/lesser.html)
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from future.builtins import * # NOQA
from future.utils import native_str
import os
import time
import warnings
import numpy as np
from obspy import Trace, UTCDateTime
from obspy.core.compatibility import frombuffer
from obspy.core.util import AttribDict, gps2DistAzimuth
# we put here everything but the time, they are going to stats.starttime
# left SAC attributes, right trace attributes, see also
# http://www.iris.edu/KB/questions/13/SAC+file+format
convert_dict = {'npts': 'npts',
'delta': 'delta',
'kcmpnm': 'channel',
'kstnm': 'station',
'scale': 'calib',
'knetwk': 'network',
'khole': 'location'}
# all the sac specific extras, the SAC reference time specific headers are
# handled separately and are directly controlled by trace.stats.starttime.
SAC_EXTRA = ('depmin', 'depmax', 'odelta', 'o', 'a', 't0', 't1', 't2', 't3',
't4', 't5', 't6', 't7', 't8', 't9', 'f', 'stla', 'stlo', 'stel',
'stdp', 'evla', 'evlo', 'evdp', 'mag', 'user0', 'user1', 'user2',
'user3', 'user4', 'user5', 'user6', 'user7', 'user8', 'user9',
'dist', 'az', 'baz', 'gcarc', 'depmen', 'cmpaz', 'cmpinc',
'nvhdr', 'norid', 'nevid', 'nwfid', 'iftype', 'idep', 'iztype',
'iinst', 'istreg', 'ievreg', 'ievtype', 'iqual', 'isynth',
'imagtyp', 'imagsrc', 'leven', 'lpspol', 'lovrok', 'lcalda',
'kevnm', 'ko', 'ka', 'kt0', 'kt1', 'kt2', 'kt3', 'kt4', 'kt5',
'kt6', 'kt7', 'kt8', 'kt9', 'kf', 'kuser0', 'kuser1', 'kuser2',
'kdatrd', 'kinst', 'cmpinc', 'xminimum', 'xmaximum', 'yminimum',
'ymaximum', 'unused6', 'unused7', 'unused8', 'unused9',
'unused10', 'unused11', 'unused12', 'unused13')
FDICT = {'delta': 0, 'depmin': 1, 'depmax': 2, 'scale': 3,
'odelta': 4, 'b': 5, 'e': 6, 'o': 7, 'a': 8, 'int1': 9,
't0': 10, 't1': 11, 't2': 12, 't3': 13, 't4': 14,
't5': 15, 't6': 16, 't7': 17, 't8': 18, 't9': 19,
'f': 20, 'stla': 31, 'stlo': 32, 'stel': 33, 'stdp': 34,
'evla': 35, 'evlo': 36, 'evdp': 38, 'mag': 39,
'user0': 40, 'user1': 41, 'user2': 42, 'user3': 43,
'user4': 44, 'user5': 45, 'user6': 46, 'user7': 47,
'user8': 48, 'user9': 49, 'dist': 50, 'az': 51,
'baz': 52, 'gcarc': 53, 'depmen': 56, 'cmpaz': 57,
'cmpinc': 58, 'xminimum': 59, 'xmaximum': 60,
'yminimum': 61, 'ymaximum': 62, 'unused6': 63,
'unused7': 64, 'unused8': 65, 'unused9': 66,
'unused10': 67, 'unused11': 68, 'unused12': 69}
IDICT = {'nzyear': 0, 'nzjday': 1, 'nzhour': 2, 'nzmin': 3,
'nzsec': 4, 'nzmsec': 5, 'nvhdr': 6, 'norid': 7,
'nevid': 8, 'npts': 9, 'nwfid': 11,
'iftype': 15, 'idep': 16, 'iztype': 17, 'iinst': 19,
'istreg': 20, 'ievreg': 21, 'ievtype': 22, 'iqual': 23,
'isynth': 24, 'imagtyp': 25, 'imagsrc': 26,
'leven': 35, 'lpspol': 36, 'lovrok': 37,
'lcalda': 38, 'unused13': 39}
SDICT = {'kstnm': 0, 'kevnm': 1, 'khole': 2, 'ko': 3, 'ka': 4,
'kt0': 5, 'kt1': 6, 'kt2': 7, 'kt3': 8, 'kt4': 9,
'kt5': 10, 'kt6': 11, 'kt7': 12, 'kt8': 13,
'kt9': 14, 'kf': 15, 'kuser0': 16, 'kuser1': 17,
'kuser2': 18, 'kcmpnm': 19, 'knetwk': 20,
'kdatrd': 21, 'kinst': 22}
TWO_DIGIT_YEAR_MSG = ("SAC file with 2-digit year header field encountered. "
"This is not supported by the SAC file format standard. "
"Prepending '19'.")
[docs]class SacError(Exception):
"""
Raised if the SAC file is corrupt or if necessary information
in the SAC file is missing.
"""
pass
[docs]class SacIOError(Exception):
"""
Raised if the given SAC file can't be read.
"""
pass
[docs]class SacIO(object):
"""
Class for SAC file IO.
Functions are given below, attributes/header
fields (described below) can be directly accessed (via the
:meth:`~obspy.sac.sacio.SacIO.__getattr__` method, see the link for
an example).
.. rubric::Description of attributes/header fields (based on SacIris_).
.. _SacIris: http://www.iris.edu/manuals/sac/SAC_Manuals/FileFormatPt2.html
============ ==== =========================================================
Field Name Type Description
============ ==== =========================================================
npts N Number of points per data component. [required]
nvhdr N Header version number. Current value is the integer 6.
Older version data (NVHDR < 6) are automatically updated
when read into sac. [required]
b F Beginning value of the independent variable. [required]
e F Ending value of the independent variable. [required]
iftype I Type of file [required]:
* ITIME {Time series file}
* IRLIM {Spectral file---real and imaginary}
* IAMPH {Spectral file---amplitude and phase}
* IXY {General x versus y data}
* IXYZ {General XYZ (3-D) file}
leven L TRUE if data is evenly spaced. [required]
delta F Increment between evenly spaced samples (nominal value).
[required]
odelta F Observed increment if different from nominal value.
idep I Type of dependent variable:
* IUNKN (Unknown)
* IDISP (Displacement in nm)
* IVEL (Velocity in nm/sec)
* IVOLTS (Velocity in volts)
* IACC (Acceleration in nm/sec/sec)
scale F Multiplying scale factor for dependent variable
[not currently used]
depmin F Minimum value of dependent variable.
depmax F Maximum value of dependent variable.
depmen F Mean value of dependent variable.
nzyear N GMT year corresponding to reference (zero) time in file.
nyjday N GMT julian day.
nyhour N GMT hour.
nzmin N GMT minute.
nzsec N GMT second.
nzmsec N GMT millisecond.
iztype I Reference time equivalence:
* IUNKN (5): Unknown
* IB (9): Begin time
* IDAY (10): Midnight of reference GMT day
* IO (11): Event origin time
* IA (12): First arrival time
* ITn (13-22): User defined time pick n, n=0,9
o F Event origin time (seconds relative to reference time.)
a F First arrival time (seconds relative to reference time.)
ka K First arrival time identification.
f F Fini or end of event time (seconds relative to reference
time.)
tn F User defined time {ai n}=0,9 (seconds picks or markers
relative to reference time).
kt{ai n} K A User defined time {ai n}=0,9. pick identifications
kinst K Generic name of recording instrument
iinst I Type of recording instrument. [currently not used]
knetwk K Name of seismic network.
kstnm K Station name.
istreg I Station geographic region. [not currently used]
stla F Station latitude (degrees, north positive)
stlo F Station longitude (degrees, east positive).
stel F Station elevation (meters). [not currently used]
stdp F Station depth below surface (meters). [not currently
used]
cmpaz F Component azimuth (degrees, clockwise from north).
cmpinc F Component incident angle (degrees, from vertical).
kcmpnm K Component name.
lpspol L TRUE if station components have a positive polarity
(left-hand rule).
kevnm K Event name.
ievreg I Event geographic region. [not currently used]
evla F Event latitude (degrees north positive).
evlo F Event longitude (degrees east positive).
evel F Event elevation (meters). [not currently used]
evdp F Event depth below surface (meters). [not currently used]
mag F Event magnitude.
imagtyp I Magnitude type:
* IMB (Bodywave Magnitude)
* IMS (Surfacewave Magnitude)
* IML (Local Magnitude)
* IMW (Moment Magnitude)
* IMD (Duration Magnitude)
* IMX (User Defined Magnitude)
imagsrc I Source of magnitude information:
* INEIC (National Earthquake Information Center)
* IPDE (Preliminary Determination of Epicenter)
* IISC (International Seismological Centre)
* IREB (Reviewed Event Bulletin)
* IUSGS (US Geological Survey)
* IBRK (UC Berkeley)
* ICALTECH (California Institute of Technology)
* ILLNL (Lawrence Livermore National Laboratory)
* IEVLOC (Event Location (computer program) )
* IJSOP (Joint Seismic Observation Program)
* IUSER (The individual using SAC2000)
* IUNKNOWN (unknown)
ievtyp I Type of event:
* IUNKN (Unknown)
* INUCL (Nuclear event)
* IPREN (Nuclear pre-shot event)
* IPOSTN (Nuclear post-shot event)
* IQUAKE (Earthquake)
* IPREQ (Foreshock)
* IPOSTQ (Aftershock)
* ICHEM (Chemical explosion)
* IQB (Quarry or mine blast confirmed by quarry)
* IQB1 (Quarry/mine blast with designed shot
info-ripple fired)
* IQB2 (Quarry/mine blast with observed shot
info-ripple fired)
* IQMT (Quarry/mining-induced events:
tremors and rockbursts)
* IEQ (Earthquake)
* IEQ1 (Earthquakes in a swarm or aftershock
sequence)
* IEQ2 (Felt earthquake)
* IME (Marine explosion)
* IEX (Other explosion)
* INU (Nuclear explosion)
* INC (Nuclear cavity collapse)
* IO\_ (Other source of known origin)
* IR (Regional event of unknown origin)
* IT (Teleseismic event of unknown origin)
* IU (Undetermined or conflicting information)
* IOTHER (Other)
nevid N Event ID (CSS 3.0)
norid N Origin ID (CSS 3.0)
nwfid N Waveform ID (CSS 3.0)
khole k Hole identification if nuclear event.
dist F Station to event distance (km).
az F Event to station azimuth (degrees).
baz F Station to event azimuth (degrees).
gcarc F Station to event great circle arc length (degrees).
lcalda L TRUE if DIST AZ BAZ and GCARC are to be calculated from
st event coordinates.
iqual I Quality of data [not currently used]:
* IGOOD (Good data)
* IGLCH (Glitches)
* IDROP (Dropouts)
* ILOWSN (Low signal to noise ratio)
* IOTHER (Other)
isynth I Synthetic data flag [not currently used]:
* IRLDTA (Real data)
* ????? (Flags for various synthetic seismogram
codes)
user{ai n} F User defined variable storage area {ai n}=0,9.
kuser{ai n} K User defined variable storage area {ai n}=0,2.
lovrok L TRUE if it is okay to overwrite this file on disk.
============ ==== =========================================================
"""
[docs] def __init__(self, filen=False, headonly=False, alpha=False,
debug_headers=False):
self.byteorder = 'little'
self.InitArrays()
self.debug_headers = debug_headers
if filen is False:
return
# parse Trace object if we get one
if isinstance(filen, Trace):
self.readTrace(filen)
return
if alpha:
if headonly:
self.ReadSacXYHeader(filen)
else:
self.ReadSacXY(filen)
elif headonly:
self.ReadSacHeader(filen)
else:
self.ReadSacFile(filen)
[docs] def InitArrays(self):
"""
Function to initialize the floating, character and integer
header arrays (self.hf, self.hs, self.hi) with dummy values. This
function is useful for writing SAC files from artificial data,
thus the header arrays are not filled by a read method
beforehand
:return: Nothing
"""
# The SAC header has 70 floats, then 40 integers, then 192 bytes
# in strings. Store them in array (and convert the char to a
# list). That's a total of 632 bytes.
#
# allocate the array for header floats
self.hf = np.ndarray(70, dtype=native_str('<f4'))
self.hf[:] = -12345.0
#
# allocate the array for header integers
self.hi = np.ndarray(40, dtype=native_str('<i4'))
self.hi[:] = -12345
#
# allocate the array for header characters
self.hs = np.ndarray(24, dtype=native_str('|S8'))
self.hs[:] = b'-12345 ' # setting default value
# allocate the array for the points
self.seis = np.ndarray([], dtype=native_str('<f4'))
[docs] def fromarray(self, trace, begin=0.0, delta=1.0, distkm=0,
starttime=UTCDateTime("1970-01-01T00:00:00.000000")):
"""
Create a SAC file from an numpy.ndarray instance
>>> t = SacIO()
>>> b = np.arange(10)
>>> t.fromarray(b)
>>> t.GetHvalue('npts')
10
"""
if not isinstance(trace, np.ndarray):
raise SacError("input needs to be of instance numpy.ndarray")
else:
# Only copy the data if they are not of the required type
self.seis = np.require(trace, native_str('<f4'))
# convert start time to sac reference time, if it is not default
if begin == -12345:
reftime = starttime
else:
reftime = starttime - begin
# if there are any micro-seconds, use begin to store them
# integer arithmetic
millisecond = reftime.microsecond // 1000
# integer arithmetic
microsecond = (reftime.microsecond - millisecond * 1000)
if microsecond != 0:
begin += microsecond * 1e-6
# set a few values that are required to create a valid SAC-file
self.SetHvalue('int1', 2)
self.SetHvalue('cmpaz', 0)
self.SetHvalue('cmpinc', 0)
self.SetHvalue('nvhdr', 6)
self.SetHvalue('leven', 1)
self.SetHvalue('lpspol', 1)
self.SetHvalue('lcalda', 0)
self.SetHvalue('lovrok', 1)
self.SetHvalue('nzyear', reftime.year)
self.SetHvalue('nzjday', reftime.strftime("%j"))
self.SetHvalue('nzhour', reftime.hour)
self.SetHvalue('nzmin', reftime.minute)
self.SetHvalue('nzsec', reftime.second)
self.SetHvalue('nzmsec', millisecond)
self.SetHvalue('kcmpnm', 'Z')
self.SetHvalue('evla', 0)
self.SetHvalue('evlo', 0)
self.SetHvalue('iftype', 1)
self.SetHvalue('npts', len(trace))
self.SetHvalue('delta', delta)
self.SetHvalue('b', begin)
self.SetHvalue('e', begin + (len(trace) - 1) * delta)
self.SetHvalue('iztype', 9)
self.SetHvalue('dist', distkm)
[docs] def GetHvalue(self, item):
"""
Read SAC-header variable.
:param item: header variable name (e.g. 'npts' or 'delta')
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> tr = SacIO('test.sac') # doctest: +SKIP
>>> tr.GetHvalue('npts') # doctest: +SKIP
100
This is equivalent to:
>>> SacIO().GetHvalueFromFile('test.sac','npts') # doctest: +SKIP
100
Or:
>>> tr = SacIO('test.sac') # doctest: +SKIP
>>> tr.npts # doctest: +SKIP
100
"""
key = item.lower() # convert the item to lower case
if key in FDICT:
index = FDICT[key]
return(self.hf[index])
elif key in IDICT:
index = IDICT[key]
return(self.hi[index])
elif key in SDICT:
index = SDICT[key]
if index == 0:
myarray = self.hs[0].decode()
elif index == 1:
myarray = self.hs[1].decode() + self.hs[2].decode()
else:
myarray = self.hs[index + 1].decode() # extra 1 from item #2
return myarray
else:
raise SacError("Cannot find header entry for: " + item)
[docs] def SetHvalue(self, item, value):
"""
Assign new value to SAC-header variable.
:param item: SAC-header variable name
:param value: numeric or string value to be assigned to header
variable.
>>> from obspy.sac import SacIO
>>> tr = SacIO()
>>> print(tr.GetHvalue('kstnm').strip())
-12345
>>> tr.SetHvalue('kstnm', 'STA_NEW')
>>> print(tr.GetHvalue('kstnm').strip())
STA_NEW
"""
key = item.lower() # convert the item to lower case
#
if key in FDICT:
index = FDICT[key]
self.hf[index] = float(value)
elif key in IDICT:
index = IDICT[key]
self.hi[index] = int(value)
elif key in SDICT:
index = SDICT[key]
if value:
value = '%-8s' % value
else:
value = '-12345 '
if index == 0:
self.hs[0] = value.encode('ascii', 'strict')
elif index == 1:
value1 = '%-8s' % value[0:8]
value2 = '%-8s' % value[8:16]
self.hs[1] = value1.encode('ascii', 'strict')
self.hs[2] = value2.encode('ascii', 'strict')
else:
self.hs[index + 1] = value.encode('ascii', 'strict')
else:
raise SacError("Cannot find header entry for: " + item)
[docs] def IsSACfile(self, fh, fsize=True, lenchk=False):
"""
Test for a valid SAC file using arrays.
"""
cur_pos = fh.tell()
fh.seek(0, os.SEEK_END)
length = fh.tell()
fh.seek(cur_pos, os.SEEK_SET)
try:
npts = self.GetHvalue('npts')
except:
raise SacError("Unable to read number of points from header")
if lenchk and npts != len(self.seis):
raise SacError("Number of points in header and " +
"length of trace inconsistent!")
if fsize:
sizecheck = length - (632 + 4 * int(npts))
# size check info
if sizecheck != 0:
msg = "File-size and theoretical size are inconsistent.\n" \
"Check that headers are consistent with time series."
raise SacError(msg)
# get the SAC file version number
version = self.GetHvalue('nvhdr')
if version < 0 or version > 20:
raise SacError("Unknown header version!")
if self.GetHvalue('delta') <= 0:
raise SacError("Delta < 0 is not a valid header entry!")
[docs] def ReadSacFile(self, fh, fsize=True):
"""
Read read in the header and data in a SAC file
The header is split into three arrays - floats, ints, and strings and
the data points are returned in the array seis
:param fh: file or file-like object.
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> tr = SacIO() # doctest: +SKIP
>>> with open('test.sac') as fh:
... tr.ReadSacFile(fh) # doctest: +SKIP
This is equivalent to:
>>> with open('test.sac') as fh:
... tr = SacIO(fh) # doctest: +SKIP
"""
# --------------------------------------------------------------
# parse the header
#
# The sac header has 70 floats, 40 integers, then 192 bytes
# in strings. Store them in array (and convert the char to a
# list). That's a total of 632 bytes.
# --------------------------------------------------------------
self.hf = frombuffer(fh.read(4 * 70), dtype=native_str('<f4'))
self.hi = frombuffer(fh.read(4 * 40), dtype=native_str('<i4'))
# read in the char values
self.hs = frombuffer(fh.read(24 * 8), dtype=native_str('|S8'))
if len(self.hf) != 70 or len(self.hi) != 40 or len(self.hs) != 24:
self.hf = self.hi = self.hs = None
fh.close()
raise SacIOError("Cannot read all header values")
# only continue if it is a SAC file
try:
self.IsSACfile(fh, fsize)
except SacError:
try:
# if it is not a valid SAC-file try with big endian
# byte order
fh.seek(0, os.SEEK_SET)
self.hf = frombuffer(fh.read(4 * 70), dtype=native_str('>f4'))
self.hi = frombuffer(fh.read(4 * 40), dtype=native_str('>i4'))
# read in the char values
self.hs = frombuffer(fh.read(24 * 8), dtype=native_str('|S8'))
self.IsSACfile(fh, fsize)
self.byteorder = 'big'
except SacError as e:
raise SacError(e)
# --------------------------------------------------------------
# read in the seismogram points
# --------------------------------------------------------------
# you just have to know it's in the 10th place
# actually, it's in the SAC manual
npts = int(self.hi[9])
if self.byteorder == 'big':
self.seis = frombuffer(fh.read(npts * 4), dtype=native_str('>f4'))
else:
self.seis = frombuffer(fh.read(npts * 4), dtype=native_str('<f4'))
if len(self.seis) != npts:
self.hf = self.hi = self.hs = self.seis = None
raise SacIOError("Cannot read all data points")
try:
self._get_date()
except SacError:
warnings.warn('Cannot determine date')
if self.GetHvalue('lcalda'):
try:
self._get_dist()
except SacError:
pass
[docs] def ReadSacXY(self, fh):
"""
Read SAC XY files (ascii)
:param f: File or file-like object.
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> tr = SacIO() # doctest: +SKIP
>>> tr.ReadSacXY('testxy.sac') # doctest: +SKIP
>>> tr.GetHvalue('npts') # doctest: +SKIP
100
This is equivalent to:
>>> tr = SacIO('testxy.sac',alpha=True) # doctest: +SKIP
Reading only the header portion of alphanumeric SAC-files is currently
not supported.
"""
data = bytes(fh.read())
data = [_i.rstrip(b"\n\r") for _i in data.splitlines(True)]
if len(data) < 14 + 8 + 8:
raise SacIOError("Not a valid SAC file.")
# --------------------------------------------------------------
# parse the header
#
# The sac header has 70 floats, 40 integers, then 192 bytes
# in strings. Store them in array (and convert the char to a
# list). That's a total of 632 bytes.
# --------------------------------------------------------------
# read in the float values
self.hf = np.array([i.split() for i in data[:14]],
dtype=native_str('<f4')).ravel()
# read in the int values
self.hi = np.array([i.split() for i in data[14: 14 + 8]],
dtype=native_str('<i4')).ravel()
# reading in the string part is a bit more complicated
# because every string field has to be 8 characters long
# apart from the second field which is 16 characters long
# resulting in a total length of 192 characters
for i, j in enumerate(range(0, 24, 3)):
line = data[14 + 8 + i]
self.hs[j:j + 3] = np.fromstring(line, dtype=native_str('|S8'),
count=3)
# --------------------------------------------------------------
# read in the seismogram points
# --------------------------------------------------------------
self.seis = np.array([i.split() for i in data[30:]],
dtype=native_str('<f4')).ravel()
try:
self._get_date()
except SacError:
warnings.warn('Cannot determine date')
if self.GetHvalue('lcalda'):
try:
self._get_dist()
except SacError:
pass
[docs] def readTrace(self, trace):
"""
Fill in SacIO object with data from obspy trace.
Warning: Currently only the case of a previously empty SacIO object is
safe!
"""
# extracting relative SAC time as specified with b
try:
b = float(trace.stats['sac']['b'])
except KeyError:
b = 0.0
# filling in SAC/sacio specific defaults
self.fromarray(trace.data, begin=b, delta=trace.stats.delta,
starttime=trace.stats.starttime)
# overwriting with ObsPy defaults
for _j, _k in convert_dict.items():
self.SetHvalue(_j, trace.stats[_k])
# overwriting up SAC specific values
# note that the SAC reference time values (including B and E) are
# not used in here any more, they are already set by t.fromarray
# and directly deduce from tr.starttime
for _i in SAC_EXTRA:
try:
self.SetHvalue(_i, trace.stats.sac[_i])
except (AttributeError, KeyError):
pass
return
[docs] def WriteSacXY(self, fh):
"""
Write SAC XY file (ascii)
:param fh: open file or file-like object.
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> with open('test.sac', 'rb') as fh:
... tr = SacIO(fh) # doctest: +SKIP
>>> with open('test2.sac', 'wb') as fh:
... tr.WriteSacXY(fh) # doctest: +SKIP
>>> with open('test2.sac', 'wb') as fh:
... tr.IsValidXYSacFile(fh) # doctest: +SKIP
True
"""
# header
try:
np.savetxt(fh, np.reshape(self.hf, (14, 5)),
fmt=native_str("%#15.7g%#15.7g%#15.7g%#15.7g%#15.7g"))
np.savetxt(fh, np.reshape(self.hi, (8, 5)),
fmt=native_str("%10d%10d%10d%10d%10d"))
for i in range(0, 24, 3):
# numpy 1.6 compatibility
fh.write(self.hs[i:i + 3].tostring())
fh.write(b'\n')
except Exception as e:
raise SacIOError("Cannot write header values.", e)
# traces
npts = self.GetHvalue('npts')
if npts == -12345 or npts == 0:
return
try:
rows = npts // 5
np.savetxt(fh, np.reshape(self.seis[0:5 * rows], (rows, 5)),
fmt=native_str("%#15.7g%#15.7g%#15.7g%#15.7g%#15.7g"))
np.savetxt(fh, self.seis[5 * rows:], delimiter=b'\t')
except Exception as e:
raise SacIOError("Cannot write trace values.", e)
[docs] def WriteSacBinary(self, fh):
"""
Write a SAC binary file using the head arrays and array seis.
:param fh: open file or file-like object.
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> with open('test.sac', 'rb') as fh:
... tr = SacIO(fh) # doctest: +SKIP
>>> with open('test2.sac', 'wb') as fh:
... tr.WriteSacBinary(fh) # doctest: +SKIP
>>> import os
>>> os.stat('test2.sac')[6] == os.stat('test.sac')[6] # doctest: +SKIP
True
"""
try:
self._chck_header()
# numpy 1.6 compatibility
fh.write(self.hf.tostring())
fh.write(self.hi.tostring())
fh.write(self.hs.tostring())
fh.write(self.seis.tostring())
except Exception as e:
msg = "Cannot write SAC-buffer to file: "
raise SacIOError(msg, e)
[docs] def PrintIValue(self, label='=', value=-12345):
"""
Convenience function for printing undefined integer header values.
"""
if value != -12345:
print(label, value)
[docs] def PrintFValue(self, label='=', value=-12345.0):
"""
Convenience function for printing undefined float header values.
"""
if value != -12345.0:
print('%s %.8g' % (label, value))
[docs] def PrintSValue(self, label='=', value='-12345'):
"""
Convenience function for printing undefined string header values.
"""
if value.find('-12345') == -1:
print(label, value)
[docs] def ListStdValues(self): # h is a header list, s is a float list
"""
Convenience function for printing common header values.
:param: None
:return: None
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> t = SacIO('test.sac') # doctest: +SKIP
>>> t.ListStdValues() # doctest: +SKIP +NORMALIZE_WHITESPACE
<BLANKLINE>
Reference Time = 07/18/1978 (199) 8:0:0.0
Npts = 100
Delta = 1
Begin = 10
End = 109
Min = -1
Mean = 8.7539462e-08
Max = 1
Header Version = 6
Station = STA
Channel = Q
Event = FUNCGEN: SINE
If no header values are defined (i.e. all are equal 12345) than this
function won't do anything.
"""
#
# Seismogram Info:
#
try:
nzyear = self.GetHvalue('nzyear')
nzjday = self.GetHvalue('nzjday')
month = time.strptime(repr(nzyear) + " " + repr(nzjday),
"%Y %j").tm_mon
date = time.strptime(repr(nzyear) + " " + repr(nzjday),
"%Y %j").tm_mday
pattern = '\nReference Time = %2.2d/%2.2d/%d (%d) %d:%d:%d.%d'
print(pattern % (month, date,
self.GetHvalue('nzyear'),
self.GetHvalue('nzjday'),
self.GetHvalue('nzhour'),
self.GetHvalue('nzmin'),
self.GetHvalue('nzsec'),
self.GetHvalue('nzmsec')))
except ValueError:
pass
self.PrintIValue('Npts = ', self.GetHvalue('npts'))
self.PrintFValue('Delta = ', self.GetHvalue('delta'))
self.PrintFValue('Begin = ', self.GetHvalue('b'))
self.PrintFValue('End = ', self.GetHvalue('e'))
self.PrintFValue('Min = ', self.GetHvalue('depmin'))
self.PrintFValue('Mean = ', self.GetHvalue('depmen'))
self.PrintFValue('Max = ', self.GetHvalue('depmax'))
#
self.PrintIValue('Header Version = ', self.GetHvalue('nvhdr'))
#
# station Info:
#
self.PrintSValue('Station = ', self.GetHvalue('kstnm'))
self.PrintSValue('Channel = ', self.GetHvalue('kcmpnm'))
self.PrintFValue('Station Lat = ', self.GetHvalue('stla'))
self.PrintFValue('Station Lon = ', self.GetHvalue('stlo'))
self.PrintFValue('Station Elev = ', self.GetHvalue('stel'))
#
# Event Info:
#
self.PrintSValue('Event = ', self.GetHvalue('kevnm'))
self.PrintFValue('Event Lat = ', self.GetHvalue('evla'))
self.PrintFValue('Event Lon = ', self.GetHvalue('evlo'))
self.PrintFValue('Event Depth = ', self.GetHvalue('evdp'))
self.PrintFValue('Origin Time = ', self.GetHvalue('o'))
#
self.PrintFValue('Azimuth = ', self.GetHvalue('az'))
self.PrintFValue('Back Azimuth = ', self.GetHvalue('baz'))
self.PrintFValue('Distance (km) = ', self.GetHvalue('dist'))
self.PrintFValue('Distance (deg) = ', self.GetHvalue('gcarc'))
[docs] def GetHvalueFromFile(self, thePath, theItem):
"""
Quick access to a specific header item in specified file.
:param f: filename (SAC binary)
:type hn: str
:param hn: header variable name
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> t = SacIO() # doctest: +SKIP
>>> t.GetHvalueFromFile('test.sac','kcmpnm').rstrip() # doctest: +SKIP
'Q'
String header values have a fixed length of 8 or 16 characters. This
can lead to errors for example if you concatenate strings and forget to
strip off the trailing whitespace.
"""
#
# Read in the Header
#
with open(thePath, "rb") as fh:
self.ReadSacHeader(fh)
return(self.GetHvalue(theItem))
[docs] def SetHvalueInFile(self, thePath, theItem, theValue):
"""
Quick access to change a specific header item in a specified file.
:param f: filename (SAC binary)
:type hn: str
:param hn: header variable name
:type hv: str, float or int
:param hv: header variable value (numeric or string value to be
assigned to hn)
:return: None
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> t = SacIO() # doctest: +SKIP
>>> t.GetHvalueFromFile('test.sac','kstnm').rstrip() # doctest: +SKIP
'STA'
>>> t.SetHvalueInFile('test.sac','kstnm','blub') # doctest: +SKIP
>>> t.GetHvalueFromFile('test.sac','kstnm').rstrip() # doctest: +SKIP
'blub'
"""
# Read the header.
with open(thePath, "rb") as fh:
self.ReadSacHeader(fh)
# Modify it.
self.SetHvalue(theItem, theValue)
# Write it.
with open(thePath, "rb+") as fh:
self.WriteSacHeader(fh)
[docs] def IsValidSacFile(self, thePath):
"""
Quick test for a valid SAC binary file (wraps 'IsSACfile').
:param f: filename (SAC binary)
:rtype: boolean (True or False)
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> SacIO().IsValidSacFile('test.sac') # doctest: +SKIP
True
>>> SacIO().IsValidSacFile('testxy.sac') # doctest: +SKIP
False
"""
#
# Read in the Header
#
try:
self.ReadSacHeader(thePath)
except SacError:
return False
except SacIOError:
return False
else:
return True
[docs] def IsValidXYSacFile(self, fh):
"""
Quick test for a valid SAC ascii file.
:param file: file or file-like object.
:rtype: boolean (True or False)
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> SacIO().IsValidXYSacFile('testxy.sac') # doctest: +SKIP
True
>>> SacIO().IsValidXYSacFile('test.sac') # doctest: +SKIP
False
"""
try:
self.ReadSacXY(fh)
return True
except:
return False
[docs] def _get_date(self):
"""
If date header values are set calculate date in julian seconds
>>> t = SacIO()
>>> t.fromarray(np.random.randn(100), delta=1.0,
... starttime=UTCDateTime(1970,1,1))
>>> t._get_date()
>>> t.reftime.timestamp
0.0
>>> t.endtime.timestamp - t.reftime.timestamp
100.0
"""
# if any of the time-header values are still set to -12345 then
# UTCDateTime raises an exception and reftime is set to 0.0
try:
ms = self.GetHvalue('nzmsec') * 1000
yr = self.GetHvalue('nzyear')
if 0 <= yr <= 99:
warnings.warn(TWO_DIGIT_YEAR_MSG)
yr += 1900
self.reftime = UTCDateTime(year=yr,
julday=self.GetHvalue('nzjday'),
hour=self.GetHvalue('nzhour'),
minute=self.GetHvalue('nzmin'),
second=self.GetHvalue('nzsec'),
microsecond=ms)
b = float(self.GetHvalue('b'))
if b != -12345.0:
self.starttime = self.reftime + b
else:
self.starttime = self.reftime
self.endtime = self.starttime + \
self.GetHvalue('npts') * float(self.GetHvalue('delta'))
except:
try:
self.reftime = UTCDateTime(0.0)
b = float(self.GetHvalue('b'))
if b != -12345.0:
self.starttime = self.reftime + b
else:
self.starttime = self.reftime
self.endtime = self.reftime + \
self.GetHvalue('npts') * float(self.GetHvalue('delta'))
except:
raise SacError("Cannot calculate date")
[docs] def _get_dist(self):
"""
calculate distance from station and event coordinates
>>> t = SacIO()
>>> t.SetHvalue('evla',48.15)
>>> t.SetHvalue('evlo',11.58333)
>>> t.SetHvalue('stla',-41.2869)
>>> t.SetHvalue('stlo',174.7746)
>>> t._get_dist()
>>> print('%.2f' % t.GetHvalue('dist'))
18486.53
>>> print('%.5f' % t.GetHvalue('az'))
65.65415
>>> print('%.4f' % t.GetHvalue('baz'))
305.9755
The original SAC-program calculates the distance assuming a
average radius of 6371 km. Therefore, our routine should be more
accurate.
"""
eqlat = self.GetHvalue('evla')
eqlon = self.GetHvalue('evlo')
stlat = self.GetHvalue('stla')
stlon = self.GetHvalue('stlo')
d = self.GetHvalue('dist')
if eqlat == -12345.0 or eqlon == -12345.0 or \
stlat == -12345.0 or stlon == -12345.0:
raise SacError('Insufficient information to calculate distance.')
if d != -12345.0:
raise SacError('Distance is already set.')
dist, az, baz = gps2DistAzimuth(eqlat, eqlon, stlat, stlon)
self.SetHvalue('dist', dist / 1000.)
self.SetHvalue('az', az)
self.SetHvalue('baz', baz)
[docs] def swap_byte_order(self):
"""
Swap byte order of SAC-file in memory.
:param: None
:return: None
>>> from obspy.sac import SacIO # doctest: +SKIP
>>> t = SacIO('test.sac') # doctest: +SKIP
>>> t.swap_byte_order() # doctest: +SKIP
"""
if self.byteorder == 'big':
bs = '<'
self.byteorder = 'little'
elif self.byteorder == 'little':
bs = '>'
self.byteorder = 'big'
self.seis = self.seis.byteswap(True).newbyteorder(bs)
self.hf = self.hf.byteswap(True).newbyteorder(bs)
self.hi = self.hi.byteswap(True).newbyteorder(bs)
[docs] def __getattr__(self, hname):
"""
convenience function to access header values
:param hname: header variable name
>>> tr = SacIO()
>>> tr.fromarray(np.random.randn(100))
>>> tr.npts == tr.GetHvalue('npts') # doctest: +SKIP
True
"""
return self.GetHvalue(hname)
[docs]def attach_paz(tr, paz_file, todisp=False, tovel=False, torad=False,
tohz=False):
'''
Attach tr.stats.paz AttribDict to trace from SAC paz_file
This is experimental code, taken from
obspy.gse2.libgse2.attach_paz and adapted to the SAC-pole-zero
conventions. Especially the conversion from velocity to
displacement and vice versa is still under construction. It works
but I cannot guarantee that the values are correct. For more
information on the SAC-pole-zero format see:
http://www.iris.edu/files/sac-manual/commands/transfer.html. For a
useful discussion on polezero files and transfer functions in
general see:
http://seis-uk.le.ac.uk/equipment/downloads/data_management/\
seisuk_instrument_resp_removal.pdf
Also bear in mind that according to the SAC convention for
pole-zero files CONSTANT is defined as:
digitizer_gain*seismometer_gain*A0. This means that it does not
have explicit information on the digitizer gain and seismometer
gain which we therefore set to 1.0.
Attaches to a trace a paz AttribDict containing poles zeros and gain.
:param tr: An ObsPy :class:`~obspy.core.trace.Trace` object
:param paz_file: path to pazfile or file pointer
:param todisp: change a velocity transfer function to a displacement
transfer function by adding another zero
:param tovel: change a displacement transfer function to a velocity
transfer function by removing one 0,0j zero
:param torad: change to radians
:param tohz: change to Hertz
>>> from obspy import Trace
>>> import io
>>> tr = Trace()
>>> f = io.StringIO("""ZEROS 3
... -5.032 0.0
... POLES 6
... -0.02365 0.02365
... -0.02365 -0.02365
... -39.3011 0.
... -7.74904 0.
... -53.5979 21.7494
... -53.5979 -21.7494
... CONSTANT 2.16e18""")
>>> attach_paz(tr, f,torad=True)
>>> for z in tr.stats.paz['zeros']:
... print("%.2f %.2f" % (z.real, z.imag))
-31.62 0.00
0.00 0.00
0.00 0.00
'''
poles = []
zeros = []
if isinstance(paz_file, (str, native_str)):
paz_file = open(paz_file, 'r')
while True:
line = paz_file.readline()
if not line:
break
# lines starting with * are comments
if line.startswith('*'):
continue
if line.find('ZEROS') != -1:
a = line.split()
noz = int(a[1])
for _k in range(noz):
line = paz_file.readline()
a = line.split()
if line.find('POLES') != -1 or line.find('CONSTANT') != -1 or \
line.startswith('*') or not line:
while len(zeros) < noz:
zeros.append(complex(0, 0j))
break
else:
zeros.append(complex(float(a[0]), float(a[1])))
if line.find('POLES') != -1:
a = line.split()
nop = int(a[1])
for _k in range(nop):
line = paz_file.readline()
a = line.split()
if line.find('CONSTANT') != -1 or line.find('ZEROS') != -1 or \
line.startswith('*') or not line:
while len(poles) < nop:
poles.append(complex(0, 0j))
break
else:
poles.append(complex(float(a[0]), float(a[1])))
if line.find('CONSTANT') != -1:
a = line.split()
# in the observatory this is the seismometer gain [muVolt/nm/s]
# the A0_normalization_factor is hardcoded to 1.0
constant = float(a[1])
paz_file.close()
# To convert the velocity response to the displacement response,
# multiplication with jw is used. This is equivalent to one more
# zero in the pole-zero representation
if todisp:
zeros.append(complex(0, 0j))
# To convert the displacement response to the velocity response,
# division with jw is used. This is equivalent to one less zero
# in the pole-zero representation
if tovel:
for i, zero in enumerate(list(zeros)):
if zero == complex(0, 0j):
zeros.pop(i)
break
else:
raise Exception("Could not remove (0,0j) zero to change \
displacement response to velocity response")
# convert poles, zeros and gain in Hertz to radians
if torad:
tmp = [z * 2. * np.pi for z in zeros]
zeros = tmp
tmp = [p * 2. * np.pi for p in poles]
poles = tmp
# When extracting RESP files and SAC_PZ files
# from a dataless SEED using the rdseed program
# where the former is in Hz and the latter in radians,
# there gains seem to be unaffected by this.
# According to this document:
# http://www.le.ac.uk/
# seis-uk/downloads/seisuk_instrument_resp_removal.pdf
# the gain should also be converted when changing from
# hertz to radians or vice versa. However, the rdseed programs
# does not do this. I'm not entirely sure at this stage which one is
# correct or if I have missed something. I've therefore decided
# to leave it out for now, in order to stay compatible with the
# rdseed program and the SAC program.
# constant *= (2. * np.pi) ** 3
# convert poles, zeros and gain in radian to Hertz
if tohz:
for i, z in enumerate(zeros):
if abs(z) > 0.0:
zeros[i] /= 2 * np.pi
for i, p in enumerate(poles):
if abs(p) > 0.0:
poles[i] /= 2 * np.pi
# constant /= (2. * np.pi) ** 3
# fill up ObsPy Poles and Zeros AttribDict
# In SAC pole-zero files CONSTANT is defined as:
# digitizer_gain*seismometer_gain*A0
tr.stats.paz = AttribDict()
tr.stats.paz.seismometer_gain = 1.0
tr.stats.paz.digitizer_gain = 1.0
tr.stats.paz.poles = poles
tr.stats.paz.zeros = zeros
# taken from obspy.gse2.paz:145
tr.stats.paz.sensitivity = tr.stats.paz.digitizer_gain * \
tr.stats.paz.seismometer_gain
tr.stats.paz.gain = constant
[docs]def attach_resp(tr, resp_file, todisp=False, tovel=False, torad=False,
tohz=False):
"""
Extract key instrument response information from a RESP file, which
can be extracted from a dataless SEED volume by, for example, using
the script obspy-dataless2resp or the rdseed program. At the moment,
you have to determine yourself if the given response is for velocity
or displacement and if the values are given in rad or Hz. This is
still experimental code (see also documentation for
:func:`obspy.sac.sacio.attach_paz`).
Attaches to a trace a paz AttribDict containing poles, zeros, and gain.
:param tr: An ObsPy :class:`~obspy.core.trace.Trace` object
:param resp_file: path to RESP-file or file pointer
:param todisp: change a velocity transfer function to a displacement
transfer function by adding another zero
:param tovel: change a displacement transfer function to a velocity
transfer function by removing one 0,0j zero
:param torad: change to radians
:param tohz: change to Hertz
>>> from obspy import Trace
>>> import os
>>> tr = Trace()
>>> respfile = os.path.join(os.path.dirname(__file__), 'tests', 'data',
... 'RESP.NZ.CRLZ.10.HHZ')
>>> attach_resp(tr, respfile, torad=True, todisp=False)
>>> for k in sorted(tr.stats.paz): # doctest: +NORMALIZE_WHITESPACE
... print(k)
digitizer_gain
gain
poles
seismometer_gain
sensitivity
t_shift
zeros
>>> print(tr.stats.paz.poles) # doctest: +SKIP
[(-0.15931644664884559+0.15931644664884559j),
(-0.15931644664884559-0.15931644664884559j),
(-314.15926535897933+202.31856689118268j),
(-314.15926535897933-202.31856689118268j)]
"""
if not hasattr(resp_file, 'write'):
resp_filep = open(resp_file, 'r')
else:
resp_filep = resp_file
zeros_pat = r'B053F10-13'
poles_pat = r'B053F15-18'
a0_pat = r'B053F07'
sens_pat = r'B058F04'
t_shift_pat = r'B057F08'
t_shift = 0.0
poles = []
zeros = []
while True:
line = resp_filep.readline()
if not line:
break
if line.startswith(a0_pat):
a0 = float(line.split(':')[1])
if line.startswith(sens_pat):
sens = float(line.split(':')[1])
if line.startswith(poles_pat):
tmp = line.split()
poles.append(complex(float(tmp[2]), float(tmp[3])))
if line.startswith(zeros_pat):
tmp = line.split()
zeros.append(complex(float(tmp[2]), float(tmp[3])))
if line.startswith(t_shift_pat):
t_shift += float(line.split(':')[1])
constant = a0 * sens
if not hasattr(resp_file, 'write'):
resp_filep.close()
if torad:
tmp = [z * 2. * np.pi for z in zeros]
zeros = tmp
tmp = [p * 2. * np.pi for p in poles]
poles = tmp
if todisp:
zeros.append(complex(0, 0j))
# To convert the displacement response to the velocity response,
# division with jw is used. This is equivalent to one less zero
# in the pole-zero representation
if tovel:
for i, zero in enumerate(list(zeros)):
if zero == complex(0, 0j):
zeros.pop(i)
break
else:
raise Exception("Could not remove (0,0j) zero to change \
displacement response to velocity response")
# convert poles, zeros and gain in radian to Hertz
if tohz:
for i, z in enumerate(zeros):
if abs(z) > 0.0:
zeros[i] /= 2 * np.pi
for i, p in enumerate(poles):
if abs(p) > 0.0:
poles[i] /= 2 * np.pi
constant /= (2. * np.pi) ** 3
# fill up ObsPy Poles and Zeros AttribDict
# In SAC pole-zero files CONSTANT is defined as:
# digitizer_gain*seismometer_gain*A0
tr.stats.paz = AttribDict()
tr.stats.paz.seismometer_gain = sens
tr.stats.paz.digitizer_gain = 1.0
tr.stats.paz.poles = poles
tr.stats.paz.zeros = zeros
# taken from obspy.gse2.paz:145
tr.stats.paz.sensitivity = tr.stats.paz.digitizer_gain * \
tr.stats.paz.seismometer_gain
tr.stats.paz.gain = constant
tr.stats.paz.t_shift = t_shift
if __name__ == "__main__":
import doctest
doctest.testmod()