bugfix: add new tests and refactor get_none
This commit is contained in:
Sebastian Wehling-Benatelli
parent
221743fe20
commit
7fbc3bc5ae
10
autoPyLoT.py
10
autoPyLoT.py
@ -28,7 +28,7 @@ from pylot.core.util.dataprocessing import restitute_data, 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 get_None, trim_station_components, check4gapsAndRemove, check4doubled, \
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from pylot.core.util.utils import get_none, trim_station_components, check4gapsAndRemove, 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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@ -91,9 +91,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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sp=sp_info)
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print(splash)
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parameter = get_None(parameter)
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inputfile = get_None(inputfile)
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eventid = get_None(eventid)
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parameter = get_none(parameter)
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inputfile = get_none(inputfile)
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eventid = get_none(eventid)
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fig_dict = None
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fig_dict_wadatijack = None
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@ -154,7 +154,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
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datastructure.setExpandFields(exf)
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# check if default location routine NLLoc is available and all stations are used
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if get_None(parameter['nllocbin']) and station == 'all':
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if get_none(parameter['nllocbin']) and station == 'all':
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locflag = 1
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# get NLLoc-root path
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nllocroot = parameter.get('nllocroot')
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@ -22,7 +22,7 @@ from pylot.core.pick.picker import AICPicker, PragPicker
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from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
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getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
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from pylot.core.util.utils import getPatternLine, gen_Pool, \
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get_bool, identifyPhaseID, get_None, correct_iplot
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get_bool, identifyPhaseID, get_none, correct_iplot
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def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
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@ -258,7 +258,7 @@ class AutopickStation(object):
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self.pickparams = copy.deepcopy(pickparam)
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self.verbose = verbose
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self.iplot = correct_iplot(iplot)
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self.fig_dict = get_None(fig_dict)
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self.fig_dict = get_none(fig_dict)
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self.metadata = metadata
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self.origin = origin
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@ -15,7 +15,7 @@ import numpy as np
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from obspy.core import Stream, UTCDateTime
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from scipy.signal import argrelmax
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from pylot.core.util.utils import get_bool, get_None, SetChannelComponents
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from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
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def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
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@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
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PickError = symmetrize_error(diffti_te, diffti_tl)
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if iplot > 1:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # iplot)
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plt_flag = 1
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fig._tight = True
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@ -344,7 +344,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
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print("fmpicker: Found polarity %s" % FM)
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if iplot > 1:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # iplot)
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plt_flag = 1
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fig._tight = True
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@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
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returnflag = 0
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if iplot > 1:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # iplot)
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plt_flag = 1
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fig._tight = True
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@ -1213,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
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t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
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trace.stats.npts)
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if i == 0:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # self.iplot) ### WHY? MP MP
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plt_flag = 1
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ax1 = fig.add_subplot(3, 1, i + 1)
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ax = ax1
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ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
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else:
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if get_None(fig) is None:
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if get_none(fig) is None:
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fig = plt.figure() # self.iplot) ### WHY? MP MP
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plt_flag = 1
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ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
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@ -1494,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
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# set initial quality to 4 (worst) and change only if one condition is hit
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quality = 4
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if get_None(uncertainty) is None:
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if get_none(uncertainty) is None:
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return quality
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if uncertainty <= Errors[0]:
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@ -315,15 +315,32 @@ def fnConstructor(s):
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return fn
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def get_None(value):
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def get_none(value):
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"""
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Convert "None" to None
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:param value:
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:type value: str, bool
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:type value: str, NoneType
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:return:
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:rtype: bool
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:rtype: type(value) or NoneType
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>>> st = read()
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>>> print(get_none(st))
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3 Trace(s) in Stream:
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BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
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BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
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BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
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>>> get_none('Stream')
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'Stream'
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>>> get_none(0)
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0
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>>> get_none(0.)
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0.0
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>>> print(get_none('None'))
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None
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>>> print(get_none(None))
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None
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"""
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if value == 'None':
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if value is None or (type(value) is str and value == 'None'):
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return None
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else:
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return value
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@ -53,7 +53,7 @@ from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorte
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pick_linestyle_plt, pick_color_plt, \
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check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
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loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
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identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
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identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
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station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
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from autoPyLoT import autoPyLoT
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from pylot.core.util.thread import Thread
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@ -860,26 +860,13 @@ class WaveformWidgetPG(QtWidgets.QWidget):
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def clearPlotDict(self):
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self.plotdict = dict()
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def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
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component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
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def station_sort(nslc):
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"""Try to sort after station integer in case of a line array (e.g. active seismics)"""
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try:
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rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
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return rval
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except ValueError as e:
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# this is the standard case for seismological stations
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pass
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except Exception as e:
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print(f'Sorting by station integer failed with unknown exception: {e}')
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# fallback to default sorting
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return sorted(nslc)
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def plotWFData(self, wfdata, wfsyn=None, title=None, zoomx=None, zoomy=None,
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noiselevel=None, scaleddata=False, mapping=True,
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component='*', nth_sample=1, iniPick=None, verbosity=0,
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method='normal', gain=1.):
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if not wfdata:
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print('Nothing to plot.')
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return
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self.title = title
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self.clearPlotDict()
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self.wfstart, self.wfend = full_range(wfdata)
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@ -897,12 +884,14 @@ class WaveformWidgetPG(QtWidgets.QWidget):
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else:
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st_select = wfdata
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st_select, gaps = merge_stream(st_select)
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# list containing tuples of network, station, channel (for sorting)
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nslc = []
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for trace in st_select:
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nslc.append(
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trace.get_id()) # (trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
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nslc = station_sort(nslc)
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nslc.sort()
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nslc.reverse()
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plots = []
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@ -966,7 +955,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
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self.ylabel = ''
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self.setXLims([0, self.wfend - self.wfstart])
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self.setYLims([0.5, nmax + 0.5])
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return plots
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return plots, gaps
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def minMax(self, trace, time_ax):
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'''
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@ -988,7 +977,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
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min_ = data.min(axis=1)
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max_ = data.max(axis=1)
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if remaining_samples:
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extreme_values = np.empty((npixel + 1, 2), dtype=float)
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extreme_values = np.empty((npixel + 1, 2), dtype=np.float)
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extreme_values[:-1, 0] = min_
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extreme_values[:-1, 1] = max_
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extreme_values[-1, 0] = \
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@ -996,7 +985,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
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extreme_values[-1, 1] = \
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trace.data[-remaining_samples:].max()
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else:
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extreme_values = np.empty((npixel, 2), dtype=float)
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extreme_values = np.empty((npixel, 2), dtype=np.float)
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extreme_values[:, 0] = min_
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extreme_values[:, 1] = max_
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data = extreme_values.flatten()
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@ -1566,114 +1555,6 @@ class PylotCanvas(FigureCanvas):
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self.draw()
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class SearchFileByExtensionDialog(QtWidgets.QDialog):
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def __init__(self, parent=None, label='Text: ', default_text='.xml', events=None):
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super(SearchFileByExtensionDialog, self).__init__(parent)
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self.events = events
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self.filepaths = []
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self.file_extensions = []
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self.default_text = default_text
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self.label = label
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self.setButtons()
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self.setupUi()
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self.connectSignals()
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self.showPaths()
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self.refreshSelectionBox()
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self.refresh_timer = QTimer(self)
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self.refresh_timer.timeout.connect(self.showPaths)
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self.refresh_timer.start(10000)
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self.resize(800, 450)
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def setupUi(self):
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self.main_layout = QtWidgets.QVBoxLayout()
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self.header_layout = QtWidgets.QHBoxLayout()
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#
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self.setLayout(self.main_layout)
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# widgets inside the dialog
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self.textLabel = QtWidgets.QLabel(self.label)
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self.comboBox = QtWidgets.QComboBox()
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self.comboBox.addItem(self.default_text)
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self.comboBox.setEditable(True)
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# optional search button, currently disabled. List refreshed when text changes
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self.searchButton = QtWidgets.QPushButton('Search')
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self.searchButton.setVisible(False)
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self.tableWidget = QtWidgets.QTableWidget()
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tableWidget = self.tableWidget
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tableWidget.setColumnCount(3)
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tableWidget.setRowCount(len(self.events))
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tableWidget.setHorizontalHeaderLabels(('Event ID', 'Filename', 'Last modified'))
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tableWidget.setEditTriggers(tableWidget.NoEditTriggers)
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tableWidget.setSortingEnabled(True)
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header = tableWidget.horizontalHeader()
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header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
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header.setStretchLastSection(True)
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self.statusText = QtWidgets.QLabel()
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self.header_layout.addWidget(self.textLabel)
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self.header_layout.addWidget(self.comboBox)
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self.header_layout.addWidget(self.searchButton)
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self.main_layout.addLayout(self.header_layout)
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self.main_layout.addWidget(self.tableWidget)
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self.main_layout.addWidget(self.statusText)
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self.main_layout.addWidget(self._buttonbox)
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def showPaths(self):
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self.filepaths = []
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fext = self.comboBox.currentText()
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self.tableWidget.clearContents()
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for index, event in enumerate(self.events):
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filename = get_pylot_eventfile_with_extension(event, fext)
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self.tableWidget.setItem(index, 0, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
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if filename:
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self.filepaths.append(filename)
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ts = int(os.path.getmtime(filename))
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# create QTableWidgetItems of filepath and last modification time
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fname_item = QtWidgets.QTableWidgetItem(f'{os.path.split(filename)[-1]}')
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ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
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self.tableWidget.setItem(index, 1, fname_item)
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self.tableWidget.setItem(index, 2, ts_item)
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# TODO: Idea -> only refresh if table contents changed. Use selection to load only a subset of files
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if len(self.filepaths) > 0:
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status_text = f'Found {len(self.filepaths)} eventfiles. Do you want to load them?'
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else:
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status_text = 'Did not find any files for specified file mask.'
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self.statusText.setText(status_text)
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def refreshSelectionBox(self):
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fext = self.comboBox.currentText()
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self.file_extensions = [fext]
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for event in self.events:
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extensions = get_possible_pylot_eventfile_extensions(event, '*.xml')
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for ext in extensions:
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if not ext in self.file_extensions:
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self.file_extensions.append(ext)
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self.comboBox.clear()
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for ext in sorted(self.file_extensions):
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self.comboBox.addItem(ext)
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def setButtons(self):
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self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
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QDialogButtonBox.Cancel)
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def connectSignals(self):
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self._buttonbox.accepted.connect(self.accept)
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self._buttonbox.rejected.connect(self.reject)
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self.comboBox.editTextChanged.connect(self.showPaths)
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self.searchButton.clicked.connect(self.showPaths)
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class SingleTextLineDialog(QtWidgets.QDialog):
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def __init__(self, parent=None, label='Text: ', default_text='.xml'):
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super(SingleTextLineDialog, self).__init__(parent)
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@ -1905,7 +1786,7 @@ class PickDlg(QDialog):
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# init expected picks using obspy Taup
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try:
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if self.metadata and model != "None":
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if self.metadata and model is not None:
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self.model = TauPyModel(model)
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self.get_arrivals()
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self.drawArrivals()
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@ -2632,9 +2513,7 @@ class PickDlg(QDialog):
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data.normalize()
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if not data:
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QtWidgets.QMessageBox.warning(self, 'No channel to plot',
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'No channel to plot for phase: {}. '
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'Make sure to select the correct channels for P and S '
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'in the menu in the top panel.'.format(phase))
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'No channel to plot for phase: {}.'.format(phase))
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self.leave_picking_mode()
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return
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@ -2774,7 +2653,7 @@ class PickDlg(QDialog):
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minFMSNR = parameter.get('minFMSNR')
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quality = get_quality_class(spe, parameter.get('timeerrorsP'))
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if quality <= minFMweight and snr >= minFMSNR:
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FM = fmpicker(self.getWFData().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
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FM = fmpicker(self.getWFData().select(channel=channel), wfdata, parameter.get('fmpickwin'),
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pick - stime_diff)
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# save pick times for actual phase
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@ -3687,9 +3566,8 @@ class TuneAutopicker(QWidget):
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# wfdat = remove_underscores(wfdat)
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# rotate misaligned stations to ZNE
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# check for gaps and doubled channels
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wfdat, _ = check_for_gaps_and_merge(wfdat)
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# check for nans
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check_for_nan(wfdat)
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wfdat, gaps = merge_stream(wfdat)
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# check4gaps(wfdat)
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check4doubled(wfdat)
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wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
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# trim station components to same start value
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@ -3733,14 +3611,14 @@ class TuneAutopicker(QWidget):
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self.listWidget.scrollToBottom()
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def get_current_event(self):
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path = self.get_current_event_fp()
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path = self.eventBox.currentText()
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return self.parent().project.getEventFromPath(path)
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def get_current_event_name(self):
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return self.eventBox.currentText().split('/')[-1].rstrip('*')
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return self.eventBox.currentText().split('/')[-1].split('*')[0]
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def get_current_event_fp(self):
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return self.eventBox.currentText().rstrip('*')
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return self.eventBox.currentText().split('*')[0]
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def get_current_event_picks(self, station):
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event = self.get_current_event()
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@ -3844,7 +3722,6 @@ class TuneAutopicker(QWidget):
|
||||
st = self.data.getWFData()
|
||||
tr = st.select(station=self.get_current_station())[0]
|
||||
starttime = tr.stats.starttime
|
||||
# create two lists with figure names and subindices (for subplots) to get the correct axes
|
||||
p_axes = [
|
||||
('mainFig', 0),
|
||||
('aicFig', 0),
|
||||
@ -4792,8 +4669,8 @@ class InputsTab(PropTab):
|
||||
self.tstopBox = QSpinBox()
|
||||
for spinbox in [self.tstartBox, self.tstopBox]:
|
||||
spinbox.setRange(-99999, 99999)
|
||||
self.tstartBox.setValue(float(settings.value('tstart')) if get_None(settings.value('tstart')) else 0)
|
||||
self.tstopBox.setValue(float(settings.value('tstop')) if get_None(settings.value('tstop')) else 1e6)
|
||||
self.tstartBox.setValue(float(settings.value('tstart')) if get_none(settings.value('tstart')) else 0)
|
||||
self.tstopBox.setValue(float(settings.value('tstop')) if get_none(settings.value('tstop')) else 1e6)
|
||||
self.cuttimesLayout.addWidget(self.tstartBox, 10)
|
||||
self.cuttimesLayout.addWidget(QLabel('[s] and'), 0)
|
||||
self.cuttimesLayout.addWidget(self.tstopBox, 10)
|
||||
@ -5786,20 +5663,9 @@ class ChooseWaveFormWindow(QWidget):
|
||||
def submit(self):
|
||||
matplotlib.pyplot.close(self.currentSpectro)
|
||||
t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
|
||||
self.applyFFT()
|
||||
|
||||
def applyFFT(self, trace):
|
||||
tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
|
||||
transformed = abs(np.fft.rfft(tra.data))
|
||||
print ( transformed )
|
||||
matplotlib.pyplot.plot ( transformed )
|
||||
matplotlib.pyplot.show()
|
||||
|
||||
def applyFFTs(self, tra):
|
||||
transformed = abs(np.fft.rfft(tra.data))
|
||||
print ( transformed )
|
||||
matplotlib.pyplot.plot ( transformed )
|
||||
matplotlib.pyplot.show()
|
||||
self.currentSpectro = self.traces[
|
||||
self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
|
||||
self.currentSpectro.show()
|
||||
|
||||
def submitN(self):
|
||||
matplotlib.pyplot.close(self.currentSpectro)
|
||||
@ -5815,6 +5681,13 @@ class ChooseWaveFormWindow(QWidget):
|
||||
self.chooseBoxTraces.currentText()[3:]]['E'].spectrogram(show=False, title=t)
|
||||
self.currentSpectro.show()
|
||||
|
||||
def submitZ(self):
|
||||
matplotlib.pyplot.close(self.currentSpectro)
|
||||
t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
|
||||
self.currentSpectro = self.traces[
|
||||
self.chooseBoxTraces.currentText()[3:]]['Z'].spectrogram(show=False, title=t)
|
||||
self.currentSpectro.show()
|
||||
|
||||
# Creates a QComboBox and adds all traces provided
|
||||
def createComboBoxTraces(self):
|
||||
if len(self.wFs) <= 0:
|
||||
@ -5841,55 +5714,6 @@ class ChooseWaveFormWindow(QWidget):
|
||||
pass
|
||||
|
||||
|
||||
class SpectrogramTab(QWidget):
|
||||
def __init__(self, traces, wfdata, parent=None):
|
||||
super(SpectrogramTab, self).__init__(parent)
|
||||
self.setupUi()
|
||||
self.traces = traces
|
||||
self.wfdata = wfdata
|
||||
|
||||
def setupUi(self):
|
||||
pass
|
||||
def makeSpecFig(self, direction = 'Z', height = 0, width = 0, parent = None):
|
||||
|
||||
i = 0
|
||||
grams = []
|
||||
figure, axis = matplotlib.pyplot.subplots(len(self.traces), sharex=True)
|
||||
|
||||
start, end = full_range(self.wfdata)
|
||||
|
||||
if height != 0 and width != 0:
|
||||
figure.figsize = (width, height)
|
||||
figure.set_figwidth = width
|
||||
figure.set_figheight = height
|
||||
|
||||
#figure.tight_layout()
|
||||
|
||||
for t in self.traces:
|
||||
tra = self.traces[t][direction]
|
||||
#print(start, end)
|
||||
|
||||
# Set Title
|
||||
if i == 0:
|
||||
if direction == 'Z':
|
||||
figure.suptitle("section: vertical components")
|
||||
elif direction == 'E':
|
||||
figure.suptitle("section: east-west components")
|
||||
elif direction == 'N':
|
||||
figure.suptitle("section: north-south components")
|
||||
axis[i].vlines(0, axis[i].get_ylim()[0], axis[i].get_ylim()[1],
|
||||
colors='m', linestyles='dashed',
|
||||
linewidth=2)
|
||||
|
||||
grams.append(tra.spectrogram(show=False, axes=axis[i]))
|
||||
i+=1
|
||||
|
||||
#figure.setXLims([0, end - start])
|
||||
figure.set_tight_layout(True)
|
||||
fC = FigureCanvas(figure)
|
||||
return fC
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
import doctest
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user