Merge branch 'develop' of ariadne.geophysik.ruhr-uni-bochum.de:/data/git/pylot into develop
This commit is contained in:
commit
5f740783f0
@ -43,7 +43,7 @@ from obspy import UTCDateTime
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from pylot.core.io.data import Data
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from pylot.core.io.inputs import FilterOptions, AutoPickParameter
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from pylot.core.pick.autopick import autopickevent
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from pylot.core.io.phases import picks_to_dict
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from pylot.core.io.phases import picksdict_from_picks
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from pylot.core.loc.nll import locate as locateNll
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from pylot.core.util.defaults import FILTERDEFAULTS, COMPNAME_MAP,\
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AUTOMATIC_DEFAULTS
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@ -735,7 +735,7 @@ class MainWindow(QMainWindow):
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return rval
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def updatePicks(self, type='manual'):
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picks = picks_to_dict(evt=self.getData().getEvtData())
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picks = picksdict_from_picks(evt=self.getData().getEvtData())
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if type == 'manual':
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self.picks.update(picks)
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elif type == 'auto':
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|
@ -9,7 +9,7 @@ from obspy.core import read, Stream, UTCDateTime
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from obspy import read_events, read_inventory
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from obspy.core.event import Event, ResourceIdentifier, Pick, WaveformStreamID
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from pylot.core.io.phases import readPILOTEvent, picks_from_dict
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from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict
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from pylot.core.util.utils import fnConstructor, getGlobalTimes
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from pylot.core.util.errors import FormatError, OverwriteError
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@ -411,19 +411,18 @@ class Data(object):
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:raise OverwriteError: raises an OverwriteError if the picks list is
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not empty. The GUI will then ask for a decision.
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"""
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firstonset = None
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#firstonset = find_firstonset(picks)
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if self.getEvtData().picks:
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raise OverwriteError('Actual picks would be overwritten!')
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picks, firstonset = picks_from_dict(picks)
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picks = picks_from_picksdict(picks)
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self.getEvtData().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.getEvtData().resource_id = ID
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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.getEvtData().resource_id = ID
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else:
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print('No picks to apply!')
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def applyArrivals(arrivals):
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"""
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@ -8,9 +8,9 @@ import scipy.io as sio
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import obspy.core.event as ope
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from obspy.core import UTCDateTime
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from pylot.core.pick.utils import select_for_phase
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from pylot.core.util.utils import getOwner, createPick, createArrival, \
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createEvent, createOrigin, createMagnitude
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createEvent, createOrigin, createMagnitude, getGlobalTimes
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def readPILOTEvent(phasfn=None, locfn=None, authority_id=None, **kwargs):
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"""
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@ -192,14 +192,14 @@ def picksdict_from_obs(fn):
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return picks
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def picks_to_dict(evt):
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'''
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def picksdict_from_picks(evt):
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"""
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Takes an Event object and return the pick dictionary commonly used within
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PyLoT
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:param evt: Event object contain all available information
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:type evt: `~obspy.core.event.Event`
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:return: pick dictionary
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'''
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"""
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picks = {}
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for pick in evt.picks:
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phase = {}
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@ -229,12 +229,12 @@ def picks_to_dict(evt):
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picks[station] = onsets.copy()
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return picks
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def picks_from_dict(picks):
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firstonset = None
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def picks_from_picksdict(picks):
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picks_list = list()
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for station, onsets in picks.items():
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print('Reading picks on station %s' % station)
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for label, phase in onsets.items():
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if not isinstance(phase, dict):
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if not isinstance(phase, dict) or len(phase) < 3:
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continue
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onset = phase['mpp']
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epp = phase['epp']
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@ -262,52 +262,90 @@ def picks_from_dict(picks):
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else:
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pick.polarity = 'undecidable'
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except KeyError as e:
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print('No polarity information found for %s' % phase)
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if firstonset is None or firstonset > onset:
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firstonset = onset
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print(e.message, 'No polarity information found for %s' % phase)
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picks_list.append(pick)
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return picks_list
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def reassess_pilot_event(root_dir, event_id):
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def reassess_pilot_db(root_dir, out_dir=None, fn_param=None):
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import glob
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evt_list = glob.glob1(root_dir,'e????.???.??')
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for evt in evt_list:
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reassess_pilot_event(root_dir, evt, out_dir, fn_param)
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def reassess_pilot_event(root_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
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from obspy import read
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from pylot.core.util.defaults import AUTOMATIC_DEFAULTS
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from pylot.core.io.inputs import AutoPickParameter
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from pylot.core.pick.utils import earllatepicker
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default = AutoPickParameter(AUTOMATIC_DEFAULTS)
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if fn_param is None:
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import pylot.core.util.defaults as defaults
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fn_param = defaults.AUTOMATIC_DEFAULTS
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default = AutoPickParameter(fn_param)
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search_base = os.path.join(root_dir, event_id)
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phases_file = glob.glob(os.path.join(search_base, 'PHASES.mat'))
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picks_dict = picks_from_pilot(phases_file)
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if not phases_file:
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return
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print('Opening PILOT phases file: {fn}'.format(fn=phases_file[0]))
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picks_dict = picks_from_pilot(phases_file[0])
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print('Dictionary read from PHASES.mat:\n{0}'.format(picks_dict))
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for station in picks_dict.keys():
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fn_pattern = os.path.join(search_base, '{0}*'.format(station))
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try:
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st = read(fn_pattern)
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st = read(fn_pattern, format='GSE2')
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except TypeError as e:
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print(e.message)
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st = read(fn_pattern, format='GSE2')
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if not st:
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raise RuntimeError('no waveform data found for station {station}'.format(station=station))
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st = read(fn_pattern)
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for phase in picks_dict[station].keys():
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try:
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mpp = picks_dict[station][phase]['mpp']
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except KeyError as e:
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print(e.message, station)
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continue
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epp, lpp, spe = earllatepicker(st,
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sel_st = select_for_phase(st, phase)
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if not sel_st:
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raise warnings.formatwarning(
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'no waveform data found for station {station}'.format(
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station=station), category=RuntimeWarning)
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print(sel_st)
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stime, etime = getGlobalTimes(sel_st)
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rel_pick = mpp - stime
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epp, lpp, spe = earllatepicker(sel_st,
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default.get('nfac{0}'.format(phase)),
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default.get('tsnrz' if phase == 'P' else 'tsnrh'),
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mpp
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Pick1=rel_pick,
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iplot=None,
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)
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if epp is None or lpp is None:
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continue
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epp = stime + epp
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lpp = stime + lpp
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min_diff = 3 * st[0].stats.delta
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if lpp - mpp < min_diff:
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lpp = mpp + min_diff
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if mpp - epp < min_diff:
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epp = mpp - min_diff
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picks_dict[station][phase] = dict(epp=epp, mpp=mpp, lpp=lpp, spe=spe)
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# create Event object for export
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evt = ope.Event(resource_id=event_id)
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evt.picks = picks_from_dict(picks_dict)
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evt.picks = picks_from_picksdict(picks_dict)
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# write phase information to file
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evt.write('{0}.xml'.format(event_id), format='QUAKEML')
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if not out_dir:
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fnout_prefix = os.path.join(root_dir, event_id, '{0}.'.format(event_id))
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else:
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fnout_prefix = os.path.join(out_dir, '{0}.'.format(event_id))
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evt.write(fnout_prefix + 'xml', format='QUAKEML')
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#evt.write(fnout_prefix + 'cnv', format='VELEST')
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def writephases(arrivals, fformat, filename):
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'''
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"""
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Function of methods to write phases to the following standard file
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formats used for locating earthquakes:
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@ -325,7 +363,7 @@ def writephases(arrivals, fformat, filename):
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:param: filename, full path and name of phase file
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:type: string
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'''
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"""
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if fformat == 'NLLoc':
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print ("Writing phases to %s for NLLoc" % filename)
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@ -387,7 +425,6 @@ def writephases(arrivals, fformat, filename):
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sweight))
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fid.close()
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elif fformat == 'HYPO71':
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print ("Writing phases to %s for HYPO71" % filename)
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fid = open("%s" % filename, 'w')
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@ -9,7 +9,7 @@ import matplotlib.pyplot as plt
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from obspy import read_events
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from pylot.core.io.phases import picks_to_dict
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from pylot.core.io.phases import picksdict_from_picks
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from pylot.core.util.pdf import ProbabilityDensityFunction
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from pylot.core.util.version import get_git_version as _getVersionString
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@ -86,8 +86,8 @@ class Comparison(object):
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"""
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compare_pdfs = dict()
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pdf_a = self.get(self.names[0]).pdf_data(type)
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pdf_b = self.get(self.names[1]).pdf_data(type)
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pdf_a = self.get(self.names[0]).generate_pdf_data(type)
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pdf_b = self.get(self.names[1]).generate_pdf_data(type)
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for station, phases in pdf_a.items():
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if station in pdf_b.keys():
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@ -206,6 +206,7 @@ class PDFDictionary(object):
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def __init__(self, data):
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self._pickdata = data
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self._pdfdata = self.generate_pdf_data()
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def __nonzero__(self):
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if len(self.pick_data) < 1:
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@ -213,6 +214,14 @@ class PDFDictionary(object):
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else:
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return True
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@property
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def pdf_data(self):
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return self._pdfdata
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@pdf_data.setter
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def pdf_data(self, data):
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self._pdfdata = data
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@property
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def pick_data(self):
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return self._pickdata
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@ -221,15 +230,23 @@ class PDFDictionary(object):
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def pick_data(self, data):
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self._pickdata = data
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@property
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def stations(self):
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return self.pick_data.keys()
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@property
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def nstations(self):
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return len(self.stations)
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@classmethod
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def from_quakeml(self, fn):
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cat = read_events(fn)
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if len(cat) > 1:
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raise NotImplementedError('reading more than one event at the same '
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'time is not implemented yet! Sorry!')
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return PDFDictionary(picks_to_dict(cat[0]))
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return PDFDictionary(picksdict_from_picks(cat[0]))
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def pdf_data(self, type='exp'):
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def generate_pdf_data(self, type='exp'):
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"""
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Returns probabiliy density function dictionary containing the
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representation of the actual pick_data.
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@ -251,3 +268,57 @@ class PDFDictionary(object):
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return pdf_picks
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def plot(self, stations=None):
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'''
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plots the all probability density function for either desired STATIONS
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or all available date
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:param stations: list of stations to be plotted
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:type stations: list
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:return: matplotlib figure object containing the plot
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'''
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assert stations is not None or not isinstance(stations, list), \
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'parameter stations should be a list not {0}'.format(type(stations))
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if not stations:
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nstations = self.nstations
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stations = self.stations
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else:
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nstations = len(stations)
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istations = range(nstations)
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fig, axarr = plt.subplots(nstations, 2, sharex='col', sharey='row')
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hide_labels = True
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for n in istations:
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station = stations[n]
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pdfs = self.pdf_data[station]
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for l, phase in enumerate(pdfs.keys()):
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try:
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axarr[n, l].plot(pdfs[phase].axis, pdfs[phase].data)
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if n is 0:
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axarr[n, l].set_title(phase)
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if l is 0:
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axann = axarr[n, l].annotate(station, xy=(.05, .5),
|
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xycoords='axes fraction')
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bbox_props = dict(boxstyle='round', facecolor='lightgrey',
|
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alpha=.7)
|
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axann.set_bbox(bbox_props)
|
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if n == int(np.median(istations)) and l is 0:
|
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label = 'probability density (qualitative)'
|
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axarr[n, l].set_ylabel(label)
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except IndexError as e:
|
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print('trying aligned plotting\n{0}'.format(e))
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hide_labels = False
|
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axarr[l].plot(pdfs[phase].axis, pdfs[phase].data)
|
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axarr[l].set_title(phase)
|
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if l is 0:
|
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axann = axarr[l].annotate(station, xy=(.05, .5),
|
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xycoords='axes fraction')
|
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bbox_props = dict(boxstyle='round', facecolor='lightgrey',
|
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alpha=.7)
|
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axann.set_bbox(bbox_props)
|
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if hide_labels:
|
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plt.setp([a.get_xticklabels() for a in axarr[0, :]], visible=False)
|
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plt.setp([a.get_yticklabels() for a in axarr[:, 1]], visible=False)
|
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plt.setp([a.get_yticklabels() for a in axarr[:, 0]], visible=False)
|
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|
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return fig
|
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|
@ -464,6 +464,37 @@ def getResolutionWindow(snr):
|
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return time_resolution / 2
|
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|
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|
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def select_for_phase(st, phase):
|
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'''
|
||||
takes a STream object and a phase name and returns that particular component
|
||||
which presumably shows the chosen PHASE best
|
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|
||||
:param st: stream object containing one or more component[s]
|
||||
:type st: `~obspy.core.stream.Stream`
|
||||
:param phase: label of the phase for which the stream selection is carried
|
||||
out; 'P' or 'S'
|
||||
:type phase: str
|
||||
:return:
|
||||
'''
|
||||
from pylot.core.util.defaults import COMPNAME_MAP
|
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|
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sel_st = Stream()
|
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if phase.upper() == 'P':
|
||||
comp = 'Z'
|
||||
alter_comp = COMPNAME_MAP[comp]
|
||||
sel_st += st.select(component=comp)
|
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sel_st += st.select(component=alter_comp)
|
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elif phase.upper() == 'S':
|
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comps = 'NE'
|
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for comp in comps:
|
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alter_comp = COMPNAME_MAP[comp]
|
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sel_st += st.select(component=comp)
|
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sel_st += st.select(component=alter_comp)
|
||||
else:
|
||||
raise TypeError('Unknown phase label: {0}'.format(phase))
|
||||
return sel_st
|
||||
|
||||
|
||||
def wadaticheck(pickdic, dttolerance, iplot):
|
||||
'''
|
||||
Function to calculate Wadati-diagram from given P and S onsets in order
|
||||
@ -938,10 +969,6 @@ def checkZ4S(X, pick, zfac, checkwin, iplot):
|
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return returnflag
|
||||
|
||||
|
||||
def reassess_pilot_event():
|
||||
pass
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
import doctest
|
||||
|
||||
|
34
pylot/core/util/dataprocessing.py
Normal file
34
pylot/core/util/dataprocessing.py
Normal file
@ -0,0 +1,34 @@
|
||||
#!/usr/bin/env python
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
import os
|
||||
import glob
|
||||
from obspy import UTCDateTime
|
||||
|
||||
def gse_time_header(lines):
|
||||
'''
|
||||
takes a path FILE to a GSE data file and returns the time header of the file
|
||||
:param file: path to GSE data file
|
||||
:type file: str
|
||||
:return: time header from FILE
|
||||
:rtype: str
|
||||
|
||||
>>> gse_time_header('test.gse')
|
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"WID2 2005/10/09 20:17:25.000 ATH SHZ NSP CM6 9000 50.000000 0.10E+01 1.000 NSP -1.0 0.0"
|
||||
'''
|
||||
|
||||
return lines[1]
|
||||
|
||||
def time_from_header(header):
|
||||
timeline = header.split(' ')
|
||||
time = timeline[1].split('/') + timeline[2].split(':')
|
||||
time = time[:-1] + time[-1].split('.')
|
||||
time[-1] += '000'
|
||||
return [int(t) for t in time]
|
||||
|
||||
def check_time(time):
|
||||
try:
|
||||
UTCDateTime(time)
|
||||
return True
|
||||
except ValueError:
|
||||
return False
|
@ -256,9 +256,10 @@ class ProbabilityDensityFunction(object):
|
||||
'''
|
||||
|
||||
rval = 0
|
||||
for n, x in enumerate(self.axis):
|
||||
axis = self.axis - self.x0
|
||||
for n, x in enumerate(axis):
|
||||
rval += x * self.data[n]
|
||||
return rval * self.incr
|
||||
return rval * self.incr + self.x0
|
||||
|
||||
def standard_deviation(self):
|
||||
mu = self.expectation()
|
||||
|
0
scripts/pylot-noisewindow.py
Normal file → Executable file
0
scripts/pylot-noisewindow.py
Normal file → Executable file
33
scripts/pylot-reasses-pilot-db.py
Executable file
33
scripts/pylot-reasses-pilot-db.py
Executable file
@ -0,0 +1,33 @@
|
||||
#!/usr/bin/env python
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
import argparse
|
||||
|
||||
from pylot.core.util.version import get_git_version as _getVersionString
|
||||
from pylot.core.io.phases import reassess_pilot_db
|
||||
|
||||
__version__ = _getVersionString()
|
||||
__author__ = 'S. Wehling-Benatelli'
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser(
|
||||
description='reassess old PILOT event data base in terms of consistent '
|
||||
'automatic uncertainty estimation',
|
||||
epilog='Script written by {author} belonging to PyLoT version'
|
||||
' {version}\n'.format(author=__author__,
|
||||
version=__version__)
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'dbroot', type=str, help='specifies the root directory (in '
|
||||
'most cases PILOT database folder)'
|
||||
)
|
||||
parser.add_argument(
|
||||
'--output', '-o', type=str, help='path to the output directory', dest='output'
|
||||
)
|
||||
parser.add_argument(
|
||||
'--parameterfile', '-p', type=str, help='full path to the parameterfile', dest='parfile'
|
||||
)
|
||||
|
||||
args = parser.parse_args()
|
||||
reassess_pilot_db(args.dbroot, args.output, args.parfile)
|
23
scripts/pylot-reasses-pilot-event.py
Normal file → Executable file
23
scripts/pylot-reasses-pilot-event.py
Normal file → Executable file
@ -3,23 +3,34 @@
|
||||
|
||||
import argparse
|
||||
|
||||
from pylot.core.pick.utils import reassess_pilot_event
|
||||
from pylot.core.util.version import get_git_version as _getVersionString
|
||||
from pylot.core.io.phases import reassess_pilot_event
|
||||
|
||||
__version__ = _getVersionString()
|
||||
__author__ = 'sebastianw'
|
||||
__author__ = 'S. Wehling-Benatelli'
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser()
|
||||
parser = argparse.ArgumentParser(
|
||||
description='reassess old PILOT event data in terms of consistent '
|
||||
'automatic uncertainty estimation',
|
||||
epilog='Script written by {author} belonging to PyLoT version'
|
||||
' {version}\n'.format(author=__author__,
|
||||
version=__version__)
|
||||
)
|
||||
|
||||
parser.add_argument(
|
||||
'--directory', '-d', type=str, help='specifies the root directory (in '
|
||||
'dbroot', type=str, help='specifies the root directory (in '
|
||||
'most cases PILOT database folder)'
|
||||
)
|
||||
parser.add_argument(
|
||||
'--eventid', '-i', type=str, help='PILOT event identifier'
|
||||
'id', type=str, help='PILOT event identifier'
|
||||
)
|
||||
parser.add_argument(
|
||||
'--output', '-o', type=str, help='path to the output directory', dest='output'
|
||||
)
|
||||
parser.add_argument(
|
||||
'--parameterfile', '-p', type=str, help='full path to the parameterfile', dest='parfile'
|
||||
)
|
||||
|
||||
args = parser.parse_args()
|
||||
reassess_pilot_event(args.dir, args.id)
|
||||
reassess_pilot_event(args.dbroot, args.id, args.output, args.parfile)
|
||||
|
0
scripts/pylot-signalwindow.py
Normal file → Executable file
0
scripts/pylot-signalwindow.py
Normal file → Executable file
0
scripts/pylot-snr.py
Normal file → Executable file
0
scripts/pylot-snr.py
Normal file → Executable file
Loading…
Reference in New Issue
Block a user