WIP: Simplify data structure #39
@ -4,13 +4,16 @@
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import copy
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import logging
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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 typing import List
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from PySide2.QtWidgets import QMessageBox
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from obspy import read_events
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from obspy.core import read, Stream, 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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import pylot.core.loc.focmec as focmec
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import pylot.core.loc.hypodd as hypodd
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import pylot.core.loc.velest as velest
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@ -139,29 +142,6 @@ class Data(object):
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def setNew(self):
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self._new = True
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def getCutTimes(self):
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"""
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Returns earliest start and latest end of all waveform data
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:return: minimum start time and maximum end time as a tuple
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:rtype: (UTCDateTime, UTCDateTime)
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"""
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if self.cuttimes is None:
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self.updateCutTimes()
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return self.cuttimes
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def updateCutTimes(self):
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"""
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Update cuttimes to contain earliest start and latest end time
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of all waveform data
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:rtype: None
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"""
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self.cuttimes = full_range(self.getWFData())
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def getEventFileName(self):
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ID = self.getID()
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# handle forbidden filenames especially on windows systems
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return fnConstructor(str(ID))
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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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@ -252,184 +232,6 @@ class Data(object):
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if picktype in str(pick.method_id.id):
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picks.append(pick)
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def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
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"""
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Export event to file
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:param fnout: basename of file
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:param fnext: file extensions xml, cnv, obs, focmec, or/and pha
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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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"""
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from pylot.core.util.defaults import OUTPUTFORMATS
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if not type(fcheck) == list:
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fcheck = [fcheck]
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try:
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evtformat = OUTPUTFORMATS[fnext]
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except KeyError as e:
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errmsg = '{0}; selected file extension {1} not ' \
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'supported'.format(e, fnext)
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raise FormatError(errmsg)
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if hasattr(self.get_evt_data(), 'notes'):
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try:
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with open(os.path.join(os.path.dirname(fnout), 'notes.txt'), 'w') as notes_file:
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notes_file.write(self.get_evt_data().notes)
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except Exception as e:
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print('Warning: Could not save notes.txt: ', str(e))
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# check for already existing xml-file
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if fnext == '.xml':
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if os.path.isfile(fnout + fnext):
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print("xml-file already exists! Check content ...")
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cat = read_events(fnout + fnext)
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if len(cat) > 1:
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raise IOError('Ambigious event information in file {}'.format(fnout + fnext))
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if len(cat) < 1:
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raise IOError('No event information in file {}'.format(fnout + fnext))
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event = cat[0]
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if not event.resource_id == self.get_evt_data().resource_id:
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QMessageBox.warning(self, 'Warning', 'Different resource IDs!')
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return
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self.checkEvent(event, fcheck)
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self.setEvtData(event)
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self.get_evt_data().write(fnout + fnext, format=evtformat)
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# try exporting event
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else:
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evtdata_org = self.get_evt_data()
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picks = evtdata_org.picks
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eventpath = evtdata_org.path
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picks_copy = copy.deepcopy(picks)
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evtdata_copy = Event(eventpath)
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evtdata_copy.picks = picks_copy
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# check for stations picked automatically as well as manually
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# Prefer manual picks!
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for i in range(len(picks)):
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if picks[i].method_id == 'manual':
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mstation = picks[i].waveform_id.station_code
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mstation_ext = mstation + '_'
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for k in range(len(picks_copy)):
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if ((picks_copy[k].waveform_id.station_code == mstation) or
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(picks_copy[k].waveform_id.station_code == mstation_ext)) and \
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(picks_copy[k].method_id == 'auto'):
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del picks_copy[k]
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break
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lendiff = len(picks) - len(picks_copy)
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if lendiff != 0:
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print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
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no_uncertainties_p = []
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no_uncertainties_s = []
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if upperErrors:
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# check for pick uncertainties exceeding adjusted upper errors
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# Picks with larger uncertainties will not be saved in output file!
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for j in range(len(picks)):
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for i in range(len(picks_copy)):
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if picks_copy[i].phase_hint[0] == 'P':
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# Skipping pick if no upper_uncertainty is found and warning user
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if picks_copy[i].time_errors['upper_uncertainty'] is None:
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#print("{1} P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
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# picks_copy[i].waveform_id.station_code,
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# picks_copy[i].method_id))
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if not picks_copy[i].waveform_id.station_code in no_uncertainties_p:
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no_uncertainties_p.append(picks_copy[i].waveform_id.station_code)
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continue
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#print ("checking for upper_uncertainty")
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if (picks_copy[i].time_errors['uncertainty'] is None) or \
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(picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]):
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print("Uncertainty exceeds or equal adjusted upper time error!")
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print("Adjusted uncertainty: {}".format(upperErrors[0]))
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print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
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print("{1} P-Pick of station {0} will not be saved in outputfile".format(
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picks_copy[i].waveform_id.station_code,
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picks_copy[i].method_id))
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del picks_copy[i]
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break
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if picks_copy[i].phase_hint[0] == 'S':
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# Skipping pick if no upper_uncertainty is found and warning user
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if picks_copy[i].time_errors['upper_uncertainty'] is None:
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#print("{1} S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
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#picks_copy[i].waveform_id.station_code,
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#picks_copy[i].method_id))
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if not picks_copy[i].waveform_id.station_code in no_uncertainties_s:
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no_uncertainties_s.append(picks_copy[i].waveform_id.station_code)
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continue
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if (picks_copy[i].time_errors['uncertainty'] is None) or \
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(picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]):
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print("Uncertainty exceeds or equal adjusted upper time error!")
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print("Adjusted uncertainty: {}".format(upperErrors[1]))
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print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
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print("{1} S-Pick of station {0} will not be saved in outputfile".format(
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picks_copy[i].waveform_id.station_code,
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picks_copy[i].method_id))
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del picks_copy[i]
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break
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for s in no_uncertainties_p:
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print("P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
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for s in no_uncertainties_s:
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print("S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
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if fnext == '.obs':
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try:
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evtdata_copy.write(fnout + fnext, format=evtformat)
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# write header afterwards
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evid = str(evtdata_org.resource_id).split('/')[1]
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header = '# EQEVENT: Label: EQ%s Loc: X 0.00 Y 0.00 Z 10.00 OT 0.00 \n' % evid
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nllocfile = open(fnout + fnext)
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l = nllocfile.readlines()
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# Adding A0/Generic Amplitude to .obs file
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# l2 = []
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# for li in l:
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# for amp in evtdata_org.amplitudes:
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# if amp.waveform_id.station_code == li[0:5].strip():
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# li = li[0:64] + '{:0.2e}'.format(amp.generic_amplitude) + li[73:-1] + '\n'
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# l2.append(li)
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# l = l2
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nllocfile.close()
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l.insert(0, header)
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nllocfile = open(fnout + fnext, 'w')
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nllocfile.write("".join(l))
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nllocfile.close()
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except KeyError as e:
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raise KeyError('''{0} export format
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not implemented: {1}'''.format(evtformat, e))
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if fnext == '.cnv':
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try:
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velest.export(picks_copy, fnout + fnext, eventinfo=self.get_evt_data())
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except KeyError as e:
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raise KeyError('''{0} export format
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not implemented: {1}'''.format(evtformat, e))
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if fnext == '_focmec.in':
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try:
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parameter = PylotParameter()
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logging.warning('Using default input parameter')
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focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
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except KeyError as e:
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raise KeyError('''{0} export format
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not implemented: {1}'''.format(evtformat, e))
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if fnext == '.pha':
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try:
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parameter = PylotParameter()
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logging.warning('Using default input parameter')
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hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
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except KeyError as e:
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raise KeyError('''{0} export format
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not implemented: {1}'''.format(evtformat, e))
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def getComp(self):
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"""
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Get component (ZNE)
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"""
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return self.comp
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def getID(self):
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"""
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Get unique resource id
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@ -470,23 +272,10 @@ class Data(object):
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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 obspy_dmt:
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# wfdir = 'raw'
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# self.processed = False
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# for fname in fnames:
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# if fname.endswith('processed'):
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# wfdir = 'processed'
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# self.processed = True
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# break
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# for fpath in fnames:
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# if fpath.endswith(wfdir):
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# wffnames = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
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# if 'syngine' in fpath.split('/')[-1]:
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# wffnames_syn = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
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# else:
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# wffnames = fnames
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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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@ -494,9 +283,6 @@ class Data(object):
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else:
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return False
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# various pre-processing steps:
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# remove possible underscores in station names
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# self.wfdata = remove_underscores(self.wfdata)
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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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@ -618,11 +404,6 @@ class Data(object):
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picks = picks_from_picksdict(picks)
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break
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self.get_evt_data().picks = picks
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# if 'smi:local' in self.getID() and firstonset:
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# fonset_str = firstonset.strftime('%Y_%m_%d_%H_%M_%S')
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# ID = ResourceIdentifier('event/' + fonset_str)
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# ID.convertIDToQuakeMLURI(authority_id=authority_id)
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# self.get_evt_data().resource_id = ID
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def applyEvent(event):
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"""
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@ -654,6 +435,171 @@ class Data(object):
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applydata[typ](data)
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self._new = False
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@dataclass
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class SeismicEventData:
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event_id: str = ""
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catalog: Catalog = field(default_factory=Catalog)
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def find_event_files(self, directory: str, extensions: List[str]) -> List[str]:
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"""
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Browse the directory to find event files with specified extensions.
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Parameters:
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directory (str): The directory path to search for event files.
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extensions (List[str]): List of file extensions to search for.
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Returns:
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List[str]: List of file paths that match the given extensions.
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Example:
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>>> sed = SeismicEventData()
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>>> sed.find_event_files('test_directory', ['.xml', '.quakeml']) # doctest: +SKIP
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['test_directory/event1.xml', 'test_directory/event2.quakeml']
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"""
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matches = []
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for root, _, files in os.walk(directory):
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for ext in extensions:
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for filename in fnmatch.filter(files, f'*{ext}'):
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matches.append(os.path.join(root, filename))
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return matches
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def read_event_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
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"""
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Read a seismic event from the first found file in the directory with specified format.
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Parameters:
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directory (str): The directory path to search for event files.
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extensions (List[str]): List of file extensions to search for.
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format (str): The format to read the event file.
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Example:
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>>> sed = SeismicEventData()
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>>> sed.read_event_from_directory('test_directory', ['.xml', '.quakeml'], 'QUAKEML') # doctest: +SKIP
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"""
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event_files = self.find_event_files(directory, extensions)
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if event_files:
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self.read_event(event_files[0], format)
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else:
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raise FileNotFoundError(f"No event files found in directory {directory} with extensions {extensions}.")
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def read_event(self, file_path: str, format: str) -> None:
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"""
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Read a seismic event from a file with specified format.
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Parameters:
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file_path (str): The path to the event file.
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format (str): The format to read the event file.
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Example:
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>>> sed = SeismicEventData()
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>>> sed.read_event('test_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
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"""
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if os.path.exists(file_path):
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self.catalog = read_events(file_path, format=format)
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self.event_id = self.catalog[0].resource_id.id.split('/')[-1] if self.catalog else ""
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else:
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raise FileNotFoundError(f"File {file_path} does not exist.")
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def write_event(self, file_path: str, format: str) -> None:
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"""
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Write the seismic event to a file with specified format.
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Parameters:
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file_path (str): The path to the output file.
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format (str): The format to write the event file.
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Example:
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>>> sed = SeismicEventData(event_id='12345')
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>>> sed.write_event('output_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
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"""
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self.catalog.write(file_path, format=format)
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@dataclass
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class WaveformData:
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stream: Stream = field(default_factory=Stream)
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def find_waveform_files(self, directory: str, extensions: List[str]) -> List[str]:
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"""
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Browse the directory to find waveform files with specified extensions.
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Parameters:
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directory (str): The directory path to search for waveform files.
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extensions (List[str]): List of file extensions to search for.
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Returns:
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List[str]: List of file paths that match the given extensions.
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Example:
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>>> wd = WaveformData()
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>>> wd.find_waveform_files('test_directory', ['.mseed']) # doctest: +SKIP
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['test_directory/waveform1.mseed']
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"""
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matches = []
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for root, _, files in os.walk(directory):
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for ext in extensions:
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for filename in fnmatch.filter(files, f'*{ext}'):
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matches.append(os.path.join(root, filename))
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return matches
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def read_waveform_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
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"""
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Read waveform data from the first found file in the directory with specified format.
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Parameters:
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directory (str): The directory path to search for waveform files.
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extensions (List[str]): List of file extensions to search for.
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format (str): The format to read the waveform file.
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Example:
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>>> wd = WaveformData()
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>>> wd.read_waveform_from_directory('test_directory', ['.mseed'], 'MSEED') # doctest: +SKIP
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"""
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waveform_files = self.find_waveform_files(directory, extensions)
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if waveform_files:
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self.read_waveform(waveform_files[0], format)
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else:
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raise FileNotFoundError(f"No waveform files found in directory {directory} with extensions {extensions}.")
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def read_waveform(self, file_path: str, format: str) -> None:
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"""
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Read waveform data from a file with specified format.
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Parameters:
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file_path (str): The path to the waveform file.
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format (str): The format to read the waveform file.
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Example:
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>>> wd = WaveformData()
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>>> wd.read_waveform('test_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
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"""
|
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if os.path.exists(file_path):
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self.stream = read(file_path, format=format)
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else:
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raise FileNotFoundError(f"File {file_path} does not exist.")
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def write_waveform(self, file_path: str, format: str) -> None:
|
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"""
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Write the waveform data to a file with specified format.
|
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Parameters:
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file_path (str): The path to the output file.
|
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format (str): The format to write the waveform file.
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|
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Example:
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>>> 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")
|
||||
|
||||
|
||||
class GenericDataStructure(object):
|
||||
"""
|
||||
@ -837,22 +783,6 @@ class PilotDataStructure(GenericDataStructure):
|
||||
self.setExpandFields(['root', 'database'])
|
||||
|
||||
|
||||
class ObspyDMTdataStructure(GenericDataStructure):
|
||||
"""
|
||||
Object containing the data access information for the old PILOT data
|
||||
structure.
|
||||
"""
|
||||
|
||||
def __init__(self, **fields):
|
||||
if not fields:
|
||||
fields = {'database': '',
|
||||
'root': ''}
|
||||
|
||||
GenericDataStructure.__init__(self, **fields)
|
||||
|
||||
self.setExpandFields(['root', 'database'])
|
||||
|
||||
|
||||
class SeiscompDataStructure(GenericDataStructure):
|
||||
"""
|
||||
Dictionary containing the data access information for an SDS data archive:
|
||||
|
||||
Loading…
Reference in New Issue
Block a user