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Merge remote-tracking branch 'origin/develop' into feature/refactor

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Darius Arnold 2018-08-03 11:55:13 +02:00
commit a45e817213
35 changed files with 1708 additions and 1056 deletions
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502
PyLoT.py
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47
autoPyLoT.py
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@ -7,6 +7,7 @@ import argparse
import datetime import datetime
import glob import glob
import os import os
import traceback
import pylot.core.loc.focmec as focmec import pylot.core.loc.focmec as focmec
import pylot.core.loc.hash as hash import pylot.core.loc.hash as hash
@ -22,7 +23,7 @@ from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
from pylot.core.io.data import Data from pylot.core.io.data import Data
from pylot.core.io.inputs import PylotParameter from pylot.core.io.inputs import PylotParameter
from pylot.core.pick.autopick import autopickevent, iteratepicker from pylot.core.pick.autopick import autopickevent, iteratepicker
from pylot.core.util.dataprocessing import restitute_data, read_metadata from pylot.core.util.dataprocessing import restitute_data, read_metadata, Metadata
from pylot.core.util.defaults import SEPARATOR from pylot.core.util.defaults import SEPARATOR
from pylot.core.util.event import Event from pylot.core.util.event import Event
from pylot.core.util.structure import DATASTRUCTURE from pylot.core.util.structure import DATASTRUCTURE
@ -38,6 +39,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
""" """
Determine phase onsets automatically utilizing the automatic picking Determine phase onsets automatically utilizing the automatic picking
algorithms by Kueperkoch et al. 2010/2012. algorithms by Kueperkoch et al. 2010/2012.
:param obspyDMT_wfpath: if obspyDMT is used, name of data directory ("raw" or "processed")
:param input_dict: :param input_dict:
:type input_dict: :type input_dict:
:param parameter: PylotParameter object containing parameters used for automatic picking :param parameter: PylotParameter object containing parameters used for automatic picking
@ -53,7 +55,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
:type savepath: str :type savepath: str
:param savexml: export results in XML file if True :param savexml: export results in XML file if True
:type savexml: bool :type savexml: bool
:param station: list of station names or 'all' to pick all stations :param station: choose specific station name or 'all' to pick all stations
:type station: str :type station: str
:param iplot: logical variable for plotting: 0=none, 1=partial, 2=all :param iplot: logical variable for plotting: 0=none, 1=partial, 2=all
:type iplot: int :type iplot: int
@ -117,7 +119,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
if not parameter: if not parameter:
if inputfile: if inputfile:
parameter = PylotParameter(inputfile) parameter = PylotParameter(inputfile)
#iplot = parameter['iplot'] # iplot = parameter['iplot']
else: else:
infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in') infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
print('Using default input file {}'.format(infile)) print('Using default input file {}'.format(infile))
@ -149,8 +151,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
datastructure.modifyFields(**dsfields) datastructure.modifyFields(**dsfields)
datastructure.setExpandFields(exf) datastructure.setExpandFields(exf)
# check if default location routine NLLoc is available # check if default location routine NLLoc is available and all stations are used
if real_None(parameter['nllocbin']): if real_None(parameter['nllocbin']) and station == 'all':
locflag = 1 locflag = 1
# get NLLoc-root path # get NLLoc-root path
nllocroot = parameter.get('nllocroot') nllocroot = parameter.get('nllocroot')
@ -200,8 +202,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
events.append(os.path.join(datapath, eventID)) events.append(os.path.join(datapath, eventID))
else: else:
# autoPyLoT was initialized from GUI # autoPyLoT was initialized from GUI
events = [] events = [eventid]
events.append(eventid)
evID = os.path.split(eventid)[-1] evID = os.path.split(eventid)[-1]
locflag = 2 locflag = 2
else: else:
@ -271,24 +272,26 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
if not wfdat: if not wfdat:
print('Could not find station {}. STOP!'.format(station)) print('Could not find station {}. STOP!'.format(station))
return return
wfdat = remove_underscores(wfdat) #wfdat = remove_underscores(wfdat)
# trim components for each station to avoid problems with different trace starttimes for one station # trim components for each station to avoid problems with different trace starttimes for one station
wfdat = check4gaps(wfdat) wfdat = check4gaps(wfdat)
wfdat = check4doubled(wfdat) wfdat = check4doubled(wfdat)
wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False) wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
metadata = read_metadata(parameter.get('invdir')) if not wfpath_extension:
# TODO: (idea) read metadata from obspy_dmt database metadata = Metadata(parameter.get('invdir'))
# if not wfpath_extension: else:
# metadata = read_metadata(parameter.get('invdir')) metadata = Metadata(os.path.join(eventpath, 'resp'))
# else:
# metadata = None
corr_dat = None corr_dat = None
if metadata: if metadata:
# rotate stations to ZNE # rotate stations to ZNE
wfdat = check4rotated(wfdat, metadata) try:
wfdat = check4rotated(wfdat, metadata)
except Exception as e:
print('Could not rotate station {} to ZNE:\n{}'.format(wfdat[0].stats.station,
traceback.format_exc()))
if locflag: if locflag:
print("Restitute data ...") print("Restitute data ...")
corr_dat = restitute_data(wfdat.copy(), *metadata, ncores=ncores) corr_dat = restitute_data(wfdat.copy(), metadata, ncores=ncores)
if not corr_dat and locflag: if not corr_dat and locflag:
locflag = 2 locflag = 2
print('Working on event %s. Stations: %s' % (eventpath, station)) print('Working on event %s. Stations: %s' % (eventpath, station))
@ -363,8 +366,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
WAscaling[2])) WAscaling[2]))
evt = local_mag.updated_event(magscaling) evt = local_mag.updated_event(magscaling)
net_ml = local_mag.net_magnitude(magscaling) net_ml = local_mag.net_magnitude(magscaling)
print("Network local magnitude: %4.1f" % net_ml.mag) if net_ml:
if magscaling == None: print("Network local magnitude: %4.1f" % net_ml.mag)
if magscaling is None:
scaling = False scaling = False
elif magscaling[0] != 0 and magscaling[1] != 0: elif magscaling[0] != 0 and magscaling[1] != 0:
scaling = False scaling = False
@ -447,8 +451,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
WAscaling[2])) WAscaling[2]))
evt = local_mag.updated_event(magscaling) evt = local_mag.updated_event(magscaling)
net_ml = local_mag.net_magnitude(magscaling) net_ml = local_mag.net_magnitude(magscaling)
print("Network local magnitude: %4.1f" % net_ml.mag) if net_ml:
if magscaling == None: print("Network local magnitude: %4.1f" % net_ml.mag)
if magscaling is None:
scaling = False scaling = False
elif magscaling[0] != 0 and magscaling[1] != 0: elif magscaling[0] != 0 and magscaling[1] != 0:
scaling = False scaling = False
@ -499,7 +504,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
endsplash = '''------------------------------------------\n' endsplash = '''------------------------------------------\n'
-----Finished event %s!-----\n' -----Finished event %s!-----\n'
------------------------------------------'''.format \ ------------------------------------------'''.format \
(version=_getVersionString()) % evID (version=_getVersionString()) % evID
print(endsplash) print(endsplash)
locflag = glocflag locflag = glocflag
if locflag == 0: if locflag == 0:

21
pylot/core/analysis/magnitude.py
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@ -17,6 +17,7 @@ from pylot.core.util.utils import common_range, fit_curve
from scipy import integrate, signal from scipy import integrate, signal
from scipy.optimize import curve_fit from scipy.optimize import curve_fit
def richter_magnitude_scaling(delta): def richter_magnitude_scaling(delta):
distance = np.array([0, 10, 20, 25, 30, 35, 40, 45, 50, 60, 70, 75, 85, 90, 100, 110, distance = np.array([0, 10, 20, 25, 30, 35, 40, 45, 50, 60, 70, 75, 85, 90, 100, 110,
120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 230, 240, 250, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 230, 240, 250,
@ -122,7 +123,7 @@ class Magnitude(object):
def net_magnitude(self, magscaling=None): def net_magnitude(self, magscaling=None):
if self: if self:
if magscaling == None: if magscaling is None:
scaling = False scaling = False
elif magscaling[0] != 0 and magscaling[1] != 0: elif magscaling[0] != 0 and magscaling[1] != 0:
scaling = False scaling = False
@ -225,7 +226,7 @@ class LocalMagnitude(Magnitude):
sqH = np.sqrt(power_sum) sqH = np.sqrt(power_sum)
# get time array # get time array
th=np.arange(0, st[0].stats.npts/st[0].stats.sampling_rate, st[0].stats.delta) th = np.arange(0, st[0].stats.npts / st[0].stats.sampling_rate, st[0].stats.delta)
# get maximum peak within pick window # get maximum peak within pick window
iwin = getsignalwin(th, t0 - stime, self.calc_win) iwin = getsignalwin(th, t0 - stime, self.calc_win)
ii = min([iwin[len(iwin) - 1], len(th)]) ii = min([iwin[len(iwin) - 1], len(th)])
@ -247,7 +248,7 @@ class LocalMagnitude(Magnitude):
ax.set_title('Station %s, Channel %s, RMS Horizontal Trace, ' ax.set_title('Station %s, Channel %s, RMS Horizontal Trace, '
'WA-peak-to-peak=%6.3f mm' % (st[0].stats.station, 'WA-peak-to-peak=%6.3f mm' % (st[0].stats.station,
st[0].stats.channel, st[0].stats.channel,
wapp)) wapp))
ax.set_xlabel('Time [s]') ax.set_xlabel('Time [s]')
ax.set_ylabel('Displacement [mm]') ax.set_ylabel('Displacement [mm]')
ax = fig.add_subplot(212) ax = fig.add_subplot(212)
@ -257,15 +258,16 @@ class LocalMagnitude(Magnitude):
ax.plot([t0 - stime, t0 - stime], [0, max(sqH)], 'r', linewidth=2) ax.plot([t0 - stime, t0 - stime], [0, max(sqH)], 'r', linewidth=2)
ax.set_title('Channel %s, RMS Horizontal Trace, ' ax.set_title('Channel %s, RMS Horizontal Trace, '
'WA-peak-to-peak=%6.3f mm' % (st[1].stats.channel, 'WA-peak-to-peak=%6.3f mm' % (st[1].stats.channel,
wapp)) wapp))
ax.set_xlabel('Time [s]') ax.set_xlabel('Time [s]')
ax.set_ylabel('Displacement [mm]') ax.set_ylabel('Displacement [mm]')
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return wapp, fig return wapp, fig
def calc(self): def calc(self):
@ -309,7 +311,7 @@ class LocalMagnitude(Magnitude):
a0 = a0 * 1e03 # mm to nm (see Havskov & Ottemöller, 2010) a0 = a0 * 1e03 # mm to nm (see Havskov & Ottemöller, 2010)
magnitude = ope.StationMagnitude(mag=np.log10(a0) \ magnitude = ope.StationMagnitude(mag=np.log10(a0) \
+ self.wascaling[0] * np.log10(delta) + self.wascaling[1] + self.wascaling[0] * np.log10(delta) + self.wascaling[1]
* delta + self.wascaling[ * delta + self.wascaling[
2]) 2])
magnitude.origin_id = self.origin_id magnitude.origin_id = self.origin_id
magnitude.waveform_id = pick.waveform_id magnitude.waveform_id = pick.waveform_id
@ -510,6 +512,9 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
zdat = select_for_phase(wfstream, "P") zdat = select_for_phase(wfstream, "P")
if len(zdat) == 0:
raise IOError('No vertical component found in stream:\n{}'.format(wfstream))
dt = zdat[0].stats.delta dt = zdat[0].stats.delta
freq = zdat[0].stats.sampling_rate freq = zdat[0].stats.sampling_rate

14
pylot/core/io/data.py
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@ -17,6 +17,7 @@ from pylot.core.util.utils import fnConstructor, full_range, remove_underscores,
import pylot.core.loc.velest as velest import pylot.core.loc.velest as velest
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
class Data(object): class Data(object):
""" """
Data container with attributes wfdata holding ~obspy.core.stream. Data container with attributes wfdata holding ~obspy.core.stream.
@ -284,7 +285,7 @@ class Data(object):
mstation_ext = mstation + '_' mstation_ext = mstation + '_'
for k in range(len(picks_copy)): for k in range(len(picks_copy)):
if ((picks_copy[k].waveform_id.station_code == mstation) or if ((picks_copy[k].waveform_id.station_code == mstation) or
(picks_copy[k].waveform_id.station_code == mstation_ext)) and \ (picks_copy[k].waveform_id.station_code == mstation_ext)) and \
(picks_copy[k].method_id == 'auto'): (picks_copy[k].method_id == 'auto'):
del picks_copy[k] del picks_copy[k]
break break
@ -299,7 +300,7 @@ class Data(object):
for i in range(len(picks_copy)): for i in range(len(picks_copy)):
if picks_copy[i].phase_hint[0] == 'P': if picks_copy[i].phase_hint[0] == 'P':
if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \ if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
(picks_copy[i].time_errors['uncertainty'] == None): (picks_copy[i].time_errors['uncertainty'] is None):
print("Uncertainty exceeds or equal adjusted upper time error!") print("Uncertainty exceeds or equal adjusted upper time error!")
print("Adjusted uncertainty: {}".format(upperErrors[0])) print("Adjusted uncertainty: {}".format(upperErrors[0]))
print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty'])) print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
@ -311,7 +312,7 @@ class Data(object):
break break
if picks_copy[i].phase_hint[0] == 'S': if picks_copy[i].phase_hint[0] == 'S':
if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \ if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
(picks_copy[i].time_errors['uncertainty'] == None): (picks_copy[i].time_errors['uncertainty'] is None):
print("Uncertainty exceeds or equal adjusted upper time error!") print("Uncertainty exceeds or equal adjusted upper time error!")
print("Adjusted uncertainty: {}".format(upperErrors[1])) print("Adjusted uncertainty: {}".format(upperErrors[1]))
print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty'])) print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
@ -404,7 +405,7 @@ class Data(object):
# various pre-processing steps: # various pre-processing steps:
# remove possible underscores in station names # remove possible underscores in station names
self.wfdata = remove_underscores(self.wfdata) #self.wfdata = remove_underscores(self.wfdata)
# check for stations with rotated components # check for stations with rotated components
if checkRotated and metadata is not None: if checkRotated and metadata is not None:
self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0) self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
@ -416,7 +417,6 @@ class Data(object):
self.dirty = False self.dirty = False
return True return True
def appendWFData(self, fnames, synthetic=False): def appendWFData(self, fnames, synthetic=False):
""" """
Read waveform data from fnames and append it to current wf data Read waveform data from fnames and append it to current wf data
@ -506,8 +506,10 @@ class Data(object):
# check for automatic picks # check for automatic picks
print("Writing phases to ObsPy-quakeml file") print("Writing phases to ObsPy-quakeml file")
for key in picks: for key in picks:
if not picks[key].get('P'):
continue
if picks[key]['P']['picker'] == 'auto': if picks[key]['P']['picker'] == 'auto':
print("Existing picks will be overwritten!") print("Existing auto-picks will be overwritten in pick-dictionary!")
picks = picks_from_picksdict(picks) picks = picks_from_picksdict(picks)
break break
else: else:

10
pylot/core/io/default_parameters.py
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@ -456,11 +456,11 @@ defaults = {'rootpath': {'type': str,
'namestring': 'Wadati tolerance'}, 'namestring': 'Wadati tolerance'},
'jackfactor': {'type': float, 'jackfactor': {'type': float,
'tooltip': 'pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor', 'tooltip': 'pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor',
'value': 5.0, 'value': 5.0,
'min': 0., 'min': 0.,
'max': np.inf, 'max': np.inf,
'namestring': 'Jackknife safety factor'}, 'namestring': 'Jackknife safety factor'},
'WAscaling': {'type': (float, float, float), 'WAscaling': {'type': (float, float, float),
'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] \ 'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] \

21
pylot/core/io/phases.py
View File

@ -245,7 +245,7 @@ def picksdict_from_picks(evt):
if picker.startswith('smi:local/'): if picker.startswith('smi:local/'):
picker = picker.split('smi:local/')[1] picker = picker.split('smi:local/')[1]
except IndexError: except IndexError:
picker = 'manual' # MP MP TODO maybe improve statement picker = 'manual' # MP MP TODO maybe improve statement
try: try:
onsets = picksdict[picker][station] onsets = picksdict[picker][station]
except KeyError as e: except KeyError as e:
@ -346,6 +346,7 @@ def picks_from_picksdict(picks, creation_info=None):
picks_list.append(pick) picks_list.append(pick)
return picks_list return picks_list
def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0): def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0):
import glob import glob
@ -499,7 +500,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
except KeyError as e: except KeyError as e:
print(e) print(e)
fm = None fm = None
if fm == None: if fm is None:
fm = '?' fm = '?'
onset = arrivals[key]['P']['mpp'] onset = arrivals[key]['P']['mpp']
year = onset.year year = onset.year
@ -916,9 +917,9 @@ def merge_picks(event, picks):
network = pick.waveform_id.network_code network = pick.waveform_id.network_code
method = pick.method_id method = pick.method_id
for p in event.picks: for p in event.picks:
if p.waveform_id.station_code == station\ if p.waveform_id.station_code == station \
and p.waveform_id.network_code == network\ and p.waveform_id.network_code == network \
and p.phase_hint == phase\ and p.phase_hint == phase \
and (str(p.method_id) in str(method) and (str(p.method_id) in str(method)
or str(method) in str(p.method_id)): or str(method) in str(p.method_id)):
p.time, p.time_errors, p.waveform_id.network_code, p.method_id = time, err, network, method p.time, p.time_errors, p.waveform_id.network_code, p.method_id = time, err, network, method
@ -965,22 +966,22 @@ def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
arrivals_copy = cat_copy.events[0].picks arrivals_copy = cat_copy.events[0].picks
# Prefere manual picks if qualities are sufficient! # Prefere manual picks if qualities are sufficient!
for Pick in arrivals: for Pick in arrivals:
if (Pick.method_id.id).split('/')[1] == 'manual': if Pick.method_id.id.split('/')[1] == 'manual':
mstation = Pick.waveform_id.station_code mstation = Pick.waveform_id.station_code
mstation_ext = mstation + '_' mstation_ext = mstation + '_'
for mpick in arrivals_copy: for mpick in arrivals_copy:
phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint)) phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
if phase == 'P': if phase == 'P':
if ((mpick.waveform_id.station_code == mstation) or if ((mpick.waveform_id.station_code == mstation) or
(mpick.waveform_id.station_code == mstation_ext)) and \ (mpick.waveform_id.station_code == mstation_ext)) and \
((mpick.method_id).split('/')[1] == 'auto') and \ (mpick.method_id.split('/')[1] == 'auto') and \
(mpick.time_errors['uncertainty'] <= ErrorsP[3]): (mpick.time_errors['uncertainty'] <= ErrorsP[3]):
del mpick del mpick
break break
elif phase == 'S': elif phase == 'S':
if ((mpick.waveform_id.station_code == mstation) or if ((mpick.waveform_id.station_code == mstation) or
(mpick.waveform_id.station_code == mstation_ext)) and \ (mpick.waveform_id.station_code == mstation_ext)) and \
((mpick.method_id).split('/')[1] == 'auto') and \ (mpick.method_id.split('/')[1] == 'auto') and \
(mpick.time_errors['uncertainty'] <= ErrorsS[3]): (mpick.time_errors['uncertainty'] <= ErrorsS[3]):
del mpick del mpick
break break

1
pylot/core/loc/nll.py
View File

@ -76,6 +76,7 @@ def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
def locate(fnin, parameter=None): def locate(fnin, parameter=None):
""" """
takes an external program name and tries to run it takes an external program name and tries to run it
:param parameter: PyLoT Parameter object
:param fnin: external program name :param fnin: external program name
:return: None :return: None
""" """

331
pylot/core/pick/autopick.py
View File

@ -8,6 +8,7 @@ function conglomerate utils.
:author: MAGS2 EP3 working group / Ludger Kueperkoch :author: MAGS2 EP3 working group / Ludger Kueperkoch
""" """
import traceback
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import numpy as np import numpy as np
@ -71,42 +72,34 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
for station in stations: for station in stations:
topick = data.select(station=station) topick = data.select(station=station)
input_tuples.append((topick, param, apverbose, iplot, fig_dict, metadata, origin))
if iplot is None or iplot == 'None' or iplot == 0:
input_tuples.append((topick, param, apverbose, metadata, origin))
if iplot > 0:
all_onsets[station] = autopickstation(topick, param, verbose=apverbose,
iplot=iplot, fig_dict=fig_dict,
metadata=metadata, origin=origin)
if iplot > 0: if iplot > 0:
print('iPlot Flag active: NO MULTIPROCESSING possible.') print('iPlot Flag active: NO MULTIPROCESSING possible.')
return all_onsets ncores = 1
# rename str for ncores in case ncores == 0 (use all cores) # rename ncores for string representation in case ncores == 0 (use all cores)
ncores_str = ncores if ncores != 0 else 'all available' ncores_str = ncores if ncores != 0 else 'all available'
print('Autopickstation: Distribute autopicking for {} ' print('Autopickstation: Distribute autopicking for {} '
'stations on {} cores.'.format(len(input_tuples), ncores_str)) 'stations on {} cores.'.format(len(input_tuples), ncores_str))
pool = gen_Pool(ncores) if ncores == 1:
results = pool.map(call_autopickstation, input_tuples) results = serial_picking(input_tuples)
pool.close() else:
results = parallel_picking(input_tuples, ncores)
for result, wfstream in results: for result, station in results:
if type(result) == dict: if type(result) == dict:
station = result['station']
result.pop('station')
all_onsets[station] = result all_onsets[station] = result
else: else:
if result == None: if result is None:
result = 'Picker exited unexpectedly.' result = 'Picker exited unexpectedly.'
if len(wfstream) > 0:
station = wfstream[0].stats.station
else:
station = None
print('Could not pick a station: {}\nReason: {}'.format(station, result)) print('Could not pick a station: {}\nReason: {}'.format(station, result))
# no Wadati/JK for single station (also valid for tuning mode)
if len(stations) == 1:
return all_onsets
# quality control # quality control
# median check and jackknife on P-onset times # median check and jackknife on P-onset times
jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, jackfactor, iplot, fig_dict_wadatijack) jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, jackfactor, iplot, fig_dict_wadatijack)
@ -115,6 +108,20 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
return wadationsets return wadationsets
def serial_picking(input_tuples):
result = []
for input_tuple in input_tuples:
result.append(call_autopickstation(input_tuple))
return result
def parallel_picking(input_tuples, ncores):
pool = gen_Pool(ncores)
result = pool.imap_unordered(call_autopickstation, input_tuples)
pool.close()
return result
def call_autopickstation(input_tuple): def call_autopickstation(input_tuple):
""" """
helper function used for multiprocessing helper function used for multiprocessing
@ -123,12 +130,16 @@ def call_autopickstation(input_tuple):
:return: dictionary containing P pick, S pick and station name :return: dictionary containing P pick, S pick and station name
:rtype: dict :rtype: dict
""" """
wfstream, pickparam, verbose, metadata, origin = input_tuple wfstream, pickparam, verbose, iplot, fig_dict, metadata, origin = input_tuple
if fig_dict:
print('Running in interactive mode')
# multiprocessing not possible with interactive plotting # multiprocessing not possible with interactive plotting
try: try:
return autopickstation(wfstream, pickparam, verbose, iplot=0, metadata=metadata, origin=origin), wfstream return autopickstation(wfstream, pickparam, verbose, fig_dict=fig_dict, iplot=iplot, metadata=metadata,
origin=origin)
except Exception as e: except Exception as e:
return e, wfstream tbe = traceback.format_exc()
return tbe, wfstream[0].stats.station
def get_source_coords(parser, station_id): def get_source_coords(parser, station_id):
@ -1312,9 +1323,12 @@ def nautopickstation(wfstream, pickparam, verbose=False,
# split components # split components
zdat, ndat, edat = get_components_from_waveformstream(wfstream) zdat, ndat, edat = get_components_from_waveformstream(wfstream)
picks = {}
station = wfstream[0].stats.station
if not zdat: if not zdat:
print('No z-component found for station {}. STOP'.format(wfstream[0].stats.station)) print('No z-component found for station {}. STOP'.format(station))
return return picks, station
if p_params['algoP'] == 'HOS' or p_params['algoP'] == 'ARZ' and zdat is not None: if p_params['algoP'] == 'HOS' or p_params['algoP'] == 'ARZ' and zdat is not None:
msg = '##################################################\nautopickstation:' \ msg = '##################################################\nautopickstation:' \
@ -1331,13 +1345,10 @@ def nautopickstation(wfstream, pickparam, verbose=False,
Lc = np.inf Lc = np.inf
print('autopickstation: use_taup flag active.') print('autopickstation: use_taup flag active.')
if not metadata: if not metadata:
metadata = [None, None]
if not metadata[1]:
print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.') print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.')
else: else:
station_id = wfstream[0].get_id() station_id = wfstream[0].get_id()
parser = metadata[1] station_coords = metadata.get_coordinates(station_id, time=wfstream[0].stats.starttime)
station_coords = get_source_coords(parser, station_id)
if station_coords and origin: if station_coords and origin:
source_origin = origin[0] source_origin = origin[0]
model = TauPyModel(p_params['taup_model']) model = TauPyModel(p_params['taup_model'])
@ -1377,7 +1388,7 @@ def nautopickstation(wfstream, pickparam, verbose=False,
Lwf = zdat[0].stats.endtime - zdat[0].stats.starttime Lwf = zdat[0].stats.endtime - zdat[0].stats.starttime
if not Lwf > 0: if not Lwf > 0:
print('autopickstation: empty trace! Return!') print('autopickstation: empty trace! Return!')
return return picks, station
Ldiff = Lwf - abs(Lc) Ldiff = Lwf - abs(Lc)
if Ldiff <= 0 or pstop <= pstart or pstop - pstart <= thosmw: if Ldiff <= 0 or pstop <= pstart or pstop - pstart <= thosmw:
@ -1574,8 +1585,8 @@ def nautopickstation(wfstream, pickparam, verbose=False,
msg = "autopickstation: P-weight: {0}, " \ msg = "autopickstation: P-weight: {0}, " \
"SNR: {1}, SNR[dB]: {2}, Polarity: {3}".format(Pweight, SNRP, SNRPdB, FM) "SNR: {1}, SNR[dB]: {2}, Polarity: {3}".format(Pweight, SNRP, SNRPdB, FM)
print(msg) print(msg)
msg = 'autopickstation: Refind P-Pick: {} s | P-Error: {} s'.format(zdat[0].stats.starttime \ msg = 'autopickstation: Refined P-Pick: {} s | P-Error: {} s'.format(zdat[0].stats.starttime \
+ mpickP, Perror) + mpickP, Perror)
print(msg) print(msg)
Sflag = 1 Sflag = 1
@ -1609,7 +1620,7 @@ def nautopickstation(wfstream, pickparam, verbose=False,
ndat = edat ndat = edat
pickSonset = (edat is not None and ndat is not None and len(edat) > 0 and len( pickSonset = (edat is not None and ndat is not None and len(edat) > 0 and len(
ndat) > 0 and Pweight < 4) ndat) > 0 and Pweight < 4)
if pickSonset: if pickSonset:
# determine time window for calculating CF after P onset # determine time window for calculating CF after P onset
@ -1617,8 +1628,8 @@ def nautopickstation(wfstream, pickparam, verbose=False,
round(max([mpickP + s_params['sstart'], 0])), # MP MP relative time axis round(max([mpickP + s_params['sstart'], 0])), # MP MP relative time axis
round(min([ round(min([
mpickP + s_params['sstop'], mpickP + s_params['sstop'],
edat[0].stats.endtime-edat[0].stats.starttime, edat[0].stats.endtime - edat[0].stats.starttime,
ndat[0].stats.endtime-ndat[0].stats.starttime ndat[0].stats.endtime - ndat[0].stats.starttime
])) ]))
] ]
@ -1842,7 +1853,7 @@ def nautopickstation(wfstream, pickparam, verbose=False,
Serror = pickerr[ipick] Serror = pickerr[ipick]
msg = 'autopickstation: Refined S-Pick: {} s | S-Error: {} s'.format(hdat[0].stats.starttime \ msg = 'autopickstation: Refined S-Pick: {} s | S-Error: {} s'.format(hdat[0].stats.starttime \
+ mpickS, Serror) + mpickS, Serror)
print(msg) print(msg)
# get SNR # get SNR
@ -1956,115 +1967,114 @@ def nautopickstation(wfstream, pickparam, verbose=False,
ax1.set_ylim([-1.5, 1.5]) ax1.set_ylim([-1.5, 1.5])
ax1.set_ylabel('Normalized Counts') ax1.set_ylabel('Normalized Counts')
# fig.suptitle(tr_filt.stats.starttime) # fig.suptitle(tr_filt.stats.starttime)
try: # only continue if one horizontal stream exists
len(edat[0]) if (ndat or edat) and Sflag == 1:
except: # mirror components in case one does not exist
edat = ndat if not edat:
try: edat = ndat
len(ndat[0]) if not ndat:
except: ndat = edat
ndat = edat if len(edat[0]) > 1 and len(ndat[0]) > 1:
if len(edat[0]) > 1 and len(ndat[0]) > 1 and Sflag == 1: # plot horizontal traces
# plot horizontal traces ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
ax2 = fig.add_subplot(3, 1, 2, sharex=ax1) th1data = np.arange(0,
th1data = np.arange(0, trH1_filt.stats.npts /
trH1_filt.stats.npts / trH1_filt.stats.sampling_rate,
trH1_filt.stats.sampling_rate, trH1_filt.stats.delta)
trH1_filt.stats.delta) # check equal length of arrays, sometimes they are different!?
# check equal length of arrays, sometimes they are different!? wfldiff = len(trH1_filt.data) - len(th1data)
wfldiff = len(trH1_filt.data) - len(th1data) if wfldiff < 0:
if wfldiff < 0: th1data = th1data[0:len(th1data) - abs(wfldiff)]
th1data = th1data[0:len(th1data) - abs(wfldiff)] ax2.plot(th1data, trH1_filt.data / max(trH1_filt.data), color=linecolor, linewidth=0.7, label='Data')
ax2.plot(th1data, trH1_filt.data / max(trH1_filt.data), color=linecolor, linewidth=0.7, label='Data') if Pweight < 4:
if Pweight < 4: ax2.plot(arhcf1.getTimeArray(),
ax2.plot(arhcf1.getTimeArray(), arhcf1.getCF() / max(arhcf1.getCF()), 'b', label='CF1')
arhcf1.getCF() / max(arhcf1.getCF()), 'b', label='CF1') if aicSflag == 1 and Sweight < 4:
if aicSflag == 1 and Sweight < 4: ax2.plot(arhcf2.getTimeArray(),
ax2.plot(arhcf2.getTimeArray(), arhcf2.getCF() / max(arhcf2.getCF()), 'm', label='CF2')
arhcf2.getCF() / max(arhcf2.getCF()), 'm', label='CF2') ax2.plot(
ax2.plot( [aicarhpick.getpick(), aicarhpick.getpick()],
[aicarhpick.getpick(), aicarhpick.getpick()], [-1, 1], 'g', label='Initial S Onset')
[-1, 1], 'g', label='Initial S Onset') ax2.plot(
ax2.plot( [aicarhpick.getpick() - 0.5,
[aicarhpick.getpick() - 0.5, aicarhpick.getpick() + 0.5],
aicarhpick.getpick() + 0.5], [1, 1], 'g')
[1, 1], 'g') ax2.plot(
ax2.plot( [aicarhpick.getpick() - 0.5,
[aicarhpick.getpick() - 0.5, aicarhpick.getpick() + 0.5],
aicarhpick.getpick() + 0.5], [-1, -1], 'g')
[-1, -1], 'g') ax2.plot([refSpick.getpick(), refSpick.getpick()],
ax2.plot([refSpick.getpick(), refSpick.getpick()], [-1.3, 1.3], 'g', linewidth=2, label='Final S Pick')
[-1.3, 1.3], 'g', linewidth=2, label='Final S Pick') ax2.plot(
ax2.plot( [refSpick.getpick() - 0.5, refSpick.getpick() + 0.5],
[refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [1.3, 1.3], 'g', linewidth=2)
[1.3, 1.3], 'g', linewidth=2) ax2.plot(
ax2.plot( [refSpick.getpick() - 0.5, refSpick.getpick() + 0.5],
[refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [-1.3, -1.3], 'g', linewidth=2)
[-1.3, -1.3], 'g', linewidth=2) ax2.plot([lpickS, lpickS], [-1.1, 1.1], 'g--', label='lpp')
ax2.plot([lpickS, lpickS], [-1.1, 1.1], 'g--', label='lpp') ax2.plot([epickS, epickS], [-1.1, 1.1], 'g--', label='epp')
ax2.plot([epickS, epickS], [-1.1, 1.1], 'g--', label='epp') ax2.set_title('%s, S Weight=%d, SNR=%7.2f, SNR[dB]=%7.2f' % (
ax2.set_title('%s, S Weight=%d, SNR=%7.2f, SNR[dB]=%7.2f' % ( trH1_filt.stats.channel,
trH1_filt.stats.channel, Sweight, SNRS, SNRSdB))
Sweight, SNRS, SNRSdB)) else:
else: ax2.set_title('%s, S Weight=%d, SNR=None, SNRdB=None' % (
ax2.set_title('%s, S Weight=%d, SNR=None, SNRdB=None' % ( trH1_filt.stats.channel, Sweight))
trH1_filt.stats.channel, Sweight)) ax2.legend(loc=1)
ax2.legend(loc=1) ax2.set_yticks([])
ax2.set_yticks([]) ax2.set_ylim([-1.5, 1.5])
ax2.set_ylim([-1.5, 1.5]) ax2.set_ylabel('Normalized Counts')
ax2.set_ylabel('Normalized Counts') # fig.suptitle(trH1_filt.stats.starttime)
# fig.suptitle(trH1_filt.stats.starttime)
ax3 = fig.add_subplot(3, 1, 3, sharex=ax1) ax3 = fig.add_subplot(3, 1, 3, sharex=ax1)
th2data = np.arange(0, th2data = np.arange(0,
trH2_filt.stats.npts / trH2_filt.stats.npts /
trH2_filt.stats.sampling_rate, trH2_filt.stats.sampling_rate,
trH2_filt.stats.delta) trH2_filt.stats.delta)
# check equal length of arrays, sometimes they are different!? # check equal length of arrays, sometimes they are different!?
wfldiff = len(trH2_filt.data) - len(th2data) wfldiff = len(trH2_filt.data) - len(th2data)
if wfldiff < 0: if wfldiff < 0:
th2data = th2data[0:len(th2data) - abs(wfldiff)] th2data = th2data[0:len(th2data) - abs(wfldiff)]
ax3.plot(th2data, trH2_filt.data / max(trH2_filt.data), color=linecolor, linewidth=0.7, label='Data') ax3.plot(th2data, trH2_filt.data / max(trH2_filt.data), color=linecolor, linewidth=0.7, label='Data')
if Pweight < 4: if Pweight < 4:
p22, = ax3.plot(arhcf1.getTimeArray(), p22, = ax3.plot(arhcf1.getTimeArray(),
arhcf1.getCF() / max(arhcf1.getCF()), 'b', label='CF1') arhcf1.getCF() / max(arhcf1.getCF()), 'b', label='CF1')
if aicSflag == 1: if aicSflag == 1:
ax3.plot(arhcf2.getTimeArray(), ax3.plot(arhcf2.getTimeArray(),
arhcf2.getCF() / max(arhcf2.getCF()), 'm', label='CF2') arhcf2.getCF() / max(arhcf2.getCF()), 'm', label='CF2')
ax3.plot( ax3.plot(
[aicarhpick.getpick(), aicarhpick.getpick()], [aicarhpick.getpick(), aicarhpick.getpick()],
[-1, 1], 'g', label='Initial S Onset') [-1, 1], 'g', label='Initial S Onset')
ax3.plot( ax3.plot(
[aicarhpick.getpick() - 0.5, [aicarhpick.getpick() - 0.5,
aicarhpick.getpick() + 0.5], aicarhpick.getpick() + 0.5],
[1, 1], 'g') [1, 1], 'g')
ax3.plot( ax3.plot(
[aicarhpick.getpick() - 0.5, [aicarhpick.getpick() - 0.5,
aicarhpick.getpick() + 0.5], aicarhpick.getpick() + 0.5],
[-1, -1], 'g') [-1, -1], 'g')
ax3.plot([refSpick.getpick(), refSpick.getpick()], ax3.plot([refSpick.getpick(), refSpick.getpick()],
[-1.3, 1.3], 'g', linewidth=2, label='Final S Pick') [-1.3, 1.3], 'g', linewidth=2, label='Final S Pick')
ax3.plot( ax3.plot(
[refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [refSpick.getpick() - 0.5, refSpick.getpick() + 0.5],
[1.3, 1.3], 'g', linewidth=2) [1.3, 1.3], 'g', linewidth=2)
ax3.plot( ax3.plot(
[refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [refSpick.getpick() - 0.5, refSpick.getpick() + 0.5],
[-1.3, -1.3], 'g', linewidth=2) [-1.3, -1.3], 'g', linewidth=2)
ax3.plot([lpickS, lpickS], [-1.1, 1.1], 'g--', label='lpp') ax3.plot([lpickS, lpickS], [-1.1, 1.1], 'g--', label='lpp')
ax3.plot([epickS, epickS], [-1.1, 1.1], 'g--', label='epp') ax3.plot([epickS, epickS], [-1.1, 1.1], 'g--', label='epp')
ax3.legend(loc=1) ax3.legend(loc=1)
ax3.set_yticks([]) ax3.set_yticks([])
ax3.set_ylim([-1.5, 1.5]) ax3.set_ylim([-1.5, 1.5])
ax3.set_xlabel('Time [s] after %s' % tr_filt.stats.starttime) ax3.set_xlabel('Time [s] after %s' % tr_filt.stats.starttime)
ax3.set_ylabel('Normalized Counts') ax3.set_ylabel('Normalized Counts')
ax3.set_title(trH2_filt.stats.channel) ax3.set_title(trH2_filt.stats.channel)
if plt_flag == 1: if plt_flag == 1:
fig.show() fig.show()
try: try:
input() input()
except SyntaxError: except SyntaxError:
pass pass
plt.close(fig) plt.close(fig)
########################################################################## ##########################################################################
# calculate "real" onset times # calculate "real" onset times
if lpickP is not None and lpickP == mpickP: if lpickP is not None and lpickP == mpickP:
@ -2082,12 +2092,22 @@ def nautopickstation(wfstream, pickparam, verbose=False,
epickP = zdat[0].stats.starttime - p_params['timeerrorsP'][3] epickP = zdat[0].stats.starttime - p_params['timeerrorsP'][3]
mpickP = zdat[0].stats.starttime mpickP = zdat[0].stats.starttime
# create dictionary
# for P phase
ccode = zdat[0].stats.channel
ncode = zdat[0].stats.network
ppick = dict(channel=ccode, network=ncode, lpp=lpickP, epp=epickP, mpp=mpickP, spe=Perror, snr=SNRP,
snrdb=SNRPdB, weight=Pweight, fm=FM, w0=None, fc=None, Mo=None,
Mw=None, picker=picker, marked=Pmarker)
if edat: if edat:
hdat = edat[0] hdat = edat[0]
elif ndat: elif ndat:
hdat = ndat[0] hdat = ndat[0]
else: else:
return # no horizontal components given
picks = dict(P=ppick)
return picks, station
if lpickS is not None and lpickS == mpickS: if lpickS is not None and lpickS == mpickS:
lpickS += hdat.stats.delta lpickS += hdat.stats.delta
@ -2104,21 +2124,14 @@ def nautopickstation(wfstream, pickparam, verbose=False,
epickS = hdat.stats.starttime - s_params['timeerrorsS'][3] epickS = hdat.stats.starttime - s_params['timeerrorsS'][3]
mpickS = hdat.stats.starttime mpickS = hdat.stats.starttime
# create dictionary
# for P phase
ccode = zdat[0].stats.channel
ncode = zdat[0].stats.network
ppick = dict(channel=ccode, network=ncode, lpp=lpickP, epp=epickP, mpp=mpickP, spe=Perror, snr=SNRP,
snrdb=SNRPdB, weight=Pweight, fm=FM, w0=None, fc=None, Mo=None,
Mw=None, picker=picker, marked=Pmarker)
# add S phase # add S phase
ccode = hdat.stats.channel ccode = hdat.stats.channel
ncode = hdat.stats.network ncode = hdat.stats.network
spick = dict(channel=ccode, network=ncode, lpp=lpickS, epp=epickS, mpp=mpickS, spe=Serror, snr=SNRS, spick = dict(channel=ccode, network=ncode, lpp=lpickS, epp=epickS, mpp=mpickS, spe=Serror, snr=SNRS,
snrdb=SNRSdB, weight=Sweight, fm=None, picker=picker, Ao=Ao) snrdb=SNRSdB, weight=Sweight, fm=None, picker=picker, Ao=Ao)
# merge picks into returning dictionary # merge picks into returning dictionary
picks = dict(P=ppick, S=spick, station=zdat[0].stats.station) picks = dict(P=ppick, S=spick)
return picks return picks, station
def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter, fig_dict=None): def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter, fig_dict=None):
@ -2189,11 +2202,11 @@ def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter, fig_dict=None):
print( print(
"iteratepicker: The following picking parameters have been modified for iterative picking:") "iteratepicker: The following picking parameters have been modified for iterative picking:")
print( print(
"pstart: %fs => %fs" % (pstart_old, pickparameter.get('pstart'))) "pstart: %fs => %fs" % (pstart_old, pickparameter.get('pstart')))
print( print(
"pstop: %fs => %fs" % (pstop_old, pickparameter.get('pstop'))) "pstop: %fs => %fs" % (pstop_old, pickparameter.get('pstop')))
print( print(
"sstop: %fs => %fs" % (sstop_old, pickparameter.get('sstop'))) "sstop: %fs => %fs" % (sstop_old, pickparameter.get('sstop')))
print("pickwinP: %fs => %fs" % ( print("pickwinP: %fs => %fs" % (
pickwinP_old, pickparameter.get('pickwinP'))) pickwinP_old, pickparameter.get('pickwinP')))
print("Precalcwin: %fs => %fs" % ( print("Precalcwin: %fs => %fs" % (
@ -2203,7 +2216,7 @@ def iteratepicker(wf, NLLocfile, picks, badpicks, pickparameter, fig_dict=None):
print("zfac: %f => %f" % (zfac_old, pickparameter.get('zfac'))) print("zfac: %f => %f" % (zfac_old, pickparameter.get('zfac')))
# repick station # repick station
newpicks = autopickstation(wf2pick, pickparameter, fig_dict=fig_dict) newpicks, _ = autopickstation(wf2pick, pickparameter, fig_dict=fig_dict)
# replace old dictionary with new one # replace old dictionary with new one
picks[badpicks[i][0]] = newpicks picks[badpicks[i][0]] = newpicks

3
pylot/core/pick/compare.py
View File

@ -506,7 +506,8 @@ class PDFstatistics(object):
return rlist return rlist
def writeThetaToFile(self, array, out_dir): @staticmethod
def writeThetaToFile(array, out_dir):
""" """
Method to write array like data to file. Useful since acquiring can take Method to write array like data to file. Useful since acquiring can take
serious amount of time when dealing with large databases. serious amount of time when dealing with large databases.

112
pylot/core/pick/picker.py
View File

@ -164,9 +164,9 @@ class AICPicker(AutoPicker):
iplot = int(self.iplot) iplot = int(self.iplot)
except: except:
if self.iplot == True or self.iplot == 'True': if self.iplot == True or self.iplot == 'True':
iplot = 2 iplot = 2
else: else:
iplot = 0 iplot = 0
# find NaN's # find NaN's
nn = np.isnan(self.cf) nn = np.isnan(self.cf)
@ -191,17 +191,32 @@ class AICPicker(AutoPicker):
# remove offset in AIC function # remove offset in AIC function
offset = abs(min(aic) - min(aicsmooth)) offset = abs(min(aic) - min(aicsmooth))
aicsmooth = aicsmooth - offset aicsmooth = aicsmooth - offset
cf = self.Data[0].data
# get maximum of HOS/AR-CF as startimg point for searching # get maximum of HOS/AR-CF as startimg point for searching
# minimum in AIC function # minimum in AIC function
icfmax = np.argmax(self.Data[0].data) icfmax = np.argmax(cf)
# MP MP testing threshold
thresh_hit = False
thresh_factor = 0.7
thresh = thresh_factor * cf[icfmax]
for index, sample in enumerate(cf):
if sample >= thresh:
thresh_hit = True
# go on searching for the following maximum
if index > 0 and thresh_hit:
if sample <= cf[index - 1]:
icfmax = index - 1
break
# MP MP ---
# find minimum in AIC-CF front of maximum of HOS/AR-CF # find minimum in AIC-CF front of maximum of HOS/AR-CF
lpickwindow = int(round(self.PickWindow / self.dt)) lpickwindow = int(round(self.PickWindow / self.dt))
tsafety = self.TSNR[1] # safety gap, AIC is usually a little bit too late tsafety = self.TSNR[1] # safety gap, AIC is usually a little bit too late
left_corner_ind = max([icfmax - lpickwindow, 2]) left_corner_ind = max([icfmax - lpickwindow, 2])
right_corner_ind = icfmax + int(tsafety / self.dt) right_corner_ind = icfmax + int(tsafety / self.dt)
aic_snip = aicsmooth[left_corner_ind : right_corner_ind] aic_snip = aicsmooth[left_corner_ind: right_corner_ind]
minima = argrelmin(aic_snip)[0] # 0th entry of tuples for axes minima = argrelmin(aic_snip)[0] # 0th entry of tuples for axes
if len(minima) > 0: if len(minima) > 0:
pickindex = minima[-1] + left_corner_ind pickindex = minima[-1] + left_corner_ind
self.Pick = self.Tcf[pickindex] self.Pick = self.Tcf[pickindex]
@ -233,27 +248,28 @@ class AICPicker(AutoPicker):
ii = min([isignal[len(isignal) - 1], len(self.Tcf)]) ii = min([isignal[len(isignal) - 1], len(self.Tcf)])
isignal = isignal[0:ii] isignal = isignal[0:ii]
try: try:
self.Data[0].data[isignal] cf[isignal]
except IndexError as e: except IndexError as e:
msg = "Time series out of bounds! {}".format(e) msg = "Time series out of bounds! {}".format(e)
print(msg) print(msg)
return return
# calculate SNR from CF # calculate SNR from CF
self.SNR = max(abs(self.Data[0].data[isignal])) / \ self.SNR = max(abs(cf[isignal])) / \
abs(np.mean(self.Data[0].data[inoise])) abs(np.mean(cf[inoise]))
# calculate slope from CF after initial pick # calculate slope from CF after initial pick
# get slope window # get slope window
tslope = self.TSNR[3] # slope determination window tslope = self.TSNR[3] # slope determination window
if tsafety >= 0: if tsafety >= 0:
islope = np.where((self.Tcf <= min([self.Pick + tslope + tsafety, self.Tcf[-1]])) \ islope = np.where((self.Tcf <= min([self.Pick + tslope + tsafety, self.Tcf[-1]])) \
& (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin & (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin
else: else:
islope = np.where((self.Tcf <= min([self.Pick + tslope, self.Tcf[-1]])) \ islope = np.where((self.Tcf <= min([self.Pick + tslope, self.Tcf[-1]])) \
& (self.Tcf >= self.Pick + tsafety)) # TODO: put this in a seperate function like getsignalwin & (
self.Tcf >= self.Pick + tsafety)) # TODO: put this in a seperate function like getsignalwin
# find maximum within slope determination window # find maximum within slope determination window
# 'cause slope should be calculated up to first local minimum only! # 'cause slope should be calculated up to first local minimum only!
try: try:
dataslope = self.Data[0].data[islope[0][0:-1]] dataslope = cf[islope[0][0:-1]]
except IndexError: except IndexError:
print("Slope Calculation: empty array islope, check signal window") print("Slope Calculation: empty array islope, check signal window")
return return
@ -263,7 +279,7 @@ class AICPicker(AutoPicker):
try: try:
imaxs, = argrelmax(dataslope) imaxs, = argrelmax(dataslope)
imax = imaxs[0] imax = imaxs[0]
except ValueError as e: except (ValueError, IndexError) as e:
print(e, 'picker: argrelmax not working!') print(e, 'picker: argrelmax not working!')
imax = np.argmax(dataslope) imax = np.argmax(dataslope)
iislope = islope[0][0:imax + 1] iislope = islope[0][0:imax + 1]
@ -276,14 +292,14 @@ class AICPicker(AutoPicker):
print("AICPicker: Maximum for slope determination right at the beginning of the window!") print("AICPicker: Maximum for slope determination right at the beginning of the window!")
print("Choose longer slope determination window!") print("Choose longer slope determination window!")
if self.iplot > 1: if self.iplot > 1:
if self.fig == None or self.fig == 'None': if self.fig is None or self.fig == 'None':
fig = plt.figure() fig = plt.figure()
plt_flag = iplot plt_flag = iplot
else: else:
fig = self.fig fig = self.fig
ax = fig.add_subplot(111) ax = fig.add_subplot(111)
x = self.Data[0].data cf = cf
ax.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data') ax.plot(self.Tcf, cf / max(cf), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
ax.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF') ax.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
ax.legend(loc=1) ax.legend(loc=1)
ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime) ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
@ -291,12 +307,23 @@ class AICPicker(AutoPicker):
ax.set_title(self.Data[0].stats.station) ax.set_title(self.Data[0].stats.station)
if plt_flag in [1, 2]: if plt_flag in [1, 2]:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return return
iislope = islope[0][0:imax+1] iislope = islope[0][0:imax + 1]
dataslope = self.Data[0].data[iislope] # MP MP change slope calculation
# get all maxima of aicsmooth
iaicmaxima = argrelmax(aicsmooth)[0]
# get first index of maximum after pickindex (indices saved in iaicmaxima)
aicmax = iaicmaxima[np.where(iaicmaxima > pickindex)[0]]
if len(aicmax) > 0:
iaicmax = aicmax[0]
else:
iaicmax = -1
dataslope = aicsmooth[pickindex: iaicmax]
# calculate slope as polynomal fit of order 1 # calculate slope as polynomal fit of order 1
xslope = np.arange(0, len(dataslope), 1) xslope = np.arange(0, len(dataslope), 1)
P = np.polyfit(xslope, dataslope, 1) P = np.polyfit(xslope, dataslope, 1)
@ -306,24 +333,23 @@ class AICPicker(AutoPicker):
else: else:
self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0]) self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
# normalize slope to maximum of cf to make it unit independent # normalize slope to maximum of cf to make it unit independent
self.slope /= self.Data[0].data[icfmax] self.slope /= aicsmooth[iaicmax]
else: else:
self.SNR = None self.SNR = None
self.slope = None self.slope = None
if iplot > 1: if iplot > 1:
if self.fig == None or self.fig == 'None': if self.fig is None or self.fig == 'None':
fig = plt.figure() # self.iplot) fig = plt.figure() # self.iplot)
plt_flag = iplot plt_flag = iplot
else: else:
fig = self.fig fig = self.fig
fig._tight = True fig._tight = True
ax1 = fig.add_subplot(211) ax1 = fig.add_subplot(211)
x = self.Data[0].data if len(self.Tcf) > len(cf): # why? LK
if len(self.Tcf) > len(self.Data[0].data): # why? LK self.Tcf = self.Tcf[0:len(self.Tcf) - 1]
self.Tcf = self.Tcf[0:len(self.Tcf)-1] ax1.plot(self.Tcf, cf / max(cf), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
ax1.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
ax1.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF') ax1.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
if self.Pick is not None: if self.Pick is not None:
ax1.plot([self.Pick, self.Pick], [-0.1, 0.5], 'b', linewidth=2, label='AIC-Pick') ax1.plot([self.Pick, self.Pick], [-0.1, 0.5], 'b', linewidth=2, label='AIC-Pick')
@ -333,7 +359,7 @@ class AICPicker(AutoPicker):
if self.Pick is not None: if self.Pick is not None:
ax2 = fig.add_subplot(2, 1, 2, sharex=ax1) ax2 = fig.add_subplot(2, 1, 2, sharex=ax1)
ax2.plot(self.Tcf, x, color=self._linecolor, linewidth=0.7, label='Data') ax2.plot(self.Tcf, aicsmooth, color='r', linewidth=0.7, label='Data')
ax1.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window') ax1.axvspan(self.Tcf[inoise[0]], self.Tcf[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
ax1.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0, ax1.axvspan(self.Tcf[isignal[0]], self.Tcf[isignal[-1]], color='b', alpha=0.2, lw=0,
label='Signal Window') label='Signal Window')
@ -345,7 +371,8 @@ class AICPicker(AutoPicker):
label='Signal Window') label='Signal Window')
ax2.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0, ax2.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
label='Slope Window') label='Slope Window')
ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2, label='Slope') ax2.plot(self.Tcf[pickindex: iaicmax], datafit, 'g', linewidth=2,
label='Slope') # MP MP changed temporarily!
if self.slope is not None: if self.slope is not None:
ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station, ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station,
@ -361,15 +388,17 @@ class AICPicker(AutoPicker):
if plt_flag in [1, 2]: if plt_flag in [1, 2]:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
if plt_flag == 3: if plt_flag == 3:
stats = self.Data[0].stats stats = self.Data[0].stats
netstlc = '{}.{}.{}'.format(stats.network, stats.station, stats.location) netstlc = '{}.{}.{}'.format(stats.network, stats.station, stats.location)
fig.savefig('aicfig_{}_{}.png'.format(netstlc, stats.channel)) fig.savefig('aicfig_{}_{}.png'.format(netstlc, stats.channel))
if self.Pick == None: if self.Pick is None:
print('AICPicker: Could not find minimum, picking window too short?') print('AICPicker: Could not find minimum, picking window too short?')
return return
@ -386,9 +415,9 @@ class PragPicker(AutoPicker):
iplot = int(self.getiplot()) iplot = int(self.getiplot())
except: except:
if self.getiplot() == True or self.getiplot() == 'True': if self.getiplot() == True or self.getiplot() == 'True':
iplot = 2 iplot = 2
else: else:
iplot = 0 iplot = 0
if self.getpick1() is not None: if self.getpick1() is not None:
print('PragPicker: Get most likely pick from HOS- or AR-CF using pragmatic picking algorithm ...') print('PragPicker: Get most likely pick from HOS- or AR-CF using pragmatic picking algorithm ...')
@ -427,11 +456,11 @@ class PragPicker(AutoPicker):
# prominent trend: decrease aus # prominent trend: decrease aus
# flat: use given aus # flat: use given aus
cfdiff = np.diff(cfipick) cfdiff = np.diff(cfipick)
if len(cfdiff)<20: if len(cfdiff) < 20:
print('PragPicker: Very few samples for CF. Check LTA window dimensions!') print('PragPicker: Very few samples for CF. Check LTA window dimensions!')
i0diff = np.where(cfdiff > 0) i0diff = np.where(cfdiff > 0)
cfdiff = cfdiff[i0diff] cfdiff = cfdiff[i0diff]
if len(cfdiff)<1: if len(cfdiff) < 1:
print('PragPicker: Negative slope for CF. Check LTA window dimensions! STOP') print('PragPicker: Negative slope for CF. Check LTA window dimensions! STOP')
self.Pick = None self.Pick = None
return return
@ -455,7 +484,7 @@ class PragPicker(AutoPicker):
break break
# now we look to the left # now we look to the left
if len(self.cf) > ipick1 +1: if len(self.cf) > ipick1 + 1:
for i in range(ipick1, max([ipick1 - lpickwindow + 1, 2]), -1): for i in range(ipick1, max([ipick1 - lpickwindow + 1, 2]), -1):
if self.cf[i + 1] > self.cf[i] and self.cf[i - 1] >= self.cf[i]: if self.cf[i + 1] > self.cf[i] and self.cf[i - 1] >= self.cf[i]:
if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]: if cfsmooth[i - 1] * (1 + aus1) >= cfsmooth[i]:
@ -466,7 +495,7 @@ class PragPicker(AutoPicker):
cfpick_l = self.cf[i] cfpick_l = self.cf[i]
break break
else: else:
msg ='PragPicker: Initial onset too close to start of CF! \ msg = 'PragPicker: Initial onset too close to start of CF! \
Stop finalizing pick to the left.' Stop finalizing pick to the left.'
print(msg) print(msg)
@ -486,7 +515,7 @@ class PragPicker(AutoPicker):
pickflag = 0 pickflag = 0
if iplot > 1: if iplot > 1:
if self.fig == None or self.fig == 'None': if self.fig is None or self.fig == 'None':
fig = plt.figure() # self.getiplot()) fig = plt.figure() # self.getiplot())
plt_flag = 1 plt_flag = 1
else: else:
@ -496,15 +525,18 @@ class PragPicker(AutoPicker):
ax.plot(Tcfpick, cfipick, color=self._linecolor, linewidth=0.7, label='CF') ax.plot(Tcfpick, cfipick, color=self._linecolor, linewidth=0.7, label='CF')
ax.plot(Tcfpick, cfsmoothipick, 'r', label='Smoothed CF') ax.plot(Tcfpick, cfsmoothipick, 'r', label='Smoothed CF')
if pickflag > 0: if pickflag > 0:
ax.plot([self.Pick, self.Pick], [min(cfipick), max(cfipick)], self._pickcolor_p, linewidth=2, label='Pick') ax.plot([self.Pick, self.Pick], [min(cfipick), max(cfipick)], self._pickcolor_p, linewidth=2,
label='Pick')
ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime) ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
ax.set_yticks([]) ax.set_yticks([])
ax.set_title(self.Data[0].stats.station) ax.set_title(self.Data[0].stats.station)
ax.legend(loc=1) ax.legend(loc=1)
if plt_flag == 1: if plt_flag == 1:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return return

178
pylot/core/pick/utils.py
View File

@ -14,8 +14,7 @@ import matplotlib.pyplot as plt
import numpy as np import numpy as np
from scipy.signal import argrelmax from scipy.signal import argrelmax
from obspy.core import Stream, UTCDateTime from obspy.core import Stream, UTCDateTime
from pylot.core.util.utils import real_Bool, real_None from pylot.core.util.utils import real_Bool, real_None, SetChannelComponents
def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'): def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@ -144,13 +143,16 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
ax.plot(t, x, color=linecolor, linewidth=0.7, label='Data') ax.plot(t, x, color=linecolor, linewidth=0.7, label='Data')
ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window') ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window') ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
ax.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], color=linecolor, linewidth=0.7, linestyle='dashed', label='Noise Level') ax.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], color=linecolor, linewidth=0.7, linestyle='dashed',
label='Noise Level')
ax.plot(t[pis[zc]], np.zeros(len(zc)), '*g', ax.plot(t[pis[zc]], np.zeros(len(zc)), '*g',
markersize=14, label='Zero Crossings') markersize=14, label='Zero Crossings')
ax.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], color=linecolor, linewidth=0.7, linestyle='dashed') ax.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], color=linecolor, linewidth=0.7, linestyle='dashed')
ax.plot([Pick1, Pick1], [max(x), -max(x)], 'b', linewidth=2, label='mpp') ax.plot([Pick1, Pick1], [max(x), -max(x)], 'b', linewidth=2, label='mpp')
ax.plot([LPick, LPick], [max(x) / 2, -max(x) / 2], color=linecolor, linewidth=0.7, linestyle='dashed', label='lpp') ax.plot([LPick, LPick], [max(x) / 2, -max(x) / 2], color=linecolor, linewidth=0.7, linestyle='dashed',
ax.plot([EPick, EPick], [max(x) / 2, -max(x) / 2], color=linecolor, linewidth=0.7, linestyle='dashed', label='epp') label='lpp')
ax.plot([EPick, EPick], [max(x) / 2, -max(x) / 2], color=linecolor, linewidth=0.7, linestyle='dashed',
label='epp')
ax.plot([Pick1 + PickError, Pick1 + PickError], ax.plot([Pick1 + PickError, Pick1 + PickError],
[max(x) / 2, -max(x) / 2], 'r--', label='spe') [max(x) / 2, -max(x) / 2], 'r--', label='spe')
ax.plot([Pick1 - PickError, Pick1 - PickError], ax.plot([Pick1 - PickError, Pick1 - PickError],
@ -163,8 +165,10 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
ax.legend(loc=1) ax.legend(loc=1)
if plt_flag == 1: if plt_flag == 1:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return EPick, LPick, PickError return EPick, LPick, PickError
@ -198,9 +202,9 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
iplot = int(iplot) iplot = int(iplot)
except: except:
if iplot == True or iplot == 'True': if iplot == True or iplot == 'True':
iplot = 2 iplot = 2
else: else:
iplot = 0 iplot = 0
warnings.simplefilter('ignore', np.RankWarning) warnings.simplefilter('ignore', np.RankWarning)
@ -227,8 +231,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
# get zero crossings after most likely pick # get zero crossings after most likely pick
# initial onset is assumed to be the first zero crossing # initial onset is assumed to be the first zero crossing
# first from unfiltered trace # first from unfiltered trace
zc1 = [] zc1 = [Pick]
zc1.append(Pick)
index1 = [] index1 = []
i = 0 i = 0
for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]): for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]):
@ -273,8 +276,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
# now using filterd trace # now using filterd trace
# next zero crossings after most likely pick # next zero crossings after most likely pick
zc2 = [] zc2 = [Pick]
zc2.append(Pick)
index2 = [] index2 = []
i = 0 i = 0
for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]): for j in range(ipick[0][1], ipick[0][len(t[ipick]) - 1]):
@ -362,8 +364,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
ax2.set_yticks([]) ax2.set_yticks([])
if plt_flag == 1: if plt_flag == 1:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return FM return FM
@ -573,8 +577,6 @@ def select_for_phase(st, phase):
:rtype: `~obspy.core.stream.Stream` :rtype: `~obspy.core.stream.Stream`
""" """
from pylot.core.util.defaults import SetChannelComponents
sel_st = Stream() sel_st = Stream()
compclass = SetChannelComponents() compclass = SetChannelComponents()
if phase.upper() == 'P': if phase.upper() == 'P':
@ -623,14 +625,18 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
ibad = 0 ibad = 0
for key in list(pickdic.keys()): for key in list(pickdic.keys()):
if pickdic[key]['P']['weight'] < 4 and pickdic[key]['S']['weight'] < 4: ppick = pickdic[key].get('P')
spick = pickdic[key].get('S')
if not ppick or not spick:
continue
if ppick['weight'] < 4 and spick['weight'] < 4:
# calculate S-P time # calculate S-P time
spt = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp'] spt = spick['mpp'] - ppick['mpp']
# add S-P time to dictionary # add S-P time to dictionary
pickdic[key]['SPt'] = spt pickdic[key]['SPt'] = spt
# add P onsets and corresponding S-P times to list # add P onsets and corresponding S-P times to list
UTCPpick = UTCDateTime(pickdic[key]['P']['mpp']) UTCPpick = UTCDateTime(ppick['mpp'])
UTCSpick = UTCDateTime(pickdic[key]['S']['mpp']) UTCSpick = UTCDateTime(spick['mpp'])
Ppicks.append(UTCPpick.timestamp) Ppicks.append(UTCPpick.timestamp)
Spicks.append(UTCSpick.timestamp) Spicks.append(UTCSpick.timestamp)
SPtimes.append(spt) SPtimes.append(spt)
@ -660,11 +666,11 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
# check, if deviation is larger than adjusted # check, if deviation is larger than adjusted
if wddiff > dttolerance: if wddiff > dttolerance:
# remove pick from dictionary # remove pick from dictionary
pickdic.pop(key) # # mark onset and downgrade S-weight to 9, also set SPE to None (disregarded in GUI)
# # mark onset and downgrade S-weight to 9
# # (not used anymore) # # (not used anymore)
# marker = 'badWadatiCheck' marker = 'badWadatiCheck'
# pickdic[key]['S']['weight'] = 9 pickdic[key]['S']['weight'] = 9
pickdic[key]['S']['spe'] = None
badstations.append(key) badstations.append(key)
ibad += 1 ibad += 1
else: else:
@ -676,8 +682,7 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
checkedSPtime = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp'] checkedSPtime = pickdic[key]['S']['mpp'] - pickdic[key]['P']['mpp']
checkedSPtimes.append(checkedSPtime) checkedSPtimes.append(checkedSPtime)
pickdic[key]['S']['marked'] = marker pickdic[key]['S']['marked'] = marker
#pickdic[key]['S']['marked'] = marker
print("wadaticheck: the following stations failed the check:") print("wadaticheck: the following stations failed the check:")
print(badstations) print(badstations)
@ -719,8 +724,8 @@ def wadaticheck(pickdic, dttolerance, iplot=0, fig_dict=None):
ax.plot(Ppicks, SPtimes, 'ro', label='Skipped S-Picks') ax.plot(Ppicks, SPtimes, 'ro', label='Skipped S-Picks')
if wfitflag == 0: if wfitflag == 0:
ax.plot(Ppicks, wdfit, color=linecolor, linewidth=0.7, label='Wadati 1') ax.plot(Ppicks, wdfit, color=linecolor, linewidth=0.7, label='Wadati 1')
ax.plot(Ppicks, wdfit+dttolerance, color='0.9', linewidth=0.5, label='Wadati 1 Tolerance') ax.plot(Ppicks, wdfit + dttolerance, color='0.9', linewidth=0.5, label='Wadati 1 Tolerance')
ax.plot(Ppicks, wdfit-dttolerance, color='0.9', linewidth=0.5) ax.plot(Ppicks, wdfit - dttolerance, color='0.9', linewidth=0.5)
ax.plot(checkedPpicks, wdfit2, 'g', label='Wadati 2') ax.plot(checkedPpicks, wdfit2, 'g', label='Wadati 2')
ax.plot(checkedPpicks, checkedSPtimes, color=linecolor, ax.plot(checkedPpicks, checkedSPtimes, color=linecolor,
linewidth=0, marker='o', label='Reliable S-Picks') linewidth=0, marker='o', label='Reliable S-Picks')
@ -787,9 +792,9 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
iplot = int(iplot) iplot = int(iplot)
except: except:
if real_Bool(iplot): if real_Bool(iplot):
iplot = 2 iplot = 2
else: else:
iplot = 0 iplot = 0
assert isinstance(X, Stream), "%s is not a stream object" % str(X) assert isinstance(X, Stream), "%s is not a stream object" % str(X)
@ -851,8 +856,10 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
ax.set_yticks([]) ax.set_yticks([])
if plt_flag == 1: if plt_flag == 1:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return returnflag return returnflag
@ -886,9 +893,12 @@ def checkPonsets(pickdic, dttolerance, jackfactor=5, iplot=0, fig_dict=None):
Ppicks = [] Ppicks = []
stations = [] stations = []
for station in pickdic: for station in pickdic:
if pickdic[station]['P']['weight'] < 4: pick = pickdic[station].get('P')
if not pick:
continue
if pick['weight'] < 4:
# add P onsets to list # add P onsets to list
UTCPpick = UTCDateTime(pickdic[station]['P']['mpp']) UTCPpick = UTCDateTime(pick['mpp'])
Ppicks.append(UTCPpick.timestamp) Ppicks.append(UTCPpick.timestamp)
stations.append(station) stations.append(station)
@ -1083,10 +1093,9 @@ def checkZ4S(X, pick, zfac, checkwin, iplot, fig=None, linecolor='k'):
iplot = int(iplot) iplot = int(iplot)
except: except:
if real_Bool(iplot): if real_Bool(iplot):
iplot = 2 iplot = 2
else: else:
iplot = 0 iplot = 0
assert isinstance(X, Stream), "%s is not a stream object" % str(X) assert isinstance(X, Stream), "%s is not a stream object" % str(X)
@ -1188,12 +1197,81 @@ def checkZ4S(X, pick, zfac, checkwin, iplot, fig=None, linecolor='k'):
ax.set_xlabel('Time [s] since %s' % zdat[0].stats.starttime) ax.set_xlabel('Time [s] since %s' % zdat[0].stats.starttime)
if plt_flag == 1: if plt_flag == 1:
fig.show() fig.show()
try: input() try:
except SyntaxError: pass input()
except SyntaxError:
pass
plt.close(fig) plt.close(fig)
return returnflag return returnflag
def getPickQuality(wfdata, picks, inputs, phase, compclass=None):
quality = 4
components4phases = {'P': ['Z'],
'S': ['N', 'E']}
timeErrors4phases = {'P': 'timeerrorsP',
'S': 'timeerrorsS'}
tsnr4phases = {'P': 'tsnrz',
'S': 'tsnrh'}
if not phase in components4phases.keys():
raise IOError('getPickQuality: Could not understand phase: {}'.format(phase))
if not compclass:
print('Warning: No settings for channel components found. Using default')
compclass = SetChannelComponents()
picks = picks[phase]
mpp = picks.get('mpp')
uncertainty = picks.get('spe')
if not mpp:
print('getPickQuality: No pick found!')
return quality
if not uncertainty:
print('getPickQuality: No pick uncertainty (spe) found!')
return quality
tsnr = inputs[tsnr4phases[phase]]
timeErrors = inputs[timeErrors4phases[phase]]
snrdb_final = 0
for component in components4phases[phase]:
alter_comp = compclass.getCompPosition(component)
st_select = wfdata.select(component=component)
st_select += wfdata.select(component=alter_comp)
if st_select:
trace = st_select[0]
_, snrdb, _ = getSNR(st_select, tsnr,
mpp - trace.stats.starttime)
if snrdb > snrdb_final:
snrdb_final = snrdb
quality = getQualityFromUncertainty(uncertainty, timeErrors)
quality += getQualityFromSNR(snrdb_final)
return quality
def getQualityFromSNR(snrdb):
quality_modifier = 4
if not snrdb:
print('getQualityFromSNR: No snrdb!')
return quality_modifier
# MP MP ++++ experimental,
# raise pick quality by x classes if snrdb is lower than corresponding key
quality4snrdb = {3: 4,
5: 3,
7: 2,
9: 1,
11: 0}
# MP MP ---
# iterate over all thresholds and check whether snrdb is larger, if so, set new quality_modifier
for snrdb_threshold in sorted(list(quality4snrdb.keys())):
if snrdb > snrdb_threshold:
quality_modifier = quality4snrdb[snrdb_threshold]
return quality_modifier
def get_quality_class(uncertainty, weight_classes): def get_quality_class(uncertainty, weight_classes):
""" """
Script to transform uncertainty into quality classes 0-4 regarding adjusted time errors Script to transform uncertainty into quality classes 0-4 regarding adjusted time errors
@ -1378,6 +1456,26 @@ def get_pickparams(pickparam):
return p_params, s_params, first_motion_params, signal_length_params return p_params, s_params, first_motion_params, signal_length_params
def getQualityFromUncertainty(uncertainty, Errors):
# set initial quality to 4 (worst) and change only if one condition is hit
quality = 4
if real_None(uncertainty) is None:
return quality
if uncertainty <= Errors[0]:
quality = 0
elif (uncertainty > Errors[0]) and \
(uncertainty <= Errors[1]):
quality = 1
elif (uncertainty > Errors[1]) and \
(uncertainty <= Errors[2]):
quality = 2
elif (uncertainty > Errors[2]) and \
(uncertainty <= Errors[3]):
quality = 3
elif uncertainty > Errors[3]:
quality = 4
if __name__ == '__main__': if __name__ == '__main__':
import doctest import doctest

80
pylot/core/util/array_map.py
View File

@ -23,8 +23,7 @@ class Array_map(QtGui.QWidget):
''' '''
QtGui.QWidget.__init__(self) QtGui.QWidget.__init__(self)
self._parent = parent self._parent = parent
self.metadata_type = parent.metadata[0] self.metadata = parent.metadata
self.metadata = parent.metadata[1]
self.picks = None self.picks = None
self.picks_dict = None self.picks_dict = None
self.autopicks_dict = None self.autopicks_dict = None
@ -74,15 +73,11 @@ class Array_map(QtGui.QWidget):
if pickDlg.exec_(): if pickDlg.exec_():
pyl_mw.setDirty(True) pyl_mw.setDirty(True)
pyl_mw.update_status('picks accepted ({0})'.format(station)) pyl_mw.update_status('picks accepted ({0})'.format(station))
replot = pyl_mw.get_current_event().setPick(station, pickDlg.getPicks()) pyl_mw.addPicks(station, pickDlg.getPicks(picktype='manual'), type='manual')
pyl_mw.addPicks(station, pickDlg.getPicks(picktype='auto'), type='auto')
self._refresh_drawings() self._refresh_drawings()
if replot: pyl_mw.drawPicks(station)
pyl_mw.plotWaveformData() pyl_mw.draw()
pyl_mw.drawPicks()
pyl_mw.draw()
else:
pyl_mw.drawPicks(station)
pyl_mw.draw()
else: else:
pyl_mw.update_status('picks discarded ({0})'.format(station)) pyl_mw.update_status('picks discarded ({0})'.format(station))
except Exception as e: except Exception as e:
@ -94,7 +89,7 @@ class Array_map(QtGui.QWidget):
self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings) self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
self.comboBox_am.currentIndexChanged.connect(self._refresh_drawings) self.comboBox_am.currentIndexChanged.connect(self._refresh_drawings)
self.canvas.mpl_connect('motion_notify_event', self.mouse_moved) self.canvas.mpl_connect('motion_notify_event', self.mouse_moved)
#self.zoom_id = self.basemap.ax.figure.canvas.mpl_connect('scroll_event', self.zoom) # self.zoom_id = self.basemap.ax.figure.canvas.mpl_connect('scroll_event', self.zoom)
def _from_dict(self, function, key): def _from_dict(self, function, key):
return function(self.stations_dict.values(), key=lambda x: x[key])[key] return function(self.stations_dict.values(), key=lambda x: x[key])[key]
@ -159,35 +154,8 @@ class Array_map(QtGui.QWidget):
self.main_box.addWidget(self.canvas, 1) self.main_box.addWidget(self.canvas, 1)
self.main_box.addWidget(self.status_label, 0) self.main_box.addWidget(self.status_label, 0)
def init_stations(self): def init_stations(self):
def stat_info_from_parser(parser): self.stations_dict = self.metadata.get_all_coordinates()
stations_dict = {}
for station in parser.stations:
station_name = station[0].station_call_letters
network_name = station[0].network_code
if not station_name in stations_dict.keys():
st_id = network_name + '.' + station_name
stations_dict[st_id] = {'latitude': station[0].latitude,
'longitude': station[0].longitude}
return stations_dict
def stat_info_from_inventory(inventory):
stations_dict = {}
for network in inventory.networks:
for station in network.stations:
station_name = station.code
network_name = network_name.code
if not station_name in stations_dict.keys():
st_id = network_name + '.' + station_name
stations_dict[st_id] = {'latitude': station[0].latitude,
'longitude': station[0].longitude}
return stations_dict
read_stat = {'xml': stat_info_from_inventory,
'dless': stat_info_from_parser}
self.stations_dict = read_stat[self.metadata_type](self.metadata)
self.latmin = self.get_min_from_stations('latitude') self.latmin = self.get_min_from_stations('latitude')
self.lonmin = self.get_min_from_stations('longitude') self.lonmin = self.get_min_from_stations('longitude')
self.latmax = self.get_max_from_stations('latitude') self.latmax = self.get_max_from_stations('latitude')
@ -196,13 +164,15 @@ class Array_map(QtGui.QWidget):
def init_picks(self): def init_picks(self):
def get_picks(station_dict): def get_picks(station_dict):
picks = {} picks = {}
# selected phase
phase = self.comboBox_phase.currentText() phase = self.comboBox_phase.currentText()
for st_id in station_dict.keys(): for st_id in station_dict.keys():
try: try:
station_name = st_id.split('.')[-1] station_name = st_id.split('.')[-1]
# current_picks_dict: auto or manual
pick = self.current_picks_dict()[station_name][phase] pick = self.current_picks_dict()[station_name][phase]
if pick['picker'] == 'auto': if pick['picker'] == 'auto':
if pick['weight'] > 3: if not pick['spe']:
continue continue
picks[st_id] = pick['mpp'] picks[st_id] = pick['mpp']
except KeyError: except KeyError:
@ -217,11 +187,12 @@ class Array_map(QtGui.QWidget):
for pick in picks.values(): for pick in picks.values():
if type(pick) is obspy.core.utcdatetime.UTCDateTime: if type(pick) is obspy.core.utcdatetime.UTCDateTime:
picks_utc.append(pick) picks_utc.append(pick)
self._earliest_picktime = min(picks_utc) if picks_utc:
for st_id, pick in picks.items(): self._earliest_picktime = min(picks_utc)
if type(pick) is obspy.core.utcdatetime.UTCDateTime: for st_id, pick in picks.items():
pick -= self._earliest_picktime if type(pick) is obspy.core.utcdatetime.UTCDateTime:
picks_rel[st_id] = pick pick -= self._earliest_picktime
picks_rel[st_id] = pick
return picks_rel return picks_rel
self.picks = get_picks(self.stations_dict) self.picks = get_picks(self.stations_dict)
@ -331,6 +302,8 @@ class Array_map(QtGui.QWidget):
def scatter_picked_stations(self): def scatter_picked_stations(self):
picks, lats, lons = self.get_picks_lat_lon() picks, lats, lons = self.get_picks_lat_lon()
if len(lons) < 1 and len(lats) < 1:
return
# workaround because of an issue with latlon transformation of arrays with len <3 # workaround because of an issue with latlon transformation of arrays with len <3
if len(lons) <= 2 and len(lats) <= 2: if len(lons) <= 2 and len(lats) <= 2:
self.sc_picked = self.basemap.scatter(lons[0], lats[0], s=50, facecolor='white', self.sc_picked = self.basemap.scatter(lons[0], lats[0], s=50, facecolor='white',
@ -354,7 +327,7 @@ class Array_map(QtGui.QWidget):
def add_cbar(self, label): def add_cbar(self, label):
self.cbax_bg = inset_axes(self.main_ax, width="6%", height="75%", loc=5) self.cbax_bg = inset_axes(self.main_ax, width="6%", height="75%", loc=5)
cbax = inset_axes(self.main_ax, width='2%', height='70%', loc=5) cbax = inset_axes(self.main_ax, width='2%', height='70%', loc=5)
cbar = self.main_ax.figure.colorbar(self.sc_picked, cax = cbax) cbar = self.main_ax.figure.colorbar(self.sc_picked, cax=cbax)
cbar.set_label(label) cbar.set_label(label)
cbax.yaxis.tick_left() cbax.yaxis.tick_left()
cbax.yaxis.set_label_position('left') cbax.yaxis.set_label_position('left')
@ -375,13 +348,16 @@ class Array_map(QtGui.QWidget):
self.draw_everything() self.draw_everything()
def draw_everything(self): def draw_everything(self):
if self.picks_dict or self.autopicks_dict: picktype = self.comboBox_am.currentText()
if (self.picks_dict and picktype == 'manual') \
or (self.autopicks_dict and picktype == 'auto'):
self.init_picks() self.init_picks()
if len(self.picks) >= 3: if len(self.picks) >= 3:
self.init_picksgrid() self.init_picksgrid()
self.draw_contour_filled() self.draw_contour_filled()
self.scatter_all_stations() self.scatter_all_stations()
if self.picks_dict or self.autopicks_dict: if (self.picks_dict and picktype == 'manual') \
or (self.autopicks_dict and picktype == 'auto'):
self.scatter_picked_stations() self.scatter_picked_stations()
self.cbar = self.add_cbar(label='Time relative to first onset ({}) [s]'.format(self._earliest_picktime)) self.cbar = self.add_cbar(label='Time relative to first onset ({}) [s]'.format(self._earliest_picktime))
self.comboBox_phase.setEnabled(True) self.comboBox_phase.setEnabled(True)
@ -397,16 +373,16 @@ class Array_map(QtGui.QWidget):
del (self.cbar, self.cbax_bg) del (self.cbar, self.cbax_bg)
if hasattr(self, 'sc_picked'): if hasattr(self, 'sc_picked'):
self.sc_picked.remove() self.sc_picked.remove()
del (self.sc_picked) del self.sc_picked
if hasattr(self, 'sc_event'): if hasattr(self, 'sc_event'):
self.sc_event.remove() self.sc_event.remove()
del (self.sc_event) del self.sc_event
if hasattr(self, 'contourf'): if hasattr(self, 'contourf'):
self.remove_contourf() self.remove_contourf()
del (self.contourf) del self.contourf
if hasattr(self, 'cid'): if hasattr(self, 'cid'):
self.canvas.mpl_disconnect(self.cid) self.canvas.mpl_disconnect(self.cid)
del (self.cid) del self.cid
try: try:
self.sc.remove() self.sc.remove()
except Exception as e: except Exception as e:

213
pylot/core/util/dataprocessing.py
View File

@ -13,86 +13,95 @@ from pylot.core.util.utils import key_for_set_value, find_in_list, \
class Metadata(object): class Metadata(object):
def __init__(self, inventory=None): def __init__(self, inventory=None):
self.inventories = [] self.inventories = []
# saves read metadata objects (Parser/inventory) for a filename # saves read metadata objects (Parser/inventory) for a filename
self.inventory_files = {} self.inventory_files = {}
# saves filenames holding metadata for a seed_id # saves filenames holding metadata for a seed_id
# seed id as key, path to file as value
self.seed_ids = {} self.seed_ids = {}
self.stations_dict = {}
if inventory: if inventory:
if os.path.isdir(inventory): if os.path.isdir(inventory):
self.add_inventory(inventory) self.add_inventory(inventory)
if os.path.isfile(inventory): if os.path.isfile(inventory):
self.add_inventory_file(inventory) self.add_inventory_file(inventory)
def __str__(self): def __str__(self):
repr = 'PyLoT Metadata object including the following inventories:\n\n' repr = 'PyLoT Metadata object including the following inventories:\n\n'
ntotal = len(self.inventories) ntotal = len(self.inventories)
for index, inventory in enumerate(self.inventories): for index, inventory in enumerate(self.inventories):
if index < 2 or (ntotal - index) < 3: if index < 2 or (ntotal - index) < 3:
repr += '{}\n'.format(inventory) repr += '{}\n'.format(inventory)
if ntotal > 4 and int(ntotal/2) == index: if ntotal > 4 and int(ntotal / 2) == index:
repr += '...\n' repr += '...\n'
if ntotal > 4: if ntotal > 4:
repr += '\nTotal of {} inventories. Use Metadata.inventories to see all.'.format(ntotal) repr += '\nTotal of {} inventories. Use Metadata.inventories to see all.'.format(ntotal)
return repr return repr
def __repr__(self): def __repr__(self):
return self.__str__() return self.__str__()
def add_inventory(self, path_to_inventory): def add_inventory(self, path_to_inventory):
''' """
add paths to list of inventories Add path to list of inventories.
:param path_to_inventory: Path to a folder
:param path_to_inventory: :type path_to_inventory: str
:return: :return: None
''' """
assert (os.path.isdir(path_to_inventory)), '{} is no directory'.format(path_to_inventory) assert (os.path.isdir(path_to_inventory)), '{} is no directory'.format(path_to_inventory)
if not path_to_inventory in self.inventories: if not path_to_inventory in self.inventories:
self.inventories.append(path_to_inventory) self.inventories.append(path_to_inventory)
def add_inventory_file(self, path_to_inventory_file): def add_inventory_file(self, path_to_inventory_file):
''' """
add a single file to inventory files Add the folder in which the file exists to the list of inventories.
:param path_to_inventory_file: full path including filename
:param path_to_inventory_file: :type path_to_inventory_file: str
:return: :return: None
"""
'''
assert (os.path.isfile(path_to_inventory_file)), '{} is no file'.format(path_to_inventory_file) assert (os.path.isfile(path_to_inventory_file)), '{} is no file'.format(path_to_inventory_file)
self.add_inventory(os.path.split(path_to_inventory_file)[0]) self.add_inventory(os.path.split(path_to_inventory_file)[0])
if not path_to_inventory_file in self.inventory_files.keys(): if not path_to_inventory_file in self.inventory_files.keys():
self.read_single_file(path_to_inventory_file) self.read_single_file(path_to_inventory_file)
def remove_all_inventories(self): def remove_all_inventories(self):
self.__init__() self.__init__()
def remove_inventory(self, path_to_inventory): def remove_inventory(self, path_to_inventory):
''' """
remove a path from inventories list Remove a path from inventories list. If path is not in inventories list, do nothing.
:param path_to_inventory: Path to a folder
:param path_to_inventory: """
:return:
'''
if not path_to_inventory in self.inventories: if not path_to_inventory in self.inventories:
print('Path {} not in inventories list.'.format(path_to_inventory)) print('Path {} not in inventories list.'.format(path_to_inventory))
return return
self.inventories.remove(path_to_inventory) self.inventories.remove(path_to_inventory)
for filename in self.inventory_files.keys(): for filename in self.inventory_files.keys():
if filename.startswith(path_to_inventory): if filename.startswith(path_to_inventory):
del(self.inventory_files[filename]) del (self.inventory_files[filename])
for seed_id in self.seed_ids.keys(): for seed_id in self.seed_ids.keys():
if self.seed_ids[seed_id].startswith(path_to_inventory): if self.seed_ids[seed_id].startswith(path_to_inventory):
del(self.seed_ids[seed_id]) del (self.seed_ids[seed_id])
def get_metadata(self, seed_id, time=None):
def get_metadata(self, seed_id): """
Get metadata for seed id at time. When time is not specified, metadata for current time is fetched.
:param seed_id: Seed id such as BW.WETR..HHZ (Network.Station.Location.Channel)
:type seed_id: str
:param time: Time for which the metadata should be returned
:type time: UTCDateTime
:return: Dictionary with keys data and invtype.
data is a obspy.io.xseed.parser.Parser or an obspy.core.inventory.inventory.Inventory depending on the metadata
file.
invtype is a string denoting of which type the value of the data key is. It can take the values 'dless',
'dseed', 'xml', 'resp', according to the filetype of the metadata.
:rtype: dict
"""
# try most recent data if no time is specified
if not time:
time = UTCDateTime()
# get metadata for a specific seed_id, if not already read, try to read from inventories # get metadata for a specific seed_id, if not already read, try to read from inventories
if not seed_id in self.seed_ids.keys(): if not seed_id in self.seed_ids.keys():
self._read_inventory_data(seed_id) self._read_inventory_data(seed_id)
@ -100,12 +109,13 @@ class Metadata(object):
if not seed_id in self.seed_ids.keys(): if not seed_id in self.seed_ids.keys():
print('No data found for seed id {}. Trying to find it in all known inventories...'.format(seed_id)) print('No data found for seed id {}. Trying to find it in all known inventories...'.format(seed_id))
self.read_all() self.read_all()
for inv_fname, metadata in self.inventory_files.items(): for inv_fname, metadata_dict in self.inventory_files.items():
# use get_coordinates to check for seed_id # use get_coordinates to check for seed_id
try: try:
metadata['data'].get_coordinates(seed_id) metadata_dict['data'].get_coordinates(seed_id, time)
self.seed_ids[seed_id] = inv_fname self.seed_ids[seed_id] = inv_fname
return metadata print('Found metadata for station {}!'.format(seed_id))
return metadata_dict
except Exception as e: except Exception as e:
continue continue
print('Could not find metadata for station {}'.format(seed_id)) print('Could not find metadata for station {}'.format(seed_id))
@ -113,30 +123,30 @@ class Metadata(object):
fname = self.seed_ids[seed_id] fname = self.seed_ids[seed_id]
return self.inventory_files[fname] return self.inventory_files[fname]
def read_all(self): def read_all(self):
''' """
read all metadata files found in all inventories Read all metadata files found in all inventories
:return: """
'''
for inventory in self.inventories: for inventory in self.inventories:
for inv_fname in os.listdir(inventory): for inv_fname in os.listdir(inventory):
inv_fname = os.path.join(inventory, inv_fname) inv_fname = os.path.join(inventory, inv_fname)
if not self.read_single_file(inv_fname): if not self.read_single_file(inv_fname):
continue continue
def read_single_file(self, inv_fname): def read_single_file(self, inv_fname):
if not inv_fname in self.inventory_files.keys(): """
pass Try to read a single file as Parser/Inventory and add its dictionary to inventory files if reading sudceeded.
else: :param inv_fname: path/filename of inventory file
if not self.inventory_files[inv_fname]: :type inv_fname: str
pass :rtype: None
else: """
return # return if it was read already
if self.inventory_files.get(inv_fname, None):
return
try: try:
invtype, robj = self._read_metadata_file(inv_fname) invtype, robj = self._read_metadata_file(inv_fname)
if robj == None: if robj is None:
return return
except Exception as e: except Exception as e:
print('Could not read file {}'.format(inv_fname)) print('Could not read file {}'.format(inv_fname))
@ -145,15 +155,64 @@ class Metadata(object):
'data': robj} 'data': robj}
return True return True
def get_coordinates(self, seed_id, time=None):
def get_coordinates(self, seed_id): """
metadata = self.get_metadata(seed_id) Get coordinates of given seed id.
:param seed_id: Seed id such as BW.WETR..HHZ (Network.Station.Location.Channel)
:type seed_id: str
:param time: Used when a station has data available at multiple time intervals
:type time: UTCDateTime
:return: dict containing position information of the station
:rtype: dict
"""
# try most recent data if no time is specified
if not time:
time = UTCDateTime()
metadata = self.get_metadata(seed_id, time)
if not metadata: if not metadata:
return return
return metadata['data'].get_coordinates(seed_id) return metadata['data'].get_coordinates(seed_id, time)
def get_all_coordinates(self):
def stat_info_from_parser(parser):
for station in parser.stations:
station_name = station[0].station_call_letters
network_name = station[0].network_code
if not station_name in self.stations_dict.keys():
st_id = network_name + '.' + station_name
self.stations_dict[st_id] = {'latitude': station[0].latitude,
'longitude': station[0].longitude}
def stat_info_from_inventory(inventory):
for network in inventory.networks:
for station in network.stations:
station_name = station.code
network_name = network_name.code
if not station_name in self.stations_dict.keys():
st_id = network_name + '.' + station_name
self.stations_dict[st_id] = {'latitude': station[0].latitude,
'longitude': station[0].longitude}
read_stat = {'xml': stat_info_from_inventory,
'dless': stat_info_from_parser}
self.read_all()
for item in self.inventory_files.values():
inventory = item['data']
invtype = item['invtype']
read_stat[invtype](inventory)
return self.stations_dict
def get_paz(self, seed_id, time): def get_paz(self, seed_id, time):
"""
:param seed_id: Seed id such as BW.WETR..HHZ (Network.Station.Location.Channel)
:type seed_id: str
:param time: Used when a station has data available at multiple time intervals
:type time: UTCDateTime
:rtype: dict
"""
metadata = self.get_metadata(seed_id) metadata = self.get_metadata(seed_id)
if not metadata: if not metadata:
return return
@ -163,18 +222,17 @@ class Metadata(object):
resp = metadata['data'].get_response(seed_id, time) resp = metadata['data'].get_response(seed_id, time)
return resp.get_paz(seed_id) return resp.get_paz(seed_id)
def _read_inventory_data(self, seed_id=None): def _read_inventory_data(self, seed_id=None):
for inventory in self.inventories: for inventory in self.inventories:
if self._read_metadata_iterator(path_to_inventory=inventory, station_seed_id=seed_id): if self._read_metadata_iterator(path_to_inventory=inventory, station_seed_id=seed_id):
return return
def _read_metadata_iterator(self, path_to_inventory, station_seed_id): def _read_metadata_iterator(self, path_to_inventory, station_seed_id):
''' """
search for metadata for a specific station iteratively Search for metadata for a specific station iteratively.
''' """
station, network, location, channel = station_seed_id.split('.') station, network, location, channel = station_seed_id.split('.')
# seach for station seed id in filenames in invetory
fnames = glob.glob(os.path.join(path_to_inventory, '*' + station_seed_id + '*')) fnames = glob.glob(os.path.join(path_to_inventory, '*' + station_seed_id + '*'))
if not fnames: if not fnames:
# search for station name in filename # search for station name in filename
@ -203,13 +261,13 @@ class Metadata(object):
continue continue
print('Could not find metadata for station_seed_id {} in path {}'.format(station_seed_id, path_to_inventory)) print('Could not find metadata for station_seed_id {} in path {}'.format(station_seed_id, path_to_inventory))
def _read_metadata_file(self, path_to_inventory_filename): def _read_metadata_file(self, path_to_inventory_filename):
''' """
function reading metadata files (either dataless seed, xml or resp) function reading metadata files (either dataless seed, xml or resp)
:param path_to_inventory_filename: :param path_to_inventory_filename:
:return: file type/ending, inventory object (Parser or Inventory) :return: file type/ending, inventory object (Parser or Inventory)
''' :rtype: (str, obspy.io.xseed.Parser or obspy.core.inventory.inventory.Inventory)
"""
# functions used to read metadata for different file endings (or file types) # functions used to read metadata for different file endings (or file types)
read_functions = {'dless': self._read_dless, read_functions = {'dless': self._read_dless,
'dseed': self._read_dless, 'dseed': self._read_dless,
@ -228,8 +286,8 @@ class Metadata(object):
return file_type, robj return file_type, robj
return None, None return None, None
@staticmethod
def _read_dless(self, path_to_inventory): def _read_dless(path_to_inventory):
exc = None exc = None
try: try:
parser = Parser(path_to_inventory) parser = Parser(path_to_inventory)
@ -237,8 +295,8 @@ class Metadata(object):
parser = None parser = None
return parser, exc return parser, exc
@staticmethod
def _read_inventory_file(self, path_to_inventory): def _read_inventory_file(path_to_inventory):
exc = None exc = None
try: try:
inv = read_inventory(path_to_inventory) inv = read_inventory(path_to_inventory)
@ -247,7 +305,6 @@ class Metadata(object):
return inv, exc return inv, exc
def time_from_header(header): def time_from_header(header):
""" """
Function takes in the second line from a .gse file and takes out the date and time from that line. Function takes in the second line from a .gse file and takes out the date and time from that line.
@ -458,15 +515,22 @@ def read_metadata(path_to_inventory):
# return metadata_objects # return metadata_objects
def restitute_trace(input_tuple): def restitute_trace(input_tuple):
def no_metadata(tr, seed_id):
print('no metadata file found '
'for trace {0}'.format(seed_id))
return tr, True
tr, metadata, unit, force = input_tuple tr, metadata, unit, force = input_tuple
remove_trace = False remove_trace = False
seed_id = tr.get_id() seed_id = tr.get_id()
mdata = metadata.get_metadata(seed_id) mdata = metadata.get_metadata(seed_id, time=tr.stats.starttime)
if not mdata:
return no_metadata(tr, seed_id)
invtype = mdata['invtype'] invtype = mdata['invtype']
inobj = mdata['data'] inobj = mdata['data']
@ -481,8 +545,7 @@ def restitute_trace(input_tuple):
if invtype == 'resp': if invtype == 'resp':
fresp = find_in_list(inobj, seed_id) fresp = find_in_list(inobj, seed_id)
if not fresp: if not fresp:
raise IOError('no response file found ' return no_metadata(tr, seed_id)
'for trace {0}'.format(seed_id))
fname = fresp fname = fresp
seedresp = dict(filename=fname, seedresp = dict(filename=fname,
date=stime, date=stime,
@ -504,9 +567,8 @@ def restitute_trace(input_tuple):
else: else:
finv = invlist[0] finv = invlist[0]
inventory = read_inventory(finv, format='STATIONXML') inventory = read_inventory(finv, format='STATIONXML')
elif invtype == None: elif invtype is None:
print("No restitution possible, as there are no station-meta data available!") return no_metadata(tr, seed_id)
return tr, True
else: else:
remove_trace = True remove_trace = True
# apply restitution to data # apply restitution to data
@ -542,9 +604,6 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
takes a data stream and a path_to_inventory and returns the corrected takes a data stream and a path_to_inventory and returns the corrected
waveform data stream waveform data stream
:param data: seismic data stream :param data: seismic data stream
:param invtype: type of found metadata
:param inobj: either list of metadata files or `obspy.io.xseed.Parser`
object
:param unit: unit to correct for (default: 'VEL') :param unit: unit to correct for (default: 'VEL')
:param force: force restitution for already corrected traces (default: :param force: force restitution for already corrected traces (default:
False) False)
@ -553,7 +612,7 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
restflag = list() restflag = list()
data = remove_underscores(data) #data = remove_underscores(data)
# loop over traces # loop over traces
input_tuples = [] input_tuples = []
@ -562,7 +621,7 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
data.remove(tr) data.remove(tr)
pool = gen_Pool(ncores) pool = gen_Pool(ncores)
result = pool.map(restitute_trace, input_tuples) result = pool.imap_unordered(restitute_trace, input_tuples)
pool.close() pool.close()
for tr, remove_trace in result: for tr, remove_trace in result:
@ -612,7 +671,7 @@ def get_prefilt(trace, tlow=(0.5, 0.9), thi=(5., 2.), verbosity=0):
fny = trace.stats.sampling_rate / 2 fny = trace.stats.sampling_rate / 2
fc21 = fny - (fny * thi[0] / 100.) fc21 = fny - (fny * thi[0] / 100.)
fc22 = fny - (fny * thi[1] / 100.) fc22 = fny - (fny * thi[1] / 100.)
return (tlow[0], tlow[1], fc21, fc22) return tlow[0], tlow[1], fc21, fc22
if __name__ == "__main__": if __name__ == "__main__":

52
pylot/core/util/defaults.py
View File

@ -16,7 +16,6 @@ from pylot.core.loc import hyposat
from pylot.core.loc import nll from pylot.core.loc import nll
from pylot.core.loc import velest from pylot.core.loc import velest
# determine system dependent path separator # determine system dependent path separator
system_name = platform.system() system_name = platform.system()
if system_name in ["Linux", "Darwin"]: if system_name in ["Linux", "Darwin"]:
@ -42,54 +41,3 @@ OUTPUTFORMATS = {'.xml': 'QUAKEML',
LOCTOOLS = dict(nll=nll, hyposat=hyposat, velest=velest, hypo71=hypo71, hypodd=hypodd) LOCTOOLS = dict(nll=nll, hyposat=hyposat, velest=velest, hypo71=hypo71, hypodd=hypodd)
class SetChannelComponents(object):
def __init__(self):
self.setDefaultCompPosition()
def setDefaultCompPosition(self):
# default component order
self.compPosition_Map = dict(Z=2, N=1, E=0)
self.compName_Map = {'3': 'Z',
'1': 'N',
'2': 'E'}
def _getCurrentPosition(self, component):
for key, value in self.compName_Map.items():
if value == component:
return key, value
errMsg = 'getCurrentPosition: Could not find former position of component {}.'.format(component)
raise ValueError(errMsg)
def _switch(self, component, component_alter):
# Without switching, multiple definitions of the same alter_comp are possible
old_alter_comp, _ = self._getCurrentPosition(component)
old_comp = self.compName_Map[component_alter]
if not old_alter_comp == component_alter and not old_comp == component:
self.compName_Map[old_alter_comp] = old_comp
print('switch: Automatically switched component {} to {}'.format(old_alter_comp, old_comp))
def setCompPosition(self, component_alter, component, switch=True):
component_alter = str(component_alter)
if not component_alter in self.compName_Map.keys():
errMsg = 'setCompPosition: Unrecognized alternative component {}. Expecting one of {}.'
raise ValueError(errMsg.format(component_alter, self.compName_Map.keys()))
if not component in self.compPosition_Map.keys():
errMsg = 'setCompPosition: Unrecognized target component {}. Expecting one of {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys()))
print('setCompPosition: set component {} to {}'.format(component_alter, component))
if switch:
self._switch(component, component_alter)
self.compName_Map[component_alter] = component
def getCompPosition(self, component):
return self._getCurrentPosition(component)[0]
def getPlotPosition(self, component):
component = str(component)
if component in self.compPosition_Map.keys():
return self.compPosition_Map[component]
elif component in self.compName_Map.keys():
return self.compPosition_Map[self.compName_Map[component]]
else:
errMsg = 'getCompPosition: Unrecognized component {}. Expecting one of {} or {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys(), self.compName_Map.keys()))

17
pylot/core/util/event.py
View File

@ -35,6 +35,7 @@ class Event(ObsPyEvent):
self._refEvent = False self._refEvent = False
self.get_notes() self.get_notes()
self.get_obspy_event_info() self.get_obspy_event_info()
self.dirty = False
def get_notes_path(self): def get_notes_path(self):
""" """
@ -143,6 +144,7 @@ class Event(ObsPyEvent):
for index, pick in reversed(list(enumerate(self.picks))): for index, pick in reversed(list(enumerate(self.picks))):
if picktype in str(pick.method_id): if picktype in str(pick.method_id):
self.picks.pop(index) self.picks.pop(index)
self.dirty = True
def addPicks(self, picks): def addPicks(self, picks):
""" """
@ -157,12 +159,12 @@ class Event(ObsPyEvent):
# add ObsPy picks (clear old manual and copy all new manual from pylot) # add ObsPy picks (clear old manual and copy all new manual from pylot)
self.clearObsPyPicks('manual') self.clearObsPyPicks('manual')
self.picks += picks_from_picksdict(self.pylot_picks) self.picks += picks_from_picksdict(self.pylot_picks)
self.dirty = True
def addAutopicks(self, autopicks): def addAutopicks(self, autopicks):
""" """
Add automatic picks to event Add automatic picks to event
:param autopicks: automatic picks to add to event :param autopicks: automatic picks to add to event
:type autopicks dict:
:return: :return:
:rtype: None :rtype: None
""" """
@ -171,6 +173,7 @@ class Event(ObsPyEvent):
# add ObsPy picks (clear old auto and copy all new auto from pylot) # add ObsPy picks (clear old auto and copy all new auto from pylot)
self.clearObsPyPicks('auto') self.clearObsPyPicks('auto')
self.picks += picks_from_picksdict(self.pylot_autopicks) self.picks += picks_from_picksdict(self.pylot_autopicks)
self.dirty = True
def setPick(self, station, pick): def setPick(self, station, pick):
""" """
@ -186,11 +189,13 @@ class Event(ObsPyEvent):
self.pylot_picks[station] = pick self.pylot_picks[station] = pick
else: else:
try: try:
self.pylot_picks.pop(station) if station in self.pylot_picks:
self.pylot_picks.pop(station)
except Exception as e: except Exception as e:
print('Could not remove pick {} from station {}: {}'.format(pick, station, e)) print('Could not remove pick {} from station {}: {}'.format(pick, station, e))
self.clearObsPyPicks('manual') self.clearObsPyPicks('manual')
self.picks += picks_from_picksdict(self.pylot_picks) self.picks += picks_from_picksdict(self.pylot_picks)
self.dirty = True
def setPicks(self, picks): def setPicks(self, picks):
""" """
@ -203,6 +208,7 @@ class Event(ObsPyEvent):
self.pylot_picks = picks self.pylot_picks = picks
self.clearObsPyPicks('manual') self.clearObsPyPicks('manual')
self.picks += picks_from_picksdict(self.pylot_picks) self.picks += picks_from_picksdict(self.pylot_picks)
self.dirty = True
def getPick(self, station): def getPick(self, station):
""" """
@ -237,11 +243,13 @@ class Event(ObsPyEvent):
self.pylot_autopicks[station] = pick self.pylot_autopicks[station] = pick
else: else:
try: try:
self.pylot_autopicks.pop(station) if station in self.pylot_autopicks:
self.pylot_autopicks.pop(station)
except Exception as e: except Exception as e:
print('Could not remove pick {} from station {}: {}'.format(pick, station, e)) print('Could not remove pick {} from station {}: {}'.format(pick, station, e))
self.clearObsPyPicks('auto') self.clearObsPyPicks('auto')
self.picks += picks_from_picksdict(self.pylot_autopicks) self.picks += picks_from_picksdict(self.pylot_autopicks)
self.dirty = True
def setAutopicks(self, picks): def setAutopicks(self, picks):
""" """
@ -254,6 +262,7 @@ class Event(ObsPyEvent):
self.pylot_autopicks = picks self.pylot_autopicks = picks
self.clearObsPyPicks('auto') self.clearObsPyPicks('auto')
self.picks += picks_from_picksdict(self.pylot_autopicks) self.picks += picks_from_picksdict(self.pylot_autopicks)
self.dirty = True
def getAutopick(self, station): def getAutopick(self, station):
""" """
@ -292,6 +301,7 @@ class Event(ObsPyEvent):
try: try:
outfile = open(filename, 'wb') outfile = open(filename, 'wb')
cPickle.dump(self, outfile, -1) cPickle.dump(self, outfile, -1)
self.dirty = False
except Exception as e: except Exception as e:
print('Could not pickle PyLoT event. Reason: {}'.format(e)) print('Could not pickle PyLoT event. Reason: {}'.format(e))
@ -310,5 +320,6 @@ class Event(ObsPyEvent):
import _pickle as cPickle import _pickle as cPickle
infile = open(filename, 'rb') infile = open(filename, 'rb')
event = cPickle.load(infile) event = cPickle.load(infile)
event.dirty = False
print('Loaded %s' % filename) print('Loaded %s' % filename)
return event return event

4
pylot/core/util/obspyDMT_interface.py
View File

@ -4,6 +4,7 @@
import os import os
from obspy import UTCDateTime from obspy import UTCDateTime
def check_obspydmt_structure(path): def check_obspydmt_structure(path):
''' '''
Check path for obspyDMT event structure. Check path for obspyDMT event structure.
@ -16,6 +17,7 @@ def check_obspydmt_structure(path):
return True return True
return False return False
def check_obspydmt_eventfolder(folder): def check_obspydmt_eventfolder(folder):
try: try:
time = folder.split('.')[0] time = folder.split('.')[0]
@ -25,6 +27,7 @@ def check_obspydmt_eventfolder(folder):
except Exception as e: except Exception as e:
return False, e return False, e
def qml_from_obspyDMT(path): def qml_from_obspyDMT(path):
import pickle import pickle
from obspy.core.event import Event, Magnitude, Origin from obspy.core.event import Event, Magnitude, Origin
@ -41,4 +44,3 @@ def qml_from_obspyDMT(path):
ev.magnitudes.append(mag) ev.magnitudes.append(mag)
ev.origins.append(origin) ev.origins.append(origin)
return ev return ev

37
pylot/core/util/thread.py
View File

@ -33,31 +33,21 @@ class Thread(QThread):
self._executed = False self._executed = False
self._executedError = e self._executedError = e
traceback.print_exc() traceback.print_exc()
exctype, value = sys.exc_info ()[:2] exctype, value = sys.exc_info()[:2]
self._executedErrorInfo = '{} {} {}'.\ self._executedErrorInfo = '{} {} {}'. \
format(exctype, value, traceback.format_exc()) format(exctype, value, traceback.format_exc())
sys.stdout = sys.__stdout__ sys.stdout = sys.__stdout__
def showProgressbar(self): def showProgressbar(self):
if self.progressText: if self.progressText:
# generate widget if not given in init # # generate widget if not given in init
if not self.pb_widget: # if not self.pb_widget:
self.pb_widget = QDialog(self.parent()) # self.pb_widget = ProgressBarWidget(self.parent())
self.pb_widget.setWindowFlags(Qt.SplashScreen) # self.pb_widget.setWindowFlags(Qt.SplashScreen)
self.pb_widget.setModal(True) # self.pb_widget.setModal(True)
# add button self.pb_widget.label.setText(self.progressText)
delete_button = QPushButton('X')
delete_button.clicked.connect(self.exit)
hl = QHBoxLayout()
pb = QProgressBar()
pb.setRange(0, 0)
hl.addWidget(pb)
hl.addWidget(QLabel(self.progressText))
if self.abortButton:
hl.addWidget(delete_button)
self.pb_widget.setLayout(hl)
self.pb_widget.show() self.pb_widget.show()
def hideProgressbar(self): def hideProgressbar(self):
@ -75,6 +65,7 @@ class Worker(QRunnable):
''' '''
Worker class to be run by MultiThread(QThread). Worker class to be run by MultiThread(QThread).
''' '''
def __init__(self, fun, args, def __init__(self, fun, args,
progressText=None, progressText=None,
pb_widget=None, pb_widget=None,
@ -82,7 +73,7 @@ class Worker(QRunnable):
super(Worker, self).__init__() super(Worker, self).__init__()
self.fun = fun self.fun = fun
self.args = args self.args = args
#self.kwargs = kwargs # self.kwargs = kwargs
self.signals = WorkerSignals() self.signals = WorkerSignals()
self.progressText = progressText self.progressText = progressText
self.pb_widget = pb_widget self.pb_widget = pb_widget
@ -96,9 +87,9 @@ class Worker(QRunnable):
try: try:
result = self.fun(self.args) result = self.fun(self.args)
except: except:
exctype, value = sys.exc_info ()[:2] exctype, value = sys.exc_info()[:2]
print(exctype, value, traceback.format_exc()) print(exctype, value, traceback.format_exc())
self.signals.error.emit ((exctype, value, traceback.format_exc ())) self.signals.error.emit((exctype, value, traceback.format_exc()))
else: else:
self.signals.result.emit(result) self.signals.result.emit(result)
finally: finally:
@ -140,13 +131,13 @@ class MultiThread(QThread):
def run(self): def run(self):
if self.redirect_stdout: if self.redirect_stdout:
sys.stdout = self sys.stdout = self
try: try:
if not self.ncores: if not self.ncores:
self.ncores = multiprocessing.cpu_count() self.ncores = multiprocessing.cpu_count()
pool = multiprocessing.Pool(self.ncores) pool = multiprocessing.Pool(self.ncores)
self.data = pool.map_async(self.func, self.args, callback=self.emitDone) self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
#self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
pool.close() pool.close()
self._executed = True self._executed = True
except Exception as e: except Exception as e:

238
pylot/core/util/utils.py
View File

@ -22,11 +22,7 @@ from pylot.styles import style_settings
from scipy.interpolate import splrep, splev from scipy.interpolate import splrep, splev
from PySide import QtCore, QtGui from PySide import QtCore, QtGui
try: import pyqtgraph as pg
import pyqtgraph as pg
except Exception as e:
print('PyLoT: Could not import pyqtgraph. {}'.format(e))
pg = None
def _pickle_method(m): def _pickle_method(m):
if m.im_self is None: if m.im_self is None:
@ -34,6 +30,7 @@ def _pickle_method(m):
else: else:
return getattr, (m.im_self, m.im_func.func_name) return getattr, (m.im_self, m.im_func.func_name)
def getAutoFilteroptions(phase, parameter): def getAutoFilteroptions(phase, parameter):
filtername = {'P': 'bpz2', filtername = {'P': 'bpz2',
'S': 'bph2'} 'S': 'bph2'}
@ -41,9 +38,10 @@ def getAutoFilteroptions(phase, parameter):
print('autoPickParameter: No filter options for phase {}.'.format(phase)) print('autoPickParameter: No filter options for phase {}.'.format(phase))
return return
freqmin, freqmax = parameter.get(filtername[phase]) freqmin, freqmax = parameter.get(filtername[phase])
filteroptions = FilterOptions(type='bandpass', freq=[freqmin, freqmax], order=4) # order=4 default from obspy filteroptions = FilterOptions(type='bandpass', freq=[freqmin, freqmax], order=4) # order=4 default from obspy
return filteroptions return filteroptions
def readDefaultFilterInformation(fname): def readDefaultFilterInformation(fname):
""" """
Read default filter information from pylot.in file Read default filter information from pylot.in file
@ -118,8 +116,12 @@ def gen_Pool(ncores=0):
""" """
import multiprocessing import multiprocessing
if ncores == 0: ncores_max = multiprocessing.cpu_count()
ncores = multiprocessing.cpu_count()
if ncores == 0 or ncores > ncores_max:
ncores = ncores_max
if ncores > ncores_max:
print('Reduced number of requested CPU slots to available number: {}'.format(ncores))
print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores)) print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
@ -397,6 +399,10 @@ def full_range(stream):
:return: minimum start time and maximum end time :return: minimum start time and maximum end time
:rtype: (`~maximum start time and minimum end time`, maximum start time and minimum end time) :rtype: (`~maximum start time and minimum end time`, maximum start time and minimum end time)
""" """
if not stream:
print('full_range: Empty Stream!')
return None, None
min_start = min([trace.stats.starttime for trace in stream]) min_start = min([trace.stats.starttime for trace in stream])
max_end = max([trace.stats.endtime for trace in stream]) max_end = max([trace.stats.endtime for trace in stream])
@ -537,7 +543,7 @@ def isSorted(iterable):
False False
""" """
assert isIterable(iterable), 'object is not iterable; object: {' \ assert isIterable(iterable), 'object is not iterable; object: {' \
'0}'.format(iterable) '}'.format(iterable)
if type(iterable) is str: if type(iterable) is str:
iterable = [s for s in iterable] iterable = [s for s in iterable]
return sorted(iterable) == iterable return sorted(iterable) == iterable
@ -675,7 +681,7 @@ def pick_color(picktype, phase, quality=0):
bpc = base_phase_colors(picktype, phase) # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)} bpc = base_phase_colors(picktype, phase) # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
rgba = bpc['rgba'] rgba = bpc['rgba']
modifier = bpc['modifier'] modifier = bpc['modifier']
intensity = 255.*quality/min_quality intensity = 255. * quality / min_quality
rgba = modify_rgba(rgba, modifier, intensity) rgba = modify_rgba(rgba, modifier, intensity)
return rgba return rgba
@ -787,6 +793,7 @@ def base_phase_colors(picktype, phase):
phasecolors = style_settings.phasecolors phasecolors = style_settings.phasecolors
return phasecolors[picktype][phase] return phasecolors[picktype][phase]
def transform_colors_mpl_str(colors, no_alpha=False): def transform_colors_mpl_str(colors, no_alpha=False):
""" """
Transforms rgba color values to a matplotlib string of color values with a range of [0, 1] Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
@ -805,6 +812,7 @@ def transform_colors_mpl_str(colors, no_alpha=False):
colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl) colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
return colors_mpl return colors_mpl
def transform_colors_mpl(colors): def transform_colors_mpl(colors):
""" """
Transform rgba colors from [0, 255] to [0, 1] Transform rgba colors from [0, 255] to [0, 1]
@ -817,6 +825,7 @@ def transform_colors_mpl(colors):
colors_mpl = tuple([color / 255. for color in colors]) colors_mpl = tuple([color / 255. for color in colors])
return colors_mpl return colors_mpl
def remove_underscores(data): def remove_underscores(data):
""" """
takes a `obspy.core.stream.Stream` object and removes all underscores takes a `obspy.core.stream.Stream` object and removes all underscores
@ -826,9 +835,9 @@ def remove_underscores(data):
:return: data stream :return: data stream
:rtype: `~obspy.core.stream.Stream` :rtype: `~obspy.core.stream.Stream`
""" """
for tr in data: #for tr in data:
# remove underscores # # remove underscores
tr.stats.station = tr.stats.station.strip('_') # tr.stats.station = tr.stats.station.strip('_')
return data return data
@ -926,7 +935,10 @@ def get_stations(data):
def check4rotated(data, metadata=None, verbosity=1): def check4rotated(data, 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 data: stream object containing seismic traces :param data: stream object containing seismic traces
:type data: `~obspy.core.stream.Stream` :type data: `~obspy.core.stream.Stream`
:param metadata: tuple containing metadata type string and metadata parser object :param metadata: tuple containing metadata type string and metadata parser object
@ -943,100 +955,59 @@ def check4rotated(data, metadata=None, verbosity=1):
Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length. 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 Returns unrotated traces of no metadata is provided
:param wfstream: stream containing seismic traces :param wfstream: stream containing seismic traces of a station
:type wfstream: `~obspy.core.stream.Stream` :type wfstream: `~obspy.core.stream.Stream`
:param metadata: tuple containing metadata type string and metadata parser object :param metadata: tuple containing metadata type string and metadata parser object
:type metadata: (str, `~obspy.io.xseed.parser.Parser`) :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
:return: stream object with traditionally oriented traces (ZNE) :return: stream object with traditionally oriented traces (ZNE)
:rtype: `~obspy.core.stream.Stream` :rtype: `~obspy.core.stream.Stream`
""" """
try:
# indexing fails if metadata is None
metadata[0]
except TypeError:
if verbosity:
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
print(msg)
return wfstream
if metadata[0] is None:
# sometimes metadata is (None, (None,))
if verbosity:
msg = 'Warning: could not rotate traces since no metadata was given\nCheck inventory directory!'
print(msg)
return wfstream
else:
parser = metadata[1]
def get_dip_azimut(parser, trace_id):
"""
Gets azimuth and dip by trace id out of the metadata parser
:param parser: metadata parser object
:type parser: `~obspy.io.xseed.parser.Parser`
:param trace_id: eg. 'BW.RJOB..EHZ',
:type trace_id: str
:return: tuple containing dip and azimuth of the trace corresponding to trace_id
:rtype: (float, float)
"""
dip = None
azimut = None
try:
blockettes = parser._select(trace_id)
except SEEDParserException as e:
print(e)
raise ValueError
for blockette_ in blockettes:
if blockette_.id != 52:
continue
dip = blockette_.dip
azimut = blockette_.azimuth
break
if (dip is None or azimut is None) or (dip == 0 and azimut == 0):
error_msg = 'Dip and azimuth not available for trace_id {}'.format(trace_id)
raise ValueError(error_msg)
return dip, azimut
# check if any traces in this station need to be rotated
trace_ids = [trace.id for trace in wfstream] trace_ids = [trace.id for trace in wfstream]
for trace_id in trace_ids: orientations = [trace_id[-1] for trace_id in trace_ids]
orientation = trace_id[-1] # last letter if trace id is orientation code, ZNE or 123 rotation_required = [orientation.isnumeric() for orientation in orientations]
if orientation.isnumeric(): if any(rotation_required):
# misaligned channels have a number as orientation t_start = full_range(wfstream)
azimuts = [] try:
dips = [] azimuts = [metadata.get_coordinates(tr_id, t_start)['azimuth'] for tr_id in trace_ids]
for trace_id in trace_ids: dips = [metadata.get_coordinates(tr_id, t_start)['dip'] for tr_id in trace_ids]
try: except (KeyError, TypeError) as e:
dip, azimut = get_dip_azimut(parser, trace_id) print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(trace_id))
except ValueError as e: return wfstream
print(e) if len(wfstream) < 3:
print('Failed to rotate station {}, no azimuth or dip available in metadata'.format(trace_id)) print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
return wfstream return wfstream
azimuts.append(azimut) # to rotate all traces must have same length, so trim them
dips.append(dip) wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
# to rotate all traces must have same length z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True) wfstream[1], azimuts[1], dips[1],
z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0], wfstream[2], azimuts[2], dips[2])
wfstream[1], azimuts[1], dips[1], print('check4rotated: rotated trace {} to ZNE'.format(trace_id))
wfstream[2], azimuts[2], dips[2]) # replace old data with rotated data, change the channel code to ZNE
print('check4rotated: rotated station {} to ZNE'.format(trace_id)) z_index = dips.index(min(
z_index = dips.index(min(dips)) # get z-trace index (dip is measured from 0 to -90) dips)) # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
wfstream[z_index].data = z wfstream[z_index].data = z
wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z' wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
del trace_ids[z_index] del trace_ids[z_index]
for trace_id in trace_ids: for trace_id in trace_ids:
dip, az = get_dip_azimut(parser, trace_id) coordinates = metadata.get_coordinates(trace_id, t_start)
trace = wfstream.select(id=trace_id)[0] dip, az = coordinates['dip'], coordinates['azimuth']
if az > 315 or az <= 45 or az > 135 and az <= 225: trace = wfstream.select(id=trace_id)[0]
trace.data = n if az > 315 or az <= 45 or az > 135 and az <= 225:
trace.stats.channel = trace.stats.channel[0:-1] + 'N' trace.data = n
elif az > 45 and az <= 135 or az > 225 and az <= 315: trace.stats.channel = trace.stats.channel[0:-1] + 'N'
trace.data = e elif az > 45 and az <= 135 or az > 225 and az <= 315:
trace.stats.channel = trace.stats.channel[0:-1] + 'E' trace.data = e
break trace.stats.channel = trace.stats.channel[0:-1] + 'E'
else:
continue
return wfstream return wfstream
if metadata is None:
if verbosity:
msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
print(msg)
return data
stations = get_stations(data) stations = get_stations(data)
for station in stations: # loop through all stations and rotate data if neccessary for station in stations: # loop through all stations and rotate data if neccessary
wf_station = data.select(station=station) wf_station = data.select(station=station)
rotate_components(wf_station, metadata) rotate_components(wf_station, metadata)
@ -1149,7 +1120,7 @@ def loopIdentifyPhase(phase):
""" """
from pylot.core.util.defaults import ALTSUFFIX from pylot.core.util.defaults import ALTSUFFIX
if phase == None: if phase is None:
raise NameError('Can not identify phase that is None') raise NameError('Can not identify phase that is None')
phase_copy = phase phase_copy = phase
@ -1199,20 +1170,6 @@ def identifyPhaseID(phase):
return identifyPhase(loopIdentifyPhase(phase)) return identifyPhase(loopIdentifyPhase(phase))
def has_spe(pick):
"""
Check for 'spe' key (symmetric picking error) in dict and return its value if found, else return None
:param pick: pick dictionary
:type pick: dict
:return: value of 'spe' key
:rtype: float or None
"""
if not 'spe' in pick.keys():
return None
else:
return pick['spe']
def check_all_obspy(eventlist): def check_all_obspy(eventlist):
ev_type = 'obspydmt' ev_type = 'obspydmt'
return check_event_folders(eventlist, ev_type) return check_event_folders(eventlist, ev_type)
@ -1245,8 +1202,8 @@ def check_event_folder(path):
folder = path.split('/')[-1] folder = path.split('/')[-1]
# for pylot: select only folders that start with 'e', containin two dots and have length 12 # for pylot: select only folders that start with 'e', containin two dots and have length 12
if (folder.startswith('e') if (folder.startswith('e')
and len(folder.split('.')) == 3 and len(folder.split('.')) == 3
and len(folder) == 12): and len(folder) == 12):
ev_type = 'pylot' ev_type = 'pylot'
elif check_obspydmt_eventfolder(folder)[0]: elif check_obspydmt_eventfolder(folder)[0]:
ev_type = 'obspydmt' ev_type = 'obspydmt'
@ -1276,3 +1233,56 @@ if __name__ == "__main__":
import doctest import doctest
doctest.testmod() doctest.testmod()
class SetChannelComponents(object):
def __init__(self):
self.setDefaultCompPosition()
def setDefaultCompPosition(self):
# default component order
self.compPosition_Map = dict(Z=2, N=1, E=0)
self.compName_Map = {'3': 'Z',
'1': 'N',
'2': 'E'}
def _getCurrentPosition(self, component):
for key, value in self.compName_Map.items():
if value == component:
return key, value
errMsg = 'getCurrentPosition: Could not find former position of component {}.'.format(component)
raise ValueError(errMsg)
def _switch(self, component, component_alter):
# Without switching, multiple definitions of the same alter_comp are possible
old_alter_comp, _ = self._getCurrentPosition(component)
old_comp = self.compName_Map[component_alter]
if not old_alter_comp == component_alter and not old_comp == component:
self.compName_Map[old_alter_comp] = old_comp
print('switch: Automatically switched component {} to {}'.format(old_alter_comp, old_comp))
def setCompPosition(self, component_alter, component, switch=True):
component_alter = str(component_alter)
if not component_alter in self.compName_Map.keys():
errMsg = 'setCompPosition: Unrecognized alternative component {}. Expecting one of {}.'
raise ValueError(errMsg.format(component_alter, self.compName_Map.keys()))
if not component in self.compPosition_Map.keys():
errMsg = 'setCompPosition: Unrecognized target component {}. Expecting one of {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys()))
print('setCompPosition: set component {} to {}'.format(component_alter, component))
if switch:
self._switch(component, component_alter)
self.compName_Map[component_alter] = component
def getCompPosition(self, component):
return self._getCurrentPosition(component)[0]
def getPlotPosition(self, component):
component = str(component)
if component in self.compPosition_Map.keys():
return self.compPosition_Map[component]
elif component in self.compName_Map.keys():
return self.compPosition_Map[self.compName_Map[component]]
else:
errMsg = 'getCompPosition: Unrecognized component {}. Expecting one of {} or {}.'
raise ValueError(errMsg.format(component, self.compPosition_Map.keys(), self.compName_Map.keys()))

501
pylot/core/util/widgets.py
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15
pylot/styles/style_settings.py
View File

@ -5,18 +5,18 @@
# the base color # the base color
phasecolors = { phasecolors = {
'manual': { 'manual': {
'P':{ 'P': {
'rgba': (0, 0, 255, 255), 'rgba': (0, 0, 255, 255),
'modifier': 'g'}, 'modifier': 'g'},
'S':{ 'S': {
'rgba': (255, 0, 0, 255), 'rgba': (255, 0, 0, 255),
'modifier': 'b'} 'modifier': 'b'}
}, },
'auto':{ 'auto': {
'P':{ 'P': {
'rgba': (140, 0, 255, 255), 'rgba': (140, 0, 255, 255),
'modifier': 'g'}, 'modifier': 'g'},
'S':{ 'S': {
'rgba': (255, 140, 0, 255), 'rgba': (255, 140, 0, 255),
'modifier': 'b'} 'modifier': 'b'}
} }
@ -24,8 +24,8 @@ phasecolors = {
# Set plot colors and stylesheet for each style # Set plot colors and stylesheet for each style
stylecolors = { stylecolors = {
'default':{ 'default': {
'linecolor':{ 'linecolor': {
'rgba': (0, 0, 0, 255)}, 'rgba': (0, 0, 0, 255)},
'background': { 'background': {
'rgba': (255, 255, 255, 255)}, 'rgba': (255, 255, 255, 255)},
@ -67,4 +67,3 @@ stylecolors = {
'filename': 'bright.qss'} 'filename': 'bright.qss'}
} }
} }

2
setup.py
View File

@ -8,7 +8,7 @@ setup(
packages=['pylot', 'pylot.core', 'pylot.core.loc', 'pylot.core.pick', packages=['pylot', 'pylot.core', 'pylot.core.loc', 'pylot.core.pick',
'pylot.core.io', 'pylot.core.util', 'pylot.core.active', 'pylot.core.io', 'pylot.core.util', 'pylot.core.active',
'pylot.core.analysis', 'pylot.testing'], 'pylot.core.analysis', 'pylot.testing'],
requires=['obspy', 'PySide', 'matplotlib', 'numpy'], requires=['obspy', 'PySide', 'matplotlib', 'numpy', 'scipy', 'pyqtgraph'],
url='dummy', url='dummy',
license='LGPLv3', license='LGPLv3',
author='Sebastian Wehling-Benatelli', author='Sebastian Wehling-Benatelli',

27
tests/__init__.py Normal file
View File

@ -0,0 +1,27 @@
# -*- coding: utf-8 -*-
# --------------------------------------------------------
# Purpose: Convience imports for PyLoT
#
'''
================================================
PyLoT - the Python picking and Localization Tool
================================================
This python library contains a graphical user interfaces for picking
seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
and the Qt4 libraries to be installed first.
PILOT has been developed in Mathworks' MatLab. In order to distribute
PILOT without facing portability problems, it has been decided to re-
develop the software package in Python. The great work of the ObsPy
group allows easy handling of a bunch of seismic data and PyLoT will
benefit a lot compared to the former MatLab version.
The development of PyLoT is part of the joint research project MAGS2.
:copyright:
The PyLoT Development Team
:license:
GNU Lesser General Public License, Version 3
(http://www.gnu.org/copyleft/lesser.html)
'''

250
tests/test_Metadata/test_Metadata.py
View File

@ -1,32 +1,59 @@
import unittest import unittest
import os import os
from obspy import UTCDateTime
from obspy.io.xseed.utils import SEEDParserException
from obspy.io.xseed import Parser
from pylot.core.util.dataprocessing import Metadata from pylot.core.util.dataprocessing import Metadata
from tests.utils import HidePrints
class TestMetadata(unittest.TestCase): class TestMetadata(unittest.TestCase):
def setUp(self): def setUp(self):
self.station_id = 'BW.WETR..HH' self.station_id = 'BW.WETR..HH'
metadata_folder = 'metadata1' self.time = UTCDateTime('2012-08-01')
metadata_folder = os.path.join('test_data', 'dless_multiple_files', 'metadata1')
self.m = Metadata(metadata_folder) self.m = Metadata(metadata_folder)
def test_get_coordinates_sucess(self): def test_get_coordinates_sucess(self):
expected = {'Z': {u'elevation': 607.0, u'longitude': 12.87571, u'local_depth': 0.0, u'azimuth': 0.0, u'latitude': 49.14502, u'dip': -90.0}, expected = {'Z': {u'elevation': 607.0, u'longitude': 12.87571, u'local_depth': 0.0, u'azimuth': 0.0,
'E': {u'azimuth': 90.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0, u'longitude': 12.87571}, u'latitude': 49.14502, u'dip': -90.0},
'N': {u'azimuth': 0.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0, u'longitude': 12.87571} 'E': {u'azimuth': 90.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502,
u'local_depth': 0.0, u'longitude': 12.87571},
'N': {u'azimuth': 0.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0,
u'longitude': 12.87571}
} }
result = {} result = {}
for channel in ('Z', 'N', 'E'): for channel in ('Z', 'N', 'E'):
coords = self.m.get_coordinates(self.station_id+channel) with HidePrints():
coords = self.m.get_coordinates(self.station_id+channel, time=self.time)
result[channel] = coords result[channel] = coords
self.assertDictEqual(result[channel], expected[channel]) self.assertDictEqual(result[channel], expected[channel])
def test_get_coordinates_sucess_no_time(self):
expected = {'Z': {u'elevation': 607.0, u'longitude': 12.87571, u'local_depth': 0.0, u'azimuth': 0.0,
u'latitude': 49.14502, u'dip': -90.0},
'E': {u'azimuth': 90.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502,
u'local_depth': 0.0, u'longitude': 12.87571},
'N': {u'azimuth': 0.0, u'dip': 0.0, u'elevation': 607.0, u'latitude': 49.14502, u'local_depth': 0.0,
u'longitude': 12.87571}
}
result = {}
for channel in ('Z', 'N', 'E'):
with HidePrints():
coords = self.m.get_coordinates(self.station_id+channel)
result[channel] = coords
self.assertDictEqual(result[channel], expected[channel])
class TestMetadataAdding(unittest.TestCase): class TestMetadataAdding(unittest.TestCase):
"""Tests if adding files and directories to a metadata object works.""" """Tests if adding files and directories to a metadata object works."""
def setUp(self): def setUp(self):
self.station_id = 'BW.WETR..HH' self.station_id = 'BW.WETR..HH'
self.metadata_folders = ('metadata1', 'metadata2') self.metadata_folders = (os.path.join('test_data', 'dless_multiple_files', 'metadata1'),
os.path.join('test_data', 'dless_multiple_files', 'metadata2'))
self.m = Metadata() self.m = Metadata()
def test_add_inventory_folder(self): def test_add_inventory_folder(self):
@ -43,8 +70,10 @@ class TestMetadataAdding(unittest.TestCase):
fpath = os.path.join(self.metadata_folders[0], 'DATALESS.BW.WETR..HHZ') fpath = os.path.join(self.metadata_folders[0], 'DATALESS.BW.WETR..HHZ')
self.m.add_inventory_file(fpath) self.m.add_inventory_file(fpath)
# adding an inventory file should append its folder to the list of inventories and the file to the # adding an inventory file should append its folder to the list of inventories and the file to the
self.assertEqual(['metadata1/DATALESS.BW.WETR..HHZ'], self.m.inventory_files.keys()) # does the filename exist in inventory files? self.assertEqual([os.path.join(self.metadata_folders[0], 'DATALESS.BW.WETR..HHZ')],
self.assertEqual(['data', 'invtype'], self.m.inventory_files['metadata1/DATALESS.BW.WETR..HHZ'].keys()) # is the required information attacht to the filename? self.m.inventory_files.keys()) # does the filename exist in inventory files?
self.assertEqual(['data', 'invtype'], self.m.inventory_files[os.path.join(self.metadata_folders[0],
'DATALESS.BW.WETR..HHZ')].keys()) # is the required information attacht to the filename?
self.assertDictEqual({}, self.m.seed_ids) self.assertDictEqual({}, self.m.seed_ids)
self.assertEqual([self.metadata_folders[0]], self.m.inventories) self.assertEqual([self.metadata_folders[0]], self.m.inventories)
@ -66,7 +95,8 @@ class TestMetadataRemoval(unittest.TestCase):
def setUp(self): def setUp(self):
self.station_id = 'BW.WETR..HH' self.station_id = 'BW.WETR..HH'
self.metadata_folders = ('metadata1', 'metadata2') self.metadata_folders = (os.path.join('test_data', 'dless_multiple_files', 'metadata1'),
os.path.join('test_data', 'dless_multiple_files', 'metadata2'))
self.m = Metadata() self.m = Metadata()
def test_remove_all_inventories(self): def test_remove_all_inventories(self):
@ -93,7 +123,8 @@ class TestMetadataRemoval(unittest.TestCase):
exist in the instance.""" exist in the instance."""
# add multiple inventories # add multiple inventories
self.m.add_inventory(self.metadata_folders[0]) self.m.add_inventory(self.metadata_folders[0])
self.m.remove_inventory('metadata_not_existing') with HidePrints():
self.m.remove_inventory('metadata_not_existing')
self.assertIn(self.metadata_folders[0], self.m.inventories) self.assertIn(self.metadata_folders[0], self.m.inventories)
def isEmpty(self, metadata): def isEmpty(self, metadata):
@ -102,3 +133,202 @@ class TestMetadataRemoval(unittest.TestCase):
self.assertDictEqual({}, metadata.seed_ids) self.assertDictEqual({}, metadata.seed_ids)
self.assertEqual([], metadata.inventories) self.assertEqual([], metadata.inventories)
class TestMetadata_read_single_file(unittest.TestCase):
def setUp(self):
self.station_id = 'BW.WETR..HHZ'
self.metadata_folders = (os.path.join('test_data', 'dless_multiple_files', 'metadata1'),
os.path.join('test_data', 'dless_multiple_files', 'metadata2'))
self.metadata_paths = []
self.m = Metadata()
def test_read_single_file(self):
"""Test if reading a single file works"""
fname = os.path.join(self.metadata_folders[0], 'DATALESS.'+self.station_id)
with HidePrints():
res = self.m.read_single_file(fname)
# method should return true if file is successfully read
self.assertTrue(res)
# list of inventories (folders) should be empty
self.assertEqual([], self.m.inventories)
# list of inventory files should contain the added file
self.assertIn(fname, self.m.inventory_files.keys())
self.assertEqual({}, self.m.seed_ids)
def test_read_single_file_invalid_path(self):
"""Test if reading from a non existing file fails. The filename should not be
added to the metadata object"""
fname = os.path.join("this", "path", "doesnt", "exist")
with HidePrints():
res = self.m.read_single_file(fname)
# method should return None if file reading fails
self.assertIsNone(res)
# list of inventories (folders) should be empty
self.assertEqual([], self.m.inventories)
# list of inventory files should not contain the added file
self.assertNotIn(fname, self.m.inventory_files.keys())
self.assertEqual({}, self.m.seed_ids)
def test_read_single_file_multiple_times(self):
"""Test if reading a file twice doesnt add it twice to the metadata object"""
fname = os.path.join(self.metadata_folders[0], 'DATALESS.'+self.station_id)
with HidePrints():
res1 = self.m.read_single_file(fname)
res2 = self.m.read_single_file(fname)
self.assertTrue(res1)
self.assertIsNone(res2)
self.assertItemsEqual([fname], self.m.inventory_files.keys())
class TestMetadataMultipleTime(unittest.TestCase):
"""Test if stations with multiple metadata entries in a single file are handled correctly.
The user must specify the time where he wants to get metadata.
The station ROTT changed has metadata available at multiple times
LE.ROTT..HNE | 200.00 Hz | Titan 4g-EDR-209, Very Low gain, 200 sps | 2015-01-08 - 2015-03-19 | Lat: 49.1, Lng: 8.1
LE.ROTT..HNE | 200.00 Hz | Titan 4g-EDR-209, Very Low gain, 200 sps | 2015-03-19 - | Lat: 49.1, Lng: 8.1
LE.ROTT..HNN | 200.00 Hz | Titan 4g-EDR-209, Very Low gain, 200 sps | 2015-01-08 - 2015-03-19 | Lat: 49.1, Lng: 8.1
LE.ROTT..HNN | 200.00 Hz | Titan 4g-EDR-209, Very Low gain, 200 sps | 2015-03-19 - | Lat: 49.1, Lng: 8.1
LE.ROTT..HNZ | 200.00 Hz | Titan 4g-EDR-209, Very Low gain, 200 sps | 2015-01-08 - 2015-03-19 | Lat: 49.1, Lng: 8.1
LE.ROTT..HNZ | 200.00 Hz | Titan 4g-EDR-209, Very Low gain, 200 sps | 2015-03-19 - | Lat: 49.1, Lng: 8.1
"""
def setUp(self):
self.seed_id = 'LE.ROTT..HN'
path = os.path.dirname(__file__) # gets path to currently running script
metadata = os.path.join('test_data', 'dless_multiple_times', 'MAGS2_LE_ROTT.dless') # specific subfolder of test data
metadata_path = os.path.join(path, metadata)
self.m = Metadata(metadata_path)
self.p = Parser(metadata_path)
def test_get_metadata_works_without_datetime(self):
"""Test if get_metadata works if multiple metadata entries are available but no time is
specified."""
for channel in ('Z', 'N', 'E'):
with HidePrints():
md = self.m.get_metadata(self.seed_id + channel)
self.assertDictEqual(md['data'].get_inventory(), self.p.get_inventory())
def test_get_metadata_works_with_first_datetime(self):
"""Test if get_metadata works if multiple metadata entries are available and the older time is specified."""
t = UTCDateTime('2015-02-08')
for channel in ('Z', 'N', 'E'):
with HidePrints():
md = self.m.get_metadata(self.seed_id + channel, t)
self.assertDictEqual(md['data'].get_inventory(), self.p.get_inventory())
def test_get_metadata_fails_when_time_before_starttime(self):
"""Tests if get_metadata returns None when given a data that is before the start date
of the metadata"""
with HidePrints():
md = self.m.get_metadata(self.seed_id, UTCDateTime('1960-07-20'))
self.assertIs(md, None)
def test_get_metadata_invalid_seed_id(self):
"""Tes if get metadata returns none when asked for a seed id that does not exist"""
with HidePrints():
res = self.m.get_metadata("this.doesnt..exist")
self.assertIsNone(res)
class TestMetadataMultipleEntries(unittest.TestCase):
"""
The station KB.TMO07 has changed instruments multiple times.
Networks:
KB (KB network)
Stations:
KB.TMO07 (Karlsruhe GPI)
Channels:
KB.TMO07.00.BHE | 50.00 Hz | Streckeisen KABBA-STS-2 | 2004-12-06 - 2005-04-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHE | 50.00 Hz | Streckeisen KABBA-STS-2 | 2005-04-18 - 2006-07-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHE | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2006-10-10 - 2006-11-14 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHE | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2006-11-24 - 2007-01-12 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHE | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-01-18 - 2007-03-15 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHE | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-10-25 - 2007-11-21 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHE | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-11-21 - 2008-01-17 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Streckeisen KABBA-STS-2 | 2004-12-06 - 2005-04-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Streckeisen KABBA-STS-2 | 2005-04-18 - 2006-07-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2006-10-10 - 2006-11-14 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2006-11-24 - 2007-01-12 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-01-18 - 2007-03-15 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-10-25 - 2007-11-21 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHN | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-11-21 - 2008-01-17 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Streckeisen KABBA-STS-2 | 2004-12-06 - 2005-04-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Streckeisen KABBA-STS-2 | 2005-04-18 - 2006-07-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2006-10-10 - 2006-11-14 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2006-11-24 - 2007-01-12 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-01-18 - 2007-03-15 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-10-25 - 2007-11-21 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.BHZ | 50.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-11-21 - 2008-01-17 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-01-12 - 2007-01-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-10-10 - 2007-10-25 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Streckeisen KABBA-STS-2 | 2008-07-11 - 2008-12-05 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Streckeisen KABBA-STS-2 | 2009-05-12 - 2010-02-15 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Streckeisen KABBA-STS-2 | 2010-02-15 - 2010-04-07 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Lennartz KABBA-LE-3D/1 | 2010-04-07 - 2010-08-03 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 200.00 Hz | Streckeisen KABBA-STS-2 | 2010-08-05 - 2010-12-20 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 100.00 Hz | Streckeisen KABBA-STS-2 | 2010-12-20 - 2010-12-22 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 200.00 Hz | Streckeisen KABBA-STS-2 | 2010-12-22 - 2011-04-02 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 200.00 Hz | Streckeisen KABBA-STS-2 | 2011-04-15 - 2012-05-07 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHE | 200.00 Hz | Streckeisen KABBA-STS-2 | 2012-05-07 - | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-01-12 - 2007-01-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-10-10 - 2007-10-25 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Streckeisen KABBA-STS-2 | 2008-07-11 - 2008-12-05 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Streckeisen KABBA-STS-2 | 2009-05-12 - 2010-02-15 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Streckeisen KABBA-STS-2 | 2010-02-15 - 2010-04-07 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Lennartz KABBA-LE-3D/1 | 2010-04-07 - 2010-08-03 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 200.00 Hz | Streckeisen KABBA-STS-2 | 2010-08-05 - 2010-12-20 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 100.00 Hz | Streckeisen KABBA-STS-2 | 2010-12-20 - 2010-12-22 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 200.00 Hz | Streckeisen KABBA-STS-2 | 2010-12-22 - 2011-04-02 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 200.00 Hz | Streckeisen KABBA-STS-2 | 2011-04-15 - 2012-05-07 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHN | 200.00 Hz | Streckeisen KABBA-STS-2 | 2012-05-07 - | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-01-12 - 2007-01-18 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Lennartz KABBA-LE-3D/5 | 2007-10-10 - 2007-10-25 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Streckeisen KABBA-STS-2 | 2008-07-11 - 2008-12-05 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Streckeisen KABBA-STS-2 | 2009-05-12 - 2010-02-15 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Streckeisen KABBA-STS-2 | 2010-02-15 - 2010-04-07 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Lennartz KABBA-LE-3D/1 | 2010-04-07 - 2010-08-03 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 200.00 Hz | Streckeisen KABBA-STS-2 | 2010-08-05 - 2010-12-20 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 100.00 Hz | Streckeisen KABBA-STS-2 | 2010-12-20 - 2010-12-22 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 200.00 Hz | Streckeisen KABBA-STS-2 | 2010-12-22 - 2011-04-02 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 200.00 Hz | Streckeisen KABBA-STS-2 | 2011-04-15 - 2012-05-07 | Lat: 49.0, Lng: 8.4
KB.TMO07.00.HHZ | 200.00 Hz | Streckeisen KABBA-STS-2 | 2012-05-07 - | Lat: 49.0, Lng: 8.4
"""
def setUp(self):
self.seed_id = 'KB.TMO07.00.HHZ'
path = os.path.dirname(__file__) # gets path to currently running script
metadata = os.path.join('test_data', 'dless_multiple_instruments', 'MAGS2_KB_TMO07.dless') # specific subfolder of test data
metadata_path = os.path.join(path, metadata)
self.m = Metadata(metadata_path)
self.p = Parser(metadata_path)
def test_get_paz_current_time(self):
"""Test if getting the paz from the metadata object with the current time works"""
t = UTCDateTime()
with HidePrints():
pazm = self.m.get_paz(self.seed_id, t)
pazp = self.p.get_paz(self.seed_id, t)
self.assertEqual(pazm, pazp)
def test_get_paz_past(self):
"""Test if getting paz from metadata object with a time in the past works"""
t = UTCDateTime('2007-01-13')
with HidePrints():
pazm = self.m.get_paz(self.seed_id, t)
pazp = self.p.get_paz(self.seed_id, t)
self.assertEqual(pazm, pazp)
def test_get_paz_time_not_exisiting(self):
"""Test if getting paz from metadata at a time where there is no metadata
available fails correctly"""
with self.assertRaises(SEEDParserException):
with HidePrints():
self.m.get_paz(self.seed_id, UTCDateTime('1990-1-1'))
def test_get_paz_seed_id_not_existing(self):
"""Test if getting paz from a non existing seed id returns None as expected."""
with HidePrints():
res = self.m.get_paz('This.doesnt..exist', UTCDateTime)
self.assertIsNone(res)

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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Utilities/helpers for testing"""
import sys
import os
class HidePrints:
"""
Context manager that hides all standard output within its body.
The optional hide_prints argument can be used to quickly enable printing during debugging of tests.
Use (This will result in all console output of noisy_function to be suppressed):
from tests.utils import HidePrints
with HidePrints():
noise_function()
"""
@staticmethod
def hide(func, *args, **kwargs):
"""Decorator that hides all prints of the decorated function.
Use:
from tests.utils import HidePrints
@HidePrints.hide
def noise()
print("NOISE")
"""
def silencer(*args, **kwargs):
with HidePrints():
func(*args, **kwargs)
return silencer
def __init__(self, hide_prints=True):
"""Create object with hide_prints=False to disable print hiding"""
self.hide = hide_prints
def __enter__(self):
"""Redirect stdout to /dev/null, save old stdout"""
if self.hide:
self._original_stdout = sys.stdout
devnull = open(os.devnull, "w")
sys.stdout = devnull
def __exit__(self, exc_type, exc_val, exc_tb):
"""Reinstate old stdout"""
if self.hide:
sys.stdout = self._original_stdout