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
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@ -0,0 +1,90 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os
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import argparse
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from pylot.core.util import _getVersionString
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from pylot.core.read import Data, AutoPickParameter
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from pylot.core.pick.CharFuns import HOScf, AICcf
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from pylot.core.util.structure import DATASTRUCTURE
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__version__ = _getVersionString()
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METHOD = {'HOS':HOScf, 'AIC':AICcf}
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def autoPyLoT(fnames, inputfile):
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'''
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Determine phase onsets automatically utilizing the automatic picking
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algorithm by Kueperkoch et al. 2011.
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:param fnames: list of strings containing the paths or urls to the
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waveform data to be picked
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:type fnames: list
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:param inputfile: path to the input file containing all parameter
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information for automatic picking (for formatting details, see.
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`~pylot.core.read.input.AutoPickParameter`
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:type inputfile: str
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:return:
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.. rubric:: Example
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'''
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parameter = AutoPickParameter(inputfile)
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data = Data()
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meth = parameter.getParam('algoP')
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tsnr1 = parameter.getParam('tsnr1')
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tsnr2 = parameter.getParam('tsnr2')
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tnoise = parameter.getParam('pnoiselen')
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tsignal = parameter.getParam('tlim')
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order = parameter.getParam('hosorder')
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thosmw = parameter.getParam('tlta')
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if parameter.hasParam('datastructure'):
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datastructure = DATASTRUCTURE[parameter.getParam('datastructure')]()
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dsfields = {'root':parameter.getParam('rootpath')} #see TODO: in data.py
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datastructure.modifyFields(dsfields)
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def expandSDS(datastructure):
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return datastructure.expandDataPath()
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def expandPDS(datastructure):
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return os.path.join(datastructure.expandDataPath(),'*')
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dsem = {'PDS':expandPDS, 'SDS':expandSDS}
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expandMethod = dsem[datastructure.getName()]
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data.setWFData(expandMethod())
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else:
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data.setWFData()
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cfP = METHOD[meth](data.getWFData(), (tnoise, tsignal), thosmw, order)
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if __name__ == "__main__":
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# parse arguments
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parser = argparse.ArgumentParser(
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description='''This program visualizes Probabilistic Power Spectral Densities.''')
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parser.add_argument('-d', '-D', '--data', type=str, action='store',
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help='''path or url to the data to be picked''',
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default='http://examples.obspy.org/BW.KW1..EHZ.D.2011.037'
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)
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parser.add_argument('-i', '-I', '--inputfile', type=str,
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action='store',
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help='''full path to the file containing the input
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parameters for autoPyLoT''',
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default=os.path.join(os.path.expanduser('~'), '.pylot',
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'autoPyLoT.in')
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)
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parser.add_argument('-v', '-V', '--version', action='version',
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version='autoPyLoT ' + __version__,
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help='show version information and exit')
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cla = parser.parse_args()
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autoPyLoT(cla.data, str(cla.inputfile))
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@ -1 +1 @@
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043c-dirty
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694a-dirty
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@ -53,32 +53,22 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None):
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#get signal window
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isignal = getsignalwin(t, Pick1, TSNR[2])
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#calculate noise level
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nlevel = max(abs(x[inoise])) * nfac
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nlevel = np.sqrt(np.mean(np.square(x[inoise]))) * nfac
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#get time where signal exceeds nlevel
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ilup = np.where(x[isignal] > nlevel)
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ildown = np.where(x[isignal] < -nlevel)
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if len(ilup[0]) <= 1 and len(ildown[0]) <= 1:
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print 'earllatepicker: Signal lower than noise level, misspick?'
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return
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il = min([ilup[0][0], ildown[0][0]])
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ilup, = np.where(x[isignal] > nlevel)
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ildown, = np.where(x[isignal] < -nlevel)
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if not ilup.size and not ildown.size:
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raise ValueError('earllatepicker: Signal lower than noise level')
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il = min(np.min(ilup) if ilup.size else float('inf'),
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np.min(ildown) if ildown.size else float('inf'))
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LPick = t[isignal][il]
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#get earliest possible pick
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#get next 2 zero crossings after most likely pick
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#initial onset is assumed to be the first zero crossing
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zc = []
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zc.append(Pick1)
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i = 0
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for j in range(isignal[0][1], isignal[0][len(t[isignal]) - 1]):
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i = i + 1
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if x[j - 1] <= 0 and x[j] >= 0:
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zc.append(t[isignal][i])
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elif x[j - 1] > 0 and x[j] <= 0:
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zc.append(t[isignal][i])
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if len(zc) == 3:
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break
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#calculate maximum period T0 of signal out of zero crossings
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T0 = max(np.diff(zc)) #this is half wave length!
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#determine all zero crossings in signal window
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zc = crossings_nonzero_all(x[isignal])
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#calculate mean half period T0 of signal as the average of the
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T0 = np.mean(np.diff(zc)) * X[0].stats.delta #this is half wave length!
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#T0/4 is assumed as time difference between most likely and earliest possible pick!
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EPick = Pick1 - T0 / 2
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@ -288,6 +278,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
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return FM
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def crossings_nonzero_all(data):
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pos = data > 0
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npos = ~pos
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return ((pos[:-1] & npos[1:]) | (npos[:-1] & pos[1:])).nonzero()[0]
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def getSNR(X, TSNR, t1):
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'''
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@ -3,15 +3,13 @@
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import os
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import numpy as np
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from obspy.core import (read, Stream, UTCDateTime)
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from obspy import readEvents
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from obspy.core.event import (Event, Catalog)
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from pylot.core.read import readPILOTEvent
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from pylot.core.util import fnConstructor, createEvent, FormatError, \
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prepTimeAxis, getGlobalTimes
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from pylot.core.util import fnConstructor, FormatError, \
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getGlobalTimes
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class Data(object):
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@ -129,8 +127,8 @@ class Data(object):
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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:
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warnmsg += '{0}\n'.format(fname)
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except Exception, 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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@ -148,6 +146,7 @@ class Data(object):
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def getEvtData(self):
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return self.evtdata
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#TODO: write superclass DataStructure instead of three fully featured individual classes
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class GenericDataStructure(object):
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'''
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@ -157,6 +156,7 @@ class GenericDataStructure(object):
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def __init__(self, structexp='$R/$D/$E', folderdepth=2, **kwargs):
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structureOptions = ('$R', '$D', '$E')
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self.__name = 'GDS'
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structExpression = []
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depth = 0
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while structexp is not os.path.sep:
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@ -182,6 +182,9 @@ class GenericDataStructure(object):
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key = str(key).upper()
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self.__gdsFields[key] = value
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def getName(self):
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return self.__name
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def getFields(self):
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return self.__gdsFields
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@ -198,7 +201,9 @@ class PilotDataStructure(object):
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def __init__(self, dataformat='GSE2', fsuffix='gse',
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root='/data/Egelados/EVENT_DATA/LOCAL/', database='2006.01',
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**kwargs):
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self.dataType = dataformat
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self.__name = 'PDS'
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self.dataFormat = dataformat
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self.dataType = 'waveform'
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self.__pdsFields = {'ROOT': root,
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'DATABASE': database,
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'SUFFIX': fsuffix
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@ -233,6 +238,9 @@ class PilotDataStructure(object):
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def getFields(self):
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return self.__pdsFields
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def getName(self):
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return self.__name
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def expandDataPath(self):
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datapath = os.path.join(self.getFields()['ROOT'],
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self.getFields()['DATABASE'])
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@ -260,8 +268,8 @@ class SeiscompDataStructure(object):
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}
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def __init__(self, dataType='waveform', sdate=None, edate=None, **kwargs):
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# imports
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from obspy.core import UTCDateTime
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self.__name = 'SDS'
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def checkDate(date):
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if not isinstance(date, UTCDateTime):
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@ -337,6 +345,9 @@ class SeiscompDataStructure(object):
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def getFields(self):
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return self.__sdsFields
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def getName(self):
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return self.__name
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def expandDataPath(self):
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fullChan = '{0}.{1}'.format(self.getFields()['CHAN'], self.getType())
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dataPath = os.path.join(self.getFields()['SDSdir'],
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@ -5,7 +5,7 @@
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class AutoPickParameter(object):
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'''
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AutoPickParameters is a parameter type object capable to read and/or write
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parameter ASCII and binary files.
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parameter ASCII.
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:param fn str: Filename of the input file
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@ -34,51 +34,64 @@ class AutoPickParameter(object):
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========== ========== =======================================
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'''
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def __init__(self, fn=None):
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def __init__(self, fnin=None, fnout=None, **kwargs):
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'''
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Initialize parameter object:
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read content of an ASCII file an form a type consistent dictionary
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contain all parameters.
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'''
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self.__filename = fn
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self.__filename = fnin
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parFileCont = {}
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try:
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if self.__filename is not None:
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# read from parsed arguments alternatively
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for key, val in kwargs.iteritems():
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parFileCont[key] = val
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if self.__filename is not None:
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inputFile = open(self.__filename, 'r')
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lines = inputFile.readlines()
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for line in lines:
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parspl = line.split('\t')[:2]
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parFileCont[parspl[0].strip()] = parspl[1]
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for key, value in parFileCont.iteritems():
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try:
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val = int(value)
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except:
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try:
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val = float(value)
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except:
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if value.find(';') > 0:
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vallist = value.strip().split(';')
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val = []
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for val0 in vallist:
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val0 = float(val0)
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val.append(val0)
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else:
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val = str(value.strip())
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parFileCont[key] = val
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else:
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parFileCont = {}
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else:
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return
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try:
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lines = inputFile.readlines()
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for line in lines:
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parspl = line.split('\t')[:2]
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parFileCont[parspl[0].strip()] = parspl[1]
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except Exception, e:
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self._printParameterError(e)
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parFileCont = {}
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inputFile.seek(0)
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lines = inputFile.readlines()
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for line in lines:
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if not line.startswith(('#', '%', '\n', ' ')):
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parspl = line.split('#')[:2]
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parFileCont[parspl[1].strip()] = parspl[0].strip()
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for key, value in parFileCont.iteritems():
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try:
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val = int(value)
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except:
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try:
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val = float(value)
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except:
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if len(value.split(' ')) > 1:
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vallist = value.strip().split(' ')
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val = []
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for val0 in vallist:
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val0 = float(val0)
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val.append(val0)
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else:
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val = str(value.strip())
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parFileCont[key] = val
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self.__parameter = parFileCont
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if fnout:
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self.export2File(fnout)
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# Human-readable string representation of the object
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def __str__(self):
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string = ''
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string += 'Automated picking parameter:\n\n'
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if self.__parameter:
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for key, value in self.__parameter.iteritems():
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for key, value in self.iteritems():
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string += '%s:\t\t%s\n' % (key, value)
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else:
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string += 'Empty parameter dictionary.'
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@ -107,6 +120,25 @@ class AutoPickParameter(object):
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def __len__(self):
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return len(self.__parameter.keys())
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def iteritems(self):
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for key, value in self.__parameter.iteritems():
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yield key, value
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def hasParam(self, *args):
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def test(param):
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try:
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self.__parameter[param]
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return True
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except KeyError:
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return False
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try:
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for param in args:
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test(param)
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except TypeError:
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test(args)
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def getParam(self, *args):
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try:
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for param in args:
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@ -122,15 +154,19 @@ class AutoPickParameter(object):
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def setParam(self, **kwargs):
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for param, value in kwargs.iteritems():
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try:
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self.__setitem__(param, value)
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except KeyError, e:
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self._printParameterError(e)
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self.__setitem__(param, value)
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print self
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def _printParameterError(self, errmsg):
|
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print 'ParameterError:\n non-existent parameter %s' % errmsg
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def export2File(self, fnout):
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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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lines.append('{key}\t{value}'.format(key=key, value=value))
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fid_out.writelines(lines)
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class FilterOptions(object):
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'''
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@ -285,9 +285,9 @@ class PickDlg(QDialog):
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# connect button press event to an action
|
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self.cidpress = self.connectPressEvent(self.panPress)
|
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self.cidmotion = self.connectMotionEvent()
|
||||
self.cidrelease = self.connectReleaseEvent()
|
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self.cidscroll = self.connectScrollEvent()
|
||||
self.cidmotion = self.connectMotionEvent(self.panMotion)
|
||||
self.cidrelease = self.connectReleaseEvent(self.panRelease)
|
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self.cidscroll = self.connectScrollEvent(self.scrollZoom)
|
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def setupUi(self):
|
||||
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||||
@ -328,6 +328,7 @@ class PickDlg(QDialog):
|
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|
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_dialtoolbar.addAction(self.filterAction)
|
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_dialtoolbar.addWidget(self.selectPhase)
|
||||
_dialtoolbar.addAction(self.zoomAction)
|
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_innerlayout = QVBoxLayout()
|
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||||
@ -346,39 +347,40 @@ class PickDlg(QDialog):
|
||||
self.setLayout(_outerlayout)
|
||||
|
||||
def disconnectPressEvent(self):
|
||||
self.getPlotWidget().mpl_disconnect(self.cidpress)
|
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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):
|
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widget = self.getPlotWidget()
|
||||
widget.mpl_disconnect(self.cidmotion)
|
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self.cidmotion = None
|
||||
|
||||
def connectMotionEvent(self):
|
||||
def connectMotionEvent(self, slot):
|
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widget = self.getPlotWidget()
|
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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