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Merge remote-tracking branch 'origin/develop' into feature/refactor

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This commit is contained in:
Darius Arnold 2018-07-06 09:49:52 +02:00
commit 5258a7e9b4
19 changed files with 1382 additions and 640 deletions
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1
.gitignore vendored
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@ -1,3 +1,4 @@
*.pyc *.pyc
*~ *~
pylot/RELEASE-VERSION pylot/RELEASE-VERSION
*.idea

329
PyLoT.py
View File

@ -86,7 +86,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \ PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
getDataType, ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \ getDataType, ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
CompareEventsWidget CompareEventsWidget
from pylot.core.util.map_projection import map_projection from pylot.core.util.array_map import Array_map
from pylot.core.util.structure import DATASTRUCTURE from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.thread import Thread, Worker from pylot.core.util.thread import Thread, Worker
from pylot.core.util.version import get_git_version as _getVersionString from pylot.core.util.version import get_git_version as _getVersionString
@ -138,6 +138,9 @@ class MainWindow(QMainWindow):
self._eventChanged = [False, False] self._eventChanged = [False, False]
self.apd_local = None self.apd_local = None
self.apd_sge = None self.apd_sge = None
self.stations_highlighted = []
self.obspy_dmt = False
self.nextStation = False
self.poS_id = None self.poS_id = None
self.ae_id = None self.ae_id = None
@ -615,6 +618,10 @@ class MainWindow(QMainWindow):
# add scroll area used in case number of traces gets too high # add scroll area used in case number of traces gets too high
self.wf_scroll_area = QtGui.QScrollArea(self) self.wf_scroll_area = QtGui.QScrollArea(self)
self.wf_scroll_area.setVisible(False)
self.no_data_label = QLabel('No Data')
self.no_data_label.setStyleSheet('color: red')
self.no_data_label.setAlignment(Qt.AlignCenter)
# create central matplotlib figure canvas widget # create central matplotlib figure canvas widget
self.init_wfWidget() self.init_wfWidget()
@ -632,11 +639,17 @@ class MainWindow(QMainWindow):
array_tab.setLayout(self.array_layout) array_tab.setLayout(self.array_layout)
events_tab.setLayout(self.events_layout) events_tab.setLayout(self.events_layout)
# tighten up layouts inside tabs
for layout in [self.wf_layout, self.array_layout, self.events_layout]:
layout.setSpacing(0)
layout.setContentsMargins(0, 0, 0, 0)
# add tabs to main tab widget # add tabs to main tab widget
self.tabs.addTab(wf_tab, 'Waveform Plot') self.tabs.addTab(wf_tab, 'Waveform Plot')
self.tabs.addTab(array_tab, 'Array Map') self.tabs.addTab(array_tab, 'Array Map')
self.tabs.addTab(events_tab, 'Eventlist') self.tabs.addTab(events_tab, 'Eventlist')
self.wf_layout.addWidget(self.no_data_label)
self.wf_layout.addWidget(self.wf_scroll_area) self.wf_layout.addWidget(self.wf_scroll_area)
self.wf_scroll_area.setWidgetResizable(True) self.wf_scroll_area.setWidgetResizable(True)
self.init_array_tab() self.init_array_tab()
@ -1217,6 +1230,8 @@ class MainWindow(QMainWindow):
tv.verticalHeader().hide() tv.verticalHeader().hide()
tv.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows) tv.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
current_event = self.get_current_event()
eventBox.setView(tv) eventBox.setView(tv)
eventBox.clear() eventBox.clear()
model = eventBox.model() model = eventBox.model()
@ -1249,6 +1264,17 @@ class MainWindow(QMainWindow):
event_ref = event.isRefEvent() event_ref = event.isRefEvent()
event_test = event.isTestEvent() event_test = event.isTestEvent()
time = lat = lon = depth = mag = None
if len(event.origins) == 1:
origin = event.origins[0]
time = origin.time + 0 # add 0 because there was an exception for time = 0s
lat = origin.latitude
lon = origin.longitude
depth = origin.depth
if len(event.magnitudes) == 1:
magnitude = event.magnitudes[0]
mag = magnitude.mag
# text = '{path:{plen}} | manual: [{p:3d}] | auto: [{a:3d}]' # text = '{path:{plen}} | manual: [{p:3d}] | auto: [{a:3d}]'
# text = text.format(path=event_path, # text = text.format(path=event_path,
# plen=plmax, # plen=plmax,
@ -1256,6 +1282,11 @@ class MainWindow(QMainWindow):
# a=event_nautopicks) # a=event_nautopicks)
item_path = QtGui.QStandardItem('{path:{plen}}'.format(path=event_path, plen=plmax)) item_path = QtGui.QStandardItem('{path:{plen}}'.format(path=event_path, plen=plmax))
item_time = QtGui.QStandardItem('{}'.format(time))
item_lat = QtGui.QStandardItem('{}'.format(lat))
item_lon = QtGui.QStandardItem('{}'.format(lon))
item_depth = QtGui.QStandardItem('{}'.format(depth))
item_mag = QtGui.QStandardItem('{}'.format(mag))
item_nmp = QtGui.QStandardItem(str(ma_count['manual'])) item_nmp = QtGui.QStandardItem(str(ma_count['manual']))
item_nmp.setIcon(self.manupicksicon_small) item_nmp.setIcon(self.manupicksicon_small)
item_nap = QtGui.QStandardItem(str(ma_count['auto'])) item_nap = QtGui.QStandardItem(str(ma_count['auto']))
@ -1281,10 +1312,17 @@ class MainWindow(QMainWindow):
# item.setFont(font) # item.setFont(font)
# item2.setForeground(QtGui.QColor('black')) # item2.setForeground(QtGui.QColor('black'))
# item2.setFont(font) # item2.setFont(font)
itemlist = [item_path, item_nmp, item_nap, item_ref, item_test, item_notes] itemlist = [item_path, item_time, item_lat, item_lon, item_depth,
if event_test and select_events == 'ref': item_mag, item_nmp, item_nap, item_ref, item_test, item_notes]
for item in itemlist:
item.setTextAlignment(Qt.AlignCenter)
if event_test and select_events == 'ref' or self.isEmpty(event_path):
for item in itemlist: for item in itemlist:
item.setEnabled(False) item.setEnabled(False)
#item color
self.setItemColor(itemlist, id, event, current_event)
model.appendRow(itemlist) model.appendRow(itemlist)
if not event.path == self.eventBox.itemText(id).strip(): if not event.path == self.eventBox.itemText(id).strip():
message = ('Path missmatch creating eventbox.\n' message = ('Path missmatch creating eventbox.\n'
@ -1296,6 +1334,23 @@ class MainWindow(QMainWindow):
eventBox.setCurrentIndex(index) eventBox.setCurrentIndex(index)
self.refreshRefTestButtons() self.refreshRefTestButtons()
def isEmpty(self, event_path):
wf_stat = {True: 'processed',
False: 'raw',
None: None}
# self.data.processed is only None for PyLoT datastructure, else True or False
wf_dir = wf_stat[self.data.processed]
if wf_dir is not None:
wf_path = os.path.join(event_path, wf_dir)
if wf_dir is 'processed' and not os.path.exists(wf_path):
wf_path = os.path.join(event_path, 'raw')
else:
wf_path = event_path
if not os.path.exists(wf_path):
return True
return not bool(os.listdir(wf_path))
def filename_from_action(self, action): def filename_from_action(self, action):
if action.data() is None: if action.data() is None:
filt = "Supported file formats" \ filt = "Supported file formats" \
@ -1373,7 +1428,10 @@ class MainWindow(QMainWindow):
def exportAllEvents(self, outformats=['.xml']): def exportAllEvents(self, outformats=['.xml']):
for event in self.project.eventlist: for event in self.project.eventlist:
self.get_data().setEvtData(event) self.get_data().setEvtData(event)
self.saveData(event, event.path, outformats) try:
self.saveData(event, event.path, outformats)
except Exception as e:
print('WARNING! Could not save event {}. Reason: {}'.format(event.path, e))
def enableSaveEventAction(self): def enableSaveEventAction(self):
self.saveEventAction.setEnabled(True) self.saveEventAction.setEnabled(True)
@ -1617,10 +1675,10 @@ class MainWindow(QMainWindow):
if self._eventChanged[1]: if self._eventChanged[1]:
self.refresh_array_map() self.refresh_array_map()
if not plotted and self._eventChanged[0]: if not plotted and self._eventChanged[0]:
# newWF(False) = load data without plotting # newWF(plot=False) = load data without plotting
self.newWF(plot=False) self.newWF(plot=False)
def newWF(self, plot=True): def newWF(self, event=None, plot=True):
''' '''
Load new data and plot if necessary. Load new data and plot if necessary.
''' '''
@ -1634,6 +1692,7 @@ class MainWindow(QMainWindow):
call modal plot thread method when finished. call modal plot thread method when finished.
''' '''
if load: if load:
self.prepareLoadWaveformData()
self.wfd_thread = Thread(self, self.loadWaveformData, self.wfd_thread = Thread(self, self.loadWaveformData,
progressText='Reading data input...', progressText='Reading data input...',
pb_widget=self.mainProgressBarWidget) pb_widget=self.mainProgressBarWidget)
@ -1646,6 +1705,16 @@ class MainWindow(QMainWindow):
if plot and not load: if plot and not load:
self.plotWaveformDataThread() self.plotWaveformDataThread()
def prepareLoadWaveformData(self):
self.fnames = self.getWFFnames_from_eventbox()
self.fnames_syn = []
eventpath = self.get_current_event_path()
basepath = eventpath.split(os.path.basename(eventpath))[0]
self.obspy_dmt = check_obspydmt_structure(basepath)
self.dataPlot.activateObspyDMToptions(self.obspy_dmt)
if self.obspy_dmt:
self.prepareObspyDMT_data(eventpath)
def loadWaveformData(self): def loadWaveformData(self):
''' '''
Load waveform data corresponding to current selected event. Load waveform data corresponding to current selected event.
@ -1657,14 +1726,48 @@ class MainWindow(QMainWindow):
# ans = self.data.setWFData(self.getWFFnames()) # ans = self.data.setWFData(self.getWFFnames())
# else: # else:
# ans = False # ans = False
self.fnames = self.getWFFnames_from_eventbox()
eventpath = self.get_current_event_path()
basepath = eventpath.split(os.path.basename(eventpath))[0]
obspy_dmt = check_obspydmt_structure(basepath)
self.data.setWFData(self.fnames, self.data.setWFData(self.fnames,
self.fnames_syn,
checkRotated=True, checkRotated=True,
metadata=self.metadata, metadata=self.metadata)
obspy_dmt=obspy_dmt)
def prepareObspyDMT_data(self, eventpath):
qcbox_processed = self.dataPlot.qcombo_processed
qcheckb_syn = self.dataPlot.syn_checkbox
qcbox_processed.setEnabled(False)
qcheckb_syn.setEnabled(False)
for fpath in os.listdir(eventpath):
fpath = fpath.split('/')[-1]
if 'syngine' in fpath:
eventpath_syn = os.path.join(eventpath, fpath)
qcheckb_syn.setEnabled(True)
if self.dataPlot.syn_checkbox.isChecked():
self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
if 'processed' in fpath:
qcbox_processed.setEnabled(True)
if qcbox_processed.isEnabled():
wftype = qcbox_processed.currentText()
else:
wftype = 'raw'
qcbox_processed.setCurrentIndex(qcbox_processed.findText(wftype))
eventpath_dmt = os.path.join(eventpath, wftype)
self.fnames = [os.path.join(eventpath_dmt, filename) for filename in os.listdir(eventpath_dmt)]
# def setWFstatus(self):
# '''
# show status of current data, can be either 'raw' or 'processed'
# :param status:
# :return:
# '''
# status = self.data.processed
# wf_stat_color = {True: 'green',
# False: 'black',
# None: None}
# wf_stat = {True: 'processed',
# False: 'raw',
# None: None}
# self.dataPlot.setQCboxItem(wf_stat[status])
def check_plot_quantity(self): def check_plot_quantity(self):
""" """
@ -1757,7 +1860,10 @@ class MainWindow(QMainWindow):
def finish_pg_plot(self): def finish_pg_plot(self):
self.getPlotWidget().updateWidget() self.getPlotWidget().updateWidget()
plots = self.wfp_thread.data plots, gaps = self.wfp_thread.data
# do not show plot if no data are given
self.wf_scroll_area.setVisible(len(plots) > 0)
self.no_data_label.setVisible(not len(plots) > 0)
for times, data, times_syn, data_syn in plots: for times, data, times_syn, data_syn in plots:
self.dataPlot.plotWidget.getPlotItem().plot(times, data, self.dataPlot.plotWidget.getPlotItem().plot(times, data,
pen=self.dataPlot.pen_linecolor) pen=self.dataPlot.pen_linecolor)
@ -1765,8 +1871,7 @@ class MainWindow(QMainWindow):
self.dataPlot.plotWidget.getPlotItem().plot(times_syn, data_syn, self.dataPlot.plotWidget.getPlotItem().plot(times_syn, data_syn,
pen=self.dataPlot.pen_linecolor_syn) pen=self.dataPlot.pen_linecolor_syn)
self.dataPlot.reinitMoveProxy() self.dataPlot.reinitMoveProxy()
self.dataPlot.plotWidget.showAxis('left') self.highlight_stations()
self.dataPlot.plotWidget.showAxis('bottom')
def finishWaveformDataPlot(self): def finishWaveformDataPlot(self):
self.comparable = self.checkEvents4comparison() self.comparable = self.checkEvents4comparison()
@ -1842,12 +1947,10 @@ class MainWindow(QMainWindow):
comparable[event.pylot_id] = self.checkEvent4comparison(event) comparable[event.pylot_id] = self.checkEvent4comparison(event)
return comparable return comparable
def clearWaveformDataPlot(self): def clearWaveformDataPlot(self, refresh_plot=False):
self.disconnectWFplotEvents() self.disconnectWFplotEvents()
if self.pg: if self.pg:
self.dataPlot.plotWidget.getPlotItem().clear() self.dataPlot.plotWidget.getPlotItem().clear()
self.dataPlot.plotWidget.hideAxis('bottom')
self.dataPlot.plotWidget.hideAxis('left')
else: else:
for ax in self.dataPlot.axes: for ax in self.dataPlot.axes:
ax.cla() ax.cla()
@ -1863,6 +1966,9 @@ class MainWindow(QMainWindow):
self.openEventAction.setEnabled(False) self.openEventAction.setEnabled(False)
self.openEventsAutoAction.setEnabled(False) self.openEventsAutoAction.setEnabled(False)
self.loadpilotevent.setEnabled(False) self.loadpilotevent.setEnabled(False)
if not refresh_plot:
self.wf_scroll_area.setVisible(False)
self.no_data_label.setVisible(True)
self.disableSaveEventAction() self.disableSaveEventAction()
self.draw() self.draw()
@ -1871,7 +1977,7 @@ class MainWindow(QMainWindow):
Open a modal thread to plot current waveform data. Open a modal thread to plot current waveform data.
''' '''
self.check_plot_quantity() self.check_plot_quantity()
self.clearWaveformDataPlot() self.clearWaveformDataPlot(refresh_plot=True)
self.wfp_thread = Thread(self, self.plotWaveformData, self.wfp_thread = Thread(self, self.plotWaveformData,
arg=filter, arg=filter,
progressText='Plotting waveform data...', progressText='Plotting waveform data...',
@ -1904,9 +2010,10 @@ class MainWindow(QMainWindow):
self.plot_method = 'fast' self.plot_method = 'fast'
else: else:
self.plot_method = 'normal' self.plot_method = 'normal'
plots = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp, rval = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp,
nth_sample=int(nth_sample), method=self.plot_method) nth_sample=int(nth_sample), method=self.plot_method)
return plots plots, gaps = rval if rval else ([], [])
return plots, gaps
def adjustPlotHeight(self): def adjustPlotHeight(self):
if self.pg: if self.pg:
@ -2135,10 +2242,12 @@ class MainWindow(QMainWindow):
def pickOnStation(self, gui_event): def pickOnStation(self, gui_event):
if self.pg: if self.pg:
if not gui_event.button() == 1: button = gui_event.button()
if not button in [1, 4]:
return return
else: else:
if not gui_event.button == 1: button = gui_event.button
if not button == 1:
return return
if self.pg: if self.pg:
@ -2149,27 +2258,59 @@ class MainWindow(QMainWindow):
wfID = self.getWFID(ycoord) wfID = self.getWFID(ycoord)
if wfID is None: return if wfID is None: return
self.pickDialog(wfID)
def pickDialog(self, wfID, nextStation=False):
station = self.getStationName(wfID)
network = self.getNetworkName(wfID) network = self.getNetworkName(wfID)
station = self.getStationName(wfID)
if button == 1:
self.pickDialog(wfID, network, station)
elif button == 4:
self.toggle_station_color(wfID, network, station)
def toggle_station_color(self, wfID, network, station):
black_pen = pg.mkPen((0, 0, 0))
red_pen = pg.mkPen((200, 50, 50))
line_item = self.dataPlot.plotWidget.getPlotItem().listDataItems()[wfID - 1]
current_pen = line_item.opts['pen']
nwst = '{}.{}'.format(network, station)
if current_pen == black_pen:
line_item.setPen(red_pen)
if not nwst in self.stations_highlighted:
self.stations_highlighted.append(nwst)
else:
line_item.setPen(black_pen)
if nwst in self.stations_highlighted:
self.stations_highlighted.pop(self.stations_highlighted.index(nwst))
def highlight_stations(self):
for wfID, value in self.getPlotWidget().getPlotDict().items():
station, channel, network = value
nwst = '{}.{}'.format(network, station)
if nwst in self.stations_highlighted:
self.toggle_station_color(wfID, network, station)
def pickDialog(self, wfID, network=None, station=None):
if not network:
network = self.getNetworkName(wfID)
if not station: if not station:
station = self.getStationName(wfID)
if not station or not network:
return return
self.update_status('picking on station {0}'.format(station)) self.update_status('picking on station {0}'.format(station))
data = self.get_data().getOriginalWFData().copy() data = self.get_data().getOriginalWFData().copy()
event = self.get_current_event() event = self.get_current_event()
wftype = self.dataPlot.qcombo_processed.currentText() if self.obspy_dmt else None
pickDlg = PickDlg(self, parameter=self._inputs, pickDlg = PickDlg(self, parameter=self._inputs,
data=data.select(station=station), data=data.select(station=station),
station=station, network=network, station=station, network=network,
picks=self.getPicksOnStation(station, 'manual'), picks=self.getPicksOnStation(station, 'manual'),
autopicks=self.getPicksOnStation(station, 'auto'), autopicks=self.getPicksOnStation(station, 'auto'),
metadata=self.metadata, event=event, metadata=self.metadata, event=event,
filteroptions=self.filteroptions) filteroptions=self.filteroptions, wftype=wftype)
if self.filterActionP.isChecked() or self.filterActionS.isChecked(): if self.filterActionP.isChecked() or self.filterActionS.isChecked():
pickDlg.currentPhase = self.getSeismicPhase() pickDlg.currentPhase = self.getSeismicPhase()
pickDlg.filterWFData() pickDlg.filterWFData()
pickDlg.nextStation.setChecked(nextStation) pickDlg.nextStation.setChecked(self.nextStation)
pickDlg.nextStation.stateChanged.connect(self.toggle_next_station)
if pickDlg.exec_(): if pickDlg.exec_():
if pickDlg._dirty: if pickDlg._dirty:
self.setDirty(True) self.setDirty(True)
@ -2179,13 +2320,13 @@ class MainWindow(QMainWindow):
self.enableSaveEventAction() self.enableSaveEventAction()
if replot1 or replot2: if replot1 or replot2:
self.plotWaveformDataThread() self.plotWaveformDataThread()
self.drawPicks()
self.draw() self.draw()
else: else:
self.drawPicks(station) self.drawPicks(station)
self.draw() self.draw()
if pickDlg.nextStation.isChecked(): if self.nextStation:
self.pickDialog(wfID - 1, nextStation=pickDlg.nextStation.isChecked()) self.pickDialog(wfID - 1)
else: else:
self.update_status('picks discarded ({0})'.format(station)) self.update_status('picks discarded ({0})'.format(station))
if not self.get_loc_flag() and self.check4Loc(): if not self.get_loc_flag() and self.check4Loc():
@ -2194,8 +2335,13 @@ class MainWindow(QMainWindow):
elif self.get_loc_flag() and not self.check4Loc(): elif self.get_loc_flag() and not self.check4Loc():
self.set_loc_flag(False) self.set_loc_flag(False)
def toggle_next_station(self, signal):
self.nextStation = bool(signal)
def addListItem(self, text): def addListItem(self, text):
self.listWidget.addItem(text) textlist = text.split('\n')
for text in textlist:
self.listWidget.addItem(text)
self.listWidget.scrollToBottom() self.listWidget.scrollToBottom()
def init_fig_dict(self): def init_fig_dict(self):
@ -2254,7 +2400,7 @@ class MainWindow(QMainWindow):
def tune_autopicker(self): def tune_autopicker(self):
''' '''
Initiates TuneAutopicker widget use to interactively Initiates TuneAutopicker widget used to interactively
tune parameters for autopicking algorithm. tune parameters for autopicking algorithm.
''' '''
# figures and canvas have to be iniated from the main GUI # figures and canvas have to be iniated from the main GUI
@ -2263,7 +2409,7 @@ class MainWindow(QMainWindow):
self.init_fig_dict() self.init_fig_dict()
#if not self.tap: #if not self.tap:
# init TuneAutopicker object # init TuneAutopicker object
self.tap = TuneAutopicker(self) self.tap = TuneAutopicker(self, self.obspy_dmt)
# first call of update to init tabs with empty canvas # first call of update to init tabs with empty canvas
self.update_autopicker() self.update_autopicker()
# connect update signal of TuneAutopicker with update function # connect update signal of TuneAutopicker with update function
@ -2345,6 +2491,7 @@ class MainWindow(QMainWindow):
# export current picks etc. # export current picks etc.
self.exportAllEvents(['.xml']) self.exportAllEvents(['.xml'])
wfpath = self.dataPlot.qcombo_processed.currentText() if self.obspy_dmt else ''
# define arguments for picker # define arguments for picker
args = {'parameter': self._inputs, args = {'parameter': self._inputs,
'station': 'all', 'station': 'all',
@ -2353,8 +2500,8 @@ class MainWindow(QMainWindow):
'iplot': 0, 'iplot': 0,
'fig_dict': None, 'fig_dict': None,
'fig_dict_wadatijack': self.fig_dict_wadatijack, 'fig_dict_wadatijack': self.fig_dict_wadatijack,
'locflag': 0} 'savexml': False,
'obspyDMT_wfpath': wfpath}
# init pick thread # init pick thread
self.mp_thread = QtCore.QThreadPool() self.mp_thread = QtCore.QThreadPool()
self.mp_worker = Worker(autoPyLoT, args, redirect_stdout=True) self.mp_worker = Worker(autoPyLoT, args, redirect_stdout=True)
@ -2363,6 +2510,7 @@ class MainWindow(QMainWindow):
self.mp_worker.signals.message.connect(self.addListItem) self.mp_worker.signals.message.connect(self.addListItem)
self.mp_worker.signals.result.connect(self.finalizeAutoPick) self.mp_worker.signals.result.connect(self.finalizeAutoPick)
self.mp_worker.signals.finished.connect(self.enableAutoPickWidget)
self.mp_thread.start(self.mp_worker) self.mp_thread.start(self.mp_worker)
@ -2377,7 +2525,6 @@ class MainWindow(QMainWindow):
self.apd_sge.show() self.apd_sge.show()
def finalizeAutoPick(self, result): def finalizeAutoPick(self, result):
self.apw.enable(True)
if result: if result:
self.init_canvas_dict_wadatijack() self.init_canvas_dict_wadatijack()
for eventID in result.keys(): for eventID in result.keys():
@ -2393,6 +2540,9 @@ class MainWindow(QMainWindow):
self.drawPicks(picktype='auto') self.drawPicks(picktype='auto')
self.draw() self.draw()
def enableAutoPickWidget(self, event=None):
self.apw.enable(True)
def get_event_from_id(self, eventID): def get_event_from_id(self, eventID):
for event in self.project.eventlist: for event in self.project.eventlist:
if event.pylot_id == eventID: if event.pylot_id == eventID:
@ -2607,55 +2757,28 @@ class MainWindow(QMainWindow):
""" """
if not self.okToContinue(): if not self.okToContinue():
return return
settings = QSettings() parameter = self._inputs
# get location tool hook loctool = 'nll'
loctool = settings.value("loc/tool", "nll")
lt = locateTool[loctool] lt = locateTool[loctool]
# get working directory # get working directory
locroot = settings.value("{0}/rootPath".format(loctool), None) locroot = parameter['nllocroot']
if locroot is None: if locroot is None:
self.PyLoTprefs() self.PyLoTprefs()
self.locate_event() self.locate_event()
infile = settings.value("{0}/inputFile".format(loctool), None) ctrfile = os.path.join(locroot, 'run', parameter['ctrfile'])
if not infile: ttt = parameter['ttpatter']
caption = 'Select {0} input file'.format(loctool) outfile = parameter['outpatter']
filt = "Supported file formats" \
" (*.in *.ini *.conf *.cfg)"
ans = QFileDialog().getOpenFileName(self, caption=caption,
filter=filt, dir=locroot)
if ans[0]:
infile = ans[0]
else:
QMessageBox.information(self,
self.tr('No infile selected'),
self.tr('Inputfile necessary for localization.'))
return
settings.setValue("{0}/inputFile".format(loctool), infile)
settings.sync()
if loctool == 'nll':
ttt = settings.value("{0}/travelTimeTables", None)
ok = False
if ttt is None:
while not ok:
text, ok = QInputDialog.getText(self, 'Pattern for travel time tables',
'Base name of travel time tables',
echo=QLineEdit.Normal,
text="ttime")
ttt = text
outfile = settings.value("{0}/outputFile".format(loctool),
os.path.split(os.tempnam())[-1])
eventname = self.get_current_event_name() eventname = self.get_current_event_name()
obsdir = os.path.join(self._inputs['rootpath'], self._inputs['datapath'], self._inputs['database'], eventname) obsdir = os.path.join(self._inputs['rootpath'], self._inputs['datapath'], self._inputs['database'], eventname)
self.saveData(event=self.get_current_event(), directory=obsdir, outformats='.obs') self.saveData(event=self.get_current_event(), directory=obsdir, outformats='.obs')
filename = 'PyLoT_' + eventname filename = 'PyLoT_' + eventname
locpath = os.path.join(locroot, 'loc', filename) locpath = os.path.join(locroot, 'loc', filename)
phasefile = os.path.join(obsdir, filename + '.obs') phasefile = os.path.join(obsdir, filename + '.obs')
lt.modify_inputs(infile, locroot, filename, phasefile, ttt) lt.modify_inputs(ctrfile, locroot, filename, phasefile, ttt)
try: try:
lt.locate(infile) lt.locate(ctrfile)
except RuntimeError as e: except RuntimeError as e:
print(e.message) print(e.message)
#finally: #finally:
@ -2721,10 +2844,7 @@ class MainWindow(QMainWindow):
self.init_metadata() self.init_metadata()
if not self.metadata: if not self.metadata:
return return
self.am_figure = Figure() self.array_map = Array_map(self)
self.am_canvas = FigureCanvas(self.am_figure)
self.am_toolbar = NavigationToolbar(self.am_canvas, self)
self.array_map = map_projection(self)
# self.array_map_thread() # self.array_map_thread()
self.array_layout.addWidget(self.array_map) self.array_layout.addWidget(self.array_map)
self.tabs.setCurrentIndex(index) self.tabs.setCurrentIndex(index)
@ -2763,7 +2883,8 @@ class MainWindow(QMainWindow):
lon = event.origins[0].longitude lon = event.origins[0].longitude
self.array_map.eventLoc = (lat, lon) self.array_map.eventLoc = (lat, lon)
if self.get_current_event(): if self.get_current_event():
self.array_map.refresh_drawings(self.get_current_event().getPicks()) self.array_map.refresh_drawings(self.get_current_event().getPicks(),
self.get_current_event().getAutopicks(),)
self._eventChanged[1] = False self._eventChanged[1] = False
def init_event_table(self, tabindex=2): def init_event_table(self, tabindex=2):
@ -2817,14 +2938,6 @@ class MainWindow(QMainWindow):
event.addNotes(notes) event.addNotes(notes)
self.fill_eventbox() self.fill_eventbox()
def set_background_color(items, color):
for item in items:
item.setBackground(color)
def set_foreground_color(items, color):
for item in items:
item.setForeground(color)
current_event = self.get_current_event() current_event = self.get_current_event()
# generate delete icon # generate delete icon
@ -2894,7 +3007,7 @@ class MainWindow(QMainWindow):
if hasattr(event, 'origins'): if hasattr(event, 'origins'):
if event.origins: if event.origins:
origin = event.origins[0] origin = event.origins[0]
item_time.setText(str(origin.time).split('.')[0]) item_time.setText(str(origin.time + 0).split('.')[0]) # +0 as workaround in case time=0s
item_lon.setText(str(origin.longitude)) item_lon.setText(str(origin.longitude))
item_lat.setText(str(origin.latitude)) item_lat.setText(str(origin.latitude))
item_depth.setText(str(origin.depth)) item_depth.setText(str(origin.depth))
@ -2928,11 +3041,7 @@ class MainWindow(QMainWindow):
item_nmp, item_nap, item_ref, item_test, item_notes] item_nmp, item_nap, item_ref, item_test, item_notes]
self.project._table.append(column) self.project._table.append(column)
if index%2: self.setItemColor(column, index, event, current_event)
set_background_color(column, QtGui.QColor(*(245, 245, 245, 255)))
if event == current_event:
set_foreground_color(column, QtGui.QColor(*(0, 143, 143, 255)))
# manipulate items # manipulate items
item_ref.setBackground(self._ref_test_colors['ref']) item_ref.setBackground(self._ref_test_colors['ref'])
@ -2954,6 +3063,24 @@ class MainWindow(QMainWindow):
self.events_layout.addWidget(self.event_table) self.events_layout.addWidget(self.event_table)
self.tabs.setCurrentIndex(tabindex) self.tabs.setCurrentIndex(tabindex)
def setItemColor(self, item_list, index, event, current_event):
def set_background_color(items, color):
for item in items:
item.setBackground(color)
def set_foreground_color(items, color):
for item in items:
item.setForeground(color)
if index % 2:
set_background_color(item_list, QtGui.QColor(*(245, 245, 245, 255)))
if self.isEmpty(event.path):
set_foreground_color(item_list, QtGui.QColor(*(180, 180, 180, 255)))
if event == current_event:
set_background_color(item_list, QtGui.QColor(*(0, 143, 143, 255)))
def read_metadata_thread(self, fninv): def read_metadata_thread(self, fninv):
self.rm_thread = Thread(self, read_metadata, arg=fninv, progressText='Reading metadata...', self.rm_thread = Thread(self, read_metadata, arg=fninv, progressText='Reading metadata...',
pb_widget=self.mainProgressBarWidget) pb_widget=self.mainProgressBarWidget)
@ -3003,20 +3130,18 @@ class MainWindow(QMainWindow):
settings.setValue("inventoryFile", self.project.inv_path) settings.setValue("inventoryFile", self.project.inv_path)
fninv = settings.value("inventoryFile", None) fninv = settings.value("inventoryFile", None)
if fninv and ask_default: if (fninv and ask_default) and not new:
ans = QMessageBox.question(self, self.tr("Use default metadata..."), ans = QMessageBox.question(self, self.tr("Use default metadata..."),
self.tr( self.tr(
"Do you want to use the default value for metadata?\n({})".format(fninv)), "Do you want to use the default value for metadata?\n({})".format(fninv)),
QMessageBox.Yes | QMessageBox.No, QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes) QMessageBox.Yes)
if ans == QMessageBox.No: if ans == QMessageBox.Yes:
if not set_inv(settings):
return None
elif ans == QMessageBox.Yes:
self.read_metadata_thread(fninv) self.read_metadata_thread(fninv)
if fninv and not ask_default: return
self.read_metadata_thread(fninv) set_inv(settings)
def calc_magnitude(self, type='ML'): def calc_magnitude(self, type='ML'):
self.init_metadata() self.init_metadata()
if not self.metadata: if not self.metadata:
@ -3197,9 +3322,11 @@ class MainWindow(QMainWindow):
self.fill_eventbox() self.fill_eventbox()
self.getPlotWidget().draw() self.getPlotWidget().draw()
if self.plot_method == 'fast': if self.plot_method == 'fast':
self.dataPlot.setPermText('MIN/MAX plot', color='red') self.dataPlot.setPermText(1, ' MIN/MAX plot ', color='red')
else: else:
self.dataPlot.setPermText() self.dataPlot.setPermText(1)
self.dataPlot.setPermText(0, '| Number of traces: {} |'.format(len(self.getPlotWidget().getPlotDict())))
def _setDirty(self): def _setDirty(self):
self.setDirty(True) self.setDirty(True)

72
autoPyLoT.py
View File

@ -34,7 +34,7 @@ __version__ = _getVersionString()
def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None, def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, eventid=None, savepath=None,
savexml=True, station='all', iplot=0, ncores=0): savexml=True, station='all', iplot=0, ncores=0, obspyDMT_wfpath=False):
""" """
Determine phase onsets automatically utilizing the automatic picking Determine phase onsets automatically utilizing the automatic picking
algorithms by Kueperkoch et al. 2010/2012. algorithms by Kueperkoch et al. 2010/2012.
@ -94,7 +94,6 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
fig_dict = None fig_dict = None
fig_dict_wadatijack = None fig_dict_wadatijack = None
locflag = 1
if input_dict and isinstance(input_dict, dict): if input_dict and isinstance(input_dict, dict):
if 'parameter' in input_dict: if 'parameter' in input_dict:
parameter = input_dict['parameter'] parameter = input_dict['parameter']
@ -110,10 +109,10 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
eventid = input_dict['eventid'] eventid = input_dict['eventid']
if 'iplot' in input_dict: if 'iplot' in input_dict:
iplot = input_dict['iplot'] iplot = input_dict['iplot']
if 'locflag' in input_dict:
locflag = input_dict['locflag']
if 'savexml' in input_dict: if 'savexml' in input_dict:
savexml = input_dict['savexml'] savexml = input_dict['savexml']
if 'obspyDMT_wfpath' in input_dict:
obspyDMT_wfpath = input_dict['obspyDMT_wfpath']
if not parameter: if not parameter:
if inputfile: if inputfile:
@ -151,7 +150,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
datastructure.setExpandFields(exf) datastructure.setExpandFields(exf)
# check if default location routine NLLoc is available # check if default location routine NLLoc is available
if real_None(parameter['nllocbin']) and locflag: if real_None(parameter['nllocbin']):
locflag = 1
# get NLLoc-root path # get NLLoc-root path
nllocroot = parameter.get('nllocroot') nllocroot = parameter.get('nllocroot')
# get path to NLLoc executable # get path to NLLoc executable
@ -167,7 +167,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
ttpat = parameter.get('ttpatter') ttpat = parameter.get('ttpatter')
# pattern of NLLoc-output file # pattern of NLLoc-output file
nllocoutpatter = parameter.get('outpatter') nllocoutpatter = parameter.get('outpatter')
maxnumit = 3 # maximum number of iterations for re-picking maxnumit = 2 # maximum number of iterations for re-picking
else: else:
locflag = 0 locflag = 0
print(" !!! ") print(" !!! ")
@ -175,6 +175,14 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
print("!!No source parameter estimation possible!!") print("!!No source parameter estimation possible!!")
print(" !!! ") print(" !!! ")
wfpath_extension = ''
if obspyDMT_wfpath not in [None, False, 'False', '']:
wfpath_extension = obspyDMT_wfpath
print('Using obspyDMT structure. There will be no restitution, as pre-processed data are expected.')
if wfpath_extension != 'processed':
print('WARNING: Expecting wfpath_extension to be "processed" for'
' pre-processed data but received "{}" instead!!!'.format(wfpath_extension))
if not input_dict: if not input_dict:
# started in production mode # started in production mode
datapath = datastructure.expandDataPath() datapath = datastructure.expandDataPath()
@ -219,6 +227,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
glocflag = locflag glocflag = locflag
for eventpath in events: for eventpath in events:
evID = os.path.split(eventpath)[-1] evID = os.path.split(eventpath)[-1]
event_datapath = os.path.join(eventpath, wfpath_extension)
fext = '.xml' fext = '.xml'
filename = os.path.join(eventpath, 'PyLoT_' + evID + fext) filename = os.path.join(eventpath, 'PyLoT_' + evID + fext)
try: try:
@ -231,7 +240,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
pylot_event = Event(eventpath) # event should be path to event directory pylot_event = Event(eventpath) # event should be path to event directory
data.setEvtData(pylot_event) data.setEvtData(pylot_event)
if fnames == 'None': if fnames == 'None':
data.setWFData(glob.glob(os.path.join(datapath, eventpath, '*'))) data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*')))
# the following is necessary because within # the following is necessary because within
# multiple event processing no event ID is provided # multiple event processing no event ID is provided
# in autopylot.in # in autopylot.in
@ -268,12 +277,18 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
wfdat = check4doubled(wfdat) wfdat = check4doubled(wfdat)
wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False) wfdat = trim_station_components(wfdat, trim_start=True, trim_end=False)
metadata = read_metadata(parameter.get('invdir')) metadata = read_metadata(parameter.get('invdir'))
# rotate stations to ZNE # TODO: (idea) read metadata from obspy_dmt database
wfdat = check4rotated(wfdat, metadata) # if not wfpath_extension:
# metadata = read_metadata(parameter.get('invdir'))
# else:
# metadata = None
corr_dat = None corr_dat = None
if locflag: if metadata:
print("Restitute data ...") # rotate stations to ZNE
corr_dat = restitute_data(wfdat.copy(), *metadata, ncores=ncores) wfdat = check4rotated(wfdat, metadata)
if locflag:
print("Restitute data ...")
corr_dat = restitute_data(wfdat.copy(), *metadata, ncores=ncores)
if not corr_dat and locflag: if not corr_dat and locflag:
locflag = 2 locflag = 2
print('Working on event %s. Stations: %s' % (eventpath, station)) print('Working on event %s. Stations: %s' % (eventpath, station))
@ -331,7 +346,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
picks[stats]['P'].update(props) picks[stats]['P'].update(props)
evt = moment_mag.updated_event() evt = moment_mag.updated_event()
net_mw = moment_mag.net_magnitude() net_mw = moment_mag.net_magnitude()
print("Network moment magnitude: %4.1f" % net_mw.mag) if net_mw is not None:
print("Network moment magnitude: %4.1f" % net_mw.mag)
# calculate local (Richter) magntiude # calculate local (Richter) magntiude
WAscaling = parameter.get('WAscaling') WAscaling = parameter.get('WAscaling')
magscaling = parameter.get('magscaling') magscaling = parameter.get('magscaling')
@ -348,8 +364,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
evt = local_mag.updated_event(magscaling) evt = local_mag.updated_event(magscaling)
net_ml = local_mag.net_magnitude(magscaling) net_ml = local_mag.net_magnitude(magscaling)
print("Network local magnitude: %4.1f" % net_ml.mag) print("Network local magnitude: %4.1f" % net_ml.mag)
print("Network local magnitude scaled with:") if magscaling == None:
print("%f * Ml + %f" % (magscaling[0], magscaling[1])) scaling = False
elif magscaling[0] != 0 and magscaling[1] != 0:
scaling = False
else:
scaling = True
if scaling:
print("Network local magnitude scaled with:")
print("%f * Ml + %f" % (magscaling[0], magscaling[1]))
else: else:
print("autoPyLoT: No NLLoc-location file available!") print("autoPyLoT: No NLLoc-location file available!")
print("No source parameter estimation possible!") print("No source parameter estimation possible!")
@ -406,7 +429,8 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
picks[stats]['P'].update(props) picks[stats]['P'].update(props)
evt = moment_mag.updated_event() evt = moment_mag.updated_event()
net_mw = moment_mag.net_magnitude() net_mw = moment_mag.net_magnitude()
print("Network moment magnitude: %4.1f" % net_mw.mag) if net_mw is not None:
print("Network moment magnitude: %4.1f" % net_mw.mag)
# calculate local (Richter) magntiude # calculate local (Richter) magntiude
WAscaling = parameter.get('WAscaling') WAscaling = parameter.get('WAscaling')
magscaling = parameter.get('magscaling') magscaling = parameter.get('magscaling')
@ -424,8 +448,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
evt = local_mag.updated_event(magscaling) evt = local_mag.updated_event(magscaling)
net_ml = local_mag.net_magnitude(magscaling) net_ml = local_mag.net_magnitude(magscaling)
print("Network local magnitude: %4.1f" % net_ml.mag) print("Network local magnitude: %4.1f" % net_ml.mag)
print("Network local magnitude scaled with:") if magscaling == None:
print("%f * Ml + %f" % (magscaling[0], magscaling[1])) scaling = False
elif magscaling[0] != 0 and magscaling[1] != 0:
scaling = False
else:
scaling = True
if scaling:
print("Network local magnitude scaled with:")
print("%f * Ml + %f" % (magscaling[0], magscaling[1]))
else: else:
print("autoPyLoT: No NLLoc-location file available! Stop iteration!") print("autoPyLoT: No NLLoc-location file available! Stop iteration!")
locflag = 9 locflag = 9
@ -512,9 +543,12 @@ if __name__ == "__main__":
parser.add_argument('-c', '-C', '--ncores', type=int, parser.add_argument('-c', '-C', '--ncores', type=int,
action='store', default=0, action='store', default=0,
help='''optional, number of CPU cores used for parallel processing (default: all available(=0))''') help='''optional, number of CPU cores used for parallel processing (default: all available(=0))''')
parser.add_argument('-dmt', '-DMT', '--obspy_dmt_wfpath', type=str,
action='store', default=False,
help='''optional, wftype (raw, processed) used for obspyDMT database structure''')
cla = parser.parse_args() cla = parser.parse_args()
picks = autoPyLoT(inputfile=str(cla.inputfile), fnames=str(cla.fnames), picks = autoPyLoT(inputfile=str(cla.inputfile), fnames=str(cla.fnames),
eventid=str(cla.eventid), savepath=str(cla.spath), eventid=str(cla.eventid), savepath=str(cla.spath),
ncores=cla.ncores, iplot=int(cla.iplot)) ncores=cla.ncores, iplot=int(cla.iplot), obspyDMT_wfpath=str(cla.obspy_dmt_wfpath))

2
icons_rc_2.py
View File

@ -7,7 +7,7 @@
# #
# WARNING! All changes made in this file will be lost! # WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore from PySide import QtCore
qt_resource_data = "\ qt_resource_data = "\
\x00\x00\x9e\x04\ \x00\x00\x9e\x04\

2
icons_rc_3.py
View File

@ -7,7 +7,7 @@
# #
# WARNING! All changes made in this file will be lost! # WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore from PySide import QtCore
qt_resource_data = "\ qt_resource_data = "\
\x00\x00\x9e\x04\ \x00\x00\x9e\x04\

66
inputs/pylot_local.in
View File

@ -4,19 +4,19 @@
%Parameters are optimized for %extent data sets! %Parameters are optimized for %extent data sets!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#main settings# #main settings#
#rootpath# %project path /DATA/Insheim #rootpath# %project path
#datapath# %data path EVENT_DATA/LOCAL #datapath# %data path
#database# %name of data base 2018.02_Insheim #database# %name of data base
#eventID# %event ID for single event processing (* for all events found in database) e0006.038.18 #eventID# %event ID for single event processing (* for all events found in database)
#invdir# %full path to inventory or dataless-seed file /DATA/Insheim/STAT_INFO #invdir# %full path to inventory or dataless-seed file
PILOT #datastructure# %choose data structure PILOT #datastructure# %choose data structure
True #apverbose# %choose 'True' or 'False' for terminal output True #apverbose# %choose 'True' or 'False' for terminal output
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#NLLoc settings# #NLLoc settings#
None #nllocbin# %path to NLLoc executable /home/ludger/NLLOC #nllocbin# %path to NLLoc executable
None #nllocroot# %root of NLLoc-processing directory /home/ludger/NLLOC/Insheim #nllocroot# %root of NLLoc-processing directory
None #phasefile# %name of autoPyLoT-output phase file for NLLoc AUTOPHASES.obs #phasefile# %name of autoPyLoT-output phase file for NLLoc
None #ctrfile# %name of autoPyLoT-output control file for NLLoc Insheim_min1d032016_auto.in #ctrfile# %name of autoPyLoT-output control file for NLLoc
ttime #ttpatter# %pattern of NLLoc ttimes from grid ttime #ttpatter# %pattern of NLLoc ttimes from grid
AUTOLOC_nlloc #outpatter# %pattern of NLLoc-output file AUTOLOC_nlloc #outpatter# %pattern of NLLoc-output file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -27,31 +27,31 @@ AUTOLOC_nlloc #outpatter# %pattern of
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#settings local magnitude# #settings local magnitude#
1.11 0.0009 -2.0 #WAscaling# %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] If zeros are set, original Richter magnitude is calculated! 1.11 0.0009 -2.0 #WAscaling# %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm] If zeros are set, original Richter magnitude is calculated!
1.0382 -0.447 #magscaling# %Scaling relation for derived local magnitude [a*Ml+b]. If zeros are set, no scaling of network magnitude is applied! 0.0 0.0 #magscaling# %Scaling relation for derived local magnitude [a*Ml+b]. If zeros are set, no scaling of network magnitude is applied!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#filter settings# #filter settings#
1.0 1.0 #minfreq# %Lower filter frequency [P, S] 2.0 2.0 #minfreq# %Lower filter frequency [P, S]
10.0 10.0 #maxfreq# %Upper filter frequency [P, S] 30.0 15.0 #maxfreq# %Upper filter frequency [P, S]
2 2 #filter_order# %filter order [P, S] 3 3 #filter_order# %filter order [P, S]
bandpass bandpass #filter_type# %filter type (bandpass, bandstop, lowpass, highpass) [P, S] bandpass bandpass #filter_type# %filter type (bandpass, bandstop, lowpass, highpass) [P, S]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#common settings picker# #common settings picker#
local #extent# %extent of array ("local", "regional" or "global") local #extent# %extent of array ("local", "regional" or "global")
15.0 #pstart# %start time [s] for calculating CF for P-picking 7.0 #pstart# %start time [s] for calculating CF for P-picking
60.0 #pstop# %end time [s] for calculating CF for P-picking 16.0 #pstop# %end time [s] for calculating CF for P-picking
-1.0 #sstart# %start time [s] relative to P-onset for calculating CF for S-picking -0.5 #sstart# %start time [s] relative to P-onset for calculating CF for S-picking
10.0 #sstop# %end time [s] after P-onset for calculating CF for S-picking 10.0 #sstop# %end time [s] after P-onset for calculating CF for S-picking
True #use_taup# %use estimated traveltimes from TauPy for calculating windows for CF False #use_taup# %use estimated traveltimes from TauPy for calculating windows for CF
iasp91 #taup_model# %define TauPy model for traveltime estimation iasp91 #taup_model# %define TauPy model for traveltime estimation
2.0 10.0 #bpz1# %lower/upper corner freq. of first band pass filter Z-comp. [Hz] 2.0 20.0 #bpz1# %lower/upper corner freq. of first band pass filter Z-comp. [Hz]
2.0 12.0 #bpz2# %lower/upper corner freq. of second band pass filter Z-comp. [Hz] 2.0 30.0 #bpz2# %lower/upper corner freq. of second band pass filter Z-comp. [Hz]
2.0 8.0 #bph1# %lower/upper corner freq. of first band pass filter H-comp. [Hz] 2.0 10.0 #bph1# %lower/upper corner freq. of first band pass filter H-comp. [Hz]
2.0 10.0 #bph2# %lower/upper corner freq. of second band pass filter z-comp. [Hz] 2.0 15.0 #bph2# %lower/upper corner freq. of second band pass filter z-comp. [Hz]
#special settings for calculating CF# #special settings for calculating CF#
%!!Edit the following only if you know what you are doing!!% %!!Edit the following only if you know what you are doing!!%
#Z-component# #Z-component#
HOS #algoP# %choose algorithm for P-onset determination (HOS, ARZ, or AR3) HOS #algoP# %choose algorithm for P-onset determination (HOS, ARZ, or AR3)
7.0 #tlta# %for HOS-/AR-AIC-picker, length of LTA window [s] 4.0 #tlta# %for HOS-/AR-AIC-picker, length of LTA window [s]
4 #hosorder# %for HOS-picker, order of Higher Order Statistics 4 #hosorder# %for HOS-picker, order of Higher Order Statistics
2 #Parorder# %for AR-picker, order of AR process of Z-component 2 #Parorder# %for AR-picker, order of AR process of Z-component
1.2 #tdet1z# %for AR-picker, length of AR determination window [s] for Z-component, 1st pick 1.2 #tdet1z# %for AR-picker, length of AR determination window [s] for Z-component, 1st pick
@ -59,12 +59,12 @@ HOS #algoP# %choose algo
0.6 #tdet2z# %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick 0.6 #tdet2z# %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick
0.2 #tpred2z# %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick 0.2 #tpred2z# %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick
0.001 #addnoise# %add noise to seismogram for stable AR prediction 0.001 #addnoise# %add noise to seismogram for stable AR prediction
3.0 0.1 0.5 1.0 #tsnrz# %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s] 3.0 0.0 1.0 0.5 #tsnrz# %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]
3.0 #pickwinP# %for initial AIC pick, length of P-pick window [s] 3.0 #pickwinP# %for initial AIC pick, length of P-pick window [s]
6.0 #Precalcwin# %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick) 6.0 #Precalcwin# %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)
0.2 #aictsmooth# %for HOS/AR, take average of samples for smoothing of AIC-function [s] 0.4 #aictsmooth# %for HOS/AR, take average of samples for smoothing of AIC-function [s]
0.1 #tsmoothP# %for HOS/AR, take average of samples for smoothing CF [s] 0.1 #tsmoothP# %for HOS/AR, take average of samples for smoothing CF [s]
0.001 #ausP# %for HOS/AR, artificial uplift of samples (aus) of CF (P) 0.4 #ausP# %for HOS/AR, artificial uplift of samples (aus) of CF (P)
1.3 #nfacP# %for HOS/AR, noise factor for noise level determination (P) 1.3 #nfacP# %for HOS/AR, noise factor for noise level determination (P)
#H-components# #H-components#
ARH #algoS# %choose algorithm for S-onset determination (ARH or AR3) ARH #algoS# %choose algorithm for S-onset determination (ARH or AR3)
@ -75,7 +75,7 @@ ARH #algoS# %choose algo
4 #Sarorder# %for AR-picker, order of AR process of H-components 4 #Sarorder# %for AR-picker, order of AR process of H-components
5.0 #Srecalcwin# %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H) 5.0 #Srecalcwin# %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)
4.0 #pickwinS# %for initial AIC pick, length of S-pick window [s] 4.0 #pickwinS# %for initial AIC pick, length of S-pick window [s]
2.0 0.3 1.5 1.0 #tsnrh# %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s] 2.0 0.2 1.5 1.0 #tsnrh# %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]
1.0 #aictsmoothS# %for AIC-picker, take average of samples for smoothing of AIC-function [s] 1.0 #aictsmoothS# %for AIC-picker, take average of samples for smoothing of AIC-function [s]
0.7 #tsmoothS# %for AR-picker, take average of samples for smoothing CF [s] (S) 0.7 #tsmoothS# %for AR-picker, take average of samples for smoothing CF [s] (S)
0.9 #ausS# %for HOS/AR, artificial uplift of samples (aus) of CF (S) 0.9 #ausS# %for HOS/AR, artificial uplift of samples (aus) of CF (S)
@ -85,16 +85,16 @@ ARH #algoS# %choose algo
2.0 #minFMSNR# %miniumum required SNR for first-motion determination 2.0 #minFMSNR# %miniumum required SNR for first-motion determination
0.2 #fmpickwin# %pick window around P onset for calculating zero crossings 0.2 #fmpickwin# %pick window around P onset for calculating zero crossings
#quality assessment# #quality assessment#
0.02 0.04 0.08 0.16 #timeerrorsP# %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P 0.04 0.08 0.16 0.32 #timeerrorsP# %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P
0.04 0.08 0.16 0.32 #timeerrorsS# %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S 0.05 0.10 0.20 0.40 #timeerrorsS# %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S
0.8 #minAICPslope# %below this slope [counts/s] the initial P pick is rejected 0.8 #minAICPslope# %below this slope [counts/s] the initial P pick is rejected
1.1 #minAICPSNR# %below this SNR the initial P pick is rejected 1.1 #minAICPSNR# %below this SNR the initial P pick is rejected
1.0 #minAICSslope# %below this slope [counts/s] the initial S pick is rejected 1.0 #minAICSslope# %below this slope [counts/s] the initial S pick is rejected
1.5 #minAICSSNR# %below this SNR the initial S pick is rejected 1.5 #minAICSSNR# %below this SNR the initial S pick is rejected
1.0 #minsiglength# %length of signal part for which amplitudes must exceed noiselevel [s] 1.0 #minsiglength# %length of signal part for which amplitudes must exceed noiselevel [s]
1.0 #noisefactor# %noiselevel*noisefactor=threshold 1.1 #noisefactor# %noiselevel*noisefactor=threshold
10.0 #minpercent# %required percentage of amplitudes exceeding threshold 50.0 #minpercent# %required percentage of amplitudes exceeding threshold
1.5 #zfac# %P-amplitude must exceed at least zfac times RMS-S amplitude 1.1 #zfac# %P-amplitude must exceed at least zfac times RMS-S amplitude
6.0 #mdttolerance# %maximum allowed deviation of P picks from median [s] 5.0 #mdttolerance# %maximum allowed deviation of P picks from median [s]
1.0 #wdttolerance# %maximum allowed deviation from Wadati-diagram 1.0 #wdttolerance# %maximum allowed deviation from Wadati-diagram
5.0 #jackfactor# %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 2.0 #jackfactor# %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

12
pylot/core/analysis/magnitude.py
View File

@ -6,6 +6,7 @@ Revised/extended summer 2017.
:author: Ludger Küperkoch / MAGS2 EP3 working group :author: Ludger Küperkoch / MAGS2 EP3 working group
""" """
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import numpy as np import numpy as np
import obspy.core.event as ope import obspy.core.event as ope
@ -121,7 +122,13 @@ class Magnitude(object):
def net_magnitude(self, magscaling=None): def net_magnitude(self, magscaling=None):
if self: if self:
if magscaling is not None and str(magscaling) is not '[0.0, 0.0]': if magscaling == None:
scaling = False
elif magscaling[0] != 0 and magscaling[1] != 0:
scaling = False
else:
scaling = True
if scaling:
# scaling necessary # scaling necessary
print("Scaling network magnitude ...") print("Scaling network magnitude ...")
mag = ope.Magnitude( mag = ope.Magnitude(
@ -140,7 +147,6 @@ class Magnitude(object):
station_count=len(self.magnitudes), station_count=len(self.magnitudes),
azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap) azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap)
return mag return mag
return None
class LocalMagnitude(Magnitude): class LocalMagnitude(Magnitude):
@ -219,7 +225,7 @@ class LocalMagnitude(Magnitude):
sqH = np.sqrt(power_sum) sqH = np.sqrt(power_sum)
# get time array # get time array
th = np.arange(0, len(sqH) * dt, dt) th=np.arange(0, st[0].stats.npts/st[0].stats.sampling_rate, st[0].stats.delta)
# get maximum peak within pick window # get maximum peak within pick window
iwin = getsignalwin(th, t0 - stime, self.calc_win) iwin = getsignalwin(th, t0 - stime, self.calc_win)
ii = min([iwin[len(iwin) - 1], len(th)]) ii = min([iwin[len(iwin) - 1], len(th)])

48
pylot/core/io/data.py
View File

@ -15,7 +15,7 @@ from pylot.core.util.event import Event
from pylot.core.util.utils import fnConstructor, full_range, remove_underscores, check4gaps, check4doubled, \ from pylot.core.util.utils import fnConstructor, full_range, remove_underscores, check4gaps, check4doubled, \
check4rotated, trim_station_components check4rotated, trim_station_components
import pylot.core.loc.velest as velest import pylot.core.loc.velest as velest
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
class Data(object): class Data(object):
""" """
@ -43,7 +43,7 @@ class Data(object):
elif isinstance(evtdata, dict): elif isinstance(evtdata, dict):
evt = readPILOTEvent(**evtdata) evt = readPILOTEvent(**evtdata)
evtdata = evt evtdata = evt
elif isinstance(evtdata, str): elif type(evtdata) in [str, unicode]:
try: try:
cat = read_events(evtdata) cat = read_events(evtdata)
if len(cat) is not 1: if len(cat) is not 1:
@ -60,6 +60,8 @@ class Data(object):
raise NotImplementedError('PILOT location information ' raise NotImplementedError('PILOT location information '
'read support not yet ' 'read support not yet '
'implemeted.') 'implemeted.')
elif 'event.pkl' in evtdata:
evtdata = qml_from_obspyDMT(evtdata)
else: else:
raise e raise e
else: else:
@ -72,6 +74,7 @@ class Data(object):
self.wforiginal = None self.wforiginal = None
self.cuttimes = None self.cuttimes = None
self.dirty = False self.dirty = False
self.processed = None
def __str__(self): def __str__(self):
return str(self.wfdata) return str(self.wfdata)
@ -368,7 +371,7 @@ class Data(object):
data.filter(**kwargs) data.filter(**kwargs)
self.dirty = True self.dirty = True
def setWFData(self, fnames, checkRotated=False, metadata=None, obspy_dmt=False): def setWFData(self, fnames, fnames_syn=None, checkRotated=False, metadata=None):
""" """
Clear current waveform data and set given waveform data Clear current waveform data and set given waveform data
:param fnames: waveform data names to append :param fnames: waveform data names to append
@ -377,30 +380,31 @@ class Data(object):
self.wfdata = Stream() self.wfdata = Stream()
self.wforiginal = None self.wforiginal = None
self.wfsyn = Stream() self.wfsyn = Stream()
wffnames = None # if obspy_dmt:
wffnames_syn = None # wfdir = 'raw'
wfdir = 'processed' if 'processed' in [fname.split('/')[-1] for fname in fnames] else 'raw' # self.processed = False
if obspy_dmt: # for fname in fnames:
for fpath in fnames: # if fname.endswith('processed'):
if fpath.endswith(wfdir): # wfdir = 'processed'
wffnames = [os.path.join(fpath, fname) for fname in os.listdir(fpath)] # self.processed = True
if 'syngine' in fpath.split('/')[-1]: # break
wffnames_syn = [os.path.join(fpath, fname) for fname in os.listdir(fpath)] # for fpath in fnames:
else: # if fpath.endswith(wfdir):
wffnames = fnames # wffnames = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
if wffnames is not None: # if 'syngine' in fpath.split('/')[-1]:
self.appendWFData(wffnames) # wffnames_syn = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
if wffnames_syn is not None: # else:
self.appendWFData(wffnames_syn, synthetic=True) # wffnames = fnames
if fnames is not None:
self.appendWFData(fnames)
if fnames_syn is not None:
self.appendWFData(fnames_syn, synthetic=True)
else: else:
return False return False
# various pre-processing steps: # various pre-processing steps:
# remove possible underscores in station names # remove possible underscores in station names
self.wfdata = remove_underscores(self.wfdata) self.wfdata = remove_underscores(self.wfdata)
# check for gaps and doubled channels
check4gaps(self.wfdata)
check4doubled(self.wfdata)
# check for stations with rotated components # check for stations with rotated components
if checkRotated and metadata is not None: if checkRotated and metadata is not None:
self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0) self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
@ -441,7 +445,7 @@ class Data(object):
except SacIOError as se: except SacIOError as se:
warnmsg += '{0}\n{1}\n'.format(fname, se) warnmsg += '{0}\n{1}\n'.format(fname, se)
if warnmsg: if warnmsg:
warnmsg = 'WARNING: unable to read\n' + warnmsg warnmsg = 'WARNING in appendWFData: unable to read waveform data\n' + warnmsg
print(warnmsg) print(warnmsg)
def getWFData(self): def getWFData(self):

78
pylot/core/pick/autopick.py
View File

@ -100,9 +100,9 @@ def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None,
# quality control # quality control
# median check and jackknife on P-onset times # median check and jackknife on P-onset times
jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, jackfactor, 1, fig_dict_wadatijack) jk_checked_onsets = checkPonsets(all_onsets, mdttolerance, jackfactor, iplot, fig_dict_wadatijack)
# check S-P times (Wadati) # check S-P times (Wadati)
wadationsets = wadaticheck(jk_checked_onsets, wdttolerance, 1, fig_dict_wadatijack) wadationsets = wadaticheck(jk_checked_onsets, wdttolerance, iplot, fig_dict_wadatijack)
return wadationsets return wadationsets
@ -1057,8 +1057,64 @@ def nautopickstation(wfstream, pickparam, verbose=False,
# read your pylot.in for details! # read your pylot.in for details!
plt_flag = 0 plt_flag = 0
# get picking parameter dictionaries # special parameters for P picking
p_params, s_params, first_motion_params, signal_length_params = get_pickparams(pickparam) algoP = pickparam.get('algoP')
pstart = pickparam.get('pstart')
pstop = pickparam.get('pstop')
thosmw = pickparam.get('tlta')
tsnrz = pickparam.get('tsnrz')
hosorder = pickparam.get('hosorder')
bpz1 = pickparam.get('bpz1')
bpz2 = pickparam.get('bpz2')
pickwinP = pickparam.get('pickwinP')
aictsmoothP = pickparam.get('aictsmooth')
tsmoothP = pickparam.get('tsmoothP')
ausP = pickparam.get('ausP')
nfacP = pickparam.get('nfacP')
tpred1z = pickparam.get('tpred1z')
tdet1z = pickparam.get('tdet1z')
tpred2z = pickparam.get('tpred2z')
tdet2z = pickparam.get('tdet2z')
Parorder = pickparam.get('Parorder')
addnoise = pickparam.get('addnoise')
Precalcwin = pickparam.get('Precalcwin')
minAICPslope = pickparam.get('minAICPslope')
minAICPSNR = pickparam.get('minAICPSNR')
timeerrorsP = pickparam.get('timeerrorsP')
# special parameters for S picking
algoS = pickparam.get('algoS')
sstart = pickparam.get('sstart')
sstop = pickparam.get('sstop')
use_taup = real_Bool(pickparam.get('use_taup'))
taup_model = pickparam.get('taup_model')
bph1 = pickparam.get('bph1')
bph2 = pickparam.get('bph2')
tsnrh = pickparam.get('tsnrh')
pickwinS = pickparam.get('pickwinS')
tpred1h = pickparam.get('tpred1h')
tdet1h = pickparam.get('tdet1h')
tpred2h = pickparam.get('tpred2h')
tdet2h = pickparam.get('tdet2h')
Sarorder = pickparam.get('Sarorder')
aictsmoothS = pickparam.get('aictsmoothS')
tsmoothS = pickparam.get('tsmoothS')
ausS = pickparam.get('ausS')
minAICSslope = pickparam.get('minAICSslope')
minAICSSNR = pickparam.get('minAICSSNR')
Srecalcwin = pickparam.get('Srecalcwin')
nfacS = pickparam.get('nfacS')
timeerrorsS = pickparam.get('timeerrorsS')
# parameters for first-motion determination
minFMSNR = pickparam.get('minFMSNR')
fmpickwin = pickparam.get('fmpickwin')
minfmweight = pickparam.get('minfmweight')
# parameters for checking signal length
minsiglength = pickparam.get('minsiglength')
minpercent = pickparam.get('minpercent')
nfacsl = pickparam.get('noisefactor')
# parameter to check for spuriously picked S onset
zfac = pickparam.get('zfac')
# path to inventory-, dataless- or resp-files
# initialize output # initialize output
Pweight = 4 # weight for P onset Pweight = 4 # weight for P onset
@ -1159,6 +1215,8 @@ def nautopickstation(wfstream, pickparam, verbose=False,
if p_params['use_taup'] is True: if p_params['use_taup'] is True:
Lc = np.inf Lc = np.inf
print('autopickstation: use_taup flag active.') print('autopickstation: use_taup flag active.')
if not metadata:
metadata = [None, None]
if not metadata[1]: if not metadata[1]:
print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.') print('Warning: Could not use TauPy to estimate onsets as there are no metadata given.')
else: else:
@ -1207,7 +1265,7 @@ def nautopickstation(wfstream, pickparam, verbose=False,
return return
Ldiff = Lwf - abs(Lc) Ldiff = Lwf - abs(Lc)
if Ldiff < 0 or pstop <= pstart: if Ldiff <= 0 or pstop <= pstart or pstop - pstart <= thosmw:
msg = 'autopickstation: Cutting times are too large for actual ' \ msg = 'autopickstation: Cutting times are too large for actual ' \
'waveform!\nUsing entire waveform instead!' 'waveform!\nUsing entire waveform instead!'
if verbose: print(msg) if verbose: print(msg)
@ -1345,8 +1403,8 @@ def nautopickstation(wfstream, pickparam, verbose=False,
elif p_params['algoP'] == 'ARZ': elif p_params['algoP'] == 'ARZ':
# calculate ARZ-CF using subclass ARZcf of class # calculate ARZ-CF using subclass ARZcf of class
# CharcteristicFunction # CharcteristicFunction
cf2 = ARZcf(z_copy, cuttimes2, p_params['tpred1z'], p_params['Parorder'], p_params['tdet1z'], cf2 = ARZcf(z_copy, cuttimes2, tpred2z, Parorder, tdet2z,
p_params['addnoise']) # instance of ARZcf addnoise) # instance of ARZcf
############################################################## ##############################################################
# get refined onset time from CF2 using class Picker # get refined onset time from CF2 using class Picker
assert isinstance(cf2, CharacteristicFunction), 'cf2 is not set ' \ assert isinstance(cf2, CharacteristicFunction), 'cf2 is not set ' \
@ -1401,7 +1459,8 @@ def nautopickstation(wfstream, pickparam, verbose=False,
msg = "autopickstation: P-weight: {0}, " \ msg = "autopickstation: P-weight: {0}, " \
"SNR: {1}, SNR[dB]: {2}, Polarity: {3}".format(Pweight, SNRP, SNRPdB, FM) "SNR: {1}, SNR[dB]: {2}, Polarity: {3}".format(Pweight, SNRP, SNRPdB, FM)
print(msg) print(msg)
msg = 'autopickstation: Refined P-Pick: {} s | P-Error: {} s'.format(mpickP, Perror) msg = 'autopickstation: Refind P-Pick: {} s | P-Error: {} s'.format(zdat[0].stats.starttime \
+ mpickP, Perror)
print(msg) print(msg)
Sflag = 1 Sflag = 1
@ -1667,7 +1726,8 @@ def nautopickstation(wfstream, pickparam, verbose=False,
lpickS = lpick[ipick] lpickS = lpick[ipick]
Serror = pickerr[ipick] Serror = pickerr[ipick]
msg = 'autopickstation: Refined S-Pick: {} s | S-Error: {} s'.format(mpickS, Serror) msg = 'autopickstation: Refined S-Pick: {} s | S-Error: {} s'.format(hdat[0].stats.starttime \
+ mpickS, Serror)
print(msg) print(msg)
# get SNR # get SNR

2
pylot/core/pick/charfuns.py
View File

@ -78,7 +78,7 @@ class CharacteristicFunction(object):
return self.cut return self.cut
def setCut(self, cut): def setCut(self, cut):
self.cut = cut self.cut = (int(cut[0]), int(cut[1]))
def getTime1(self): def getTime1(self):
return self.t1 return self.t1

110
pylot/core/pick/picker.py
View File

@ -233,12 +233,41 @@ class AICPicker(AutoPicker):
# quality assessment using SNR and slope from CF # quality assessment using SNR and slope from CF
if self.Pick is not None: if self.Pick is not None:
self.Data[0].data = check_counts_ms(self.Data[0].data) # get noise window
inoise = getnoisewin(self.Tcf, self.Pick, self.TSNR[0], self.TSNR[1])
# check, if these are counts or m/s, important for slope estimation!
# this is quick and dirty, better solution? #Todo wtf
if max(self.Data[0].data < 1e-3) and max(self.Data[0].data >= 1e-6):
self.Data[0].data = self.Data[0].data * 1000000.
elif max(self.Data[0].data < 1e-6):
self.Data[0].data = self.Data[0].data * 1e13
# get signal window
isignal = getsignalwin(self.Tcf, self.Pick, self.TSNR[2])
if len(isignal) == 0:
return
ii = min([isignal[len(isignal) - 1], len(self.Tcf)])
isignal = isignal[0:ii]
try:
self.Data[0].data[isignal]
except IndexError as e:
msg = "Time series out of bounds! {}".format(e)
print(msg)
return
# calculate SNR from CF # calculate SNR from CF
# subtract beginning of Tcf to get sample index in self.Data, which self.SNR = max(abs(self.Data[0].data[isignal])) / \
# is cut out off trace abs(np.mean(self.Data[0].data[inoise]))
self.SNR = getSNR(self.Data, self.TSNR, self.Pick-self.Tcf[0])[0] # TODO Check wether this yields similar results
# calculate slope from CF after initial pick # calculate slope from CF after initial pick
# get slope window
tslope = self.TSNR[3] # slope determination window
tsafety = self.TSNR[1] # safety gap, AIC is usually a little bit too late
if tsafety >= 0:
islope = np.where((self.Tcf <= min([self.Pick + tslope + tsafety, self.Tcf[-1]])) \
& (self.Tcf >= self.Pick)) # TODO: put this in a seperate function like getsignalwin
else:
islope = np.where((self.Tcf <= min([self.Pick + tslope, self.Tcf[-1]])) \
& (self.Tcf >= self.Pick + tsafety)) # TODO: put this in a seperate function like getsignalwin
# find maximum within slope determination window
# 'cause slope should be calculated up to first local minimum only!
try: try:
self.slope, iislope, datafit = calcSlope(self.Data, self.aicsmooth, self.Tcf, self.Pick, self.TSNR) self.slope, iislope, datafit = calcSlope(self.Data, self.aicsmooth, self.Tcf, self.Pick, self.TSNR)
except Exception: except Exception:
@ -264,6 +293,56 @@ class AICPicker(AutoPicker):
pass pass
plt.close(fig) plt.close(fig)
return return
if len(dataslope) < 2:
print('No or not enough data in slope window found!')
return
try:
imaxs, = argrelmax(dataslope)
imaxs.size
imax = imaxs[0]
except ValueError as e:
print(e, 'picker: argrelmax not working!')
imax = np.argmax(dataslope)
iislope = islope[0][0:imax + 1]
if len(iislope) < 2:
# calculate slope from initial onset to maximum of AIC function
print("AICPicker: Not enough data samples left for slope calculation!")
print("Calculating slope from initial onset to maximum of AIC function ...")
imax = np.argmax(aicsmooth[islope[0][0:-1]])
if imax == 0:
print("AICPicker: Maximum for slope determination right at the beginning of the window!")
print("Choose longer slope determination window!")
if self.iplot > 1:
if self.fig == None or self.fig == 'None':
fig = plt.figure()
plt_flag = 1
else:
fig = self.fig
ax = fig.add_subplot(111)
x = self.Data[0].data
ax.plot(self.Tcf, x / max(x), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
ax.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
ax.legend(loc=1)
ax.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
ax.set_yticks([])
ax.set_title(self.Data[0].stats.station)
if plt_flag == 1:
fig.show()
try: input()
except SyntaxError: pass
plt.close(fig)
return
iislope = islope[0][0:imax+1]
dataslope = self.Data[0].data[iislope]
# calculate slope as polynomal fit of order 1
xslope = np.arange(0, len(dataslope), 1)
P = np.polyfit(xslope, dataslope, 1)
datafit = np.polyval(P, xslope)
if datafit[0] >= datafit[-1]:
print('AICPicker: Negative slope, bad onset skipped!')
else:
self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
else: else:
self.SNR = -1 self.SNR = -1
self.slope = -1 self.slope = -1
@ -305,24 +384,23 @@ class AICPicker(AutoPicker):
label='Slope Window') label='Slope Window')
ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2, label='Slope') ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2, label='Slope')
ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station, if self.slope is not None:
self.SNR, self.slope)) ax1.set_title('Station %s, SNR=%7.2f, Slope= %12.2f counts/s' % (self.Data[0].stats.station,
self.SNR, self.slope))
else:
ax1.set_title('Station %s, SNR=%7.2f' % (self.Data[0].stats.station, self.SNR))
ax2.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime) ax2.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
ax2.set_ylabel('Counts') ax2.set_ylabel('Counts')
ax2.set_yticks([]) ax2.set_yticks([])
ax2.legend(loc=1) ax2.legend(loc=1)
if plt_flag == 1:
fig.show()
try: input()
except SyntaxError: pass
plt.close(fig)
else: else:
ax1.set_title(self.Data[0].stats.station) ax1.set_title(self.Data[0].stats.station)
if plt_flag == 1:
fig.show() if plt_flag == 1:
try: input() fig.show()
except SyntaxError: pass try: input()
plt.close(fig) except SyntaxError: pass
plt.close(fig)
if self.Pick == None: if self.Pick == None:
print('AICPicker: Could not find minimum, picking window too short?') print('AICPicker: Could not find minimum, picking window too short?')

458
pylot/core/util/array_map.py Normal file
View File

@ -0,0 +1,458 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import numpy as np
import obspy
from PySide import QtGui
from mpl_toolkits.basemap import Basemap
from matplotlib.figure import Figure
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from pylot.core.util.widgets import PickDlg, PylotCanvas
from scipy.interpolate import griddata
plt.interactive(False)
class Array_map(QtGui.QWidget):
def __init__(self, parent, figure=None):
'''
Create a map of the array.
:param parent: PyLoT Mainwindow class
:param figure:
'''
QtGui.QWidget.__init__(self)
self._parent = parent
self.metadata_type = parent.metadata[0]
self.metadata = parent.metadata[1]
self.picks = None
self.picks_dict = None
self.autopicks_dict = None
self.eventLoc = None
self.figure = figure
self.init_graphics()
self.init_stations()
self.init_basemap(resolution='l')
self.init_map()
self._style = parent._style
# self.show()
def init_map(self):
self.init_lat_lon_dimensions()
self.init_lat_lon_grid()
self.init_x_y_dimensions()
self.connectSignals()
self.draw_everything()
self.canvas.setZoomBorders2content()
def onpick(self, event):
ind = event.ind
button = event.mouseevent.button
if ind == [] or not button == 1:
return
data = self._parent.get_data().getWFData()
for index in ind:
station = str(self._station_onpick_ids[index].split('.')[-1])
try:
data = data.select(station=station)
if not data:
self._warn('No data for station {}'.format(station))
return
pickDlg = PickDlg(self._parent, parameter=self._parent._inputs,
data=data,
station=station,
picks=self._parent.get_current_event().getPick(station),
autopicks=self._parent.get_current_event().getAutopick(station),
filteroptions=self._parent.filteroptions)
except Exception as e:
message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
self._warn(message)
print(message, e)
return
pyl_mw = self._parent
try:
if pickDlg.exec_():
pyl_mw.setDirty(True)
pyl_mw.update_status('picks accepted ({0})'.format(station))
replot = pyl_mw.get_current_event().setPick(station, pickDlg.getPicks())
self._refresh_drawings()
if replot:
pyl_mw.plotWaveformData()
pyl_mw.drawPicks()
pyl_mw.draw()
else:
pyl_mw.drawPicks(station)
pyl_mw.draw()
else:
pyl_mw.update_status('picks discarded ({0})'.format(station))
except Exception as e:
message = 'Could not save picks for station {st}.\n{er}'.format(st=station, er=e)
self._warn(message)
print(message, e)
def connectSignals(self):
self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
self.comboBox_am.currentIndexChanged.connect(self._refresh_drawings)
self.canvas.mpl_connect('motion_notify_event', self.mouse_moved)
#self.zoom_id = self.basemap.ax.figure.canvas.mpl_connect('scroll_event', self.zoom)
def _from_dict(self, function, key):
return function(self.stations_dict.values(), key=lambda x: x[key])[key]
def get_min_from_stations(self, key):
return self._from_dict(min, key)
def get_max_from_stations(self, key):
return self._from_dict(max, key)
def get_min_from_picks(self):
return min(self.picks_rel.values())
def get_max_from_picks(self):
return max(self.picks_rel.values())
def mouse_moved(self, event):
if not event.inaxes == self.main_ax:
return
x = event.xdata
y = event.ydata
lat, lon = self.basemap(x, y, inverse=True)
self.status_label.setText('Latitude: {}, Longitude: {}'.format(lat, lon))
def current_picks_dict(self):
picktype = self.comboBox_am.currentText()
auto_manu = {'auto': self.autopicks_dict,
'manual': self.picks_dict}
return auto_manu[picktype]
def init_graphics(self):
if not self.figure:
self.figure = Figure()
self.status_label = QtGui.QLabel()
self.main_ax = self.figure.add_subplot(111)
self.canvas = PylotCanvas(self.figure, parent=self._parent, multicursor=True,
panZoomX=False, panZoomY=False)
self.main_box = QtGui.QVBoxLayout()
self.setLayout(self.main_box)
self.top_row = QtGui.QHBoxLayout()
self.main_box.addLayout(self.top_row, 1)
self.comboBox_phase = QtGui.QComboBox()
self.comboBox_phase.insertItem(0, 'P')
self.comboBox_phase.insertItem(1, 'S')
self.comboBox_am = QtGui.QComboBox()
self.comboBox_am.insertItem(0, 'auto')
self.comboBox_am.insertItem(1, 'manual')
self.top_row.addWidget(QtGui.QLabel('Select a phase: '))
self.top_row.addWidget(self.comboBox_phase)
self.top_row.setStretch(1, 1) # set stretch of item 1 to 1
self.top_row.addWidget(QtGui.QLabel('Pick type: '))
self.top_row.addWidget(self.comboBox_am)
self.top_row.setStretch(3, 1) # set stretch of item 1 to 1
self.main_box.addWidget(self.canvas, 1)
self.main_box.addWidget(self.status_label, 0)
def init_stations(self):
def stat_info_from_parser(parser):
stations_dict = {}
for station in parser.stations:
station_name = station[0].station_call_letters
network_name = station[0].network_code
if not station_name in stations_dict.keys():
st_id = network_name + '.' + station_name
stations_dict[st_id] = {'latitude': station[0].latitude,
'longitude': station[0].longitude}
return stations_dict
def stat_info_from_inventory(inventory):
stations_dict = {}
for network in inventory.networks:
for station in network.stations:
station_name = station.code
network_name = network_name.code
if not station_name in stations_dict.keys():
st_id = network_name + '.' + station_name
stations_dict[st_id] = {'latitude': station[0].latitude,
'longitude': station[0].longitude}
return stations_dict
read_stat = {'xml': stat_info_from_inventory,
'dless': stat_info_from_parser}
self.stations_dict = read_stat[self.metadata_type](self.metadata)
self.latmin = self.get_min_from_stations('latitude')
self.lonmin = self.get_min_from_stations('longitude')
self.latmax = self.get_max_from_stations('latitude')
self.lonmax = self.get_max_from_stations('longitude')
def init_picks(self):
def get_picks(station_dict):
picks = {}
phase = self.comboBox_phase.currentText()
for st_id in station_dict.keys():
try:
station_name = st_id.split('.')[-1]
pick = self.current_picks_dict()[station_name][phase]
if pick['picker'] == 'auto':
if pick['weight'] > 3:
continue
picks[st_id] = pick['mpp']
except KeyError:
continue
except Exception as e:
print('Cannot display pick for station {}. Reason: {}'.format(station_name, e))
return picks
def get_picks_rel(picks):
picks_rel = {}
picks_utc = []
for pick in picks.values():
if type(pick) is obspy.core.utcdatetime.UTCDateTime:
picks_utc.append(pick)
self._earliest_picktime = min(picks_utc)
for st_id, pick in picks.items():
if type(pick) is obspy.core.utcdatetime.UTCDateTime:
pick -= self._earliest_picktime
picks_rel[st_id] = pick
return picks_rel
self.picks = get_picks(self.stations_dict)
self.picks_rel = get_picks_rel(self.picks)
def init_lat_lon_dimensions(self):
# init minimum and maximum lon and lat dimensions
self.londim = self.lonmax - self.lonmin
self.latdim = self.latmax - self.latmin
def init_x_y_dimensions(self):
# transformation of lat/lon to ax coordinate system
for st_id, coords in self.stations_dict.items():
lat, lon = coords['latitude'], coords['longitude']
coords['x'], coords['y'] = self.basemap(lon, lat)
self.xdim = self.get_max_from_stations('x') - self.get_min_from_stations('x')
self.ydim = self.get_max_from_stations('y') - self.get_min_from_stations('y')
def init_basemap(self, resolution='l'):
# basemap = Basemap(projection=projection, resolution = resolution, ax=self.main_ax)
width = 5e6
height = 2e6
basemap = Basemap(projection='lcc', resolution=resolution, ax=self.main_ax,
width=width, height=height,
lat_0=(self.latmin + self.latmax) / 2.,
lon_0=(self.lonmin + self.lonmax) / 2.)
# basemap.fillcontinents(color=None, lake_color='aqua',zorder=1)
basemap.drawmapboundary(zorder=2) # fill_color='darkblue')
basemap.shadedrelief(zorder=3)
basemap.drawcountries(zorder=4)
basemap.drawstates(zorder=5)
basemap.drawcoastlines(zorder=6)
# labels = [left,right,top,bottom]
parallels = np.arange(-90, 90, 5.)
parallels_small = np.arange(-90, 90, 2.5)
basemap.drawparallels(parallels_small, linewidth=0.5, zorder=7)
basemap.drawparallels(parallels, zorder=7)
meridians = np.arange(-180, 180, 5.)
meridians_small = np.arange(-180, 180, 2.5)
basemap.drawmeridians(meridians_small, linewidth=0.5, zorder=7)
basemap.drawmeridians(meridians, zorder=7)
self.basemap = basemap
self.figure._tight = True
self.figure.tight_layout()
def init_lat_lon_grid(self, nstep=250):
# create a regular grid to display colormap
lataxis = np.linspace(self.latmin, self.latmax, nstep)
lonaxis = np.linspace(self.lonmin, self.lonmax, nstep)
self.longrid, self.latgrid = np.meshgrid(lonaxis, lataxis)
def init_picksgrid(self):
picks, lats, lons = self.get_picks_lat_lon()
try:
self.picksgrid_active = griddata((lats, lons), picks, (self.latgrid, self.longrid),
method='linear')
except Exception as e:
self._warn('Could not init picksgrid: {}'.format(e))
def get_st_lat_lon_for_plot(self):
stations = []
latitudes = []
longitudes = []
for st_id, coords in self.stations_dict.items():
stations.append(st_id)
latitudes.append(coords['latitude'])
longitudes.append(coords['longitude'])
return stations, latitudes, longitudes
def get_st_x_y_for_plot(self):
stations = []
xs = []
ys = []
for st_id, coords in self.stations_dict.items():
stations.append(st_id)
xs.append(coords['x'])
ys.append(coords['y'])
return stations, xs, ys
def get_picks_lat_lon(self):
picks = []
latitudes = []
longitudes = []
for st_id, pick in self.picks_rel.items():
picks.append(pick)
latitudes.append(self.stations_dict[st_id]['latitude'])
longitudes.append(self.stations_dict[st_id]['longitude'])
return picks, latitudes, longitudes
def draw_contour_filled(self, nlevel='50'):
levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
self.contourf = self.basemap.contourf(self.longrid, self.latgrid, self.picksgrid_active,
levels, latlon=True, zorder=9, alpha=0.5)
def scatter_all_stations(self):
stations, lats, lons = self.get_st_lat_lon_for_plot()
self.sc = self.basemap.scatter(lons, lats, s=50, facecolor='none', latlon=True,
zorder=10, picker=True, edgecolor='m', label='Not Picked')
self.cid = self.canvas.mpl_connect('pick_event', self.onpick)
self._station_onpick_ids = stations
if self.eventLoc:
lats, lons = self.eventLoc
self.sc_event = self.basemap.scatter(lons, lats, s=100, facecolor='red',
latlon=True, zorder=11, label='Event (might be outside map region)')
def scatter_picked_stations(self):
picks, lats, lons = self.get_picks_lat_lon()
# workaround because of an issue with latlon transformation of arrays with len <3
if len(lons) <= 2 and len(lats) <= 2:
self.sc_picked = self.basemap.scatter(lons[0], lats[0], s=50, facecolor='white',
c=picks[0], latlon=True, zorder=11, label='Picked')
if len(lons) == 2 and len(lats) == 2:
self.sc_picked = self.basemap.scatter(lons[1], lats[1], s=50, facecolor='white',
c=picks[1], latlon=True, zorder=11)
else:
self.sc_picked = self.basemap.scatter(lons, lats, s=50, facecolor='white',
c=picks, latlon=True, zorder=11, label='Picked')
def annotate_ax(self):
self.annotations = []
stations, xs, ys = self.get_st_x_y_for_plot()
for st, x, y in zip(stations, xs, ys):
self.annotations.append(self.main_ax.annotate(' %s' % st, xy=(x, y),
fontsize='x-small', color='white', zorder=12))
self.legend = self.main_ax.legend(loc=1)
self.legend.get_frame().set_facecolor((1, 1, 1, 0.75))
def add_cbar(self, label):
self.cbax_bg = inset_axes(self.main_ax, width="6%", height="75%", loc=5)
cbax = inset_axes(self.main_ax, width='2%', height='70%', loc=5)
cbar = self.main_ax.figure.colorbar(self.sc_picked, cax = cbax)
cbar.set_label(label)
cbax.yaxis.tick_left()
cbax.yaxis.set_label_position('left')
for spine in self.cbax_bg.spines.values():
spine.set_visible(False)
self.cbax_bg.yaxis.set_ticks([])
self.cbax_bg.xaxis.set_ticks([])
self.cbax_bg.patch.set_facecolor((1, 1, 1, 0.75))
return cbar
def refresh_drawings(self, picks=None, autopicks=None):
self.picks_dict = picks
self.autopicks_dict = autopicks
self._refresh_drawings()
def _refresh_drawings(self):
self.remove_drawings()
self.draw_everything()
def draw_everything(self):
if self.picks_dict or self.autopicks_dict:
self.init_picks()
if len(self.picks) >= 3:
self.init_picksgrid()
self.draw_contour_filled()
self.scatter_all_stations()
if self.picks_dict or self.autopicks_dict:
self.scatter_picked_stations()
self.cbar = self.add_cbar(label='Time relative to first onset ({}) [s]'.format(self._earliest_picktime))
self.comboBox_phase.setEnabled(True)
else:
self.comboBox_phase.setEnabled(False)
self.annotate_ax()
self.canvas.draw()
def remove_drawings(self):
if hasattr(self, 'cbar'):
self.cbar.remove()
self.cbax_bg.remove()
del (self.cbar, self.cbax_bg)
if hasattr(self, 'sc_picked'):
self.sc_picked.remove()
del (self.sc_picked)
if hasattr(self, 'sc_event'):
self.sc_event.remove()
del (self.sc_event)
if hasattr(self, 'contourf'):
self.remove_contourf()
del (self.contourf)
if hasattr(self, 'cid'):
self.canvas.mpl_disconnect(self.cid)
del (self.cid)
try:
self.sc.remove()
except Exception as e:
print('Warning: could not remove station scatter plot.\nReason: {}'.format(e))
try:
self.legend.remove()
except Exception as e:
print('Warning: could not remove legend. Reason: {}'.format(e))
self.canvas.draw()
def remove_contourf(self):
for item in self.contourf.collections:
item.remove()
def remove_annotations(self):
for annotation in self.annotations:
annotation.remove()
def zoom(self, event):
map = self.basemap
xlim = map.ax.get_xlim()
ylim = map.ax.get_ylim()
x, y = event.xdata, event.ydata
zoom = {'up': 1. / 2.,
'down': 2.}
if not event.xdata or not event.ydata:
return
if event.button in zoom:
factor = zoom[event.button]
xdiff = (xlim[1] - xlim[0]) * factor
xl = x - 0.5 * xdiff
xr = x + 0.5 * xdiff
ydiff = (ylim[1] - ylim[0]) * factor
yb = y - 0.5 * ydiff
yt = y + 0.5 * ydiff
if xl < map.xmin or yb < map.ymin or xr > map.xmax or yt > map.ymax:
xl, xr = map.xmin, map.xmax
yb, yt = map.ymin, map.ymax
map.ax.set_xlim(xl, xr)
map.ax.set_ylim(yb, yt)
map.ax.figure.canvas.draw()
def _warn(self, message):
self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Warning,
'Warning', message)
self.qmb.show()

207
pylot/core/util/dataprocessing.py
View File

@ -12,6 +12,186 @@ from pylot.core.util.utils import key_for_set_value, find_in_list, \
remove_underscores, gen_Pool remove_underscores, gen_Pool
class Metadata(object):
def __init__(self, inventory=None):
self.inventories = []
if os.path.isdir(inventory):
self.add_inventory(inventory)
if os.path.isfile(inventory):
self.add_inventory_file(inventory)
self.seed_ids = {}
self.inventory_files = {}
def add_inventory(self, path_to_inventory):
# add paths to list of inventories
assert (os.path.isdir(path_to_inventory)), '{} is no directory'.format(path_to_inventory)
if not path_to_inventory in self.inventories:
self.inventories.append(path_to_inventory)
def add_inventory_file(self, path_to_inventory_file):
assert (os.path.isfile(path_to_inventory_file)), '{} is no directory'.format(path_to_inventory_file)
self.add_inventory(os.path.split(path_to_inventory_file)[0])
if not path_to_inventory_file in self.inventory_files.keys():
self.read_single_file(path_to_inventory_file)
def remove_inventory(self, path_to_inventory):
if not path_to_inventory in self.inventories:
print('Path {} not in inventories list.'.format(path_to_inventory))
return
self.inventories.remove(path_to_inventory)
def get_metadata(self, seed_id):
# get metadata for a specific seed_id, if not already read, try to read from inventories
if not seed_id in self.seed_ids.keys():
self._read_inventory_data(seed_id)
# if seed id is not found read all inventories and try to find it there
if not seed_id in self.seed_ids.keys():
print('No data found for seed id {}. Trying to find it in all known inventories...'.format(seed_id))
self.read_all()
for inv_fname, metadata in self.inventory_files.items():
# use get_coordinates to check for seed_id
if metadata['data'].get_coordinates(seed_id):
self.seed_ids[seed_id] = inv_fname
return metadata
print('Could not find metadata for station {}'.format(seed_id))
return None
fname = self.seed_ids[seed_id]
return self.inventory_files[fname]
def read_all(self):
for inventory in self.inventories:
for inv_fname in os.listdir(inventory):
inv_fname = os.path.join(inventory, inv_fname)
if not self.read_single_file(inv_fname):
continue
def read_single_file(self, inv_fname):
if not inv_fname in self.inventory_files.keys():
pass
else:
if not self.inventory_files[inv_fname]:
pass
else:
return
try:
invtype, robj = self._read_metadata_file(inv_fname)
if robj == None:
return
except Exception as e:
print('Could not read file {}'.format(inv_fname))
return
self.inventory_files[inv_fname] = {'invtype': invtype,
'data': robj}
return True
def get_coordinates(self, seed_id):
metadata = self.get_metadata(seed_id)
return metadata['data'].get_coordinates(seed_id)
def get_paz(self, seed_id, time=None):
metadata = self.get_metadata(seed_id)
if metadata['invtype'] in ['dless', 'dseed']:
return metadata['data'].get_paz(seed_id)
elif metadata['invtype'] in ['resp', 'xml']:
if not time:
print('Time needed to extract metadata from station inventory.')
return None
resp = metadata['data'].get_response(seed_id, time)
return resp.get_paz(seed_id)
def _read_inventory_data(self, seed_id=None):
for inventory in self.inventories:
if self._read_metadata_iterator(path_to_inventory=inventory, station_seed_id=seed_id):
return
def _read_metadata_iterator(self, path_to_inventory, station_seed_id):
'''
search for metadata for a specific station iteratively
'''
station, network, location, channel = station_seed_id.split('.')
fnames = glob.glob(os.path.join(path_to_inventory, '*' + station_seed_id + '*'))
if not fnames:
# search for station name in filename
fnames = glob.glob(os.path.join(path_to_inventory, '*' + station + '*'))
if not fnames:
# search for network name in filename
fnames = glob.glob(os.path.join(path_to_inventory, '*' + network + '*'))
if not fnames:
print('Could not find filenames matching station name, network name or seed id')
return
for fname in fnames:
if fname in self.inventory_files.keys():
if self.inventory_files[fname]:
# file already read
continue
invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
try:
robj.get_coordinates(station_seed_id)
self.inventory_files[fname] = {'invtype': invtype,
'data': robj}
if station_seed_id in self.seed_ids.keys():
print('WARNING: Overwriting metadata for station {}'.format(station_seed_id))
self.seed_ids[station_seed_id] = fname
return True
except Exception as e:
continue
print('Could not find metadata for station_seed_id {} in path {}'.format(station_seed_id, path_to_inventory))
def _read_metadata_file(self, path_to_inventory_filename):
'''
function reading metadata files (either dataless seed, xml or resp)
:param path_to_inventory_filename:
:return: file type/ending, inventory object (Parser or Inventory)
'''
# functions used to read metadata for different file endings (or file types)
read_functions = {'dless': self._read_dless,
'dseed': self._read_dless,
'xml': self._read_inventory_file,
'resp': self._read_inventory_file}
file_ending = path_to_inventory_filename.split('.')[-1]
if file_ending in read_functions.keys():
robj, exc = read_functions[file_ending](path_to_inventory_filename)
if exc is not None:
raise exc
return file_ending, robj
# in case file endings did not match the above keys, try and error
for file_type in ['dless', 'xml']:
robj, exc = read_functions[file_type](path_to_inventory_filename)
if exc is None:
return file_type, robj
return None, None
def _read_dless(self, path_to_inventory):
exc = None
try:
parser = Parser(path_to_inventory)
except Exception as exc:
parser = None
return parser, exc
def _read_inventory_file(self, path_to_inventory):
exc = None
try:
inv = read_inventory(path_to_inventory)
except Exception as exc:
inv = None
return inv, exc
def time_from_header(header): def time_from_header(header):
""" """
Function takes in the second line from a .gse file and takes out the date and time from that line. Function takes in the second line from a .gse file and takes out the date and time from that line.
@ -196,6 +376,33 @@ def read_metadata(path_to_inventory):
return invtype, robj return invtype, robj
# idea to optimize read_metadata
# def read_metadata_new(path_to_inventory):
# metadata_objects = []
# # read multiple files from directory
# if os.path.isdir(path_to_inventory):
# fnames = os.listdir(path_to_inventory)
# # read single file
# elif os.path.isfile(path_to_inventory):
# fnames = [path_to_inventory]
# else:
# print("Neither dataless-SEED file, inventory-xml file nor "
# "RESP-file found!")
# print("!!WRONG CALCULATION OF SOURCE PARAMETERS!!")
# fnames = []
#
# for fname in fnames:
# path_to_inventory_filename = os.path.join(path_to_inventory, fname)
# try:
# ftype, robj = read_metadata_file(path_to_inventory_filename)
# metadata_objects.append((ftype, robj))
# except Exception as e:
# print('Could not read metadata file {} '
# 'because of the following Exception: {}'.format(path_to_inventory_filename, e))
# return metadata_objects
def restitute_trace(input_tuple): def restitute_trace(input_tuple):
tr, invtype, inobj, unit, force = input_tuple tr, invtype, inobj, unit, force = input_tuple

14
pylot/core/util/event.py
View File

@ -7,6 +7,7 @@ from obspy import UTCDateTime
from obspy.core.event import Event as ObsPyEvent from obspy.core.event import Event as ObsPyEvent
from obspy.core.event import Origin, ResourceIdentifier from obspy.core.event import Origin, ResourceIdentifier
from pylot.core.io.phases import picks_from_picksdict from pylot.core.io.phases import picks_from_picksdict
from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
class Event(ObsPyEvent): class Event(ObsPyEvent):
@ -33,6 +34,7 @@ class Event(ObsPyEvent):
self._testEvent = False self._testEvent = False
self._refEvent = False self._refEvent = False
self.get_notes() self.get_notes()
self.get_obspy_event_info()
def get_notes_path(self): def get_notes_path(self):
""" """
@ -43,6 +45,18 @@ class Event(ObsPyEvent):
notesfile = os.path.join(self.path, 'notes.txt') notesfile = os.path.join(self.path, 'notes.txt')
return notesfile 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): def get_notes(self):
""" """
set self.note attribute to content of notes file set self.note attribute to content of notes file

377
pylot/core/util/map_projection.py
View File

@ -1,377 +0,0 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import numpy as np
import obspy
from PySide import QtGui
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
from mpl_toolkits.basemap import Basemap
from pylot.core.util.widgets import PickDlg
from scipy.interpolate import griddata
plt.interactive(False)
class map_projection(QtGui.QWidget):
def __init__(self, parent, figure=None):
'''
:param: picked, can be False, auto, manual
:value: str
'''
QtGui.QWidget.__init__(self)
self._parent = parent
self.metadata = parent.metadata
self.parser = parent.metadata[1]
self.picks = None
self.picks_dict = None
self.eventLoc = None
self.figure = figure
self.init_graphics()
self.init_stations()
self.init_basemap(resolution='l')
self.init_map()
self._style = parent._style
# self.show()
def init_map(self):
self.init_lat_lon_dimensions()
self.init_lat_lon_grid()
self.init_x_y_dimensions()
self.connectSignals()
self.draw_everything()
def onpick(self, event):
ind = event.ind
button = event.mouseevent.button
if ind == [] or not button == 1:
return
data = self._parent.get_data().getWFData()
for index in ind:
station = str(self.station_names[index].split('.')[-1])
try:
pickDlg = PickDlg(self, parameter=self._parent._inputs,
data=data.select(station=station),
station=station,
picks=self._parent.get_current_event().getPick(station),
autopicks=self._parent.get_current_event().getAutopick(station))
except Exception as e:
message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
self._warn(message)
print(message, e)
return
pyl_mw = self._parent
try:
if pickDlg.exec_():
pyl_mw.setDirty(True)
pyl_mw.update_status('picks accepted ({0})'.format(station))
replot = pyl_mw.get_current_event().setPick(station, pickDlg.getPicks())
self._refresh_drawings()
if replot:
pyl_mw.plotWaveformData()
pyl_mw.drawPicks()
pyl_mw.draw()
else:
pyl_mw.drawPicks(station)
pyl_mw.draw()
else:
pyl_mw.update_status('picks discarded ({0})'.format(station))
except Exception as e:
message = 'Could not save picks for station {st}.\n{er}'.format(st=station, er=e)
self._warn(message)
print(message, e)
def connectSignals(self):
self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
self.zoom_id = self.basemap.ax.figure.canvas.mpl_connect('scroll_event', self.zoom)
def init_graphics(self):
if not self.figure:
if not hasattr(self._parent, 'am_figure'):
self.figure = plt.figure()
self.toolbar = NavigationToolbar(self.figure.canvas, self)
else:
self.figure = self._parent.am_figure
self.toolbar = self._parent.am_toolbar
self.main_ax = self.figure.add_subplot(111)
self.canvas = self.figure.canvas
self.main_box = QtGui.QVBoxLayout()
self.setLayout(self.main_box)
self.top_row = QtGui.QHBoxLayout()
self.main_box.addLayout(self.top_row)
self.comboBox_phase = QtGui.QComboBox()
self.comboBox_phase.insertItem(0, 'P')
self.comboBox_phase.insertItem(1, 'S')
self.comboBox_am = QtGui.QComboBox()
self.comboBox_am.insertItem(0, 'auto')
self.comboBox_am.insertItem(1, 'manual')
self.top_row.addWidget(QtGui.QLabel('Select a phase: '))
self.top_row.addWidget(self.comboBox_phase)
self.top_row.setStretch(1, 1) # set stretch of item 1 to 1
self.main_box.addWidget(self.canvas)
self.main_box.addWidget(self.toolbar)
def init_stations(self):
def get_station_names_lat_lon(parser):
station_names = []
lat = []
lon = []
for station in parser.stations:
station_name = station[0].station_call_letters
network = station[0].network_code
if not station_name in station_names:
station_names.append(network + '.' + station_name)
lat.append(station[0].latitude)
lon.append(station[0].longitude)
return station_names, lat, lon
station_names, lat, lon = get_station_names_lat_lon(self.parser)
self.station_names = station_names
self.lat = lat
self.lon = lon
def init_picks(self):
phase = self.comboBox_phase.currentText()
def get_picks(station_names):
picks = []
for station in station_names:
try:
station = station.split('.')[-1]
picks.append(self.picks_dict[station][phase]['mpp'])
except:
picks.append(np.nan)
return picks
def get_picks_rel(picks):
picks_rel = []
picks_utc = []
for pick in picks:
if type(pick) is obspy.core.utcdatetime.UTCDateTime:
picks_utc.append(pick)
minp = min(picks_utc)
for pick in picks:
if type(pick) is obspy.core.utcdatetime.UTCDateTime:
pick -= minp
picks_rel.append(pick)
return picks_rel
self.picks = get_picks(self.station_names)
self.picks_rel = get_picks_rel(self.picks)
def init_picks_active(self):
def remove_nan_picks(picks):
picks_no_nan = []
for pick in picks:
if not np.isnan(pick):
picks_no_nan.append(pick)
return picks_no_nan
self.picks_no_nan = remove_nan_picks(self.picks_rel)
def init_stations_active(self):
def remove_nan_lat_lon(picks, lat, lon):
lat_no_nan = []
lon_no_nan = []
for index, pick in enumerate(picks):
if not np.isnan(pick):
lat_no_nan.append(lat[index])
lon_no_nan.append(lon[index])
return lat_no_nan, lon_no_nan
self.lat_no_nan, self.lon_no_nan = remove_nan_lat_lon(self.picks_rel, self.lat, self.lon)
def init_lat_lon_dimensions(self):
def get_lon_lat_dim(lon, lat):
londim = max(lon) - min(lon)
latdim = max(lat) - min(lat)
return londim, latdim
self.londim, self.latdim = get_lon_lat_dim(self.lon, self.lat)
def init_x_y_dimensions(self):
def get_x_y_dim(x, y):
xdim = max(x) - min(x)
ydim = max(y) - min(y)
return xdim, ydim
self.x, self.y = self.basemap(self.lon, self.lat)
self.xdim, self.ydim = get_x_y_dim(self.x, self.y)
def init_basemap(self, resolution='l'):
# basemap = Basemap(projection=projection, resolution = resolution, ax=self.main_ax)
basemap = Basemap(projection='lcc', resolution=resolution, ax=self.main_ax,
width=5e6, height=2e6,
lat_0=(min(self.lat) + max(self.lat)) / 2.,
lon_0=(min(self.lon) + max(self.lon)) / 2.)
# basemap.fillcontinents(color=None, lake_color='aqua',zorder=1)
basemap.drawmapboundary(zorder=2) # fill_color='darkblue')
basemap.shadedrelief(zorder=3)
basemap.drawcountries(zorder=4)
basemap.drawstates(zorder=5)
basemap.drawcoastlines(zorder=6)
self.basemap = basemap
self.figure.tight_layout()
def init_lat_lon_grid(self):
def get_lat_lon_axis(lat, lon):
steplat = (max(lat) - min(lat)) / 250
steplon = (max(lon) - min(lon)) / 250
lataxis = np.arange(min(lat), max(lat), steplat)
lonaxis = np.arange(min(lon), max(lon), steplon)
return lataxis, lonaxis
def get_lat_lon_grid(lataxis, lonaxis):
longrid, latgrid = np.meshgrid(lonaxis, lataxis)
return latgrid, longrid
self.lataxis, self.lonaxis = get_lat_lon_axis(self.lat, self.lon)
self.latgrid, self.longrid = get_lat_lon_grid(self.lataxis, self.lonaxis)
def init_picksgrid(self):
self.picksgrid_no_nan = griddata((self.lat_no_nan, self.lon_no_nan),
self.picks_no_nan, (self.latgrid, self.longrid),
method='linear') ##################
def draw_contour_filled(self, nlevel='50'):
levels = np.linspace(min(self.picks_no_nan), max(self.picks_no_nan), nlevel)
self.contourf = self.basemap.contourf(self.longrid, self.latgrid, self.picksgrid_no_nan,
levels, latlon=True, zorder=9, alpha=0.5)
def scatter_all_stations(self):
self.sc = self.basemap.scatter(self.lon, self.lat, s=50, facecolor='none', latlon=True,
zorder=10, picker=True, edgecolor='m', label='Not Picked')
self.cid = self.canvas.mpl_connect('pick_event', self.onpick)
if self.eventLoc:
lat, lon = self.eventLoc
self.sc_event = self.basemap.scatter(lon, lat, s=100, facecolor='red',
latlon=True, zorder=11, label='Event (might be outside map region)')
def scatter_picked_stations(self):
lon = self.lon_no_nan
lat = self.lat_no_nan
# workaround because of an issue with latlon transformation of arrays with len <3
if len(lon) <= 2 and len(lat) <= 2:
self.sc_picked = self.basemap.scatter(lon[0], lat[0], s=50, facecolor='white',
c=self.picks_no_nan[0], latlon=True, zorder=11, label='Picked')
if len(lon) == 2 and len(lat) == 2:
self.sc_picked = self.basemap.scatter(lon[1], lat[1], s=50, facecolor='white',
c=self.picks_no_nan[1], latlon=True, zorder=11)
else:
self.sc_picked = self.basemap.scatter(lon, lat, s=50, facecolor='white',
c=self.picks_no_nan, latlon=True, zorder=11, label='Picked')
def annotate_ax(self):
self.annotations = []
for index, name in enumerate(self.station_names):
self.annotations.append(self.main_ax.annotate(' %s' % name, xy=(self.x[index], self.y[index]),
fontsize='x-small', color='white', zorder=12))
self.legend = self.main_ax.legend(loc=1)
def add_cbar(self, label):
cbar = self.main_ax.figure.colorbar(self.sc_picked, fraction=0.025)
cbar.set_label(label)
return cbar
def refresh_drawings(self, picks=None):
self.picks_dict = picks
self._refresh_drawings()
def _refresh_drawings(self):
self.remove_drawings()
self.draw_everything()
def draw_everything(self):
if self.picks_dict:
self.init_picks()
self.init_picks_active()
self.init_stations_active()
if len(self.picks_no_nan) >= 3:
self.init_picksgrid()
self.draw_contour_filled()
self.scatter_all_stations()
if self.picks_dict:
self.scatter_picked_stations()
self.cbar = self.add_cbar(label='Time relative to first onset [s]')
self.comboBox_phase.setEnabled(True)
else:
self.comboBox_phase.setEnabled(False)
self.annotate_ax()
self.canvas.draw()
def remove_drawings(self):
if hasattr(self, 'sc_picked'):
self.sc_picked.remove()
del (self.sc_picked)
if hasattr(self, 'sc_event'):
self.sc_event.remove()
del (self.sc_event)
if hasattr(self, 'cbar'):
self.cbar.remove()
del (self.cbar)
if hasattr(self, 'contourf'):
self.remove_contourf()
del (self.contourf)
if hasattr(self, 'cid'):
self.canvas.mpl_disconnect(self.cid)
del (self.cid)
try:
self.sc.remove()
except Exception as e:
print('Warning: could not remove station scatter plot.\nReason: {}'.format(e))
try:
self.legend.remove()
except Exception as e:
print('Warning: could not remove legend. Reason: {}'.format(e))
self.canvas.draw()
def remove_contourf(self):
for item in self.contourf.collections:
item.remove()
def remove_annotations(self):
for annotation in self.annotations:
annotation.remove()
def zoom(self, event):
map = self.basemap
xlim = map.ax.get_xlim()
ylim = map.ax.get_ylim()
x, y = event.xdata, event.ydata
zoom = {'up': 1. / 2.,
'down': 2.}
if not event.xdata or not event.ydata:
return
if event.button in zoom:
factor = zoom[event.button]
xdiff = (xlim[1] - xlim[0]) * factor
xl = x - 0.5 * xdiff
xr = x + 0.5 * xdiff
ydiff = (ylim[1] - ylim[0]) * factor
yb = y - 0.5 * ydiff
yt = y + 0.5 * ydiff
if xl < map.xmin or yb < map.ymin or xr > map.xmax or yt > map.ymax:
xl, xr = map.xmin, map.xmax
yb, yt = map.ymin, map.ymax
map.ax.set_xlim(xl, xr)
map.ax.set_ylim(yb, yt)
map.ax.figure.canvas.draw()
def _warn(self, message):
self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Warning,
'Warning', message)
self.qmb.show()

18
pylot/core/util/obspyDMT_interface.py
View File

@ -25,4 +25,20 @@ def check_obspydmt_eventfolder(folder):
except Exception as e: except Exception as e:
return False, 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

214
pylot/core/util/widgets.py
View File

@ -16,6 +16,9 @@ import time
import numpy as np import numpy as np
import matplotlib
matplotlib.use('QT4Agg')
from matplotlib.figure import Figure from matplotlib.figure import Figure
try: try:
@ -26,6 +29,7 @@ from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT
from matplotlib.widgets import MultiCursor from matplotlib.widgets import MultiCursor
from matplotlib.tight_layout import get_renderer, get_subplotspec_list, get_tight_layout_figure from matplotlib.tight_layout import get_renderer, get_subplotspec_list, get_tight_layout_figure
from scipy.signal import argrelmin, argrelmax from scipy.signal import argrelmin, argrelmax
from obspy import read
from PySide import QtCore, QtGui from PySide import QtCore, QtGui
from PySide.QtGui import QAction, QApplication, QCheckBox, QComboBox, \ from PySide.QtGui import QAction, QApplication, QCheckBox, QComboBox, \
@ -447,23 +451,25 @@ class WaveformWidgetPG(QtGui.QWidget):
self.orig_parent = parent self.orig_parent = parent
# attribute plotdict is a dictionary connecting position and a name # attribute plotdict is a dictionary connecting position and a name
self.plotdict = dict() self.plotdict = dict()
# init labels
self.xlabel = None
self.ylabel = None
self.title = None
# create plot # create plot
self.main_layout = QtGui.QVBoxLayout() self.main_layout = QtGui.QVBoxLayout()
self.label_layout = QtGui.QHBoxLayout() self.label_layout = QtGui.QHBoxLayout()
self.status_label = QtGui.QLabel() self.add_labels()
self.perm_label = QtGui.QLabel() self.connect_signals()
self.setLayout(self.main_layout)
self.plotWidget = self.pg.PlotWidget(self.parent(), title=title) self.plotWidget = self.pg.PlotWidget(self.parent(), title=title)
self.main_layout.addWidget(self.plotWidget) self.main_layout.addWidget(self.plotWidget)
self.main_layout.addLayout(self.label_layout) self.main_layout.addLayout(self.label_layout)
self.label_layout.addWidget(self.status_label) self.init_labels()
self.label_layout.addWidget(self.perm_label) self.activateObspyDMToptions(False)
self.plotWidget.showGrid(x=False, y=True, alpha=0.3) 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.wfstart, self.wfend = 0, 0
self.pen_multicursor = self.pg.mkPen(self.parent()._style['multicursor']['rgba']) 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 = 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.pen_linecolor_syn = self.pg.mkPen((100, 0, 255, 255))
self.reinitMoveProxy() self.reinitMoveProxy()
self._proxy = self.pg.SignalProxy(self.plotWidget.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved) self._proxy = self.pg.SignalProxy(self.plotWidget.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)
@ -489,12 +495,59 @@ class WaveformWidgetPG(QtGui.QWidget):
self.vLine.setPos(mousePoint.x()) self.vLine.setPos(mousePoint.x())
self.hLine.setPos(mousePoint.y()) self.hLine.setPos(mousePoint.y())
def connect_signals(self):
self.qcombo_processed.activated.connect(self.parent().newWF)
self.syn_checkbox.clicked.connect(self.parent().newWF)
def init_labels(self):
self.label_layout.addWidget(self.status_label)
for label in self.perm_labels:
self.label_layout.addWidget(label)
self.label_layout.addWidget(self.syn_checkbox)
self.label_layout.addWidget(self.qcombo_processed)
self.syn_checkbox.setLayoutDirection(Qt.RightToLeft)
self.label_layout.setStretch(0, 4)
self.label_layout.setStretch(1, 0)
self.label_layout.setStretch(2, 0)
self.label_layout.setStretch(3, 0)
self.label_layout.setStretch(4, 3)
self.label_layout.setStretch(5, 1)
def add_labels(self):
self.status_label = QtGui.QLabel()
self.perm_labels = []
for index in range(3):
label = QtGui.QLabel()
self.perm_labels.append(label)
self.qcombo_processed = QtGui.QComboBox()
self.syn_checkbox = QtGui.QCheckBox('synthetics')
self.addQCboxItem('processed', 'green')
self.addQCboxItem('raw', 'black')
#self.perm_qcbox_right.setAlignment(2)
self.setLayout(self.main_layout)
def getPlotDict(self): def getPlotDict(self):
return self.plotdict return self.plotdict
def setPermText(self, text=None, color='black'): def activateObspyDMToptions(self, activate):
self.perm_label.setText(text) self.syn_checkbox.setVisible(activate)
self.perm_label.setStyleSheet('color: {}'.format(color)) self.qcombo_processed.setVisible(activate)
def setPermText(self, number, text=None, color='black'):
if not 0 <= number < len(self.perm_labels):
raise ValueError('No label for number {}'.format(number))
self.perm_labels[number].setText(text)
self.perm_labels[number].setStyleSheet('color: {}'.format(color))
def addQCboxItem(self, text=None, color='black'):
item = QtGui.QStandardItem(text)
model = self.qcombo_processed.model()
model.appendRow(item)
item.setForeground(QtGui.QColor('{}'.format(color)))
def setQCboxItem(self, text):
index = self.qcombo_processed.findText(text)
self.qcombo_processed.setCurrentIndex(index)
def setPlotDict(self, key, value): def setPlotDict(self, key, value):
self.plotdict[key] = value self.plotdict[key] = value
@ -529,6 +582,14 @@ class WaveformWidgetPG(QtGui.QWidget):
else: else:
st_select = wfdata 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) # list containing tuples of network, station, channel (for sorting)
nsc = [] nsc = []
for trace in st_select: for trace in st_select:
@ -552,6 +613,8 @@ class WaveformWidgetPG(QtGui.QWidget):
st_syn = wfsyn.select(network=network, station=station, channel=channel) st_syn = wfsyn.select(network=network, station=station, channel=channel)
if st_syn: if st_syn:
trace_syn = st_syn[0].copy() trace_syn = st_syn[0].copy()
else:
trace_syn = Trace()
if mapping: if mapping:
comp = channel[-1] comp = channel[-1]
n = compclass.getPlotPosition(str(comp)) n = compclass.getPlotPosition(str(comp))
@ -568,9 +631,11 @@ class WaveformWidgetPG(QtGui.QWidget):
time_ax_syn = prepTimeAxis(stime_syn, trace_syn) time_ax_syn = prepTimeAxis(stime_syn, trace_syn)
if method == 'fast': if method == 'fast':
trace.data, time_ax = self.minMax(trace, time_ax) 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: if not scaleddata:
trace.detrend('constant') trace.detrend('constant')
trace.normalize(np.max(np.abs(trace.data)) * 2) trace.normalize(np.max(np.abs(trace.data)) * 2)
@ -581,23 +646,23 @@ class WaveformWidgetPG(QtGui.QWidget):
times = np.array([time for index, time in enumerate(time_ax) if not index % nth_sample]) 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 []) 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 = 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 []) if not index % nth_sample] if st_syn else [])
plots.append((times, trace.data, plots.append((times, trace.data,
times_syn, trace.data_syn)) times_syn, trace_syn.data))
self.setPlotDict(n, (station, channel, network)) self.setPlotDict(n, (station, channel, network))
self.xlabel = 'seconds since {0}'.format(self.wfstart) self.xlabel = 'seconds since {0}'.format(self.wfstart)
self.ylabel = '' self.ylabel = ''
self.setXLims([0, self.wfend - self.wfstart]) self.setXLims([0, self.wfend - self.wfstart])
self.setYLims([0.5, nmax + 0.5]) self.setYLims([0.5, nmax + 0.5])
return plots return plots, gaps
def minMax(self, trace, time_ax): def minMax(self, trace, time_ax):
''' '''
create min/max array for fast plotting (approach based on obspy __plot_min_max function) create min/max array for fast plotting (approach based on obspy __plot_min_max function)
:returns data, time_ax :returns data, time_ax
''' '''
npixel = self.width() npixel = self.orig_parent.width()
ndata = len(trace.data) ndata = len(trace.data)
pts_per_pixel = ndata/npixel pts_per_pixel = ndata/npixel
if pts_per_pixel < 2: if pts_per_pixel < 2:
@ -1013,6 +1078,14 @@ class PylotCanvas(FigureCanvas):
if mapping: if mapping:
plot_positions = self.calcPlotPositions(st_select, compclass) 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) # list containing tuples of network, station, channel and plot position (for sorting)
nsc = [] nsc = []
for plot_pos, trace in enumerate(st_select): for plot_pos, trace in enumerate(st_select):
@ -1245,9 +1318,10 @@ class PickDlg(QDialog):
def __init__(self, parent=None, data=None, station=None, network=None, picks=None, def __init__(self, parent=None, data=None, station=None, network=None, picks=None,
autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None,
event=None, filteroptions=None, model='iasp91'): event=None, filteroptions=None, model='iasp91', wftype=None):
super(PickDlg, self).__init__(parent, 1) super(PickDlg, self).__init__(parent, 1)
self.orig_parent = parent self.orig_parent = parent
self.setAttribute(Qt.WA_DeleteOnClose)
# initialize attributes # initialize attributes
self.parameter = parameter self.parameter = parameter
@ -1256,6 +1330,7 @@ class PickDlg(QDialog):
self.network = network self.network = network
self.rotate = rotate self.rotate = rotate
self.metadata = metadata self.metadata = metadata
self.wftype = wftype
self.pylot_event = event self.pylot_event = event
self.components = 'ZNE' self.components = 'ZNE'
self.currentPhase = None self.currentPhase = None
@ -1305,7 +1380,7 @@ class PickDlg(QDialog):
self.cur_ylim = None self.cur_ylim = None
# set attribute holding data # set attribute holding data
if data is None: if data is None or not data:
try: try:
data = parent.get_data().getWFData().copy() data = parent.get_data().getWFData().copy()
self.data = data.select(station=station) self.data = data.select(station=station)
@ -1328,7 +1403,7 @@ class PickDlg(QDialog):
# fill compare and scale channels # fill compare and scale channels
self.compareChannel.addItem('-', None) self.compareChannel.addItem('-', None)
self.scaleChannel.addItem('normalized', None) self.scaleChannel.addItem('individual', None)
for trace in self.getWFData(): for trace in self.getWFData():
channel = trace.stats.channel channel = trace.stats.channel
@ -1345,8 +1420,12 @@ class PickDlg(QDialog):
actionS.setChecked(self.getChannelSettingsS(channel)) actionS.setChecked(self.getChannelSettingsS(channel))
# plot data # plot data
title = self.getStation()
if self.wftype is not None:
title += ' | ({})'.format(self.wftype)
self.multicompfig.plotWFData(wfdata=self.getWFData(), self.multicompfig.plotWFData(wfdata=self.getWFData(),
title=self.getStation()) title=title)
self.multicompfig.setZoomBorders2content() self.multicompfig.setZoomBorders2content()
@ -1380,7 +1459,6 @@ class PickDlg(QDialog):
self.setWindowTitle('Pickwindow on station: {}'.format(self.getStation())) self.setWindowTitle('Pickwindow on station: {}'.format(self.getStation()))
self.setWindowState(QtCore.Qt.WindowMaximized) self.setWindowState(QtCore.Qt.WindowMaximized)
self.deleteLater()
def setupUi(self): def setupUi(self):
menuBar = QtGui.QMenuBar(self) menuBar = QtGui.QMenuBar(self)
@ -1526,7 +1604,7 @@ class PickDlg(QDialog):
_dialtoolbar.addWidget(QtGui.QLabel('Compare to channel: ')) _dialtoolbar.addWidget(QtGui.QLabel('Compare to channel: '))
_dialtoolbar.addWidget(self.compareChannel) _dialtoolbar.addWidget(self.compareChannel)
_dialtoolbar.addSeparator() _dialtoolbar.addSeparator()
_dialtoolbar.addWidget(QtGui.QLabel('Scale by: ')) _dialtoolbar.addWidget(QtGui.QLabel('Scaling: '))
_dialtoolbar.addWidget(self.scaleChannel) _dialtoolbar.addWidget(self.scaleChannel)
# layout the innermost widget # layout the innermost widget
@ -1649,7 +1727,7 @@ class PickDlg(QDialog):
self.arrivalsText.append(ax.text(time_rel, ylims[0], arrival.name, color='0.5')) self.arrivalsText.append(ax.text(time_rel, ylims[0], arrival.name, color='0.5'))
def drawArrivalsText(self): def drawArrivalsText(self):
return self.drawArrivals(True) return self.drawArrivals(textOnly=True)
def refreshArrivalsText(self, event=None): def refreshArrivalsText(self, event=None):
self.removeArrivalsText() self.removeArrivalsText()
@ -2514,6 +2592,9 @@ class PickDlg(QDialog):
filtops_str = transformFilteroptions2String(filtoptions) filtops_str = transformFilteroptions2String(filtoptions)
title += ' | Filteroptions: {}'.format(filtops_str) title += ' | Filteroptions: {}'.format(filtops_str)
if self.wftype is not None:
title += ' | ({})'.format(self.wftype)
plot_additional = bool(self.compareChannel.currentText()) plot_additional = bool(self.compareChannel.currentText())
additional_channel = self.compareChannel.currentText() additional_channel = self.compareChannel.currentText()
scale_channel = self.scaleChannel.currentText() scale_channel = self.scaleChannel.currentText()
@ -2601,6 +2682,7 @@ class PickDlg(QDialog):
phase = 'S' phase = 'S'
filter = True filter = True
self.plotWFData(phase=phase, filter=filter) self.plotWFData(phase=phase, filter=filter)
self.drawArrivals()
def resetZoom(self): def resetZoom(self):
ax = self.multicompfig.axes[0] ax = self.multicompfig.axes[0]
@ -2864,7 +2946,7 @@ class AutoPickWidget(MultiEventWidget):
def reinitEvents2plot(self): def reinitEvents2plot(self):
for eventID, eventDict in self.events2plot.items(): for eventID, eventDict in self.events2plot.items():
for widget_key, widget in eventDict.items(): for widget_key, widget in eventDict.items():
widget.setParent(None) del(widget)
self.events2plot = {} self.events2plot = {}
self.eventbox.clear() self.eventbox.clear()
self.refresh_plot_tabs() self.refresh_plot_tabs()
@ -2946,13 +3028,15 @@ class TuneAutopicker(QWidget):
:type: PyLoT Mainwindow :type: PyLoT Mainwindow
''' '''
def __init__(self, parent): def __init__(self, parent, obspy_dmt=False):
QtGui.QWidget.__init__(self, parent, 1) QtGui.QWidget.__init__(self, parent, 1)
self._style = parent._style self._style = parent._style
self.setWindowTitle('PyLoT - Tune Autopicker') self.setWindowTitle('PyLoT - Tune Autopicker')
self.parameter = self.parent()._inputs self.parameter = self.parent()._inputs
self.fig_dict = self.parent().fig_dict self.fig_dict = self.parent().fig_dict
self.data = Data() self.data = Data()
self.obspy_dmt = obspy_dmt
self.wftype = None
self.pdlg_widget = None self.pdlg_widget = None
self.pylot_picks = None self.pylot_picks = None
self.init_main_layouts() self.init_main_layouts()
@ -3009,8 +3093,45 @@ class TuneAutopicker(QWidget):
self.eventBox.activated.connect(self.fill_tabs) self.eventBox.activated.connect(self.fill_tabs)
self.stationBox.activated.connect(self.fill_tabs) self.stationBox.activated.connect(self.fill_tabs)
def catch_station_ids(self):
self.station_ids = {}
eventpath = self.get_current_event_fp()
self.wftype = 'processed' if self.obspy_dmt else ''
wf_path = os.path.join(eventpath, self.wftype)
if not os.path.exists(wf_path) and self.obspy_dmt:
self.wftype = 'raw'
wf_path = os.path.join(eventpath, self.wftype)
for filename in os.listdir(wf_path):
filename = os.path.join(eventpath, self.wftype, filename)
try:
st = read(filename, headonly=True)
except Exception as e:
print('Warning: Could not read file {} as a stream object: {}'.format(filename, e))
continue
for trace in st:
network = trace.stats.network
station = trace.stats.station
location = trace.stats.location
station_id = '{}.{}.{}'.format(network, station, location)
if not station_id in self.station_ids:
self.station_ids[station_id] = []
self.station_ids[station_id].append(filename)
def fill_stationbox(self): def fill_stationbox(self):
fnames = self.parent().getWFFnames_from_eventbox(eventbox=self.eventBox) self.stationBox.clear()
model = self.stationBox.model()
self.catch_station_ids()
st_ids_list = list(self.station_ids.keys())
st_ids_list.sort()
for station_id in st_ids_list:
item = QtGui.QStandardItem(station_id)
if station_id.split('.')[1] in self.get_current_event().pylot_picks:
item.setBackground(self.parent()._ref_test_colors['ref'])
model.appendRow(item)
def load_wf_data(self):
fnames = self.station_ids[self.get_current_station_id()]
self.data.setWFData(fnames) self.data.setWFData(fnames)
wfdat = self.data.getWFData() # all available streams wfdat = self.data.getWFData() # all available streams
# remove possible underscores in station names # remove possible underscores in station names
@ -3022,21 +3143,6 @@ class TuneAutopicker(QWidget):
wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0) wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
# trim station components to same start value # trim station components to same start value
trim_station_components(wfdat, trim_start=True, trim_end=False) trim_station_components(wfdat, trim_start=True, trim_end=False)
self.stationBox.clear()
stations = []
for trace in self.data.getWFData():
station = trace.stats.station
network = trace.stats.network
ns_tup = (str(network), str(station))
if not ns_tup in stations:
stations.append(ns_tup)
stations.sort()
model = self.stationBox.model()
for network, station in stations:
item = QtGui.QStandardItem(network + '.' + station)
if station in self.get_current_event().pylot_picks:
item.setBackground(self.parent()._ref_test_colors['ref'])
model.appendRow(item)
def init_figure_tabs(self): def init_figure_tabs(self):
self.figure_tabs = QtGui.QTabWidget() self.figure_tabs = QtGui.QTabWidget()
@ -3093,10 +3199,14 @@ class TuneAutopicker(QWidget):
def get_current_event_autopicks(self, station): def get_current_event_autopicks(self, station):
event = self.get_current_event() event = self.get_current_event()
if event.pylot_autopicks: if event.pylot_autopicks:
return event.pylot_autopicks[station] if station in event.pylot_autopicks:
return event.pylot_autopicks[station]
def get_current_station(self): def get_current_station(self):
return str(self.stationBox.currentText()).split('.')[-1] return str(self.stationBox.currentText()).split('.')[1]
def get_current_station_id(self):
return str(self.stationBox.currentText())
def gen_tab_widget(self, name, canvas): def gen_tab_widget(self, name, canvas):
widget = QtGui.QWidget() widget = QtGui.QWidget()
@ -3111,17 +3221,19 @@ class TuneAutopicker(QWidget):
self.pdlg_widget.setParent(None) self.pdlg_widget.setParent(None)
self.pdlg_widget = None self.pdlg_widget = None
return return
self.load_wf_data()
station = self.get_current_station() station = self.get_current_station()
data = self.data.getWFData() wfdata = self.data.getWFData()
metadata = self.parent().metadata metadata = self.parent().metadata
event = self.get_current_event() event = self.get_current_event()
filteroptions = self.parent().filteroptions filteroptions = self.parent().filteroptions
self.pickDlg = PickDlg(self.parent(), data=data.select(station=station), wftype = self.wftype if self.obspy_dmt else ''
self.pickDlg = PickDlg(self.parent(), data=wfdata.select(station=station).copy(),
station=station, parameter=self.parameter, station=station, parameter=self.parameter,
picks=self.get_current_event_picks(station), picks=self.get_current_event_picks(station),
autopicks=self.get_current_event_autopicks(station), autopicks=self.get_current_event_autopicks(station),
metadata=metadata, event=event, filteroptions=filteroptions, metadata=metadata, event=event, filteroptions=filteroptions,
embedded=True) embedded=True, wftype=wftype)
self.pickDlg.update_picks.connect(self.picks_from_pickdlg) self.pickDlg.update_picks.connect(self.picks_from_pickdlg)
self.pickDlg.update_picks.connect(self.fill_eventbox) self.pickDlg.update_picks.connect(self.fill_eventbox)
self.pickDlg.update_picks.connect(self.fill_stationbox) self.pickDlg.update_picks.connect(self.fill_stationbox)
@ -3301,14 +3413,17 @@ class TuneAutopicker(QWidget):
if not station: if not station:
self._warn('No station selected') self._warn('No station selected')
return return
wfpath = self.wftype if self.obspy_dmt else ''
args = {'parameter': self.parameter, args = {'parameter': self.parameter,
'station': station, 'station': station,
'fnames': 'None', 'fnames': 'None',
'eventid': [self.get_current_event_fp()], 'eventid': [self.get_current_event_fp()],
'iplot': 2, 'iplot': 2,
'fig_dict': self.fig_dict, 'fig_dict': self.fig_dict,
'locflag': 0, 'savexml': False,
'savexml': False} 'obspyDMT_wfpath': wfpath}
event = self.get_current_event()
self.parent().saveData(event, event.path, '.xml')
for key in self.fig_dict.keys(): for key in self.fig_dict.keys():
if not key == 'plot_style': if not key == 'plot_style':
self.fig_dict[key].clear() self.fig_dict[key].clear()
@ -3364,8 +3479,7 @@ class TuneAutopicker(QWidget):
if hasattr(self, 'pdlg_widget'): if hasattr(self, 'pdlg_widget'):
if self.pdlg_widget: if self.pdlg_widget:
self.pdlg_widget.setParent(None) self.pdlg_widget.setParent(None)
# TODO: removing widget by parent deletion raises exception when activating stationbox: del(self.pdlg_widget)
# RuntimeError: Internal C++ object (PylotCanvas) already deleted.
if hasattr(self, 'overview'): if hasattr(self, 'overview'):
self.overview.setParent(None) self.overview.setParent(None)
if hasattr(self, 'p_tabs'): if hasattr(self, 'p_tabs'):

6
pylot/styles/bright.qss
View File

@ -179,9 +179,9 @@ background-color:transparent;
QTabWidget::pane{ QTabWidget::pane{
background-color:rgba(0, 0, 0, 255); background-color:rgba(0, 0, 0, 255);
border-style:solid; margin: 0px, 0px, 0px, 0px;
border-color:rgba(245, 245, 245, 255); padding: 0px;
border-width:1px; border-width:0px;
} }
QTabWidget::tab{ QTabWidget::tab{

6
pylot/styles/dark.qss
View File

@ -178,9 +178,9 @@ background-color:transparent;
QTabWidget::pane{ QTabWidget::pane{
background-color:rgba(70, 70, 80, 255); background-color:rgba(70, 70, 80, 255);
border-style:solid; margin: 0px, 0px, 0px, 0px;
border-color:rgba(70, 70, 80, 255); padding: 0px;
border-width:1px; border-width:0px;
} }
QTabWidget::tab{ QTabWidget::tab{