Sebastianw Wehling-Benatelli
438b2706b7
with the last update of obspy some modules and functions names will be removed in future releases and consequently have been marked as deprecated; PyLoT now uses the desired names
739 lines
22 KiB
Python
739 lines
22 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os
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import glob
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from obspy.io.xseed import Parser
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from obspy.core import read, Stream, UTCDateTime
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from obspy import read_events, read_inventory
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from obspy.core.event import Event, ResourceIdentifier, Pick, WaveformStreamID
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from pylot.core.read.io import readPILOTEvent
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from pylot.core.util.utils import fnConstructor, getGlobalTimes
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from pylot.core.util.errors import FormatError, OverwriteError
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class Data(object):
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"""
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Data container with attributes wfdata holding ~obspy.core.stream.
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:type parent: PySide.QtGui.QWidget object, optional
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:param parent: A PySide.QtGui.QWidget object utilized when
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called by a GUI to display a PySide.QtGui.QMessageBox instead of printing
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to standard out.
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:type evtdata: ~obspy.core.event.Event object, optional
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:param evtdata ~obspy.core.event.Event object containing all derived or
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loaded event. Container object holding, e.g. phase arrivals, etc.
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"""
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def __init__(self, parent=None, evtdata=None):
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self._parent = parent
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if self.getParent():
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self.comp = parent.getComponent()
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else:
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self.comp = 'Z'
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self.wfdata = Stream()
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self._new = False
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if isinstance(evtdata, Event):
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self.evtdata = evtdata
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elif isinstance(evtdata, dict):
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evt = readPILOTEvent(**evtdata)
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self.evtdata = evt
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elif evtdata:
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cat = read_events(evtdata)
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self.evtdata = cat[0]
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else: # create an empty Event object
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self.setNew()
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self.evtdata = Event()
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self.getEvtData().picks = []
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self.wforiginal = None
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self.cuttimes = None
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self.dirty = False
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def __str__(self):
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return str(self.wfdata)
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def __add__(self, other):
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assert isinstance(other, Data), "operands must be of same type 'Data'"
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if other.isNew() and not self.isNew():
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picks_to_add = other.getEvtData().picks
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old_picks = self.getEvtData().picks
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for pick in picks_to_add:
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if pick not in old_picks:
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old_picks.append(pick)
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elif not other.isNew() and self.isNew():
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new = other + self
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self.evtdata = new.getEvtData()
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elif self.isNew() and other.isNew():
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pass
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elif self.getEvtData().get('id') == other.getEvtData().get('id'):
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other.setNew()
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return self + other
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else:
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raise ValueError("both Data objects have differing "
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"unique Event identifiers")
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return self
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def getPicksStr(self):
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picks_str = ''
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for pick in self.getEvtData().picks:
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picks_str += str(pick) + '\n'
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return picks_str
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def getParent(self):
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"""
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:return:
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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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self._new = True
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def getCutTimes(self):
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"""
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:return:
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"""
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if self.cuttimes is None:
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self.updateCutTimes()
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return self.cuttimes
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def updateCutTimes(self):
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"""
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"""
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self.cuttimes = getGlobalTimes(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 exportEvent(self, fnout, fnext='.xml'):
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"""
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:param fnout:
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:param fnext:
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:raise KeyError:
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"""
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from pylot.core.util.defaults import OUTPUTFORMATS
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try:
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evtformat = OUTPUTFORMATS[fnext]
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except KeyError as e:
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errmsg = '{0}; selected file extension {1} not ' \
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'supported'.format(e, fnext)
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raise FormatError(errmsg)
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# try exporting event via ObsPy
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try:
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self.getEvtData().write(fnout + fnext, format=evtformat)
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except KeyError as e:
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raise KeyError('''{0} export format
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not implemented: {1}'''.format(evtformat, e))
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def getComp(self):
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"""
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:return:
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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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"""
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try:
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return self.evtdata.get('resource_id').id
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except:
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return None
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def filterWFData(self, kwargs):
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"""
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:param kwargs:
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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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"""
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self.wfdata = Stream()
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self.wforiginal = None
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if fnames is not None:
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self.appendWFData(fnames)
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else:
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return False
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self.wforiginal = self.getWFData().copy()
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self.dirty = False
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return True
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def appendWFData(self, fnames):
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"""
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:param fnames:
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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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"but is actually" \
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" {0}".format(type(fnames))
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if self.dirty:
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self.resetWFData()
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warnmsg = ''
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for fname in fnames:
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try:
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self.wfdata += read(fname)
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except TypeError:
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try:
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self.wfdata += read(fname, format='GSE2')
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except Exception as e:
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warnmsg += '{0}\n{1}\n'.format(fname, e)
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if warnmsg:
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warnmsg = 'WARNING: unable to read\n' + warnmsg
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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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"""
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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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"""
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self.getEvtData().picks = []
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def restituteWFData(self, invdlpath, streams=None):
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"""
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:param invdlpath:
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:param streams:
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:return:
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"""
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restflag = 0
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if streams is None:
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st_raw = self.getWFData()
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st = st_raw.copy()
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else:
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st = streams
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for tr in st:
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# remove underscores
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if len(tr.stats.station) > 3 and tr.stats.station[3] == '_':
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tr.stats.station = tr.stats.station[0:3]
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dlp = '%s/*.dless' % invdlpath
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invp = '%s/*.xml' % invdlpath
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respp = '%s/*.resp' % invdlpath
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dlfile = glob.glob(dlp)
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invfile = glob.glob(invp)
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respfile = glob.glob(respp)
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# check for dataless-SEED file
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if len(dlfile) >= 1:
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print("Found dataless-SEED file(s)!")
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print("Reading meta data information ...")
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for j in range(len(dlfile)):
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print("Found dataless-SEED file %s" % dlfile[j])
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parser = Parser('%s' % dlfile[j])
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for i in range(len(st)):
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# check, whether this trace has already been corrected
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try:
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st[i].stats.processing
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except:
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try:
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print(
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"Correcting %s, %s for instrument response "
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"..." % (st[i].stats.station,
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st[i].stats.channel))
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# get corner frequencies for pre-filtering
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fny = st[i].stats.sampling_rate / 2
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fc21 = fny - (fny * 0.05)
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fc22 = fny - (fny * 0.02)
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prefilt = [0.5, 0.9, fc21, fc22]
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# instrument correction
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st[i].simulate(pre_filt=prefilt,
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seedresp={'filename': parser,
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'date': st[
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i].stats.starttime,
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'units': "VEL"})
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restflag = 1
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except ValueError as e:
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vmsg = '{0}'.format(e)
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print(vmsg)
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else:
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print("Trace has already been corrected!")
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# check for inventory-xml file
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if len(invfile) >= 1:
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print("Found inventory-xml file(s)!")
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print("Reading meta data information ...")
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for j in range(len(invfile)):
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print("Found inventory-xml file %s" % invfile[j])
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inv = read_inventory(invfile[j], format="STATIONXML")
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for i in range(len(st)):
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# check, whether this trace has already been corrected
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try:
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st[i].stats.processing
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except:
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try:
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print("Correcting %s, %s for instrument response "
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"..." % (st[i].stats.station,
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st[i].stats.channel))
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# get corner frequencies for pre-filtering
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fny = st[i].stats.sampling_rate / 2
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fc21 = fny - (fny * 0.05)
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fc22 = fny - (fny * 0.02)
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prefilt = [0.5, 0.9, fc21, fc22]
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# instrument correction
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st[i].attach_response(inv)
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st[i].remove_response(output='VEL',
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pre_filt=prefilt)
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restflag = 1
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except ValueError as e:
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vmsg = '{0}'.format(e)
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print(vmsg)
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else:
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print("Trace has already been corrected!")
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# check for RESP-file
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if len(respfile) >= 1:
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print("Found response file(s)!")
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print("Reading meta data information ...")
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for j in range(len(respfile)):
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print("Found RESP-file %s" % respfile[j])
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for i in range(len(st)):
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# check, whether this trace has already been corrected
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try:
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st[i].stats.processing
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except:
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try:
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print("Correcting %s, %s for instrument response "
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"..." % (st[i].stats.station,
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st[i].stats.channel))
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# get corner frequencies for pre-filtering
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fny = st[i].stats.sampling_rate / 2
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fc21 = fny - (fny * 0.05)
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fc22 = fny - (fny * 0.02)
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prefilt = [0.5, 0.9, fc21, fc22]
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# instrument correction
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seedresp = {'filename': respfile[0],
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'date': st[0].stats.starttime,
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'units': "VEL"}
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st[i].simulate(paz_remove=None, pre_filt=prefilt,
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seedresp=seedresp)
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restflag = 1
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except ValueError as e:
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vmsg = '{0}'.format(e)
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print(vmsg)
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else:
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print("Trace has already been corrected!")
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if len(respfile) < 1 and len(invfile) < 1 and len(dlfile) < 1:
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print("No dataless-SEED file,inventory-xml file nor RESP-file "
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"found!")
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print("Go on processing data without source parameter "
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"determination!")
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return st, restflag
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def getEvtData(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, type='pick', authority_id='rub'):
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"""
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:param data:
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:param type:
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:param authority_id:
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:raise OverwriteError:
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"""
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def applyPicks(picks):
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"""
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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.
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:param picks:
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:raise OverwriteError: raises an OverwriteError if the picks list is
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not empty. The GUI will then ask for a decision.
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"""
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firstonset = None
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if self.getEvtData().picks:
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raise OverwriteError('Actual picks would be overwritten!')
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for station, onsets in picks.items():
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print('Reading picks on station %s' % station)
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for label, phase in onsets.items():
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onset = phase['mpp']
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epp = phase['epp']
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lpp = phase['lpp']
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error = phase['spe']
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pick = Pick()
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pick.time = onset
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pick.time_errors.lower_uncertainty = onset - epp
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pick.time_errors.upper_uncertainty = lpp - onset
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pick.time_errors.uncertainty = error
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pick.phase_hint = label
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pick.waveform_id = WaveformStreamID(station_code=station)
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self.getEvtData().picks.append(pick)
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try:
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polarity = phase['fm']
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except KeyError as e:
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print('No polarity information found for %s' % phase)
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if firstonset is None or firstonset > onset:
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firstonset = onset
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if 'smi:local' in self.getID() and firstonset:
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fonset_str = firstonset.strftime('%Y_%m_%d_%H_%M_%S')
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ID = ResourceIdentifier('event/' + fonset_str)
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ID.convertIDToQuakeMLURI(authority_id=authority_id)
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self.getEvtData().resource_id = ID
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else:
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print('No picks to apply!')
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def applyArrivals(arrivals):
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"""
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:param arrivals:
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"""
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pass
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def applyEvent(event):
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"""
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:param event:
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"""
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if not self.isNew():
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self.setEvtData(event)
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else:
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raise OverwriteError('Acutal event would be overwritten!')
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applydata = {'pick': applyPicks,
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'arrival': applyArrivals,
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'event': applyEvent}
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applydata[type](data)
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class GenericDataStructure(object):
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"""
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GenericDataBase type holds all information about the current data-
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base working on.
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"""
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def __init__(self, **kwargs):
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self.allowedFields = []
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self.expandFields = ['root']
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self.dsFields = {}
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self.modifyFields(**kwargs)
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def modifyFields(self, **kwargs):
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"""
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:param kwargs:
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"""
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assert isinstance(kwargs, dict), 'dictionary type object expected'
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if not self.extraAllowed():
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kwargs = self.updateNotAllowed(kwargs)
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for key, value in kwargs.iteritems():
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key = str(key).lower()
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if value is not None:
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if type(value) not in (str, int, float):
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for n, val in enumerate(value):
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value[n] = str(val)
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else:
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value = str(value)
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try:
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self.setFieldValue(key, value)
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except KeyError as e:
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errmsg = ''
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errmsg += 'WARNING:\n'
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errmsg += 'unable to set values for datastructure fields\n'
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errmsg += '%s; desired value was: %s\n' % (e, value)
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print(errmsg)
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def isField(self, key):
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"""
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:param key:
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:return:
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"""
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return key in self.getFields().keys()
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def getFieldValue(self, key):
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"""
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:param key:
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:return:
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"""
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if self.isField(key):
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return self.getFields()[key]
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else:
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return
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def setFieldValue(self, key, value):
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"""
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:param key:
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:param value:
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:raise KeyError:
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"""
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if not self.extraAllowed() and key not in self.getAllowed():
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raise KeyError
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else:
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if not self.isField(key):
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print('creating new field "%s"' % key)
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self.getFields()[key] = value
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def getFields(self):
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"""
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:return:
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"""
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return self.dsFields
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def getExpandFields(self):
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"""
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:return:
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"""
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return self.expandFields
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def setExpandFields(self, keys):
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"""
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:param keys:
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"""
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expandFields = []
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for key in keys:
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if self.isField(key):
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expandFields.append(key)
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self.expandFields = expandFields
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def getAllowed(self):
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"""
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|
|
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:return:
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"""
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return self.allowedFields
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def extraAllowed(self):
|
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"""
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|
|
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:return:
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"""
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return not self.allowedFields
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|
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def updateNotAllowed(self, kwargs):
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"""
|
|
|
|
:param kwargs:
|
|
:return:
|
|
"""
|
|
for key in kwargs:
|
|
if key not in self.getAllowed():
|
|
kwargs.__delitem__(key)
|
|
return kwargs
|
|
|
|
def hasSuffix(self):
|
|
"""
|
|
|
|
|
|
:return:
|
|
"""
|
|
try:
|
|
self.getFieldValue('suffix')
|
|
except KeyError:
|
|
return False
|
|
else:
|
|
if self.getFieldValue('suffix'):
|
|
return True
|
|
return False
|
|
|
|
def expandDataPath(self):
|
|
"""
|
|
|
|
|
|
:return:
|
|
"""
|
|
expandList = []
|
|
for item in self.getExpandFields():
|
|
expandList.append(self.getFieldValue(item))
|
|
if self.hasSuffix():
|
|
expandList.append('*%s' % self.getFieldValue('suffix'))
|
|
return os.path.join(*expandList)
|
|
|
|
def getCatalogName(self):
|
|
"""
|
|
|
|
|
|
:return:
|
|
"""
|
|
return os.path.join(self.getFieldValue('root'), 'catalog.qml')
|
|
|
|
|
|
class PilotDataStructure(GenericDataStructure):
|
|
"""
|
|
Object containing the data access information for the old PILOT data
|
|
structure.
|
|
"""
|
|
|
|
def __init__(self, **fields):
|
|
if not fields:
|
|
fields = {'database': '2006.01',
|
|
'root': '/data/Egelados/EVENT_DATA/LOCAL'}
|
|
|
|
GenericDataStructure.__init__(self, **fields)
|
|
|
|
self.setExpandFields(['root', 'database'])
|
|
|
|
|
|
class SeiscompDataStructure(GenericDataStructure):
|
|
"""
|
|
Dictionary containing the data access information for an SDS data archive:
|
|
|
|
:param str dataType: Desired data type. Default: ``'waveform'``
|
|
:param sdate, edate: Either date string or an instance of
|
|
:class:`obspy.core.utcdatetime.UTCDateTime. Default: ``None``
|
|
:type sdate, edate: str or UTCDateTime or None
|
|
"""
|
|
|
|
def __init__(self, rootpath='/data/SDS', dataformat='MSEED',
|
|
filesuffix=None, **kwargs):
|
|
super(GenericDataStructure, self).__init__()
|
|
|
|
edate = UTCDateTime()
|
|
halfyear = UTCDateTime('1970-07-01')
|
|
sdate = UTCDateTime(edate - halfyear)
|
|
del halfyear
|
|
|
|
year = ''
|
|
if not edate.year == sdate.year:
|
|
nyears = edate.year - sdate.year
|
|
for yr in range(nyears):
|
|
year += '{0:04d},'.format(sdate.year + yr)
|
|
year = '{' + year[:-1] + '}'
|
|
else:
|
|
year = '{0:04d}'.format(sdate.year)
|
|
|
|
# SDS fields' default values
|
|
# definitions from
|
|
# http://www.seiscomp3.org/wiki/doc/applications/slarchive/SDS
|
|
|
|
self.dsFields = {'root': '/data/SDS', 'YEAR': year, 'NET': '??',
|
|
'STA': '????', 'CHAN': 'HH?', 'TYPE': 'D', 'LOC': '',
|
|
'DAY': '{0:03d}'.format(sdate.julday)
|
|
}
|
|
self.modifiyFields(**kwargs)
|
|
|
|
def modifiyFields(self, **kwargs):
|
|
"""
|
|
|
|
:param kwargs:
|
|
"""
|
|
if kwargs and isinstance(kwargs, dict):
|
|
for key, value in kwargs.iteritems():
|
|
key = str(key)
|
|
if type(value) not in (str, int, float):
|
|
for n, val in enumerate(value):
|
|
value[n] = str(val)
|
|
else:
|
|
value = str(value)
|
|
try:
|
|
self.setFieldValue(key, value)
|
|
except KeyError as e:
|
|
errmsg = ''
|
|
errmsg += 'WARNING:\n'
|
|
errmsg += 'unable to set values for SDS fields\n'
|
|
errmsg += '%s; desired value was: %s\n' % (e, value)
|
|
print(errmsg)
|
|
|
|
def setFieldValue(self, key, value):
|
|
"""
|
|
|
|
:param key:
|
|
:param value:
|
|
"""
|
|
if self.isField(key):
|
|
self.getFields()[key] = value
|
|
else:
|
|
print('Warning: trying to set value of non-existent field '
|
|
'{field}'.format(field=key))
|
|
|
|
def expandDataPath(self):
|
|
"""
|
|
|
|
|
|
:return:
|
|
"""
|
|
fullChan = '{0}.{1}'.format(self.getFields()['CHAN'], self.getType())
|
|
dataPath = os.path.join(self.getFields()['SDSdir'],
|
|
self.getFields()['YEAR'],
|
|
self.getFields()['NET'],
|
|
self.getFields()['STA'],
|
|
fullChan,
|
|
'*{0}'.format(self.getFields()['DAY']))
|
|
return dataPath
|