Merge branch 'feature/obspy_dmt_interface' into develop
This commit is contained in:
commit
d57c193a0b
1
.gitignore
vendored
1
.gitignore
vendored
@ -1,3 +1,4 @@
|
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*.pyc
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*~
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pylot/RELEASE-VERSION
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*.idea
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133
PyLoT.py
133
PyLoT.py
@ -138,6 +138,7 @@ class MainWindow(QMainWindow):
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self._eventChanged = [False, False]
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self.apd_local = None
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self.apd_sge = None
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self.stations_highlighted = []
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self.poS_id = None
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self.ae_id = None
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@ -615,6 +616,10 @@ class MainWindow(QMainWindow):
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# add scroll area used in case number of traces gets too high
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self.wf_scroll_area = QtGui.QScrollArea(self)
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self.wf_scroll_area.setVisible(False)
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self.no_data_label = QLabel('No Data')
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self.no_data_label.setStyleSheet('color: red')
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self.no_data_label.setAlignment(Qt.AlignCenter)
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# create central matplotlib figure canvas widget
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self.init_wfWidget()
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@ -637,6 +642,7 @@ class MainWindow(QMainWindow):
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self.tabs.addTab(array_tab, 'Array Map')
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self.tabs.addTab(events_tab, 'Eventlist')
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self.wf_layout.addWidget(self.no_data_label)
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self.wf_layout.addWidget(self.wf_scroll_area)
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self.wf_scroll_area.setWidgetResizable(True)
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self.init_array_tab()
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@ -1249,6 +1255,17 @@ class MainWindow(QMainWindow):
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event_ref = event.isRefEvent()
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event_test = event.isTestEvent()
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time = lat = lon = depth = mag = None
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if len(event.origins) == 1:
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origin = event.origins[0]
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time = origin.time + 0 # add 0 because there was an exception for time = 0s
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lat = origin.latitude
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lon = origin.longitude
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depth = origin.depth
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if len(event.magnitudes) == 1:
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magnitude = event.magnitudes[0]
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mag = magnitude.mag
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# text = '{path:{plen}} | manual: [{p:3d}] | auto: [{a:3d}]'
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# text = text.format(path=event_path,
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# plen=plmax,
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@ -1256,6 +1273,11 @@ class MainWindow(QMainWindow):
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# a=event_nautopicks)
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item_path = QtGui.QStandardItem('{path:{plen}}'.format(path=event_path, plen=plmax))
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item_time = QtGui.QStandardItem('{}'.format(time))
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item_lat = QtGui.QStandardItem('{}'.format(lat))
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item_lon = QtGui.QStandardItem('{}'.format(lon))
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item_depth = QtGui.QStandardItem('{}'.format(depth))
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item_mag = QtGui.QStandardItem('{}'.format(mag))
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item_nmp = QtGui.QStandardItem(str(ma_count['manual']))
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item_nmp.setIcon(self.manupicksicon_small)
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item_nap = QtGui.QStandardItem(str(ma_count['auto']))
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@ -1281,8 +1303,11 @@ class MainWindow(QMainWindow):
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# item.setFont(font)
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# item2.setForeground(QtGui.QColor('black'))
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# item2.setFont(font)
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itemlist = [item_path, item_nmp, item_nap, item_ref, item_test, item_notes]
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if event_test and select_events == 'ref':
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itemlist = [item_path, item_time, item_lat, item_lon, item_depth,
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item_mag, item_nmp, item_nap, item_ref, item_test, item_notes]
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for item in itemlist:
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item.setTextAlignment(Qt.AlignCenter)
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if event_test and select_events == 'ref' or self.isEmpty(event_path):
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for item in itemlist:
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item.setEnabled(False)
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model.appendRow(itemlist)
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@ -1296,6 +1321,23 @@ class MainWindow(QMainWindow):
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eventBox.setCurrentIndex(index)
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self.refreshRefTestButtons()
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def isEmpty(self, event_path):
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wf_stat = {True: 'processed',
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False: 'raw',
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None: None}
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# self.data.processed is only None for PyLoT datastructure, else True or False
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wf_dir = wf_stat[self.data.processed]
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if wf_dir is not None:
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wf_path = os.path.join(event_path, wf_dir)
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if wf_dir is 'processed' and not os.path.exists(wf_path):
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wf_path = os.path.join(event_path, 'raw')
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else:
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wf_path = event_path
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if not os.path.exists(wf_path):
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return True
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return not bool(os.listdir(wf_path))
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def filename_from_action(self, action):
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if action.data() is None:
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filt = "Supported file formats" \
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@ -1666,6 +1708,21 @@ class MainWindow(QMainWindow):
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metadata=self.metadata,
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obspy_dmt=obspy_dmt)
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def setWFstatus(self):
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'''
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show status of current data, can be either 'raw' or 'processed'
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:param status:
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:return:
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'''
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status = self.data.processed
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wf_stat_color = {True: 'green',
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False: 'black',
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None: None}
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wf_stat = {True: 'processed',
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False: 'raw',
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None: None}
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self.dataPlot.setPermTextRight(wf_stat[status], wf_stat_color[status])
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def check_plot_quantity(self):
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"""
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Check the amount of samples to be plotted and ask user to reduce the amount if it is too large.
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@ -1757,7 +1814,10 @@ class MainWindow(QMainWindow):
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def finish_pg_plot(self):
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self.getPlotWidget().updateWidget()
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plots = self.wfp_thread.data
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plots, gaps = 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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for times, data, times_syn, data_syn in plots:
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self.dataPlot.plotWidget.getPlotItem().plot(times, data,
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pen=self.dataPlot.pen_linecolor)
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@ -1765,8 +1825,7 @@ class MainWindow(QMainWindow):
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self.dataPlot.plotWidget.getPlotItem().plot(times_syn, data_syn,
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pen=self.dataPlot.pen_linecolor_syn)
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self.dataPlot.reinitMoveProxy()
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self.dataPlot.plotWidget.showAxis('left')
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self.dataPlot.plotWidget.showAxis('bottom')
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self.highlight_stations()
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def finishWaveformDataPlot(self):
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self.comparable = self.checkEvents4comparison()
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@ -1808,6 +1867,7 @@ class MainWindow(QMainWindow):
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if True in self.comparable.values():
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self.compare_action.setEnabled(True)
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self.draw()
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self.setWFstatus()
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def checkEvent4comparison(self, event):
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if event.pylot_picks and event.pylot_autopicks:
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@ -1842,12 +1902,10 @@ class MainWindow(QMainWindow):
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comparable[event.pylot_id] = self.checkEvent4comparison(event)
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return comparable
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def clearWaveformDataPlot(self):
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def clearWaveformDataPlot(self, refresh_plot=False):
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self.disconnectWFplotEvents()
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if self.pg:
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self.dataPlot.plotWidget.getPlotItem().clear()
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self.dataPlot.plotWidget.hideAxis('bottom')
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self.dataPlot.plotWidget.hideAxis('left')
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else:
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for ax in self.dataPlot.axes:
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ax.cla()
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@ -1863,6 +1921,9 @@ class MainWindow(QMainWindow):
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self.openEventAction.setEnabled(False)
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self.openEventsAutoAction.setEnabled(False)
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self.loadpilotevent.setEnabled(False)
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if not refresh_plot:
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self.wf_scroll_area.setVisible(False)
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self.no_data_label.setVisible(True)
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self.disableSaveEventAction()
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self.draw()
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@ -1871,7 +1932,7 @@ class MainWindow(QMainWindow):
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Open a modal thread to plot current waveform data.
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'''
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self.check_plot_quantity()
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self.clearWaveformDataPlot()
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self.clearWaveformDataPlot(refresh_plot=True)
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self.wfp_thread = Thread(self, self.plotWaveformData,
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arg=filter,
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progressText='Plotting waveform data...',
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@ -1904,9 +1965,10 @@ class MainWindow(QMainWindow):
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self.plot_method = 'fast'
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else:
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self.plot_method = 'normal'
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plots = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp,
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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)
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return plots
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plots, gaps = rval if rval else ([], [])
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return plots, gaps
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def adjustPlotHeight(self):
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if self.pg:
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@ -2135,10 +2197,12 @@ class MainWindow(QMainWindow):
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def pickOnStation(self, gui_event):
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if self.pg:
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if not gui_event.button() == 1:
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button = gui_event.button()
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if not button in [1, 4]:
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return
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else:
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if not gui_event.button == 1:
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button = gui_event.button
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if not button == 1:
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return
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if self.pg:
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@ -2149,12 +2213,42 @@ class MainWindow(QMainWindow):
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wfID = self.getWFID(ycoord)
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if wfID is None: return
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self.pickDialog(wfID)
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def pickDialog(self, wfID, nextStation=False):
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network = self.getNetworkName(wfID)
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station = self.getStationName(wfID)
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if button == 1:
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self.pickDialog(wfID, network, station)
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elif button == 4:
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self.toggle_station_color(wfID, network, station)
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def toggle_station_color(self, wfID, network, station):
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black_pen = pg.mkPen((0, 0, 0))
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red_pen = pg.mkPen((200, 50, 50))
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line_item = self.dataPlot.plotWidget.getPlotItem().listDataItems()[wfID - 1]
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current_pen = line_item.opts['pen']
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nwst = '{}.{}'.format(network, station)
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if current_pen == black_pen:
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line_item.setPen(red_pen)
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if not nwst in self.stations_highlighted:
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self.stations_highlighted.append(nwst)
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else:
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line_item.setPen(black_pen)
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if nwst in self.stations_highlighted:
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self.stations_highlighted.pop(self.stations_highlighted.index(nwst))
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def highlight_stations(self):
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for wfID, value in self.getPlotWidget().getPlotDict().items():
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station, channel, network = value
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nwst = '{}.{}'.format(network, station)
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if nwst in self.stations_highlighted:
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self.toggle_station_color(wfID, network, station)
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def pickDialog(self, wfID, network=None, station=None, nextStation=False):
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if not network:
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network = self.getNetworkName(wfID)
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if not station:
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station = self.getStationName(wfID)
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if not station or not network:
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return
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self.update_status('picking on station {0}'.format(station))
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data = self.get_data().getOriginalWFData().copy()
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@ -2894,7 +2988,7 @@ class MainWindow(QMainWindow):
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if hasattr(event, 'origins'):
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if event.origins:
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origin = event.origins[0]
|
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item_time.setText(str(origin.time).split('.')[0])
|
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item_time.setText(str(origin.time + 0).split('.')[0]) # +0 as workaround in case time=0s
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item_lon.setText(str(origin.longitude))
|
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item_lat.setText(str(origin.latitude))
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item_depth.setText(str(origin.depth))
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@ -2931,6 +3025,9 @@ class MainWindow(QMainWindow):
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if index%2:
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set_background_color(column, QtGui.QColor(*(245, 245, 245, 255)))
|
||||
|
||||
if self.isEmpty(event.path):
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set_foreground_color(column, QtGui.QColor(*(180, 180, 180, 255)))
|
||||
|
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if event == current_event:
|
||||
set_foreground_color(column, QtGui.QColor(*(0, 143, 143, 255)))
|
||||
|
||||
@ -3197,9 +3294,9 @@ class MainWindow(QMainWindow):
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||||
self.fill_eventbox()
|
||||
self.getPlotWidget().draw()
|
||||
if self.plot_method == 'fast':
|
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self.dataPlot.setPermText('MIN/MAX plot', color='red')
|
||||
self.dataPlot.setPermTextMid('MIN/MAX plot', color='red')
|
||||
else:
|
||||
self.dataPlot.setPermText()
|
||||
self.dataPlot.setPermTextMid()
|
||||
|
||||
def _setDirty(self):
|
||||
self.setDirty(True)
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
#
|
||||
# WARNING! All changes made in this file will be lost!
|
||||
|
||||
from PyQt4 import QtCore
|
||||
from PySide import QtCore
|
||||
|
||||
qt_resource_data = "\
|
||||
\x00\x00\x9e\x04\
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
#
|
||||
# WARNING! All changes made in this file will be lost!
|
||||
|
||||
from PyQt4 import QtCore
|
||||
from PySide import QtCore
|
||||
|
||||
qt_resource_data = "\
|
||||
\x00\x00\x9e\x04\
|
||||
|
||||
@ -15,7 +15,7 @@ from pylot.core.util.event import Event
|
||||
from pylot.core.util.utils import fnConstructor, full_range, remove_underscores, check4gaps, check4doubled, \
|
||||
check4rotated, trim_station_components
|
||||
import pylot.core.loc.velest as velest
|
||||
|
||||
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
|
||||
|
||||
class Data(object):
|
||||
"""
|
||||
@ -60,6 +60,8 @@ class Data(object):
|
||||
raise NotImplementedError('PILOT location information '
|
||||
'read support not yet '
|
||||
'implemeted.')
|
||||
elif 'event.pkl' in evtdata:
|
||||
evtdata = qml_from_obspyDMT(evtdata)
|
||||
else:
|
||||
raise e
|
||||
else:
|
||||
@ -72,6 +74,7 @@ class Data(object):
|
||||
self.wforiginal = None
|
||||
self.cuttimes = None
|
||||
self.dirty = False
|
||||
self.processed = None
|
||||
|
||||
def __str__(self):
|
||||
return str(self.wfdata)
|
||||
@ -379,8 +382,14 @@ class Data(object):
|
||||
self.wfsyn = Stream()
|
||||
wffnames = None
|
||||
wffnames_syn = None
|
||||
wfdir = 'processed' if 'processed' in [fname.split('/')[-1] for fname in fnames] else 'raw'
|
||||
if obspy_dmt:
|
||||
wfdir = 'raw'
|
||||
self.processed = False
|
||||
for fname in fnames:
|
||||
if fname.endswith('processed'):
|
||||
wfdir = 'processed'
|
||||
self.processed = True
|
||||
break
|
||||
for fpath in fnames:
|
||||
if fpath.endswith(wfdir):
|
||||
wffnames = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
|
||||
@ -398,9 +407,6 @@ class Data(object):
|
||||
# various pre-processing steps:
|
||||
# remove possible underscores in station names
|
||||
self.wfdata = remove_underscores(self.wfdata)
|
||||
# check for gaps and doubled channels
|
||||
check4gaps(self.wfdata)
|
||||
check4doubled(self.wfdata)
|
||||
# check for stations with rotated components
|
||||
if checkRotated and metadata is not None:
|
||||
self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
|
||||
|
||||
@ -7,6 +7,7 @@ from obspy import UTCDateTime
|
||||
from obspy.core.event import Event as ObsPyEvent
|
||||
from obspy.core.event import Origin, ResourceIdentifier
|
||||
from pylot.core.io.phases import picks_from_picksdict
|
||||
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
|
||||
|
||||
|
||||
class Event(ObsPyEvent):
|
||||
@ -33,6 +34,7 @@ class Event(ObsPyEvent):
|
||||
self._testEvent = False
|
||||
self._refEvent = False
|
||||
self.get_notes()
|
||||
self.get_obspy_event_info()
|
||||
|
||||
def get_notes_path(self):
|
||||
"""
|
||||
@ -43,6 +45,18 @@ class Event(ObsPyEvent):
|
||||
notesfile = os.path.join(self.path, 'notes.txt')
|
||||
return notesfile
|
||||
|
||||
def get_obspy_event_info(self):
|
||||
infile_pickle = os.path.join(self.path, 'info/event.pkl')
|
||||
if not os.path.isfile(infile_pickle):
|
||||
return
|
||||
try:
|
||||
event_dmt = qml_from_obspyDMT(infile_pickle)
|
||||
except Exception as e:
|
||||
print('Could not get obspy event info: {}'.format(e))
|
||||
return
|
||||
self.magnitudes = event_dmt.magnitudes
|
||||
self.origins = event_dmt.origins
|
||||
|
||||
def get_notes(self):
|
||||
"""
|
||||
set self.note attribute to content of notes file
|
||||
|
||||
@ -25,4 +25,20 @@ def check_obspydmt_eventfolder(folder):
|
||||
except Exception as e:
|
||||
return False, e
|
||||
|
||||
check_obspydmt_eventfolder('20110311_054623.a')
|
||||
def qml_from_obspyDMT(path):
|
||||
import pickle
|
||||
from obspy.core.event import Event, Magnitude, Origin
|
||||
|
||||
if not os.path.exists(path):
|
||||
return IOError('Could not find Event at {}'.format(path))
|
||||
infile = open(path, 'rb')
|
||||
event_dmt = pickle.load(infile)
|
||||
ev = Event(resource_id=event_dmt['event_id'])
|
||||
origin = Origin(resource_id=event_dmt['origin_id'], time=event_dmt['datetime'], longitude=event_dmt['longitude'],
|
||||
latitude=event_dmt['latitude'], depth=event_dmt['depth'])
|
||||
mag = Magnitude(mag=event_dmt['magnitude'], magnitude_type=event_dmt['magnitude_type'],
|
||||
origin_id=event_dmt['origin_id'])
|
||||
ev.magnitudes.append(mag)
|
||||
ev.origins.append(origin)
|
||||
return ev
|
||||
|
||||
|
||||
@ -447,23 +447,25 @@ class WaveformWidgetPG(QtGui.QWidget):
|
||||
self.orig_parent = parent
|
||||
# attribute plotdict is a dictionary connecting position and a name
|
||||
self.plotdict = dict()
|
||||
# init labels
|
||||
self.xlabel = None
|
||||
self.ylabel = None
|
||||
self.title = None
|
||||
# create plot
|
||||
self.main_layout = QtGui.QVBoxLayout()
|
||||
self.label_layout = QtGui.QHBoxLayout()
|
||||
self.status_label = QtGui.QLabel()
|
||||
self.perm_label = QtGui.QLabel()
|
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self.setLayout(self.main_layout)
|
||||
self.add_labels()
|
||||
self.plotWidget = self.pg.PlotWidget(self.parent(), title=title)
|
||||
self.main_layout.addWidget(self.plotWidget)
|
||||
self.main_layout.addLayout(self.label_layout)
|
||||
self.label_layout.addWidget(self.status_label)
|
||||
self.label_layout.addWidget(self.perm_label)
|
||||
self.label_layout.addWidget(self.perm_label_mid)
|
||||
self.label_layout.addWidget(self.perm_label_right)
|
||||
self.plotWidget.showGrid(x=False, y=True, alpha=0.3)
|
||||
self.plotWidget.hideAxis('bottom')
|
||||
self.plotWidget.hideAxis('left')
|
||||
self.wfstart, self.wfend = 0, 0
|
||||
self.pen_multicursor = self.pg.mkPen(self.parent()._style['multicursor']['rgba'])
|
||||
self.pen_linecolor = self.pg.mkPen(self.parent()._style['linecolor']['rgba'])
|
||||
self.pen_linecolor_highlight = self.pg.mkPen((255, 100, 100, 255))
|
||||
self.pen_linecolor_syn = self.pg.mkPen((100, 0, 255, 255))
|
||||
self.reinitMoveProxy()
|
||||
self._proxy = self.pg.SignalProxy(self.plotWidget.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)
|
||||
@ -489,12 +491,24 @@ class WaveformWidgetPG(QtGui.QWidget):
|
||||
self.vLine.setPos(mousePoint.x())
|
||||
self.hLine.setPos(mousePoint.y())
|
||||
|
||||
def add_labels(self):
|
||||
self.status_label = QtGui.QLabel()
|
||||
self.perm_label_mid = QtGui.QLabel()
|
||||
self.perm_label_mid.setAlignment(4)
|
||||
self.perm_label_right = QtGui.QLabel()
|
||||
self.perm_label_right.setAlignment(2)
|
||||
self.setLayout(self.main_layout)
|
||||
|
||||
def getPlotDict(self):
|
||||
return self.plotdict
|
||||
|
||||
def setPermText(self, text=None, color='black'):
|
||||
self.perm_label.setText(text)
|
||||
self.perm_label.setStyleSheet('color: {}'.format(color))
|
||||
def setPermTextMid(self, text=None, color='black'):
|
||||
self.perm_label_mid.setText(text)
|
||||
self.perm_label_mid.setStyleSheet('color: {}'.format(color))
|
||||
|
||||
def setPermTextRight(self, text=None, color='black'):
|
||||
self.perm_label_right.setText(text)
|
||||
self.perm_label_right.setStyleSheet('color: {}'.format(color))
|
||||
|
||||
def setPlotDict(self, key, value):
|
||||
self.plotdict[key] = value
|
||||
@ -529,6 +543,14 @@ class WaveformWidgetPG(QtGui.QWidget):
|
||||
else:
|
||||
st_select = wfdata
|
||||
|
||||
gaps = st_select.get_gaps()
|
||||
if gaps:
|
||||
merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
|
||||
st_select.merge()
|
||||
print('Merged the following stations because of gaps:')
|
||||
for merged_station in merged:
|
||||
print(merged_station)
|
||||
|
||||
# list containing tuples of network, station, channel (for sorting)
|
||||
nsc = []
|
||||
for trace in st_select:
|
||||
@ -552,6 +574,8 @@ class WaveformWidgetPG(QtGui.QWidget):
|
||||
st_syn = wfsyn.select(network=network, station=station, channel=channel)
|
||||
if st_syn:
|
||||
trace_syn = st_syn[0].copy()
|
||||
else:
|
||||
trace_syn = Trace()
|
||||
if mapping:
|
||||
comp = channel[-1]
|
||||
n = compclass.getPlotPosition(str(comp))
|
||||
@ -569,8 +593,10 @@ class WaveformWidgetPG(QtGui.QWidget):
|
||||
|
||||
if method == 'fast':
|
||||
trace.data, time_ax = self.minMax(trace, time_ax)
|
||||
if trace_syn:
|
||||
trace_syn.data, time_ax_syn = self.minMax(trace_syn, time_ax_syn)
|
||||
|
||||
if time_ax not in [None, []]:
|
||||
if len(time_ax) > 0:
|
||||
if not scaleddata:
|
||||
trace.detrend('constant')
|
||||
trace.normalize(np.max(np.abs(trace.data)) * 2)
|
||||
@ -581,16 +607,16 @@ class WaveformWidgetPG(QtGui.QWidget):
|
||||
times = np.array([time for index, time in enumerate(time_ax) if not index % nth_sample])
|
||||
times_syn = np.array([time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else [])
|
||||
trace.data = np.array([datum + n for index, datum in enumerate(trace.data) if not index % nth_sample])
|
||||
trace.data_syn = np.array([datum + n for index, datum in enumerate(trace.data_syn)
|
||||
trace_syn.data = np.array([datum + n for index, datum in enumerate(trace_syn.data)
|
||||
if not index % nth_sample] if st_syn else [])
|
||||
plots.append((times, trace.data,
|
||||
times_syn, trace.data_syn))
|
||||
times_syn, trace_syn.data))
|
||||
self.setPlotDict(n, (station, channel, network))
|
||||
self.xlabel = 'seconds since {0}'.format(self.wfstart)
|
||||
self.ylabel = ''
|
||||
self.setXLims([0, self.wfend - self.wfstart])
|
||||
self.setYLims([0.5, nmax + 0.5])
|
||||
return plots
|
||||
return plots, gaps
|
||||
|
||||
def minMax(self, trace, time_ax):
|
||||
'''
|
||||
@ -1013,6 +1039,14 @@ class PylotCanvas(FigureCanvas):
|
||||
if mapping:
|
||||
plot_positions = self.calcPlotPositions(st_select, compclass)
|
||||
|
||||
gaps = st_select.get_gaps()
|
||||
if gaps:
|
||||
merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
|
||||
st_select.merge()
|
||||
print('Merged the following stations because of gaps:')
|
||||
for merged_station in merged:
|
||||
print(merged_station)
|
||||
|
||||
# list containing tuples of network, station, channel and plot position (for sorting)
|
||||
nsc = []
|
||||
for plot_pos, trace in enumerate(st_select):
|
||||
|
||||
Loading…
Reference in New Issue
Block a user