[update] added check for nan values in waveforms which crashed obspy filter routines
[minor] some tweaks and optimisations
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9
PyLoT.py
9
PyLoT.py
@ -2127,7 +2127,7 @@ class MainWindow(QMainWindow):
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def finish_pg_plot(self):
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self.getPlotWidget().updateWidget()
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plots, gaps = self.wfp_thread.data
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plots = self.wfp_thread.data
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# do not show plot if no data are given
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self.wf_scroll_area.setVisible(len(plots) > 0)
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self.no_data_label.setVisible(not len(plots) > 0)
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@ -2301,8 +2301,8 @@ class MainWindow(QMainWindow):
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self.plot_method = 'normal'
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rval = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp,
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nth_sample=int(nth_sample), method=self.plot_method, gain=self.gain)
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plots, gaps = rval if rval else ([], [])
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return plots, gaps
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plots = rval if rval else []
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return plots
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def adjustPlotHeight(self):
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if self.pg:
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@ -3807,7 +3807,8 @@ class MainWindow(QMainWindow):
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def closeEvent(self, event):
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if self.okToContinue():
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self.logwidget.close()
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if hasattr(self, 'logwidget'):
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self.logwidget.close()
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event.accept()
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else:
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event.ignore()
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@ -9,4 +9,4 @@
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conda activate pylot_38
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python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_janis_noisy.in -c $NSLOTS
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python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_adriaarray.in -c 20 -dmt processed
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@ -19,7 +19,7 @@ from pylot.core.util.errors import FormatError, OverwriteError
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from pylot.core.util.event import Event
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from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
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from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
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check4gapsAndMerge, trim_station_components
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check_for_gaps_and_merge, trim_station_components, check_for_nan
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class Data(object):
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@ -64,7 +64,7 @@ class Data(object):
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elif 'LOC' in evtdata:
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raise NotImplementedError('PILOT location information '
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'read support not yet '
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'implemeted.')
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'implemented.')
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elif 'event.pkl' in evtdata:
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evtdata = qml_from_obspyDMT(evtdata)
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else:
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@ -457,6 +457,11 @@ class Data(object):
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:param fnames: waveform data names to append
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:type fnames: list
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"""
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def check_fname_exists(filenames: list) -> list:
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if filenames:
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filenames = [fn for fn in filenames if os.path.isfile(fn)]
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return filenames
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self.wfdata = Stream()
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self.wforiginal = None
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self.wfsyn = Stream()
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@ -465,6 +470,8 @@ class Data(object):
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self.tstart = tstart
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self.tstop = tstop
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fnames = check_fname_exists(fnames)
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fnames_syn = check_fname_exists(fnames_syn)
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# if obspy_dmt:
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# wfdir = 'raw'
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# self.processed = False
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@ -491,7 +498,9 @@ class Data(object):
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# remove possible underscores in station names
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# self.wfdata = remove_underscores(self.wfdata)
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# check for gaps and merge
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self.wfdata = check4gapsAndMerge(self.wfdata)
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self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
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# check for nans
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check_for_nan(self.wfdata)
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# check for stations with rotated components
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if checkRotated and metadata is not None:
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self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
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@ -660,7 +660,7 @@ class AutopickStation(object):
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ax1.set_ylim([-1.5, 1.5])
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ax1.set_ylabel('Normalized Counts')
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if self.horizontal_traces_exist() and self.s_data.Sflag == 1:
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if self.horizontal_traces_exist():# and self.s_data.Sflag == 1:
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# plot E trace
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ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
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th1data = np.linspace(0, self.etrace.stats.endtime - self.etrace.stats.starttime,
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@ -1332,22 +1332,6 @@ def get_quality_class(uncertainty, weight_classes):
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return quality
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def set_NaNs_to(data, nan_value):
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"""
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Replace all NaNs in data with nan_value
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:param data: array holding data
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:type data: `~numpy.ndarray`
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:param nan_value: value which all NaNs are set to
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:type nan_value: float, int
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:return: data array with all NaNs replaced with nan_value
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:rtype: `~numpy.ndarray`
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"""
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nn = np.isnan(data)
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if np.any(nn):
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data[nn] = nan_value
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return data
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def taper_cf(cf):
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"""
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Taper cf data to get rid off of side maximas
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@ -818,19 +818,6 @@ def trim_station_components(data, trim_start=True, trim_end=True):
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return data
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def merge_stream(stream):
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gaps = stream.get_gaps()
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if gaps:
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# list of merged stations (seed_ids)
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merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
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stream.merge(method=1)
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print('Merged the following stations because of gaps:')
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for merged_station in merged:
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print(merged_station)
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return stream, gaps
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def check4gapsAndRemove(data):
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"""
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check for gaps in Stream and remove them
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@ -851,12 +838,12 @@ def check4gapsAndRemove(data):
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return data
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def check4gapsAndMerge(data):
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def check_for_gaps_and_merge(data):
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"""
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check for gaps in Stream and merge if gaps are found
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:param data: stream of seismic data
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:type data: `~obspy.core.stream.Stream`
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:return: data stream
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:return: data stream, gaps returned from obspy get_gaps
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:rtype: `~obspy.core.stream.Stream`
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"""
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gaps = data.get_gaps()
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@ -867,7 +854,7 @@ def check4gapsAndMerge(data):
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for merged_station in merged:
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print(merged_station)
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return data
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return data, gaps
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def check4doubled(data):
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@ -897,6 +884,21 @@ def check4doubled(data):
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return data
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def check_for_nan(data, nan_value=0.):
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"""
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Replace all NaNs in data with nan_value (in place)
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:param data: stream of seismic data
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:type data: `~obspy.core.stream.Stream`
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:param nan_value: value which all NaNs are set to
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:type nan_value: float, int
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:return: None
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"""
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if not data:
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return
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for trace in data:
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np.nan_to_num(trace.data, copy=False, nan=nan_value)
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def get_stations(data):
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"""
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Get list of all station names in data stream
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@ -51,7 +51,7 @@ from pylot.core.pick.autopick import fmpicker
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from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
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from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
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pick_linestyle_plt, pick_color_plt, \
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check4rotated, check4doubled, merge_stream, identifyPhase, \
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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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station_id_remove_channel
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@ -897,7 +897,7 @@ 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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# st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice
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# list containing tuples of network, station, channel (for sorting)
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nslc = []
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@ -968,7 +968,7 @@ 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, gaps
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return plots
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def minMax(self, trace, time_ax):
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'''
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@ -990,7 +990,7 @@ 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=np.float)
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extreme_values = np.empty((npixel + 1, 2), dtype=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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@ -998,7 +998,7 @@ 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=np.float)
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extreme_values = np.empty((npixel, 2), dtype=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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@ -3581,8 +3581,9 @@ 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, gaps = merge_stream(wfdat)
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# check4gaps(wfdat)
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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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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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@ -3737,6 +3738,7 @@ class TuneAutopicker(QWidget):
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st = self.data.getWFData()
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tr = st.select(station=self.get_current_station())[0]
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starttime = tr.stats.starttime
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# create two lists with figure names and subindices (for subplots) to get the correct axes
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p_axes = [
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('mainFig', 0),
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('aicFig', 0),
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