Merge branch 'develop' into update_waveformwidget
This commit is contained in:
commit
e2b69d043c
13
QtPyLoT.py
13
QtPyLoT.py
@ -74,7 +74,7 @@ from pylot.core.util.connection import checkurl
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from pylot.core.util.dataprocessing import read_metadata, restitute_data
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from pylot.core.util.utils import fnConstructor, getLogin, \
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full_range, readFilterInformation, trim_station_components, check4gaps, make_pen, pick_color_plt, \
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pick_linestyle_plt, remove_underscores, check4doubled, identifyPhaseID, excludeQualityClasses, has_spe
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pick_linestyle_plt, remove_underscores, check4doubled, identifyPhaseID, excludeQualityClasses, has_spe, check4rotated
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from pylot.core.util.event import Event
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from pylot.core.io.location import create_creation_info, create_event
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from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
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@ -1421,6 +1421,8 @@ class MainWindow(QMainWindow):
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# check for gaps and doubled channels
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check4gaps(wfdat)
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check4doubled(wfdat)
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# check for stations with rotated components
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wfdat = check4rotated(wfdat, self.metadata)
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# trim station components to same start value
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trim_station_components(wfdat, trim_start=True, trim_end=False)
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self._stime = full_range(self.get_data().getWFData())[0]
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@ -1925,15 +1927,6 @@ class MainWindow(QMainWindow):
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self.apw.insert_log_widget(self.listWidget)
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self.apw.refresh_tooltips()
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# self.logDockWidget = QDockWidget("AutoPickLog", self)
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# self.logDockWidget.setObjectName("LogDockWidget")
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# self.logDockWidget.setAllowedAreas(
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# Qt.LeftDockWidgetArea | Qt.RightDockWidgetArea)
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# self.logDockWidget.setWidget(self.listWidget)
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# self.addDockWidget(Qt.LeftDockWidgetArea, self.logDockWidget)
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# self.addListItem('Loading default values from PyLoT-input file %s'
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# % self.infile)
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self.apw.start.connect(self.start_autopick)
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self.apw.show()
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@ -26,7 +26,8 @@ from pylot.core.util.dataprocessing import restitute_data, read_metadata
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from pylot.core.util.defaults import SEPARATOR
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from pylot.core.util.event import Event
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from pylot.core.util.structure import DATASTRUCTURE
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from pylot.core.util.utils import real_None, remove_underscores, trim_station_components, check4gaps, check4doubled
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from pylot.core.util.utils import real_None, remove_underscores, trim_station_components, check4gaps, check4doubled, \
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check4rotated
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from pylot.core.util.version import get_git_version as _getVersionString
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__version__ = _getVersionString()
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@ -254,6 +255,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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wfdat = check4doubled(wfdat)
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wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
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metadata = read_metadata(parameter.get('invdir'))
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# rotate stations to ZNE
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wfdat = check4rotated(wfdat, metadata)
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corr_dat = None
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if locflag:
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print("Restitute data ...")
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@ -348,6 +348,11 @@ defaults = {'rootpath': {'type': str,
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'value': 1.0,
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'namestring': 'Wadati tolerance'},
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'jackfactor': {'type': float,
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'tooltip': 'pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor',
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'value': 5.0,
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'namestring': 'Jackknife safety factor'},
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'WAscaling': {'type': (float, float, float),
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'tooltip': 'Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] \
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If zeros are set, original Richter magnitude is calculated!',
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@ -386,7 +391,7 @@ defaults = {'rootpath': {'type': str,
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'namestring': 'Use TauPy'},
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'taup_model': {'type': str,
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'tooltip': 'define TauPy model for traveltime estimation',
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'tooltip': 'define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6',
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'value': 'iasp91',
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'namestring': 'TauPy model'}
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}
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@ -481,5 +486,6 @@ settings_special_pick = {
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'minpercent',
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'zfac',
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'mdttolerance',
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'wdttolerance']
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'wdttolerance',
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'jackfactor'],
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}
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@ -41,6 +41,7 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
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# parameter input file (usually autoPyLoT.in).
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wdttolerance = param.get('wdttolerance')
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mdttolerance = param.get('mdttolerance')
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jackfactor = param.get('jackfactor')
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apverbose = param.get('apverbose')
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for n in range(len(data)):
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station = data[n].stats.station
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@ -80,7 +81,7 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
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# quality control
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# median check and jackknife on P-onset times
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jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, 1, fig_dict_wadatijack)
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jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, jackfactor, 1, fig_dict_wadatijack)
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#return jk_checked_onsets
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# check S-P times (Wadati)
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wadationsets = wadaticheck(jk_checked_onsets, wdttolerance, 1, fig_dict_wadatijack)
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@ -499,6 +500,8 @@ def autopickstation(wfstream, pickparam, verbose=False,
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SNRPdB,
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FM)
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print(msg)
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msg = 'autopickstation: Refined P-Pick: {} s | P-Error: {} s'.format(mpickP, Perror)
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print(msg)
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Sflag = 1
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else:
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@ -759,6 +762,9 @@ def autopickstation(wfstream, pickparam, verbose=False,
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lpickS = lpick[ipick]
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Serror = pickerr[ipick]
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msg = 'autopickstation: Refined S-Pick: {} s | S-Error: {} s'.format(mpickS, Serror)
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print(msg)
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# get SNR
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[SNRS, SNRSdB, Snoiselevel] = getSNR(h_copy, tsnrh, mpickS)
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@ -296,9 +296,12 @@ class HOScf(CharacteristicFunction):
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elif self.getOrder() == 4:
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LTA[j] = lta / np.power(lta1, 2)
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nn = np.isnan(LTA)
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if len(nn) > 1:
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LTA[nn] = 0
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# remove NaN's with first not-NaN-value,
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# so autopicker doesnt pick discontinuity at start of the trace
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ind = np.where(~np.isnan(LTA))[0]
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if ind.size:
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first = ind[0]
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LTA[:first] = LTA[first]
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self.cf = LTA
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self.xcf = x
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@ -244,7 +244,11 @@ class AICPicker(AutoPicker):
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& (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin
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# find maximum within slope determination window
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# 'cause slope should be calculated up to first local minimum only!
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dataslope = self.Data[0].data[islope[0][0]:islope[0][len(islope[0]) - 1]]
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try:
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dataslope = self.Data[0].data[islope[0][0:-1]]
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except IndexError:
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print("Slope Calculation: empty array islope, check signal window")
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return
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if len(dataslope) < 1:
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print('No data in slope window found!')
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return
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@ -254,7 +258,7 @@ class AICPicker(AutoPicker):
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# calculate slope from initial onset to maximum of AIC function
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print("AICPicker: Not enough data samples left for slope calculation!")
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print("Calculating slope from initial onset to maximum of AIC function ...")
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imax = np.argmax(aicsmooth[islope[0][0]:islope[0][len(islope[0])-1]])
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imax = np.argmax(aicsmooth[islope[0][0:-1]])
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if imax == 0:
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print("AICPicker: Maximum for slope determination right at the beginning of the window!")
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print("Choose longer slope determination window!")
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@ -284,10 +288,10 @@ class AICPicker(AutoPicker):
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xslope = np.arange(0, len(dataslope), 1)
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P = np.polyfit(xslope, dataslope, 1)
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datafit = np.polyval(P, xslope)
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if datafit[0] >= datafit[len(datafit) - 1]:
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if datafit[0] >= datafit[-1]:
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print('AICPicker: Negative slope, bad onset skipped!')
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return
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self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[len(dataslope) - 1] - datafit[0])
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self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
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else:
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self.SNR = None
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@ -135,7 +135,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None):
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ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
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ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
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ax.plot([t[0], t[int(len(t)) - 1]], [nlevel, nlevel], '--k', label='Noise Level')
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ax.plot(t[isignal[zc]], np.zeros(len(zc)), '*g',
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ax.plot(t[pis[zc]], np.zeros(len(zc)), '*g',
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markersize=14, label='Zero Crossings')
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ax.plot([t[0], t[int(len(t)) - 1]], [-nlevel, -nlevel], '--k')
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ax.plot([Pick1, Pick1], [max(x), -max(x)], 'b', linewidth=2, label='mpp')
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@ -205,8 +205,10 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None):
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t = np.arange(0, Xraw[0].stats.npts / Xraw[0].stats.sampling_rate,
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Xraw[0].stats.delta)
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# get pick window
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ipick = np.where(
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(t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
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ipick = np.where((t <= min([Pick + pickwin, len(Xraw[0])])) & (t >= Pick))
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if len(ipick[0]) <= 1:
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print('fmpicker: Zero crossings window to short!')
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return
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# remove mean
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xraw[ipick] = xraw[ipick] - np.mean(xraw[ipick])
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xfilt[ipick] = xfilt[ipick] - np.mean(xfilt[ipick])
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@ -801,7 +803,7 @@ def checksignallength(X, pick, TSNR, minsiglength, nfac, minpercent, iplot=0, fi
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return returnflag
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def checkPonsets(pickdic, dttolerance, iplot=0, fig_dict=None):
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def checkPonsets(pickdic, dttolerance, jackfactor=5, iplot=0, fig_dict=None):
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'''
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Function to check statistics of P-onset times: Control deviation from
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median (maximum adjusted deviation = dttolerance) and apply pseudo-
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@ -838,9 +840,9 @@ def checkPonsets(pickdic, dttolerance, iplot=0, fig_dict=None):
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return
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# get pseudo variances smaller than average variances
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# (times safety factor), these picks passed jackknife test
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ij = np.where(PHI_pseudo <= 5 * xjack)
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ij = np.where(PHI_pseudo <= jackfactor * xjack)
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# these picks did not pass jackknife test
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badjk = np.where(PHI_pseudo > 5 * xjack)
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badjk = np.where(PHI_pseudo > jackfactor * xjack)
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badjkstations = np.array(stations)[badjk]
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print("checkPonsets: %d pick(s) did not pass jackknife test!" % len(badjkstations))
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print(badjkstations)
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@ -9,6 +9,9 @@ import subprocess
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import numpy as np
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from obspy import UTCDateTime, read
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from obspy.signal.rotate import rotate2zne
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from obspy.io.xseed.utils import SEEDParserException
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from pylot.core.io.inputs import PylotParameter
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from scipy.interpolate import splrep, splev
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@ -696,6 +699,94 @@ def get_stations(data):
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return stations
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def check4rotated(data, metadata=None):
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def rotate_components(wfstream, metadata=None):
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"""rotates components if orientation code is numeric.
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azimut and dip are fetched from metadata"""
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try:
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# indexing fails if metadata is None
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metadata[0]
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except:
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msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
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print(msg)
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return wfstream
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if metadata[0] is None:
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# sometimes metadata is (None, (None,))
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msg = 'Warning: could not rotate traces since no metadata was given\nCheck inventory directory!'
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print(msg)
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return wfstream
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else:
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parser = metadata[1]
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def get_dip_azimut(parser, trace_id):
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"""gets azimut and dip for a trace out of the metadata parser"""
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dip = None
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azimut = None
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try:
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blockettes = parser._select(trace_id)
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except SEEDParserException as e:
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print(e)
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raise ValueError
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for blockette_ in blockettes:
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if blockette_.id != 52:
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continue
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dip = blockette_.dip
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azimut = blockette_.azimuth
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break
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if dip is None or azimut is None:
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error_msg = 'Dip and azimuth not available for trace_id {}'.format(trace_id)
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raise ValueError(error_msg)
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return dip, azimut
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trace_ids = [trace.id for trace in wfstream]
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for trace_id in trace_ids:
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orientation = trace_id[-1]
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if orientation.isnumeric():
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# misaligned channels have a number as orientation
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azimuts = []
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dips = []
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for trace_id in trace_ids:
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try:
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dip, azimut = get_dip_azimut(parser, trace_id)
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except ValueError as e:
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print(e)
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print('Failed to rotate station {}, no azimuth or dip available in metadata'.format(trace_id))
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return wfstream
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azimuts.append(azimut)
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dips.append(dip)
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# to rotate all traces must have same length
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wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
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z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
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wfstream[1], azimuts[1], dips[1],
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wfstream[2], azimuts[2], dips[2])
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print('check4rotated: rotated station {} to ZNE'.format(trace_id))
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z_index = dips.index(min(dips)) # get z-trace index (dip is measured from 0 to -90
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wfstream[z_index].data = z
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wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
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del trace_ids[z_index]
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for trace_id in trace_ids:
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dip, az = get_dip_azimut(parser, trace_id)
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trace = wfstream.select(id=trace_id)[0]
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if az > 315 and az <= 45 or az > 135 and az <= 225:
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trace.data = n
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trace.stats.channel = trace.stats.channel[0:-1] + 'N'
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elif az > 45 and az <= 135 or az > 225 and az <= 315:
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trace.data = e
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trace.stats.channel = trace.stats.channel[0:-1] + 'E'
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break
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else:
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continue
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return wfstream
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stations = get_stations(data)
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for station in stations:
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wf_station = data.select(station=station)
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wf_station = rotate_components(wf_station, metadata)
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return data
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def scaleWFData(data, factor=None, components='all'):
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"""
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produce scaled waveforms from given waveform data and a scaling factor,
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@ -23,7 +23,7 @@ except:
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from matplotlib.figure import Figure
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from pylot.core.util.utils import find_horizontals, identifyPhase, loopIdentifyPhase, trim_station_components, \
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identifyPhaseID
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identifyPhaseID, check4rotated
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try:
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from matplotlib.backends.backend_qt4agg import FigureCanvas
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@ -440,6 +440,7 @@ class WaveformWidgetPG(QtGui.QWidget):
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self.plotWidget.showGrid(x=False, y=True, alpha=0.2)
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self.plotWidget.hideAxis('bottom')
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self.plotWidget.hideAxis('left')
|
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self.wfstart, self.wfend = 0, 0
|
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self.reinitMoveProxy()
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self._proxy = pg.SignalProxy(self.plotWidget.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)
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|
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@ -457,8 +458,9 @@ class WaveformWidgetPG(QtGui.QWidget):
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# if x > 0:# and index < len(data1):
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wfID = self._parent.getWFID(y)
|
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station = self._parent.getStationName(wfID)
|
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abstime = self.wfstart + x
|
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if self._parent.get_current_event():
|
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self.label.setText("station = {}, t = {} [s]".format(station, x))
|
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self.label.setText("station = {}, T = {}, t = {} [s]".format(station, abstime, x))
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self.vLine.setPos(mousePoint.x())
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self.hLine.setPos(mousePoint.y())
|
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@ -482,7 +484,7 @@ class WaveformWidgetPG(QtGui.QWidget):
|
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component='*', nth_sample=1, iniPick=None, verbosity=0):
|
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self.title = title
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self.clearPlotDict()
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wfstart, wfend = full_range(wfdata)
|
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self.wfstart, self.wfend = full_range(wfdata)
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nmax = 0
|
||||
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settings = QSettings()
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@ -510,7 +512,7 @@ class WaveformWidgetPG(QtGui.QWidget):
|
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|
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try:
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self.plotWidget.getPlotItem().vb.setLimits(xMin=float(0),
|
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xMax=float(wfend - wfstart),
|
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xMax=float(self.wfend - self.wfstart),
|
||||
yMin=-0.5,
|
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yMax=len(nsc) + 0.5)
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except:
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@ -528,7 +530,7 @@ class WaveformWidgetPG(QtGui.QWidget):
|
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if verbosity:
|
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msg = 'plotting %s channel of station %s' % (channel, station)
|
||||
print(msg)
|
||||
stime = trace.stats.starttime - wfstart
|
||||
stime = trace.stats.starttime - self.wfstart
|
||||
time_ax = prepTimeAxis(stime, trace)
|
||||
if time_ax is not None:
|
||||
if not scaleddata:
|
||||
@ -538,9 +540,9 @@ class WaveformWidgetPG(QtGui.QWidget):
|
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data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
|
||||
plots.append((times, data))
|
||||
self.setPlotDict(n, (station, channel, network))
|
||||
self.xlabel = 'seconds since {0}'.format(wfstart)
|
||||
self.xlabel = 'seconds since {0}'.format(self.wfstart)
|
||||
self.ylabel = ''
|
||||
self.setXLims([0, wfend - wfstart])
|
||||
self.setXLims([0, self.wfend - self.wfstart])
|
||||
self.setYLims([-0.5, nmax + 0.5])
|
||||
return plots
|
||||
|
||||
@ -2291,6 +2293,8 @@ class TuneAutopicker(QWidget):
|
||||
wfdat = self.data.getWFData() # all available streams
|
||||
# trim station components to same start value
|
||||
trim_station_components(wfdat, trim_start=True, trim_end=False)
|
||||
# rotate misaligned stations to ZNE
|
||||
wfdat = check4rotated(wfdat, self.parent.metadata)
|
||||
self.stationBox.clear()
|
||||
stations = []
|
||||
for trace in self.data.getWFData():
|
||||
|
||||
Loading…
Reference in New Issue
Block a user