[add] docstrings in pylot/core/io
This commit is contained in:
Darius Arnold
parent
b2f211516a
commit
6aacd2dd55
@ -99,6 +99,11 @@ class Data(object):
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return self
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def getPicksStr(self):
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"""
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Return picks in event data
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:return: picks seperated by newlines
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:rtype: str
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"""
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picks_str = ''
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for pick in self.get_evt_data().picks:
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picks_str += str(pick) + '\n'
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@ -106,18 +111,11 @@ class Data(object):
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def getParent(self):
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"""
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:return:
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Get PySide.QtGui.QWidget parent object
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"""
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return self._parent
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def isNew(self):
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"""
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:return:
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"""
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return self._new
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def setNew(self):
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@ -125,9 +123,9 @@ class Data(object):
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def getCutTimes(self):
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"""
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:return:
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Returns earliest start and latest end of all waveform data
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:return: minimum start time and maximum end time as a tuple
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:rtype: (UTCDateTime, UTCDateTime)
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"""
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if self.cuttimes is None:
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self.updateCutTimes()
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@ -135,22 +133,34 @@ class Data(object):
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def updateCutTimes(self):
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"""
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Update cuttimes to contain earliest start and latest end time
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of all waveform data
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:rtype: None
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"""
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self.cuttimes = full_range(self.getWFData())
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def getEventFileName(self):
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"""
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:return:
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"""
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ID = self.getID()
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# handle forbidden filenames especially on windows systems
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return fnConstructor(str(ID))
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def checkEvent(self, event, fcheck, forceOverwrite=False):
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"""
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Check information in supplied event and own event and replace own
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information with supplied information if own information not exiisting
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or forced by forceOverwrite
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param fcheck: check and delete existing information
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can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
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:type fcheck: str, [str]
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:param forceOverwrite: Set to true to force overwrite own information. If false,
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supplied information from event is only used if there is no own information in that
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category (given in fcheck: manual, auto, origin, magnitude)
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:type forceOverwrite: bool
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:return:
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:rtype: None
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"""
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if 'origin' in fcheck:
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self.replaceOrigin(event, forceOverwrite)
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if 'magnitude' in fcheck:
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@ -161,18 +171,47 @@ class Data(object):
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self.replacePicks(event, 'manual')
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def replaceOrigin(self, event, forceOverwrite=False):
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"""
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Replace own origin with the one supplied in event if own origin is not
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existing or forced by forceOverwrite = True
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param forceOverwrite: always replace own information with supplied one if true
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:type forceOverwrite: bool
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:return:
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:rtype: None
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"""
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if self.get_evt_data().origins or forceOverwrite:
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if event.origins:
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print("Found origin, replace it by new origin.")
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event.origins = self.get_evt_data().origins
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def replaceMagnitude(self, event, forceOverwrite=False):
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"""
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Replace own magnitude with the one supplied in event if own magnitude is not
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existing or forced by forceOverwrite = True
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param forceOverwrite: always replace own information with supplied one if true
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:type forceOverwrite: bool
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:return:
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:rtype: None
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"""
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if self.get_evt_data().magnitudes or forceOverwrite:
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if event.magnitudes:
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print("Found magnitude, replace it by new magnitude")
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event.magnitudes = self.get_evt_data().magnitudes
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def replacePicks(self, event, picktype):
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"""
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Replace own picks with the one in event
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:param event: Event that supplies information for comparison
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:type event: pylot.core.util.event.Event
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:param picktype: 'auto' or 'manual' picks
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:type picktype: str
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:return:
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:rtype: None
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"""
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checkflag = 0
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picks = event.picks
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# remove existing picks
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@ -189,10 +228,10 @@ class Data(object):
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picks.append(pick)
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def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
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"""
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Export event to file
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:param fnout: basename of file
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:param fnext: file extension
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:param fnext: file extension, xml, cnv, obs
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:param fcheck: check and delete existing information
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can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
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"""
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@ -304,17 +343,13 @@ class Data(object):
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def getComp(self):
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"""
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:return:
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Get component (ZNE)
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"""
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return self.comp
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def getID(self):
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"""
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:return:
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Get unique resource id
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"""
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try:
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return self.evtdata.get('resource_id').id
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@ -323,16 +358,17 @@ class Data(object):
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def filterWFData(self, kwargs):
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"""
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:param kwargs:
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Filter waveform data
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:param kwargs: arguments to pass through to filter function
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"""
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self.getWFData().filter(**kwargs)
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self.dirty = True
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def setWFData(self, fnames):
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"""
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:param fnames:
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Clear current waveform data and set given waveform data
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:param fnames: waveform data names to append
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:type fnames: list
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"""
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self.wfdata = Stream()
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self.wforiginal = None
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@ -346,8 +382,9 @@ class Data(object):
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def appendWFData(self, fnames):
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"""
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:param fnames:
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Read waveform data from fnames and append it to current wf data
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:param fnames: waveform data to append
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:type fnames: list
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"""
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assert isinstance(fnames, list), "input parameter 'fnames' is " \
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"supposed to be of type 'list' " \
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@ -372,54 +409,42 @@ class Data(object):
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print(warnmsg)
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def getWFData(self):
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"""
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:return:
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"""
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return self.wfdata
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def getOriginalWFData(self):
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"""
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:return:
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"""
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return self.wforiginal
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def resetWFData(self):
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"""
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Set waveform data to original waveform data
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"""
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self.wfdata = self.getOriginalWFData().copy()
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self.dirty = False
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def resetPicks(self):
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"""
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Clear all picks from event
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"""
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self.get_evt_data().picks = []
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def get_evt_data(self):
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"""
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:return:
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"""
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return self.evtdata
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def setEvtData(self, event):
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self.evtdata = event
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def applyEVTData(self, data, typ='pick', authority_id='rub'):
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"""
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:param data:
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:param typ:
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:param authority_id:
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Either takes an `obspy.core.event.Event` object and applies all new
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information on the event to the actual data if typ is 'event or
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creates ObsPy pick objects and append it to the picks list from the
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PyLoT dictionary contain all picks if type is pick
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:param data: data to apply, either picks or complete event
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:type data:
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:param typ: which event data to apply, 'pick' or 'event'
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:type typ: str
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:param authority_id: (currently unused)
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:type: str
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:raise OverwriteError:
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"""
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@ -1,6 +1,10 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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"""
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Default parameters used for picking
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"""
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defaults = {'rootpath': {'type': str,
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'tooltip': 'project path',
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'value': '',
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@ -70,6 +70,7 @@ class PylotParameter(object):
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# Set default values of parameter names
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def __init_default_paras(self):
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"""set default values of parameter names"""
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parameters = default_parameters.defaults
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self.__defaults = parameters
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@ -104,15 +105,34 @@ class PylotParameter(object):
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return len(self.__parameter.keys())
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def iteritems(self):
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"""
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Iterate over parameters
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:return: key, value tupel
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:rtype:
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"""
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for key, value in self.__parameter.items():
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yield key, value
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def hasParam(self, parameter):
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"""
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Check if parameter is in keys
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:param parameter: parameter to look for in keys
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:type parameter:
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:return:
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:rtype: bool
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"""
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if parameter in self.__parameter.keys():
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return True
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return False
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def get(self, *args):
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"""
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Get first available parameter in args
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:param args:
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:type args:
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:return:
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:rtype:
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"""
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try:
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for param in args:
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try:
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@ -128,15 +148,35 @@ class PylotParameter(object):
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raise ParameterError(e)
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def get_defaults(self):
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"""
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get default parameters
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:return:
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:rtype: dict
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"""
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return self.__defaults
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def get_main_para_names(self):
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"""
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Get main parameter names
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:return: list of keys available in parameters
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:rtype:
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"""
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return self._settings_main
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def get_special_para_names(self):
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"""
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Get pick parameter names
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:return: list of keys available in parameters
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:rtype:
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"""
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return self._settings_special_pick
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def get_all_para_names(self):
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"""
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Get all parameter names
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:return:
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:rtype: list
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"""
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all_names = []
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all_names += self.get_main_para_names()['dirs']
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all_names += self.get_main_para_names()['nlloc']
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@ -151,6 +191,16 @@ class PylotParameter(object):
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return all_names
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def checkValue(self, param, value):
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"""
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Check type of value against expected type of param.
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Print warning message if type check fails
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:param param:
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:type param:
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:param value:
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:type value:
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:return:
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:rtype:
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"""
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is_type = type(value)
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expect_type = self.get_defaults()[param]['type']
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if not is_type == expect_type and not is_type == tuple:
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@ -159,9 +209,25 @@ class PylotParameter(object):
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print(Warning(message))
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def setParamKV(self, param, value):
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"""
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set parameter param to value
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:param param:
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:type param:
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:param value:
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:type value:
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:return:
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:rtype: None
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"""
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self.__setitem__(param, value)
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def setParam(self, **kwargs):
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"""
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Set multiple parameters
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:param kwargs:
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:type kwargs:
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:return:
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:rtype: None
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"""
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for key in kwargs:
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self.__setitem__(key, kwargs[key])
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@ -170,11 +236,23 @@ class PylotParameter(object):
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print('ParameterError:\n non-existent parameter %s' % errmsg)
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def reset_defaults(self):
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"""
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Reset current parameters to default parameters
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:return:
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:rtype: None
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"""
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defaults = self.get_defaults()
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for param in defaults:
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self.setParamKV(param, defaults[param]['value'])
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def from_file(self, fnin=None):
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"""
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read parameters from file and set values to read values
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:param fnin: filename
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:type fnin:
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:return:
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:rtype: None
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"""
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if not fnin:
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if self.__filename is not None:
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fnin = self.__filename
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@ -221,6 +299,13 @@ class PylotParameter(object):
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self.__parameter = self._parFileCont
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def export2File(self, fnout):
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"""
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Export parameters to file
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:param fnout: Filename of export file
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:type fnout: str
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:return:
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:rtype:
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"""
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fid_out = open(fnout, 'w')
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lines = []
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# for key, value in self.iteritems():
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@ -257,6 +342,19 @@ class PylotParameter(object):
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'quality assessment', None)
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def write_section(self, fid, names, title, separator):
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"""
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write a section of parameters to file
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:param fid: File object to write to
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:type fid:
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:param names: which parameter names to write to file
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:type names:
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:param title: title of section
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:type title: str
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:param separator: section separator, written at start of section
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:type separator: str
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:return:
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:rtype:
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"""
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if separator:
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fid.write(separator)
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fid.write('#{}#\n'.format(title))
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@ -54,7 +54,7 @@ def create_arrival(pickresID, cinfo, phase, azimuth=None, dist=None):
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def create_creation_info(agency_id=None, creation_time=None, author=None):
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'''
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get creation info of obspy event
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:param agency_id:
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:param creation_time:
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:param author:
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@ -197,9 +197,9 @@ def create_pick(origintime, picknum, picktime, eventnum, cinfo, phase, station,
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def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
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'''
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:param timetohash:
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:type timetohash
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create unique resource id
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:param timetohash: event origin time to hash
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:type timetohash: class: `~obspy.core.utcdatetime.UTCDateTime` object
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:param restype: type of the resource, e.g. 'orig', 'earthquake' ...
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:type restype: str
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:param authority_id: name of the institution carrying out the processing
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@ -118,6 +118,13 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
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def picksdict_from_pilot(fn):
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"""
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Create pick dictionary from matlab file
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:param fn: matlab file
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:type fn:
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:return: pick dictionary
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:rtype: dict
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"""
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from pylot.core.util.defaults import TIMEERROR_DEFAULTS
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picks = dict()
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phases_pilot = sio.loadmat(fn)
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@ -147,6 +154,13 @@ def picksdict_from_pilot(fn):
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def stations_from_pilot(stat_array):
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"""
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Create stations list from pilot station array
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:param stat_array:
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:type stat_array:
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:return:
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:rtype: list
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"""
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stations = list()
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cur_stat = None
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for stat in stat_array:
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@ -164,6 +178,13 @@ def stations_from_pilot(stat_array):
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def convert_pilot_times(time_array):
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"""
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Convert pilot times to UTCDateTimes
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:param time_array: pilot times
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:type time_array:
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:return:
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:rtype:
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"""
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times = [int(time) for time in time_array]
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microseconds = int((time_array[-1] - times[-1]) * 1e6)
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times.append(microseconds)
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@ -171,6 +192,13 @@ def convert_pilot_times(time_array):
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def picksdict_from_obs(fn):
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"""
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create pick dictionary from obs file
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:param fn: filename
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:type fn:
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:return:
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:rtype:
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"""
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picks = dict()
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station_name = str()
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for line in open(fn, 'r'):
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@ -240,6 +268,16 @@ def picksdict_from_picks(evt):
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def picks_from_picksdict(picks, creation_info=None):
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"""
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Create a list of picks out of a pick dictionary
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:param picks: pick dictionary
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: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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user