Add object based approach to autopickstation: preparing traces, modifying cuttimes with taupy
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Darius Arnold
parent
9b787ac4e8
commit
0230f0bf2e
@ -137,6 +137,274 @@ def get_source_coords(parser, station_id):
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print('Could not get source coordinates for station {}: {}'.format(station_id, e))
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return station_coords
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class PickingParameters(object):
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"""
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Stores parameters used for picking a single station.
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"""
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def __init__(self, *args, **kwargs):
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"""
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Add dictionaries given as positional arguments and the keyword argument dictionary to the instance
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as attributes. Positional arguments with types differing from dict are ignored.
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"""
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# add entries from dictionaries given as positional arguments
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for arg in args:
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if type(arg) == dict:
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self.add_params_from_dict(arg)
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# add values given as keyword arguments
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self.add_params_from_dict(kwargs)
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def add_params_from_dict(self, d):
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"""
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Add all key-value pairs from dictionary d to the class namespace as attributes.
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:param d:
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:type d: dict
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:rtype: None
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"""
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for key, value in d.items():
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setattr(self, key, value)
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class PickingResults(object):
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def __init__(self):
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# initialize output
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self.Pweight = 4 # weight for P onset
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self.Sweight = 4 # weight for S onset
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self.FM = 'N' # first motion (polarity)
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self.SNRP = None # signal-to-noise ratio of P onset
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self.SNRPdB = None # signal-to-noise ratio of P onset [dB]
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self.SNRS = None # signal-to-noise ratio of S onset
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self.SNRSdB = None # signal-to-noise ratio of S onset [dB]
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self.mpickP = None # most likely P onset
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self.lpickP = None # latest possible P onset
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self.epickP = None # earliest possible P onset
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self.mpickS = None # most likely S onset
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self.lpickS = None # latest possible S onset
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self.epickS = None # earliest possible S onset
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self.Perror = None # symmetrized picking error P onset
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self.Serror = None # symmetrized picking error S onset
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self.aicSflag = 0
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self.aicPflag = 0
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self.Pflag = 0
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self.Sflag = 0
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self.Pmarker = []
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self.Ao = None # Wood-Anderson peak-to-peak amplitude
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self.picker = 'auto' # type of picks
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class MissingTraceException(ValueError):
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"""
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Used to indicate missing traces in a obspy.core.stream.Stream object
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"""
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pass
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class AutopickStation(object):
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def __init__(self, wfstream, pickparam, verbose, iplot, fig_dict, metadata, origin):
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# save given parameters
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self.wfstream = wfstream
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self.pickparam = pickparam
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self.verbose = verbose
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self.iplot = iplot
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self.fig_dict = fig_dict
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self.metadata = metadata
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self.origin = origin
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# extract additional information
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pickparams = self.extract_pickparams(pickparam)
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self.p_params, self.s_params, self.first_motion_params, self.signal_length_params = pickparams
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self.results = PickingResults()
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self.channelorder = {'Z': 3, 'N': 1, 'E': 2} # TODO get this from the pylot preferences
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self.station_name = wfstream[0].stats.station
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self.network_name = wfstream[0].stats.network
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self.station_id = '{}.{}'.format(self.network_name, self.station_name)
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# default values used in old autopickstation function #TODO way for user to set those
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self.detrend_type = 'demean'
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self.filter_type = 'bandpass'
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self.zerophase = False
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self.taper_max_percentage = 0.05
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self.taper_type = 'hann'
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def vprint(self, s):
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"""Only print statement if verbose picking is set to true."""
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if self.verbose:
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print(s)
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def extract_pickparams(self, pickparam):
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"""
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Get parameter names out of pickparam dictionary into PickingParameters objects and return them.
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:return: PickingParameters objects containing 1. p pick parameters, 2. s pick parameters, 3. first motion determinatiion
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parameters, 4. signal length parameters
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:rtype: (PickingParameters, PickingParameters, PickingParameters, PickingParameters)
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"""
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# Define names of all parameters in different groups
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p_parameter_names = 'algoP pstart pstop use_taup taup_model tlta tsnrz hosorder bpz1 bpz2 pickwinP aictsmooth tsmoothP ausP nfacP tpred1z tdet1z Parorder addnoise Precalcwin minAICPslope minAICPSNR timeerrorsP checkwindowP minfactorP'.split(
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' ')
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s_parameter_names = 'algoS sstart sstop bph1 bph2 tsnrh pickwinS tpred1h tdet1h tpred2h tdet2h Sarorder aictsmoothS tsmoothS ausS minAICSslope minAICSSNR Srecalcwin nfacS timeerrorsS zfac checkwindowS minfactorS'.split(
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' ')
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first_motion_names = 'minFMSNR fmpickwin minfmweight'.split(' ')
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signal_length_names = 'minsiglength minpercent noisefactor'.split(' ')
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# Get list of values from pickparam by name
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p_parameter_values = map(pickparam.get, p_parameter_names)
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s_parameter_values = map(pickparam.get, s_parameter_names)
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fm_parameter_values = map(pickparam.get, first_motion_names)
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sl_parameter_values = map(pickparam.get, signal_length_names)
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# construct dicts from names and values
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p_params = dict(zip(p_parameter_names, p_parameter_values))
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s_params = dict(zip(s_parameter_names, s_parameter_values))
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first_motion_params = dict(zip(first_motion_names, fm_parameter_values))
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signal_length_params = dict(zip(signal_length_names, sl_parameter_values))
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p_params['use_taup'] = real_Bool(p_params['use_taup'])
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return PickingParameters(p_params), PickingParameters(s_params), PickingParameters(first_motion_params), PickingParameters(signal_length_params)
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def get_components_from_waveformstream(self):
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"""
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Splits waveformstream into multiple components zdat, ndat, edat. For traditional orientation (ZNE) these contain
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the vertical, north-south or east-west component. Otherwise they contain components numbered 123 with
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orientation diverging from the traditional orientation.
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:param waveformstream: Stream containing all three components for one station either by ZNE or 123 channel code
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(mixture of both options is handled as well)
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:type waveformstream: obspy.core.stream.Stream
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:return: Tuple containing (z waveform, n waveform, e waveform) selected by the given channels
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:rtype: (obspy.core.stream.Stream, obspy.core.stream.Stream, obspy.core.stream.Stream)
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"""
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waveform_data = {}
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for key in self.channelorder:
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waveform_data[key] = self.wfstream.select(component=key) # try ZNE first
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if len(waveform_data[key]) == 0:
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waveform_data[key] = self.wfstream.select(component=str(self.channelorder[key])) # use 123 as second option
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return waveform_data['Z'], waveform_data['N'], waveform_data['E']
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def prepare_wfstream(self, wfstream, freqmin=None, freqmax=None):
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"""
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Prepare a waveformstream for picking by applying detrending, filtering and tapering. Creates a copy of the
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waveform the leave the original unchanged.
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:param wfstream:
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:type wfstream:
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:param freqmin:
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:type freqmin:
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:param freqmax:
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:type freqmax:
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:return: Tuple containing the changed waveform stream and the first trace of the stream
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:rtype: (obspy.core.stream.Stream, obspy.core.trace.Trace)
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"""
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wfstream_copy = wfstream.copy()
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trace_copy = wfstream[0].copy()
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trace_copy.detrend(type=self.detrend_type)
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trace_copy.filter(self.filter_type, freqmin=freqmin, freqmax=freqmax, zerophase=self.zerophase)
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trace_copy.taper(max_percentage=self.taper_max_percentage, type=self.taper_type)
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wfstream_copy[0].data = trace_copy.data
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return wfstream_copy, trace_copy
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def modify_starttimes_taupy(self):
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"""
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Calculate theoretical arrival times for a source at self.origin and a station at self.metadata. Modify
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self.pstart and self.pstop so they are based on a time window around these theoretical arrival times.
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:rtype: None
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"""
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def create_arrivals(metadata, origin, station_id, taup_model):
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"""
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Create List of arrival times for all phases for a given origin and station
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:param metadata: tuple containing metadata type string and Parser object read from inventory file
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:type metadata: tuple (str, ~obspy.io.xseed.parser.Parser)
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:param origin: list containing origin objects representing origins for all events
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:type origin: list(~obspy.core.event.origin)
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:param station_id: Station id with format NETWORKNAME.STATIONNAME
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:type station_id: str
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:param taup_model: Model name to use. See obspy.taup.tau.TauPyModel for options
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:type taup_model: str
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:return: List of Arrival objects
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:rtype: obspy.taup.tau.Arrivals
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"""
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parser = metadata[1]
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station_coords = get_source_coords(parser, station_id)
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source_origin = origin[0]
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model = TauPyModel(taup_model)
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arrivals = model.get_travel_times_geo(source_depth_in_km=source_origin.depth,
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source_latitude_in_deg=source_origin.latitude,
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source_longitude_in_deg=source_origin.longitude,
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receiver_latitude_in_deg=station_coords['latitude'],
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receiver_longitude_in_deg=station_coords['longitude'])
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return arrivals
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def first_PS_onsets(arrivals):
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"""
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Get first P and S onsets from arrivals list
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:param arrivals: List of Arrival objects
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:type arrivals: obspy.taup.tau.Arrivals
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:return:
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:rtype:
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"""
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phases = {'P': [], 'S': []}
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# sort phases in P and S phases
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for arr in arrivals:
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phases[identifyPhaseID(arr.phase.name)].append(arr)
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# get first P and S onsets from arrivals list
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arrP, estFirstP = min([(arr, arr.time) for arr in phases['P']], key=lambda t: t[1])
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arrS, estFirstS = min([(arr, arr.time) for arr in phases['S']], key=lambda t: t[1])
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print('autopick: estimated first arrivals for P: {} s, S:{} s after event'
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' origin time using TauPy'.format(estFirstP, estFirstS))
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return estFirstP, estFirstS
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print('autopickstation: use_taup flag active.')
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if not self.metadata[1]:
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raise AttributeError('Warning: Could not use TauPy to estimate onsets as there are no metadata given.')
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if not self.origin:
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raise AttributeError('No source origins given!')
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arrivals = create_arrivals(self.metadata, self.origin, self.station_id, self.p_params.taup_model)
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estFirstP, estFirstS = first_PS_onsets(arrivals)
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# modifiy pstart and pstop relative to estimated first P arrival (relative to station time axis)
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self.p_params.pstart += (self.origin[0].time + estFirstP) - self.zstream[0].stats.starttime
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self.p_params.pstop += (self.origin[0].time + estFirstP) - self.zstream[0].stats.starttime
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print('autopick: CF calculation times respectively:'
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' pstart: {} s, pstop: {} s'.format(self.p_params.pstart, self.p_params.pstop))
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# make sure pstart and pstop are inside the starttime/endtime of vertical trace
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self.p_params.pstart = max(self.p_params.pstart, 0)
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self.p_params.pstop = min(self.p_params.pstop, len(self.zstream[0]) * self.zstream[0].stats.starttime)
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def autopickstation(self):
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self.zstream, self.nstream, self.estream = self.get_components_from_waveformstream()
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self.ztrace, self.ntrace, self.etrace = self.zstream[0], self.nstream[0], self.estream[0]
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try:
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self.pick_p_phase()
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#TODO handle exceptions correctly
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# requires an overlook of what should be returned in case picking fails at various stages
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except MissingTraceException as mte:
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print(mte)
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return
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def pick_p_phase(self):
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"""
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Pick p phase, return results
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:return: P pick results
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:rtype: PickingResults
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:raises:
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MissingTraceException: If vertical trace is missing.
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"""
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if not self.zstream or self.zstream is None:
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raise MissingTraceException('No z-component found for station {}'.format(self.station_name))
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msg = '##################################################\nautopickstation:' \
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' Working on P onset of station {station}\nFiltering vertical ' \
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'trace ...\n{data}'.format(station=self.station_name, data=str(self.zstream))
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self.vprint(msg)
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z_copy, tr_filt = self.prepare_wfstream(self.wfstream, self.p_params.bpz1[0], self.p_params.bpz2[0])
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if self.p_params.use_taup is True and self.origin is not None:
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Lc = np.inf # what is Lc? DA
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try:
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self.modify_starttimes_taupy()
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except AttributeError as ae:
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print(ae)
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else:
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Lc = self.p_params.pstop - self.p_params.pstop
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Lwf = self.ztrace.stats.endtime - self.ztrace.stats.starttime
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def autopickstation(wfstream, pickparam, verbose=False,
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iplot=0, fig_dict=None, metadata=None, origin=None):
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