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

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This commit is contained in:
Marcel Paffrath 2017-12-06 14:53:18 +01:00
commit 1296e914c3
18 changed files with 504 additions and 161 deletions
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2
autoPyLoT.py
View File

@ -338,6 +338,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
local_mag = LocalMagnitude(corr_dat, evt,
parameter.get('sstop'),
WAscaling, True, iplot)
# update pick with local magnitude property values
for stats, amplitude in local_mag.amplitudes.items():
picks[stats]['S']['Ao'] = amplitude.generic_amplitude
print("Local station magnitudes scaled with:")
@ -412,6 +413,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
local_mag = LocalMagnitude(corr_dat, evt,
parameter.get('sstop'),
WAscaling, True, iplot)
# update pick with local magnitude property values
for stats, amplitude in local_mag.amplitudes.items():
if stats in picks:
picks[stats]['S']['Ao'] = amplitude.generic_amplitude

39
pylot/core/analysis/magnitude.py
View File

@ -16,7 +16,6 @@ from pylot.core.util.utils import common_range, fit_curve
from scipy import integrate, signal
from scipy.optimize import curve_fit
def richter_magnitude_scaling(delta):
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,
@ -133,7 +132,7 @@ class Magnitude(object):
station_count=len(self.magnitudes),
azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap)
else:
# no saling necessary
# no scaling necessary
mag = ope.Magnitude(
mag=np.median([M.mag for M in self.magnitudes.values()]),
magnitude_type=self.type,
@ -233,17 +232,33 @@ class LocalMagnitude(Magnitude):
# check for plot flag (for debugging only)
fig = None
if iplot > 1:
st.plot()
fig = plt.figure()
ax = fig.add_subplot(111)
ax = fig.add_subplot(211)
ax.plot(th, st[0].data, 'k')
ax.plot(th, sqH)
ax.plot(th[iwin], sqH[iwin], 'g')
ax.plot([t0, t0], [0, max(sqH)], 'r', linewidth=2)
ax.title(
'Station %s, RMS Horizontal Traces, WA-peak-to-peak=%4.1f mm' \
% (st[0].stats.station, wapp))
ax.plot([t0 - stime, t0 - stime], [0, max(sqH)], 'r', linewidth=2)
ax.set_title('Station %s, Channel %s, RMS Horizontal Trace, '
'WA-peak-to-peak=%6.3f mm' % (st[0].stats.station,
st[0].stats.channel,
wapp))
ax.set_xlabel('Time [s]')
ax.set_ylabel('Displacement [mm]')
ax = fig.add_subplot(212)
ax.plot(th, st[1].data, 'k')
ax.plot(th, sqH)
ax.plot(th[iwin], sqH[iwin], 'g')
ax.plot([t0 - stime, t0 - stime], [0, max(sqH)], 'r', linewidth=2)
ax.set_title('Channel %s, RMS Horizontal Trace, '
'WA-peak-to-peak=%6.3f mm' % (st[1].stats.channel,
wapp))
ax.set_xlabel('Time [s]')
ax.set_ylabel('Displacement [mm]')
fig.show()
try: input()
except SyntaxError: pass
plt.close(fig)
return wapp, fig
@ -251,6 +266,10 @@ class LocalMagnitude(Magnitude):
for a in self.arrivals:
if a.phase not in 'sS':
continue
# make sure calculating Ml only from reliable onsets
# NLLoc: time_weight = 0 => do not use onset!
if a.time_weight == 0:
continue
pick = a.pick_id.get_referred_object()
station = pick.waveform_id.station_code
wf = select_for_phase(self.stream.select(
@ -349,6 +368,10 @@ class MomentMagnitude(Magnitude):
for a in self.arrivals:
if a.phase not in 'pP':
continue
# make sure calculating Mo only from reliable onsets
# NLLoc: time_weight = 0 => do not use onset!
if a.time_weight == 0:
continue
pick = a.pick_id.get_referred_object()
station = pick.waveform_id.station_code
scopy = self.stream.copy()

137
pylot/core/io/data.py
View File

@ -99,6 +99,11 @@ class Data(object):
return self
def getPicksStr(self):
"""
Return picks in event data
:return: picks seperated by newlines
:rtype: str
"""
picks_str = ''
for pick in self.get_evt_data().picks:
picks_str += str(pick) + '\n'
@ -106,18 +111,11 @@ class Data(object):
def getParent(self):
"""
:return:
Get PySide.QtGui.QWidget parent object
"""
return self._parent
def isNew(self):
"""
:return:
"""
return self._new
def setNew(self):
@ -125,9 +123,9 @@ class Data(object):
def getCutTimes(self):
"""
:return:
Returns earliest start and latest end of all waveform data
:return: minimum start time and maximum end time as a tuple
:rtype: (UTCDateTime, UTCDateTime)
"""
if self.cuttimes is None:
self.updateCutTimes()
@ -135,22 +133,34 @@ class Data(object):
def updateCutTimes(self):
"""
Update cuttimes to contain earliest start and latest end time
of all waveform data
:rtype: None
"""
self.cuttimes = full_range(self.getWFData())
def getEventFileName(self):
"""
:return:
"""
ID = self.getID()
# handle forbidden filenames especially on windows systems
return fnConstructor(str(ID))
def checkEvent(self, event, fcheck, forceOverwrite=False):
"""
Check information in supplied event and own event and replace own
information with supplied information if own information not exiisting
or forced by forceOverwrite
:param event: Event that supplies information for comparison
:type event: pylot.core.util.event.Event
:param fcheck: check and delete existing information
can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
:type fcheck: str, [str]
:param forceOverwrite: Set to true to force overwrite own information. If false,
supplied information from event is only used if there is no own information in that
category (given in fcheck: manual, auto, origin, magnitude)
:type forceOverwrite: bool
:return:
:rtype: None
"""
if 'origin' in fcheck:
self.replaceOrigin(event, forceOverwrite)
if 'magnitude' in fcheck:
@ -161,18 +171,47 @@ class Data(object):
self.replacePicks(event, 'manual')
def replaceOrigin(self, event, forceOverwrite=False):
"""
Replace own origin with the one supplied in event if own origin is not
existing or forced by forceOverwrite = True
:param event: Event that supplies information for comparison
:type event: pylot.core.util.event.Event
:param forceOverwrite: always replace own information with supplied one if true
:type forceOverwrite: bool
:return:
:rtype: None
"""
if self.get_evt_data().origins or forceOverwrite:
if event.origins:
print("Found origin, replace it by new origin.")
event.origins = self.get_evt_data().origins
def replaceMagnitude(self, event, forceOverwrite=False):
"""
Replace own magnitude with the one supplied in event if own magnitude is not
existing or forced by forceOverwrite = True
:param event: Event that supplies information for comparison
:type event: pylot.core.util.event.Event
:param forceOverwrite: always replace own information with supplied one if true
:type forceOverwrite: bool
:return:
:rtype: None
"""
if self.get_evt_data().magnitudes or forceOverwrite:
if event.magnitudes:
print("Found magnitude, replace it by new magnitude")
event.magnitudes = self.get_evt_data().magnitudes
def replacePicks(self, event, picktype):
"""
Replace own picks with the one in event
:param event: Event that supplies information for comparison
:type event: pylot.core.util.event.Event
:param picktype: 'auto' or 'manual' picks
:type picktype: str
:return:
:rtype: None
"""
checkflag = 0
picks = event.picks
# remove existing picks
@ -189,10 +228,10 @@ class Data(object):
picks.append(pick)
def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
"""
Export event to file
:param fnout: basename of file
:param fnext: file extension
:param fnext: file extension, xml, cnv, obs
:param fcheck: check and delete existing information
can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
"""
@ -304,17 +343,13 @@ class Data(object):
def getComp(self):
"""
:return:
Get component (ZNE)
"""
return self.comp
def getID(self):
"""
:return:
Get unique resource id
"""
try:
return self.evtdata.get('resource_id').id
@ -323,16 +358,17 @@ class Data(object):
def filterWFData(self, kwargs):
"""
:param kwargs:
Filter waveform data
:param kwargs: arguments to pass through to filter function
"""
self.getWFData().filter(**kwargs)
self.dirty = True
def setWFData(self, fnames):
"""
:param fnames:
Clear current waveform data and set given waveform data
:param fnames: waveform data names to append
:type fnames: list
"""
self.wfdata = Stream()
self.wforiginal = None
@ -346,8 +382,9 @@ class Data(object):
def appendWFData(self, fnames):
"""
:param fnames:
Read waveform data from fnames and append it to current wf data
:param fnames: waveform data to append
:type fnames: list
"""
assert isinstance(fnames, list), "input parameter 'fnames' is " \
"supposed to be of type 'list' " \
@ -372,54 +409,42 @@ class Data(object):
print(warnmsg)
def getWFData(self):
"""
:return:
"""
return self.wfdata
def getOriginalWFData(self):
"""
:return:
"""
return self.wforiginal
def resetWFData(self):
"""
Set waveform data to original waveform data
"""
self.wfdata = self.getOriginalWFData().copy()
self.dirty = False
def resetPicks(self):
"""
Clear all picks from event
"""
self.get_evt_data().picks = []
def get_evt_data(self):
"""
:return:
"""
return self.evtdata
def setEvtData(self, event):
self.evtdata = event
def applyEVTData(self, data, typ='pick', authority_id='rub'):
"""
:param data:
:param typ:
:param authority_id:
Either takes an `obspy.core.event.Event` object and applies all new
information on the event to the actual data if typ is 'event or
creates ObsPy pick objects and append it to the picks list from the
PyLoT dictionary contain all picks if type is pick
:param data: data to apply, either picks or complete event
:type data:
:param typ: which event data to apply, 'pick' or 'event'
:type typ: str
:param authority_id: (currently unused)
:type: str
:raise OverwriteError:
"""

4
pylot/core/io/default_parameters.py
View File

@ -1,6 +1,10 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Default parameters used for picking
"""
defaults = {'rootpath': {'type': str,
'tooltip': 'project path',
'value': '',

98
pylot/core/io/inputs.py
View File

@ -70,6 +70,7 @@ class PylotParameter(object):
# Set default values of parameter names
def __init_default_paras(self):
"""set default values of parameter names"""
parameters = default_parameters.defaults
self.__defaults = parameters
@ -104,15 +105,34 @@ class PylotParameter(object):
return len(self.__parameter.keys())
def iteritems(self):
"""
Iterate over parameters
:return: key, value tupel
:rtype:
"""
for key, value in self.__parameter.items():
yield key, value
def hasParam(self, parameter):
"""
Check if parameter is in keys
:param parameter: parameter to look for in keys
:type parameter:
:return:
:rtype: bool
"""
if parameter in self.__parameter.keys():
return True
return False
def get(self, *args):
"""
Get first available parameter in args
:param args:
:type args:
:return:
:rtype:
"""
try:
for param in args:
try:
@ -128,15 +148,35 @@ class PylotParameter(object):
raise ParameterError(e)
def get_defaults(self):
"""
get default parameters
:return:
:rtype: dict
"""
return self.__defaults
def get_main_para_names(self):
"""
Get main parameter names
:return: list of keys available in parameters
:rtype:
"""
return self._settings_main
def get_special_para_names(self):
"""
Get pick parameter names
:return: list of keys available in parameters
:rtype:
"""
return self._settings_special_pick
def get_all_para_names(self):
"""
Get all parameter names
:return:
:rtype: list
"""
all_names = []
all_names += self.get_main_para_names()['dirs']
all_names += self.get_main_para_names()['nlloc']
@ -151,6 +191,16 @@ class PylotParameter(object):
return all_names
def checkValue(self, param, value):
"""
Check type of value against expected type of param.
Print warning message if type check fails
:param param:
:type param:
:param value:
:type value:
:return:
:rtype:
"""
is_type = type(value)
expect_type = self.get_defaults()[param]['type']
if not is_type == expect_type and not is_type == tuple:
@ -159,9 +209,25 @@ class PylotParameter(object):
print(Warning(message))
def setParamKV(self, param, value):
"""
set parameter param to value
:param param:
:type param:
:param value:
:type value:
:return:
:rtype: None
"""
self.__setitem__(param, value)
def setParam(self, **kwargs):
"""
Set multiple parameters
:param kwargs:
:type kwargs:
:return:
:rtype: None
"""
for key in kwargs:
self.__setitem__(key, kwargs[key])
@ -170,11 +236,23 @@ class PylotParameter(object):
print('ParameterError:\n non-existent parameter %s' % errmsg)
def reset_defaults(self):
"""
Reset current parameters to default parameters
:return:
:rtype: None
"""
defaults = self.get_defaults()
for param in defaults:
self.setParamKV(param, defaults[param]['value'])
def from_file(self, fnin=None):
"""
read parameters from file and set values to read values
:param fnin: filename
:type fnin:
:return:
:rtype: None
"""
if not fnin:
if self.__filename is not None:
fnin = self.__filename
@ -221,6 +299,13 @@ class PylotParameter(object):
self.__parameter = self._parFileCont
def export2File(self, fnout):
"""
Export parameters to file
:param fnout: Filename of export file
:type fnout: str
:return:
:rtype:
"""
fid_out = open(fnout, 'w')
lines = []
# for key, value in self.iteritems():
@ -257,6 +342,19 @@ class PylotParameter(object):
'quality assessment', None)
def write_section(self, fid, names, title, separator):
"""
write a section of parameters to file
:param fid: File object to write to
:type fid:
:param names: which parameter names to write to file
:type names:
:param title: title of section
:type title: str
:param separator: section separator, written at start of section
:type separator: str
:return:
:rtype:
"""
if separator:
fid.write(separator)
fid.write('#{}#\n'.format(title))

8
pylot/core/io/location.py
View File

@ -54,7 +54,7 @@ def create_arrival(pickresID, cinfo, phase, azimuth=None, dist=None):
def create_creation_info(agency_id=None, creation_time=None, author=None):
'''
get creation info of obspy event
:param agency_id:
:param creation_time:
:param author:
@ -197,9 +197,9 @@ def create_pick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
'''
:param timetohash:
:type timetohash
create unique resource id
:param timetohash: event origin time to hash
:type timetohash: class: `~obspy.core.utcdatetime.UTCDateTime` object
:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
:type restype: str
:param authority_id: name of the institution carrying out the processing

79
pylot/core/io/phases.py
View File

@ -118,6 +118,13 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
def picksdict_from_pilot(fn):
"""
Create pick dictionary from matlab file
:param fn: matlab file
:type fn:
:return: pick dictionary
:rtype: dict
"""
from pylot.core.util.defaults import TIMEERROR_DEFAULTS
picks = dict()
phases_pilot = sio.loadmat(fn)
@ -147,6 +154,13 @@ def picksdict_from_pilot(fn):
def stations_from_pilot(stat_array):
"""
Create stations list from pilot station array
:param stat_array:
:type stat_array:
:return:
:rtype: list
"""
stations = list()
cur_stat = None
for stat in stat_array:
@ -164,6 +178,13 @@ def stations_from_pilot(stat_array):
def convert_pilot_times(time_array):
"""
Convert pilot times to UTCDateTimes
:param time_array: pilot times
:type time_array:
:return:
:rtype:
"""
times = [int(time) for time in time_array]
microseconds = int((time_array[-1] - times[-1]) * 1e6)
times.append(microseconds)
@ -171,6 +192,13 @@ def convert_pilot_times(time_array):
def picksdict_from_obs(fn):
"""
create pick dictionary from obs file
:param fn: filename
:type fn:
:return:
:rtype:
"""
picks = dict()
station_name = str()
for line in open(fn, 'r'):
@ -240,6 +268,16 @@ def picksdict_from_picks(evt):
def picks_from_picksdict(picks, creation_info=None):
"""
Create a list of picks out of a pick dictionary
:param picks: pick dictionary
:type picks: dict
:param creation_info: obspy creation information to apply to picks
:type creation_info:
:param creation_info: obspy creation information to apply to picks
:return: list of picks
:rtype: list
"""
picks_list = list()
for station, onsets in picks.items():
for label, phase in onsets.items():
@ -410,25 +448,24 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
HYPO71, NLLoc, VELEST, HYPOSAT, and hypoDD
:param: arrivals
:type: dictionary containing all phase information including
station ID, phase, first motion, weight (uncertainty),
....
:param arrivals:dictionary containing all phase information including
station ID, phase, first motion, weight (uncertainty), ...
:type arrivals: dict
:param: fformat
:type: string, chosen file format (location routine),
choose between NLLoc, HYPO71, HYPOSAT, VELEST,
HYPOINVERSE, and hypoDD
:param fformat: chosen file format (location routine),
choose between NLLoc, HYPO71, HYPOSAT, VELEST,
HYPOINVERSE, and hypoDD
:type fformat: str
:param: filename, full path and name of phase file
:type: string
:param filename: full path and name of phase file
:type filename: string
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
:param: eventinfo, optional, needed for VELEST-cnv file
:param eventinfo: optional, needed for VELEST-cnv file
and FOCMEC- and HASH-input files
:type: `obspy.core.event.Event` object
:type eventinfo: `obspy.core.event.Event` object
"""
if fformat == 'NLLoc':
@ -874,10 +911,20 @@ def merge_picks(event, picks):
def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
"""
Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
Uncertainties are tranformed into quality classes and visualized via histogram if desired.
Ludger Küperkoch, BESTEC GmbH, 07/2017
"""
:param xmlnames: list of xml obspy event files containing picks
:type xmlnames: list
:param ErrorsP: time errors of P waves for the four discrete quality classes
:type ErrorsP:
:param ErrorsS: time errors of S waves for the four discrete quality classes
:type ErrorsS:
:param plotflag:
:type plotflag:
:return:
:rtype:
"""
from pylot.core.pick.utils import getQualityFromUncertainty
from pylot.core.util.utils import loopIdentifyPhase, identifyPhase

8
pylot/core/loc/focmec.py
View File

@ -18,11 +18,11 @@ def export(picks, fnout, parameter, eventinfo):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
:param: eventinfo, source information needed for focmec format
:type: list object
:param eventinfo: source information needed for focmec format
:type eventinfo: list object
'''
# write phases to FOCMEC-phase file
writephases(picks, 'FOCMEC', fnout, parameter, eventinfo)

8
pylot/core/loc/hash.py
View File

@ -18,11 +18,11 @@ def export(picks, fnout, parameter, eventinfo):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
:param: eventinfo, source information needed for HASH format
:type: list object
:param eventinfo: source information needed for HASH format
:type eventinfo: list object
'''
# write phases to HASH-phase file
writephases(picks, 'HASH', fnout, parameter, eventinfo)

4
pylot/core/loc/hypo71.py
View File

@ -18,8 +18,8 @@ def export(picks, fnout, parameter):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
'''
# write phases to HYPO71-phase file
writephases(picks, 'HYPO71', fnout, parameter)

8
pylot/core/loc/hypodd.py
View File

@ -18,11 +18,11 @@ def export(picks, fnout, parameter, eventinfo):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
:param: eventinfo, source information needed for hypoDD format
:type: list object
:param eventinfo: source information needed for hypoDD format
:type eventinfo: list object
'''
# write phases to hypoDD-phase file
writephases(picks, 'hypoDD', fnout, parameter, eventinfo)

4
pylot/core/loc/hyposat.py
View File

@ -18,8 +18,8 @@ def export(picks, fnout, parameter):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
'''
# write phases to HYPOSAT-phase file
writephases(picks, 'HYPOSAT', fnout, parameter)

20
pylot/core/loc/nll.py
View File

@ -28,8 +28,8 @@ def export(picks, fnout, parameter):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
'''
# write phases to NLLoc-phase file
writephases(picks, 'NLLoc', fnout, parameter)
@ -38,19 +38,19 @@ def export(picks, fnout, parameter):
def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
'''
:param ctrfn: name of NLLoc-control file
:type: str
:type ctrfn: str
:param root: root path to NLLoc working directory
:type: str
:type root: str
:param nllocoutn: name of NLLoc-location output file
:type: str
:type nllocoutn: str
:param phasefn: name of NLLoc-input phase file
:type: str
:type phasefn: str
:param tttn: pattern of precalculated NLLoc traveltime tables
:type: str
:type tttn: str
'''
# For locating the event the NLLoc-control file has to be modified!
# create comment line for NLLoc-control file NLLoc-output file
@ -75,9 +75,9 @@ def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
def locate(fnin, infile=None):
"""
takes an external program name
:param fnin:
:return:
takes an external program name and tries to run it
:param fnin: external program name
:return: None
"""
if infile is None:

8
pylot/core/loc/velest.py
View File

@ -18,11 +18,11 @@ def export(picks, fnout, eventinfo, parameter=None):
:param fnout: complete path to the exporting obs file
:type fnout: str
:param: eventinfo, source time needed for VELEST-cnv format
:type: list object
:param eventinfo: source time needed for VELEST-cnv format
:type eventinfo: list object
:param: parameter, all input information
:type: object
:param parameter: all input information
:type parameter: object
'''
# write phases to VELEST-phase file
writephases(picks, 'VELEST', fnout, parameter, eventinfo)

2
pylot/core/pick/autopick.py
View File

@ -155,7 +155,7 @@ def autopickstation(wfstream, pickparam, verbose=False,
:type metadata: tuple (str, ~obspy.io.xseed.parser.Parser)
:param origin: list containing origin objects representing origins for all events
:type origin: list(~obspy.core.event.origin)
:return: :dictionary containing P pick, S pick and station name
:return: dictionary containing P pick, S pick and station name
:rtype: dict
"""

71
pylot/core/pick/picker.py
View File

@ -29,38 +29,36 @@ from pylot.core.pick.utils import getnoisewin, getsignalwin
class AutoPicker(object):
'''
"""
Superclass of different, automated picking algorithms applied on a CF determined
using AIC, HOS, or AR prediction.
'''
"""
warnings.simplefilter('ignore')
def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None, fig=None, linecolor='k'):
'''
:param: cf, characteristic function, on which the picking algorithm is applied
:type: `~pylot.core.pick.CharFuns.CharacteristicFunction` object
:param: TSNR, length of time windows around pick used to determine SNR [s]
:type: tuple (T_noise, T_gap, T_signal)
:param: PickWindow, length of pick window [s]
:type: float
:param: iplot, no. of figure window for plotting interims results
:type: integer
:param: aus ("artificial uplift of samples"), find local minimum at i if aic(i-1)*(1+aus) >= aic(i)
:type: float
:param: Tsmooth, length of moving smoothing window to calculate smoothed CF [s]
:type: float
:param: Pick1, initial (prelimenary) onset time, starting point for PragPicker and
EarlLatePicker
:type: float
'''
"""
Create AutoPicker object
:param cf: characteristic function, on which the picking algorithm is applied
:type cf: `~pylot.core.pick.CharFuns.CharacteristicFunction`
:param TSNR: length of time windows around pick used to determine SNR [s], tuple (T_noise, T_gap, T_signal)
:type TSNR: (float, float, float)
:param PickWindow: length of pick window [s]
:type PickWindow: float
:param iplot: flag used for plotting, if > 1, results will be plotted. Use iplot = 0 to disable plotting
:type iplot: int
:param aus: ("artificial uplift of samples"), find local minimum at i if aic(i-1)*(1+aus) >= aic(i)
:type aus: float
:param Tsmooth: length of moving smoothing window to calculate smoothed CF [s]
:type Tsmooth: float
:param Pick1: initial (preliminary) onset time, starting point for PragPicker and EarlLatePicker
:type Pick1: float
:param fig: matplotlib figure used for plotting. If not given and plotting is enabled, a new figure will
be created
:type fig: `~matplotlib.figure.Figure`
:param linecolor: matplotlib line color string
:type linecolor: str
"""
assert isinstance(cf, CharacteristicFunction), "%s is not a CharacteristicFunction object" % str(cf)
self._linecolor = linecolor
@ -79,6 +77,11 @@ class AutoPicker(object):
self.calcPick()
def __str__(self):
"""
String representation of AutoPicker object
:return:
:rtype: str
"""
return '''\n\t{name} object:\n
TSNR:\t\t\t{TSNR}\n
PickWindow:\t{PickWindow}\n
@ -142,12 +145,12 @@ class AutoPicker(object):
class AICPicker(AutoPicker):
'''
"""
Method to derive the onset time of an arriving phase based on CF
derived from AIC. In order to get an impression of the quality of this inital pick,
derived from AIC. In order to get an impression of the quality of this initial pick,
a quality assessment is applied based on SNR and slope determination derived from the CF,
from which the AIC has been calculated.
'''
"""
def calcPick(self):
@ -214,6 +217,12 @@ class AICPicker(AutoPicker):
self.Pick = self.Tcf[i]
break
def calcPick(self):
"""
Calculate pick using cf derived from AIC
:return:
:rtype: None
"""
# quality assessment using SNR and slope from CF
if self.Pick is not None:
# get noise window
@ -364,9 +373,9 @@ class AICPicker(AutoPicker):
class PragPicker(AutoPicker):
'''
"""
Method of pragmatic picking exploiting information given by CF.
'''
"""
def calcPick(self):

7
pylot/core/util/connection.py
View File

@ -8,6 +8,13 @@ except:
def checkurl(url='https://ariadne.geophysik.ruhr-uni-bochum.de/trac/PyLoT/'):
"""
check if URL is available
:param url: url
:type url: str
:return: available: True/False
:rtype: bool
"""
try:
urlopen(url, timeout=1)
return True

154
pylot/core/util/event.py
View File

@ -15,6 +15,11 @@ class Event(ObsPyEvent):
'''
def __init__(self, path):
"""
Initialize event by event directory
:param path: path to event directory
:type path: str
"""
self.pylot_id = path.split('/')[-1]
# initialize super class
super(Event, self).__init__(resource_id=ResourceIdentifier('smi:local/' + self.pylot_id))
@ -30,10 +35,20 @@ class Event(ObsPyEvent):
self.get_notes()
def get_notes_path(self):
"""
Notes files is freely editable by the user and can contain notes regarding the event
:return: path to notes file
:rtype: str
"""
notesfile = os.path.join(self.path, 'notes.txt')
return notesfile
def get_notes(self):
"""
set self.note attribute to content of notes file
:return:
:rtype: None
"""
notesfile = self.get_notes_path()
if os.path.isfile(notesfile):
with open(notesfile) as infile:
@ -48,34 +63,81 @@ class Event(ObsPyEvent):
pass
def addNotes(self, notes):
"""
Set new notes string
:param notes: notes to save in Event object
:type notes: str
:return:
:rtype: None
"""
self.notes = str(notes)
def clearNotes(self):
"""
Clear event notes
:return:
:rtype: None
"""
self.notes = None
def isRefEvent(self):
"""
Return reference event flag
:return: True if event is refence event
:rtype: bool
"""
return self._refEvent
def isTestEvent(self):
"""
Return test event flag
:return: True if event is test event
:rtype: bool
"""
return self._testEvent
def setRefEvent(self, bool):
"""
Set reference event flag
:param bool: new reference event flag
:type bool: bool
:return:
:rtype: None
"""
self._refEvent = bool
if bool: self._testEvent = False
def setTestEvent(self, bool):
"""
Set test event flag
:param bool: new test event flag
:type bool: bool
:return:
:rtype: None
"""
self._testEvent = bool
if bool: self._refEvent = False
def clearObsPyPicks(self, picktype):
"""
Remove picks of a certain type from event
:param picktype: type of picks to remove, 'auto' or 'manual'
:type picktype: str
:return:
:rtype: None
"""
for index, pick in reversed(list(enumerate(self.picks))):
if picktype in str(pick.method_id):
self.picks.pop(index)
def addPicks(self, picks):
'''
"""
add pylot picks and overwrite existing ones
'''
:param picks: picks to add to event in pick dictionary
:type picks: dict
:return:
:rtype: None
"""
for station in picks:
self.pylot_picks[station] = picks[station]
# add ObsPy picks (clear old manual and copy all new manual from pylot)
@ -83,6 +145,13 @@ class Event(ObsPyEvent):
self.picks += picks_from_picksdict(self.pylot_picks)
def addAutopicks(self, autopicks):
"""
Add automatic picks to event
:param autopicks: automatic picks to add to event
:type autopicks dict:
:return:
:rtype: None
"""
for station in autopicks:
self.pylot_autopicks[station] = autopicks[station]
# add ObsPy picks (clear old auto and copy all new auto from pylot)
@ -90,6 +159,15 @@ class Event(ObsPyEvent):
self.picks += picks_from_picksdict(self.pylot_autopicks)
def setPick(self, station, pick):
"""
Set pick for a station
:param station: station name
:type station: str
:param pick:
:type pick: dict
:return:
:rtype:
"""
if pick:
self.pylot_picks[station] = pick
else:
@ -101,21 +179,46 @@ class Event(ObsPyEvent):
self.picks += picks_from_picksdict(self.pylot_picks)
def setPicks(self, picks):
'''
set pylot picks and delete and overwrite all existing
'''
"""
Set pylot picks and delete and overwrite all existing
:param picks: new picks
:type picks: dict
:return:
:rtype: None
"""
self.pylot_picks = picks
self.clearObsPyPicks('manual')
self.picks += picks_from_picksdict(self.pylot_picks)
def getPick(self, station):
"""
Get pick at station
:param station: station name
:type station: str
:return: pick dictionary of station
:rtype: dict
"""
if station in self.pylot_picks.keys():
return self.pylot_picks[station]
def getPicks(self):
"""
Return pylot picks
:return:
:rtype: dict
"""
return self.pylot_picks
def setAutopick(self, station, pick):
"""
Set pick at station
:param station: station name
:type station: str
:param pick:
:type pick: dict
:return:
:rtype: None
"""
if pick:
self.pylot_autopicks[station] = pick
else:
@ -127,25 +230,46 @@ class Event(ObsPyEvent):
self.picks += picks_from_picksdict(self.pylot_autopicks)
def setAutopicks(self, picks):
'''
set pylot picks and delete and overwrite all existing
'''
"""
Set pylot picks and delete and overwrite all existing
:param picks: new picks
:type picks: dict
:return:
:rtype: None
"""
self.pylot_autopicks = picks
self.clearObsPyPicks('auto')
self.picks += picks_from_picksdict(self.pylot_autopicks)
def getAutopick(self, station):
"""
Return autopick at station
:param station: station name
:type station: str
:return: pick dictionary
:rtype: dict
"""
if station in self.pylot_autopicks.keys():
return self.pylot_autopicks[station]
def getAutopicks(self):
"""
Get autopicks of event
:return: dict containing automatic picks
:rtype: dict
"""
return self.pylot_autopicks
def save(self, filename):
'''
"""
Save PyLoT Event to a file.
Can be loaded by using event.load(filename).
'''
Uses pickling to save event object to file
:param filename: filename to save project under
:type filename: str
:return:
:rtype: None
"""
try:
import cPickle
except ImportError:
@ -159,9 +283,13 @@ class Event(ObsPyEvent):
@staticmethod
def load(filename):
'''
Load project from filename.
'''
"""
Load project from filename
:param filename: to load event file
:type filename: str
:return: event loaded from file
:rtype: Event
"""
try:
import cPickle
except ImportError: