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Merge branch 'develop' of ariadne.geophysik.ruhr-uni-bochum.de:/data/git/pylot into develop

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Marcel Paffrath 2016-05-19 11:20:47 +02:00
commit 5f740783f0
12 changed files with 268 additions and 55 deletions
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4
QtPyLoT.py
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@ -43,7 +43,7 @@ from obspy import UTCDateTime
from pylot.core.io.data import Data
from pylot.core.io.inputs import FilterOptions, AutoPickParameter
from pylot.core.pick.autopick import autopickevent
from pylot.core.io.phases import picks_to_dict
from pylot.core.io.phases import picksdict_from_picks
from pylot.core.loc.nll import locate as locateNll
from pylot.core.util.defaults import FILTERDEFAULTS, COMPNAME_MAP,\
AUTOMATIC_DEFAULTS
@ -735,7 +735,7 @@ class MainWindow(QMainWindow):
return rval
def updatePicks(self, type='manual'):
picks = picks_to_dict(evt=self.getData().getEvtData())
picks = picksdict_from_picks(evt=self.getData().getEvtData())
if type == 'manual':
self.picks.update(picks)
elif type == 'auto':

19
pylot/core/io/data.py
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@ -9,7 +9,7 @@ from obspy.core import read, Stream, UTCDateTime
from obspy import read_events, read_inventory
from obspy.core.event import Event, ResourceIdentifier, Pick, WaveformStreamID
from pylot.core.io.phases import readPILOTEvent, picks_from_dict
from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict
from pylot.core.util.utils import fnConstructor, getGlobalTimes
from pylot.core.util.errors import FormatError, OverwriteError
@ -411,19 +411,18 @@ class Data(object):
:raise OverwriteError: raises an OverwriteError if the picks list is
not empty. The GUI will then ask for a decision.
"""
firstonset = None
#firstonset = find_firstonset(picks)
if self.getEvtData().picks:
raise OverwriteError('Actual picks would be overwritten!')
picks, firstonset = picks_from_dict(picks)
picks = picks_from_picksdict(picks)
self.getEvtData().picks = picks
# if 'smi:local' in self.getID() and firstonset:
# fonset_str = firstonset.strftime('%Y_%m_%d_%H_%M_%S')
# ID = ResourceIdentifier('event/' + fonset_str)
# ID.convertIDToQuakeMLURI(authority_id=authority_id)
# self.getEvtData().resource_id = ID
if 'smi:local' in self.getID() and firstonset:
fonset_str = firstonset.strftime('%Y_%m_%d_%H_%M_%S')
ID = ResourceIdentifier('event/' + fonset_str)
ID.convertIDToQuakeMLURI(authority_id=authority_id)
self.getEvtData().resource_id = ID
else:
print('No picks to apply!')
def applyArrivals(arrivals):
"""

89
pylot/core/io/phases.py
View File

@ -8,9 +8,9 @@ import scipy.io as sio
import obspy.core.event as ope
from obspy.core import UTCDateTime
from pylot.core.pick.utils import select_for_phase
from pylot.core.util.utils import getOwner, createPick, createArrival, \
createEvent, createOrigin, createMagnitude
createEvent, createOrigin, createMagnitude, getGlobalTimes
def readPILOTEvent(phasfn=None, locfn=None, authority_id=None, **kwargs):
"""
@ -192,14 +192,14 @@ def picksdict_from_obs(fn):
return picks
def picks_to_dict(evt):
'''
def picksdict_from_picks(evt):
"""
Takes an Event object and return the pick dictionary commonly used within
PyLoT
:param evt: Event object contain all available information
:type evt: `~obspy.core.event.Event`
:return: pick dictionary
'''
"""
picks = {}
for pick in evt.picks:
phase = {}
@ -229,12 +229,12 @@ def picks_to_dict(evt):
picks[station] = onsets.copy()
return picks
def picks_from_dict(picks):
firstonset = None
def picks_from_picksdict(picks):
picks_list = list()
for station, onsets in picks.items():
print('Reading picks on station %s' % station)
for label, phase in onsets.items():
if not isinstance(phase, dict):
if not isinstance(phase, dict) or len(phase) < 3:
continue
onset = phase['mpp']
epp = phase['epp']
@ -262,52 +262,90 @@ def picks_from_dict(picks):
else:
pick.polarity = 'undecidable'
except KeyError as e:
print('No polarity information found for %s' % phase)
if firstonset is None or firstonset > onset:
firstonset = onset
print(e.message, 'No polarity information found for %s' % phase)
picks_list.append(pick)
return picks_list
def reassess_pilot_event(root_dir, event_id):
def reassess_pilot_db(root_dir, out_dir=None, fn_param=None):
import glob
evt_list = glob.glob1(root_dir,'e????.???.??')
for evt in evt_list:
reassess_pilot_event(root_dir, evt, out_dir, fn_param)
def reassess_pilot_event(root_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
from obspy import read
from pylot.core.util.defaults import AUTOMATIC_DEFAULTS
from pylot.core.io.inputs import AutoPickParameter
from pylot.core.pick.utils import earllatepicker
default = AutoPickParameter(AUTOMATIC_DEFAULTS)
if fn_param is None:
import pylot.core.util.defaults as defaults
fn_param = defaults.AUTOMATIC_DEFAULTS
default = AutoPickParameter(fn_param)
search_base = os.path.join(root_dir, event_id)
phases_file = glob.glob(os.path.join(search_base, 'PHASES.mat'))
picks_dict = picks_from_pilot(phases_file)
if not phases_file:
return
print('Opening PILOT phases file: {fn}'.format(fn=phases_file[0]))
picks_dict = picks_from_pilot(phases_file[0])
print('Dictionary read from PHASES.mat:\n{0}'.format(picks_dict))
for station in picks_dict.keys():
fn_pattern = os.path.join(search_base, '{0}*'.format(station))
try:
st = read(fn_pattern)
st = read(fn_pattern, format='GSE2')
except TypeError as e:
print(e.message)
st = read(fn_pattern, format='GSE2')
if not st:
raise RuntimeError('no waveform data found for station {station}'.format(station=station))
st = read(fn_pattern)
for phase in picks_dict[station].keys():
try:
mpp = picks_dict[station][phase]['mpp']
except KeyError as e:
print(e.message, station)
continue
epp, lpp, spe = earllatepicker(st,
sel_st = select_for_phase(st, phase)
if not sel_st:
raise warnings.formatwarning(
'no waveform data found for station {station}'.format(
station=station), category=RuntimeWarning)
print(sel_st)
stime, etime = getGlobalTimes(sel_st)
rel_pick = mpp - stime
epp, lpp, spe = earllatepicker(sel_st,
default.get('nfac{0}'.format(phase)),
default.get('tsnrz' if phase == 'P' else 'tsnrh'),
mpp
Pick1=rel_pick,
iplot=None,
)
if epp is None or lpp is None:
continue
epp = stime + epp
lpp = stime + lpp
min_diff = 3 * st[0].stats.delta
if lpp - mpp < min_diff:
lpp = mpp + min_diff
if mpp - epp < min_diff:
epp = mpp - min_diff
picks_dict[station][phase] = dict(epp=epp, mpp=mpp, lpp=lpp, spe=spe)
# create Event object for export
evt = ope.Event(resource_id=event_id)
evt.picks = picks_from_dict(picks_dict)
evt.picks = picks_from_picksdict(picks_dict)
# write phase information to file
evt.write('{0}.xml'.format(event_id), format='QUAKEML')
if not out_dir:
fnout_prefix = os.path.join(root_dir, event_id, '{0}.'.format(event_id))
else:
fnout_prefix = os.path.join(out_dir, '{0}.'.format(event_id))
evt.write(fnout_prefix + 'xml', format='QUAKEML')
#evt.write(fnout_prefix + 'cnv', format='VELEST')
def writephases(arrivals, fformat, filename):
'''
"""
Function of methods to write phases to the following standard file
formats used for locating earthquakes:
@ -325,7 +363,7 @@ def writephases(arrivals, fformat, filename):
:param: filename, full path and name of phase file
:type: string
'''
"""
if fformat == 'NLLoc':
print ("Writing phases to %s for NLLoc" % filename)
@ -387,7 +425,6 @@ def writephases(arrivals, fformat, filename):
sweight))
fid.close()
elif fformat == 'HYPO71':
print ("Writing phases to %s for HYPO71" % filename)
fid = open("%s" % filename, 'w')

81
pylot/core/pick/compare.py
View File

@ -9,7 +9,7 @@ import matplotlib.pyplot as plt
from obspy import read_events
from pylot.core.io.phases import picks_to_dict
from pylot.core.io.phases import picksdict_from_picks
from pylot.core.util.pdf import ProbabilityDensityFunction
from pylot.core.util.version import get_git_version as _getVersionString
@ -86,8 +86,8 @@ class Comparison(object):
"""
compare_pdfs = dict()
pdf_a = self.get(self.names[0]).pdf_data(type)
pdf_b = self.get(self.names[1]).pdf_data(type)
pdf_a = self.get(self.names[0]).generate_pdf_data(type)
pdf_b = self.get(self.names[1]).generate_pdf_data(type)
for station, phases in pdf_a.items():
if station in pdf_b.keys():
@ -206,6 +206,7 @@ class PDFDictionary(object):
def __init__(self, data):
self._pickdata = data
self._pdfdata = self.generate_pdf_data()
def __nonzero__(self):
if len(self.pick_data) < 1:
@ -213,6 +214,14 @@ class PDFDictionary(object):
else:
return True
@property
def pdf_data(self):
return self._pdfdata
@pdf_data.setter
def pdf_data(self, data):
self._pdfdata = data
@property
def pick_data(self):
return self._pickdata
@ -221,15 +230,23 @@ class PDFDictionary(object):
def pick_data(self, data):
self._pickdata = data
@property
def stations(self):
return self.pick_data.keys()
@property
def nstations(self):
return len(self.stations)
@classmethod
def from_quakeml(self, fn):
cat = read_events(fn)
if len(cat) > 1:
raise NotImplementedError('reading more than one event at the same '
'time is not implemented yet! Sorry!')
return PDFDictionary(picks_to_dict(cat[0]))
return PDFDictionary(picksdict_from_picks(cat[0]))
def pdf_data(self, type='exp'):
def generate_pdf_data(self, type='exp'):
"""
Returns probabiliy density function dictionary containing the
representation of the actual pick_data.
@ -251,3 +268,57 @@ class PDFDictionary(object):
return pdf_picks
def plot(self, stations=None):
'''
plots the all probability density function for either desired STATIONS
or all available date
:param stations: list of stations to be plotted
:type stations: list
:return: matplotlib figure object containing the plot
'''
assert stations is not None or not isinstance(stations, list), \
'parameter stations should be a list not {0}'.format(type(stations))
if not stations:
nstations = self.nstations
stations = self.stations
else:
nstations = len(stations)
istations = range(nstations)
fig, axarr = plt.subplots(nstations, 2, sharex='col', sharey='row')
hide_labels = True
for n in istations:
station = stations[n]
pdfs = self.pdf_data[station]
for l, phase in enumerate(pdfs.keys()):
try:
axarr[n, l].plot(pdfs[phase].axis, pdfs[phase].data)
if n is 0:
axarr[n, l].set_title(phase)
if l is 0:
axann = axarr[n, l].annotate(station, xy=(.05, .5),
xycoords='axes fraction')
bbox_props = dict(boxstyle='round', facecolor='lightgrey',
alpha=.7)
axann.set_bbox(bbox_props)
if n == int(np.median(istations)) and l is 0:
label = 'probability density (qualitative)'
axarr[n, l].set_ylabel(label)
except IndexError as e:
print('trying aligned plotting\n{0}'.format(e))
hide_labels = False
axarr[l].plot(pdfs[phase].axis, pdfs[phase].data)
axarr[l].set_title(phase)
if l is 0:
axann = axarr[l].annotate(station, xy=(.05, .5),
xycoords='axes fraction')
bbox_props = dict(boxstyle='round', facecolor='lightgrey',
alpha=.7)
axann.set_bbox(bbox_props)
if hide_labels:
plt.setp([a.get_xticklabels() for a in axarr[0, :]], visible=False)
plt.setp([a.get_yticklabels() for a in axarr[:, 1]], visible=False)
plt.setp([a.get_yticklabels() for a in axarr[:, 0]], visible=False)
return fig

35
pylot/core/pick/utils.py
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@ -464,6 +464,37 @@ def getResolutionWindow(snr):
return time_resolution / 2
def select_for_phase(st, phase):
'''
takes a STream object and a phase name and returns that particular component
which presumably shows the chosen PHASE best
: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
sel_st = Stream()
if phase.upper() == 'P':
comp = 'Z'
alter_comp = COMPNAME_MAP[comp]
sel_st += st.select(component=comp)
sel_st += st.select(component=alter_comp)
elif phase.upper() == 'S':
comps = 'NE'
for comp in comps:
alter_comp = COMPNAME_MAP[comp]
sel_st += st.select(component=comp)
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):
return returnflag
def reassess_pilot_event():
pass
if __name__ == '__main__':
import doctest

34
pylot/core/util/dataprocessing.py Normal file
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@ -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')
"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

5
pylot/core/util/pdf.py
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@ -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
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33
scripts/pylot-reasses-pilot-db.py Executable file
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@ -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
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@ -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
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0
scripts/pylot-snr.py Normal file → Executable file
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