first time commiting, please rectify and tell me what is wrong.
This commit is contained in:
parent
b49206407a
commit
d4bb265c37
@ -11,140 +11,70 @@ import numpy as np
|
||||
from obspy.core import UTCDateTime
|
||||
import obspy.core.event as ope
|
||||
|
||||
def runProgram(cmd, parameter=None):
|
||||
"""
|
||||
run an external program specified by cmd with parameters input returning the
|
||||
stdout output
|
||||
|
||||
:param cmd: name of the command to run
|
||||
:type cmd: str
|
||||
:param parameter: filename of parameter file or parameter string
|
||||
:type parameter: str
|
||||
:return: stdout output
|
||||
:rtype: str
|
||||
"""
|
||||
|
||||
if parameter:
|
||||
cmd.strip()
|
||||
cmd += ' %s 2>&1' % parameter
|
||||
|
||||
output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
|
||||
shell = True)
|
||||
|
||||
|
||||
|
||||
def fnConstructor(s):
|
||||
if type(s) is str:
|
||||
s = s.split(':')[-1]
|
||||
else:
|
||||
s = getHash(UTCDateTime())
|
||||
|
||||
badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
|
||||
badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
|
||||
|
||||
fn = badchars.sub('_', s)
|
||||
|
||||
if badsuffix.match(fn):
|
||||
fn = '_' + fn
|
||||
return fn
|
||||
|
||||
|
||||
def getLogin():
|
||||
return pwd.getpwuid(os.getuid())[0]
|
||||
|
||||
|
||||
def getHash(time):
|
||||
def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
|
||||
'''
|
||||
:param time: time object for which a hash should be calculated
|
||||
:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
|
||||
:return: str
|
||||
createArrival - function to create an Obspy Arrival
|
||||
:param pickresID: Resource identifier of the created pick
|
||||
:type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
|
||||
|
||||
# eventnum is no input for this function
|
||||
:param eventnum: human-readable event identifier
|
||||
:type eventnum: str
|
||||
|
||||
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
|
||||
holding information on the creation of the returned object
|
||||
:type cinfo: :class: `~obspy.core.event.CreationInfo` object
|
||||
:param phase: name of the arrivals seismic phase
|
||||
:type phase: str
|
||||
|
||||
# also no input for this function
|
||||
:param station: name of the station at which the seismic phase has been
|
||||
picked
|
||||
:type station: str
|
||||
:param authority_id: name of the institution carrying out the processing
|
||||
:type authority_id: str
|
||||
|
||||
:param azimuth: azimuth between source and receiver
|
||||
:type azimuth: float or int, optional
|
||||
:param dist: distance between source and receiver
|
||||
:type dist: float or int, optional
|
||||
:return: An ObsPy :class: `~obspy.core.event.Arrival` object
|
||||
'''
|
||||
hg = hashlib.sha1()
|
||||
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
|
||||
return hg.hexdigest()
|
||||
|
||||
|
||||
def getOwner(fn):
|
||||
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
|
||||
|
||||
|
||||
def prepTimeAxis(stime, trace):
|
||||
nsamp = trace.stats.npts
|
||||
srate = trace.stats.sampling_rate
|
||||
tincr = trace.stats.delta
|
||||
etime = stime + nsamp / srate
|
||||
time_ax = np.arange(stime, etime, tincr)
|
||||
if len(time_ax) < nsamp:
|
||||
print 'elongate time axes by one datum'
|
||||
time_ax = np.arange(stime, etime + tincr, tincr)
|
||||
elif len(time_ax) > nsamp:
|
||||
print 'shorten time axes by one datum'
|
||||
time_ax = np.arange(stime, etime - tincr, tincr)
|
||||
if len(time_ax) != nsamp:
|
||||
raise ValueError('{0} samples of data \n '
|
||||
'{1} length of time vector \n'
|
||||
'delta: {2}'.format(nsamp, len(time_ax), tincr))
|
||||
return time_ax
|
||||
|
||||
|
||||
def scaleWFData(data, factor=None, components='all'):
|
||||
"""
|
||||
produce scaled waveforms from given waveform data and a scaling factor,
|
||||
waveform may be selected by their components name
|
||||
:param data: waveform data to be scaled
|
||||
:type data: `~obspy.core.stream.Stream` object
|
||||
:param factor: scaling factor
|
||||
:type factor: float
|
||||
:param components: components labels for the traces in data to be scaled by
|
||||
the scaling factor (optional, default: 'all')
|
||||
:type components: tuple
|
||||
:return: scaled waveform data
|
||||
:rtype: `~obspy.core.stream.Stream` object
|
||||
"""
|
||||
if components is not 'all':
|
||||
for comp in components:
|
||||
if factor is None:
|
||||
max_val = np.max(np.abs(data.select(component=comp)[0].data))
|
||||
data.select(component=comp)[0].data /= 2 * max_val
|
||||
else:
|
||||
data.select(component=comp)[0].data /= 2 * factor
|
||||
arrival = ope.Arrival()
|
||||
arrival.creation_info = cinfo
|
||||
arrival.pick_id = pickresID
|
||||
arrival.phase = phase
|
||||
if azimuth is not None:
|
||||
arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360. #what about azimuth > 180?
|
||||
else:
|
||||
for tr in data:
|
||||
if factor is None:
|
||||
max_val = float(np.max(np.abs(tr.data)))
|
||||
tr.data /= 2 * max_val
|
||||
else:
|
||||
tr.data /= 2 * factor
|
||||
|
||||
return data
|
||||
|
||||
def demeanTrace(trace, window):
|
||||
"""
|
||||
returns the DATA where each trace is demean by the average value within
|
||||
WINDOW
|
||||
:param trace: waveform trace object
|
||||
:type trace: `~obspy.core.stream.Trace`
|
||||
:param inoise: range of indices of DATA within the WINDOW
|
||||
:type window: tuple
|
||||
:return: trace
|
||||
:rtype: `~obspy.core.stream.Trace`
|
||||
"""
|
||||
trace.data -= trace.data[window].mean()
|
||||
return trace
|
||||
|
||||
|
||||
def getGlobalTimes(stream):
|
||||
min_start = UTCDateTime()
|
||||
max_end = None
|
||||
for trace in stream:
|
||||
if trace.stats.starttime < min_start:
|
||||
min_start = trace.stats.starttime
|
||||
if max_end is None or trace.stats.endtime > max_end:
|
||||
max_end = trace.stats.endtime
|
||||
return min_start, max_end
|
||||
arrival.azimuth = azimuth
|
||||
arrival.distance = dist
|
||||
return arrival
|
||||
|
||||
def createAmplitude(pickID, amp, unit, category, cinfo):
|
||||
'''
|
||||
:param pickID:
|
||||
:param amp:
|
||||
:param unit:
|
||||
:param category:
|
||||
:param cinfo:
|
||||
:return:
|
||||
'''
|
||||
amplitude = ope.Amplitude()
|
||||
amplitude.creation_info = cinfo
|
||||
amplitude.generic_amplitude = amp
|
||||
amplitude.unit = ope.AmplitudeUnit(unit)
|
||||
amplitude.type = ope.AmplitudeCategory(category)
|
||||
amplitude.pick_id = pickID
|
||||
return amplitude
|
||||
|
||||
def createCreationInfo(agency_id=None, creation_time=None, author=None):
|
||||
'''
|
||||
:param agency_id:
|
||||
:param creation_time:
|
||||
:param author:
|
||||
:return:
|
||||
'''
|
||||
if author is None:
|
||||
author = getLogin()
|
||||
if creation_time is None:
|
||||
@ -153,56 +83,6 @@ def createCreationInfo(agency_id=None, creation_time=None, author=None):
|
||||
creation_time=creation_time)
|
||||
|
||||
|
||||
def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
|
||||
'''
|
||||
|
||||
:param timetohash:
|
||||
:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
|
||||
:type restype: str
|
||||
:param authority_id: name of the institution carrying out the processing
|
||||
:type authority_id: str, optional
|
||||
:return:
|
||||
'''
|
||||
assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
|
||||
"UTCDateTime object"
|
||||
hid = getHash(timetohash)
|
||||
if hrstr is None:
|
||||
resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
|
||||
else:
|
||||
resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
|
||||
if authority_id is not None:
|
||||
resID.convertIDToQuakeMLURI(authority_id=authority_id)
|
||||
return resID
|
||||
|
||||
|
||||
def createOrigin(origintime, cinfo, latitude, longitude, depth):
|
||||
'''
|
||||
createOrigin - function to create an ObsPy Origin
|
||||
:param origintime: the origins time of occurence
|
||||
:type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
|
||||
:param latitude: latitude in decimal degree of the origins location
|
||||
:type latitude: float
|
||||
:param longitude: longitude in decimal degree of the origins location
|
||||
:type longitude: float
|
||||
:param depth: hypocentral depth of the origin
|
||||
:type depth: float
|
||||
:return: An ObsPy :class: `~obspy.core.event.Origin` object
|
||||
'''
|
||||
|
||||
assert isinstance(origintime, UTCDateTime), "origintime has to be " \
|
||||
"a UTCDateTime object, but " \
|
||||
"actually is of type " \
|
||||
"'%s'" % type(origintime)
|
||||
|
||||
origin = ope.Origin()
|
||||
origin.time = origintime
|
||||
origin.creation_info = cinfo
|
||||
origin.latitude = latitude
|
||||
origin.longitude = longitude
|
||||
origin.depth = depth
|
||||
return origin
|
||||
|
||||
|
||||
def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
|
||||
authority_id=None):
|
||||
'''
|
||||
@ -247,14 +127,56 @@ def createEvent(origintime, cinfo, originloc=None, etype=None, resID=None,
|
||||
event.origins = [o]
|
||||
return event
|
||||
|
||||
def createMagnitude(originID, cinfo):
|
||||
'''
|
||||
createMagnitude - function to create an ObsPy Magnitude object
|
||||
:param originID:
|
||||
:param cinfo:
|
||||
:param authority_id: # is no input
|
||||
:return:
|
||||
'''
|
||||
magnitude = ope.Magnitude()
|
||||
magnitude.creation_info = cinfo
|
||||
magnitude.origin_id = originID
|
||||
return magnitude
|
||||
|
||||
def createOrigin(origintime, cinfo, latitude, longitude, depth):
|
||||
'''
|
||||
createOrigin - function to create an ObsPy Origin
|
||||
:param origintime: the origins time of occurence
|
||||
:type origintime: :class: `~obspy.core.utcdatetime.UTCDateTime` object
|
||||
# cinfo missing
|
||||
:param latitude: latitude in decimal degree of the origins location
|
||||
:type latitude: float
|
||||
:param longitude: longitude in decimal degree of the origins location
|
||||
:type longitude: float
|
||||
:param depth: hypocentral depth of the origin
|
||||
:type depth: float
|
||||
:return: An ObsPy :class: `~obspy.core.event.Origin` object
|
||||
'''
|
||||
|
||||
assert isinstance(origintime, UTCDateTime), "origintime has to be " \
|
||||
"a UTCDateTime object, but " \
|
||||
"actually is of type " \
|
||||
"'%s'" % type(origintime)
|
||||
|
||||
origin = ope.Origin()
|
||||
origin.time = origintime
|
||||
origin.creation_info = cinfo
|
||||
origin.latitude = latitude
|
||||
origin.longitude = longitude
|
||||
origin.depth = depth
|
||||
return origin
|
||||
|
||||
def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
|
||||
wfseedstr, authority_id):
|
||||
'''
|
||||
createPick - function to create an ObsPy Pick
|
||||
|
||||
# origintime missing
|
||||
:param picknum: number of the created pick
|
||||
:type picknum: int
|
||||
# picktime missing
|
||||
:param eventnum: human-readable event identifier
|
||||
:type eventnum: str
|
||||
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
|
||||
@ -282,61 +204,175 @@ def createPick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
|
||||
pick.waveform_id = ope.ResourceIdentifier(id=wfseedstr, prefix='file:/')
|
||||
return pick
|
||||
|
||||
|
||||
def createArrival(pickresID, cinfo, phase, azimuth=None, dist=None):
|
||||
def createResourceID(timetohash, restype, authority_id=None, hrstr=None):
|
||||
'''
|
||||
createArrival - function to create an Obspy Arrival
|
||||
:param pickresID: Resource identifier of the created pick
|
||||
:type pickresID: :class: `~obspy.core.event.ResourceIdentifier` object
|
||||
:param eventnum: human-readable event identifier
|
||||
:type eventnum: str
|
||||
:param cinfo: An ObsPy :class: `~obspy.core.event.CreationInfo` object
|
||||
holding information on the creation of the returned object
|
||||
:type cinfo: :class: `~obspy.core.event.CreationInfo` object
|
||||
:param phase: name of the arrivals seismic phase
|
||||
:type phase: str
|
||||
:param station: name of the station at which the seismic phase has been
|
||||
picked
|
||||
:type station: str
|
||||
|
||||
:param timetohash:
|
||||
# type (timetohas) missing
|
||||
:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
|
||||
:type restype: str
|
||||
:param authority_id: name of the institution carrying out the processing
|
||||
:type authority_id: str
|
||||
:param azimuth: azimuth between source and receiver
|
||||
:type azimuth: float or int, optional
|
||||
:param dist: distance between source and receiver
|
||||
:type dist: float or int, optional
|
||||
:return: An ObsPy :class: `~obspy.core.event.Arrival` object
|
||||
'''
|
||||
arrival = ope.Arrival()
|
||||
arrival.creation_info = cinfo
|
||||
arrival.pick_id = pickresID
|
||||
arrival.phase = phase
|
||||
if azimuth is not None:
|
||||
arrival.azimuth = float(azimuth) if azimuth > -180 else azimuth + 360.
|
||||
else:
|
||||
arrival.azimuth = azimuth
|
||||
arrival.distance = dist
|
||||
return arrival
|
||||
|
||||
|
||||
def createMagnitude(originID, cinfo):
|
||||
'''
|
||||
createMagnitude - function to create an ObsPy Magnitude object
|
||||
:param originID:
|
||||
:param cinfo:
|
||||
:param authority_id:
|
||||
:type authority_id: str, optional
|
||||
# hrstr missing
|
||||
:return:
|
||||
'''
|
||||
magnitude = ope.Magnitude()
|
||||
magnitude.creation_info = cinfo
|
||||
magnitude.origin_id = originID
|
||||
return magnitude
|
||||
assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
|
||||
"UTCDateTime object"
|
||||
hid = getHash(timetohash)
|
||||
if hrstr is None:
|
||||
resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
|
||||
else:
|
||||
resID = ope.ResourceIdentifier(restype + '/' + hrstr + '_' + hid[0:6])
|
||||
if authority_id is not None:
|
||||
resID.convertIDToQuakeMLURI(authority_id=authority_id)
|
||||
return resID
|
||||
|
||||
def demeanTrace(trace, window):
|
||||
"""
|
||||
returns the DATA where each trace is demean by the average value within
|
||||
WINDOW
|
||||
:param trace: waveform trace object
|
||||
:type trace: `~obspy.core.stream.Trace`
|
||||
:param inoise: range of indices of DATA within the WINDOW # not used
|
||||
# param (window) mising
|
||||
:type window: tuple
|
||||
:return: trace
|
||||
:rtype: `~obspy.core.stream.Trace`
|
||||
"""
|
||||
trace.data -= trace.data[window].mean()
|
||||
return trace
|
||||
|
||||
def createAmplitude(pickID, amp, unit, category, cinfo):
|
||||
amplitude = ope.Amplitude()
|
||||
amplitude.creation_info = cinfo
|
||||
amplitude.generic_amplitude = amp
|
||||
amplitude.unit = ope.AmplitudeUnit(unit)
|
||||
amplitude.type = ope.AmplitudeCategory(category)
|
||||
amplitude.pick_id = pickID
|
||||
return amplitude
|
||||
def fnConstructor(s):
|
||||
'''
|
||||
|
||||
:param s:
|
||||
:return:
|
||||
'''
|
||||
if type(s) is str:
|
||||
s = s.split(':')[-1]
|
||||
else:
|
||||
s = getHash(UTCDateTime())
|
||||
|
||||
badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
|
||||
badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
|
||||
|
||||
fn = badchars.sub('_', s)
|
||||
|
||||
if badsuffix.match(fn):
|
||||
fn = '_' + fn
|
||||
return fn
|
||||
|
||||
def getGlobalTimes(stream):
|
||||
'''
|
||||
|
||||
:param stream:
|
||||
:return:
|
||||
'''
|
||||
min_start = UTCDateTime()
|
||||
max_end = None
|
||||
for trace in stream:
|
||||
if trace.stats.starttime < min_start:
|
||||
min_start = trace.stats.starttime
|
||||
if max_end is None or trace.stats.endtime > max_end:
|
||||
max_end = trace.stats.endtime
|
||||
return min_start, max_end
|
||||
|
||||
def getHash(time):
|
||||
'''
|
||||
:param time: time object for which a hash should be calculated
|
||||
:type time: :class: `~obspy.core.utcdatetime.UTCDateTime` object
|
||||
:return: str
|
||||
'''
|
||||
hg = hashlib.sha1()
|
||||
hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
|
||||
return hg.hexdigest()
|
||||
|
||||
def getLogin():
|
||||
'''
|
||||
|
||||
:return:
|
||||
'''
|
||||
return pwd.getpwuid(os.getuid())[0]
|
||||
|
||||
def getOwner(fn):
|
||||
'''
|
||||
|
||||
:param fn:
|
||||
:return:
|
||||
'''
|
||||
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
|
||||
|
||||
def prepTimeAxis(stime, trace):
|
||||
'''
|
||||
|
||||
:param stime:
|
||||
:param trace:
|
||||
:return:
|
||||
'''
|
||||
nsamp = trace.stats.npts
|
||||
srate = trace.stats.sampling_rate
|
||||
tincr = trace.stats.delta
|
||||
etime = stime + nsamp / srate
|
||||
time_ax = np.arange(stime, etime, tincr)
|
||||
if len(time_ax) < nsamp:
|
||||
print 'elongate time axes by one datum'
|
||||
time_ax = np.arange(stime, etime + tincr, tincr)
|
||||
elif len(time_ax) > nsamp:
|
||||
print 'shorten time axes by one datum'
|
||||
time_ax = np.arange(stime, etime - tincr, tincr)
|
||||
if len(time_ax) != nsamp:
|
||||
raise ValueError('{0} samples of data \n '
|
||||
'{1} length of time vector \n'
|
||||
'delta: {2}'.format(nsamp, len(time_ax), tincr))
|
||||
return time_ax
|
||||
|
||||
def runProgram(cmd, parameter=None):
|
||||
"""
|
||||
run an external program specified by cmd with parameters input returning the
|
||||
stdout output
|
||||
|
||||
:param cmd: name of the command to run
|
||||
:type cmd: str
|
||||
:param parameter: filename of parameter file or parameter string
|
||||
:type parameter: str
|
||||
:return: stdout output
|
||||
:rtype: str
|
||||
"""
|
||||
|
||||
if parameter:
|
||||
cmd.strip()
|
||||
cmd += ' %s 2>&1' % parameter
|
||||
|
||||
output = subprocess.check_output('{} | tee /dev/stderr'.format(cmd),
|
||||
shell = True)
|
||||
# no return command?
|
||||
|
||||
def scaleWFData(data, factor=None, components='all'):
|
||||
"""
|
||||
produce scaled waveforms from given waveform data and a scaling factor,
|
||||
waveform may be selected by their components name
|
||||
:param data: waveform data to be scaled
|
||||
:type data: `~obspy.core.stream.Stream` object
|
||||
:param factor: scaling factor
|
||||
:type factor: float
|
||||
:param components: components labels for the traces in data to be scaled by
|
||||
the scaling factor (optional, default: 'all')
|
||||
:type components: tuple
|
||||
:return: scaled waveform data
|
||||
:rtype: `~obspy.core.stream.Stream` object
|
||||
"""
|
||||
if components is not 'all':
|
||||
for comp in components:
|
||||
if factor is None:
|
||||
max_val = np.max(np.abs(data.select(component=comp)[0].data))
|
||||
data.select(component=comp)[0].data /= 2 * max_val
|
||||
else:
|
||||
data.select(component=comp)[0].data /= 2 * factor
|
||||
else:
|
||||
for tr in data:
|
||||
if factor is None:
|
||||
max_val = float(np.max(np.abs(tr.data)))
|
||||
tr.data /= 2 * max_val
|
||||
else:
|
||||
tr.data /= 2 * factor
|
||||
return data
|
Loading…
Reference in New Issue
Block a user