refactor: restructure data objects
This commit is contained in:
Sebastian Wehling-Benatelli
parent
b15cfe2e1d
commit
63dac0fff6
@ -1,605 +1,61 @@
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#!/usr/bin/env python
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# -*- coding: utf-8 -*-
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import copy
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import logging
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import os
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import os
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import fnmatch
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from dataclasses import dataclass, field
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from dataclasses import dataclass, field
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from typing import List
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from typing import List, Union
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from PySide2.QtWidgets import QMessageBox
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from obspy import UTCDateTime
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from obspy import read, read_events, Stream, Catalog, UTCDateTime
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from obspy.core.event import Event as ObsPyEvent
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from obspy.io.sac import SacIOError
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from pylot.core.io.event import EventData
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from pylot.core.io.waveformdata import WaveformData
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import pylot.core.loc.focmec as focmec
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@dataclass
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import pylot.core.loc.hypodd as hypodd
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class Data:
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import pylot.core.loc.velest as velest
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event_data: EventData = field(default_factory=EventData)
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from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
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waveform_data: WaveformData = field(default_factory=WaveformData)
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picksdict_from_pilot, merge_picks, PylotParameter
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_parent: Union[None, 'QtWidgets.QWidget'] = None
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from pylot.core.util.errors import FormatError, OverwriteError
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from pylot.core.util.event import Event
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from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
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from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
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check_for_gaps_and_merge, trim_station_components, check_for_nan
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class Data(object):
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"""
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Data container with attributes wfdata holding ~obspy.core.stream.
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:type parent: PySide2.QtWidgets.QWidget object, optional
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:param parent: A PySide2.QtWidgets.QWidget object utilized when
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called by a GUI to display a PySide2.QtWidgets.QMessageBox instead of printing
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to standard out.
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:type evtdata: ~obspy.core.event.Event object, optional
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:param evtdata ~obspy.core.event.Event object containing all derived or
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loaded event. Container object holding, e.g. phase arrivals, etc.
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"""
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def __init__(self, parent=None, evtdata=None):
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def __init__(self, parent=None, evtdata=None):
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self._parent = parent
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self._parent = parent
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if self.getParent():
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self.event_data = EventData(evtdata)
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self.comp = parent.getComponent()
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self.waveform_data = WaveformData()
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else:
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self.comp = 'Z'
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self.wfdata = Stream()
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self._new = False
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if isinstance(evtdata, ObsPyEvent) or isinstance(evtdata, Event):
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pass
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elif isinstance(evtdata, dict):
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evt = readPILOTEvent(**evtdata)
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evtdata = evt
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elif isinstance(evtdata, str):
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try:
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cat = read_events(evtdata)
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if len(cat) != 1:
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raise ValueError('ambiguous event information for file: '
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'{file}'.format(file=evtdata))
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evtdata = cat[0]
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except TypeError as e:
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if 'Unknown format for file' in e.message:
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if 'PHASES' in evtdata:
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picks = picksdict_from_pilot(evtdata)
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evtdata = ObsPyEvent()
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evtdata.picks = picks_from_picksdict(picks)
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elif 'LOC' in evtdata:
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raise NotImplementedError('PILOT location information '
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'read support not yet '
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'implemented.')
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elif 'event.pkl' in evtdata:
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evtdata = qml_from_obspyDMT(evtdata)
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else:
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raise e
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else:
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raise e
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else: # create an empty Event object
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self.setNew()
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evtdata = ObsPyEvent()
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evtdata.picks = []
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self.evtdata = evtdata
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self.wforiginal = None
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self.cuttimes = None
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self.dirty = False
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self.processed = None
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def __str__(self):
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def __str__(self):
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return str(self.wfdata)
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return str(self.waveform_data.wfdata)
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def __add__(self, other):
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def __add__(self, other):
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assert isinstance(other, Data), "operands must be of same type 'Data'"
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if not isinstance(other, Data):
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rs_id = self.get_evt_data().get('resource_id')
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raise TypeError("Operands must be of type 'Data'")
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rs_id_other = other.get_evt_data().get('resource_id')
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if self.event_data.is_new() and other.event_data.is_new():
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if other.isNew() and not self.isNew():
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picks_to_add = other.get_evt_data().picks
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old_picks = self.get_evt_data().picks
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wf_ids_old = [pick.waveform_id for pick in old_picks]
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for new_pick in picks_to_add:
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wf_id = new_pick.waveform_id
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if wf_id in wf_ids_old:
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for old_pick in old_picks:
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comparison = [old_pick.waveform_id == new_pick.waveform_id,
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old_pick.phase_hint == new_pick.phase_hint,
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old_pick.method_id == new_pick.method_id]
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if all(comparison):
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del (old_pick)
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old_picks.append(new_pick)
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elif not other.isNew() and self.isNew():
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new = other + self
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self.evtdata = new.get_evt_data()
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elif self.isNew() and other.isNew():
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pass
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pass
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elif rs_id == rs_id_other:
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elif other.event_data.is_new():
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other.setNew()
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new_picks = other.event_data.evtdata.picks
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old_picks = self.event_data.evtdata.picks
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old_picks.extend([pick for pick in new_picks if pick not in old_picks])
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elif self.event_data.is_new():
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return other + self
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elif self.event_data.get_id() == other.event_data.get_id():
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other.event_data.set_new()
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return self + other
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return self + other
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else:
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else:
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raise ValueError("both Data objects have differing "
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raise ValueError("Both Data objects have differing unique Event identifiers")
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"unique Event identifiers")
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return self
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return self
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def getPicksStr(self):
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def get_parent(self):
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"""
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Return picks in event data
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:return: picks seperated by newlines
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:rtype: str
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"""
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picks_str = ''
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for pick in self.get_evt_data().picks:
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picks_str += str(pick) + '\n'
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return picks_str
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def getParent(self):
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"""
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Get PySide.QtGui.QWidget parent object
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"""
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return self._parent
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return self._parent
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def isNew(self):
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def filter_wf_data(self, **kwargs):
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return self._new
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self.waveform_data.wfdata.detrend('linear')
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self.waveform_data.wfdata.taper(0.02, type='cosine')
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self.waveform_data.wfdata.filter(**kwargs)
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self.waveform_data.dirty = True
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def setNew(self):
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def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
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self._new = True
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return self.waveform_data.set_wf_data(fnames, fnames_alt, check_rotated, metadata, tstart, tstop)
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def checkEvent(self, event, fcheck, forceOverwrite=False):
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"""
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Check information in supplied event and own event and replace with own
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information if no other information are given or forced by forceOverwrite
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param fcheck: check and delete existing information
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can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
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:type fcheck: str, [str]
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:param forceOverwrite: Set to true to force overwrite own information. If false,
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supplied information from event is only used if there is no own information in that
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category (given in fcheck: manual, auto, origin, magnitude)
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:type forceOverwrite: bool
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:return:
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:rtype: None
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"""
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if 'origin' in fcheck:
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self.replaceOrigin(event, forceOverwrite)
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if 'magnitude' in fcheck:
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self.replaceMagnitude(event, forceOverwrite)
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if 'auto' in fcheck:
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self.replacePicks(event, 'auto')
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if 'manual' in fcheck:
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self.replacePicks(event, 'manual')
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def replaceOrigin(self, event, forceOverwrite=False):
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"""
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Replace own origin with the one supplied in event if own origin is not
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existing or forced by forceOverwrite = True
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param forceOverwrite: always replace own information with supplied one if true
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:type forceOverwrite: bool
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:return:
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:rtype: None
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"""
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if self.get_evt_data().origins or forceOverwrite:
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if event.origins:
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print("Found origin, replace it by new origin.")
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event.origins = self.get_evt_data().origins
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def replaceMagnitude(self, event, forceOverwrite=False):
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"""
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Replace own magnitude with the one supplied in event if own magnitude is not
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existing or forced by forceOverwrite = True
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param forceOverwrite: always replace own information with supplied one if true
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:type forceOverwrite: bool
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:return:
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:rtype: None
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"""
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if self.get_evt_data().magnitudes or forceOverwrite:
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if event.magnitudes:
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print("Found magnitude, replace it by new magnitude")
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event.magnitudes = self.get_evt_data().magnitudes
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def replacePicks(self, event, picktype):
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"""
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Replace picks in event with own picks
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param picktype: 'auto' or 'manual' picks
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:type picktype: str
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:return:
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:rtype: None
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"""
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checkflag = 1
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picks = event.picks
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# remove existing picks
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for j, pick in reversed(list(enumerate(picks))):
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try:
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if picktype in str(pick.method_id.id):
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picks.pop(j)
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checkflag = 2
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except AttributeError as e:
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msg = '{}'.format(e)
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print(e)
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checkflag = 0
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if checkflag > 0:
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if checkflag == 1:
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print("Write new %s picks to catalog." % picktype)
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if checkflag == 2:
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print("Found %s pick(s), remove them and append new picks to catalog." % picktype)
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# append new picks
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for pick in self.get_evt_data().picks:
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if picktype in str(pick.method_id.id):
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picks.append(pick)
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def getID(self):
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"""
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Get unique resource id
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"""
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try:
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return self.evtdata.get('resource_id').id
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except:
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return None
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def filterWFData(self, kwargs):
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"""
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Filter waveform data
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:param kwargs: arguments to pass through to filter function
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"""
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data = self.getWFData()
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data.detrend('linear')
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data.taper(0.02, type='cosine')
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data.filter(**kwargs)
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self.dirty = True
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def setWFData(self, fnames, fnames_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
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"""
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Clear current waveform data and set given waveform data
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:param fnames: waveform data names to append
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:param fnames_alt: alternative data to show (e.g. synthetic/processed)
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:type fnames: list
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"""
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def check_fname_exists(filenames: list) -> list:
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if filenames:
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filenames = [fn for fn in filenames if os.path.isfile(fn)]
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return filenames
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self.wfdata = Stream()
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self.wforiginal = None
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self.wf_alt = Stream()
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if tstart == tstop:
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tstart = tstop = None
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self.tstart = tstart
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self.tstop = tstop
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# remove directories
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fnames = check_fname_exists(fnames)
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fnames_alt = check_fname_exists(fnames_alt)
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if fnames is not None:
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self.appendWFData(fnames)
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if fnames_alt is not None:
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self.appendWFData(fnames_alt, alternative=True)
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else:
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return False
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# check for gaps and merge
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self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
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# check for nans
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check_for_nan(self.wfdata)
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# check for stations with rotated components
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if checkRotated and metadata is not None:
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self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
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# trim station components to same start value
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trim_station_components(self.wfdata, trim_start=True, trim_end=False)
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# make a copy of original data
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self.wforiginal = self.getWFData().copy()
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self.dirty = False
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return True
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def appendWFData(self, fnames, alternative=False):
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"""
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Read waveform data from fnames and append it to current wf data
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:param fnames: waveform data to append
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:type fnames: list
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"""
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assert isinstance(fnames, list), "input parameter 'fnames' is " \
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"supposed to be of type 'list' " \
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"but is actually" \
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" {0}".format(type(fnames))
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if self.dirty:
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self.resetWFData()
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orig_or_alternative_data = {True: self.wf_alt,
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False: self.wfdata}
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warnmsg = ''
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for fname in set(fnames):
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try:
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orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
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except TypeError:
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try:
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orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
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except Exception as e:
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try:
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orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
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endtime=self.tstop)
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except Exception as e:
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warnmsg += '{0}\n{1}\n'.format(fname, e)
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except SacIOError as se:
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warnmsg += '{0}\n{1}\n'.format(fname, se)
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if warnmsg:
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warnmsg = 'WARNING in appendWFData: unable to read waveform data\n' + warnmsg
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print(warnmsg)
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def getWFData(self):
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return self.wfdata
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def getOriginalWFData(self):
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return self.wforiginal
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def getAltWFdata(self):
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return self.wf_alt
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def resetWFData(self):
|
|
||||||
"""
|
|
||||||
Set waveform data to original waveform data
|
|
||||||
"""
|
|
||||||
if self.getOriginalWFData():
|
|
||||||
self.wfdata = self.getOriginalWFData().copy()
|
|
||||||
else:
|
|
||||||
self.wfdata = Stream()
|
|
||||||
self.dirty = False
|
|
||||||
|
|
||||||
def resetPicks(self):
|
|
||||||
"""
|
|
||||||
Clear all picks from event
|
|
||||||
"""
|
|
||||||
self.get_evt_data().picks = []
|
|
||||||
|
|
||||||
def get_evt_data(self):
|
|
||||||
return self.evtdata
|
|
||||||
|
|
||||||
def setEvtData(self, event):
|
|
||||||
self.evtdata = event
|
|
||||||
|
|
||||||
def applyEVTData(self, data, typ='pick'):
|
|
||||||
"""
|
|
||||||
Either takes an `obspy.core.event.Event` object and applies all new
|
|
||||||
information on the event to the actual data if typ is 'event or
|
|
||||||
creates ObsPy pick objects and append it to the picks list from the
|
|
||||||
PyLoT dictionary contain all picks if type is pick
|
|
||||||
:param data: data to apply, either picks or complete event
|
|
||||||
:type data:
|
|
||||||
:param typ: which event data to apply, 'pick' or 'event'
|
|
||||||
:type typ: str
|
|
||||||
:param authority_id: (currently unused)
|
|
||||||
:type: str
|
|
||||||
:raise OverwriteError:
|
|
||||||
"""
|
|
||||||
|
|
||||||
def applyPicks(picks):
|
|
||||||
"""
|
|
||||||
Creates ObsPy pick objects and append it to the picks list from the
|
|
||||||
PyLoT dictionary contain all picks.
|
|
||||||
:param picks:
|
|
||||||
:raise OverwriteError: raises an OverwriteError if the picks list is
|
|
||||||
not empty. The GUI will then ask for a decision.
|
|
||||||
"""
|
|
||||||
# firstonset = find_firstonset(picks)
|
|
||||||
# check for automatic picks
|
|
||||||
print("Writing phases to ObsPy-quakeml file")
|
|
||||||
for key in picks:
|
|
||||||
if not picks[key].get('P'):
|
|
||||||
continue
|
|
||||||
if picks[key]['P']['picker'] == 'auto':
|
|
||||||
print("Existing auto-picks will be overwritten in pick-dictionary!")
|
|
||||||
picks = picks_from_picksdict(picks)
|
|
||||||
break
|
|
||||||
else:
|
|
||||||
if self.get_evt_data().picks:
|
|
||||||
raise OverwriteError('Existing picks would be overwritten!')
|
|
||||||
else:
|
|
||||||
picks = picks_from_picksdict(picks)
|
|
||||||
break
|
|
||||||
self.get_evt_data().picks = picks
|
|
||||||
|
|
||||||
def applyEvent(event):
|
|
||||||
"""
|
|
||||||
takes an `obspy.core.event.Event` object and applies all new
|
|
||||||
information on the event to the actual data
|
|
||||||
:param event:
|
|
||||||
"""
|
|
||||||
if event is None:
|
|
||||||
print("applyEvent: Received None")
|
|
||||||
return
|
|
||||||
if self.isNew():
|
|
||||||
self.setEvtData(event)
|
|
||||||
else:
|
|
||||||
# prevent overwriting original pick information
|
|
||||||
event_old = self.get_evt_data()
|
|
||||||
if not event_old.resource_id == event.resource_id:
|
|
||||||
print("WARNING: Missmatch in event resource id's: {} and {}".format(
|
|
||||||
event_old.resource_id,
|
|
||||||
event.resource_id))
|
|
||||||
else:
|
|
||||||
picks = copy.deepcopy(event_old.picks)
|
|
||||||
event = merge_picks(event, picks)
|
|
||||||
# apply event information from location
|
|
||||||
event_old.update(event)
|
|
||||||
|
|
||||||
applydata = {'pick': applyPicks,
|
|
||||||
'event': applyEvent}
|
|
||||||
|
|
||||||
applydata[typ](data)
|
|
||||||
self._new = False
|
|
||||||
|
|
||||||
@dataclass
|
|
||||||
class SeismicEventData:
|
|
||||||
event_id: str = ""
|
|
||||||
catalog: Catalog = field(default_factory=Catalog)
|
|
||||||
|
|
||||||
def find_event_files(self, directory: str, extensions: List[str]) -> List[str]:
|
|
||||||
"""
|
|
||||||
Browse the directory to find event files with specified extensions.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
directory (str): The directory path to search for event files.
|
|
||||||
extensions (List[str]): List of file extensions to search for.
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
List[str]: List of file paths that match the given extensions.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> sed = SeismicEventData()
|
|
||||||
>>> sed.find_event_files('test_directory', ['.xml', '.quakeml']) # doctest: +SKIP
|
|
||||||
['test_directory/event1.xml', 'test_directory/event2.quakeml']
|
|
||||||
"""
|
|
||||||
matches = []
|
|
||||||
for root, _, files in os.walk(directory):
|
|
||||||
for ext in extensions:
|
|
||||||
for filename in fnmatch.filter(files, f'*{ext}'):
|
|
||||||
matches.append(os.path.join(root, filename))
|
|
||||||
return matches
|
|
||||||
|
|
||||||
def read_event_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
|
|
||||||
"""
|
|
||||||
Read a seismic event from the first found file in the directory with specified format.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
directory (str): The directory path to search for event files.
|
|
||||||
extensions (List[str]): List of file extensions to search for.
|
|
||||||
format (str): The format to read the event file.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> sed = SeismicEventData()
|
|
||||||
>>> sed.read_event_from_directory('test_directory', ['.xml', '.quakeml'], 'QUAKEML') # doctest: +SKIP
|
|
||||||
"""
|
|
||||||
event_files = self.find_event_files(directory, extensions)
|
|
||||||
if event_files:
|
|
||||||
self.read_event(event_files[0], format)
|
|
||||||
else:
|
|
||||||
raise FileNotFoundError(f"No event files found in directory {directory} with extensions {extensions}.")
|
|
||||||
|
|
||||||
def read_event(self, file_path: str, format: str) -> None:
|
|
||||||
"""
|
|
||||||
Read a seismic event from a file with specified format.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
file_path (str): The path to the event file.
|
|
||||||
format (str): The format to read the event file.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> sed = SeismicEventData()
|
|
||||||
>>> sed.read_event('test_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
|
|
||||||
"""
|
|
||||||
if os.path.exists(file_path):
|
|
||||||
self.catalog = read_events(file_path, format=format)
|
|
||||||
self.event_id = self.catalog[0].resource_id.id.split('/')[-1] if self.catalog else ""
|
|
||||||
else:
|
|
||||||
raise FileNotFoundError(f"File {file_path} does not exist.")
|
|
||||||
|
|
||||||
def write_event(self, file_path: str, format: str) -> None:
|
|
||||||
"""
|
|
||||||
Write the seismic event to a file with specified format.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
file_path (str): The path to the output file.
|
|
||||||
format (str): The format to write the event file.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> sed = SeismicEventData(event_id='12345')
|
|
||||||
>>> sed.write_event('output_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
|
|
||||||
"""
|
|
||||||
self.catalog.write(file_path, format=format)
|
|
||||||
|
|
||||||
@dataclass
|
|
||||||
class WaveformData:
|
|
||||||
stream: Stream = field(default_factory=Stream)
|
|
||||||
|
|
||||||
def find_waveform_files(self, directory: str, extensions: List[str]) -> List[str]:
|
|
||||||
"""
|
|
||||||
Browse the directory to find waveform files with specified extensions.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
directory (str): The directory path to search for waveform files.
|
|
||||||
extensions (List[str]): List of file extensions to search for.
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
List[str]: List of file paths that match the given extensions.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> wd = WaveformData()
|
|
||||||
>>> wd.find_waveform_files('test_directory', ['.mseed']) # doctest: +SKIP
|
|
||||||
['test_directory/waveform1.mseed']
|
|
||||||
"""
|
|
||||||
matches = []
|
|
||||||
for root, _, files in os.walk(directory):
|
|
||||||
for ext in extensions:
|
|
||||||
for filename in fnmatch.filter(files, f'*{ext}'):
|
|
||||||
matches.append(os.path.join(root, filename))
|
|
||||||
return matches
|
|
||||||
|
|
||||||
def read_waveform_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
|
|
||||||
"""
|
|
||||||
Read waveform data from the first found file in the directory with specified format.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
directory (str): The directory path to search for waveform files.
|
|
||||||
extensions (List[str]): List of file extensions to search for.
|
|
||||||
format (str): The format to read the waveform file.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> wd = WaveformData()
|
|
||||||
>>> wd.read_waveform_from_directory('test_directory', ['.mseed'], 'MSEED') # doctest: +SKIP
|
|
||||||
"""
|
|
||||||
waveform_files = self.find_waveform_files(directory, extensions)
|
|
||||||
if waveform_files:
|
|
||||||
self.read_waveform(waveform_files[0], format)
|
|
||||||
else:
|
|
||||||
raise FileNotFoundError(f"No waveform files found in directory {directory} with extensions {extensions}.")
|
|
||||||
|
|
||||||
def read_waveform(self, file_path: str, format: str) -> None:
|
|
||||||
"""
|
|
||||||
Read waveform data from a file with specified format.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
file_path (str): The path to the waveform file.
|
|
||||||
format (str): The format to read the waveform file.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> wd = WaveformData()
|
|
||||||
>>> wd.read_waveform('test_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
|
|
||||||
"""
|
|
||||||
if os.path.exists(file_path):
|
|
||||||
self.stream = read(file_path, format=format)
|
|
||||||
else:
|
|
||||||
raise FileNotFoundError(f"File {file_path} does not exist.")
|
|
||||||
|
|
||||||
def write_waveform(self, file_path: str, format: str) -> None:
|
|
||||||
"""
|
|
||||||
Write the waveform data to a file with specified format.
|
|
||||||
|
|
||||||
Parameters:
|
|
||||||
file_path (str): The path to the output file.
|
|
||||||
format (str): The format to write the waveform file.
|
|
||||||
|
|
||||||
Example:
|
|
||||||
>>> wd = WaveformData()
|
|
||||||
>>> wd.write_waveform('output_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
|
|
||||||
"""
|
|
||||||
self.stream.write(file_path, format=format)
|
|
||||||
|
|
||||||
# Example usage:
|
|
||||||
# seismic_event = SeismicEventData()
|
|
||||||
# seismic_event.read_event_from_directory("path_to_directory", extensions=[".xml", ".quakeml"], format="QUAKEML")
|
|
||||||
# seismic_event.write_event("output_event_file.xml", format="QUAKEML")
|
|
||||||
|
|
||||||
# waveform_data = WaveformData()
|
|
||||||
# waveform_data.read_waveform_from_directory("path_to_directory", extensions=[".mseed"], format="MSEED")
|
|
||||||
# waveform_data.write_waveform("output_waveform_file.mseed", format="MSEED")
|
|
||||||
|
|
||||||
|
def reset_wf_data(self):
|
||||||
|
self.waveform_data.reset_wf_data()
|
||||||
|
|
||||||
class GenericDataStructure(object):
|
class GenericDataStructure(object):
|
||||||
"""
|
"""
|
||||||
|
|||||||
106
pylot/core/io/event.py
Normal file
106
pylot/core/io/event.py
Normal file
@ -0,0 +1,106 @@
|
|||||||
|
import copy
|
||||||
|
from dataclasses import dataclass
|
||||||
|
from typing import Union
|
||||||
|
|
||||||
|
from obspy import read_events
|
||||||
|
from obspy.core.event import Event as ObsPyEvent
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass
|
||||||
|
class EventData:
|
||||||
|
evtdata: Union[ObsPyEvent, None] = None
|
||||||
|
_new: bool = False
|
||||||
|
|
||||||
|
def __init__(self, evtdata=None):
|
||||||
|
self.set_event_data(evtdata)
|
||||||
|
|
||||||
|
def set_event_data(self, evtdata):
|
||||||
|
if isinstance(evtdata, ObsPyEvent):
|
||||||
|
self.evtdata = evtdata
|
||||||
|
elif isinstance(evtdata, dict):
|
||||||
|
self.evtdata = self.read_pilot_event(**evtdata)
|
||||||
|
elif isinstance(evtdata, str):
|
||||||
|
self.evtdata = self.read_event_file(evtdata)
|
||||||
|
else:
|
||||||
|
self.set_new()
|
||||||
|
self.evtdata = ObsPyEvent(picks=[])
|
||||||
|
|
||||||
|
def read_event_file(self, evtdata: str) -> ObsPyEvent:
|
||||||
|
try:
|
||||||
|
cat = read_events(evtdata)
|
||||||
|
if len(cat) != 1:
|
||||||
|
raise ValueError(f'ambiguous event information for file: {evtdata}')
|
||||||
|
return cat[0]
|
||||||
|
except TypeError as e:
|
||||||
|
self.handle_event_file_error(e, evtdata)
|
||||||
|
|
||||||
|
def handle_event_file_error(self, e: TypeError, evtdata: str):
|
||||||
|
if 'Unknown format for file' in str(e):
|
||||||
|
if 'PHASES' in evtdata:
|
||||||
|
picks = self.picksdict_from_pilot(evtdata)
|
||||||
|
evtdata = ObsPyEvent(picks=self.picks_from_picksdict(picks))
|
||||||
|
elif 'LOC' in evtdata:
|
||||||
|
raise NotImplementedError('PILOT location information read support not yet implemented.')
|
||||||
|
elif 'event.pkl' in evtdata:
|
||||||
|
evtdata = self.qml_from_obspy_dmt(evtdata)
|
||||||
|
else:
|
||||||
|
raise e
|
||||||
|
else:
|
||||||
|
raise e
|
||||||
|
|
||||||
|
def set_new(self):
|
||||||
|
self._new = True
|
||||||
|
|
||||||
|
def is_new(self) -> bool:
|
||||||
|
return self._new
|
||||||
|
|
||||||
|
def get_picks_str(self) -> str:
|
||||||
|
return '\n'.join(str(pick) for pick in self.evtdata.picks)
|
||||||
|
|
||||||
|
def replace_origin(self, event: ObsPyEvent, force_overwrite: bool = False):
|
||||||
|
if self.evtdata.origins or force_overwrite:
|
||||||
|
event.origins = self.evtdata.origins
|
||||||
|
|
||||||
|
def replace_magnitude(self, event: ObsPyEvent, force_overwrite: bool = False):
|
||||||
|
if self.evtdata.magnitudes or force_overwrite:
|
||||||
|
event.magnitudes = self.evtdata.magnitudes
|
||||||
|
|
||||||
|
def replace_picks(self, event: ObsPyEvent, picktype: str):
|
||||||
|
checkflag = 1
|
||||||
|
picks = event.picks
|
||||||
|
for j, pick in reversed(list(enumerate(picks))):
|
||||||
|
if picktype in str(pick.method_id.id):
|
||||||
|
picks.pop(j)
|
||||||
|
checkflag = 2
|
||||||
|
|
||||||
|
if checkflag > 0:
|
||||||
|
for pick in self.evtdata.picks:
|
||||||
|
if picktype in str(pick.method_id.id):
|
||||||
|
picks.append(pick)
|
||||||
|
|
||||||
|
def get_id(self) -> Union[str, None]:
|
||||||
|
try:
|
||||||
|
return self.evtdata.resource_id.id
|
||||||
|
except:
|
||||||
|
return None
|
||||||
|
|
||||||
|
def apply_event_data(self, data, typ='pick'):
|
||||||
|
if typ == 'pick':
|
||||||
|
self.apply_picks(data)
|
||||||
|
elif typ == 'event':
|
||||||
|
self.apply_event(data)
|
||||||
|
|
||||||
|
def apply_picks(self, picks):
|
||||||
|
self.evtdata.picks = picks
|
||||||
|
|
||||||
|
def apply_event(self, event: ObsPyEvent):
|
||||||
|
if self.is_new():
|
||||||
|
self.evtdata = event
|
||||||
|
else:
|
||||||
|
old_event = self.evtdata
|
||||||
|
if old_event.resource_id == event.resource_id:
|
||||||
|
picks = copy.deepcopy(old_event.picks)
|
||||||
|
event = self.merge_picks(event, picks)
|
||||||
|
old_event.update(event)
|
||||||
|
else:
|
||||||
|
print(f"WARNING: Mismatch in event resource id's: {old_event.resource_id} and {event.resource_id}")
|
||||||
243
pylot/core/io/waveformdata.py
Normal file
243
pylot/core/io/waveformdata.py
Normal file
@ -0,0 +1,243 @@
|
|||||||
|
import logging
|
||||||
|
import os
|
||||||
|
from dataclasses import dataclass, field
|
||||||
|
from typing import Union, List
|
||||||
|
|
||||||
|
import numpy as np
|
||||||
|
from obspy import Stream, read
|
||||||
|
from obspy.io.sac import SacIOError
|
||||||
|
from obspy.signal.rotate import rotate2zne
|
||||||
|
|
||||||
|
from pylot.core.util.utils import full_range, get_stations
|
||||||
|
|
||||||
|
|
||||||
|
@dataclass
|
||||||
|
class WaveformData:
|
||||||
|
wfdata: Stream = field(default_factory=Stream)
|
||||||
|
wforiginal: Union[Stream, None] = None
|
||||||
|
wf_alt: Stream = field(default_factory=Stream)
|
||||||
|
dirty: bool = False
|
||||||
|
|
||||||
|
def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
|
||||||
|
self.clear_data()
|
||||||
|
fnames = self.check_fname_exists(fnames)
|
||||||
|
fnames_alt = self.check_fname_exists(fnames_alt)
|
||||||
|
|
||||||
|
if fnames:
|
||||||
|
self.append_wf_data(fnames)
|
||||||
|
if fnames_alt:
|
||||||
|
self.append_wf_data(fnames_alt, alternative=True)
|
||||||
|
self.wfdata, _ = self.check_for_gaps_and_merge(self.wfdata)
|
||||||
|
self.check_for_nan(self.wfdata)
|
||||||
|
if check_rotated and metadata:
|
||||||
|
self.wfdata = self.check4rotated(self.wfdata, metadata, verbosity=0)
|
||||||
|
self.trim_station_components(self.wfdata, trim_start=True, trim_end=False)
|
||||||
|
self.wforiginal = self.wfdata.copy()
|
||||||
|
self.dirty = False
|
||||||
|
return True
|
||||||
|
return False
|
||||||
|
|
||||||
|
def append_wf_data(self, fnames: List[str], alternative: bool = False):
|
||||||
|
data_stream = self.wf_alt if alternative else self.wfdata
|
||||||
|
warnmsg = ''
|
||||||
|
for fname in set(fnames):
|
||||||
|
try:
|
||||||
|
data_stream += read(fname)
|
||||||
|
except TypeError:
|
||||||
|
try:
|
||||||
|
data_stream += read(fname, format='GSE2')
|
||||||
|
except Exception as e:
|
||||||
|
try:
|
||||||
|
data_stream += read(fname, format='SEGY')
|
||||||
|
except Exception as e:
|
||||||
|
warnmsg += f'{fname}\n{e}\n'
|
||||||
|
except SacIOError as se:
|
||||||
|
warnmsg += f'{fname}\n{se}\n'
|
||||||
|
|
||||||
|
if warnmsg:
|
||||||
|
print(f'WARNING in appendWFData: unable to read waveform data\n{warnmsg}')
|
||||||
|
|
||||||
|
def clear_data(self):
|
||||||
|
self.wfdata = Stream()
|
||||||
|
self.wforiginal = None
|
||||||
|
self.wf_alt = Stream()
|
||||||
|
|
||||||
|
def reset_wf_data(self):
|
||||||
|
if self.wforiginal:
|
||||||
|
self.wfdata = self.wforiginal.copy()
|
||||||
|
else:
|
||||||
|
self.wfdata = Stream()
|
||||||
|
self.dirty = False
|
||||||
|
|
||||||
|
def check_fname_exists(self, filenames: List[str]) -> List[str]:
|
||||||
|
return [fn for fn in filenames if os.path.isfile(fn)]
|
||||||
|
|
||||||
|
def check_for_gaps_and_merge(self, stream):
|
||||||
|
"""
|
||||||
|
check for gaps in Stream and merge if gaps are found
|
||||||
|
:param stream: stream of seismic data
|
||||||
|
:type stream: `~obspy.core.stream.Stream`
|
||||||
|
:return: data stream, gaps returned from obspy get_gaps
|
||||||
|
:rtype: `~obspy.core.stream.Stream`
|
||||||
|
"""
|
||||||
|
gaps = stream.get_gaps()
|
||||||
|
if gaps:
|
||||||
|
merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
|
||||||
|
stream.merge(method=1)
|
||||||
|
print('Merged the following stations because of gaps:')
|
||||||
|
for merged_station in merged:
|
||||||
|
print(merged_station)
|
||||||
|
|
||||||
|
return stream, gaps
|
||||||
|
|
||||||
|
def check_for_nan(self, stream):
|
||||||
|
"""
|
||||||
|
Replace all NaNs in data with nan_value (in place)
|
||||||
|
:param stream: stream of seismic data
|
||||||
|
:type stream: `~obspy.core.stream.Stream`
|
||||||
|
:param nan_value: value which all NaNs are set to
|
||||||
|
:type nan_value: float, int
|
||||||
|
:return: None
|
||||||
|
"""
|
||||||
|
if not stream:
|
||||||
|
return
|
||||||
|
for trace in stream:
|
||||||
|
np.nan_to_num(trace.data, copy=False, nan=0.)
|
||||||
|
|
||||||
|
|
||||||
|
def check4rotated(self, stream, metadata=None, verbosity=1):
|
||||||
|
"""
|
||||||
|
Check all traces in data. If a trace is not in ZNE rotation (last symbol of channel code is numeric) and the trace
|
||||||
|
is in the metadata with azimuth and dip, rotate it to classical ZNE orientation.
|
||||||
|
Rotating the traces requires them to be of the same length, so, all traces will be trimmed to a common length as a
|
||||||
|
side effect.
|
||||||
|
:param stream: stream object containing seismic traces
|
||||||
|
:type stream: `~obspy.core.stream.Stream`
|
||||||
|
:param metadata: tuple containing metadata type string and metadata parser object
|
||||||
|
:type metadata: (str, `~obspy.io.xseed.parser.Parser`)
|
||||||
|
:param verbosity: if 0 print no information at runtime
|
||||||
|
:type verbosity: int
|
||||||
|
:return: stream object with traditionally oriented traces (ZNE) for stations that had misaligned traces (123) before
|
||||||
|
:rtype: `~obspy.core.stream.Stream`
|
||||||
|
"""
|
||||||
|
|
||||||
|
def rotation_required(trace_ids):
|
||||||
|
"""
|
||||||
|
Derive if any rotation is required from the orientation code of the input.
|
||||||
|
|
||||||
|
:param trace_ids: string identifier of waveform data trace
|
||||||
|
:type trace_ids: List(str)
|
||||||
|
:return: boolean representing if rotation is necessary for any of the traces
|
||||||
|
:rtype: bool
|
||||||
|
"""
|
||||||
|
orientations = [trace_id[-1] for trace_id in trace_ids]
|
||||||
|
return any([orientation.isnumeric() for orientation in orientations])
|
||||||
|
|
||||||
|
def rotate_components(wfs_in, metadata=None):
|
||||||
|
"""
|
||||||
|
Rotate components if orientation code is numeric (= non traditional orientation).
|
||||||
|
|
||||||
|
Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
|
||||||
|
Returns unrotated traces of no metadata is provided
|
||||||
|
:param wfs_in: stream containing seismic traces of a station
|
||||||
|
:type wfs_in: `~obspy.core.stream.Stream`
|
||||||
|
:param metadata: tuple containing metadata type string and metadata parser object
|
||||||
|
:type metadata: (str, `~obspy.io.xseed.parser.Parser`)
|
||||||
|
:return: stream object with traditionally oriented traces (ZNE)
|
||||||
|
:rtype: `~obspy.core.stream.Stream`
|
||||||
|
"""
|
||||||
|
|
||||||
|
if len(wfs_in) < 3:
|
||||||
|
print(f"Stream {wfs_in=}, has not enough components to rotate.")
|
||||||
|
return wfs_in
|
||||||
|
|
||||||
|
# check if any traces in this station need to be rotated
|
||||||
|
trace_ids = [trace.id for trace in wfs_in]
|
||||||
|
if not rotation_required(trace_ids):
|
||||||
|
logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
|
||||||
|
return wfs_in
|
||||||
|
|
||||||
|
# check metadata quality
|
||||||
|
t_start = full_range(wfs_in)
|
||||||
|
try:
|
||||||
|
azimuths = []
|
||||||
|
dips = []
|
||||||
|
for tr_id in trace_ids:
|
||||||
|
azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
|
||||||
|
dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
|
||||||
|
except (KeyError, TypeError) as err:
|
||||||
|
logging.error(
|
||||||
|
f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
|
||||||
|
f"available in metadata. Stream remains unchanged.")
|
||||||
|
return wfs_in
|
||||||
|
except Exception as err:
|
||||||
|
print(f"Unexpected {err=}, {type(err)=}")
|
||||||
|
raise
|
||||||
|
|
||||||
|
# to rotate all traces must have same length, so trim them
|
||||||
|
wfs_out = self.trim_station_components(wfs_in, trim_start=True, trim_end=True)
|
||||||
|
try:
|
||||||
|
z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
|
||||||
|
wfs_out[1], azimuths[1], dips[1],
|
||||||
|
wfs_out[2], azimuths[2], dips[2])
|
||||||
|
print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
|
||||||
|
# replace old data with rotated data, change the channel code to ZNE
|
||||||
|
z_index = dips.index(min(
|
||||||
|
dips)) # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90
|
||||||
|
# being vertical)
|
||||||
|
wfs_out[z_index].data = z
|
||||||
|
wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
|
||||||
|
del trace_ids[z_index]
|
||||||
|
for trace_id in trace_ids:
|
||||||
|
coordinates = metadata.get_coordinates(trace_id, t_start)
|
||||||
|
dip, az = coordinates['dip'], coordinates['azimuth']
|
||||||
|
trace = wfs_out.select(id=trace_id)[0]
|
||||||
|
if az > 315 or az <= 45 or 135 < az <= 225:
|
||||||
|
trace.data = n
|
||||||
|
trace.stats.channel = trace.stats.channel[0:-1] + 'N'
|
||||||
|
elif 45 < az <= 135 or 225 < az <= 315:
|
||||||
|
trace.data = e
|
||||||
|
trace.stats.channel = trace.stats.channel[0:-1] + 'E'
|
||||||
|
except ValueError as err:
|
||||||
|
print(f"{err=} Rotation failed. Stream remains unchanged.")
|
||||||
|
return wfs_in
|
||||||
|
|
||||||
|
return wfs_out
|
||||||
|
|
||||||
|
if metadata is None:
|
||||||
|
if verbosity:
|
||||||
|
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
|
||||||
|
print(msg)
|
||||||
|
return stream
|
||||||
|
stations = get_stations(stream)
|
||||||
|
for station in stations: # loop through all stations and rotate data if neccessary
|
||||||
|
wf_station = stream.select(station=station)
|
||||||
|
rotate_components(wf_station, metadata)
|
||||||
|
return stream
|
||||||
|
|
||||||
|
def trim_station_components(stream, trim_start=True, trim_end=True):
|
||||||
|
"""
|
||||||
|
cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
|
||||||
|
:param stream: stream of seismic data
|
||||||
|
:type stream: `~obspy.core.stream.Stream`
|
||||||
|
:param trim_start: trim start of stream
|
||||||
|
:type trim_start: bool
|
||||||
|
:param trim_end: trim end of stream
|
||||||
|
:type trim_end: bool
|
||||||
|
:return: data stream
|
||||||
|
:rtype: `~obspy.core.stream.Stream`
|
||||||
|
"""
|
||||||
|
starttime = {False: None}
|
||||||
|
endtime = {False: None}
|
||||||
|
|
||||||
|
stations = get_stations(stream)
|
||||||
|
|
||||||
|
print('trim_station_components: Will trim stream for trim_start: {} and for '
|
||||||
|
'trim_end: {}.'.format(trim_start, trim_end))
|
||||||
|
for station in stations:
|
||||||
|
wf_station = stream.select(station=station)
|
||||||
|
starttime[True] = max([trace.stats.starttime for trace in wf_station])
|
||||||
|
endtime[True] = min([trace.stats.endtime for trace in wf_station])
|
||||||
|
wf_station.trim(starttime=starttime[trim_start], endtime=endtime[trim_end])
|
||||||
|
|
||||||
|
return stream
|
||||||
Loading…
x
Reference in New Issue
Block a user