Merge branch 'feature/dae' into develop

# Conflicts:
#	pylot/core/io/data.py
#	pylot/core/util/widgets.py

PyLoT.py

@@ -25,6 +25,7 @@ https://www.iconfinder.com/iconsets/flavour
 
 import argparse
 import json
+import logging
 import os
 import platform
 import shutil
@@ -72,24 +73,25 @@ from pylot.core.util.errors import DatastructureError, \
     OverwriteError
 from pylot.core.util.connection import checkurl
 from pylot.core.util.dataprocessing import Metadata, restitute_data
-from pylot.core.util.utils import fnConstructor, getLogin, \
+from pylot.core.util.utils import fnConstructor, get_login, \
     full_range, readFilterInformation, pick_color_plt, \
     pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
     transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
-    check_all_pylot, get_Bool, get_None
+    check_all_pylot, get_bool, get_none
 from pylot.core.util.gui import make_pen
 from pylot.core.util.event import Event
 from pylot.core.io.location import create_creation_info, create_event
 from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
-    CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget
+    CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
+    SpectrogramTab, SearchFileByExtensionDialog
 from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
 from pylot.core.util.version import get_git_version as _getVersionString
 from pylot.core.io.getEventListFromXML import geteventlistfromxml
-from pylot.core.io.getQualitiesfromxml import getQualitiesfromxml
+from pylot.core.io.phases import getQualitiesfromxml
 
 from pylot.styles import style_settings
 
@@ -112,21 +114,19 @@ class MainWindow(QMainWindow):
     def __init__(self, parent=None, infile=None, reset_qsettings=False):
         super(MainWindow, self).__init__(parent)
 
-        # check for default pylot.in-file
+        if infile and os.path.isfile(infile) is False:
-        if not infile:
+            infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-        if os.path.isfile(infile) == False:
-            infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')
 
-            if not os.path.exists(infile[0]):
+            if not os.path.exists(infile):
                 QMessageBox.warning(self, "PyLoT Warning",
-                                    "No PyLoT-input file declared!")
+                                    "No PyLoT-input file declared! Using default parameters!")
-                sys.exit(0)
+                infile = None
-            self.infile = infile[0]
+
-        else:
-            self.infile = infile
         self._inputs = PylotParameter(infile)
+        if not infile:
+            self._inputs.reset_defaults()
+
+        self.infile = infile
         self._props = None
 
         self.gain = 1.
@@ -178,6 +178,7 @@ class MainWindow(QMainWindow):
         self.autodata = Data(self)
 
         self.fnames = None
+        self.fnames_comp = None
         self._stime = None
 
         # track deleted picks for logging
@@ -193,7 +194,7 @@ class MainWindow(QMainWindow):
                 if settings.value("user/FullName", None) is None:
                     fulluser = QInputDialog.getText(self, "Enter Name:", "Full name")
                     settings.setValue("user/FullName", fulluser)
-                    settings.setValue("user/Login", getLogin())
+                    settings.setValue("user/Login", get_login())
                 if settings.value("agency_id", None) is None:
                     agency = QInputDialog.getText(self,
                                                   "Enter authority/institution name:",
@@ -250,11 +251,11 @@ class MainWindow(QMainWindow):
             self._inputs.reset_defaults()
             # check for default pylot.in-file
             infile = os.path.join(pylot_config_dir, '.pylot.in')
-            print('Using default input file {}'.format(infile))
+            logging.warning('Using default input file {}'.format(infile))
             self._inputs.export2File(infile)
         self.infile = infile
 
-    def setupUi(self):
+    def setupUi(self, use_logwidget=False):
         try:
             self.startTime = min(
                 [tr.stats.starttime for tr in self.data.wfdata])
@@ -480,7 +481,7 @@ class MainWindow(QMainWindow):
                                                               "automatic pick "
                                                               "data.", False)
         self.compare_action.setEnabled(False)
-        self.qualities_action = self.createAction(parent=self, text='Show pick qualitites...',
+        self.qualities_action = self.createAction(parent=self, text='Show pick qualities...',
                                                   slot=self.pickQualities, shortcut='Alt+Q',
                                                   icon=qualities_icon, tip='Histogram of pick qualities')
         self.qualities_action.setEnabled(False)
@@ -493,7 +494,6 @@ class MainWindow(QMainWindow):
                                                       icon=eventlist_xml_icon,
                                                       tip='Create an Eventlist from a XML File')
         self.eventlist_xml_action.setEnabled(False)
-
         printAction = self.createAction(self, "&Print event ...",
                                         self.show_event_information, QKeySequence.Print,
                                         print_icon,
@@ -506,6 +506,8 @@ class MainWindow(QMainWindow):
         logAction = self.createAction(self, "&Show Log", self.showLogWidget,
                                       tip="""Display Log""")
 
+        logAction.setEnabled(use_logwidget)
+
         # create button group for component selection
 
         componentGroup = QActionGroup(self)
@@ -695,14 +697,17 @@ class MainWindow(QMainWindow):
         wf_tab = QtWidgets.QWidget(self)
         array_tab = QtWidgets.QWidget(self)
         events_tab = QtWidgets.QWidget(self)
+        spectro_tab = QtWidgets.QWidget(self)
 
         # init main widgets layouts
         self.wf_layout = QtWidgets.QVBoxLayout()
         self.array_layout = QtWidgets.QVBoxLayout()
         self.events_layout = QtWidgets.QVBoxLayout()
+        self.spectro_layout = QtWidgets.QVBoxLayout()
         wf_tab.setLayout(self.wf_layout)
         array_tab.setLayout(self.array_layout)
         events_tab.setLayout(self.events_layout)
+        spectro_tab.setLayout(self.spectro_layout)
 
         # tighten up layouts inside tabs
         for layout in [self.wf_layout, self.array_layout, self.events_layout]:
@@ -713,12 +718,14 @@ class MainWindow(QMainWindow):
         self.tabs.addTab(wf_tab, 'Waveform Plot')
         self.tabs.addTab(array_tab, 'Array Map')
         self.tabs.addTab(events_tab, 'Eventlist')
+        self.tabs.addTab(spectro_tab, 'Spectro')
 
         self.wf_layout.addWidget(self.no_data_label)
         self.wf_layout.addWidget(self.wf_scroll_area)
         self.wf_scroll_area.setWidgetResizable(True)
         self.init_array_tab()
         self.init_event_table()
+        self.init_spectro_tab()
         self.tabs.setCurrentIndex(0)
 
         self.eventLabel = QLabel()
@@ -731,13 +738,19 @@ class MainWindow(QMainWindow):
         _widget.setLayout(self._main_layout)
         _widget.showFullScreen()
 
+
+        if use_logwidget:
             self.logwidget = LogWidget(parent=None)
             self.logwidget.show()
-        sys.stdout = self.logwidget.stdout
+            self.stdout = self.logwidget.stdout
-        sys.stderr = self.logwidget.stderr
+            self.stderr = self.logwidget.stderr
 
         self.setCentralWidget(_widget)
 
+        # Need to store PickQualities Window somewhere so it doesnt disappear
+        self.pickQualitiesWindow = None
+
+
     def init_wfWidget(self):
         xlab = self.startTime.strftime('seconds since %Y/%m/%d %H:%M:%S (%Z)')
         plottitle = None  # "Overview: {0} components ".format(self.getComponent())
@@ -991,17 +1004,16 @@ class MainWindow(QMainWindow):
             return
         refresh = False
         events = self.project.eventlist
-        sld = SingleTextLineDialog(label='Specify file extension: ', default_text='.xml')
+        sld = SearchFileByExtensionDialog(label='Specify file extension: ', default_text='.xml',
+                                          events=events)
         if not sld.exec_():
             return
-        fext = sld.lineEdit.text()
+
-        # fext = '.xml'
+        filenames = sld.getChecked()
         for event in events:
-            path = event.path
+            for filename in filenames:
-            eventname = path.split('/')[-1]  # or event.pylot_id
+                if os.path.isfile(filename) and event.pylot_id in filename:
-            filename = os.path.join(path, 'PyLoT_' + eventname + fext)
+                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
-            if os.path.isfile(filename):
-                self.load_data(filename, draw=False, event=event, overwrite=True)
                     refresh = True
         if not refresh:
             return
@@ -1010,8 +1022,8 @@ class MainWindow(QMainWindow):
         self.fill_eventbox()
         self.setDirty(True)
 
-    def load_data(self, fname=None, loc=False, draw=True, event=None, overwrite=False):
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
-        if not overwrite:
+        if not ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1025,9 +1037,12 @@ class MainWindow(QMainWindow):
         data = Data(self, event)
         try:
             data_new = Data(self, evtdata=str(fname))
-            # MP MP commented because adding several picks might cause inconsistencies
+            if merge_strategy == 'Overwrite':
                 data = data_new
-            # data += data_new
+            elif merge_strategy == 'Merge':
+                data += data_new
+            else:
+                raise NotImplementedError(f'Unknown merge strategy: {merge_strategy}')
         except ValueError:
             qmb = QMessageBox(self, icon=QMessageBox.Question,
                               text='Warning: Missmatch in event identifiers {} and {}. Continue?'.format(
@@ -1115,16 +1130,19 @@ class MainWindow(QMainWindow):
             else:
                 return
 
-    def getWFFnames_from_eventbox(self, eventbox=None):
+    def getWFFnames_from_eventbox(self, eventbox: str = None, subpath: str = None) -> list:
         '''
         Return waveform filenames from event in eventbox.
         '''
         # TODO: add dataStructure class for obspyDMT here, this is just a workaround!
         eventpath = self.get_current_event_path(eventbox)
-        basepath = eventpath.split(os.path.basename(eventpath))[0]
+        if subpath:
+            eventpath = os.path.join(eventpath, subpath)
+        if not os.path.isdir(eventpath):
+            return []
         if self.dataStructure:
             if not eventpath:
-                return
+                return []
             fnames = [os.path.join(eventpath, f) for f in os.listdir(eventpath)]
         else:
             raise DatastructureError('not specified')
@@ -1168,7 +1186,7 @@ class MainWindow(QMainWindow):
         '''
         if not self.project:
             self.createNewProject()
-        ed = getExistingDirectories(self, 'Select event directories...')
+        ed = GetExistingDirectories(self, 'Select event directories...')
         if ed.exec_():
             eventlist = [event for event in ed.selectedFiles() if not event.endswith('EVENTS-INFO')]
             basepath = eventlist[0].split(os.path.basename(eventlist[0]))[0]
@@ -1369,7 +1387,7 @@ class MainWindow(QMainWindow):
         index = eventBox.currentIndex()
         tv = QtWidgets.QTableView()
         header = tv.horizontalHeader()
-        header.setResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
         header.setStretchLastSection(True)
         header.hide()
         tv.verticalHeader().hide()
@@ -1389,25 +1407,28 @@ class MainWindow(QMainWindow):
 
         for id, event in enumerate(self.project.eventlist):
             event_path = event.path
-            phaseErrors = {'P': self._inputs['timeerrorsP'],
+            #phaseErrors = {'P': self._inputs['timeerrorsP'],
-                           'S': self._inputs['timeerrorsS']}
+            #               'S': self._inputs['timeerrorsS']}
 
-            ma_props = {'manual': event.pylot_picks,
+            man_au_picks = {'manual': event.pylot_picks,
                             'auto': event.pylot_autopicks}
-            ma_count = {'manual': 0,
+            npicks = {'manual': {'P': 0, 'S': 0},
-                        'auto': 0}
+                      'auto': {'P': 0, 'S': 0}}
-            ma_count_total = {'manual': 0,
+            npicks_total = {'manual': {'P': 0, 'S': 0},
-                              'auto': 0}
+                            'auto': {'P': 0, 'S': 0}}
 
-            for ma in ma_props.keys():
+            for ma in man_au_picks.keys():
-                if ma_props[ma]:
+                if man_au_picks[ma]:
-                    for picks in ma_props[ma].values():
+                    for picks in man_au_picks[ma].values():
                         for phasename, pick in picks.items():
                             if not type(pick) in [dict, AttribDict]:
                                 continue
+                            phase_ID = identifyPhaseID(phasename)
+                            if not phase_ID in npicks[ma].keys():
+                                continue
                             if pick.get('spe'):
-                                ma_count[ma] += 1
+                                npicks[ma][phase_ID] += 1
-                            ma_count_total[ma] += 1
+                            npicks_total[ma][phase_ID] += 1
 
             event_ref = event.isRefEvent()
             event_test = event.isTestEvent()
@@ -1442,16 +1463,23 @@ class MainWindow(QMainWindow):
             if event.dirty:
                 event_str += '*'
             item_path = QStandardItem(event_str)
-            item_time = QStandardItem('{}'.format(time))
+            item_time = QStandardItem('{}'.format(time.strftime("%Y-%m-%d %H:%M:%S") if time else ''))
             item_lat = QStandardItem('{}'.format(lat))
             item_lon = QStandardItem('{}'.format(lon))
             item_depth = QStandardItem('{}'.format(depth))
             item_localmag = QStandardItem('{}'.format(localmag))
             item_momentmag = QStandardItem('{}'.format(momentmag))
-            item_nmp = QStandardItem('{}({})'.format(ma_count['manual'], ma_count_total['manual']))
+
+            item_nmp = QStandardItem()
+            item_nap = QStandardItem()
             item_nmp.setIcon(self.manupicksicon_small)
-            item_nap = QStandardItem('{}({})'.format(ma_count['auto'], ma_count_total['auto']))
             item_nap.setIcon(self.autopicksicon_small)
+
+            for picktype, item_np in [('manual', item_nmp), ('auto', item_nap)]:
+                npicks_str = f"{npicks[picktype]['P']}|{npicks[picktype]['S']}"
+                #npicks_str += f"({npicks_total[picktype]['P']}/{npicks_total[picktype]['S']})"
+                item_np.setText(npicks_str)
+
             item_ref = QStandardItem()  # str(event_ref))
             item_test = QStandardItem()  # str(event_test))
             if event_ref:
@@ -1665,16 +1693,55 @@ class MainWindow(QMainWindow):
         self.cmpw.show()
 
     def pickQualities(self):
-        path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
+        path = self.get_current_event_path()
-        getQualitiesfromxml(path)
+        (_, plot) = getQualitiesfromxml(path, self._inputs.get('timeerrorsP'), self._inputs.get('timeerrorsS'),plotflag=1)
+        self.pickQualitiesWindow = PickQualitiesFromXml(figure=plot, path=self.get_current_event_path(),inputVar=self._inputs)
+        self.pickQualitiesWindow.showUI()
         return 
 
+    # WIP JG
     def eventlistXml(self):
         path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
         outpath = self.project.location[:self.project.location.rfind('/')]
         geteventlistfromxml(path, outpath)
         return
 
+        # WIP JG
+    def spectogramView(self):
+        global test
+        stations = []
+        names = []
+        traces = {}
+        for tr in self.get_data().wfdata.traces:
+            if not tr.stats.station in stations:
+                stations.append(tr.stats.station)
+                names.append(tr.stats.network + '.' + tr.stats.station)
+        for station in stations:
+            traces[station] = {}
+        for ch in ['Z', 'N', 'E']:
+            for tr in self.get_data().wfdata.select(component=ch).traces:
+                traces[tr.stats.station][ch] = tr
+
+        names.sort()
+        a = self.get_current_event()
+
+        print (self.get_data().wfdata.traces[0])
+
+        test = SpectrogramTab(traces, self.get_data().wfdata)
+        height = self.tabs.widget(0).height()
+        width = self.tabs.widget(0).width()
+        self.tabs.setCurrentIndex(3)
+        figCanvas = test.makeSpecFig(direction=self.dispComponent, height = height, width = width, parent = self.tabs.widget)
+        return figCanvas
+        #self.spectro_layout.addWidget()
+        # self.get_data().wfdata.spectrogram()
+        # self.tabs.addTab(figCanvas, 'Spectrogram')
+        # self.tabs[3] = figCanvas
+        # self.refreshTabs()
+        # test.show()
+
+
+
     def compareMulti(self):
         if not self.compareoptions:
             return
@@ -1833,6 +1900,7 @@ class MainWindow(QMainWindow):
         # which will read in data input twice. Therefore current tab is changed to 0
         # in loadProject before calling this function.
         self.fill_eventbox()
+        #print(f'{self.get_current_event()=}')
         plotted = False
         if self.tabs.currentIndex() == 2:
             self.init_event_table()
@@ -1860,6 +1928,12 @@ class MainWindow(QMainWindow):
                     self.newWF(plot=False)
                 self.update_obspy_dmt()
                 self.refresh_array_map()
+        if self.tabs.currentIndex() == 3:
+            if self.spectroWidget != None:
+                self.spectro_layout.removeWidget(self.spectroWidget)
+            newSpectroWidget = self.spectogramView()
+            self.spectro_layout.addWidget(newSpectroWidget)
+            self.spectroWidget = newSpectroWidget
 
     def newWF(self, event=None, plot=True):
         '''
@@ -1890,13 +1964,20 @@ class MainWindow(QMainWindow):
 
     def prepareLoadWaveformData(self):
         self.fnames = self.getWFFnames_from_eventbox()
-        self.fnames_syn = []
+        self.fnames_comp = []
+        fnames_comp = self.getWFFnames_from_eventbox(subpath='compare')
+        self.dataPlot.activateCompareOptions(bool(fnames_comp))
+        if fnames_comp:
+            if self.dataPlot.comp_checkbox.isChecked():
+                self.fnames_comp = fnames_comp
+
         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)
+            self.dataPlot.activateCompareOptions(True)
 
     def loadWaveformData(self):
         '''
@@ -1911,6 +1992,8 @@ class MainWindow(QMainWindow):
         #     ans = False
 
         settings = QSettings()
+        # process application events to wait for event items to appear in event box
+        QApplication.processEvents()
         curr_event = self.get_current_event()
         if not curr_event:
             print('Could not find current event. Try reload?')
@@ -1918,8 +2001,8 @@ class MainWindow(QMainWindow):
 
         if len(curr_event.origins) > 0:
             origin_time = curr_event.origins[0].time
-            tstart = settings.value('tstart') if get_None(settings.value('tstart')) else 0
+            tstart = settings.value('tstart') if get_none(settings.value('tstart')) else 0
-            tstop = settings.value('tstop') if get_None(settings.value('tstop')) else 0
+            tstop = settings.value('tstop') if get_none(settings.value('tstop')) else 0
             tstart = origin_time + float(tstart)
             tstop = origin_time + float(tstop)
         else:
@@ -1927,7 +2010,7 @@ class MainWindow(QMainWindow):
             tstop = None
 
         self.data.setWFData(self.fnames,
-                            self.fnames_syn,
+                            self.fnames_comp,
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
@@ -1935,7 +2018,7 @@ class MainWindow(QMainWindow):
 
     def prepareObspyDMT_data(self, eventpath):
         qcbox_processed = self.dataPlot.qcombo_processed
-        qcheckb_syn = self.dataPlot.syn_checkbox
+        qcheckb_syn = self.dataPlot.comp_checkbox
         qcbox_processed.setEnabled(False)
         qcheckb_syn.setEnabled(False)
         for fpath in os.listdir(eventpath):
@@ -1943,8 +2026,8 @@ class MainWindow(QMainWindow):
             if 'syngine' in fpath:
                 eventpath_syn = os.path.join(eventpath, fpath)
                 qcheckb_syn.setEnabled(True)
-                if self.dataPlot.syn_checkbox.isChecked():
+                if self.dataPlot.comp_checkbox.isChecked():
-                    self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                    self.fnames_comp = [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():
@@ -2066,7 +2149,7 @@ class MainWindow(QMainWindow):
 
     def finish_pg_plot(self):
         self.getPlotWidget().updateWidget()
-        plots, gaps = self.wfp_thread.data
+        plots = 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)
@@ -2117,6 +2200,7 @@ class MainWindow(QMainWindow):
             self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
+
         if True in self.comparable.values():
             self.compare_action.setEnabled(True)
         self.draw()
@@ -2224,7 +2308,7 @@ class MainWindow(QMainWindow):
         comp = self.getComponent()
         title = 'section: {0} components'.format(zne_text[comp])
         wfst = self.get_data().getWFData()
-        wfsyn = self.get_data().getSynWFData()
+        wfsyn = self.get_data().getAltWFdata()
         if self.filterActionP.isChecked() and filter:
             self.filterWaveformData(plot=False, phase='P')
         elif self.filterActionS.isChecked() and filter:
@@ -2233,14 +2317,14 @@ class MainWindow(QMainWindow):
         # wfst += self.get_data().getWFData().select(component=alter_comp)
         plotWidget = self.getPlotWidget()
         self.adjustPlotHeight()
-        if get_Bool(settings.value('large_dataset')) == True:
+        if get_bool(settings.value('large_dataset')) == True:
             self.plot_method = 'fast'
         else:
             self.plot_method = 'normal'
         rval = plotWidget.plotWFData(wfdata=wfst, wfsyn=wfsyn, title=title, mapping=False, component=comp,
                                      nth_sample=int(nth_sample), method=self.plot_method, gain=self.gain)
-        plots, gaps = rval if rval else ([], [])
+        plots = rval if rval else []
-        return plots, gaps
+        return plots
 
     def adjustPlotHeight(self):
         if self.pg:
@@ -2536,17 +2620,21 @@ class MainWindow(QMainWindow):
             print("Warning! No network, station, and location info available!")
             return
         self.update_status('picking on station {0}'.format(station))
-        data = self.get_data().getOriginalWFData().copy()
+        wfdata = self.get_data().getOriginalWFData().copy()
+        wfdata_comp = self.get_data().getAltWFdata().copy()
         event = self.get_current_event()
         wftype = self.dataPlot.qcombo_processed.currentText() if self.obspy_dmt else None
         pickDlg = PickDlg(self, parameter=self._inputs,
-                          data=data.select(station=station),
+                          data=wfdata.select(station=station),
+                          data_compare=wfdata_comp.select(station=station),
                           station=station, network=network,
                           location=location,
                           picks=self.getPicksOnStation(station, 'manual'),
                           autopicks=self.getPicksOnStation(station, 'auto'),
                           metadata=self.metadata, event=event,
-                          filteroptions=self.filteroptions, wftype=wftype)
+                          model=self.inputs.get('taup_model'),
+                          filteroptions=self.filteroptions, wftype=wftype,
+                          show_comp_data=self.dataPlot.comp_checkbox.isChecked())
         if self.filterActionP.isChecked():
             pickDlg.currentPhase = "P"
             pickDlg.filterWFData()
@@ -2659,7 +2747,7 @@ class MainWindow(QMainWindow):
         self.init_fig_dict()
         # if not self.tap:
         # init TuneAutopicker object
-        self.tap = TuneAutopicker(self)
+        self.tap = TuneAutopicker(self, self.obspy_dmt)
         # first call of update to init tabs with empty canvas
         self.update_autopicker()
         # connect update signal of TuneAutopicker with update function
@@ -2858,7 +2946,9 @@ class MainWindow(QMainWindow):
         self.log_deleted_picks([deleted_pick])
 
     def log_deleted_picks(self, deleted_picks, event_path=None):
-        ''' Log deleted picks to list self.deleted_picks '''
+        '''
+        Log deleted picks to list self.deleted_picks
+        '''
         if not event_path:
             event_path = self.get_current_event_path()
         for deleted_pick in deleted_picks:
@@ -2872,7 +2962,9 @@ class MainWindow(QMainWindow):
             self.deleted_picks[event_path].append(deleted_pick)
 
     def dump_deleted_picks(self, event_path):
-        ''' Save deleted picks to json file for event in event_path. Load old file before and merge'''
+        '''
+        Save deleted picks to json file for event in event_path. Load old file before and merge
+        '''
         try:
             deleted_picks_from_file = self.load_deleted_picks(event_path)
         except Exception as e:
@@ -2921,10 +3013,16 @@ class MainWindow(QMainWindow):
             event = self.get_current_event()
         event.pylot_picks = {}
         event.pylot_autopicks = {}
-        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data())
+        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data(), parameter=self.getParameter())
         event.addPicks(picksdict['manual'])
         event.addAutopicks(picksdict['auto'])
 
+    def getParameter(self):
+        if hasattr(self.project, 'parameter') and isinstance(self.project.parameter, PylotParameter):
+            return self.project.parameter
+        else:
+            return self._inputs
+
     def drawPicks(self, station=None, picktype=None, stime=None):
         # if picktype not specified, draw both
         if not stime:
@@ -3068,11 +3166,13 @@ class MainWindow(QMainWindow):
         lt = locateTool[loctool]
         # get working directory
         locroot = parameter['nllocroot']
+        #locroot = 'E:/NLL/src/Insheim'
         if locroot is None:
             self.PyLoTprefs()
             self.locate_event()
 
         ctrfile = os.path.join(locroot, 'run', parameter['ctrfile'])
+        #ctrfile = 'E:/NLL/src/Insheim/run/Insheim_min1d032016.in'
         ttt = parameter['ttpatter']
         outfile = parameter['outpatter']
         eventname = self.get_current_event_name()
@@ -3083,7 +3183,7 @@ class MainWindow(QMainWindow):
         phasefile = os.path.join(obsdir, filename + '.obs')
         lt.modify_inputs(ctrfile, locroot, filename, phasefile, ttt)
         try:
-            lt.locate(ctrfile)
+            lt.locate(ctrfile, self._inputs)
         except RuntimeError as e:
             print(e.message)
         # finally:
@@ -3137,7 +3237,7 @@ class MainWindow(QMainWindow):
         '''
         if checked: pass  # dummy argument for QAction trigger signal
         self.tabs.setCurrentIndex(1)
-        # if there is no metadata (invetories is an empty list), just initialize the default empty tab
+        # if there is no metadata (inventories is an empty list), just initialize the default empty tab
         if not self.metadata.inventories:
             self.init_array_tab()
             return
@@ -3159,6 +3259,15 @@ class MainWindow(QMainWindow):
         self.tabs.setCurrentIndex(index)
         self.refresh_array_map()
 
+    def init_spectro_tab(self):
+        '''
+        Init spectrogram tab with currently selected event.
+        '''
+        self.spectroWidget = None
+        #self.spectro_layout.addWidget( self.spectogramView() )
+        pass
+
+
     def array_map_thread(self):
         '''
         Start modal thread to init the array_map object.
@@ -3381,7 +3490,7 @@ class MainWindow(QMainWindow):
                     self.event_table.setCellWidget(r_index, c_index, item)
 
         header = self.event_table.horizontalHeader()
-        header.setResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
         header.setStretchLastSection(True)
         self.event_table.cellChanged[int, int].connect(cell_changed)
         self.event_table.cellClicked[int, int].connect(cell_clicked)
@@ -3488,7 +3597,7 @@ class MainWindow(QMainWindow):
 
         wf_select = Stream()
         # restitute only picked traces
-        for station in np.unique(self.getPicks('manual').keys() + self.getPicks('auto').keys()):
+        for station in np.unique(list(self.getPicks('manual').keys()) + list(self.getPicks('auto').keys())):
             wf_select += wf_copy.select(station=station)
 
         corr_wf = restitute_data(wf_select, self.metadata)
@@ -3555,7 +3664,7 @@ class MainWindow(QMainWindow):
             return True
         return False
 
-    def update_status(self, message, duration=5000):
+    def update_status(self, message, duration=10000):
         self.statusBar().showMessage(message, duration)
         if self.get_data() is not None:
             if not self.get_current_event() or not self.project.location:
@@ -3608,10 +3717,13 @@ class MainWindow(QMainWindow):
         if not self.okToContinue():
             return
         if not fnm:
-            dlg = QFileDialog(parent=self)
+            settings = QSettings()
+            dir = settings.value('current_project_path')
+            dlg = QFileDialog(parent=self, directory=dir)
             fnm = dlg.getOpenFileName(self, 'Open project file...', filter='Pylot project (*.plp)')[0]
             if not fnm:
                 return
+            settings.setValue('current_project_path', os.path.split(fnm)[0])
         if not os.path.exists(fnm):
             QMessageBox.warning(self, 'Could not open file',
                                 'Could not open project file {}. File does not exist.'.format(fnm))
@@ -3667,7 +3779,7 @@ class MainWindow(QMainWindow):
             filename = fnm[0] + '.plp'
         self.project.parameter = self._inputs
         settings = QSettings()
-        autosaveXML = get_Bool(settings.value('autosaveXML', True))
+        autosaveXML = get_bool(settings.value('autosaveXML', True))
         if autosaveXML:
             self.exportEvents()
         if not self.project.save(filename): return False
@@ -3691,7 +3803,7 @@ class MainWindow(QMainWindow):
                 self.metadata.clear_inventory()
                 self.project.parameter = self._inputs
                 settings = QSettings()
-                autosaveXML = get_Bool(settings.value('autosaveXML', True))
+                autosaveXML = get_bool(settings.value('autosaveXML', True))
                 if autosaveXML:
                     self.exportEvents()
                 if not self.project.save(): return False
@@ -3729,6 +3841,7 @@ class MainWindow(QMainWindow):
 
     def closeEvent(self, event):
         if self.okToContinue():
+            if hasattr(self, 'logwidget'):
                 self.logwidget.close()
             event.accept()
         else:
@@ -3780,7 +3893,7 @@ class MainWindow(QMainWindow):
     def helpHelp(self):
         if checkurl():
             form = HelpForm(self,
-                            'https://ariadne.geophysik.ruhr-uni-bochum.de/trac/PyLoT/wiki')
+                            'https://github.com/seismology-RUB/PyLoT')
         else:
             form = HelpForm(self, ':/help.html')
         form.show()
@@ -3960,13 +4073,13 @@ class Project(object):
         return project
 
 
-class getExistingDirectories(QFileDialog):
+class GetExistingDirectories(QFileDialog):
     '''
     File dialog with possibility to select multiple folders.
     '''
 
     def __init__(self, *args):
-        super(getExistingDirectories, self).__init__(*args)
+        super(GetExistingDirectories, self).__init__(*args)
         self.setOption(self.DontUseNativeDialog, True)
         self.setOption(self.ReadOnly, True)
         self.setFileMode(self.Directory)
@@ -3992,16 +4105,7 @@ def create_window():
     return app, app_created
 
 
-def main(args=None):
+def main(project_filename=None, pylot_infile=None, reset_qsettings=False):
-    project_filename = None
-    # args.project_filename = 'C:/Shared/AlpArray/alparray_data/project_alparray_test.plp'
-    pylot_infile = None
-    if args:
-        if args.project_filename:
-            project_filename = args.project_filename
-        if args.input_filename:
-            pylot_infile = args.input_filename
-        reset_qsettings = args.reset_qsettings
 
     # create the Qt application
     pylot_app, app_created = create_window()
@@ -4050,4 +4154,5 @@ if __name__ == "__main__":
     parser.add_argument('--reset_qsettings', default=False, action='store_true',
                         help='reset qsettings (debug option)')
     args = parser.parse_args()
-    sys.exit(main(args))
+    sys.exit(main(project_filename=args.project_filename, pylot_infile=args.input_filename,
+                  reset_qsettings=args.reset_qsettings))

README.md

@@ -24,10 +24,10 @@ It is highly recommended to use Anaconda for a simple creation of a Python insta
 
 Afterwards run (from the PyLoT main directory where the files *requirements.txt* and *pylot.yml* are located)
 
-    conda create --name pylot_38 --file requirements.txt
+    conda env create -f pylot.yml
 or
     
-    conda env create -f pylot.yml
+    conda create --name pylot_38 --file requirements.txt
 
 to create a new Anaconda environment called "pylot_38".
 
@@ -99,13 +99,13 @@ We hope to solve these with the next release.
 
 ## Staff
 
-Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
+Original author(s): M. Rische, S. Wehling-Benatelli, L. Kueperkoch, M. Bischoff (PILOT)
 
-Developer(s): S. Wehling-Benatelli, L. Kueperkoch, K. Olbert, M. Bischoff, C. Wollin, M. Rische, M. Paffrath
+Developer(s): S. Wehling-Benatelli, M. Paffrath, L. Kueperkoch, K. Olbert, M. Bischoff, C. Wollin, M. Rische, D. Arnold, K. Cökerim, S. Zimmermann
 
 Others: A. Bruestle, T. Meier, W. Friederich
 
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-September 2017
+April 2022

autoPyLoT.py

@@ -28,7 +28,7 @@ from pylot.core.util.dataprocessing import restitute_data, Metadata
 from pylot.core.util.defaults import SEPARATOR
 from pylot.core.util.event import Event
 from pylot.core.util.structure import DATASTRUCTURE
-from pylot.core.util.utils import get_None, trim_station_components, check4gapsAndRemove, check4doubled, \
+from pylot.core.util.utils import get_none, trim_station_components, check4gapsAndRemove, check4doubled, \
     check4rotated
 from pylot.core.util.version import get_git_version as _getVersionString
 
@@ -91,9 +91,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                                                               sp=sp_info)
     print(splash)
 
-    parameter = get_None(parameter)
+    parameter = get_none(parameter)
-    inputfile = get_None(inputfile)
+    inputfile = get_none(inputfile)
-    eventid = get_None(eventid)
+    eventid = get_none(eventid)
 
     fig_dict = None
     fig_dict_wadatijack = None
@@ -119,13 +119,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
             obspyDMT_wfpath = input_dict['obspyDMT_wfpath']
 
     if not parameter:
-        if inputfile:
+        if not inputfile:
+            print('Using default input parameter')
         parameter = PylotParameter(inputfile)
-            # iplot = parameter['iplot']
-        else:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
     else:
         if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
@@ -154,7 +150,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         datastructure.setExpandFields(exf)
 
         # check if default location routine NLLoc is available and all stations are used
-        if get_None(parameter['nllocbin']) and station == 'all':
+        if get_none(parameter['nllocbin']) and station == 'all':
             locflag = 1
             # get NLLoc-root path
             nllocroot = parameter.get('nllocroot')

autopylot.sh

@@ -3,8 +3,10 @@
 #$ -l low
 #$ -cwd
 #$ -pe smp 40
-#$ -l mem=2G
+##$ -l mem=3G
-#$ -l h_vmem=2G
+#$ -l h_vmem=6G
 #$ -l os=*stretch
 
-python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in -dmt processed -c $NSLOTS
+conda activate pylot_311
+
+python ./autoPyLoT.py -i /home/marcel/.pylot/pylot_adriaarray.in -c 20 -dmt processed

pylot.yml

@@ -8,7 +8,7 @@ dependencies:
   - numpy=1.22.3
   - obspy=1.3.0
   - pyqtgraph=0.12.4
-  - pyside2=5.13.2
+  - pyside2>=5.13.2
   - python=3.8.12
-  - qt=5.12.9
+  - qt>=5.12.9
   - scipy=1.8.0

pylot/core/analysis/magnitude.py

@@ -144,6 +144,10 @@ class Magnitude(object):
                     azimuthal_gap=self.origin_id.get_referred_object().quality.azimuthal_gap)
             else:
                 # no scaling necessary
+                # Temporary fix needs rework
+                if (len(self.magnitudes.keys()) == 0):
+                    print("Error in local magnitude calculation ")
+                    return None
                 mag = ope.Magnitude(
                     mag=np.median([M.mag for M in self.magnitudes.values()]),
                     magnitude_type=self.type,
@@ -414,6 +418,10 @@ class MomentMagnitude(Magnitude):
             distance = degrees2kilometers(a.distance)
             azimuth = a.azimuth
             incidence = a.takeoff_angle
+            if not 0. <= incidence <= 360.:
+                if self.verbose:
+                    print(f'WARNING: Incidence angle outside bounds - {incidence}')
+                return
             w0, fc = calcsourcespec(scopy, onset, self.p_velocity, distance,
                                     azimuth, incidence, self.p_attenuation,
                                     self.plot_flag, self.verbose)
@@ -432,6 +440,40 @@ class MomentMagnitude(Magnitude):
             self.event.station_magnitudes.append(magnitude)
             self.magnitudes = (station, magnitude)
 
+    # WIP JG
+    def getSourceSpec(self):
+        for a in self.arrivals:
+            if a.phase not in 'pP':
+                continue
+            # make sure calculating Mo only from reliable onsets
+            # NLLoc: time_weight = 0 => do not use onset!
+            if a.time_weight == 0:
+                continue
+            pick = a.pick_id.get_referred_object()
+            station = pick.waveform_id.station_code
+            if len(self.stream) <= 2:
+                print("Station:" '{0}'.format(station))
+                print("WARNING: No instrument corrected data available,"
+                      " no magnitude calculation possible! Go on.")
+                continue
+            wf = self.stream.select(station=station)
+            if not wf:
+                continue
+            try:
+                scopy = wf.copy()
+            except AssertionError:
+                print("WARNING: Something's wrong with the data,"
+                      "station {},"
+                      "no calculation of moment magnitude possible! Go on.".format(station))
+                continue
+            onset = pick.time
+            distance = degrees2kilometers(a.distance)
+            azimuth = a.azimuth
+            incidence = a.takeoff_angle
+            w0, fc, plt = calcsourcespec(scopy, onset, self.p_velocity, distance,
+                                    azimuth, incidence, self.p_attenuation,
+                                    3, self.verbose)
+            return w0, fc, plt
 
 def calcMoMw(wfstream, w0, rho, vp, delta, verbosity=False):
     '''
@@ -602,7 +644,7 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
         N = min(int(np.power(m, 2)), 16384)
         # N = int(np.power(m, 2))
         y = dt * np.fft.fft(xdat, N)
-        Y = abs(y[: N / 2])
+        Y = abs(y[: int(N / 2)])
         L = (N - 1) / freq
         f = np.arange(0, fny, 1 / L)
 
@@ -679,6 +721,8 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
             plt.xlabel('Frequency [Hz]')
             plt.ylabel('Amplitude [m/Hz]')
             plt.grid()
+            if iplot == 3:
+                return w0, Fc, plt
             plt.show()
             try:
                 input()

pylot/core/io/data.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import copy
+import logging
 import os
 
 from PySide2.QtWidgets import QMessageBox
@@ -19,7 +20,7 @@ from pylot.core.util.errors import FormatError, OverwriteError
 from pylot.core.util.event import Event
 from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
 from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
-    check4gapsAndMerge, trim_station_components
+    check_for_gaps_and_merge, trim_station_components, check_for_nan
 
 
 class Data(object):
@@ -64,7 +65,7 @@ class Data(object):
                     elif 'LOC' in evtdata:
                         raise NotImplementedError('PILOT location information '
                                                   'read support not yet '
-                                                  'implemeted.')
+                                                  'implemented.')
                     elif 'event.pkl' in evtdata:
                         evtdata = qml_from_obspyDMT(evtdata)
                     else:
@@ -260,7 +261,6 @@ class Data(object):
         can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
         """
         from pylot.core.util.defaults import OUTPUTFORMATS
-
         if not type(fcheck) == list:
             fcheck = [fcheck]
 
@@ -321,35 +321,61 @@ class Data(object):
             if lendiff != 0:
                 print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
 
+
+            no_uncertainties_p = []
+            no_uncertainties_s = []
             if upperErrors:
                 # check for pick uncertainties exceeding adjusted upper errors
                 # Picks with larger uncertainties will not be saved in output file!
                 for j in range(len(picks)):
                     for i in range(len(picks_copy)):
                         if picks_copy[i].phase_hint[0] == 'P':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
+                            # Skipping pick if no upper_uncertainty is found and warning user
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                 #   picks_copy[i].waveform_id.station_code,
+                                  #  picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_p:
+                                    no_uncertainties_p.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+                            #print ("checking for upper_uncertainty")
+                            if  (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                    (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]):
                                 print("Uncertainty exceeds or equal adjusted upper time error!")
                                 print("Adjusted uncertainty: {}".format(upperErrors[0]))
                                 print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                 print("{1} P-Pick of station {0} will not be saved in outputfile".format(
                                     picks_copy[i].waveform_id.station_code,
                                     picks_copy[i].method_id))
-                                print("#")
                                 del picks_copy[i]
                                 break
                         if picks_copy[i].phase_hint[0] == 'S':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
+
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
+                            # Skipping pick if no upper_uncertainty is found and warning user
+                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
+                                #print("{1} S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
+                                    #picks_copy[i].waveform_id.station_code,
+                                    #picks_copy[i].method_id))
+                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_s:
+                                    no_uncertainties_s.append(picks_copy[i].waveform_id.station_code)
+                                continue
+
+
+                            if (picks_copy[i].time_errors['uncertainty'] is None) or \
+                                (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]):
                                 print("Uncertainty exceeds or equal adjusted upper time error!")
                                 print("Adjusted uncertainty: {}".format(upperErrors[1]))
                                 print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
                                 print("{1} S-Pick of station {0} will not be saved in outputfile".format(
                                     picks_copy[i].waveform_id.station_code,
                                     picks_copy[i].method_id))
-                                print("#")
                                 del picks_copy[i]
                                 break
+            for s in no_uncertainties_p:
+                print("P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
+            for s in no_uncertainties_s:
+                print("S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
 
             if fnext == '.obs':
                 try:
@@ -383,18 +409,16 @@ class Data(object):
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '_focmec.in':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                    parameter = PylotParameter()
-                    print('Using default input file {}'.format(infile))
+                    logging.warning('Using default input parameter')
-                    parameter = PylotParameter(infile)
                     focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.pha':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                    parameter = PylotParameter()
-                    print('Using default input file {}'.format(infile))
+                    logging.warning('Using default input parameter')
-                    parameter = PylotParameter(infile)
                     hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
@@ -426,20 +450,30 @@ class Data(object):
         data.filter(**kwargs)
         self.dirty = True
 
-    def setWFData(self, fnames, fnames_syn=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
+    def setWFData(self, fnames, fnames_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
         """
         Clear current waveform data and set given waveform data
         :param fnames: waveform data names to append
+        :param fnames_alt: alternative data to show (e.g. synthetic/processed)
         :type fnames: list
         """
+        def check_fname_exists(filenames: list) -> list:
+            if filenames:
+                filenames = [fn for fn in filenames if os.path.isfile(fn)]
+            return filenames
+
         self.wfdata = Stream()
         self.wforiginal = None
-        self.wfsyn = Stream()
+        self.wf_alt = Stream()
         if tstart == tstop:
             tstart = tstop = None
         self.tstart = tstart
         self.tstop = tstop
 
+        # remove directories
+        fnames = check_fname_exists(fnames)
+        fnames_alt = check_fname_exists(fnames_alt)
+
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -457,8 +491,8 @@ class Data(object):
         #     wffnames = fnames
         if fnames is not None:
             self.appendWFData(fnames)
-            if fnames_syn is not None:
+            if fnames_alt is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
+                self.appendWFData(fnames_alt, alternative=True)
         else:
             return False
 
@@ -466,7 +500,9 @@ class Data(object):
         # remove possible underscores in station names
         # self.wfdata = remove_underscores(self.wfdata)
         # check for gaps and merge
-        self.wfdata = check4gapsAndMerge(self.wfdata)
+        self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
+        # check for nans
+        check_for_nan(self.wfdata)
         # check for stations with rotated components
         if checkRotated and metadata is not None:
             self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
@@ -478,7 +514,7 @@ class Data(object):
         self.dirty = False
         return True
 
-    def appendWFData(self, fnames, synthetic=False):
+    def appendWFData(self, fnames, alternative=False):
         """
         Read waveform data from fnames and append it to current wf data
         :param fnames: waveform data to append
@@ -491,19 +527,19 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        real_or_syn_data = {True: self.wfsyn,
+        orig_or_alternative_data = {True: self.wf_alt,
                                     False: self.wfdata}
 
         warnmsg = ''
         for fname in set(fnames):
             try:
-                real_or_syn_data[synthetic] += read(fname, starttime=self.tstart, endtime=self.tstop)
+                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
             except TypeError:
                 try:
-                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
+                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                 except Exception as e:
                     try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
+                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
                                                                       endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
@@ -519,8 +555,8 @@ class Data(object):
     def getOriginalWFData(self):
         return self.wforiginal
 
-    def getSynWFData(self):
+    def getAltWFdata(self):
-        return self.wfsyn
+        return self.wf_alt
 
     def resetWFData(self):
         """

pylot/core/io/getEventListFromXML.py

@@ -8,6 +8,11 @@
    Edited for use in PyLoT
    JG, igem, 01/2022
 """
+
+import os
+import argparse
+import numpy as np
+import matplotlib.pyplot as plt
 import glob
 
 from obspy.core.event import read_events

pylot/core/io/getQualitiesfromxml.py

@@ -1,138 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-"""
-   Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
-   Uncertainties are tranformed into quality classes and visualized via histogram if desired.
-   Ludger Küperkoch, BESTEC GmbH, 07/2017
-   rev.: Ludger Küperkoch, igem, 10/2020
-   Edited for usage in PyLoT: Jeldrik Gaal, igem, 01/2022
-"""
-
-import glob
-
-import matplotlib.pyplot as plt
-import numpy as np
-from obspy.core.event import read_events
-
-
-def getQualitiesfromxml(path):
-    # uncertainties
-    ErrorsP = [0.02, 0.04, 0.08, 0.16]
-    ErrorsS = [0.04, 0.08, 0.16, 0.32]
-
-    Pw0 = []
-    Pw1 = []
-    Pw2 = []
-    Pw3 = []
-    Pw4 = []
-    Sw0 = []
-    Sw1 = []
-    Sw2 = []
-    Sw3 = []
-    Sw4 = []
-
-    # data path
-    dp = path + '/e*/*.xml'
-    # list of all available xml-files
-    xmlnames = glob.glob(dp)
-
-    # read all onset weights
-    for names in xmlnames:
-        print("Getting onset weights from {}".format(names))
-        cat = read_events(names)
-        arrivals = cat.events[0].picks
-        for Pick in arrivals:
-            if Pick.phase_hint[0] == 'P':
-                if Pick.time_errors.uncertainty <= ErrorsP[0]:
-                    Pw0.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsP[0] and \
-                        Pick.time_errors.uncertainty <= ErrorsP[1]:
-                    Pw1.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsP[1] and \
-                        Pick.time_errors.uncertainty <= ErrorsP[2]:
-                    Pw2.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsP[2] and \
-                        Pick.time_errors.uncertainty <= ErrorsP[3]:
-                    Pw3.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsP[3]:
-                    Pw4.append(Pick.time_errors.uncertainty)
-                else:
-                    pass
-            elif Pick.phase_hint[0] == 'S':
-                if Pick.time_errors.uncertainty <= ErrorsS[0]:
-                    Sw0.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsS[0] and \
-                        Pick.time_errors.uncertainty <= ErrorsS[1]:
-                    Sw1.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsS[1] and \
-                        Pick.time_errors.uncertainty <= ErrorsS[2]:
-                    Sw2.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsS[2] and \
-                        Pick.time_errors.uncertainty <= ErrorsS[3]:
-                    Sw3.append(Pick.time_errors.uncertainty)
-                elif Pick.time_errors.uncertainty > ErrorsS[3]:
-                    Sw4.append(Pick.time_errors.uncertainty)
-                else:
-                    pass
-            else:
-                print("Phase hint not defined for picking!")
-                pass
-    # get percentage of weights
-    numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
-    numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
-    try:
-        P0perc = 100.0 / numPweights * len(Pw0)
-    except:
-        P0perc = 0
-    try:
-        P1perc = 100.0 / numPweights * len(Pw1)
-    except:
-        P1perc = 0
-    try:
-        P2perc = 100.0 / numPweights * len(Pw2)
-    except:
-        P2perc = 0
-    try:
-        P3perc = 100.0 / numPweights * len(Pw3)
-    except:
-        P3perc = 0
-    try:
-        P4perc = 100.0 / numPweights * len(Pw4)
-    except:
-        P4perc = 0
-    try:
-        S0perc = 100.0 / numSweights * len(Sw0)
-    except:
-        Soperc = 0
-    try:
-        S1perc = 100.0 / numSweights * len(Sw1)
-    except:
-        S1perc = 0
-    try:
-        S2perc = 100.0 / numSweights * len(Sw2)
-    except:
-        S2perc = 0
-    try:
-        S3perc = 100.0 / numSweights * len(Sw3)
-    except:
-        S3perc = 0
-    try:
-        S4perc = 100.0 / numSweights * len(Sw4)
-    except:
-        S4perc = 0
-
-    weights = ('0', '1', '2', '3', '4')
-    y_pos = np.arange(len(weights))
-    width = 0.34
-    p1, = plt.bar(0 - width, P0perc, width, color='black')
-    p2, = plt.bar(0, S0perc, width, color='red')
-    plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
-    plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
-    plt.ylabel('%')
-    plt.xticks(y_pos, weights)
-    plt.xlim([-0.5, 4.5])
-    plt.xlabel('Qualities')
-    plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
-    plt.legend([p1, p2], ['P-Weights', 'S-Weights'])
-    plt.show()

pylot/core/io/location.py

@@ -1,7 +1,7 @@
 from obspy import UTCDateTime
 from obspy.core import event as ope
 
-from pylot.core.util.utils import getLogin, getHash
+from pylot.core.util.utils import get_login, get_hash
 
 
 def create_amplitude(pickID, amp, unit, category, cinfo):
@@ -61,7 +61,7 @@ def create_creation_info(agency_id=None, creation_time=None, author=None):
     :return:
     '''
     if author is None:
-        author = getLogin()
+        author = get_login()
     if creation_time is None:
         creation_time = UTCDateTime()
     return ope.CreationInfo(agency_id=agency_id, author=author,
@@ -210,7 +210,7 @@ def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
     '''
     assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
                                                 "UTCDateTime object"
-    hid = getHash(timetohash)
+    hid = get_hash(timetohash)
     if hrstr is None:
         resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
     else:

pylot/core/io/phases.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import glob
+import logging
 import os
 import warnings
 
@@ -16,8 +17,8 @@ from pylot.core.io.inputs import PylotParameter
 from pylot.core.io.location import create_event, \
     create_magnitude
 from pylot.core.pick.utils import select_for_phase, get_quality_class
-from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
+from pylot.core.util.utils import get_owner, full_range, four_digits, transformFilterString4Export, \
-    backtransformFilterString
+    backtransformFilterString, loopIdentifyPhase, identifyPhase
 
 
 def add_amplitudes(event, amplitudes):
@@ -58,7 +59,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if phasfn is not None and os.path.isfile(phasfn):
         phases = sio.loadmat(phasfn)
         phasctime = UTCDateTime(os.path.getmtime(phasfn))
-        phasauthor = getOwner(phasfn)
+        phasauthor = get_owner(phasfn)
     else:
         phases = None
         phasctime = None
@@ -66,7 +67,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if locfn is not None and os.path.isfile(locfn):
         loc = sio.loadmat(locfn)
         locctime = UTCDateTime(os.path.getmtime(locfn))
-        locauthor = getOwner(locfn)
+        locauthor = get_owner(locfn)
     else:
         loc = None
         locctime = None
@@ -217,7 +218,7 @@ def picksdict_from_obs(fn):
     return picks
 
 
-def picksdict_from_picks(evt):
+def picksdict_from_picks(evt, parameter=None):
     """
     Takes an Event object and return the pick dictionary commonly used within
     PyLoT
@@ -230,6 +231,7 @@ def picksdict_from_picks(evt):
         'auto': {}
     }
     for pick in evt.picks:
+        errors = None
         phase = {}
         station = pick.waveform_id.station_code
         if pick.waveform_id.channel_code is None:
@@ -273,32 +275,29 @@ def picksdict_from_picks(evt):
         phase['epp'] = epp
         phase['lpp'] = lpp
         phase['spe'] = spe
-        try:
+        weight = phase.get('weight')
-            phase['weight'] = weight
+        if not weight:
-        except:
+            if not parameter:
-            # get onset weight from uncertainty
+                logging.warning('Using ')
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                logging.warning('Using default input parameter')
-            print('Using default input file {}'.format(infile))
+                parameter = PylotParameter()
-            parameter = PylotParameter(infile)
+            pick.phase_hint = identifyPhase(pick.phase_hint)
             if pick.phase_hint == 'P':
                 errors = parameter['timeerrorsP']
             elif pick.phase_hint == 'S':
                 errors = parameter['timeerrorsS']
+            if errors:
                 weight = get_quality_class(spe, errors)
                 phase['weight'] = weight
         phase['channel'] = channel
         phase['network'] = network
         phase['picker'] = pick_method
-        try:
         if pick.polarity == 'positive':
             phase['fm'] = 'U'
         elif pick.polarity == 'negative':
             phase['fm'] = 'D'
         else:
             phase['fm'] = 'N'
-        except:
-            print("No FM info available!")
-            phase['fm'] = 'N'
         phase['filter_id'] = filter_id if filter_id is not None else ''
 
         onsets[pick.phase_hint] = phase.copy()
@@ -375,7 +374,6 @@ def picks_from_picksdict(picks, creation_info=None):
 
 
 def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0):
-    import glob
     # TODO: change root to datapath
     db_root = os.path.join(root_dir, db_dir)
     evt_list = glob.glob1(db_root, 'e????.???.??')
@@ -518,7 +516,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                 try:
                     fm = arrivals[key]['P']['fm']
                 except KeyError as e:
@@ -552,7 +550,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                                                                            ss_ms,
                                                                                            pweight))
             # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                 fm = '?'
                 onset = arrivals[key]['S']['mpp']
                 year = onset.year
@@ -671,7 +669,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
-            if arrivals[key].has_key('P') and arrivals[key]['P']['mpp'] is not None:
+            if 'P' in  arrivals[key] and arrivals[key]['P']['mpp'] is not None:
                 if arrivals[key]['P']['weight'] < 4:
                     Ponset = arrivals[key]['P']['mpp']
                     pyear = Ponset.year
@@ -700,7 +698,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
                               % (key, pyear, pmonth, pday, phh, pmm, Pss, pstd))
             # S onsets
-            if arrivals[key].has_key('S') and arrivals[key]['S']['mpp'] is not None:
+            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
                 if arrivals[key]['S']['weight'] < 4:
                     Sonset = arrivals[key]['S']['mpp']
                     syear = Sonset.year
@@ -769,7 +767,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
             # P onsets
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 if usedarrivals[key]['P']['weight'] < 4:
                     n += 1
                     stat = key
@@ -783,7 +781,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                     else:
                         fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
                         # S onsets
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                 if usedarrivals[key]['S']['weight'] < 4:
                     n += 1
                     stat = key
@@ -829,13 +827,13 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 # P onsets
                 if usedarrivals[key]['P']['weight'] < 4:
                     Ponset = usedarrivals[key]['P']['mpp']
                     Prt = Ponset - stime  # onset time relative to source time
                     fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if usedarrivals[key].has_key('S'):
+            if 'S' in usedarrivals[key]:
                 # S onsets
                 if usedarrivals[key]['S']['weight'] < 4:
                     Sonset = usedarrivals[key]['S']['mpp']
@@ -880,7 +878,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         # prefer manual picks
         usedarrivals = chooseArrivals(arrivals)
         for key in usedarrivals:
-            if usedarrivals[key].has_key('P'):
+            if 'P' in usedarrivals[key]:
                 if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
                     stat = key
                     for i in range(len(picks)):
@@ -962,7 +960,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         # write phase lines
         for key in arrivals:
-            if arrivals[key].has_key('P'):
+            if 'P' in arrivals[key]:
                 if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
                     stat = key
                     ccode = arrivals[key]['P']['channel']
@@ -1015,7 +1013,6 @@ def chooseArrivals(arrivals):
     :return: arrivals but with the manual picks prefered if possible
     """
     # If len of arrivals is greater than 2 it comes from autopicking so only autopicks are available
-    print("=== CHOOSE ===")
     if len(arrivals) > 2:
         return arrivals
     if arrivals['auto'] and arrivals['manual']:
@@ -1056,37 +1053,63 @@ def merge_picks(event, picks):
     return event
 
 
-def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
+def getQualitiesfromxml(path, errorsP, errorsS, plotflag=1, figure=None, verbosity=0):
     """
     Script to get onset uncertainties from Quakeml.xml files created by PyLoT.
     Uncertainties are tranformed into quality classes and visualized via histogram if desired.
     Ludger Küperkoch, BESTEC GmbH, 07/2017
-    :param xmlnames: list of xml obspy event files containing picks
+    :param path: path containing xml files
-    :type xmlnames: list
+    :type path: str
-    :param ErrorsP: time errors of P waves for the four discrete quality classes
+    :param errorsP: time errors of P waves for the four discrete quality classes
-    :type ErrorsP:
+    :type errorsP:
-    :param ErrorsS: time errors of S waves for the four discrete quality classes
+    :param errorsS: time errors of S waves for the four discrete quality classes
-    :type ErrorsS:
+    :type errorsS:
     :param plotflag:
     :type plotflag:
     :return:
     :rtype:
     """
 
-    from pylot.core.pick.utils import get_quality_class
+    def calc_perc(uncertainties, ntotal):
-    from pylot.core.util.utils import loopIdentifyPhase, identifyPhase
+        ''' simple function that calculates percentage of number of uncertainties (list length)'''
+        if len(uncertainties) == 0:
+            return 0
+        else:
+            return 100. / ntotal * len(uncertainties)
+
+    def calc_weight_perc(psweights, weight_ids):
+        ''' calculate percentages of different weights (pick classes!?) of total number of uncertainties of a phase'''
+        # count total number of list items for this phase
+        numWeights = np.sum([len(weight) for weight in psweights.values()])
+
+        # iterate over all available weights to return a list with percentages for plotting
+        plot_list = []
+        for weight_id in weight_ids:
+            plot_list.append(calc_perc(psweights[weight_id], numWeights))
+
+        return plot_list, numWeights
+
+    # get all xmlfiles in path (maybe this should be changed to one xml file for this function, selectable via GUI?)
+    xmlnames = glob.glob(os.path.join(path, '*.xml'))
+    if len(xmlnames) == 0:
+        print(f'No files found in path {path}.')
+        return False
+
+    # first define possible phases here
+    phases = ['P', 'S']
+
+    # define possible weights (0-4)
+    weight_ids = list(range(5))
+
+    # put both error lists in a dictionary with P/S key so that amount of code can be halfed by simply using P/S as key
+    errors = dict(P=errorsP, S=errorsS)
+
+    # create dictionaries for each phase (P/S) with a dictionary of empty list for each weight defined in weights
+    # tuple above
+    weights = {}
+    for phase in phases:
+        weights[phase] = {weight_id: [] for weight_id in weight_ids}
 
-    # read all onset weights
-    Pw0 = []
-    Pw1 = []
-    Pw2 = []
-    Pw3 = []
-    Pw4 = []
-    Sw0 = []
-    Sw1 = []
-    Sw2 = []
-    Sw3 = []
-    Sw4 = []
     for names in xmlnames:
         print("Getting onset weights from {}".format(names))
         cat = read_events(names)
@@ -1094,117 +1117,60 @@ def getQualitiesfromxml(xmlnames, ErrorsP, ErrorsS, plotflag=1):
         arrivals = cat.events[0].picks
         arrivals_copy = cat_copy.events[0].picks
         # Prefere manual picks if qualities are sufficient!
-        for Pick in arrivals:
+        for pick in arrivals:
-            if Pick.method_id.id.split('/')[1] == 'manual':
+            if pick.method_id.id.split('/')[1] == 'manual':
-                mstation = Pick.waveform_id.station_code
+                mstation = pick.waveform_id.station_code
                 mstation_ext = mstation + '_'
                 for mpick in arrivals_copy:
-                    phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
+                    phase = identifyPhase(loopIdentifyPhase(pick.phase_hint)) # MP MP catch if this fails?
-                    if phase == 'P':
                     if ((mpick.waveform_id.station_code == mstation) or
                         (mpick.waveform_id.station_code == mstation_ext)) and \
-                                (mpick.method_id.split('/')[1] == 'auto') and \
+                            (mpick.method_id.id.split('/')[1] == 'auto') and \
-                                (mpick.time_errors['uncertainty'] <= ErrorsP[3]):
+                            (mpick.time_errors['uncertainty'] <= errors[phase][3]):
-                            del mpick
-                            break
-                    elif phase == 'S':
-                        if ((mpick.waveform_id.station_code == mstation) or
-                            (mpick.waveform_id.station_code == mstation_ext)) and \
-                                (mpick.method_id.split('/')[1] == 'auto') and \
-                                (mpick.time_errors['uncertainty'] <= ErrorsS[3]):
                         del mpick
                         break
         lendiff = len(arrivals) - len(arrivals_copy)
         if lendiff != 0:
             print("Found manual as well as automatic picks, prefered the {} manual ones!".format(lendiff))
 
-        for Pick in arrivals_copy:
+        for pick in arrivals_copy:
-            phase = identifyPhase(loopIdentifyPhase(Pick.phase_hint))
+            phase = identifyPhase(loopIdentifyPhase(pick.phase_hint))
-            if phase == 'P':
+            uncertainty = pick.time_errors.uncertainty
-                Pqual = get_quality_class(Pick.time_errors.uncertainty, ErrorsP)
+            if not uncertainty:
-                if Pqual == 0:
+                if verbosity > 0:
-                    Pw0.append(Pick.time_errors.uncertainty)
+                    print('No uncertainty, pick {} invalid!'.format(pick.method_id.id))
-                elif Pqual == 1:
+                continue
-                    Pw1.append(Pick.time_errors.uncertainty)
+            # check P/S phase
-                elif Pqual == 2:
+            if phase not in phases:
-                    Pw2.append(Pick.time_errors.uncertainty)
-                elif Pqual == 3:
-                    Pw3.append(Pick.time_errors.uncertainty)
-                elif Pqual == 4:
-                    Pw4.append(Pick.time_errors.uncertainty)
-            elif phase == 'S':
-                Squal = get_quality_class(Pick.time_errors.uncertainty, ErrorsS)
-                if Squal == 0:
-                    Sw0.append(Pick.time_errors.uncertainty)
-                elif Squal == 1:
-                    Sw1.append(Pick.time_errors.uncertainty)
-                elif Squal == 2:
-                    Sw2.append(Pick.time_errors.uncertainty)
-                elif Squal == 3:
-                    Sw3.append(Pick.time_errors.uncertainty)
-                elif Squal == 4:
-                    Sw4.append(Pick.time_errors.uncertainty)
-            else:
                 print("Phase hint not defined for picking!")
-                pass
+                continue
+
+            qual = get_quality_class(uncertainty, errors[phase])
+            weights[phase][qual].append(uncertainty)
 
     if plotflag == 0:
-        Punc = [Pw0, Pw1, Pw2, Pw3, Pw4]
+        p_unc = [weights['P'][weight_id] for weight_id in weight_ids]
-        Sunc = [Sw0, Sw1, Sw2, Sw3, Sw4]
+        s_unc = [weights['S'][weight_id] for weight_id in weight_ids]
-        return Punc, Sunc
+        return p_unc, s_unc
     else:
+        if not figure:
+            fig = plt.figure()
+        ax = fig.add_subplot(111)
         # get percentage of weights
-        numPweights = np.sum([len(Pw0), len(Pw1), len(Pw2), len(Pw3), len(Pw4)])
+        listP, numPweights = calc_weight_perc(weights['P'], weight_ids)
-        numSweights = np.sum([len(Sw0), len(Sw1), len(Sw2), len(Sw3), len(Sw4)])
+        listS, numSweights = calc_weight_perc(weights['S'], weight_ids)
-        if len(Pw0) > 0:
-            P0perc = 100 / numPweights * len(Pw0)
-        else:
-            P0perc = 0
-        if len(Pw1) > 0:
-            P1perc = 100 / numPweights * len(Pw1)
-        else:
-            P1perc = 0
-        if len(Pw2) > 0:
-            P2perc = 100 / numPweights * len(Pw2)
-        else:
-            P2perc = 0
-        if len(Pw3) > 0:
-            P3perc = 100 / numPweights * len(Pw3)
-        else:
-            P3perc = 0
-        if len(Pw4) > 0:
-            P4perc = 100 / numPweights * len(Pw4)
-        else:
-            P4perc = 0
-        if len(Sw0) > 0:
-            S0perc = 100 / numSweights * len(Sw0)
-        else:
-            S0perc = 0
-        if len(Sw1) > 0:
-            S1perc = 100 / numSweights * len(Sw1)
-        else:
-            S1perc = 0
-        if len(Sw2) > 0:
-            S2perc = 100 / numSweights * len(Sw2)
-        else:
-            S2perc = 0
-        if len(Sw3) > 0:
-            S3perc = 100 / numSweights * len(Sw3)
-        else:
-            S3perc = 0
-        if len(Sw4) > 0:
-            S4perc = 100 / numSweights * len(Sw4)
-        else:
-            S4perc = 0
 
-        weights = ('0', '1', '2', '3', '4')
+        y_pos = np.arange(len(weight_ids))
-        y_pos = np.arange(len(weights))
         width = 0.34
-        plt.bar(y_pos - width, [P0perc, P1perc, P2perc, P3perc, P4perc], width, color='black')
+        ax.bar(y_pos - width, listP, width, color='black')
-        plt.bar(y_pos, [S0perc, S1perc, S2perc, S3perc, S4perc], width, color='red')
+        ax.bar(y_pos, listS, width, color='red')
-        plt.ylabel('%')
+        ax.set_ylabel('%')
-        plt.xticks(y_pos, weights)
+        ax.set_xticks(y_pos, weight_ids)
-        plt.xlim([-0.5, 4.5])
+        ax.set_xlim([-0.5, 4.5])
-        plt.xlabel('Qualities')
+        ax.set_xlabel('Qualities')
-        plt.title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
+        ax.set_title('{0} P-Qualities, {1} S-Qualities'.format(numPweights, numSweights))
-        plt.show()
+
+        if not figure:
+            fig.show()
+
+        return listP, listS

pylot/core/loc/nll.py

@@ -82,8 +82,8 @@ def locate(fnin, parameter=None):
     :param fnin: external program name
     :return: None
     """
-    exe_path = which('NLLoc', parameter)
+    exe_path = os.path.join(parameter['nllocbin'], 'NLLoc')
-    if exe_path is None:
+    if not os.path.isfile(exe_path):
         raise NLLocError('NonLinLoc executable not found; check your '
                          'environment variables')
 

pylot/core/pick/autopick.py

@@ -20,9 +20,9 @@ from pylot.core.pick.charfuns import CharacteristicFunction
 from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
 from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
-    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class
+    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
 from pylot.core.util.utils import getPatternLine, gen_Pool, \
-    get_Bool, identifyPhaseID, get_None, correct_iplot
+    get_bool, identifyPhaseID, get_none, correct_iplot
 
 
 def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
@@ -232,20 +232,6 @@ class PickingContainer:
         self.Sflag = 0
 
 
-class MissingTraceException(ValueError):
-    """
-    Used to indicate missing traces in a obspy.core.stream.Stream object
-    """
-    pass
-
-
-class PickingFailedException(Exception):
-    """
-    Raised when picking fails due to missing values etc.
-    """
-    pass
-
-
 class AutopickStation(object):
 
     def __init__(self, wfstream, pickparam, verbose, iplot=0, fig_dict=None, metadata=None, origin=None):
@@ -272,7 +258,7 @@ class AutopickStation(object):
         self.pickparams = copy.deepcopy(pickparam)
         self.verbose = verbose
         self.iplot = correct_iplot(iplot)
-        self.fig_dict = get_None(fig_dict)
+        self.fig_dict = get_none(fig_dict)
         self.metadata = metadata
         self.origin = origin
 
@@ -429,7 +415,7 @@ class AutopickStation(object):
             if station_coords is None:
                 exit_taupy()
                 raise AttributeError('Warning: Could not find station in metadata')
-            # TODO raise when metadata.get_coordinates returns None
+            # TODO: raise when metadata.get_coordinates returns None
             source_origin = origin[0]
             model = TauPyModel(taup_model)
             taup_phases = self.pickparams['taup_phases']
@@ -471,11 +457,13 @@ class AutopickStation(object):
             """If taupy failed to calculate theoretical starttimes, picking continues.
             For this a clean exit is required, since the P starttime is no longer relative to the theoretic onset but
             to the vertical trace starttime, eg. it can't be < 0."""
-            if self.pickparams["pstart"] < 0:
             # TODO here the pickparams is modified, instead of a copy
+            if self.pickparams["pstart"] < 0:
                 self.pickparams["pstart"] = 0
+            if self.pickparams["sstart"] < 0:
+                self.pickparams["sstart"] = 0
 
-        if self.pickparams["use_taup"] is False:
+        if get_bool(self.pickparams["use_taup"]) is False:
             # correct user mistake where a relative cuttime is selected (pstart < 0) but use of taupy is disabled/ has
             # not the required parameters
             exit_taupy()
@@ -499,6 +487,20 @@ class AutopickStation(object):
         self.pickparams["pstart"] = max(self.pickparams["pstart"], 0)
         self.pickparams["pstop"] = min(self.pickparams["pstop"], len(self.ztrace) * self.ztrace.stats.delta)
 
+        if self.horizontal_traces_exist():
+            # for the two horizontal components take earliest and latest time to make sure that the s onset is not clipped
+            # if start and endtime of horizontal traces differ, the s windowsize will automatically increase
+            trace_s_start = min([self.etrace.stats.starttime, self.ntrace.stats.starttime])
+            # modifiy sstart and sstop relative to estimated first S arrival (relative to station time axis)
+            self.pickparams["sstart"] += (self.origin[0].time + estFirstS) - trace_s_start
+            self.pickparams["sstop"] += (self.origin[0].time + estFirstS) - trace_s_start
+            print('autopick: CF calculation times respectively:'
+                  ' sstart: {} s, sstop: {} s'.format(self.pickparams["sstart"], self.pickparams["sstop"]))
+            # make sure pstart and pstop are inside the starttime/endtime of horizontal traces
+            self.pickparams["sstart"] = max(self.pickparams["sstart"], 0)
+            self.pickparams["sstop"] = min(self.pickparams["sstop"], len(self.ntrace) * self.ntrace.stats.delta,
+                                           len(self.etrace) * self.etrace.stats.delta)
+
     def autopickstation(self):
         """
         Main function of autopickstation, which calculates P and S picks and returns them in a dictionary.
@@ -508,6 +510,17 @@ class AutopickStation(object):
         station's value is the station name on which the picks were calculated.
         :rtype: dict
         """
+
+        if get_bool(self.pickparams['use_taup']) is True and self.origin is not None:
+            try:
+                # modify pstart, pstop, sstart, sstop to be around theoretical onset if taupy should be used,
+                # else do nothing
+                self.modify_starttimes_taupy()
+            except AttributeError as ae:
+                print(ae)
+            except MissingTraceException as mte:
+                print(mte)
+
         try:
             self.pick_p_phase()
         except MissingTraceException as mte:
@@ -515,7 +528,9 @@ class AutopickStation(object):
         except PickingFailedException as pfe:
             print(pfe)
 
-        if self.horizontal_traces_exist() and self.p_results.weight is not None and self.p_results.weight < 4:
+        if self.horizontal_traces_exist():
+            if (self.p_results.weight is not None and self.p_results.weight < 4) or \
+                    get_bool(self.pickparams.get('use_taup')):
                 try:
                     self.pick_s_phase()
                 except MissingTraceException as mte:
@@ -631,7 +646,7 @@ class AutopickStation(object):
             ax1.set_ylim([-1.5, 1.5])
             ax1.set_ylabel('Normalized Counts')
 
-            if self.horizontal_traces_exist() and self.s_data.Sflag == 1:
+            if self.horizontal_traces_exist():# and self.s_data.Sflag == 1:
                 # plot E trace
                 ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
                 th1data = np.linspace(0, self.etrace.stats.endtime - self.etrace.stats.starttime,
@@ -661,13 +676,14 @@ class AutopickStation(object):
                         ax2.plot([self.s_results.lpp, self.s_results.lpp], [-1.1, 1.1], 'g--', label='lpp')
                         ax2.plot([self.s_results.epp, self.s_results.epp], [-1.1, 1.1], 'g--', label='epp')
                         title = '{channel}, S weight={sweight}, SNR={snr:7.2}, SNR[dB]={snrdb:7.2}'
-                        ax2.set_title(title.format(channel=self.etrace.stats.channel,
+                        ax2.set_title(title.format(channel=str(self.etrace.stats.channel),
-                                                   sweight=self.s_results.weight,
+                                                   sweight=str(self.s_results.weight),
-                                                   snr=self.s_results.snr,
+                                                   snr=str(self.s_results.snr),
-                                                   snrdb=self.s_results.snrdb))
+                                                   snrdb=str(self.s_results.snrdb)))
                     else:
                         title = '{channel}, S weight={sweight}, SNR=None, SNR[dB]=None'
-                        ax2.set_title(title.format(channel=self.etrace.stats.channel, sweight=self.s_results.weight))
+                        ax2.set_title(title.format(channel=str(self.etrace.stats.channel),
+                                                   sweight=str(self.s_results.weight)))
                 ax2.legend(loc=1)
                 ax2.set_yticks([])
                 ax2.set_ylim([-1.5, 1.5])
@@ -795,15 +811,6 @@ class AutopickStation(object):
         # save filtered trace in instance for later plotting
         self.tr_filt_z_bpz2 = tr_filt
 
-        if get_Bool(self.pickparams['use_taup']) is True and self.origin is not None:
-            try:
-                # modify pstart, pstop to be around theoretical onset if taupy should be used, else does nothing
-                self.modify_starttimes_taupy()
-            except AttributeError as ae:
-                print(ae)
-            except MissingTraceException as mte:
-                print(mte)
-
         Lc = self.pickparams['pstop'] - self.pickparams['pstart']
 
         Lwf = self.ztrace.stats.endtime - self.ztrace.stats.starttime
@@ -915,7 +922,7 @@ class AutopickStation(object):
             "minFMSNR"]:
             # if SNR is high enough, try to determine first motion of onset
             self.set_current_figure('fm_picker')
-            self.p_results.fm = fmpicker(self.zstream, z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
+            self.p_results.fm = fmpicker(self.zstream.copy(), z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
                                          self.iplot, self.current_figure, self.current_linecolor)
         msg = "autopickstation: P-weight: {}, SNR: {}, SNR[dB]: {}, Polarity: {}"
         msg = msg.format(self.p_results.weight, self.p_results.snr, self.p_results.snrdb, self.p_results.fm)
@@ -1127,7 +1134,9 @@ class AutopickStation(object):
                   ''.format(self.s_results.weight, self.s_results.snr, self.s_results.snrdb))
 
     def pick_s_phase(self):
-
+        if get_bool(self.pickparams.get('use_taup')) is True:
+            cuttimesh = (self.pickparams.get('sstart'), self.pickparams.get('sstop'))
+        else:
             # determine time window for calculating CF after P onset
             cuttimesh = self._calculate_cuttimes(type='S', iteration=1)
 

pylot/core/pick/charfuns.py

@@ -16,10 +16,11 @@ autoregressive prediction: application ot local and regional distances, Geophys.
 
 :author: MAGS2 EP3 working group
 """
-
 import numpy as np
-from obspy.core import Stream
 from scipy import signal
+from obspy.core import Stream
+
+from pylot.core.pick.utils import PickingFailedException
 
 
 class CharacteristicFunction(object):
@@ -259,7 +260,7 @@ class HOScf(CharacteristicFunction):
         """
         Function to calculate skewness (statistics of order 3) or kurtosis
         (statistics of order 4), using one long moving window, as published
-        in Kueperkoch et al. (2010).
+        in Kueperkoch et al. (2010), or order 2, i.e. STA/LTA.
         :param data: data, time series (whether seismogram or CF)
         :type data: tuple
         :return: HOS cf
@@ -276,28 +277,47 @@ class HOScf(CharacteristicFunction):
         elif self.getOrder() == 4:  # this is kurtosis
             y = np.power(xnp, 4)
             y1 = np.power(xnp, 2)
+        elif self.getOrder() == 2:  # this is variance, used for STA/LTA processing
+            y = np.power(xnp, 2)
+            y1 = np.power(xnp, 2)
 
         # Initialisation
         # t2: long term moving window
         ilta = int(round(self.getTime2() / self.getIncrement()))
+        ista = int(round((self.getTime2() / 10) / self.getIncrement()))  # TODO: still hard coded!!
         lta = y[0]
         lta1 = y1[0]
+        sta = y[0]
         # moving windows
         LTA = np.zeros(len(xnp))
+        STA = np.zeros(len(xnp))
         for j in range(0, len(xnp)):
             if j < 4:
                 LTA[j] = 0
+                STA[j] = 0
+            elif j <= ista and self.getOrder() == 2:
+                lta = (y[j] + lta * (j - 1)) / j
+                if self.getOrder() == 2:
+                    sta = (y[j] + sta * (j - 1)) / j
+            # elif j < 4:
             elif j <= ilta:
                 lta = (y[j] + lta * (j - 1)) / j
                 lta1 = (y1[j] + lta1 * (j - 1)) / j
+                if self.getOrder() == 2:
+                    sta = (y[j] - y[j - ista]) / ista + sta
             else:
                 lta = (y[j] - y[j - ilta]) / ilta + lta
                 lta1 = (y1[j] - y1[j - ilta]) / ilta + lta1
+                if self.getOrder() == 2:
+                    sta = (y[j] - y[j - ista]) / ista + sta
             # define LTA
             if self.getOrder() == 3:
                 LTA[j] = lta / np.power(lta1, 1.5)
             elif self.getOrder() == 4:
                 LTA[j] = lta / np.power(lta1, 2)
+            else:
+                LTA[j] = lta
+                STA[j] = sta
 
         # remove NaN's with first not-NaN-value,
         # so autopicker doesnt pick discontinuity at start of the trace
@@ -306,7 +326,10 @@ class HOScf(CharacteristicFunction):
             first = ind[0]
             LTA[:first] = LTA[first]
 
+        if self.getOrder() > 2:
             self.cf = LTA
+        else:  # order 2 means STA/LTA!
+            self.cf = STA / LTA
         self.xcf = x
 
 
@@ -467,6 +490,9 @@ class ARHcf(CharacteristicFunction):
         print('Calculating AR-prediction error from both horizontal traces ...')
 
         xnp = self.getDataArray(self.getCut())
+        if len(xnp[0]) == 0:
+            raise PickingFailedException('calcCF: Found empty data trace for cut times. Return')
+
         n0 = np.isnan(xnp[0].data)
         if len(n0) > 1:
             xnp[0].data[n0] = 0

pylot/core/pick/picker.py

@@ -178,7 +178,9 @@ class AICPicker(AutoPicker):
         aic = tap * self.cf + max(abs(self.cf))
         # smooth AIC-CF
         ismooth = int(round(self.Tsmooth / self.dt))
-        aicsmooth = np.zeros(len(aic))
+        # MP MP better start with original data than zeros if array shall be smoothed, created artificial value before
+        # when starting with i in range(1...) loop below and subtracting offset afterwards
+        aicsmooth = np.copy(aic)
         if len(aic) < ismooth:
             print('AICPicker: Tsmooth larger than CF!')
             return
@@ -188,7 +190,7 @@ class AICPicker(AutoPicker):
                     ii1 = i - ismooth
                     aicsmooth[i] = aicsmooth[i - 1] + (aic[i] - aic[ii1]) / ismooth
                 else:
-                    aicsmooth[i] = np.mean(aic[1: i])
+                    aicsmooth[i] = np.mean(aic[0: i]) # MP MP created np.nan for i=1
         # remove offset in AIC function
         offset = abs(min(aic) - min(aicsmooth))
         aicsmooth = aicsmooth - offset
@@ -197,7 +199,7 @@ class AICPicker(AutoPicker):
         # minimum in AIC function 
         icfmax = np.argmax(cf)
 
-        # MP MP testing threshold
+        # TODO: If this shall be kept, maybe add thresh_factor to pylot parameters
         thresh_hit = False
         thresh_factor = 0.7
         thresh = thresh_factor * cf[icfmax]
@@ -209,7 +211,6 @@ class AICPicker(AutoPicker):
                 if sample <= cf[index - 1]:
                     icfmax = index - 1
                     break
-        # MP MP ---
 
         # find minimum in AIC-CF front of maximum of HOS/AR-CF
         lpickwindow = int(round(self.PickWindow / self.dt))
@@ -336,7 +337,7 @@ class AICPicker(AutoPicker):
                     self.slope = 1 / (len(dataslope) * self.Data[0].stats.delta) * (datafit[-1] - datafit[0])
                     # normalize slope to maximum of cf to make it unit independent
                     self.slope /= aicsmooth[iaicmax]
-            except ValueError as e:
+            except Exception as e:
                 print("AICPicker: Problems with data fitting! {}".format(e))
 
         else:

pylot/core/pick/utils.py

@@ -15,7 +15,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 from scipy.signal import argrelmax
 
-from pylot.core.util.utils import get_Bool, get_None, SetChannelComponents
+from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -62,8 +62,8 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
     plt_flag = 0
     try:
         iplot = int(iplot)
-    except:
+    except ValueError:
-        if get_Bool(iplot):
+        if get_bool(iplot):
             iplot = 2
         else:
             iplot = 0
@@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
     PickError = symmetrize_error(diffti_te, diffti_tl)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -344,7 +344,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
         print("fmpicker: Found polarity %s" % FM)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -816,7 +816,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
     try:
         iplot = int(iplot)
     except:
-        if get_Bool(iplot):
+        if get_bool(iplot):
             iplot = 2
         else:
             iplot = 0
@@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
             returnflag = 0
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -890,6 +890,8 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
                 input()
             except SyntaxError:
                 pass
+            except EOFError:
+                pass
             plt.close(fig)
 
     return returnflag
@@ -1130,7 +1132,7 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
     try:
         iplot = int(iplot)
     except:
-        if get_Bool(iplot):
+        if get_bool(iplot):
             iplot = 2
         else:
             iplot = 0
@@ -1211,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
             t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
                             trace.stats.npts)
             if i == 0:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax1 = fig.add_subplot(3, 1, i + 1)
                 ax = ax1
                 ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
             else:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
@@ -1320,7 +1322,7 @@ def get_quality_class(uncertainty, weight_classes):
     :return: quality of pick (0-4)
     :rtype: int
     """
-    if not uncertainty: return max(weight_classes)
+    if not uncertainty: return len(weight_classes)
     try:
         # create generator expression containing all indices of values in weight classes that are >= than uncertainty.
         # call next on it once to receive first value
@@ -1332,22 +1334,6 @@ def get_quality_class(uncertainty, weight_classes):
     return quality
 
 
-def set_NaNs_to(data, nan_value):
-    """
-    Replace all NaNs in data with nan_value
-    :param data: array holding data
-    :type data: `~numpy.ndarray`
-    :param nan_value: value which all NaNs are set to
-    :type nan_value: float, int
-    :return: data array with all NaNs replaced with nan_value
-    :rtype: `~numpy.ndarray`
-    """
-    nn = np.isnan(data)
-    if np.any(nn):
-        data[nn] = nan_value
-    return data
-
-
 def taper_cf(cf):
     """
     Taper cf data to get rid off of side maximas
@@ -1499,7 +1485,7 @@ def get_pickparams(pickparam):
     first_motion_params = dict(zip(first_motion_names, fm_parameter_values))
     signal_length_params = dict(zip(signal_length_names, sl_parameter_values))
 
-    p_params['use_taup'] = get_Bool(p_params['use_taup'])
+    p_params['use_taup'] = get_bool(p_params['use_taup'])
 
     return p_params, s_params, first_motion_params, signal_length_params
 
@@ -1508,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
     # set initial quality to 4 (worst) and change only if one condition is hit
     quality = 4
 
-    if get_None(uncertainty) is None:
+    if get_none(uncertainty) is None:
         return quality
 
     if uncertainty <= Errors[0]:
@@ -1532,3 +1518,17 @@ if __name__ == '__main__':
     import doctest
 
     doctest.testmod()
+
+
+class PickingFailedException(Exception):
+    """
+    Raised when picking fails due to missing values etc.
+    """
+    pass
+
+
+class MissingTraceException(ValueError):
+    """
+    Used to indicate missing traces in a obspy.core.stream.Stream object
+    """
+    pass

pylot/core/util/array_map.py

@@ -13,6 +13,7 @@ import obspy
 from PySide2 import QtWidgets
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+from pylot.core.util.utils import identifyPhaseID
 from scipy.interpolate import griddata
 
 from pylot.core.pick.utils import get_quality_class
@@ -75,7 +76,6 @@ class Array_map(QtWidgets.QWidget):
 
         self._style = None if not hasattr(parent, '_style') else parent._style
 
-        self.show()
 
     def init_map(self):
         self.init_colormap()
@@ -124,8 +124,8 @@ class Array_map(QtWidgets.QWidget):
         self.cmaps_box = QtWidgets.QComboBox()
         self.cmaps_box.setMaxVisibleItems(20)
         [self.cmaps_box.addItem(map_name) for map_name in sorted(plt.colormaps())]
-        # try to set to hsv as default
+        # try to set to viridis as default
-        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('hsv'))
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('viridis'))
 
         self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
@@ -280,9 +280,12 @@ class Array_map(QtWidgets.QWidget):
         self.canvas.axes.figure.canvas.draw_idle()
 
     def onpick(self, event):
+        btn_msg = {1: ' in selection. Aborted', 2: ' to delete a pick on. Aborted', 3: ' to display info.'}
         ind = event.ind
         button = event.mouseevent.button
-        if ind == []:
+        msg_reason = None
+        if len(ind) > 1:
+            self._parent.update_status(f'Found more than one station {btn_msg.get(button)}')
             return
         if button == 1:
             self.openPickDlg(ind)
@@ -385,7 +388,14 @@ class Array_map(QtWidgets.QWidget):
                 try:
                     station_name = st_id.split('.')[-1]
                     # current_picks_dict: auto or manual
-                    pick = self.current_picks_dict()[station_name][phase]
+                    station_picks = self.current_picks_dict().get(station_name)
+                    if not station_picks:
+                        continue
+                    for phase_hint, pick in station_picks.items():
+                        if identifyPhaseID(phase_hint) == phase:
+                            break
+                    else:
+                        continue
                     if pick['picker'] == 'auto':
                         if not pick['spe']:
                             continue
@@ -464,20 +474,23 @@ class Array_map(QtWidgets.QWidget):
                                                                   transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        data = self._parent.get_data().getWFData()
+        wfdata = self._parent.get_data().getWFData()
+        wfdata_comp = self._parent.get_data().getWFDataComp()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
             pyl_mw = self._parent
             try:
-                data = data.select(station=station)
+                wfdata = wfdata.select(station=station)
-                if not data:
+                wfdata_comp = wfdata_comp.select(station=station)
+                if not wfdata:
                     self._warn('No data for station {}'.format(station))
                     return
                 pickDlg = PickDlg(self._parent, parameter=self.parameter,
-                                  data=data, network=network, station=station,
+                                  data=wfdata.copy(), data_compare=wfdata_comp.copy(), network=network, station=station,
                                   picks=self._parent.get_current_event().getPick(station),
                                   autopicks=self._parent.get_current_event().getAutopick(station),
                                   filteroptions=self._parent.filteroptions, metadata=self.metadata,
+                                  model=self.parameter.get('taup_model'),
                                   event=pyl_mw.get_current_event())
             except Exception as e:
                 message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)

pylot/core/util/dataprocessing.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import glob
+import logging
 import os
 import sys
 
@@ -189,7 +190,11 @@ class Metadata(object):
         metadata = self.get_metadata(seed_id, time)
         if not metadata:
             return
+        try:
             return metadata['data'].get_coordinates(seed_id, time)
+        # no specific exception defined in obspy inventory
+        except Exception as e:
+            logging.warning(f'Could not get metadata for {seed_id}')
 
     def get_all_coordinates(self):
         def stat_info_from_parser(parser):
@@ -271,7 +276,7 @@ class Metadata(object):
                     continue
             invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
             try:
-                robj.get_coordinates(station_seed_id)
+                # robj.get_coordinates(station_seed_id)  # TODO: Commented out, failed with Parser, is this needed?
                 self.inventory_files[fname] = {'invtype': invtype,
                                                'data': robj}
                 if station_seed_id in self.seed_ids.keys():

pylot/core/util/defaults.py

@@ -26,9 +26,7 @@ elif system_name == "Windows":
 # suffix for phase name if not phase identified by last letter (P, p, etc.)
 ALTSUFFIX = ['diff', 'n', 'g', '1', '2', '3']
 
-FILTERDEFAULTS = readDefaultFilterInformation(os.path.join(os.path.expanduser('~'),
+FILTERDEFAULTS = readDefaultFilterInformation()
-                                                           '.pylot',
-                                                           'pylot.in'))
 
 TIMEERROR_DEFAULTS = os.path.join(os.path.expanduser('~'),
                                   '.pylot',

pylot/core/util/generate_array_maps.py

@@ -42,7 +42,7 @@ def main(project_file_path, manual=False, auto=True, file_format='png', f_ext=''
         for item in input_list:
             array_map_worker(item)
     else:
-        pool = multiprocessing.Pool(ncores)
+        pool = multiprocessing.Pool(ncores, maxtasksperchild=1000)
         pool.map(array_map_worker, input_list)
         pool.close()
         pool.join()

pylot/core/util/gui.py

@@ -56,7 +56,7 @@ def which(program, parameter):
         nllocpath = ":" + parameter.get('nllocbin')
         os.environ['PATH'] += nllocpath
     except Exception as e:
-        print(e.message)
+        print(e)
 
     def is_exe(fpath):
         return os.path.exists(fpath) and os.access(fpath, os.X_OK)

pylot/core/util/thread.py

@@ -22,9 +22,11 @@ class Thread(QThread):
         self.abortButton = abortButton
         self.finished.connect(self.hideProgressbar)
         self.showProgressbar()
+        self.old_stdout = None
 
     def run(self):
         if self.redirect_stdout:
+            self.old_stdout = sys.stdout
             sys.stdout = self
         try:
             if self.arg is not None:
@@ -39,7 +41,8 @@ class Thread(QThread):
             exctype, value = sys.exc_info()[:2]
             self._executedErrorInfo = '{} {} {}'. \
                 format(exctype, value, traceback.format_exc())
-        sys.stdout = sys.__stdout__
+        if self.redirect_stdout:
+            sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:
@@ -96,10 +99,12 @@ class Worker(QRunnable):
         self.progressText = progressText
         self.pb_widget = pb_widget
         self.redirect_stdout = redirect_stdout
+        self.old_stdout = None
 
     @Slot()
     def run(self):
         if self.redirect_stdout:
+            self.old_stdout = sys.stdout
             sys.stdout = self
 
         try:
@@ -112,7 +117,7 @@ class Worker(QRunnable):
             self.signals.result.emit(result)
         finally:
             self.signals.finished.emit('Done')
-        sys.stdout = sys.__stdout__
+        sys.stdout = self.old_stdout
 
     def write(self, text):
         self.signals.message.emit(text)
@@ -144,16 +149,18 @@ class MultiThread(QThread):
         self.progressText = progressText
         self.pb_widget = pb_widget
         self.redirect_stdout = redirect_stdout
+        self.old_stdout = None
         self.finished.connect(self.hideProgressbar)
         self.showProgressbar()
 
     def run(self):
         if self.redirect_stdout:
+            self.old_stdout = sys.stdout
             sys.stdout = self
         try:
             if not self.ncores:
                 self.ncores = multiprocessing.cpu_count()
-            pool = multiprocessing.Pool(self.ncores)
+            pool = multiprocessing.Pool(self.ncores, maxtasksperchild=1000)
             self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
             # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
             pool.close()
@@ -164,7 +171,7 @@ class MultiThread(QThread):
             exc_type, exc_obj, exc_tb = sys.exc_info()
             fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
             print('Exception: {}, file: {}, line: {}'.format(exc_type, fname, exc_tb.tb_lineno))
-        sys.stdout = sys.__stdout__
+        sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:

pylot/core/util/utils.py

@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
+import glob
 import hashlib
+import logging
 import os
 import platform
 import re
 import subprocess
 import warnings
+from typing import Literal, Tuple, Type
+from functools import lru_cache
 
 import numpy as np
 from obspy import UTCDateTime, read
@@ -18,6 +21,10 @@ from pylot.core.io.inputs import PylotParameter, FilterOptions
 from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
 from pylot.styles import style_settings
 
+Rgba: Type[tuple] = Tuple[int, int, int, int]
+Mplrgba: Type[tuple] = Tuple[float, float, float, float]
+Mplrgbastr: Type[tuple] = Tuple[str, str, str, str]
+
 
 def _pickle_method(m):
     if m.im_self is None:
@@ -37,15 +44,14 @@ def getAutoFilteroptions(phase, parameter):
     return filteroptions
 
 
-def readDefaultFilterInformation(fname):
+def readDefaultFilterInformation():
     """
     Read default filter information from pylot.in file
-    :param fname: path to pylot.in file
-    :type fname: str
     :return: dictionary containing the defailt filter information
     :rtype: dict
     """
-    pparam = PylotParameter(fname)
+    pparam = PylotParameter()
+    pparam.reset_defaults()
     return readFilterInformation(pparam)
 
 
@@ -82,25 +88,6 @@ def fit_curve(x, y):
     return splev, splrep(x, y)
 
 
-def getindexbounds(f, eta):
-    """
-    Get indices of values closest below and above maximum value in an array
-    :param f: array
-    :type f: `~numpy.ndarray`
-    :param eta: look for value in array that is closes to max_value * eta
-    :type eta: float
-    :return: tuple containing index of max value, index of value closest below max value,
-     index of value closest above max value
-    :rtype: (int, int, int)
-    """
-    mi = f.argmax()  # get indices of max values
-    m = max(f)  # get maximum value
-    b = m * eta  #
-    l = find_nearest(f[:mi], b)  # find closest value below max value
-    u = find_nearest(f[mi:], b) + mi  # find closest value above max value
-    return mi, l, u
-
-
 def gen_Pool(ncores=0):
     """
     Generate mulitprocessing pool object utilizing ncores amount of cores
@@ -120,7 +107,7 @@ def gen_Pool(ncores=0):
 
     print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
 
-    pool = multiprocessing.Pool(ncores)
+    pool = multiprocessing.Pool(ncores, maxtasksperchild=100)
     return pool
 
 
@@ -166,11 +153,11 @@ def clims(lim1, lim2):
     """
     takes two pairs of limits and returns one pair of common limts
     :param lim1: limit 1
-    :type lim1: int
+    :type lim1: List[int]
     :param lim2: limit 2
-    :type lim2: int
+    :type lim2: List[int]
     :return: new upper and lower limit common to both given limits
-    :rtype: [int, int]
+    :rtype: List[int]
 
     >>> clims([0, 4], [1, 3])
     [0, 4]
@@ -302,7 +289,7 @@ def fnConstructor(s):
     if type(s) is str:
         s = s.split(':')[-1]
     else:
-        s = getHash(UTCDateTime())
+        s = get_hash(UTCDateTime())
 
     badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
     badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
@@ -314,32 +301,75 @@ def fnConstructor(s):
     return fn
 
 
-def get_None(value):
+def get_none(value):
     """
     Convert "None" to None
     :param value:
-    :type value: str, bool
+    :type value: str, NoneType
     :return:
-    :rtype: bool
+    :rtype: type(value) or NoneType
+
+    >>> st = read()
+    >>> print(get_none(st))
+    3 Trace(s) in Stream:
+    BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    >>> get_none('Stream')
+    'Stream'
+    >>> get_none(0)
+    0
+    >>> get_none(0.)
+    0.0
+    >>> print(get_none('None'))
+    None
+    >>> print(get_none(None))
+    None
     """
-    if value == 'None':
+    if value is None or (type(value) is str and value == 'None'):
         return None
     else:
         return value
 
 
-def get_Bool(value):
+def get_bool(value):
     """
-    Convert string representations of bools to their true boolean value
+    Convert string representations of bools to their true boolean value. Return value if it cannot be identified as bool.
     :param value:
-    :type value: str, bool
+    :type value: str, bool, int, float
     :return: true boolean value
     :rtype: bool
+
+    >>> get_bool(True)
+    True
+    >>> get_bool(False)
+    False
+    >>> get_bool(0)
+    False
+    >>> get_bool(0.)
+    False
+    >>> get_bool(0.1)
+    True
+    >>> get_bool(2)
+    True
+    >>> get_bool(-1)
+    False
+    >>> get_bool(-0.3)
+    False
+    >>> get_bool(None)
+    None
     """
-    if value in ['True', 'true']:
+    if type(value) is bool:
+        return value
+    elif value in ['True', 'true']:
         return True
     elif value in ['False', 'false']:
         return False
+    elif isinstance(value, float) or isinstance(value, int):
+        if value > 0. or value > 0:
+            return True
+        else:
+            return False
     else:
         return value
 
@@ -353,8 +383,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
+    >>> four_digits(75)
-    1920
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -436,36 +466,53 @@ def backtransformFilterString(st):
     return st
 
 
-def getHash(time):
+def get_hash(time):
     """
     takes a time object and returns the corresponding SHA1 hash of the formatted date string
     :param time: time object for which a hash should be calculated
     :type time: `~obspy.core.utcdatetime.UTCDateTime`
     :return: SHA1 hash
     :rtype: str
+
+    >>> time = UTCDateTime(0)
+    >>> get_hash(time)
+    '7627cce3b1b58dd21b005dac008b34d18317dd15'
+    >>> get_hash(0)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'time' is not an ObsPy UTCDateTime object
     """
+    assert isinstance(time, UTCDateTime), '\'time\' is not an ObsPy UTCDateTime object'
     hg = hashlib.sha1()
-    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f').encode('utf-8'))
     return hg.hexdigest()
 
 
-def getLogin():
+def get_login():
     """
-    returns the actual user's login ID
+    returns the actual user's name
-    :return: login ID
+    :return: login name
     :rtype: str
     """
     import getpass
     return getpass.getuser()
 
 
-def getOwner(fn):
+def get_owner(fn):
     """
     takes a filename and return the login ID of the actual owner of the file
     :param fn: filename of the file tested
     :type fn: str
     :return: login ID of the file's owner
     :rtype: str
+
+    >>> import tempfile
+    >>> with tempfile.NamedTemporaryFile() as tmpfile:
+    ...     tmpfile.write(b'') and True
+    ...     tmpfile.flush()
+    ...     get_owner(tmpfile.name) == os.path.expanduser('~').split('/')[-1]
+    0
+    True
     """
     system_name = platform.system()
     if system_name in ["Linux", "Darwin"]:
@@ -511,6 +558,11 @@ def is_executable(fn):
     :param fn: path to the file to be tested
     :return: True or False
     :rtype: bool
+
+    >>> is_executable('/bin/ls')
+    True
+    >>> is_executable('/var/log/system.log')
+    False
     """
     return os.path.isfile(fn) and os.access(fn, os.X_OK)
 
@@ -537,24 +589,36 @@ def isSorted(iterable):
     >>> isSorted([2,3,1,4])
     False
     """
-    assert isIterable(iterable), 'object is not iterable; object: {' \
+    assert is_iterable(iterable), "object is not iterable; object: {}".format(iterable)
-                                 '}'.format(iterable)
     if type(iterable) is str:
         iterable = [s for s in iterable]
     return sorted(iterable) == iterable
 
 
-def isIterable(obj):
+def is_iterable(obj):
     """
     takes a python object and returns True is the object is iterable and
     False otherwise
     :param obj: a python object
-    :type obj: object
+    :type obj: obj
     :return: True of False
     :rtype: bool
+
+    >>> is_iterable(1)
+    False
+    >>> is_iterable(True)
+    False
+    >>> is_iterable(0.)
+    False
+    >>> is_iterable((0,1,3,4))
+    True
+    >>> is_iterable([1])
+    True
+    >>> is_iterable('a')
+    True
     """
     try:
-        iterator = iter(obj)
+        iter(obj)
     except TypeError as te:
         return False
     return True
@@ -563,13 +627,19 @@ def isIterable(obj):
 def key_for_set_value(d):
     """
     takes a dictionary and returns the first key for which's value the
-    boolean is True
+    boolean representation is True
     :param d: dictionary containing values
     :type d: dict
     :return: key to the first non-False value found; None if no value's
     boolean equals True
-    :rtype:
+    :rtype: bool or NoneType
+
+    >>> key_for_set_value({'one': 0, 'two': 1})
+    'two'
+    >>> print(key_for_set_value({1: 0, 2: False}))
+    None
     """
+    assert type(d) is dict, "Function only defined for inputs of type 'dict'."
     r = None
     for k, v in d.items():
         if v:
@@ -577,32 +647,53 @@ def key_for_set_value(d):
     return r
 
 
-def prepTimeAxis(stime, trace, verbosity=0):
+def prep_time_axis(offset, trace, verbosity=0):
     """
-    takes a starttime and a trace object and returns a valid time axis for
+    takes an offset and a trace object and returns a valid time axis for
     plotting
-    :param stime: start time of the actual seismogram as UTCDateTime
+    :param offset: offset of the actual seismogram on plotting axis
-    :type stime: `~obspy.core.utcdatetime.UTCDateTime`
+    :type offset: float or int
     :param trace: seismic trace object
     :type trace: `~obspy.core.trace.Trace`
     :param verbosity: if != 0, debug output will be written to console
     :type verbosity: int
     :return: valid numpy array with time stamps for plotting
     :rtype: `~numpy.ndarray`
+
+    >>> tr = read()[0]
+    >>> prep_time_axis(0., tr)
+    array([0.00000000e+00, 1.00033344e-02, 2.00066689e-02, ...,
+           2.99799933e+01, 2.99899967e+01, 3.00000000e+01])
+    >>> prep_time_axis(22.5, tr)
+    array([22.5       , 22.51000333, 22.52000667, ..., 52.47999333,
+           52.48999667, 52.5       ])
+    >>> prep_time_axis(tr.stats.starttime, tr)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'offset' is not of type 'float' or 'int'; type: <class 'obspy.core.utcdatetime.UTCDateTime'>
+    >>> tr.stats.npts -= 1
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033356e-02, 2.00066711e-02, ...,
+           2.99699933e+01, 2.99799967e+01, 2.99900000e+01])
+    >>> tr.stats.npts += 2
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033333e-02, 2.00066667e-02, ...,
+           2.99899933e+01, 2.99999967e+01, 3.00100000e+01])
     """
+    assert isinstance(offset, (float, int)), "'offset' is not of type 'float' or 'int'; type: {}".format(type(offset))
     nsamp = trace.stats.npts
     srate = trace.stats.sampling_rate
     tincr = trace.stats.delta
-    etime = stime + nsamp / srate
+    etime = offset + nsamp / srate
-    time_ax = np.linspace(stime, etime, nsamp)
+    time_ax = np.linspace(offset, etime, nsamp)
     if len(time_ax) < nsamp:
         if verbosity:
             print('elongate time axes by one datum')
-        time_ax = np.arange(stime, etime + tincr, tincr)
+        time_ax = np.arange(offset, etime + tincr, tincr)
     elif len(time_ax) > nsamp:
         if verbosity:
             print('shorten time axes by one datum')
-        time_ax = np.arange(stime, etime - tincr, tincr)
+        time_ax = np.arange(offset, etime - tincr, tincr)
     if len(time_ax) != nsamp:
         print('Station {0}, {1} samples of data \n '
               '{2} length of time vector \n'
@@ -618,13 +709,13 @@ def find_horizontals(data):
     :param data: waveform data
     :type data: `obspy.core.stream.Stream`
     :return: components list
-    :rtype: list
+    :rtype: List(str)
 
     ..example::
 
     >>> st = read()
     >>> find_horizontals(st)
-    [u'N', u'E']
+    ['N', 'E']
     """
     rval = []
     for tr in data:
@@ -635,7 +726,7 @@ def find_horizontals(data):
     return rval
 
 
-def pick_color(picktype, phase, quality=0):
+def pick_color(picktype: Literal['manual', 'automatic'], phase: Literal['P', 'S'], quality: int = 0) -> Rgba:
     """
     Create pick color by modifying the base color by the quality.
 
@@ -648,7 +739,7 @@ def pick_color(picktype, phase, quality=0):
     :param quality: quality of pick. Decides the new intensity of the modifier color
     :type quality: int
     :return: tuple containing modified rgba color values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     min_quality = 3
     bpc = base_phase_colors(picktype, phase)  # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
@@ -704,17 +795,17 @@ def pick_linestyle_plt(picktype, key):
     return linestyles[picktype][key]
 
 
-def modify_rgba(rgba, modifier, intensity):
+def modify_rgba(rgba: Rgba, modifier: Literal['r', 'g', 'b'], intensity: float) -> Rgba:
     """
     Modify rgba color by adding the given intensity to the modifier color
     :param rgba: tuple containing rgba values
-    :type rgba: (int, int, int, int)
+    :type rgba: Rgba
-    :param modifier: which color should be modified, eg. 'r', 'g', 'b'
+    :param modifier: which color should be modified; options: 'r', 'g', 'b'
-    :type modifier: str
+    :type modifier: Literal['r', 'g', 'b']
     :param intensity: intensity to be added to selected color
     :type intensity: float
     :return: tuple containing rgba values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     rgba = list(rgba)
     index = {'r': 0,
@@ -748,18 +839,20 @@ def transform_colors_mpl_str(colors, no_alpha=False):
     Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
     :param colors: tuple of rgba color values ranging from [0, 255]
     :type colors: (float, float, float, float)
-    :param no_alpha: Wether to return a alpha value in the matplotlib color string
+    :param no_alpha: Whether to return an alpha value in the matplotlib color string
     :type no_alpha: bool
     :return: String containing r, g, b values and alpha value if no_alpha is False (default)
     :rtype: str
+
+    >>> transform_colors_mpl_str((255., 255., 255., 255.), True)
+    '(1.0, 1.0, 1.0)'
+    >>> transform_colors_mpl_str((255., 255., 255., 255.))
+    '(1.0, 1.0, 1.0, 1.0)'
     """
-    colors = list(colors)
-    colors_mpl = tuple([color / 255. for color in colors])
     if no_alpha:
-        colors_mpl = '({}, {}, {})'.format(*colors_mpl)
+        return '({}, {}, {})'.format(*transform_colors_mpl(colors))
     else:
-        colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
+        return '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
-    return colors_mpl
 
 
 def transform_colors_mpl(colors):
@@ -769,27 +862,16 @@ def transform_colors_mpl(colors):
     :type colors: (float, float, float, float)
     :return: tuple of rgba color values ranging from [0, 1]
     :rtype: (float, float, float, float)
+
+    >>> transform_colors_mpl((127.5, 0., 63.75, 255.))
+    (0.5, 0.0, 0.25, 1.0)
+    >>> transform_colors_mpl(())
     """
     colors = list(colors)
     colors_mpl = tuple([color / 255. for color in colors])
     return colors_mpl
 
 
-def remove_underscores(data):
-    """
-    takes a `obspy.core.stream.Stream` object and removes all underscores
-    from station names
-    :param data: stream of seismic data
-    :type data: `~obspy.core.stream.Stream`
-    :return: data stream
-    :rtype: `~obspy.core.stream.Stream`
-    """
-    # for tr in data:
-    #    # remove underscores
-    #    tr.stats.station = tr.stats.station.strip('_')
-    return data
-
-
 def trim_station_components(data, trim_start=True, trim_end=True):
     """
     cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
@@ -818,19 +900,6 @@ def trim_station_components(data, trim_start=True, trim_end=True):
     return data
 
 
-def merge_stream(stream):
-    gaps = stream.get_gaps()
-    if gaps:
-        # list of merged stations (seed_ids)
-        merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
-        stream.merge(method=1)
-        print('Merged the following stations because of gaps:')
-        for merged_station in merged:
-            print(merged_station)
-
-    return stream, gaps
-
-
 def check4gapsAndRemove(data):
     """
     check for gaps in Stream and remove them
@@ -851,12 +920,12 @@ def check4gapsAndRemove(data):
     return data
 
 
-def check4gapsAndMerge(data):
+def check_for_gaps_and_merge(data):
     """
     check for gaps in Stream and merge if gaps are found
     :param data: stream of seismic data
     :type data: `~obspy.core.stream.Stream`
-    :return: data stream
+    :return: data stream, gaps returned from obspy get_gaps
     :rtype: `~obspy.core.stream.Stream`
     """
     gaps = data.get_gaps()
@@ -867,7 +936,7 @@ def check4gapsAndMerge(data):
         for merged_station in merged:
             print(merged_station)
 
-    return data
+    return data, gaps
 
 
 def check4doubled(data):
@@ -897,13 +966,53 @@ def check4doubled(data):
     return data
 
 
+def check_for_nan(data, nan_value=0.):
+    """
+    Replace all NaNs in data with nan_value (in place)
+    :param data: stream of seismic data
+    :type data: `~obspy.core.stream.Stream`
+    :param nan_value: value which all NaNs are set to
+    :type nan_value: float, int
+    :return: None
+    """
+    if not data:
+        return
+    for trace in data:
+        np.nan_to_num(trace.data, copy=False, nan=nan_value)
+
+
+def get_pylot_eventfile_with_extension(event, fext):
+    if hasattr(event, 'path'):
+        eventpath = event.path
+    else:
+        logging.warning('No attribute path found for event.')
+        return
+    eventname = event.pylot_id #path.split('/')[-1]  # or event.pylot_id
+    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
+    if os.path.isfile(filename):
+        return filename
+
+
+def get_possible_pylot_eventfile_extensions(event, fext):
+    if hasattr(event, 'path'):
+        eventpath = event.path
+    else:
+        logging.warning('No attribute path found for event.')
+        return []
+    eventname = event.pylot_id
+    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
+    filenames = glob.glob(filename)
+    extensions = [os.path.split(path)[-1].split('PyLoT_' + eventname)[-1] for path in filenames]
+    return extensions
+
+
 def get_stations(data):
     """
-    Get list of all station names in data stream
+    Get list of all station names in data-stream
     :param data: stream containing seismic traces
     :type data: `~obspy.core.stream.Stream`
     :return: list of all station names in data, no duplicates
-    :rtype: list of str
+    :rtype: List(str)
     """
     stations = []
     for tr in data:
@@ -930,66 +1039,87 @@ def check4rotated(data, metadata=None, verbosity=1):
     :rtype: `~obspy.core.stream.Stream`
     """
 
-    def rotate_components(wfstream, metadata=None):
+    def rotation_required(trace_ids):
+        """
+        Derive if any rotation is required from the orientation code of the input.
+
+        :param trace_ids: string identifier of waveform data trace
+        :type trace_ids: List(str)
+        :return: boolean representing if rotation is necessary for any of the traces
+        :rtype: bool
+        """
+        orientations = [trace_id[-1] for trace_id in trace_ids]
+        return any([orientation.isnumeric() for orientation in orientations])
+
+    def rotate_components(wfs_in, metadata=None):
         """
         Rotate components if orientation code is numeric (= non traditional orientation).
 
         Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
         Returns unrotated traces of no metadata is provided
-        :param wfstream: stream containing seismic traces of a station
+        :param wfs_in: stream containing seismic traces of a station
-        :type wfstream: `~obspy.core.stream.Stream`
+        :type wfs_in: `~obspy.core.stream.Stream`
         :param metadata: tuple containing metadata type string and metadata parser object
         :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
         :return: stream object with traditionally oriented traces (ZNE)
         :rtype: `~obspy.core.stream.Stream`
         """
 
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
+
         # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
+        trace_ids = [trace.id for trace in wfs_in]
-        orientations = [trace_id[-1] for trace_id in trace_ids]
+        if not rotation_required(trace_ids):
-        rotation_required = [orientation.isnumeric() for orientation in orientations]
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
-        if any(rotation_required):
+            return wfs_in
-            t_start = full_range(wfstream)
+
+        # check metadata quality
+        t_start = full_range(wfs_in)
         try:
-                azimuts = []
+            azimuths = []
             dips = []
             for tr_id in trace_ids:
-                    azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
                 dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
-            except (KeyError, TypeError) as e:
+        except (KeyError, TypeError) as err:
-                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
+            logging.error(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
-                return wfstream
+                  f"available in metadata. Stream remains unchanged.")
-            if len(wfstream) < 3:
+            return wfs_in
-                print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
+        except Exception as err:
-                return wfstream
+            print(f"Unexpected {err=}, {type(err)=}")
+            raise
+
         # to rotate all traces must have same length, so trim them
-            wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
+        wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
         try:
-                z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
+            z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
-                                     wfstream[1], azimuts[1], dips[1],
+                                 wfs_out[1], azimuths[1], dips[1],
-                                     wfstream[2], azimuts[2], dips[2])
+                                 wfs_out[2], azimuths[2], dips[2])
             print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
             # replace old data with rotated data, change the channel code to ZNE
             z_index = dips.index(min(
-                    dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
+                dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90
-                wfstream[z_index].data = z
+            # being vertical)
-                wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
+            wfs_out[z_index].data = z
+            wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
             del trace_ids[z_index]
             for trace_id in trace_ids:
                 coordinates = metadata.get_coordinates(trace_id, t_start)
                 dip, az = coordinates['dip'], coordinates['azimuth']
-                    trace = wfstream.select(id=trace_id)[0]
+                trace = wfs_out.select(id=trace_id)[0]
-                    if az > 315 or az <= 45 or az > 135 and az <= 225:
+                if az > 315 or az <= 45 or 135 < az <= 225:
                     trace.data = n
                     trace.stats.channel = trace.stats.channel[0:-1] + 'N'
-                    elif az > 45 and az <= 135 or az > 225 and az <= 315:
+                elif 45 < az <= 135 or 225 < az <= 315:
                     trace.data = e
                     trace.stats.channel = trace.stats.channel[0:-1] + 'E'
-            except (ValueError) as e:
+        except ValueError as err:
-                print(e)
+            print(f"{err=} Rotation failed. Stream remains unchanged.")
-                return wfstream
+            return wfs_in
 
-        return wfstream
+        return wfs_out
 
     if metadata is None:
         if verbosity:
@@ -1003,38 +1133,6 @@ def check4rotated(data, metadata=None, verbosity=1):
     return data
 
 
-def scaleWFData(data, factor=None, components='all'):
-    """
-    produce scaled waveforms from given waveform data and a scaling factor,
-    waveform may be selected by their components name
-    :param data: waveform data to be scaled
-    :type data: `~obspy.core.stream.Stream` object
-    :param factor: scaling factor
-    :type factor: float
-    :param components: components labels for the traces in data to be scaled by
-     the scaling factor (optional, default: 'all')
-    :type components: tuple
-    :return:  scaled waveform data
-    :rtype: `~obspy.core.stream.Stream` object
-    """
-    if components != 'all':
-        for comp in components:
-            if factor is None:
-                max_val = np.max(np.abs(data.select(component=comp)[0].data))
-                data.select(component=comp)[0].data /= 2 * max_val
-            else:
-                data.select(component=comp)[0].data /= 2 * factor
-    else:
-        for tr in data:
-            if factor is None:
-                max_val = float(np.max(np.abs(tr.data)))
-                tr.data /= 2 * max_val
-            else:
-                tr.data /= 2 * factor
-
-    return data
-
-
 def runProgram(cmd, parameter=None):
     """
     run an external program specified by cmd with parameters input returning the
@@ -1106,6 +1204,7 @@ def identifyPhase(phase):
         return False
 
 
+@lru_cache
 def identifyPhaseID(phase):
     """
     Returns phase id (capital P or S)
@@ -1169,7 +1268,7 @@ def correct_iplot(iplot):
     try:
         iplot = int(iplot)
     except ValueError:
-        if get_Bool(iplot):
+        if get_bool(iplot):
             iplot = 2
         else:
             iplot = 0

tests/test_get_qualities_from_xml.py

@@ -0,0 +1,33 @@
+import unittest
+
+from pylot.core.io.phases import getQualitiesfromxml
+
+
+class TestQualityFromXML(unittest.TestCase):
+    def setUp(self):
+        self.path = '.'
+        self.ErrorsP = [0.02, 0.04, 0.08, 0.16]
+        self.ErrorsS = [0.04, 0.08, 0.16, 0.32]
+        self.test0_result = [[0.0136956521739, 0.0126, 0.0101612903226, 0.00734848484849, 0.0135069444444,
+                              0.00649659863946, 0.0129513888889, 0.0122747747748, 0.0119252873563, 0.0103947368421,
+                              0.0092380952381, 0.00916666666667, 0.0104444444444, 0.0125333333333, 0.00904761904762,
+                              0.00885714285714, 0.00911616161616, 0.0164166666667, 0.0128787878788, 0.0122756410256,
+                              0.013653253667966917], [0.0239333333333, 0.0223791578953, 0.0217974304255],
+                             [0.0504861111111, 0.0610833333333], [], [0.171029411765]], [
+                                [0.0195, 0.0203623188406, 0.0212121212121, 0.0345833333333, 0.0196180555556,
+                                 0.0202536231884, 0.0200347222222, 0.0189, 0.0210763888889, 0.018275862069,
+                                 0.0213888888889, 0.0319791666667, 0.0205303030303, 0.0156388888889, 0.0192,
+                                 0.0231349206349, 0.023625, 0.02875, 0.0195512820513, 0.0239393939394, 0.0234166666667,
+                                 0.0174702380952, 0.0204151307995], [0.040314343081226646], [0.148555555556], [], []]
+        self.test1_result = [77.77777777777777, 11.11111111111111, 7.407407407407407, 0, 3.7037037037037037],\
+                            [92.0, 4.0, 4.0, 0, 0]
+
+    def test_result_plotflag0(self):
+        self.assertEqual(getQualitiesfromxml(self.path, self.ErrorsP, self.ErrorsS, 0), self.test0_result)
+
+    def test_result_plotflag1(self):
+        self.assertEqual(getQualitiesfromxml(self.path, self.ErrorsP, self.ErrorsS, 1), self.test1_result)
+
+
+if __name__ == '__main__':
+    unittest.main()