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 2015-05-04 12:07:17 +02:00
commit 6ee3a1b0b4
6 changed files with 227 additions and 89 deletions

90
autoPyLoT.py Normal file
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@ -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))

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@ -1 +1 @@
043c-dirty 694a-dirty

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@ -53,32 +53,22 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
#get signal window #get signal window
isignal = getsignalwin(t, Pick1, TSNR[2]) isignal = getsignalwin(t, Pick1, TSNR[2])
#calculate noise level #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 #get time where signal exceeds nlevel
ilup = np.where(x[isignal] > nlevel) ilup, = np.where(x[isignal] > nlevel)
ildown = np.where(x[isignal] < -nlevel) ildown, = np.where(x[isignal] < -nlevel)
if len(ilup[0]) <= 1 and len(ildown[0]) <= 1: if not ilup.size and not ildown.size:
print 'earllatepicker: Signal lower than noise level, misspick?' raise ValueError('earllatepicker: Signal lower than noise level')
return il = min(np.min(ilup) if ilup.size else float('inf'),
il = min([ilup[0][0], ildown[0][0]]) np.min(ildown) if ildown.size else float('inf'))
LPick = t[isignal][il] LPick = t[isignal][il]
#get earliest possible pick #get earliest possible pick
#get next 2 zero crossings after most likely pick
#initial onset is assumed to be the first zero crossing #determine all zero crossings in signal window
zc = [] zc = crossings_nonzero_all(x[isignal])
zc.append(Pick1) #calculate mean half period T0 of signal as the average of the
i = 0 T0 = np.mean(np.diff(zc)) * X[0].stats.delta #this is half wave length!
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!
#T0/4 is assumed as time difference between most likely and earliest possible pick! #T0/4 is assumed as time difference between most likely and earliest possible pick!
EPick = Pick1 - T0 / 2 EPick = Pick1 - T0 / 2
@ -288,6 +278,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
return FM 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): def getSNR(X, TSNR, t1):
''' '''

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@ -3,15 +3,13 @@
import os import os
import numpy as np
from obspy.core import (read, Stream, UTCDateTime) from obspy.core import (read, Stream, UTCDateTime)
from obspy import readEvents from obspy import readEvents
from obspy.core.event import (Event, Catalog) from obspy.core.event import (Event, Catalog)
from pylot.core.read import readPILOTEvent from pylot.core.read import readPILOTEvent
from pylot.core.util import fnConstructor, FormatError, \
from pylot.core.util import fnConstructor, createEvent, FormatError, \ getGlobalTimes
prepTimeAxis, getGlobalTimes
class Data(object): class Data(object):
@ -129,8 +127,8 @@ class Data(object):
except TypeError: except TypeError:
try: try:
self.wfdata += read(fname, format='GSE2') self.wfdata += read(fname, format='GSE2')
except Exception: except Exception, e:
warnmsg += '{0}\n'.format(fname) warnmsg += '{0}\n{1}\n'.format(fname, e)
if warnmsg: if warnmsg:
warnmsg = 'WARNING: unable to read\n' + warnmsg warnmsg = 'WARNING: unable to read\n' + warnmsg
print warnmsg print warnmsg
@ -148,6 +146,7 @@ class Data(object):
def getEvtData(self): def getEvtData(self):
return self.evtdata return self.evtdata
#TODO: write superclass DataStructure instead of three fully featured individual classes
class GenericDataStructure(object): class GenericDataStructure(object):
''' '''
@ -157,6 +156,7 @@ class GenericDataStructure(object):
def __init__(self, structexp='$R/$D/$E', folderdepth=2, **kwargs): def __init__(self, structexp='$R/$D/$E', folderdepth=2, **kwargs):
structureOptions = ('$R', '$D', '$E') structureOptions = ('$R', '$D', '$E')
self.__name = 'GDS'
structExpression = [] structExpression = []
depth = 0 depth = 0
while structexp is not os.path.sep: while structexp is not os.path.sep:
@ -182,6 +182,9 @@ class GenericDataStructure(object):
key = str(key).upper() key = str(key).upper()
self.__gdsFields[key] = value self.__gdsFields[key] = value
def getName(self):
return self.__name
def getFields(self): def getFields(self):
return self.__gdsFields return self.__gdsFields
@ -198,7 +201,9 @@ class PilotDataStructure(object):
def __init__(self, dataformat='GSE2', fsuffix='gse', def __init__(self, dataformat='GSE2', fsuffix='gse',
root='/data/Egelados/EVENT_DATA/LOCAL/', database='2006.01', root='/data/Egelados/EVENT_DATA/LOCAL/', database='2006.01',
**kwargs): **kwargs):
self.dataType = dataformat self.__name = 'PDS'
self.dataFormat = dataformat
self.dataType = 'waveform'
self.__pdsFields = {'ROOT': root, self.__pdsFields = {'ROOT': root,
'DATABASE': database, 'DATABASE': database,
'SUFFIX': fsuffix 'SUFFIX': fsuffix
@ -233,6 +238,9 @@ class PilotDataStructure(object):
def getFields(self): def getFields(self):
return self.__pdsFields return self.__pdsFields
def getName(self):
return self.__name
def expandDataPath(self): def expandDataPath(self):
datapath = os.path.join(self.getFields()['ROOT'], datapath = os.path.join(self.getFields()['ROOT'],
self.getFields()['DATABASE']) self.getFields()['DATABASE'])
@ -260,8 +268,8 @@ class SeiscompDataStructure(object):
} }
def __init__(self, dataType='waveform', sdate=None, edate=None, **kwargs): def __init__(self, dataType='waveform', sdate=None, edate=None, **kwargs):
# imports
from obspy.core import UTCDateTime self.__name = 'SDS'
def checkDate(date): def checkDate(date):
if not isinstance(date, UTCDateTime): if not isinstance(date, UTCDateTime):
@ -337,6 +345,9 @@ class SeiscompDataStructure(object):
def getFields(self): def getFields(self):
return self.__sdsFields return self.__sdsFields
def getName(self):
return self.__name
def expandDataPath(self): def expandDataPath(self):
fullChan = '{0}.{1}'.format(self.getFields()['CHAN'], self.getType()) fullChan = '{0}.{1}'.format(self.getFields()['CHAN'], self.getType())
dataPath = os.path.join(self.getFields()['SDSdir'], dataPath = os.path.join(self.getFields()['SDSdir'],

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@ -5,7 +5,7 @@
class AutoPickParameter(object): class AutoPickParameter(object):
''' '''
AutoPickParameters is a parameter type object capable to read and/or write 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 :param fn str: Filename of the input file
@ -34,51 +34,64 @@ class AutoPickParameter(object):
========== ========== ======================================= ========== ========== =======================================
''' '''
def __init__(self, fn=None): def __init__(self, fnin=None, fnout=None, **kwargs):
''' '''
Initialize parameter object: Initialize parameter object:
read content of an ASCII file an form a type consistent dictionary read content of an ASCII file an form a type consistent dictionary
contain all parameters. contain all parameters.
''' '''
self.__filename = fn
self.__filename = fnin
parFileCont = {} parFileCont = {}
try: # read from parsed arguments alternatively
if self.__filename is not None: for key, val in kwargs.iteritems():
parFileCont[key] = val
if self.__filename is not None:
inputFile = open(self.__filename, 'r') inputFile = open(self.__filename, 'r')
lines = inputFile.readlines() else:
for line in lines: return
parspl = line.split('\t')[:2] try:
parFileCont[parspl[0].strip()] = parspl[1] lines = inputFile.readlines()
for key, value in parFileCont.iteritems(): for line in lines:
try: parspl = line.split('\t')[:2]
val = int(value) parFileCont[parspl[0].strip()] = parspl[1]
except:
try:
val = float(value)
except:
if value.find(';') > 0:
vallist = value.strip().split(';')
val = []
for val0 in vallist:
val0 = float(val0)
val.append(val0)
else:
val = str(value.strip())
parFileCont[key] = val
else:
parFileCont = {}
except Exception, e: except Exception, e:
self._printParameterError(e) self._printParameterError(e)
parFileCont = {} 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)
except:
try:
val = float(value)
except:
if len(value.split(' ')) > 1:
vallist = value.strip().split(' ')
val = []
for val0 in vallist:
val0 = float(val0)
val.append(val0)
else:
val = str(value.strip())
parFileCont[key] = val
self.__parameter = parFileCont self.__parameter = parFileCont
if fnout:
self.export2File(fnout)
# Human-readable string representation of the object # Human-readable string representation of the object
def __str__(self): def __str__(self):
string = '' string = ''
string += 'Automated picking parameter:\n\n' string += 'Automated picking parameter:\n\n'
if self.__parameter: if self.__parameter:
for key, value in self.__parameter.iteritems(): for key, value in self.iteritems():
string += '%s:\t\t%s\n' % (key, value) string += '%s:\t\t%s\n' % (key, value)
else: else:
string += 'Empty parameter dictionary.' string += 'Empty parameter dictionary.'
@ -107,6 +120,25 @@ class AutoPickParameter(object):
def __len__(self): def __len__(self):
return len(self.__parameter.keys()) 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): def getParam(self, *args):
try: try:
for param in args: for param in args:
@ -122,15 +154,19 @@ class AutoPickParameter(object):
def setParam(self, **kwargs): def setParam(self, **kwargs):
for param, value in kwargs.iteritems(): for param, value in kwargs.iteritems():
try: self.__setitem__(param, value)
self.__setitem__(param, value)
except KeyError, e:
self._printParameterError(e)
print self print self
def _printParameterError(self, errmsg): def _printParameterError(self, errmsg):
print 'ParameterError:\n non-existent parameter %s' % 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): class FilterOptions(object):
''' '''

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@ -285,9 +285,9 @@ class PickDlg(QDialog):
# connect button press event to an action # connect button press event to an action
self.cidpress = self.connectPressEvent(self.panPress) self.cidpress = self.connectPressEvent(self.panPress)
self.cidmotion = self.connectMotionEvent() self.cidmotion = self.connectMotionEvent(self.panMotion)
self.cidrelease = self.connectReleaseEvent() self.cidrelease = self.connectReleaseEvent(self.panRelease)
self.cidscroll = self.connectScrollEvent() self.cidscroll = self.connectScrollEvent(self.scrollZoom)
def setupUi(self): def setupUi(self):
@ -328,6 +328,7 @@ class PickDlg(QDialog):
_dialtoolbar.addAction(self.filterAction) _dialtoolbar.addAction(self.filterAction)
_dialtoolbar.addWidget(self.selectPhase) _dialtoolbar.addWidget(self.selectPhase)
_dialtoolbar.addAction(self.zoomAction)
_innerlayout = QVBoxLayout() _innerlayout = QVBoxLayout()
@ -346,39 +347,40 @@ class PickDlg(QDialog):
self.setLayout(_outerlayout) self.setLayout(_outerlayout)
def disconnectPressEvent(self): def disconnectPressEvent(self):
self.getPlotWidget().mpl_disconnect(self.cidpress) widget = self.getPlotWidget()
widget.mpl_disconnect(self.cidpress)
self.cidpress = None
def connectPressEvent(self, slot): def connectPressEvent(self, slot):
widget = self.getPlotWidget() widget = self.getPlotWidget()
return widget.mpl_connect('button_press_event', slot) return widget.mpl_connect('button_press_event', slot)
def reconnectPressEvent(self, slot):
self.disconnectPressEvent()
return self.connectPressEvent(slot)
def disconnectScrollEvent(self): def disconnectScrollEvent(self):
widget = self.getPlotWidget() widget = self.getPlotWidget()
widget.mpl_disconnect(self.cidscroll) widget.mpl_disconnect(self.cidscroll)
self.cidscroll = None
def connectScrollEvent(self): def connectScrollEvent(self, slot):
widget = self.getPlotWidget() widget = self.getPlotWidget()
return widget.mpl_connect('scroll_event', self.scrollZoom) return widget.mpl_connect('scroll_event', slot)
def disconnectMotionEvent(self): def disconnectMotionEvent(self):
widget = self.getPlotWidget() widget = self.getPlotWidget()
widget.mpl_disconnect(self.cidmotion) widget.mpl_disconnect(self.cidmotion)
self.cidmotion = None
def connectMotionEvent(self): def connectMotionEvent(self, slot):
widget = self.getPlotWidget() widget = self.getPlotWidget()
return widget.mpl_connect('motion_notify_event', self.panMotion) return widget.mpl_connect('motion_notify_event', slot)
def disconnectReleaseEvent(self): def disconnectReleaseEvent(self):
widget = self.getPlotWidget() widget = self.getPlotWidget()
widget.mpl_disconnect(self.cidrelease) widget.mpl_disconnect(self.cidrelease)
self.cidrelease = None
def connectReleaseEvent(self): def connectReleaseEvent(self, slot):
widget = self.getPlotWidget() widget = self.getPlotWidget()
return widget.mpl_connect('button_release_event', self.panRelease) return widget.mpl_connect('button_release_event', slot)
def verifyPhaseSelection(self): def verifyPhaseSelection(self):
phase = self.selectPhase.currentText() phase = self.selectPhase.currentText()
@ -386,12 +388,13 @@ class PickDlg(QDialog):
self.disconnectReleaseEvent() self.disconnectReleaseEvent()
self.disconnectScrollEvent() self.disconnectScrollEvent()
self.disconnectMotionEvent() self.disconnectMotionEvent()
self.reconnectPressEvent(self.setIniPick) self.disconnectPressEvent()
self.cidpress = self.connectPressEvent(self.setIniPick)
else: else:
self.cidpress = self.connectPressEvent(self.panPress) self.cidpress = self.connectPressEvent(self.panPress)
self.cidmotion = self.connectMotionEvent() self.cidmotion = self.connectMotionEvent(self.panMotion)
self.cidrelease = self.connectReleaseEvent() self.cidrelease = self.connectReleaseEvent(self.panRelease)
self.cidscroll = self.connectScrollEvent() self.cidscroll = self.connectScrollEvent(self.scrollZoom)
def getComponents(self): def getComponents(self):
return self.components return self.components
@ -438,8 +441,10 @@ class PickDlg(QDialog):
wfdata = self.selectWFData(channel) wfdata = self.selectWFData(channel)
self.disconnectScrollEvent() self.disconnectScrollEvent()
self.disconnectPressEvent()
self.cidpress = self.reconnectPressEvent(self.setPick) self.disconnectReleaseEvent()
self.disconnectMotionEvent()
self.cidpress = self.connectPressEvent(self.setPick)
ini_pick = gui_event.xdata ini_pick = gui_event.xdata
@ -457,7 +462,7 @@ class PickDlg(QDialog):
'VLRW' : 15. 'VLRW' : 15.
} }
result = getSNR(wfdata, (5., .5, 1.), ini_pick) result = getSNR(wfdata, (5., .5, 2.), ini_pick)
snr = result[0] snr = result[0]
noiselevel = result[2] * 1.5 noiselevel = result[2] * 1.5
@ -473,7 +478,7 @@ class PickDlg(QDialog):
x_res /= 2 x_res /= 2
zoomx = [ini_pick - x_res, ini_pick + x_res] 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, self.getPlotWidget().plotWFData(wfdata=wfdata,
title=self.getStation() + title=self.getStation() +
' picking mode', ' picking mode',
@ -493,7 +498,7 @@ class PickDlg(QDialog):
wfdata = self.getAPD().copy().select(channel=channel) wfdata = self.getAPD().copy().select(channel=channel)
# get earliest and latest possible pick # 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 # plotting picks
ax = self.getPlotWidget().axes ax = self.getPlotWidget().axes
@ -559,9 +564,11 @@ class PickDlg(QDialog):
def zoom(self): def zoom(self):
if self.zoomAction.isChecked(): if self.zoomAction.isChecked():
self.disconnectPressEvent() self.disconnectPressEvent()
self.disconnectMotionEvent()
self.disconnectReleaseEvent()
self.figToolBar.zoom() self.figToolBar.zoom()
else: else:
self.connectPressEvent(self.setIniPick) self.cidpress = self.connectPressEvent(self.setIniPick)
def scrollZoom(self, gui_event, factor=2.): def scrollZoom(self, gui_event, factor=2.):