Pulling latest release from server ariadne.
Merge branch 'develop' of ariadne.geophysik.rub.de:/data/git/pylot into develop
This commit is contained in:
Ludger Küperkoch
commit
6ee3a1b0b4
90
autoPyLoT.py
Normal file
90
autoPyLoT.py
Normal file
@ -0,0 +1,90 @@
|
||||
#!/usr/bin/env python
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
|
||||
import os
|
||||
import argparse
|
||||
|
||||
from pylot.core.util import _getVersionString
|
||||
from pylot.core.read import Data, AutoPickParameter
|
||||
from pylot.core.pick.CharFuns import HOScf, AICcf
|
||||
from pylot.core.util.structure import DATASTRUCTURE
|
||||
|
||||
|
||||
__version__ = _getVersionString()
|
||||
|
||||
METHOD = {'HOS':HOScf, 'AIC':AICcf}
|
||||
|
||||
def autoPyLoT(fnames, inputfile):
|
||||
'''
|
||||
Determine phase onsets automatically utilizing the automatic picking
|
||||
algorithm by Kueperkoch et al. 2011.
|
||||
|
||||
:param fnames: list of strings containing the paths or urls to the
|
||||
waveform data to be picked
|
||||
:type fnames: list
|
||||
:param inputfile: path to the input file containing all parameter
|
||||
information for automatic picking (for formatting details, see.
|
||||
`~pylot.core.read.input.AutoPickParameter`
|
||||
:type inputfile: str
|
||||
:return:
|
||||
|
||||
.. rubric:: Example
|
||||
|
||||
'''
|
||||
parameter = AutoPickParameter(inputfile)
|
||||
|
||||
data = Data()
|
||||
|
||||
meth = parameter.getParam('algoP')
|
||||
tsnr1 = parameter.getParam('tsnr1')
|
||||
tsnr2 = parameter.getParam('tsnr2')
|
||||
tnoise = parameter.getParam('pnoiselen')
|
||||
tsignal = parameter.getParam('tlim')
|
||||
order = parameter.getParam('hosorder')
|
||||
thosmw = parameter.getParam('tlta')
|
||||
|
||||
if parameter.hasParam('datastructure'):
|
||||
datastructure = DATASTRUCTURE[parameter.getParam('datastructure')]()
|
||||
dsfields = {'root':parameter.getParam('rootpath')} #see TODO: in data.py
|
||||
datastructure.modifyFields(dsfields)
|
||||
|
||||
def expandSDS(datastructure):
|
||||
return datastructure.expandDataPath()
|
||||
|
||||
def expandPDS(datastructure):
|
||||
return os.path.join(datastructure.expandDataPath(),'*')
|
||||
|
||||
dsem = {'PDS':expandPDS, 'SDS':expandSDS}
|
||||
|
||||
expandMethod = dsem[datastructure.getName()]
|
||||
|
||||
data.setWFData(expandMethod())
|
||||
else:
|
||||
data.setWFData()
|
||||
|
||||
cfP = METHOD[meth](data.getWFData(), (tnoise, tsignal), thosmw, order)
|
||||
|
||||
if __name__ == "__main__":
|
||||
# parse arguments
|
||||
parser = argparse.ArgumentParser(
|
||||
description='''This program visualizes Probabilistic Power Spectral Densities.''')
|
||||
|
||||
parser.add_argument('-d', '-D', '--data', type=str, action='store',
|
||||
help='''path or url to the data to be picked''',
|
||||
default='http://examples.obspy.org/BW.KW1..EHZ.D.2011.037'
|
||||
)
|
||||
parser.add_argument('-i', '-I', '--inputfile', type=str,
|
||||
action='store',
|
||||
help='''full path to the file containing the input
|
||||
parameters for autoPyLoT''',
|
||||
default=os.path.join(os.path.expanduser('~'), '.pylot',
|
||||
'autoPyLoT.in')
|
||||
)
|
||||
parser.add_argument('-v', '-V', '--version', action='version',
|
||||
version='autoPyLoT ' + __version__,
|
||||
help='show version information and exit')
|
||||
|
||||
cla = parser.parse_args()
|
||||
|
||||
autoPyLoT(cla.data, str(cla.inputfile))
|
||||
@ -1 +1 @@
|
||||
043c-dirty
|
||||
694a-dirty
|
||||
|
||||
@ -53,32 +53,22 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
|
||||
#get signal window
|
||||
isignal = getsignalwin(t, Pick1, TSNR[2])
|
||||
#calculate noise level
|
||||
nlevel = max(abs(x[inoise])) * nfac
|
||||
nlevel = np.sqrt(np.mean(np.square(x[inoise]))) * nfac
|
||||
#get time where signal exceeds nlevel
|
||||
ilup = np.where(x[isignal] > nlevel)
|
||||
ildown = np.where(x[isignal] < -nlevel)
|
||||
if len(ilup[0]) <= 1 and len(ildown[0]) <= 1:
|
||||
print 'earllatepicker: Signal lower than noise level, misspick?'
|
||||
return
|
||||
il = min([ilup[0][0], ildown[0][0]])
|
||||
ilup, = np.where(x[isignal] > nlevel)
|
||||
ildown, = np.where(x[isignal] < -nlevel)
|
||||
if not ilup.size and not ildown.size:
|
||||
raise ValueError('earllatepicker: Signal lower than noise level')
|
||||
il = min(np.min(ilup) if ilup.size else float('inf'),
|
||||
np.min(ildown) if ildown.size else float('inf'))
|
||||
LPick = t[isignal][il]
|
||||
|
||||
#get earliest possible pick
|
||||
#get next 2 zero crossings after most likely pick
|
||||
#initial onset is assumed to be the first zero crossing
|
||||
zc = []
|
||||
zc.append(Pick1)
|
||||
i = 0
|
||||
for j in range(isignal[0][1], isignal[0][len(t[isignal]) - 1]):
|
||||
i = i + 1
|
||||
if x[j - 1] <= 0 and x[j] >= 0:
|
||||
zc.append(t[isignal][i])
|
||||
elif x[j - 1] > 0 and x[j] <= 0:
|
||||
zc.append(t[isignal][i])
|
||||
if len(zc) == 3:
|
||||
break
|
||||
#calculate maximum period T0 of signal out of zero crossings
|
||||
T0 = max(np.diff(zc)) #this is half wave length!
|
||||
|
||||
#determine all zero crossings in signal window
|
||||
zc = crossings_nonzero_all(x[isignal])
|
||||
#calculate mean half period T0 of signal as the average of the
|
||||
T0 = np.mean(np.diff(zc)) * X[0].stats.delta #this is half wave length!
|
||||
#T0/4 is assumed as time difference between most likely and earliest possible pick!
|
||||
EPick = Pick1 - T0 / 2
|
||||
|
||||
@ -288,6 +278,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
|
||||
|
||||
return FM
|
||||
|
||||
def crossings_nonzero_all(data):
|
||||
pos = data > 0
|
||||
npos = ~pos
|
||||
return ((pos[:-1] & npos[1:]) | (npos[:-1] & pos[1:])).nonzero()[0]
|
||||
|
||||
def getSNR(X, TSNR, t1):
|
||||
'''
|
||||
|
||||
@ -3,15 +3,13 @@
|
||||
|
||||
import os
|
||||
|
||||
import numpy as np
|
||||
from obspy.core import (read, Stream, UTCDateTime)
|
||||
from obspy import readEvents
|
||||
from obspy.core.event import (Event, Catalog)
|
||||
|
||||
from pylot.core.read import readPILOTEvent
|
||||
|
||||
from pylot.core.util import fnConstructor, createEvent, FormatError, \
|
||||
prepTimeAxis, getGlobalTimes
|
||||
from pylot.core.util import fnConstructor, FormatError, \
|
||||
getGlobalTimes
|
||||
|
||||
|
||||
class Data(object):
|
||||
@ -129,8 +127,8 @@ class Data(object):
|
||||
except TypeError:
|
||||
try:
|
||||
self.wfdata += read(fname, format='GSE2')
|
||||
except Exception:
|
||||
warnmsg += '{0}\n'.format(fname)
|
||||
except Exception, e:
|
||||
warnmsg += '{0}\n{1}\n'.format(fname, e)
|
||||
if warnmsg:
|
||||
warnmsg = 'WARNING: unable to read\n' + warnmsg
|
||||
print warnmsg
|
||||
@ -148,6 +146,7 @@ class Data(object):
|
||||
def getEvtData(self):
|
||||
return self.evtdata
|
||||
|
||||
#TODO: write superclass DataStructure instead of three fully featured individual classes
|
||||
|
||||
class GenericDataStructure(object):
|
||||
'''
|
||||
@ -157,6 +156,7 @@ class GenericDataStructure(object):
|
||||
|
||||
def __init__(self, structexp='$R/$D/$E', folderdepth=2, **kwargs):
|
||||
structureOptions = ('$R', '$D', '$E')
|
||||
self.__name = 'GDS'
|
||||
structExpression = []
|
||||
depth = 0
|
||||
while structexp is not os.path.sep:
|
||||
@ -182,6 +182,9 @@ class GenericDataStructure(object):
|
||||
key = str(key).upper()
|
||||
self.__gdsFields[key] = value
|
||||
|
||||
def getName(self):
|
||||
return self.__name
|
||||
|
||||
def getFields(self):
|
||||
return self.__gdsFields
|
||||
|
||||
@ -198,7 +201,9 @@ class PilotDataStructure(object):
|
||||
def __init__(self, dataformat='GSE2', fsuffix='gse',
|
||||
root='/data/Egelados/EVENT_DATA/LOCAL/', database='2006.01',
|
||||
**kwargs):
|
||||
self.dataType = dataformat
|
||||
self.__name = 'PDS'
|
||||
self.dataFormat = dataformat
|
||||
self.dataType = 'waveform'
|
||||
self.__pdsFields = {'ROOT': root,
|
||||
'DATABASE': database,
|
||||
'SUFFIX': fsuffix
|
||||
@ -233,6 +238,9 @@ class PilotDataStructure(object):
|
||||
def getFields(self):
|
||||
return self.__pdsFields
|
||||
|
||||
def getName(self):
|
||||
return self.__name
|
||||
|
||||
def expandDataPath(self):
|
||||
datapath = os.path.join(self.getFields()['ROOT'],
|
||||
self.getFields()['DATABASE'])
|
||||
@ -260,8 +268,8 @@ class SeiscompDataStructure(object):
|
||||
}
|
||||
|
||||
def __init__(self, dataType='waveform', sdate=None, edate=None, **kwargs):
|
||||
# imports
|
||||
from obspy.core import UTCDateTime
|
||||
|
||||
self.__name = 'SDS'
|
||||
|
||||
def checkDate(date):
|
||||
if not isinstance(date, UTCDateTime):
|
||||
@ -337,6 +345,9 @@ class SeiscompDataStructure(object):
|
||||
def getFields(self):
|
||||
return self.__sdsFields
|
||||
|
||||
def getName(self):
|
||||
return self.__name
|
||||
|
||||
def expandDataPath(self):
|
||||
fullChan = '{0}.{1}'.format(self.getFields()['CHAN'], self.getType())
|
||||
dataPath = os.path.join(self.getFields()['SDSdir'],
|
||||
|
||||
@ -5,7 +5,7 @@
|
||||
class AutoPickParameter(object):
|
||||
'''
|
||||
AutoPickParameters is a parameter type object capable to read and/or write
|
||||
parameter ASCII and binary files.
|
||||
parameter ASCII.
|
||||
|
||||
:param fn str: Filename of the input file
|
||||
|
||||
@ -34,22 +34,37 @@ class AutoPickParameter(object):
|
||||
========== ========== =======================================
|
||||
'''
|
||||
|
||||
def __init__(self, fn=None):
|
||||
def __init__(self, fnin=None, fnout=None, **kwargs):
|
||||
'''
|
||||
Initialize parameter object:
|
||||
|
||||
read content of an ASCII file an form a type consistent dictionary
|
||||
contain all parameters.
|
||||
'''
|
||||
self.__filename = fn
|
||||
|
||||
self.__filename = fnin
|
||||
parFileCont = {}
|
||||
try:
|
||||
# read from parsed arguments alternatively
|
||||
for key, val in kwargs.iteritems():
|
||||
parFileCont[key] = val
|
||||
|
||||
if self.__filename is not None:
|
||||
inputFile = open(self.__filename, 'r')
|
||||
else:
|
||||
return
|
||||
try:
|
||||
lines = inputFile.readlines()
|
||||
for line in lines:
|
||||
parspl = line.split('\t')[:2]
|
||||
parFileCont[parspl[0].strip()] = parspl[1]
|
||||
except Exception, e:
|
||||
self._printParameterError(e)
|
||||
inputFile.seek(0)
|
||||
lines = inputFile.readlines()
|
||||
for line in lines:
|
||||
if not line.startswith(('#', '%', '\n', ' ')):
|
||||
parspl = line.split('#')[:2]
|
||||
parFileCont[parspl[1].strip()] = parspl[0].strip()
|
||||
for key, value in parFileCont.iteritems():
|
||||
try:
|
||||
val = int(value)
|
||||
@ -57,8 +72,8 @@ class AutoPickParameter(object):
|
||||
try:
|
||||
val = float(value)
|
||||
except:
|
||||
if value.find(';') > 0:
|
||||
vallist = value.strip().split(';')
|
||||
if len(value.split(' ')) > 1:
|
||||
vallist = value.strip().split(' ')
|
||||
val = []
|
||||
for val0 in vallist:
|
||||
val0 = float(val0)
|
||||
@ -66,19 +81,17 @@ class AutoPickParameter(object):
|
||||
else:
|
||||
val = str(value.strip())
|
||||
parFileCont[key] = val
|
||||
else:
|
||||
parFileCont = {}
|
||||
except Exception, e:
|
||||
self._printParameterError(e)
|
||||
parFileCont = {}
|
||||
self.__parameter = parFileCont
|
||||
|
||||
if fnout:
|
||||
self.export2File(fnout)
|
||||
|
||||
# Human-readable string representation of the object
|
||||
def __str__(self):
|
||||
string = ''
|
||||
string += 'Automated picking parameter:\n\n'
|
||||
if self.__parameter:
|
||||
for key, value in self.__parameter.iteritems():
|
||||
for key, value in self.iteritems():
|
||||
string += '%s:\t\t%s\n' % (key, value)
|
||||
else:
|
||||
string += 'Empty parameter dictionary.'
|
||||
@ -107,6 +120,25 @@ class AutoPickParameter(object):
|
||||
def __len__(self):
|
||||
return len(self.__parameter.keys())
|
||||
|
||||
def iteritems(self):
|
||||
for key, value in self.__parameter.iteritems():
|
||||
yield key, value
|
||||
|
||||
def hasParam(self, *args):
|
||||
|
||||
def test(param):
|
||||
try:
|
||||
self.__parameter[param]
|
||||
return True
|
||||
except KeyError:
|
||||
return False
|
||||
|
||||
try:
|
||||
for param in args:
|
||||
test(param)
|
||||
except TypeError:
|
||||
test(args)
|
||||
|
||||
def getParam(self, *args):
|
||||
try:
|
||||
for param in args:
|
||||
@ -122,15 +154,19 @@ class AutoPickParameter(object):
|
||||
|
||||
def setParam(self, **kwargs):
|
||||
for param, value in kwargs.iteritems():
|
||||
try:
|
||||
self.__setitem__(param, value)
|
||||
except KeyError, e:
|
||||
self._printParameterError(e)
|
||||
print self
|
||||
|
||||
def _printParameterError(self, errmsg):
|
||||
print 'ParameterError:\n non-existent parameter %s' % errmsg
|
||||
|
||||
def export2File(self, fnout):
|
||||
fid_out = open(fnout, 'w')
|
||||
lines = []
|
||||
for key, value in self.iteritems():
|
||||
lines.append('{key}\t{value}'.format(key=key, value=value))
|
||||
fid_out.writelines(lines)
|
||||
|
||||
|
||||
class FilterOptions(object):
|
||||
'''
|
||||
|
||||
@ -285,9 +285,9 @@ class PickDlg(QDialog):
|
||||
|
||||
# connect button press event to an action
|
||||
self.cidpress = self.connectPressEvent(self.panPress)
|
||||
self.cidmotion = self.connectMotionEvent()
|
||||
self.cidrelease = self.connectReleaseEvent()
|
||||
self.cidscroll = self.connectScrollEvent()
|
||||
self.cidmotion = self.connectMotionEvent(self.panMotion)
|
||||
self.cidrelease = self.connectReleaseEvent(self.panRelease)
|
||||
self.cidscroll = self.connectScrollEvent(self.scrollZoom)
|
||||
|
||||
def setupUi(self):
|
||||
|
||||
@ -328,6 +328,7 @@ class PickDlg(QDialog):
|
||||
|
||||
_dialtoolbar.addAction(self.filterAction)
|
||||
_dialtoolbar.addWidget(self.selectPhase)
|
||||
_dialtoolbar.addAction(self.zoomAction)
|
||||
|
||||
_innerlayout = QVBoxLayout()
|
||||
|
||||
@ -346,39 +347,40 @@ class PickDlg(QDialog):
|
||||
self.setLayout(_outerlayout)
|
||||
|
||||
def disconnectPressEvent(self):
|
||||
self.getPlotWidget().mpl_disconnect(self.cidpress)
|
||||
widget = self.getPlotWidget()
|
||||
widget.mpl_disconnect(self.cidpress)
|
||||
self.cidpress = None
|
||||
|
||||
def connectPressEvent(self, slot):
|
||||
widget = self.getPlotWidget()
|
||||
return widget.mpl_connect('button_press_event', slot)
|
||||
|
||||
def reconnectPressEvent(self, slot):
|
||||
self.disconnectPressEvent()
|
||||
return self.connectPressEvent(slot)
|
||||
|
||||
def disconnectScrollEvent(self):
|
||||
widget = self.getPlotWidget()
|
||||
widget.mpl_disconnect(self.cidscroll)
|
||||
self.cidscroll = None
|
||||
|
||||
def connectScrollEvent(self):
|
||||
def connectScrollEvent(self, slot):
|
||||
widget = self.getPlotWidget()
|
||||
return widget.mpl_connect('scroll_event', self.scrollZoom)
|
||||
return widget.mpl_connect('scroll_event', slot)
|
||||
|
||||
def disconnectMotionEvent(self):
|
||||
widget = self.getPlotWidget()
|
||||
widget.mpl_disconnect(self.cidmotion)
|
||||
self.cidmotion = None
|
||||
|
||||
def connectMotionEvent(self):
|
||||
def connectMotionEvent(self, slot):
|
||||
widget = self.getPlotWidget()
|
||||
return widget.mpl_connect('motion_notify_event', self.panMotion)
|
||||
return widget.mpl_connect('motion_notify_event', slot)
|
||||
|
||||
def disconnectReleaseEvent(self):
|
||||
widget = self.getPlotWidget()
|
||||
widget.mpl_disconnect(self.cidrelease)
|
||||
self.cidrelease = None
|
||||
|
||||
def connectReleaseEvent(self):
|
||||
def connectReleaseEvent(self, slot):
|
||||
widget = self.getPlotWidget()
|
||||
return widget.mpl_connect('button_release_event', self.panRelease)
|
||||
return widget.mpl_connect('button_release_event', slot)
|
||||
|
||||
def verifyPhaseSelection(self):
|
||||
phase = self.selectPhase.currentText()
|
||||
@ -386,12 +388,13 @@ class PickDlg(QDialog):
|
||||
self.disconnectReleaseEvent()
|
||||
self.disconnectScrollEvent()
|
||||
self.disconnectMotionEvent()
|
||||
self.reconnectPressEvent(self.setIniPick)
|
||||
self.disconnectPressEvent()
|
||||
self.cidpress = self.connectPressEvent(self.setIniPick)
|
||||
else:
|
||||
self.cidpress = self.connectPressEvent(self.panPress)
|
||||
self.cidmotion = self.connectMotionEvent()
|
||||
self.cidrelease = self.connectReleaseEvent()
|
||||
self.cidscroll = self.connectScrollEvent()
|
||||
self.cidmotion = self.connectMotionEvent(self.panMotion)
|
||||
self.cidrelease = self.connectReleaseEvent(self.panRelease)
|
||||
self.cidscroll = self.connectScrollEvent(self.scrollZoom)
|
||||
|
||||
def getComponents(self):
|
||||
return self.components
|
||||
@ -438,8 +441,10 @@ class PickDlg(QDialog):
|
||||
wfdata = self.selectWFData(channel)
|
||||
|
||||
self.disconnectScrollEvent()
|
||||
|
||||
self.cidpress = self.reconnectPressEvent(self.setPick)
|
||||
self.disconnectPressEvent()
|
||||
self.disconnectReleaseEvent()
|
||||
self.disconnectMotionEvent()
|
||||
self.cidpress = self.connectPressEvent(self.setPick)
|
||||
|
||||
ini_pick = gui_event.xdata
|
||||
|
||||
@ -457,7 +462,7 @@ class PickDlg(QDialog):
|
||||
'VLRW' : 15.
|
||||
}
|
||||
|
||||
result = getSNR(wfdata, (5., .5, 1.), ini_pick)
|
||||
result = getSNR(wfdata, (5., .5, 2.), ini_pick)
|
||||
|
||||
snr = result[0]
|
||||
noiselevel = result[2] * 1.5
|
||||
@ -473,7 +478,7 @@ class PickDlg(QDialog):
|
||||
x_res /= 2
|
||||
|
||||
zoomx = [ini_pick - x_res, ini_pick + x_res]
|
||||
zoomy = [noiselevel * 1.5, -noiselevel * 1.5]
|
||||
zoomy = [-noiselevel * 1.5, noiselevel * 1.5]
|
||||
self.getPlotWidget().plotWFData(wfdata=wfdata,
|
||||
title=self.getStation() +
|
||||
' picking mode',
|
||||
@ -493,7 +498,7 @@ class PickDlg(QDialog):
|
||||
|
||||
wfdata = self.getAPD().copy().select(channel=channel)
|
||||
# get earliest and latest possible pick
|
||||
[epp, lpp, pickerror] = earllatepicker(wfdata, 1.5, (5., .5, 1.), pick)
|
||||
[epp, lpp, pickerror] = earllatepicker(wfdata, 1.5, (5., .5, 2.), pick)
|
||||
|
||||
# plotting picks
|
||||
ax = self.getPlotWidget().axes
|
||||
@ -559,9 +564,11 @@ class PickDlg(QDialog):
|
||||
def zoom(self):
|
||||
if self.zoomAction.isChecked():
|
||||
self.disconnectPressEvent()
|
||||
self.disconnectMotionEvent()
|
||||
self.disconnectReleaseEvent()
|
||||
self.figToolBar.zoom()
|
||||
else:
|
||||
self.connectPressEvent(self.setIniPick)
|
||||
self.cidpress = self.connectPressEvent(self.setIniPick)
|
||||
|
||||
def scrollZoom(self, gui_event, factor=2.):
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user