[bugfix] reverting code from commit 3069e7d5. Checking for coordinates in dataless Parser IS necessary to make sure correct Metadata were found. Fixes #37.

[minor] Commented out search for network name in metadata filename considered being unsafe

.gitignore

@@ -2,3 +2,4 @@
 *~
 .idea
 pylot/RELEASE-VERSION
+/tests/test_autopicker/dmt_database_test/

.mailmap

@@ -0,0 +1,39 @@
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <Darius_A@web.de>
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <darius.arnold@rub.de>
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <darius.arnold@ruhr-uni-bochum.de>
+Darius Arnold <Darius.Arnold@ruhr-uni-bochum.de> <mail@dariusarnold.de>
+
+Dennis Wlecklik <dennisw@minos02.geophysik.ruhr-uni-bochum.de>
+
+Jeldrik Gaal <jeldrikgaal@gmail.com>
+
+Kaan Coekerim <kaan.coekerim@ruhr-uni-bochum.de>
+Kaan Coekerim <kaan.coekerim@ruhr-uni-bochum.de> <kaan.coekerim@rub.de>
+
+Ludger Kueperkoch <kueperkoch@igem-energie.de> <kueperkoch@bestec-for-nature.com>
+Ludger Kueperkoch <kueperkoch@igem-energie.de> <ludger@quake2.(none)>
+Ludger Kueperkoch <kueperkoch@igem-energie.de> <ludger@sauron.bestec-for-nature>
+
+Marc S. Boxberg <marc.boxberg@rub.de>
+
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel.paffrath@rub.de> 
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@minos01.geophysik.ruhr-uni-bochum.de>
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@minos02.geophysik.ruhr-uni-bochum.de>
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@minos25.geophysik.ruhr-uni-bochum.de>
+Marcel Paffrath <marcel.paffrath@ruhr-uni-bochum.de> <marcel@email.com>
+
+Sally Zimmermann <sally.zimmermann@ruhr-uni-bochum.de>
+
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastianw@minos01.geophysik.ruhr-uni-bochum.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastianw@minos02.geophysik.ruhr-uni-bochum.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastianw@minos22.geophysik.ruhr-uni-bochum.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastian.wehling-benatelli@scisys.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastian.wehling@rub.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <sebastian.wehling@rub.de>
+Sebastian Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com> <DarkBeQst@users.noreply.github.com>
+
+Thomas Moeller <thomas.moeller@rub.de>
+
+Ann-Christin Koch <ann-christin.koch@ruhr-uni-bochum.de> <Ann-Christin.Koch@ruhr-uni-bochum.de>
+
+Sebastian Priebe <sebastian.priebe@rub.de>

PyLoT.py

@@ -25,6 +25,7 @@ https://www.iconfinder.com/iconsets/flavour
 
 import argparse
 import json
+import logging
 import os
 import platform
 import shutil
@@ -60,7 +61,7 @@ except ImportError:
     from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
 
-from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude, calcsourcespec
+from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import FilterOptions, PylotParameter
 from autoPyLoT import autoPyLoT
@@ -72,19 +73,19 @@ 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, get_pylot_eventfile_with_extension
+    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, \
+    ComparisonWidget, TuneAutopicker, PylotParameterWidget, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
-    SourceSpecWindow, ChooseWaveFormWindow, SpectrogramTab, SearchFileByExtensionDialog
+    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
@@ -113,11 +114,7 @@ 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 not infile:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-        if os.path.isfile(infile) is False:
+        if infile and os.path.isfile(infile) is False:
             infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]
 
             if not os.path.exists(infile):
@@ -139,7 +136,7 @@ class MainWindow(QMainWindow):
         self.project.parameter = self._inputs
         self.tap = None
         self.apw = None
-        self.paraBox = None
+        self.parameterWidget = None
         self.array_map = None
         self._metadata = Metadata(verbosity=0)
         self._eventChanged = [False, False]
@@ -181,6 +178,7 @@ class MainWindow(QMainWindow):
         self.autodata = Data(self)
 
         self.fnames = None
+        self.fnames_comp = None
         self._stime = None
 
         # track deleted picks for logging
@@ -190,13 +188,12 @@ class MainWindow(QMainWindow):
         self.table_headers = ['', 'Event', 'Time', 'Lat', 'Lon', 'Depth', 'Ml', 'Mw', '[N] MP', '[N] AP', 'Tuning Set',
                               'Test Set', 'Notes']
 
-        # TODO: refactor rootpath to datapath
         while True:
             try:
                 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:",
@@ -253,7 +250,7 @@ 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
 
@@ -688,10 +685,9 @@ class MainWindow(QMainWindow):
         # add scroll area used in case number of traces gets too high
         self.wf_scroll_area = QtWidgets.QScrollArea(self)
         self.wf_scroll_area.setVisible(False)
-        self.no_data_label = QLabel('No Data')
+        self.no_data_label = QLabel('No Data. If data were already loaded, try to select the event again in the eventbox.')
         self.no_data_label.setStyleSheet('color: red')
         self.no_data_label.setAlignment(Qt.AlignCenter)
-
         # create central matplotlib figure canvas widget
         self.init_wfWidget()
 
@@ -720,14 +716,14 @@ 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.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.init_spectro_tab()
         self.tabs.setCurrentIndex(0)
 
         self.eventLabel = QLabel()
@@ -1010,13 +1006,13 @@ class MainWindow(QMainWindow):
                                           events=events)
         if not sld.exec_():
             return
-        fext = sld.comboBox.currentText()
-        # fext = '.xml'
+
+        filenames = sld.getChecked()
         for event in events:
-            filename = get_pylot_eventfile_with_extension(event, fext)
-            if filename:
-                self.load_data(filename, draw=False, event=event, overwrite=True)
-                refresh = True
+            for filename in filenames:
+                if os.path.isfile(filename) and event.pylot_id in filename:
+                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
+                    refresh = True
         if not refresh:
             return
         if self.get_current_event().pylot_picks:
@@ -1024,8 +1020,8 @@ class MainWindow(QMainWindow):
         self.fill_eventbox()
         self.setDirty(True)
 
-    def load_data(self, fname=None, loc=False, draw=True, event=None, overwrite=False):
-        if not overwrite:
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
+        if not ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1034,14 +1030,33 @@ class MainWindow(QMainWindow):
                 fname = self.filename_from_action(action)
                 if not fname:
                     return
+
         if not event:
             event = self.get_current_event()
+
+        if event.picks:
+            qmb = QMessageBox(self, icon=QMessageBox.Question,
+                              text='Do you want to overwrite the data?',)
+            overwrite_button = qmb.addButton('Overwrite', QMessageBox.YesRole)
+            merge_button = qmb.addButton('Merge', QMessageBox.NoRole)
+            qmb.exec_()
+
+            if qmb.clickedButton() == overwrite_button:
+                merge_strategy = 'Overwrite'
+            elif qmb.clickedButton() == merge_button:
+                merge_strategy = 'Merge'
+            else:
+                return
+
         data = Data(self, event)
         try:
             data_new = Data(self, evtdata=str(fname))
-            # MP MP commented because adding several picks might cause inconsistencies
-            data = data_new
-            # data += data_new
+            if merge_strategy == 'Overwrite':
+                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(
@@ -1129,16 +1144,19 @@ 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')
@@ -1192,7 +1210,7 @@ class MainWindow(QMainWindow):
                 with open(eventlist_file, 'r') as infile:
                     eventlist_subset = [os.path.join(basepath, filename.split('\n')[0]) for filename in
                                         infile.readlines()]
-                    msg = 'Found file "eventlist.txt" in database path. WILL ONLY USE SELECTED EVENTS out of {} events ' \
+                    msg = 'Found file "eventlist.txt" in datapath. WILL ONLY USE SELECTED EVENTS out of {} events ' \
                           'contained in this subset'
                     print(msg.format(len(eventlist_subset)))
                     eventlist = [eventname for eventname in eventlist if eventname in eventlist_subset]
@@ -1217,49 +1235,34 @@ class MainWindow(QMainWindow):
         # get path from first event in list and split them
         path = eventlist[0]
         try:
-            system_name = platform.system()
-            if system_name in ["Linux", "Darwin"]:
-                dirs = {
-                    'database': path.split('/')[-2],
-                    'datapath': os.path.split(path)[0],  # path.split('/')[-3],
-                    'rootpath': '/' + os.path.join(*path.split('/')[:-3])
-                }
-            elif system_name == "Windows":
-                rootpath = path.split('/')[:-3]
-                rootpath[0] += '/'
-                dirs = {
-                    # TODO: Arrange path to meet Win standards
-                    'database': path.split('/')[-2],
-                    'datapath': path.split('/')[-3],
-                    'rootpath': os.path.join(*rootpath)
-                }
+            datapath = os.path.split(path)[0]
+            dirs = {
+                'datapath': datapath,
+            }
         except Exception as e:
             dirs = {
-                'database': '',
                 'datapath': '',
-                'rootpath': ''
             }
             print('Warning: Could not automatically init folder structure. ({})'.format(e))
 
         settings = QSettings()
-        settings.setValue("data/dataRoot", dirs['datapath'])  # d irs['rootpath'])
+        settings.setValue("data/dataRoot", dirs['datapath'])
         settings.sync()
 
         if not self.project.eventlist:
             # init parameter object
             self.setParameter(show=False)
             # hide all parameter (show all needed parameter later)
-            self.paraBox.hide_parameter()
+            self.parameterWidget.hide_parameter()
             for directory in dirs.keys():
                 # set parameter
-                box = self.paraBox.boxes[directory]
-                self.paraBox.setValue(box, dirs[directory])
+                box = self.parameterWidget.boxes[directory]
+                self.parameterWidget.setValue(box, dirs[directory])
                 # show needed parameter in box
-                self.paraBox.show_parameter(directory)
-            dirs_box = self.paraBox.get_groupbox_dialog('Directories')
+                self.parameterWidget.show_parameter(directory)
+            dirs_box = self.parameterWidget.get_groupbox_dialog('Directories')
             if not dirs_box.exec_():
                 return
-            self.project.rootpath = dirs['rootpath']
             self.project.datapath = dirs['datapath']
         else:
             if hasattr(self.project, 'datapath'):
@@ -1268,7 +1271,6 @@ class MainWindow(QMainWindow):
                                         'Datapath missmatch to current project!')
                     return
             else:
-                self.project.rootpath = dirs['rootpath']
                 self.project.datapath = dirs['datapath']
 
         self.project.add_eventlist(eventlist)
@@ -1356,11 +1358,10 @@ class MainWindow(QMainWindow):
             return True
 
     def modify_project_path(self, new_rootpath):
-        # TODO: change root to datapath
-        self.project.rootpath = new_rootpath
+        self.project.datapath = new_rootpath
         for event in self.project.eventlist:
-            event.rootpath = new_rootpath
-            event.path = os.path.join(event.rootpath, event.datapath, event.database, event.pylot_id)
+            event.datapath = new_rootpath
+            event.path = os.path.join(event.datapath, event.pylot_id)
             event.path = event.path.replace('\\', '/')
             event.path = event.path.replace('//', '/')
 
@@ -1554,7 +1555,7 @@ class MainWindow(QMainWindow):
             self.set_fname(self.get_data().getEventFileName(), type)
         return self.get_fnames(type)
 
-    def saveData(self, event=None, directory=None, outformats=['.xml', '.cnv', '.obs', '_focmec.in', '.pha']):
+    def saveData(self, event=None, directory=None, outformats=None):
         '''
         Save event data to directory with specified output formats.
         :param event: PyLoT Event, if not set current event will be used
@@ -1562,6 +1563,8 @@ class MainWindow(QMainWindow):
         :param outformats: str/list of output formats
         :return:
         '''
+        if outformats is None:
+            outformats = ['.xml', '.cnv', '.obs', '_focmec.in', '.pha']
         if not event:
             event = self.get_current_event()
         if not type(outformats) == list:
@@ -1697,7 +1700,7 @@ class MainWindow(QMainWindow):
 
     # WIP JG
     def eventlistXml(self):
-        path = self._inputs['rootpath'] + '/' + self._inputs['datapath'] + '/' + self._inputs['database']
+        path = self._inputs['datapath']
         outpath = self.project.location[:self.project.location.rfind('/')]
         geteventlistfromxml(path, outpath)
         return
@@ -1960,7 +1963,13 @@ 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)
@@ -1990,8 +1999,8 @@ 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
-            tstop = settings.value('tstop') if get_None(settings.value('tstop')) 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
             tstart = origin_time + float(tstart)
             tstop = origin_time + float(tstop)
         else:
@@ -1999,7 +2008,7 @@ class MainWindow(QMainWindow):
             tstop = None
 
         self.data.setWFData(self.fnames,
-                            self.fnames_syn,
+                            self.fnames_comp,
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
@@ -2007,7 +2016,7 @@ 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):
@@ -2015,8 +2024,8 @@ class MainWindow(QMainWindow):
             if 'syngine' in fpath:
                 eventpath_syn = os.path.join(eventpath, fpath)
                 qcheckb_syn.setEnabled(True)
-                if self.dataPlot.syn_checkbox.isChecked():
-                    self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                if self.dataPlot.comp_checkbox.isChecked():
+                    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():
@@ -2143,10 +2152,11 @@ class MainWindow(QMainWindow):
         self.wf_scroll_area.setVisible(len(plots) > 0)
         self.no_data_label.setVisible(not len(plots) > 0)
         for times, data, times_syn, data_syn in plots:
-            self.dataPlot.plotWidget.getPlotItem().plot(times, data,
-                                                        pen=self.dataPlot.pen_linecolor)
+            self.dataPlot.plotWidget.getPlotItem().plot(np.array(times), np.array(data),
+                                                        pen=self.dataPlot.pen_linecolor,
+                                                        skipFiniteCheck=True)
             if len(data_syn) > 0:
-                self.dataPlot.plotWidget.getPlotItem().plot(times_syn, data_syn,
+                self.dataPlot.plotWidget.getPlotItem().plot(np.array(times_syn), np.array(data_syn),
                                                             pen=self.dataPlot.pen_linecolor_syn)
         self.dataPlot.reinitMoveProxy()
         self.highlight_stations()
@@ -2186,7 +2196,8 @@ class MainWindow(QMainWindow):
         if event.pylot_autopicks:
             self.drawPicks(picktype='auto')
         if event.pylot_picks or event.pylot_autopicks:
-            self.locateEventAction.setEnabled(True)
+            if not self._inputs.get('extent') == 'global':
+                self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
 
@@ -2297,7 +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:
@@ -2306,7 +2317,7 @@ class MainWindow(QMainWindow):
         # wfst += self.get_data().getWFData().select(component=alter_comp)
         plotWidget = self.getPlotWidget()
         self.adjustPlotHeight()
-        if get_bool(settings.value('large_dataset')):
+        if get_bool(settings.value('large_dataset')) == True:
             self.plot_method = 'fast'
         else:
             self.plot_method = 'normal'
@@ -2416,7 +2427,7 @@ class MainWindow(QMainWindow):
         filterS = filteroptions['S']
         minP, maxP = filterP.getFreq()
         minS, maxS = filterS.getFreq()
-        self.paraBox.params_to_gui()
+        self.parameterWidget.params_to_gui()
 
     def getFilterOptions(self):
         return self.filteroptions
@@ -2609,18 +2620,20 @@ 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,
-                          model=self.inputs.get('taup_model'),
-                          filteroptions=self.filteroptions, wftype=wftype)
+                          filteroptions=self.filteroptions, wftype=wftype,
+                          show_comp_data=self.dataPlot.comp_checkbox.isChecked())
         if self.filterActionP.isChecked():
             pickDlg.currentPhase = "P"
             pickDlg.filterWFData()
@@ -2999,10 +3012,16 @@ 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:
@@ -3077,7 +3096,7 @@ class MainWindow(QMainWindow):
 
                 if self.pg:
                     if spe:
-                        if picks['epp'] and picks['lpp']:
+                        if not self.plot_method == 'fast' and picks['epp'] and picks['lpp']:
                             pen = make_pen(picktype, phaseID, 'epp', quality)
                             self.drawnPicks[picktype][station].append(pw.plot([epp, epp], ylims,
                                                                               alpha=.25, pen=pen, name='EPP'))
@@ -3156,8 +3175,8 @@ class MainWindow(QMainWindow):
         ttt = parameter['ttpatter']
         outfile = parameter['outpatter']
         eventname = self.get_current_event_name()
-        obsdir = os.path.join(self._inputs['rootpath'], self._inputs['datapath'], self._inputs['database'], eventname)
-        self.saveData(event=self.get_current_event(), directory=obsdir, outformats='.obs')
+        obsdir = os.path.join(self._inputs['datapath'], eventname)
+        self.saveData(event=self.get_current_event(), directory=obsdir, outformats=['.obs'])
         filename = 'PyLoT_' + eventname
         locpath = os.path.join(locroot, 'loc', filename)
         phasefile = os.path.join(obsdir, filename + '.obs')
@@ -3571,7 +3590,7 @@ class MainWindow(QMainWindow):
     def calc_magnitude(self):
         self.init_metadata()
         if not self.metadata:
-            return None
+            return []
 
         wf_copy = self.get_data().getWFData().copy()
 
@@ -3580,6 +3599,10 @@ class MainWindow(QMainWindow):
         for station in np.unique(list(self.getPicks('manual').keys()) + list(self.getPicks('auto').keys())):
             wf_select += wf_copy.select(station=station)
 
+        if not wf_select:
+            logging.warning('Empty Stream in calc_magnitude. Return.')
+            return []
+
         corr_wf = restitute_data(wf_select, self.metadata)
         # calculate moment magnitude
         moment_mag = MomentMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('vp'),
@@ -3714,6 +3737,7 @@ class MainWindow(QMainWindow):
                 if self.project.parameter:
                     # do this step to update default parameter on older PyLoT projects
                     self.project.parameter.reinit_default_parameters()
+                    PylotParameter.check_deprecated_parameters(self.project.parameter)
 
                     self._inputs = self.project.parameter
                     self.updateFilteroptions()
@@ -3831,13 +3855,13 @@ class MainWindow(QMainWindow):
 
     def setParameter(self, checked=0, show=True):
         if checked: pass  # dummy argument to receive trigger signal (checked) if called by QAction
-        if not self.paraBox:
-            self.paraBox = PylotParaBox(self._inputs, parent=self, windowflag=Qt.Window)
-            self.paraBox.accepted.connect(self._setDirty)
-            self.paraBox.accepted.connect(self.filterOptionsFromParameter)
+        if not self.parameterWidget:
+            self.parameterWidget = PylotParameterWidget(self._inputs, parent=self, windowflag=Qt.Window)
+            self.parameterWidget.accepted.connect(self._setDirty)
+            self.parameterWidget.accepted.connect(self.filterOptionsFromParameter)
         if show:
-            self.paraBox.params_to_gui()
-            self.paraBox.show()
+            self.parameterWidget.params_to_gui()
+            self.parameterWidget.show()
 
     def deleteAllAutopicks(self):
         qmb = QMessageBox(self, icon=QMessageBox.Question,
@@ -3884,16 +3908,18 @@ class Project(object):
     Pickable class containing information of a PyLoT project, like event lists and file locations.
     '''
 
-    # TODO: remove rootpath
     def __init__(self):
         self.eventlist = []
         self.location = None
-        self.rootpath = None
         self.datapath = None
         self.dirty = False
         self.parameter = None
         self._table = None
 
+    @property
+    def rootpath(self):
+        return self.datapath
+
     def add_eventlist(self, eventlist):
         '''
         Add events from an eventlist containing paths to event directories.
@@ -3903,8 +3929,6 @@ class Project(object):
             return
         for item in eventlist:
             event = Event(item)
-            event.rootpath = self.parameter['rootpath']
-            event.database = self.parameter['database']
             event.datapath = self.parameter['datapath']
             if not event.path in self.getPaths():
                 self.eventlist.append(event)

README.md

@@ -11,7 +11,7 @@ PILOT has originally been developed in Mathworks' MatLab. In order to distribute
 problems, it has been decided to redevelop the software package in Python. The great work of the ObsPy group allows easy
 handling of a bunch of seismic data and PyLoT will benefit a lot compared to the former MatLab version.
 
-The development of PyLoT is part of the joint research project MAGS2 and AlpArray.
+The development of PyLoT is part of the joint research project MAGS2, AlpArray and AdriaArray.
 
 ## Installation
 
@@ -27,58 +27,44 @@ Afterwards run (from the PyLoT main directory where the files *requirements.txt*
     conda env create -f pylot.yml
 or
     
-    conda create --name pylot_38 --file requirements.txt
+    conda create -c conda-forge --name pylot_311 python=3.11 --file requirements.txt
 
-to create a new Anaconda environment called "pylot_38".
+to create a new Anaconda environment called *pylot_311*.
 
 Afterwards activate the environment by typing
 
-    conda activate pylot_38
+    conda activate pylot_311
 
 #### Prerequisites:
 
 In order to run PyLoT you need to install:
 
 - Python 3
-- obspy
-- pyside2
-- pyqtgraph
 - cartopy
+- joblib
+- obspy
+- pyaml
+- pyqtgraph
+- pyside2
 
 (the following are already dependencies of the above packages):
 - scipy
 - numpy
-- matplotlib <= 3.3.x
+- matplotlib
 
 #### Some handwork:
 
-PyLoT needs a properties folder on your system to work. It should be situated in your home directory
-(on Windows usually C:/Users/*username*):
-
-    mkdir ~/.pylot
-
-In the next step you have to copy some files to this directory:
-
-*for local distance seismicity*
-
-    cp path-to-pylot/inputs/pylot_local.in ~/.pylot/pylot.in
-
-*for regional distance seismicity*
-
-    cp path-to-pylot/inputs/pylot_regional.in ~/.pylot/pylot.in
-
-*for global distance seismicity*
-
-    cp path-to-pylot/inputs/pylot_global.in ~/.pylot/pylot.in
-
-and some extra information on error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling
+Some extra information on error estimates (just needed for reading old PILOT data) and the Richter magnitude scaling
 relation
 
     cp path-to-pylot/inputs/PILOT_TimeErrors.in path-to-pylot/inputs/richter_scaling.data ~/.pylot/
 
 You may need to do some modifications to these files. Especially folder names should be reviewed.
 
-PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
+PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10/11.
+
+## Example Dataset
+An example dataset with waveform data, metadata and automatic picks in the obspy-dmt dataset format for testing the teleseismic picking can be found at https://zenodo.org/doi/10.5281/zenodo.13759803
 
 ## Release notes
 
@@ -87,6 +73,7 @@ PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
 - event organisation in project files and waveform visualisation
 - consistent manual phase picking through predefined SNR dependant zoom level
 - consistent automatic phase picking routines using Higher Order Statistics, AIC and Autoregression
+- pick correlation correction for teleseismic waveforms
 - interactive tuning of auto-pick parameters
 - uniform uncertainty estimation from waveform's properties for automatic and manual picks
 - pdf representation and comparison of picks taking the uncertainty intrinsically into account
@@ -95,7 +82,7 @@ PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
 
 #### Known issues:
 
-We hope to solve these with the next release.
+Current release is still in development progress and has several issues. We are currently lacking manpower, but hope to assess many of the issues in the near future.
 
 ## Staff
 
@@ -108,4 +95,4 @@ Others: A. Bruestle, T. Meier, W. Friederich
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-April 2022
+September 2024

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)
-    inputfile = get_None(inputfile)
-    eventid = get_None(eventid)
+    parameter = get_none(parameter)
+    inputfile = get_none(inputfile)
+    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:
-            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)
+        if not inputfile:
+            print('Using default input parameter')
+        parameter = PylotParameter(inputfile)
     else:
         if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
@@ -140,11 +136,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
     if parameter.hasParam('datastructure'):
         # getting information on data structure
         datastructure = DATASTRUCTURE[parameter.get('datastructure')]()
-        dsfields = {'root': parameter.get('rootpath'),
-                    'dpath': parameter.get('datapath'),
-                    'dbase': parameter.get('database')}
+        dsfields = {'dpath': parameter.get('datapath'),}
 
-        exf = ['root', 'dpath', 'dbase']
+        exf = ['dpath']
 
         if parameter['eventID'] != '*' and fnames == 'None':
             dsfields['eventID'] = parameter['eventID']
@@ -154,7 +148,7 @@ 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')
@@ -190,15 +184,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         if not input_dict:
             # started in production mode
             datapath = datastructure.expandDataPath()
-            if fnames == 'None' and parameter['eventID'] == '*':
+            if fnames in [None, 'None'] and parameter['eventID'] == '*':
                 # multiple event processing
                 # read each event in database
                 events = [event for event in glob.glob(os.path.join(datapath, '*')) if
                           (os.path.isdir(event) and not event.endswith('EVENTS-INFO'))]
-            elif fnames == 'None' and parameter['eventID'] != '*' and not type(parameter['eventID']) == list:
+            elif fnames in [None, 'None'] and parameter['eventID'] != '*' and not type(parameter['eventID']) == list:
                 # single event processing
                 events = glob.glob(os.path.join(datapath, parameter['eventID']))
-            elif fnames == 'None' and type(parameter['eventID']) == list:
+            elif fnames in [None, 'None'] and type(parameter['eventID']) == list:
                 # multiple event processing
                 events = []
                 for eventID in parameter['eventID']:
@@ -210,12 +204,10 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 locflag = 2
         else:
             # started in tune or interactive mode
-            datapath = os.path.join(parameter['rootpath'],
-                                    parameter['datapath'])
+            datapath = parameter['datapath']
             events = []
             for eventID in eventid:
                 events.append(os.path.join(datapath,
-                                           parameter['database'],
                                            eventID))
 
         if not events:
@@ -242,12 +234,15 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 data.get_evt_data().path = eventpath
                 print('Reading event data from filename {}...'.format(filename))
             except Exception as e:
-                print('Could not read event from file {}: {}'.format(filename, e))
+                if type(e) == FileNotFoundError:
+                    print('Creating new event file.')
+                else:
+                    print('Could not read event from file {}: {}'.format(filename, e))
                 data = Data()
                 pylot_event = Event(eventpath)  # event should be path to event directory
                 data.setEvtData(pylot_event)
-            if fnames == 'None':
-                data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*')))
+            if fnames in [None, 'None']:
+                data.setWFData(glob.glob(os.path.join(event_datapath, '*')))
                 # the following is necessary because within
                 # multiple event processing no event ID is provided
                 # in autopylot.in

docs/correlation.md

@@ -0,0 +1,77 @@
+# Pick-Correlation Correction
+
+## Introduction
+Currently, the pick-correlation correction algorithm is not accessible from they PyLoT GUI. The main file *pick_correlation_correction.py* is located in the directory *pylot\correlation*.
+The program only works for an obspy dmt database structure.
+
+The basic workflow of the algorithm is shown in the following diagram. The first step **(1)** is the normal (automatic) picking procedure in PyLoT. Everything from step **(2)** to **(5)** is part of the correlation correction algorithm.
+
+*Note: The first step is not required in case theoretical onsets are used instead of external picks when the parameter use_taupy_onsets is set to True. However, an existing event quakeML (.xml) file generated by PyLoT might be required for each event in case not external picks are used.*
+
+![images/workflow_stacking.png](images/workflow_stacking.png)
+
+A detailed description of the algorithm can be found in the corresponding publication:
+
+*Paffrath, M., Friederich, W., and the AlpArray and AlpArray-SWATH D Working Groups: Teleseismic P waves at the AlpArray seismic network: wave fronts, absolute travel times and travel-time residuals, Solid Earth, 12, 1635–1660, https://doi.org/10.5194/se-12-1635-2021, 2021.*
+
+## How to use
+To use the program you have to call the main program providing two mandatory arguments: a path to the obspy dmt database folder *dmt_database_path* and the path to the PyLoT infile *pylot.in* for picking of the beam trace:
+
+```python pick_correlation_correction.py dmt_database_path pylot.in```
+
+By default, the parameter file *parameters.yaml* is used. You can use the command line option *--params* to specify a different parameter file and other optional arguments such as *-pd* for plotting detailed information or *-n 4* to use 4 cores for parallel processing:
+
+```python pick_correlation_correction.py dmt_database_path pylot.in --params parameters_adriaarray.yaml -pd -n 4```
+
+## Cross-Correlation Parameters
+
+The program uses the parameters in the file *parameters.yaml* by default. You can use the command line option *--params* to specify a different parameter file. An example of the parameter file is provided in the *correlation\parameters.yaml* file.
+
+In the top level of the parameter file the logging level *logging* can be set, as well as a list of pick phases *pick_phases* (e.g. ['P', 'S']).
+
+For each pick phase the different parameters can be set in the first sub-level of the parameter file, e.g.:
+
+```yaml
+logging: info
+pick_phases: ['P', 'S']
+
+P:
+ min_corr_stacking: 0.8
+ min_corr_export: 0.6
+ [...]
+
+S:
+ min_corr_stacking: 0.7
+ [...]
+```
+
+The following parameters are available:
+
+
+| Parameter Name                 | Description                                                                                        | Parameter Type |
+|--------------------------------|----------------------------------------------------------------------------------------------------|----------------|
+| min_corr_stacking              | Minimum correlation coefficient for building beam trace                                            | float          |
+| min_corr_export                | Minimum correlation coefficient for pick export                                                    | float          |
+| min_stack                      | Minimum number of stations for building beam trace                                                 | int            |
+| t_before                       | Correlation window before reference pick                                                           | float          |
+| t_after                        | Correlation window after reference pick                                                            | float          |
+| cc_maxlag                      | Maximum shift for initial correlation                                                              | float          |
+| cc_maxlag2                     | Maximum shift for second (final) correlation (also for calculating pick uncertainty)               | float          |
+| initial_pick_outlier_threshold | Threshold for excluding large outliers of initial (AIC) picks                                      | float          |
+| export_threshold               | Automatically exclude all onsets which deviate more than this threshold from corrected taup onsets | float          |
+| min_picks_export               | Minimum number of correlated picks for export                                                      | int            |
+| min_picks_autopylot            | Minimum number of reference auto picks to continue with event                                      | int            |
+| check_RMS                      | Do RMS check to search for restitution errors (very experimental)                                  | bool           |
+| use_taupy_onsets               | Use taupy onsets as reference picks instead of external picks                                      | bool           |
+| station_list                   | Use the following stations as reference for stacking                                               | list[str]      |
+| use_stacked_trace              | Use existing stacked trace if found (spare re-computation)                                         | bool           |
+| data_dir                       | obspyDMT data subdirectory (e.g. 'raw', 'processed')                                               | str            |
+| pickfile_extension             | Use quakeML files (PyLoT output) with the following extension                                      | str            |
+| dt_stacking                    | Time difference for stacking window (in seconds)                                                   | list[float]    |
+| filter_options                 | Filter for first correlation (rough)                                                               | dict           |
+| filter_options_final           | Filter for second correlation (fine)                                                               | dict           |
+| filter_type                    | Filter type (e.g. bandpass)                                                                        | str            |
+| sampfreq                       | Sampling frequency (in Hz)                                                                         | float          |
+
+## Example Dataset
+An example dataset with waveform data, metadata and automatic picks in the obspy-dmt dataset format for testing can be found at https://zenodo.org/doi/10.5281/zenodo.13759803

docs/gui.md

@@ -203,8 +203,6 @@ The meaning of the header entries is:
 PyLoT GUI starts with an empty project. To add events, use the add event data button. Select one or multiple folders
 containing events.
 
-[//]: <> (TODO: explain _Directories: Root path, Data path, Database path_)
-
 ### Saving projects
 
 Save the current project from the menu with File->Save project or File->Save project as. PyLoT uses ``.plp`` files to

docs/tuning.md

@@ -6,122 +6,123 @@ A description of the parameters used for determining automatic picks.
 
 Parameters applied to the traces before picking algorithm starts.
 
-| Name                | Description                                                                                                                                                                                                             |
-|---------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *P Start*, *P
-Stop* | Define time interval relative to trace start time for CF calculation on vertical trace. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue.    |
-| *S Start*, *S
-Stop* | Define time interval relative to trace start time for CF calculation on horizontal traces. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue. |
-| *Bandpass
-Z1*       | Filter settings for Butterworth bandpass applied to vertical trace for calculation of initial P pick.                                                                                                                   |
-| *Bandpass
-Z2*       | Filter settings for Butterworth bandpass applied to vertical trace for calculation of precise P pick.                                                                                                                   |
-| *Bandpass
-H1*       | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of initial S pick.                                                                                                                |
-| *Bandpass
-H2*       | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of precise S pick.                                                                                                                |
+| Name          | Description                                                                                                                                                                                                             |
+|---------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| *P Start*, *P |                                                                                                                                                                                                                         |
+| Stop*         | Define time interval relative to trace start time for CF calculation on vertical trace. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue.    |
+| *S Start*, *S |                                                                                                                                                                                                                         |
+| Stop*         | Define time interval relative to trace start time for CF calculation on horizontal traces. Value is relative to theoretical onset time if 'Use TauPy' option is enabled in main settings of 'Tune Autopicker' dialogue. |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| Z1*           | Filter settings for Butterworth bandpass applied to vertical trace for calculation of initial P pick.                                                                                                                   |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| Z2*           | Filter settings for Butterworth bandpass applied to vertical trace for calculation of precise P pick.                                                                                                                   |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| H1*           | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of initial S pick.                                                                                                                |
+| *Bandpass     |                                                                                                                                                                                                                         |
+| H2*           | Filter settings for Butterworth bandpass applied to horizontal traces for calculation of precise S pick.                                                                                                                |
 
 ## Inital P pick
 
 Parameters used for determination of initial P pick.
 
-| Name         | Description                                                                                                                  |
-|--------------|------------------------------------------------------------------------------------------------------------------------------|
-| *
-tLTA*       | Size of gliding LTA window in seconds used for calculation of HOS-CF.                                                        |
-| *pickwin
-P*  | Size of time window in seconds in which the minimum of the AIC-CF in front of the maximum of the HOS-CF is determined.       |
-| *
-AICtsmooth* | Average of samples in this time window will be used for smoothing of the AIC-CF.                                             |
-| *
-checkwinP*  | Time in front of the global maximum of the HOS-CF in which to search for a second local extrema.                             |
-| *minfactorP* | Used with *
-checkwinP*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorP*. |
-| *
-tsignal*    | Time window in seconds after the initial P pick used for determining signal amplitude.                                       |
-| *
-tnoise*     | Time window in seconds in front of initial P pick used for determining noise amplitude.                                      |
-| *tsafetey*   | Time in seconds between *tsignal* and *
-tnoise*.                                                                              |
-| *
-tslope*     | Time window in seconds after initial P pick in which the slope of the onset is calculated.                                   |
+| Name                                                                                                              | Description                                                                                                            |
+|-------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------|
+| *                                                                                                                 |                                                                                                                        |
+| tLTA*                                                                                                             | Size of gliding LTA window in seconds used for calculation of HOS-CF.                                                  |
+| *pickwin                                                                                                          |                                                                                                                        |
+| P*                                                                                                                | Size of time window in seconds in which the minimum of the AIC-CF in front of the maximum of the HOS-CF is determined. |
+| *                                                                                                                 |                                                                                                                        |
+| AICtsmooth*                                                                                                       | Average of samples in this time window will be used for smoothing of the AIC-CF.                                       |
+| *                                                                                                                 |                                                                                                                        |
+| checkwinP*                                                                                                        | Time in front of the global maximum of the HOS-CF in which to search for a second local extrema.                       |
+| *minfactorP*                                                                                                      | Used with *                                                                                                            |
+| checkwinP*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorP*. |                                                                                                                        |
+| *                                                                                                                 |                                                                                                                        |
+| tsignal*                                                                                                          | Time window in seconds after the initial P pick used for determining signal amplitude.                                 |
+| *                                                                                                                 |                                                                                                                        |
+| tnoise*                                                                                                           | Time window in seconds in front of initial P pick used for determining noise amplitude.                                |
+| *tsafetey*                                                                                                        | Time in seconds between *tsignal* and *                                                                                |
+| tnoise*.                                                                                                          |                                                                                                                        |
+| *                                                                                                                 |                                                                                                                        |
+| tslope*                                                                                                           | Time window in seconds after initial P pick in which the slope of the onset is calculated.                             |
 
 ## Inital S pick
 
 Parameters used for determination of initial S pick
 
-| Name          | Description                                                                                                                  |
-|---------------|------------------------------------------------------------------------------------------------------------------------------|
-| *
-tdet1h*      | Length of time window in seconds in which AR params of the waveform are determined.                                          |
-| *
-tpred1h*     | Length of time window in seconds in which the waveform is predicted using the AR model.                                      |
-| *
-AICtsmoothS* | Average of samples in this time window is used for smoothing the AIC-CF.                                                     |
-| *
-pickwinS*    | Time window in which the minimum in the AIC-CF in front of the maximum in the ARH-CF is determined.                          |
-| *
-checkwinS*   | Time in front of the global maximum of the ARH-CF in which to search for a second local extrema.                             |
-| *minfactorP*  | Used with *
-checkwinS*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorS*. |
-| *
-tsignal*     | Time window in seconds after the initial P pick used for determining signal amplitude.                                       |
-| *
-tnoise*      | Time window in seconds in front of initial P pick used for determining noise amplitude.                                      |
-| *tsafetey*    | Time in seconds between *tsignal* and *
-tnoise*.                                                                              |
-| *
-tslope*      | Time window in seconds after initial P pick in which the slope of the onset is calculated.                                   |
+| Name                                                                                                              | Description                                                                                         |
+|-------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------|
+| *                                                                                                                 |                                                                                                     |
+| tdet1h*                                                                                                           | Length of time window in seconds in which AR params of the waveform are determined.                 |
+| *                                                                                                                 |                                                                                                     |
+| tpred1h*                                                                                                          | Length of time window in seconds in which the waveform is predicted using the AR model.             |
+| *                                                                                                                 |                                                                                                     |
+| AICtsmoothS*                                                                                                      | Average of samples in this time window is used for smoothing the AIC-CF.                            |
+| *                                                                                                                 |                                                                                                     |
+| pickwinS*                                                                                                         | Time window in which the minimum in the AIC-CF in front of the maximum in the ARH-CF is determined. |
+| *                                                                                                                 |                                                                                                     |
+| checkwinS*                                                                                                        | Time in front of the global maximum of the ARH-CF in which to search for a second local extrema.    |
+| *minfactorP*                                                                                                      | Used with *                                                                                         |
+| checkwinS*. If a second local maximum is found, it has to be at least as big as the first maximum * *minfactorS*. |                                                                                                     |
+| *                                                                                                                 |                                                                                                     |
+| tsignal*                                                                                                          | Time window in seconds after the initial P pick used for determining signal amplitude.              |
+| *                                                                                                                 |                                                                                                     |
+| tnoise*                                                                                                           | Time window in seconds in front of initial P pick used for determining noise amplitude.             |
+| *tsafetey*                                                                                                        | Time in seconds between *tsignal* and *                                                             |
+| tnoise*.                                                                                                          |                                                                                                     |
+| *                                                                                                                 |                                                                                                     |
+| tslope*                                                                                                           | Time window in seconds after initial P pick in which the slope of the onset is calculated.          |
 
 ## Precise P pick
 
 Parameters used for determination of precise P pick.
 
-| Name         | Description                                                                                                                                                                                                             |
-|--------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *Precalcwin* | Time window in seconds for recalculation of the HOS-CF. The new CF will be two times the size of *
-Precalcwin*, since it will be calculated from the initial pick to +/- *Precalcwin*.                                   |
-| *
-tsmoothP*   | Average of samples in this time window will be used for smoothing the second HOS-CF.                                                                                                                                    |
-| *
-ausP*       | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed HOS-CF is found when the previous sample is larger or equal to the current sample times (1+*
-ausP*). |
+| Name                                                                                | Description                                                                                                                                                                                                      |
+|-------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| *Precalcwin*                                                                        | Time window in seconds for recalculation of the HOS-CF. The new CF will be two times the size of *                                                                                                               |
+| Precalcwin*, since it will be calculated from the initial pick to +/- *Precalcwin*. |                                                                                                                                                                                                                  |
+| *                                                                                   |                                                                                                                                                                                                                  |
+| tsmoothP*                                                                           | Average of samples in this time window will be used for smoothing the second HOS-CF.                                                                                                                             |
+| *                                                                                   |                                                                                                                                                                                                                  |
+| ausP*                                                                               | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed HOS-CF is found when the previous sample is larger or equal to the current sample times (1+* |
+| ausP*).                                                                             |                                                                                                                                                                                                                  |
 
 ## Precise S pick
 
 Parameters used for determination of precise S pick.
 
-| Name         | Description                                                                                                                                                                                                             |
-|--------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *
-tdet2h*     | Time window for determination of AR coefficients.                                                                                                                                                                       |
-| *
-tpred2h*    | Time window in which the waveform is predicted using the determined AR parameters.                                                                                                                                      |
-| *Srecalcwin* | Time window for recalculation of ARH-CF. New CF will be calculated from initial pick +/- *
-Srecalcwin*.                                                                                                                  |
-| *
-tsmoothS*   | Average of samples in this time window will be used for smoothing the second ARH-CF.                                                                                                                                    |
-| *
-ausS*       | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed ARH-CF is found when the previous sample is larger or equal to the current sample times (1+*
-ausS*). |
-| *
-pickwinS*   | Time window around initial pick in which to look for a precise pick.                                                                                                                                                    |
+| Name         | Description                                                                                                                                                                                                      |
+|--------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| *            |                                                                                                                                                                                                                  |
+| tdet2h*      | Time window for determination of AR coefficients.                                                                                                                                                                |
+| *            |                                                                                                                                                                                                                  |
+| tpred2h*     | Time window in which the waveform is predicted using the determined AR parameters.                                                                                                                               |
+| *Srecalcwin* | Time window for recalculation of ARH-CF. New CF will be calculated from initial pick +/- *                                                                                                                       |
+| Srecalcwin*. |                                                                                                                                                                                                                  |
+| *            |                                                                                                                                                                                                                  |
+| tsmoothS*    | Average of samples in this time window will be used for smoothing the second ARH-CF.                                                                                                                             |
+| *            |                                                                                                                                                                                                                  |
+| ausS*        | Controls artificial uplift of samples during precise picking. A common local minimum of the smoothed and unsmoothed ARH-CF is found when the previous sample is larger or equal to the current sample times (1+* |
+| ausS*).      |                                                                                                                                                                                                                  |
+| *            |                                                                                                                                                                                                                  |
+| pickwinS*    | Time window around initial pick in which to look for a precise pick.                                                                                                                                             |
 
 ## Pick quality control
 
 Parameters used for checking quality and integrity of automatic picks.
 
-| Name                                       | Description                                                                                                                                                                                                                                                                    |
-|--------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *
-minAICPslope*                             | Initial P picks with a slope lower than this value will be discared.                                                                                                                                                                                                           |
-| *
-minAICPSNR*                               | Initial P picks with a SNR below this value will be discarded.                                                                                                                                                                                                                 |
-| *
-minAICSslope*                             | Initial S picks with a slope lower than this value will be discarded.                                                                                                                                                                                                          |
-| *
-minAICSSNR*                               | Initial S picks with a SNR below this value will be discarded.                                                                                                                                                                                                                 |
-| *minsiglength*, *noisefacor*. *minpercent* | Parameters for checking signal length. In the time window of size *
+| Name                                       | Description                                                           |
+|--------------------------------------------|-----------------------------------------------------------------------|
+| *                                          |                                                                       |
+| minAICPslope*                              | Initial P picks with a slope lower than this value will be discared.  |
+| *                                          |                                                                       |
+| minAICPSNR*                                | Initial P picks with a SNR below this value will be discarded.        |
+| *                                          |                                                                       |
+| minAICSslope*                              | Initial S picks with a slope lower than this value will be discarded. |
+| *                                          |                                                                       |
+| minAICSSNR*                                | Initial S picks with a SNR below this value will be discarded.        |
+| *minsiglength*, *noisefacor*. *minpercent* | Parameters for checking signal length. In the time window of size *   |
+
 minsiglength* after the initial P pick *
 minpercent* of samples have to be larger than the RMS value.                                                                                                        |
 | *
@@ -139,12 +140,12 @@ wdttolerance*                             | Maximum allowed deviation of S onset
 
 Parameters for discrete quality classes.
 
-| Name             | Description                                                                                                                                                                                                           |
-|------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| *
-timeerrorsP*    | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for P onsets.                                                                           |
-| *
-timeerrorsS*    | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for S onsets.                                                                           |
-| *nfacP*, *nfacS* | For determination of latest possible onset time. The time when the signal reaches an amplitude of *
-nfac* * mean value of the RMS amplitude in the time window *tnoise* corresponds to the latest possible onset time. |
+| Name                                                                                                               | Description                                                                                                                                 |
+|--------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
+| *                                                                                                                  |                                                                                                                                             |
+| timeerrorsP*                                                                                                       | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for P onsets. |
+| *                                                                                                                  |                                                                                                                                             |
+| timeerrorsS*                                                                                                       | Width of the time windows in seconds between earliest and latest possible pick which represent the quality classes 0, 1, 2, 3 for S onsets. |
+| *nfacP*, *nfacS*                                                                                                   | For determination of latest possible onset time. The time when the signal reaches an amplitude of *                                         |
+| nfac* * mean value of the RMS amplitude in the time window *tnoise* corresponds to the latest possible onset time. |                                                                                                                                             |
 

inputs/pylot_global.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-                                                   #rootpath#       %project path                                                                                        
-                                                   #datapath#       %data path                                                                                           
-                                                   #database#       %name of data base                                                                                   
-                                                   #eventID#        %event ID for single event processing (* for all events found in database)                           
+                                                   #datapath#       %data path
+                                                   #eventID#        %event ID for single event processing (* for all events found in datapath)
                                                    #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -43,6 +41,7 @@ global                                             #extent#         %extent of a
 1150.0                                             #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
 True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
 iasp91                                             #taup_model#     %define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6
+P,Pdiff                                            #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 0.05 0.5                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
 0.001 0.5                                          #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
 0.05 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

inputs/pylot_local.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/DATA/Insheim                                      #rootpath#       %project path                                                                                        
-EVENT_DATA/LOCAL                                   #datapath#       %data path                                                                                           
-2018.02_Insheim                                    #database#       %name of data base                                                                                   
-e0006.038.18                                       #eventID#        %event ID for single event processing (* for all events found in database)                           
+/DATA/Insheim/EVENT_DATA/LOCAL/2018.02_Insheim     #datapath#       %data path
+e0006.038.18                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
 /DATA/Insheim/STAT_INFO                            #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -42,7 +40,8 @@ local                                              #extent#         %extent of a
 -0.5                                               #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
 10.0                                               #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
 False                                              #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
-iasp91                                             #taup_model#     %define TauPy model for traveltime estimation                                                        
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation
+P                                                  #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 2.0 20.0                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
 2.0 30.0                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
 2.0 10.0                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

inputs/pylot_regional.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-                                                   #rootpath#       %project path                                                                                        
-                                                   #datapath#       %data path                                                                                           
-                                                   #database#       %name of data base                                                                                   
-                                                   #eventID#        %event ID for single event processing (* for all events found in database)                           
+                                                   #datapath#       %data path
+                                                   #eventID#        %event ID for single event processing (* for all events found in datapath)
                                                    #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -42,7 +40,8 @@ local                                              #extent#         %extent of a
 -1.0                                               #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
 10.0                                               #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
 True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
-iasp91                                             #taup_model#     %define TauPy model for traveltime estimation                                                        
+iasp91                                             #taup_model#     %define TauPy model for traveltime estimation
+P                                                  #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 2.0 10.0                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
 2.0 12.0                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
 2.0 8.0                                            #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

pylot.yml

@@ -1,14 +1,12 @@
-name: pylot_38
+name: pylot_311
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - cartopy=0.20.2
-  - matplotlib-base=3.3.4
-  - numpy=1.22.3
-  - obspy=1.3.0
-  - pyqtgraph=0.12.4
-  - pyside2>=5.13.2
-  - python=3.8.12
-  - qt>=5.12.9
-  - scipy=1.8.0
+  - cartopy=0.23.0=py311hcf9f919_1
+  - joblib=1.4.2=pyhd8ed1ab_0
+  - obspy=1.4.1=py311he736701_3
+  - pyaml=24.7.0=pyhd8ed1ab_0
+  - pyqtgraph=0.13.7=pyhd8ed1ab_0
+  - pyside2=5.15.8=py311h3d699ce_4
+  - pytest=8.3.2=pyhd8ed1ab_0

pylot/__init__.py

@@ -9,7 +9,7 @@ PyLoT - the Python picking and Localization Tool
 
 This python library contains a graphical user interfaces for picking
 seismic phases. This software needs ObsPy (http://github.com/obspy/obspy/wiki)
-and the Qt4 libraries to be installed first.
+and the Qt libraries to be installed first.
 
 PILOT has been developed in Mathworks' MatLab. In order to distribute
 PILOT without facing portability problems, it has been decided to re-

pylot/core/io/data.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import copy
+import logging
 import os
 
 from PySide2.QtWidgets import QMessageBox
@@ -408,18 +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')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                     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')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                     hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
@@ -451,10 +450,11 @@ 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:
@@ -464,14 +464,16 @@ class Data(object):
 
         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_syn = check_fname_exists(fnames_syn)
+        fnames_alt = check_fname_exists(fnames_alt)
+
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -489,8 +491,8 @@ class Data(object):
         #     wffnames = fnames
         if fnames is not None:
             self.appendWFData(fnames)
-            if fnames_syn is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
+            if fnames_alt is not None:
+                self.appendWFData(fnames_alt, alternative=True)
         else:
             return False
 
@@ -512,7 +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
@@ -525,20 +527,20 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        real_or_syn_data = {True: self.wfsyn,
-                            False: self.wfdata}
+        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,
-                                                            endtime=self.tstop)
+                        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)
             except SacIOError as se:
@@ -553,8 +555,8 @@ class Data(object):
     def getOriginalWFData(self):
         return self.wforiginal
 
-    def getSynWFData(self):
-        return self.wfsyn
+    def getAltWFdata(self):
+        return self.wf_alt
 
     def resetWFData(self):
         """

pylot/core/io/default_parameters.py

@@ -6,24 +6,14 @@ import numpy as np
 Default parameters used for picking
 """
 
-defaults = {'rootpath': {'type': str,
-                         'tooltip': 'project path',
-                         'value': '',
-                         'namestring': 'Root path'},
-
-            'datapath': {'type': str,
-                         'tooltip': 'data path',
+defaults = {'datapath': {'type': str,
+                         'tooltip': 'path to eventfolders',
                          'value': '',
                          'namestring': 'Data path'},
 
-            'database': {'type': str,
-                         'tooltip': 'name of data base',
-                         'value': '',
-                         'namestring': 'Database path'},
-
             'eventID': {'type': str,
-                        'tooltip': 'event ID for single event processing (* for all events found in database)',
-                        'value': '',
+                        'tooltip': 'event ID for single event processing (* for all events found in datapath)',
+                        'value': '*',
                         'namestring': 'Event ID'},
 
             'extent': {'type': str,
@@ -511,7 +501,7 @@ defaults = {'rootpath': {'type': str,
 
             'taup_model': {'type': str,
                            'tooltip': 'Define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6',
-                           'value': None,
+                           'value': 'iasp91',
                            'namestring': 'TauPy model'},
 
             'taup_phases': {'type': str,
@@ -522,9 +512,7 @@ defaults = {'rootpath': {'type': str,
 
 settings_main = {
     'dirs': [
-        'rootpath',
         'datapath',
-        'database',
         'eventID',
         'invdir',
         'datastructure',

pylot/core/io/inputs.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+import logging
+import os
 
 from pylot.core.io import default_parameters
 from pylot.core.util.errors import ParameterError
@@ -88,10 +90,10 @@ class PylotParameter(object):
         return bool(self.__parameter)
 
     def __getitem__(self, key):
-        try:
+        if key in self.__parameter:
             return self.__parameter[key]
-        except:
-            return None
+        else:
+            logging.warning(f'{key} not found in PylotParameter')
 
     def __setitem__(self, key, value):
         try:
@@ -418,6 +420,28 @@ class PylotParameter(object):
             line = value + name + ttip
             fid.write(line)
 
+    @staticmethod
+    def check_deprecated_parameters(parameters):
+        if parameters.hasParam('database') and parameters.hasParam('rootpath'):
+            parameters['datapath'] = os.path.join(parameters['rootpath'], parameters['datapath'],
+                                                  parameters['database'])
+            logging.warning(
+                f'Parameters database and rootpath are deprecated. '
+                f'Tried to merge them to now path: {parameters["datapath"]}.'
+            )
+
+        remove_keys = []
+        for key in parameters:
+            if not key in default_parameters.defaults.keys():
+                remove_keys.append(key)
+                logging.warning(f'Removing deprecated parameter: {key}')
+
+        for key in remove_keys:
+            del parameters[key]
+
+        parameters._settings_main = default_parameters.settings_main
+        parameters._settings_special_pick = default_parameters.settings_special_pick
+
 
 class FilterOptions(object):
     '''

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
 
@@ -16,7 +17,7 @@ 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, loopIdentifyPhase, identifyPhase
 
 
@@ -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 +275,28 @@ def picksdict_from_picks(evt):
         phase['epp'] = epp
         phase['lpp'] = lpp
         phase['spe'] = spe
-        try:
-            phase['weight'] = weight
-        except:
-            # get onset weight from uncertainty
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
+        weight = phase.get('weight')
+        if not weight:
+            if not parameter:
+                logging.warning('Using ')
+                logging.warning('Using default input parameter')
+                parameter = PylotParameter()
             pick.phase_hint = identifyPhase(pick.phase_hint)
             if pick.phase_hint == 'P':
                 errors = parameter['timeerrorsP']
             elif pick.phase_hint == 'S':
                 errors = parameter['timeerrorsS']
-            weight = get_quality_class(spe, errors)
-            phase['weight'] = weight
+            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!")
+        if pick.polarity == 'positive':
+            phase['fm'] = 'U'
+        elif pick.polarity == 'negative':
+            phase['fm'] = 'D'
+        else:
             phase['fm'] = 'N'
         phase['filter_id'] = filter_id if filter_id is not None else ''
 
@@ -514,7 +512,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         fid = open("%s" % filename, 'w')
         # write header
         fid.write('# EQEVENT: %s Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' %
-                  (parameter.get('database'), parameter.get('eventID')))
+                  (parameter.get('datapath'), parameter.get('eventID')))
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets
@@ -667,7 +665,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         print("Writing phases to %s for HYPOSAT" % filename)
         fid = open("%s" % filename, 'w')
         # write header
-        fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
+        fid.write('%s, event %s \n' % (parameter.get('datapath'), parameter.get('eventID')))
         arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
         for key in arrivals:
             # P onsets

pylot/core/pick/autopick.py

@@ -22,7 +22,7 @@ from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
     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):
@@ -258,10 +258,14 @@ 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
 
+        # initialize TauPy pick estimates
+        self.estFirstP = None
+        self.estFirstS = None
+
         # initialize picking results
         self.p_results = PickingResults()
         self.s_results = PickingResults()
@@ -443,15 +447,15 @@ class AutopickStation(object):
             for arr in arrivals:
                 phases[identifyPhaseID(arr.phase.name)].append(arr)
             # get first P and S onsets from arrivals list
-            estFirstP = 0
-            estFirstS = 0
+            arrival_time_p = 0
+            arrival_time_s = 0
             if len(phases['P']) > 0:
-                arrP, estFirstP = min([(arr, arr.time) for arr in phases['P']], key=lambda t: t[1])
+                arrP, arrival_time_p = min([(arr, arr.time) for arr in phases['P']], key=lambda t: t[1])
             if len(phases['S']) > 0:
-                arrS, estFirstS = min([(arr, arr.time) for arr in phases['S']], key=lambda t: t[1])
+                arrS, arrival_time_s = min([(arr, arr.time) for arr in phases['S']], key=lambda t: t[1])
             print('autopick: estimated first arrivals for P: {} s, S:{} s after event'
-                  ' origin time using TauPy'.format(estFirstP, estFirstS))
-            return estFirstP, estFirstS
+                  ' origin time using TauPy'.format(arrival_time_p, arrival_time_s))
+            return arrival_time_p, arrival_time_s
 
         def exit_taupy():
             """If taupy failed to calculate theoretical starttimes, picking continues.
@@ -477,10 +481,13 @@ class AutopickStation(object):
             raise AttributeError('No source origins given!')
 
         arrivals = create_arrivals(self.metadata, self.origin, self.pickparams["taup_model"])
-        estFirstP, estFirstS = first_PS_onsets(arrivals)
+        arrival_P, arrival_S = first_PS_onsets(arrivals)
+
+        self.estFirstP = (self.origin[0].time + arrival_P) - self.ztrace.stats.starttime
+
         # modifiy pstart and pstop relative to estimated first P arrival (relative to station time axis)
-        self.pickparams["pstart"] += (self.origin[0].time + estFirstP) - self.ztrace.stats.starttime
-        self.pickparams["pstop"] += (self.origin[0].time + estFirstP) - self.ztrace.stats.starttime
+        self.pickparams["pstart"] += self.estFirstP
+        self.pickparams["pstop"] += self.estFirstP
         print('autopick: CF calculation times respectively:'
               ' pstart: {} s, pstop: {} s'.format(self.pickparams["pstart"], self.pickparams["pstop"]))
         # make sure pstart and pstop are inside the starttime/endtime of vertical trace
@@ -491,9 +498,10 @@ class AutopickStation(object):
             # 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])
+            self.estFirstS = (self.origin[0].time + arrival_S) - trace_s_start
             # 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
+            self.pickparams["sstart"] += self.estFirstS
+            self.pickparams["sstop"] += self.estFirstS
             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
@@ -609,6 +617,12 @@ class AutopickStation(object):
             # plot tapered trace filtered with bpz2 filter settings
             ax1.plot(tdata, self.tr_filt_z_bpz2.data / max(self.tr_filt_z_bpz2.data), color=linecolor, linewidth=0.7,
                      label='Data')
+            # plot pickwindows for P
+            pstart, pstop = self.pickparams['pstart'], self.pickparams['pstop']
+            if pstart is not None and pstop is not None:
+                ax1.axvspan(pstart, pstop, color='r', alpha=0.1, zorder=0, label='P window')
+            if self.estFirstP is not None:
+                ax1.axvline(self.estFirstP, ls='dashed', color='r', alpha=0.4, label='TauPy estimate')
             if self.p_results.weight < 4:
                 # plot CF of initial onset (HOScf or ARZcf)
                 ax1.plot(self.cf1.getTimeArray(), self.cf1.getCF() / max(self.cf1.getCF()), 'b', label='CF1')
@@ -713,6 +727,15 @@ class AutopickStation(object):
                         ax3.plot([refSpick.getpick() - 0.5, refSpick.getpick() + 0.5], [-1.3, -1.3], 'g', linewidth=2)
                         ax3.plot([self.s_results.lpp, self.s_results.lpp], [-1.1, 1.1], 'g--', label='lpp')
                         ax3.plot([self.s_results.epp, self.s_results.epp], [-1.1, 1.1], 'g--', label='epp')
+
+                # plot pickwindows for S
+                sstart, sstop = self.pickparams['sstart'], self.pickparams['sstop']
+                if sstart is not None and sstop is not None:
+                    for axis in [ax2, ax3]:
+                        axis.axvspan(sstart, sstop, color='b', alpha=0.1, zorder=0, label='S window')
+                        if self.estFirstS is not None:
+                            axis.axvline(self.estFirstS, ls='dashed', color='b', alpha=0.4, label='TauPy estimate')
+
                 ax3.legend(loc=1)
                 ax3.set_yticks([])
                 ax3.set_ylim([-1.5, 1.5])
@@ -835,14 +858,21 @@ class AutopickStation(object):
             self.cf1 = None
         assert isinstance(self.cf1, CharacteristicFunction), 'cf1 is not set correctly: maybe the algorithm name ({})' \
                                                              ' is corrupted'.format(self.pickparams["algoP"])
+        # get the original waveform stream from first CF class cut to identical length as CF for plotting
+        cut_ogstream = self.cf1.getDataArray(self.cf1.getCut())
+
+        # MP: Rename to cf_stream for further use of z_copy and to prevent chaos when z_copy suddenly becomes a cf
+        # stream and later again a waveform stream
+        cf_stream = z_copy.copy()
+        cf_stream[0].data = self.cf1.getCF()
+
         # calculate AIC cf from first cf (either HOS or ARZ)
-        z_copy[0].data = self.cf1.getCF()
-        aiccf = AICcf(z_copy, cuttimes)
+        aiccf = AICcf(cf_stream, cuttimes)
         # get preliminary onset time from AIC-CF
         self.set_current_figure('aicFig')
         aicpick = AICPicker(aiccf, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot,
                             Tsmooth=self.pickparams["aictsmooth"], fig=self.current_figure,
-                            linecolor=self.current_linecolor)
+                            linecolor=self.current_linecolor, ogstream=cut_ogstream)
         # save aicpick for plotting later
         self.p_data.aicpick = aicpick
         # add pstart and pstop to aic plot
@@ -855,7 +885,7 @@ class AutopickStation(object):
                           label='P stop')
                 ax.legend(loc=1)
 
-        Pflag = self._pick_p_quality_control(aicpick, z_copy, tr_filt)
+        Pflag = self._pick_p_quality_control(aicpick, cf_stream, tr_filt)
         # go on with processing if AIC onset passes quality control
         slope = aicpick.getSlope()
         if not slope: slope = 0
@@ -894,7 +924,7 @@ class AutopickStation(object):
         refPpick = PragPicker(self.cf2, self.pickparams["tsnrz"], self.pickparams["pickwinP"], self.iplot,
                               self.pickparams["ausP"],
                               self.pickparams["tsmoothP"], aicpick.getpick(), self.current_figure,
-                              self.current_linecolor)
+                              self.current_linecolor, ogstream=cut_ogstream)
         # save PragPicker result for plotting
         self.p_data.refPpick = refPpick
         self.p_results.mpp = refPpick.getpick()
@@ -1146,11 +1176,14 @@ class AutopickStation(object):
         # calculate AIC cf
         haiccf = self._calculate_aic_cf_s_pick(cuttimesh)
 
+        # get the original waveform stream cut to identical length as CF for plotting
+        ogstream = haiccf.getDataArray(haiccf.getCut())
+
         # get preliminary onset time from AIC cf
         self.set_current_figure('aicARHfig')
         aicarhpick = AICPicker(haiccf, self.pickparams["tsnrh"], self.pickparams["pickwinS"], self.iplot,
                                Tsmooth=self.pickparams["aictsmoothS"], fig=self.current_figure,
-                               linecolor=self.current_linecolor)
+                               linecolor=self.current_linecolor, ogstream=ogstream)
         # save pick for later plotting
         self.aicarhpick = aicarhpick
 

pylot/core/pick/charfuns.py

@@ -17,7 +17,11 @@ autoregressive prediction: application ot local and regional distances, Geophys.
 :author: MAGS2 EP3 working group
 """
 import numpy as np
-from scipy import signal
+try:
+    from scipy.signal import tukey
+except ImportError:
+    from scipy.signal.windows import tukey
+
 from obspy.core import Stream
 
 from pylot.core.pick.utils import PickingFailedException
@@ -56,7 +60,7 @@ class CharacteristicFunction(object):
         self.setOrder(order)
         self.setFnoise(fnoise)
         self.setARdetStep(t2)
-        self.calcCF(self.getDataArray())
+        self.calcCF()
         self.arpara = np.array([])
         self.xpred = np.array([])
 
@@ -208,17 +212,15 @@ class CharacteristicFunction(object):
             data = self.orig_data.copy()
             return data
 
-    def calcCF(self, data=None):
-        self.cf = data
+    def calcCF(self):
+        pass
 
 
 class AICcf(CharacteristicFunction):
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         Function to calculate the Akaike Information Criterion (AIC) after Maeda (1985).
-        :param data: data, time series (whether seismogram or CF)
-        :type data: tuple
         :return: AIC function
         :rtype:
         """
@@ -227,7 +229,7 @@ class AICcf(CharacteristicFunction):
         ind = np.where(~np.isnan(xnp))[0]
         if ind.size:
             xnp[:ind[0]] = xnp[ind[0]]
-        xnp = signal.tukey(len(xnp), alpha=0.05) * xnp
+        xnp = tukey(len(xnp), alpha=0.05) * xnp
         xnp = xnp - np.mean(xnp)
         datlen = len(xnp)
         k = np.arange(1, datlen)
@@ -256,13 +258,11 @@ class HOScf(CharacteristicFunction):
         """
         super(HOScf, self).__init__(data, cut, pickparams["tlta"], pickparams["hosorder"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         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), or order 2, i.e. STA/LTA.
-        :param data: data, time series (whether seismogram or CF)
-        :type data: tuple
         :return: HOS cf
         :rtype:
         """
@@ -277,47 +277,28 @@ 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
@@ -326,10 +307,7 @@ 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.cf = LTA
         self.xcf = x
 
 
@@ -339,12 +317,10 @@ class ARZcf(CharacteristicFunction):
         super(ARZcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Parorder"],
                                     fnoise=pickparams["addnoise"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         function used to calculate the AR prediction error from a single vertical trace. Can be used to pick
         P onsets.
-        :param data:
-        :type data: ~obspy.core.stream.Stream
         :return: ARZ cf
         :rtype:
         """
@@ -475,14 +451,12 @@ class ARHcf(CharacteristicFunction):
         super(ARHcf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"],
                                     fnoise=pickparams["addnoise"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         Function to calculate a characteristic function using autoregressive modelling of the waveform of
         both horizontal traces.
         The waveform is predicted in a moving time window using the calculated AR parameters. The difference
         between the predicted and the actual waveform servers as a characteristic function.
-        :param data: wavefor stream
-        :type data: ~obspy.core.stream.Stream
         :return: ARH cf
         :rtype:
         """
@@ -631,14 +605,12 @@ class AR3Ccf(CharacteristicFunction):
         super(AR3Ccf, self).__init__(data, cut, t1=t1, t2=t2, order=pickparams["Sarorder"],
                                      fnoise=pickparams["addnoise"])
 
-    def calcCF(self, data):
+    def calcCF(self):
         """
         Function to calculate a characteristic function using autoregressive modelling of the waveform of
         all three traces.
         The waveform is predicted in a moving time window using the calculated AR parameters. The difference
         between the predicted and the actual waveform servers as a characteristic function
-        :param data: stream holding all three traces
-        :type data: ~obspy.core.stream.Stream
         :return: AR3C cf
         :rtype:
         """

pylot/core/pick/picker.py

@@ -37,7 +37,8 @@ class AutoPicker(object):
 
     warnings.simplefilter('ignore')
 
-    def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None, fig=None, linecolor='k'):
+    def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None,
+                 fig=None, linecolor='k', ogstream=None):
         """
         Create AutoPicker object
         :param cf: characteristic function, on which the picking algorithm is applied
@@ -59,12 +60,15 @@ class AutoPicker(object):
         :type fig: `~matplotlib.figure.Figure`
         :param linecolor: matplotlib line color string
         :type linecolor: str
+        :param ogstream: original stream (waveform), e.g. for plotting purposes
+        :type ogstream: `~obspy.core.stream.Stream`
         """
 
         assert isinstance(cf, CharacteristicFunction), "%s is not a CharacteristicFunction object" % str(cf)
         self._linecolor = linecolor
         self._pickcolor_p = 'b'
         self.cf = cf.getCF()
+        self.ogstream = ogstream
         self.Tcf = cf.getTimeArray()
         self.Data = cf.getXCF()
         self.dt = cf.getIncrement()
@@ -173,7 +177,7 @@ class AICPicker(AutoPicker):
         nn = np.isnan(self.cf)
         if len(nn) > 1:
             self.cf[nn] = 0
-        # taper AIC-CF to get rid off side maxima
+        # taper AIC-CF to get rid of side maxima
         tap = np.hanning(len(self.cf))
         aic = tap * self.cf + max(abs(self.cf))
         # smooth AIC-CF
@@ -316,16 +320,7 @@ class AICPicker(AutoPicker):
                             plt.close(fig)
                     return
                 iislope = islope[0][0:imax + 1]
-            # MP MP change slope calculation
-            # get all maxima of aicsmooth
-            iaicmaxima = argrelmax(aicsmooth)[0]
-            # get first index of maximum after pickindex (indices saved in iaicmaxima)
-            aicmax = iaicmaxima[np.where(iaicmaxima > pickindex)[0]]
-            if len(aicmax) > 0:
-                iaicmax = aicmax[0]
-            else:
-                iaicmax = -1
-            dataslope = aicsmooth[pickindex: iaicmax]
+            dataslope = self.Data[0].data[iislope]
             # calculate slope as polynomal fit of order 1
             xslope = np.arange(0, len(dataslope), 1)
             try:
@@ -336,7 +331,7 @@ class AICPicker(AutoPicker):
                 else:
                     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]
+                    self.slope /= self.Data[0].data[icfmax]
             except Exception as e:
                 print("AICPicker: Problems with data fitting! {}".format(e))
 
@@ -356,6 +351,12 @@ class AICPicker(AutoPicker):
                 self.Tcf = self.Tcf[0:len(self.Tcf) - 1]
             ax1.plot(self.Tcf, cf / max(cf), color=self._linecolor, linewidth=0.7, label='(HOS-/AR-) Data')
             ax1.plot(self.Tcf, aicsmooth / max(aicsmooth), 'r', label='Smoothed AIC-CF')
+            # plot the original waveform also for evaluation of the CF and pick
+            if self.ogstream:
+                data = self.ogstream[0].data
+                if len(data) == len(self.Tcf):
+                    ax1.plot(self.Tcf, 0.5 * data / max(data), 'k', label='Seismogram', alpha=0.3, zorder=0,
+                             lw=0.5)
             if self.Pick is not None:
                 ax1.plot([self.Pick, self.Pick], [-0.1, 0.5], 'b', linewidth=2, label='AIC-Pick')
             ax1.set_xlabel('Time [s] since %s' % self.Data[0].stats.starttime)
@@ -376,7 +377,7 @@ class AICPicker(AutoPicker):
                             label='Signal Window')
                 ax2.axvspan(self.Tcf[iislope[0]], self.Tcf[iislope[-1]], color='g', alpha=0.2, lw=0,
                             label='Slope Window')
-                ax2.plot(self.Tcf[pickindex: iaicmax], datafit, 'g', linewidth=2,
+                ax2.plot(self.Tcf[iislope], datafit, 'g', linewidth=2,
                          label='Slope')  # MP MP changed temporarily!
 
                 if self.slope is not None:

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, common_range
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -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
@@ -275,7 +275,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P1 = np.polyfit(xslope1, xraw[islope1], 1)
                 datafit1 = np.polyval(P1, xslope1)
-            except Exception as e:
+            except ValueError as e:
                 print("fmpicker: Problems with data fit! {}".format(e))
                 print("Skip first motion determination!")
                 return FM
@@ -321,7 +321,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P2 = np.polyfit(xslope2, xfilt[islope2], 1)
                 datafit2 = np.polyval(P2, xslope2)
-            except Exception as e:
+            except ValueError as e:
                 emsg = 'fmpicker: polyfit failed: {}'.format(e)
                 print(emsg)
                 return FM
@@ -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
@@ -828,14 +828,22 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
     if len(X) > 1:
         # all three components available
         # make sure, all components have equal lengths
-        ilen = min([len(X[0].data), len(X[1].data), len(X[2].data)])
-        x1 = X[0][0:ilen]
-        x2 = X[1][0:ilen]
-        x3 = X[2][0:ilen]
+        earliest_starttime = min(tr.stats.starttime for tr in X)
+        cuttimes = common_range(X)
+        X = X.slice(cuttimes[0], cuttimes[1])
+        x1, x2, x3 = X[:3]
+
+        if not (len(x1) == len(x2) == len(x3)):
+            raise PickingFailedException('checksignallength: unequal lengths of components!')
+
         # get RMS trace
         rms = np.sqrt((np.power(x1, 2) + np.power(x2, 2) + np.power(x3, 2)) / 3)
+        ilen = len(rms)
+        dt = earliest_starttime - X[0].stats.starttime
+        pick -= dt
     else:
         x1 = X[0].data
+        x2 = x3 = None
         ilen = len(x1)
         rms = abs(x1)
 
@@ -868,12 +876,16 @@ 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
         ax = fig.add_subplot(111)
         ax.plot(t, rms, color=linecolor, linewidth=0.7, label='RMS Data')
+        ax.plot(t, x1, 'k', alpha=0.3, lw=0.3, zorder=0)
+        if x2 is not None and x3 is not None:
+            ax.plot(t, x2, 'r', alpha=0.3, lw=0.3, zorder=0)
+            ax.plot(t, x3, 'g', alpha=0.3, lw=0.3, zorder=0)
         ax.axvspan(t[inoise[0]], t[inoise[-1]], color='y', alpha=0.2, lw=0, label='Noise Window')
         ax.axvspan(t[isignal[0]], t[isignal[-1]], color='b', alpha=0.2, lw=0, label='Signal Window')
         ax.plot([t[isignal[0]], t[isignal[len(isignal) - 1]]],
@@ -883,6 +895,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
         ax.set_xlabel('Time [s] since %s' % X[0].stats.starttime)
         ax.set_ylabel('Counts')
         ax.set_title('Check for Signal Length, Station %s' % X[0].stats.station)
+        ax.set_xlim(pickparams["pstart"], pickparams["pstop"])
         ax.set_yticks([])
         if plt_flag == 1:
             fig.show()
@@ -1213,14 +1226,14 @@ 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)
@@ -1494,7 +1507,7 @@ 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]:

pylot/core/util/array_map.py

@@ -5,14 +5,17 @@ import traceback
 
 import cartopy.crs as ccrs
 import cartopy.feature as cf
+from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
 import matplotlib
 import matplotlib.patheffects as PathEffects
 import matplotlib.pyplot as plt
 import numpy as np
 import obspy
-from PySide2 import QtWidgets
+from PySide2 import QtWidgets, QtGui
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+from obspy import UTCDateTime
+
 from pylot.core.util.utils import identifyPhaseID
 from scipy.interpolate import griddata
 
@@ -24,10 +27,10 @@ matplotlib.use('Qt5Agg')
 
 class MplCanvas(FigureCanvas):
 
-    def __init__(self, parent=None, extern_axes=None, width=5, height=4, dpi=100):
+    def __init__(self, extern_axes=None, projection=None, width=15, height=5, dpi=100):
         if extern_axes is None:
             self.fig = plt.figure(figsize=(width, height), dpi=dpi)
-            self.axes = self.fig.add_subplot(111)
+            self.axes = self.fig.add_subplot(111, projection=projection)
         else:
             self.fig = extern_axes.figure
             self.axes = extern_axes
@@ -59,24 +62,30 @@ class Array_map(QtWidgets.QWidget):
         self.parameter = parameter if parameter else parent._inputs
 
         self.picks_rel = {}
+        self.picks_rel_mean_corrected = {}
         self.marked_stations = []
         self.highlighted_stations = []
 
         # call functions to draw everything
+        self.projection = ccrs.PlateCarree()
         self.init_graphics()
+        self.ax = self.canvas.axes
+        self.ax.set_adjustable('datalim')
+
         self.init_stations()
         self.init_crtpyMap()
         self.init_map()
+
         # set original map limits to fall back on when home button is pressed
-        self.org_xlim = self.canvas.axes.get_xlim()
-        self.org_ylim = self.canvas.axes.get_ylim()
+        self.org_xlim = self.ax.get_xlim()
+        self.org_ylim = self.ax.get_ylim()
+
         # initial map without event
-        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
-        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        self.ax.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.ax.set_ylim(self.org_ylim[0], self.org_ylim[1])
 
         self._style = None if not hasattr(parent, '_style') else parent._style
 
-
     def init_map(self):
         self.init_colormap()
         self.connectSignals()
@@ -89,23 +98,24 @@ class Array_map(QtWidgets.QWidget):
         # initialize figure elements
 
         if self.extern_plot_axes is None:
-            self.canvas = MplCanvas(self)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
+            self.canvas = MplCanvas(projection=self.projection)
         else:
-            self.canvas = MplCanvas(self, extern_axes=self.extern_plot_axes)
-            self.plotWidget = FigureCanvas(self.canvas.fig)
+            self.canvas = MplCanvas(extern_axes=self.extern_plot_axes)
+
+        self.plotWidget = self.canvas
 
         # initialize GUI elements
         self.status_label = QtWidgets.QLabel()
         self.map_reset_button = QtWidgets.QPushButton('Reset Map View')
         self.save_map_button = QtWidgets.QPushButton('Save Map')
         self.go2eq_button = QtWidgets.QPushButton('Go to Event Location')
+        self.subtract_mean_cb = QtWidgets.QCheckBox('Subtract mean')
 
         self.main_box = QtWidgets.QVBoxLayout()
         self.setLayout(self.main_box)
 
         self.top_row = QtWidgets.QHBoxLayout()
-        self.main_box.addLayout(self.top_row, 1)
+        self.main_box.addLayout(self.top_row, 0)
 
         self.comboBox_phase = QtWidgets.QComboBox()
         self.comboBox_phase.insertItem(0, 'P')
@@ -124,8 +134,8 @@ 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
-        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('hsv'))
+        # try to set to plasma as default
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('plasma'))
 
         self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
@@ -138,14 +148,15 @@ class Array_map(QtWidgets.QWidget):
         self.top_row.addWidget(self.auto_refresh_box)
         self.top_row.addWidget(self.refresh_button)
 
-        self.main_box.addWidget(self.plotWidget, 1)
+        self.main_box.addWidget(self.plotWidget, 10)
 
         self.bot_row = QtWidgets.QHBoxLayout()
-        self.main_box.addLayout(self.bot_row, 0.3)
+        self.main_box.addLayout(self.bot_row, 0)
         self.bot_row.addWidget(QtWidgets.QLabel(''), 5)
         self.bot_row.addWidget(self.map_reset_button, 2)
         self.bot_row.addWidget(self.go2eq_button, 2)
         self.bot_row.addWidget(self.save_map_button, 2)
+        self.bot_row.addWidget(self.subtract_mean_cb, 0)
         self.bot_row.addWidget(self.status_label, 5)
 
     def init_colormap(self):
@@ -153,14 +164,12 @@ class Array_map(QtWidgets.QWidget):
         self.init_lat_lon_grid()
 
     def init_crtpyMap(self):
-        self.canvas.axes.cla()
-        self.canvas.axes = plt.axes(projection=ccrs.PlateCarree())
-        self.canvas.axes.add_feature(cf.LAND)
-        self.canvas.axes.add_feature(cf.OCEAN)
-        self.canvas.axes.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
-        self.canvas.axes.add_feature(cf.BORDERS, alpha=0.7)
-        self.canvas.axes.add_feature(cf.LAKES, alpha=0.7)
-        self.canvas.axes.add_feature(cf.RIVERS, linewidth=1)
+        self.ax.add_feature(cf.LAND)
+        self.ax.add_feature(cf.OCEAN)
+        self.ax.add_feature(cf.COASTLINE, linewidth=1, edgecolor='gray')
+        self.ax.add_feature(cf.BORDERS, alpha=0.7)
+        self.ax.add_feature(cf.LAKES, alpha=0.7)
+        self.ax.add_feature(cf.RIVERS, linewidth=1)
 
         # parallels and meridians
         self.add_merid_paral()
@@ -168,12 +177,8 @@ class Array_map(QtWidgets.QWidget):
         self.canvas.fig.tight_layout()
 
     def add_merid_paral(self):
-        self.gridlines = self.canvas.axes.gridlines(draw_labels=False, alpha=0.6, color='gray',
-                                                    linewidth=self.linewidth / 2, zorder=7)
-        # TODO: current cartopy version does not support label removal. Devs are working on it.
-        #  Should be fixed in coming cartopy versions
-        # self.gridlines.xformatter = LONGITUDE_FORMATTER
-        # self.gridlines.yformatter = LATITUDE_FORMATTER
+        self.gridlines = self.ax.gridlines(draw_labels=False, alpha=0.6, color='gray',
+                                           linewidth=self.linewidth / 2, zorder=7, crs=ccrs.PlateCarree())
 
     def remove_merid_paral(self):
         if len(self.gridlines.xline_artists):
@@ -181,24 +186,24 @@ class Array_map(QtWidgets.QWidget):
             self.gridlines.yline_artists[0].remove()
 
     def org_map_view(self):
-        self.canvas.axes.set_xlim(self.org_xlim[0], self.org_xlim[1])
-        self.canvas.axes.set_ylim(self.org_ylim[0], self.org_ylim[1])
+        self.ax.set_xlim(self.org_xlim[0], self.org_xlim[1])
+        self.ax.set_ylim(self.org_ylim[0], self.org_ylim[1])
         # parallels and meridians
-        self.remove_merid_paral()
-        self.add_merid_paral()
+        #self.remove_merid_paral()
+        #self.add_merid_paral()
 
-        self.canvas.axes.figure.canvas.draw_idle()
+        self.canvas.draw_idle()
 
     def go2eq(self):
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.canvas.axes.set_xlim(lons - 10, lons + 10)
-            self.canvas.axes.set_ylim(lats - 5, lats + 5)
+            self.ax.set_xlim(lons - 10, lons + 10)
+            self.ax.set_ylim(lats - 5, lats + 5)
             # parallels and meridians
-            self.remove_merid_paral()
-            self.add_merid_paral()
+            #self.remove_merid_paral()
+            #self.add_merid_paral()
 
-            self.canvas.axes.figure.canvas.draw_idle()
+            self.canvas.draw_idle()
 
         else:
             self.status_label.setText('No event information available')
@@ -212,6 +217,7 @@ class Array_map(QtWidgets.QWidget):
         self.map_reset_button.clicked.connect(self.org_map_view)
         self.go2eq_button.clicked.connect(self.go2eq)
         self.save_map_button.clicked.connect(self.saveFigure)
+        self.subtract_mean_cb.stateChanged.connect(self.toggle_subtract_mean)
 
         self.plotWidget.mpl_connect('motion_notify_event', self.mouse_moved)
         self.plotWidget.mpl_connect('scroll_event', self.mouse_scroll)
@@ -220,21 +226,32 @@ class Array_map(QtWidgets.QWidget):
 
     # set mouse events -----------------------------------------------------
     def mouse_moved(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
+        else:
+            cont, inds = self.sc.contains(event)
         lat = event.ydata
         lon = event.xdata
-        self.status_label.setText('Latitude: {:3.5f}, Longitude: {:3.5f}'.format(lat, lon))
+        text = f'Longitude: {lon:3.3f}, Latitude: {lat:3.3f}'
+
+        if cont:
+            indices = inds['ind']
+            text += ' | Station: ' if len(indices) == 1 else ' | Stations: '
+            text += ' - '.join([self._station_onpick_ids[index] for index in indices[:5]])
+            if len(indices) > 5:
+                text += '...'
+
+        self.status_label.setText(text)
 
     def mouse_scroll(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
 
         zoom = {'up': 1. / 2., 'down': 2.}
 
         if event.button in zoom:
-            xlim = self.canvas.axes.get_xlim()
-            ylim = self.canvas.axes.get_ylim()
+            xlim = self.ax.get_xlim()
+            ylim = self.ax.get_ylim()
 
             x, y = event.xdata, event.ydata
 
@@ -246,24 +263,24 @@ class Array_map(QtWidgets.QWidget):
             yb = y - 0.5 * ydiff
             yt = y + 0.5 * ydiff
 
-            self.canvas.axes.set_xlim(xl, xr)
-            self.canvas.axes.set_ylim(yb, yt)
+            self.ax.set_xlim(xl, xr)
+            self.ax.set_ylim(yb, yt)
             # parallels and meridians
-            self.remove_merid_paral()
-            self.add_merid_paral()
+            #self.remove_merid_paral()
+            #self.add_merid_paral()
 
-            self.canvas.axes.figure.canvas.draw_idle()
+            self.ax.figure.canvas.draw_idle()
 
     def mouseLeftPress(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
         self.map_x = event.xdata
         self.map_y = event.ydata
-        self.map_xlim = self.canvas.axes.get_xlim()
-        self.map_ylim = self.canvas.axes.get_ylim()
+        self.map_xlim = self.ax.get_xlim()
+        self.map_ylim = self.ax.get_ylim()
 
     def mouseLeftRelease(self, event):
-        if not event.inaxes == self.canvas.axes:
+        if not event.inaxes == self.ax:
             return
         new_x = event.xdata
         new_y = event.ydata
@@ -271,13 +288,13 @@ class Array_map(QtWidgets.QWidget):
         dx = new_x - self.map_x
         dy = new_y - self.map_y
 
-        self.canvas.axes.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
-        self.canvas.axes.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
+        self.ax.set_xlim((self.map_xlim[0] - dx, self.map_xlim[1] - dx))
+        self.ax.set_ylim(self.map_ylim[0] - dy, self.map_ylim[1] - dy)
         # parallels and meridians
-        self.remove_merid_paral()
-        self.add_merid_paral()
+        #self.remove_merid_paral()
+        #self.add_merid_paral()
 
-        self.canvas.axes.figure.canvas.draw_idle()
+        self.ax.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.'}
@@ -357,12 +374,6 @@ class Array_map(QtWidgets.QWidget):
     def get_max_from_stations(self, key):
         return self._from_dict(max, key)
 
-    def get_min_from_picks(self):
-        return min(self.picks_rel.values())
-
-    def get_max_from_picks(self):
-        return max(self.picks_rel.values())
-
     def current_picks_dict(self):
         picktype = self.comboBox_am.currentText().split(' ')[0]
         auto_manu = {'auto': self.autopicks_dict,
@@ -407,22 +418,34 @@ class Array_map(QtWidgets.QWidget):
                     print('Cannot display pick for station {}. Reason: {}'.format(station_name, e))
             return picks, uncertainties
 
-        def get_picks_rel(picks):
+        def get_picks_rel(picks, func=min):
             picks_rel = {}
             picks_utc = []
             for pick in picks.values():
-                if type(pick) is obspy.core.utcdatetime.UTCDateTime:
-                    picks_utc.append(pick)
+                if type(pick) is UTCDateTime:
+                    picks_utc.append(pick.timestamp)
             if picks_utc:
-                self._earliest_picktime = min(picks_utc)
+                self._reference_picktime = UTCDateTime(func(picks_utc))
                 for st_id, pick in picks.items():
-                    if type(pick) is obspy.core.utcdatetime.UTCDateTime:
-                        pick -= self._earliest_picktime
+                    if type(pick) is UTCDateTime:
+                        pick -= self._reference_picktime
                     picks_rel[st_id] = pick
             return picks_rel
 
+        def get_picks_rel_mean_corr(picks):
+            return get_picks_rel(picks, func=np.nanmean)
+
         self.picks, self.uncertainties = get_picks(self.stations_dict)
         self.picks_rel = get_picks_rel(self.picks)
+        self.picks_rel_mean_corrected = get_picks_rel_mean_corr(self.picks)
+
+    def toggle_subtract_mean(self):
+        if self.subtract_mean_cb.isChecked():
+            cmap = 'seismic'
+        else:
+            cmap = 'viridis'
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText(cmap))
+        self._refresh_drawings()
 
     def init_lat_lon_dimensions(self):
         # init minimum and maximum lon and lat dimensions
@@ -453,11 +476,12 @@ class Array_map(QtWidgets.QWidget):
         return stations, latitudes, longitudes
 
     def get_picks_lat_lon(self):
+        picks_rel = self.picks_rel_mean_corrected if self.subtract_mean_cb.isChecked() else self.picks_rel
         picks = []
         uncertainties = []
         latitudes = []
         longitudes = []
-        for st_id, pick in self.picks_rel.items():
+        for st_id, pick in picks_rel.items():
             picks.append(pick)
             uncertainties.append(self.uncertainties.get(st_id))
             latitudes.append(self.stations_dict[st_id]['latitude'])
@@ -469,26 +493,34 @@ class Array_map(QtWidgets.QWidget):
         stat_dict = self.stations_dict['{}.{}'.format(network, station)]
         lat = stat_dict['latitude']
         lon = stat_dict['longitude']
-        self.highlighted_stations.append(self.canvas.axes.scatter(lon, lat, s=self.pointsize, edgecolors=color,
-                                                                  facecolors='none', zorder=12,
-                                                                  transform=ccrs.PlateCarree(), label='deleted'))
+        self.highlighted_stations.append(self.ax.scatter(lon, lat, s=self.pointsize, edgecolors=color,
+                                                         facecolors='none', zorder=12,
+                                                         transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        data = self._parent.get_data().getWFData()
+        try:
+            wfdata = self._parent.get_data().getWFData()
+        except AttributeError:
+            QtWidgets.QMessageBox.warning(
+                self, "PyLoT Warning",
+                "No waveform data found. Check if they were already loaded in Waveform plot tab."
+            )
+            return
+        wfdata_comp = self._parent.get_data().getAltWFdata()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
             pyl_mw = self._parent
             try:
-                data = data.select(station=station)
-                if not data:
+                wfdata = wfdata.select(station=station)
+                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)
@@ -516,12 +548,19 @@ class Array_map(QtWidgets.QWidget):
                 print(message, e)
                 print(traceback.format_exc())
 
-    def draw_contour_filled(self, nlevel=50):
-        levels = np.linspace(self.get_min_from_picks(), self.get_max_from_picks(), nlevel)
+    def draw_contour_filled(self, nlevel=51):
+        if self.subtract_mean_cb.isChecked():
+            abs_max = self.get_residuals_absmax()
+            levels = np.linspace(-abs_max, abs_max, nlevel)
+        else:
+            levels = np.linspace(min(self.picks_rel.values()), max(self.picks_rel.values()), nlevel)
 
-        self.contourf = self.canvas.axes.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
-                                                  linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
-                                                  alpha=0.4, zorder=8, cmap=self.get_colormap())
+        self.contourf = self.ax.contourf(self.longrid, self.latgrid, self.picksgrid_active, levels,
+                                         linewidths=self.linewidth * 5, transform=ccrs.PlateCarree(),
+                                         alpha=0.4, zorder=8, cmap=self.get_colormap())
+
+    def get_residuals_absmax(self):
+        return np.max(np.absolute(list(self.picks_rel_mean_corrected.values())))
 
     def get_colormap(self):
         return plt.get_cmap(self.cmaps_box.currentText())
@@ -529,18 +568,18 @@ class Array_map(QtWidgets.QWidget):
     def scatter_all_stations(self):
         stations, lats, lons = self.get_st_lat_lon_for_plot()
 
-        self.sc = self.canvas.axes.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
-                                           zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
-                                           transform=ccrs.PlateCarree())
+        self.sc = self.ax.scatter(lons, lats, s=self.pointsize * 3, facecolor='none', marker='.',
+                                  zorder=10, picker=True, edgecolor='0.5', label='Not Picked',
+                                  transform=ccrs.PlateCarree())
 
         self.cid = self.plotWidget.mpl_connect('pick_event', self.onpick)
         self._station_onpick_ids = stations
         if self.eventLoc:
             lats, lons = self.eventLoc
-            self.sc_event = self.canvas.axes.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
-                                                     label='Event (might be outside map region)', marker='*',
-                                                     edgecolors='black',
-                                                     transform=ccrs.PlateCarree())
+            self.sc_event = self.ax.scatter(lons, lats, s=5 * self.pointsize, facecolor='red', zorder=11,
+                                            label='Event (might be outside map region)', marker='*',
+                                            edgecolors='black',
+                                            transform=ccrs.PlateCarree())
 
     def scatter_picked_stations(self):
         picks, uncertainties, lats, lons = self.get_picks_lat_lon()
@@ -553,8 +592,13 @@ class Array_map(QtWidgets.QWidget):
                           for uncertainty in uncertainties])
 
         cmap = self.get_colormap()
-        self.sc_picked = self.canvas.axes.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap,
-                                                  c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
+
+        vmin = vmax = None
+        if self.subtract_mean_cb.isChecked():
+            vmin, vmax = -self.get_residuals_absmax(), self.get_residuals_absmax()
+
+        self.sc_picked = self.ax.scatter(lons, lats, s=sizes, edgecolors='white', cmap=cmap, vmin=vmin, vmax=vmax,
+                                         c=picks, zorder=11, label='Picked', transform=ccrs.PlateCarree())
 
     def annotate_ax(self):
         self.annotations = []
@@ -572,20 +616,20 @@ class Array_map(QtWidgets.QWidget):
             if st in self.marked_stations:
                 color = 'red'
             self.annotations.append(
-                self.canvas.axes.annotate(' %s' % st, xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
-                                          fontweight='semibold', color=color, alpha=0.8,
-                                          transform=ccrs.PlateCarree(), zorder=14,
-                                          path_effects=[PathEffects.withStroke(
-                                              linewidth=self.pointsize / 15., foreground='k')]))
+                self.ax.annotate(f'{st}', xy=(x + 0.003, y + 0.003), fontsize=self.pointsize / 4.,
+                                 fontweight='semibold', color=color, alpha=0.8,
+                                 transform=ccrs.PlateCarree(), zorder=14,
+                                 path_effects=[PathEffects.withStroke(
+                                     linewidth=self.pointsize / 15., foreground='k')]))
 
-        self.legend = self.canvas.axes.legend(loc=1, framealpha=1)
+        self.legend = self.ax.legend(loc=1, framealpha=1)
         self.legend.set_zorder(100)
         self.legend.get_frame().set_facecolor((1, 1, 1, 0.95))
 
     def add_cbar(self, label):
-        self.cbax_bg = inset_axes(self.canvas.axes, width="6%", height="75%", loc=5)
-        cbax = inset_axes(self.canvas.axes, width='2%', height='70%', loc=5)
-        cbar = self.canvas.axes.figure.colorbar(self.sc_picked, cax=cbax)
+        self.cbax_bg = inset_axes(self.ax, width="6%", height="75%", loc=5)
+        cbax = inset_axes(self.ax, width='2%', height='70%', loc=5)
+        cbar = self.ax.figure.colorbar(self.sc_picked, cax=cbax)
         cbar.set_label(label)
         cbax.yaxis.tick_left()
         cbax.yaxis.set_label_position('left')
@@ -630,7 +674,9 @@ class Array_map(QtWidgets.QWidget):
         if picks_available:
             self.scatter_picked_stations()
             if hasattr(self, 'sc_picked'):
-                self.cbar = self.add_cbar(label='Time relative to first onset ({}) [s]'.format(self._earliest_picktime))
+                self.cbar = self.add_cbar(
+                    label='Time relative to reference onset ({}) [s]'.format(self._reference_picktime)
+                )
             self.comboBox_phase.setEnabled(True)
         else:
             self.comboBox_phase.setEnabled(False)

pylot/core/util/dataprocessing.py

@@ -27,6 +27,10 @@ class Metadata(object):
         # saves which metadata files are from obspy dmt
         self.obspy_dmt_invs = []
         if inventory:
+            # make sure that no accidental backslashes mess up the path
+            if isinstance(inventory, str):
+                inventory = inventory.replace('\\', '/')
+                inventory = os.path.abspath(inventory)
             if os.path.isdir(inventory):
                 self.add_inventory(inventory)
             if os.path.isfile(inventory):
@@ -55,6 +59,8 @@ class Metadata(object):
         :type path_to_inventory: str
         :return: None
         """
+        path_to_inventory = path_to_inventory.replace('\\', '/')
+        path_to_inventory = os.path.abspath(path_to_inventory)
         assert (os.path.isdir(path_to_inventory)), '{} is no directory'.format(path_to_inventory)
         if path_to_inventory not in self.inventories:
             self.inventories.append(path_to_inventory)
@@ -262,9 +268,6 @@ class Metadata(object):
         if not fnames:
             # search for station name in filename
             fnames = glob.glob(os.path.join(path_to_inventory, '*' + station + '*'))
-        if not fnames:
-            # search for network name in filename
-            fnames = glob.glob(os.path.join(path_to_inventory, '*' + network + '*'))
         if not fnames:
             if self.verbosity:
                 print('Could not find filenames matching station name, network name or seed id')
@@ -276,7 +279,7 @@ class Metadata(object):
                     continue
             invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
             try:
-                # robj.get_coordinates(station_seed_id)  # TODO: Commented out, failed with Parser, is this needed?
+                robj.get_coordinates(station_seed_id)
                 self.inventory_files[fname] = {'invtype': invtype,
                                                'data': robj}
                 if station_seed_id in self.seed_ids.keys():
@@ -284,6 +287,7 @@ class Metadata(object):
                 self.seed_ids[station_seed_id] = fname
                 return True
             except Exception as e:
+                logging.warning(e)
                 continue
         print('Could not find metadata for station_seed_id {} in path {}'.format(station_seed_id, path_to_inventory))
 
@@ -648,6 +652,8 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
     """
 
     # data = remove_underscores(data)
+    if not data:
+        return
 
     # loop over traces
     input_tuples = []
@@ -655,9 +661,14 @@ def restitute_data(data, metadata, unit='VEL', force=False, ncores=0):
         input_tuples.append((tr, metadata, unit, force))
         data.remove(tr)
 
-    pool = gen_Pool(ncores)
-    result = pool.imap_unordered(restitute_trace, input_tuples)
-    pool.close()
+    if ncores == 0:
+        result = []
+        for input_tuple in input_tuples:
+            result.append(restitute_trace(input_tuple))
+    else:
+        pool = gen_Pool(ncores)
+        result = pool.imap_unordered(restitute_trace, input_tuples)
+        pool.close()
 
     for tr, remove_trace in result:
         if not remove_trace:

pylot/core/util/event.py

@@ -22,14 +22,11 @@ class Event(ObsPyEvent):
         :param path: path to event directory
         :type path: str
         """
-        # TODO: remove rootpath and database
         self.pylot_id = path.split('/')[-1]
         # initialize super class
         super(Event, self).__init__(resource_id=ResourceIdentifier('smi:local/' + self.pylot_id))
         self.path = path
-        self.database = path.split('/')[-2]
         self.datapath = os.path.split(path)[0]  # path.split('/')[-3]
-        self.rootpath = '/' + os.path.join(*path.split('/')[:-3])
         self.pylot_autopicks = {}
         self.pylot_picks = {}
         self.notes = ''

pylot/core/util/gui.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import os
+from functools import lru_cache
 
 try:
     import pyqtgraph as pg
@@ -25,14 +26,14 @@ def pick_linestyle_pg(picktype, key):
     :return: Qt line style parameters
     :rtype:
     """
-    linestyles_manu = {'mpp': (QtCore.Qt.SolidLine, 2.),
-                       'epp': (QtCore.Qt.DashLine, 1.),
-                       'lpp': (QtCore.Qt.DashLine, 1.),
-                       'spe': (QtCore.Qt.DashLine, 1.)}
-    linestyles_auto = {'mpp': (QtCore.Qt.DotLine, 2.),
-                       'epp': (QtCore.Qt.DashDotLine, 1.),
-                       'lpp': (QtCore.Qt.DashDotLine, 1.),
-                       'spe': (QtCore.Qt.DashDotLine, 1.)}
+    linestyles_manu = {'mpp': (QtCore.Qt.SolidLine, 2),
+                       'epp': (QtCore.Qt.DashLine, 1),
+                       'lpp': (QtCore.Qt.DashLine, 1),
+                       'spe': (QtCore.Qt.DashLine, 1)}
+    linestyles_auto = {'mpp': (QtCore.Qt.DotLine, 2),
+                       'epp': (QtCore.Qt.DashDotLine, 1),
+                       'lpp': (QtCore.Qt.DashDotLine, 1),
+                       'spe': (QtCore.Qt.DashDotLine, 1)}
     linestyles = {'manual': linestyles_manu,
                   'auto': linestyles_auto}
     return linestyles[picktype][key]
@@ -80,6 +81,7 @@ def which(program, parameter):
     return None
 
 
+@lru_cache(maxsize=128)
 def make_pen(picktype, phase, key, quality):
     """
     Make  PyQtGraph.QPen

pylot/core/util/utils.py

@@ -8,6 +8,7 @@ import platform
 import re
 import subprocess
 import warnings
+from typing import Literal, Tuple, Type
 from functools import lru_cache
 
 import numpy as np
@@ -20,6 +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:
@@ -83,25 +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
@@ -167,11 +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]
@@ -303,7 +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)(\.|$)')
@@ -315,15 +301,32 @@ 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
@@ -331,11 +334,30 @@ def get_None(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 type(value) is bool:
         return value
@@ -343,8 +365,14 @@ def get_bool(value):
         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 bool(value)
+        return value
+
 
 def four_digits(year):
     """
@@ -355,8 +383,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
-    1920
+    >>> four_digits(75)
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -438,36 +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
-    :return: login ID
+    returns the actual user's name
+    :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"]:
@@ -513,6 +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)
 
@@ -539,24 +589,36 @@ def isSorted(iterable):
     >>> isSorted([2,3,1,4])
     False
     """
-    assert isIterable(iterable), 'object is not iterable; object: {' \
-                                 '}'.format(iterable)
+    assert is_iterable(iterable), "object is not iterable; object: {}".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
@@ -565,13 +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:
@@ -579,32 +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
-    :type stime: `~obspy.core.utcdatetime.UTCDateTime`
+    :param offset: offset of the actual seismogram on plotting axis
+    :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
-    time_ax = np.linspace(stime, etime, nsamp)
+    etime = offset + nsamp / srate
+    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'
@@ -620,13 +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:
@@ -637,7 +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.
 
@@ -650,7 +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)}
@@ -706,17 +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)
-    :param modifier: which color should be modified, eg. 'r', 'g', 'b'
-    :type modifier: str
+    :type rgba: Rgba
+    :param modifier: which color should be modified; options: 'r', 'g', 'b'
+    :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,
@@ -750,18 +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 colors_mpl
+        return '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
 
 
 def transform_colors_mpl(colors):
@@ -771,27 +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
@@ -928,11 +1008,11 @@ def get_possible_pylot_eventfile_extensions(event, fext):
 
 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:
@@ -959,66 +1039,88 @@ 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
-        :type wfstream: `~obspy.core.stream.Stream`
+        :param wfs_in: stream containing seismic traces of a station
+        :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`
         """
 
-        # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
-        orientations = [trace_id[-1] for trace_id in trace_ids]
-        rotation_required = [orientation.isnumeric() for orientation in orientations]
-        if any(rotation_required):
-            t_start = full_range(wfstream)
-            try:
-                azimuts = []
-                dips = []
-                for tr_id in trace_ids:
-                    azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
-                    dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
-            except (KeyError, TypeError) as e:
-                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
-                return wfstream
-            if len(wfstream) < 3:
-                print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
-                return wfstream
-            # to rotate all traces must have same length, so trim them
-            wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
-            try:
-                z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
-                                     wfstream[1], azimuts[1], dips[1],
-                                     wfstream[2], azimuts[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)
-                wfstream[z_index].data = z
-                wfstream[z_index].stats.channel = wfstream[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]
-                    if az > 315 or az <= 45 or az > 135 and 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:
-                        trace.data = e
-                        trace.stats.channel = trace.stats.channel[0:-1] + 'E'
-            except (ValueError) as e:
-                print(e)
-                return wfstream
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
 
-        return wfstream
+        # check if any traces in this station need to be rotated
+        trace_ids = [trace.id for trace in wfs_in]
+        if not rotation_required(trace_ids):
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            return wfs_in
+
+        # check metadata quality
+        t_start = full_range(wfs_in)[0]
+        try:
+            azimuths = []
+            dips = []
+            for tr_id in trace_ids:
+                azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
+        except (KeyError, TypeError) as err:
+            logging.warning(f"Rotating not possible, not all azimuth and dip information "
+                            f"available in metadata. Stream remains unchanged.")
+            logging.debug(f"Rotating not possible, {err=}, {type(err)=}")
+            return wfs_in
+        except Exception as err:
+            print(f"Unexpected {err=}, {type(err)=}")
+            raise
+
+        # to rotate all traces must have same length, so trim them
+        wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
+        try:
+            z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
+                                 wfs_out[1], azimuths[1], dips[1],
+                                 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)
+            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 = wfs_out.select(id=trace_id)[0]
+                if az > 315 or az <= 45 or 135 < az <= 225:
+                    trace.data = n
+                    trace.stats.channel = trace.stats.channel[0:-1] + 'N'
+                elif 45 < az <= 135 or 225 < az <= 315:
+                    trace.data = e
+                    trace.stats.channel = trace.stats.channel[0:-1] + 'E'
+        except ValueError as err:
+            print(f"{err=} Rotation failed. Stream remains unchanged.")
+            return wfs_in
+
+        return wfs_out
 
     if metadata is None:
         if verbosity:
@@ -1032,38 +1134,6 @@ 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

pylot/core/util/widgets.py

@@ -7,6 +7,8 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
+import glob
+import logging
 import multiprocessing
 import os
 import subprocess
@@ -16,6 +18,7 @@ import traceback
 
 import matplotlib
 import numpy as np
+from pylot.core.io.phases import getQualitiesfromxml
 
 matplotlib.use('QT5Agg')
 
@@ -49,11 +52,11 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
 from pylot.core.pick.compare import Comparison
 from pylot.core.pick.autopick import fmpicker
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
-from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
+from pylot.core.util.utils import prep_time_axis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
     pick_linestyle_plt, pick_color_plt, \
     check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
-    identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
+    identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
     station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
@@ -793,7 +796,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
 
     def connect_signals(self):
         self.qcombo_processed.activated.connect(self.parent().newWF)
-        self.syn_checkbox.clicked.connect(self.parent().newWF)
+        self.comp_checkbox.clicked.connect(self.parent().newWF)
 
     def init_labels(self):
         self.label_layout.addWidget(self.status_label)
@@ -804,13 +807,13 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         # use widgets as placeholder, so that child widgets keep position when others are hidden
         mid_layout = QHBoxLayout()
         right_layout = QHBoxLayout()
-        mid_layout.addWidget(self.syn_checkbox)
+        mid_layout.addWidget(self.comp_checkbox)
         right_layout.addWidget(self.qcombo_processed)
         mid_widget.setLayout(mid_layout)
         right_widget.setLayout(right_layout)
         self.label_layout.addWidget(mid_widget)
         self.label_layout.addWidget(right_widget)
-        self.syn_checkbox.setLayoutDirection(Qt.RightToLeft)
+        self.comp_checkbox.setLayoutDirection(Qt.RightToLeft)
         self.label_layout.setStretch(0, 4)
         self.label_layout.setStretch(1, 0)
         self.label_layout.setStretch(2, 0)
@@ -825,7 +828,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
             label = QtWidgets.QLabel()
             self.perm_labels.append(label)
         self.qcombo_processed = QtWidgets.QComboBox()
-        self.syn_checkbox = QtWidgets.QCheckBox('synthetics')
+        self.comp_checkbox = QtWidgets.QCheckBox('Load comparison data')
         self.addQCboxItem('processed', 'green')
         self.addQCboxItem('raw', 'black')
         # self.perm_qcbox_right.setAlignment(2)
@@ -834,9 +837,11 @@ class WaveformWidgetPG(QtWidgets.QWidget):
     def getPlotDict(self):
         return self.plotdict
 
-    def activateObspyDMToptions(self, activate):
-        self.syn_checkbox.setVisible(activate)
-        self.qcombo_processed.setVisible(activate)
+    def activateObspyDMToptions(self, activate: bool) -> None:
+        self.qcombo_processed.setEnabled(activate)
+
+    def activateCompareOptions(self, activate: bool) -> None:
+        self.comp_checkbox.setEnabled(activate)
 
     def setPermText(self, number, text=None, color='black'):
         if not 0 <= number < len(self.perm_labels):
@@ -936,10 +941,10 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
             stime = trace.stats.starttime - self.wfstart
-            time_ax = prepTimeAxis(stime, trace)
+            time_ax = prep_time_axis(stime, trace)
             if st_syn:
                 stime_syn = trace_syn.stats.starttime - self.wfstart
-                time_ax_syn = prepTimeAxis(stime_syn, trace_syn)
+                time_ax_syn = prep_time_axis(stime_syn, trace_syn)
 
             if method == 'fast':
                 trace.data, time_ax = self.minMax(trace, time_ax)
@@ -959,7 +964,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                     [time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else [])
                 trace.data = np.array(
                     [datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample])
-                trace_syn.data = np.array([datum + n for index, datum in enumerate(trace_syn.data)
+                trace_syn.data = np.array([datum + n + shift_syn for index, datum in enumerate(trace_syn.data)
                                            if not index % nth_sample] if st_syn else [])
                 plots.append((times, trace.data,
                               times_syn, trace_syn.data))
@@ -1148,12 +1153,12 @@ class PylotCanvas(FigureCanvas):
         ax.set_xlim(self.cur_xlim)
         ax.set_ylim(self.cur_ylim)
         self.refreshPickDlgText()
-        ax.figure.canvas.draw()
+        ax.figure.canvas.draw_idle()
 
     def panRelease(self, gui_event):
         self.press = None
         self.press_rel = None
-        self.figure.canvas.draw()
+        self.figure.canvas.draw_idle()
 
     def panZoom(self, gui_event, threshold=2., factor=1.1):
         if not gui_event.x and not gui_event.y:
@@ -1371,11 +1376,15 @@ class PylotCanvas(FigureCanvas):
             plot_positions[channel] = plot_pos
         return plot_positions
 
-    def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None,
+    def plotWFData(self, wfdata, wfdata_compare=None, title=None, zoomx=None, zoomy=None,
                    noiselevel=None, scaleddata=False, mapping=True,
                    component='*', nth_sample=1, iniPick=None, verbosity=0,
                    plot_additional=False, additional_channel=None, scaleToChannel=None,
                    snr=None):
+        def get_wf_dict(data: Stream = Stream(), linecolor = 'k', offset: float = 0., **plot_kwargs):
+            return dict(data=data, linecolor=linecolor, offset=offset, plot_kwargs=plot_kwargs)
+
+
         ax = self.axes[0]
         ax.cla()
 
@@ -1386,21 +1395,33 @@ class PylotCanvas(FigureCanvas):
         settings = QSettings()
         compclass = SetChannelComponents.from_qsettings(settings)
 
+        linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
+
+        plot_streams = dict(wfdata=get_wf_dict(linecolor=linecolor, linewidth=0.7),
+                            wfdata_comp=get_wf_dict(offset=0.1, linecolor='b', alpha=0.7, linewidth=0.5))
+
         if not component == '*':
             alter_comp = compclass.getCompPosition(component)
             # alter_comp = str(alter_comp[0])
 
-            st_select = wfdata.select(component=component)
-            st_select += wfdata.select(component=alter_comp)
+            plot_streams['wfdata']['data'] = wfdata.select(component=component)
+            plot_streams['wfdata']['data'] += wfdata.select(component=alter_comp)
+            if wfdata_compare:
+                plot_streams['wfdata_comp']['data'] = wfdata_compare.select(component=component)
+                plot_streams['wfdata_comp']['data'] += wfdata_compare.select(component=alter_comp)
         else:
-            st_select = wfdata
+            plot_streams['wfdata']['data'] = wfdata
+            if wfdata_compare:
+                plot_streams['wfdata_comp']['data'] = wfdata_compare
+
+        st_main = plot_streams['wfdata']['data']
 
         if mapping:
-            plot_positions = self.calcPlotPositions(st_select, compclass)
+            plot_positions = self.calcPlotPositions(st_main, compclass)
 
         # list containing tuples of network, station, channel and plot position (for sorting)
         nslc = []
-        for plot_pos, trace in enumerate(st_select):
+        for plot_pos, trace in enumerate(st_main):
             if not trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                 print('Warning: Unrecognized channel {}'.format(trace.stats.channel))
                 continue
@@ -1408,44 +1429,48 @@ class PylotCanvas(FigureCanvas):
         nslc.sort()
         nslc.reverse()
 
-        linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
-
         for n, seed_id in enumerate(nslc):
             network, station, location, channel = seed_id.split('.')
-            st = st_select.select(id=seed_id)
-            trace = st[0].copy()
-            if mapping:
-                n = plot_positions[trace.stats.channel]
-            if n > nmax:
-                nmax = n
-            if verbosity:
-                msg = 'plotting %s channel of station %s' % (channel, station)
-                print(msg)
-            stime = trace.stats.starttime - wfstart
-            time_ax = prepTimeAxis(stime, trace)
-            if time_ax is not None:
-                if scaleToChannel:
-                    st_scale = wfdata.select(channel=scaleToChannel)
-                    if st_scale:
-                        tr = st_scale[0]
+            for wf_name, wf_dict in plot_streams.items():
+                st_select = wf_dict.get('data')
+                if not st_select:
+                    continue
+                st = st_select.select(id=seed_id)
+                trace = st[0].copy()
+                if mapping:
+                    n = plot_positions[trace.stats.channel]
+                if n > nmax:
+                    nmax = n
+                if verbosity:
+                    msg = 'plotting %s channel of station %s' % (channel, station)
+                    print(msg)
+                stime = trace.stats.starttime - wfstart
+                time_ax = prep_time_axis(stime, trace)
+                if time_ax is not None:
+                    if scaleToChannel:
+                        st_scale = wfdata.select(channel=scaleToChannel)
+                        if st_scale:
+                            tr = st_scale[0]
+                            trace.detrend('constant')
+                            trace.normalize(np.max(np.abs(tr.data)) * 2)
+                            scaleddata = True
+                    if not scaleddata:
                         trace.detrend('constant')
-                        trace.normalize(np.max(np.abs(tr.data)) * 2)
-                        scaleddata = True
-                if not scaleddata:
-                    trace.detrend('constant')
-                    trace.normalize(np.max(np.abs(trace.data)) * 2)
+                        trace.normalize(np.max(np.abs(trace.data)) * 2)
 
-                times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
-                data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
-                ax.axhline(n, color="0.5", lw=0.5)
-                ax.plot(times, data, color=linecolor, linewidth=0.7)
-                if noiselevel is not None:
-                    for level in [-noiselevel[channel], noiselevel[channel]]:
-                        ax.plot([time_ax[0], time_ax[-1]],
-                                [n + level, n + level],
-                                color=linecolor,
-                                linestyle='dashed')
-                self.setPlotDict(n, seed_id)
+                    offset = wf_dict.get('offset')
+
+                    times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
+                    data = [datum + n + offset for index, datum in enumerate(trace.data) if not index % nth_sample]
+                    ax.axhline(n, color="0.5", lw=0.5)
+                    ax.plot(times, data, color=wf_dict.get('linecolor'), **wf_dict.get('plot_kwargs'))
+                    if noiselevel is not None:
+                        for level in [-noiselevel[channel], noiselevel[channel]]:
+                            ax.plot([time_ax[0], time_ax[-1]],
+                                    [n + level, n + level],
+                                    color=wf_dict.get('linecolor'),
+                                    linestyle='dashed')
+                    self.setPlotDict(n, seed_id)
         if plot_additional and additional_channel:
             compare_stream = wfdata.select(channel=additional_channel)
             if compare_stream:
@@ -1460,7 +1485,7 @@ class PylotCanvas(FigureCanvas):
                 if not scaleddata:
                     trace.detrend('constant')
                     trace.normalize(np.max(np.abs(trace.data)) * 2)
-                time_ax = prepTimeAxis(stime, trace)
+                time_ax = prep_time_axis(stime, trace)
                 times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
                 p_data = compare_stream[0].data
                 # #normalize
@@ -1574,6 +1599,8 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.events = events
         self.filepaths = []
         self.file_extensions = []
+        self.check_all_state = True
+        self.merge_strategy = None
         self.default_text = default_text
         self.label = label
         self.setButtons()
@@ -1581,16 +1608,17 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.connectSignals()
         self.showPaths()
         self.refreshSelectionBox()
-        self.refresh_timer = QTimer(self)
-        self.refresh_timer.timeout.connect(self.showPaths)
-        self.refresh_timer.start(10000)
+        # self.refresh_timer = QTimer(self)
+        # self.refresh_timer.timeout.connect(self.showPaths)
+        # self.refresh_timer.start(10000)
 
         self.resize(800, 450)
 
-
     def setupUi(self):
+        ncol = 4
         self.main_layout = QtWidgets.QVBoxLayout()
         self.header_layout = QtWidgets.QHBoxLayout()
+        self.footer_layout = QtWidgets.QHBoxLayout()
         #
         self.setLayout(self.main_layout)
 
@@ -1604,11 +1632,24 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.searchButton = QtWidgets.QPushButton('Search')
         self.searchButton.setVisible(False)
 
+        # check/uncheck button for table
+        self.checkAllButton = QtWidgets.QPushButton('Check/Uncheck all')
+
+        # radiobutton for merge selection
+        self.mergeRadioButtonGroup = QtWidgets.QButtonGroup()
+        self.merge_button = QtWidgets.QRadioButton('Merge')
+        self.overwrite_button = QtWidgets.QRadioButton('Overwrite')
+        self.mergeRadioButtonGroup.addButton(self.merge_button)
+        self.mergeRadioButtonGroup.addButton(self.overwrite_button)
+        self.merge_button.setChecked(True)
+        self.merge_strategy = self.merge_button.text()
+
+        # table
         self.tableWidget = QtWidgets.QTableWidget()
         tableWidget = self.tableWidget
-        tableWidget.setColumnCount(3)
+        tableWidget.setColumnCount(ncol)
         tableWidget.setRowCount(len(self.events))
-        tableWidget.setHorizontalHeaderLabels(('Event ID', 'Filename', 'Last modified'))
+        tableWidget.setHorizontalHeaderLabels(('', 'Event ID', 'Filename', 'Last modified'))
         tableWidget.setEditTriggers(tableWidget.NoEditTriggers)
         tableWidget.setSortingEnabled(True)
         header = tableWidget.horizontalHeader()
@@ -1621,9 +1662,17 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.header_layout.addWidget(self.comboBox)
         self.header_layout.addWidget(self.searchButton)
 
+        self.footer_layout.addWidget(self.checkAllButton)
+        self.footer_layout.addWidget(self.statusText)
+        self.footer_layout.addWidget(self.merge_button)
+        self.footer_layout.addWidget(self.overwrite_button)
+
+        self.footer_layout.setStretch(0, 0)
+        self.footer_layout.setStretch(1, 1)
+
         self.main_layout.addLayout(self.header_layout)
         self.main_layout.addWidget(self.tableWidget)
-        self.main_layout.addWidget(self.statusText)
+        self.main_layout.addLayout(self.footer_layout)
         self.main_layout.addWidget(self._buttonbox)
 
     def showPaths(self):
@@ -1632,23 +1681,23 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.tableWidget.clearContents()
         for index, event in enumerate(self.events):
             filename = get_pylot_eventfile_with_extension(event, fext)
-            self.tableWidget.setItem(index, 0, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
+            pf_selected_item = QtWidgets.QTableWidgetItem()
+            check_state = QtCore.Qt.Checked if filename else QtCore.Qt.Unchecked
+            pf_selected_item.setCheckState(check_state)
+            self.tableWidget.setItem(index, 0, pf_selected_item)
+            self.tableWidget.setItem(index, 1, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
             if filename:
                 self.filepaths.append(filename)
                 ts = int(os.path.getmtime(filename))
 
                 # create QTableWidgetItems of filepath and last modification time
                 fname_item = QtWidgets.QTableWidgetItem(f'{os.path.split(filename)[-1]}')
+                fname_item.setData(3, filename)
                 ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
-                self.tableWidget.setItem(index, 1, fname_item)
-                self.tableWidget.setItem(index, 2, ts_item)
+                self.tableWidget.setItem(index, 2, fname_item)
+                self.tableWidget.setItem(index, 3, ts_item)
 
-        # TODO: Idea -> only refresh if table contents changed. Use selection to load only a subset of files
-        if len(self.filepaths) > 0:
-            status_text = f'Found {len(self.filepaths)} eventfiles. Do you want to load them?'
-        else:
-            status_text = 'Did not find any files for specified file mask.'
-        self.statusText.setText(status_text)
+        self.update_status()
 
     def refreshSelectionBox(self):
         fext = self.comboBox.currentText()
@@ -1668,12 +1717,52 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
                                            QDialogButtonBox.Cancel)
 
+    def toggleCheckAll(self):
+        self.check_all_state = not self.check_all_state
+        self.checkAll(self.check_all_state)
+
+    def checkAll(self, state):
+        state = QtCore.Qt.Checked if state else QtCore.Qt.Unchecked
+        for row_ind in range(self.tableWidget.rowCount()):
+            item = self.tableWidget.item(row_ind, 0)
+            item.setCheckState(state)
+
+    def getChecked(self):
+        filepaths = []
+        for row_ind in range(self.tableWidget.rowCount()):
+            item_check = self.tableWidget.item(row_ind, 0)
+            if item_check.checkState() == QtCore.Qt.Checked:
+                item_fname = self.tableWidget.item(row_ind, 2)
+                if item_fname:
+                    filepath = item_fname.data(3)
+                    filepaths.append(filepath)
+        return filepaths
+
+    def update_status(self, row=None, col=None):
+        if col is not None and col != 0:
+            return
+        filepaths = self.getChecked()
+        if len(filepaths) > 0:
+            status_text = f"Found {len(filepaths)} eventfile{'s' if len(filepaths) > 1 else ''}. Do you want to load them?"
+        else:
+            status_text = 'Did not find/select any files for specified file mask.'
+        self.statusText.setText(status_text)
+
+    def update_merge_strategy(self):
+        for button in (self.merge_button, self.overwrite_button):
+            if button.isChecked():
+                self.merge_strategy = button.text()
+
     def connectSignals(self):
         self._buttonbox.accepted.connect(self.accept)
         self._buttonbox.rejected.connect(self.reject)
         self.comboBox.editTextChanged.connect(self.showPaths)
         self.searchButton.clicked.connect(self.showPaths)
-
+        self.checkAllButton.clicked.connect(self.toggleCheckAll)
+        self.checkAllButton.clicked.connect(self.update_status)
+        self.tableWidget.cellClicked.connect(self.update_status)
+        self.merge_button.clicked.connect(self.update_merge_strategy)
+        self.overwrite_button.clicked.connect(self.update_merge_strategy)
 
 
 class SingleTextLineDialog(QtWidgets.QDialog):
@@ -1780,16 +1869,18 @@ class PhaseDefaults(QtWidgets.QDialog):
 class PickDlg(QDialog):
     update_picks = QtCore.Signal(dict)
 
-    def __init__(self, parent=None, data=None, station=None, network=None, location=None, picks=None,
-                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None,
-                 event=None, filteroptions=None, model=None, wftype=None):
+    def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
+                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
+                 event=None, filteroptions=None, wftype=None):
         super(PickDlg, self).__init__(parent, Qt.Window)
         self.orig_parent = parent
         self.setAttribute(Qt.WA_DeleteOnClose)
 
         # initialize attributes
         self.parameter = parameter
+        model = self.parameter.get('taup_model')
         self._embedded = embedded
+        self.showCompData = show_comp_data
         self.station = station
         self.network = network
         self.location = location
@@ -1828,22 +1919,6 @@ class PickDlg(QDialog):
         else:
             self.filteroptions = FILTERDEFAULTS
         self.pick_block = False
-        self.nextStation = QtWidgets.QCheckBox('Continue with next station ')
-
-        # comparison channel
-        self.compareChannel = QtWidgets.QComboBox()
-        self.compareChannel.activated.connect(self.resetPlot)
-
-        # scale channel
-        self.scaleChannel = QtWidgets.QComboBox()
-        self.scaleChannel.activated.connect(self.resetPlot)
-
-        # initialize panning attributes
-        self.press = None
-        self.xpress = None
-        self.ypress = None
-        self.cur_xlim = None
-        self.cur_ylim = None
 
         # set attribute holding data
         if data is None or not data:
@@ -1856,6 +1931,31 @@ class PickDlg(QDialog):
                 raise Exception(errmsg)
         else:
             self.data = data
+        self.data_compare = data_compare
+
+        self.nextStation = QtWidgets.QCheckBox('Continue with next station ')
+
+        # comparison channel
+        self.referenceChannel = QtWidgets.QComboBox()
+        self.referenceChannel.activated.connect(self.resetPlot)
+
+        # comparison channel
+        self.compareCB = QtWidgets.QCheckBox()
+        self.compareCB.setChecked(self.showCompData)
+        self.compareCB.clicked.connect(self.switchCompData)
+        self.compareCB.clicked.connect(self.resetPlot)
+        self.compareCB.setVisible(bool(self.data_compare))
+
+        # scale channel
+        self.scaleChannel = QtWidgets.QComboBox()
+        self.scaleChannel.activated.connect(self.resetPlot)
+
+        # initialize panning attributes
+        self.press = None
+        self.xpress = None
+        self.ypress = None
+        self.cur_xlim = None
+        self.cur_ylim = None
 
         self.stime, self.etime = full_range(self.getWFData())
 
@@ -1868,12 +1968,12 @@ class PickDlg(QDialog):
         self.setupUi()
 
         # fill compare and scale channels
-        self.compareChannel.addItem('-', None)
+        self.referenceChannel.addItem('-', None)
         self.scaleChannel.addItem('individual', None)
 
         for trace in self.getWFData():
             channel = trace.stats.channel
-            self.compareChannel.addItem(channel, trace)
+            self.referenceChannel.addItem(channel, trace)
             if not channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                 print('Skipping unknown channel for scaling: {}'.format(channel))
                 continue
@@ -1890,7 +1990,7 @@ class PickDlg(QDialog):
         if self.wftype is not None:
             title += ' | ({})'.format(self.wftype)
 
-        self.multicompfig.plotWFData(wfdata=self.getWFData(),
+        self.multicompfig.plotWFData(wfdata=self.getWFData(), wfdata_compare=self.getWFDataComp(),
                                      title=title)
 
         self.multicompfig.setZoomBorders2content()
@@ -2066,8 +2166,11 @@ class PickDlg(QDialog):
         _dialtoolbar.addWidget(est_label)
         _dialtoolbar.addWidget(self.plot_arrivals_button)
         _dialtoolbar.addSeparator()
-        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare to channel: '))
-        _dialtoolbar.addWidget(self.compareChannel)
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Plot reference channel: '))
+        _dialtoolbar.addWidget(self.referenceChannel)
+        _dialtoolbar.addSeparator()
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare: '))
+        _dialtoolbar.addWidget(self.compareCB)
         _dialtoolbar.addSeparator()
         _dialtoolbar.addWidget(QtWidgets.QLabel('Scaling: '))
         _dialtoolbar.addWidget(self.scaleChannel)
@@ -2152,10 +2255,12 @@ class PickDlg(QDialog):
         station_id = trace.get_id()
         starttime = trace.stats.starttime
         station_coords = self.metadata.get_coordinates(station_id, starttime)
+        if not station_coords:
+            print('get_arrivals: No station coordinates found. Return!')
+            return
         origins = self.pylot_event.origins
         if phases == ['None', 'None']:
-            print("get_arrivals: Creation info (manual or auto) not available!")
-            print("Return!")
+            print("get_arrivals: Creation info (manual or auto) not available! Return!")
             return
         if origins:
             source_origin = origins[0]
@@ -2166,8 +2271,8 @@ class PickDlg(QDialog):
         arrivals = func[plot](source_origin.depth,
                               source_origin.latitude,
                               source_origin.longitude,
-                              station_coords['latitude'],
-                              station_coords['longitude'],
+                              station_coords.get('latitude'),
+                              station_coords.get('longitude'),
                               phases)
         self.arrivals = arrivals
 
@@ -2267,7 +2372,7 @@ class PickDlg(QDialog):
 
                 # create action and add to menu
                 # phase name transferred using lambda function
-                slot = lambda phase=phase, phaseID=phaseID: phaseSelect[phaseID](phase)
+                slot = lambda ph=phase, phID=phaseID: phaseSelect[phID](ph)
                 picksAction = createAction(parent=self, text=phase,
                                            slot=slot,
                                            shortcut=shortcut)
@@ -2402,7 +2507,7 @@ class PickDlg(QDialog):
     def activatePicking(self):
         self.leave_rename_phase()
         self.renamePhaseAction.setEnabled(False)
-        self.compareChannel.setEnabled(False)
+        self.referenceChannel.setEnabled(False)
         self.scaleChannel.setEnabled(False)
         phase = self.currentPhase
         phaseID = self.getPhaseID(phase)
@@ -2434,7 +2539,7 @@ class PickDlg(QDialog):
         self.disconnectPressEvent()
         self.multicompfig.connectEvents()
         self.renamePhaseAction.setEnabled(True)
-        self.compareChannel.setEnabled(True)
+        self.referenceChannel.setEnabled(True)
         self.scaleChannel.setEnabled(True)
         self.connect_pick_delete()
         self.draw()
@@ -2507,6 +2612,12 @@ class PickDlg(QDialog):
     def getWFData(self):
         return self.data
 
+    def getWFDataComp(self):
+        if self.showCompData:
+            return self.data_compare
+        else:
+            return Stream()
+
     def selectWFData(self, channel):
         component = channel[-1].upper()
         wfdata = Stream()
@@ -2628,11 +2739,16 @@ class PickDlg(QDialog):
 
         stime = self.getStartTime()
 
-        # copy data for plotting
-        data = self.getWFData().copy()
-        data = self.getPickPhases(data, phase)
-        data.normalize()
-        if not data:
+        # copy wfdata for plotting
+        wfdata = self.getWFData().copy()
+        wfdata_comp = self.getWFDataComp().copy()
+        wfdata = self.getPickPhases(wfdata, phase)
+        wfdata_comp = self.getPickPhases(wfdata_comp, phase)
+        for wfd in [wfdata, wfdata_comp]:
+            if wfd:
+                wfd.normalize()
+
+        if not wfdata:
             QtWidgets.QMessageBox.warning(self, 'No channel to plot',
                                           'No channel to plot for phase: {}. '
                                           'Make sure to select the correct channels for P and S '
@@ -2640,14 +2756,16 @@ class PickDlg(QDialog):
             self.leave_picking_mode()
             return
 
-        # filter data and trace on which is picked prior to determination of SNR
+        # filter wfdata and trace on which is picked prior to determination of SNR
         filterphase = self.currentFilterPhase()
         if filterphase:
             filteroptions = self.getFilterOptions(filterphase).parseFilterOptions()
             try:
-                data.detrend('linear')
-                data.filter(**filteroptions)
-                # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
+                for wfd in [wfdata, wfdata_comp]:
+                    if wfd:
+                        wfd.detrend('linear')
+                        wfd.filter(**filteroptions)
+                # wfdata.filter(**filteroptions)# MP MP removed filtering of original wfdata
             except ValueError as e:
                 self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
                                                  'Denied',
@@ -2657,8 +2775,8 @@ class PickDlg(QDialog):
         snr = []
         noiselevels = {}
         # determine SNR and noiselevel
-        for trace in data.traces:
-            st = data.select(channel=trace.stats.channel)
+        for trace in wfdata.traces:
+            st = wfdata.select(channel=trace.stats.channel)
             stime_diff = trace.stats.starttime - stime
             result = getSNR(st, (noise_win, gap_win, signal_win), ini_pick - stime_diff)
             snr.append(result[0])
@@ -2669,23 +2787,25 @@ class PickDlg(QDialog):
                 noiselevel = nfac
             noiselevels[trace.stats.channel] = noiselevel
 
-        # prepare plotting of data
-        for trace in data:
-            t = prepTimeAxis(trace.stats.starttime - stime, trace)
-            inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
-            trace = demeanTrace(trace, inoise)
-            # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
-            channel = trace.stats.channel
-            noiselevel = noiselevels[channel]
-            noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
-            trace.data *= noiseScaleFactor
-            noiselevels[channel] *= noiseScaleFactor
+        # prepare plotting of wfdata
+        for wfd in [wfdata, wfdata_comp]:
+            if wfd:
+                for trace in wfd:
+                    t = prep_time_axis(trace.stats.starttime - stime, trace)
+                    inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
+                    trace = demeanTrace(trace, inoise)
+                    # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
+                    channel = trace.stats.channel
+                    noiselevel = noiselevels[channel]
+                    noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
+                    trace.data *= noiseScaleFactor
+                    noiselevels[channel] *= noiseScaleFactor
 
         mean_snr = np.mean(snr)
         x_res = getResolutionWindow(mean_snr, parameter.get('extent'))
 
         xlims = [ini_pick - x_res, ini_pick + x_res]
-        ylims = list(np.array([-.5, .5]) + [0, len(data) - 1])
+        ylims = list(np.array([-.5, .5]) + [0, len(wfdata) - 1])
 
         title = self.getStation() + ' picking mode'
         title += ' | SNR: {}'.format(mean_snr)
@@ -2693,9 +2813,10 @@ class PickDlg(QDialog):
             filtops_str = transformFilteroptions2String(filteroptions)
             title += ' | Filteroptions: {}'.format(filtops_str)
 
-        plot_additional = bool(self.compareChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data,
+        plot_additional = bool(self.referenceChannel.currentText())
+        additional_channel = self.referenceChannel.currentText()
+        self.multicompfig.plotWFData(wfdata=wfdata,
+                                     wfdata_compare=wfdata_comp,
                                      title=title,
                                      zoomx=xlims,
                                      zoomy=ylims,
@@ -3086,7 +3207,8 @@ class PickDlg(QDialog):
         self.cur_xlim = self.multicompfig.axes[0].get_xlim()
         self.cur_ylim = self.multicompfig.axes[0].get_ylim()
         # self.multicompfig.updateCurrentLimits()
-        data = self.getWFData().copy()
+        wfdata = self.getWFData().copy()
+        wfdata_comp = self.getWFDataComp().copy()
         title = self.getStation()
         if filter:
             filtoptions = None
@@ -3094,19 +3216,22 @@ class PickDlg(QDialog):
                 filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()
 
             if filtoptions is not None:
-                data.detrend('linear')
-                data.taper(0.02, type='cosine')
-                data.filter(**filtoptions)
+                for wfd in [wfdata, wfdata_comp]:
+                    if wfd:
+                        wfd.detrend('linear')
+                        wfd.taper(0.02, type='cosine')
+                        wfd.filter(**filtoptions)
                 filtops_str = transformFilteroptions2String(filtoptions)
                 title += ' | Filteroptions: {}'.format(filtops_str)
 
         if self.wftype is not None:
             title += ' | ({})'.format(self.wftype)
 
-        plot_additional = bool(self.compareChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
+        plot_additional = bool(self.referenceChannel.currentText())
+        additional_channel = self.referenceChannel.currentText()
         scale_channel = self.scaleChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data, title=title,
+        self.multicompfig.plotWFData(wfdata=wfdata, wfdata_compare=wfdata_comp,
+                                     title=title,
                                      zoomx=self.getXLims(),
                                      zoomy=self.getYLims(),
                                      plot_additional=plot_additional,
@@ -3179,6 +3304,9 @@ class PickDlg(QDialog):
         self.resetZoom()
         self.refreshPlot()
 
+    def switchCompData(self):
+        self.showCompData = self.compareCB.isChecked()
+
     def refreshPlot(self):
         if self.autoFilterAction.isChecked():
             self.filterActionP.setChecked(False)
@@ -3709,7 +3837,7 @@ class TuneAutopicker(QWidget):
         self.stb_names = ['aicARHfig', 'refSpick', 'el_S1pick', 'el_S2pick']
 
     def add_parameters(self):
-        self.paraBox = PylotParaBox(self.parameter, parent=self, windowflag=Qt.Widget)
+        self.paraBox = PylotParameterWidget(self.parameter, parent=self, windowflag=Qt.Widget)
         self.paraBox.set_tune_mode(True)
         self.update_eventID()
         self.parameter_layout.addWidget(self.paraBox)
@@ -3790,11 +3918,13 @@ class TuneAutopicker(QWidget):
             location = None
 
         wfdata = self.data.getWFData()
+        wfdata_comp = self.data.getWFDataComp()
         metadata = self.parent().metadata
         event = self.get_current_event()
         filteroptions = self.parent().filteroptions
         wftype = self.wftype if self.obspy_dmt else ''
         self.pickDlg = PickDlg(self.parent(), data=wfdata.select(station=station).copy(),
+                               data_comp=wfdata_comp.select(station=station).copy(),
                                station=station, network=network,
                                location=location, parameter=self.parameter,
                                picks=self.get_current_event_picks(station),
@@ -3879,7 +4009,7 @@ class TuneAutopicker(QWidget):
             self.plot_manual_pick_to_ax(ax=ax, picks=picks, phase='S',
                                         starttime=starttime, quality=qualitySpick)
         for canvas in self.parent().canvas_dict.values():
-            canvas.draw()
+            canvas.draw_idle()
 
     def plot_manual_pick_to_ax(self, ax, picks, phase, starttime, quality):
         mpp = picks[phase]['mpp'] - starttime
@@ -4074,7 +4204,7 @@ class TuneAutopicker(QWidget):
         self.qmb.show()
 
 
-class PylotParaBox(QtWidgets.QWidget):
+class PylotParameterWidget(QtWidgets.QWidget):
     accepted = QtCore.Signal(str)
     rejected = QtCore.Signal(str)
 
@@ -4188,6 +4318,11 @@ class PylotParaBox(QtWidgets.QWidget):
         grid = QtWidgets.QGridLayout()
 
         for index1, name in enumerate(parameter_names):
+            if name in ['rootpath', 'database']:
+                logging.warning(
+                    f'Deprecated parameter loaded: {name}. Check if datapath is still correct in parameter widget.'
+                )
+                continue
             default_item = self.parameter.get_defaults()[name]
             tooltip = default_item['tooltip']
             tooltip += ' | type: {}'.format(default_item['type'])
@@ -4757,7 +4892,7 @@ class PropTab(QWidget):
     def getValues(self):
         return None
 
-    def resetValues(self, infile=None):
+    def resetValues(self, infile):
         return None
 
 
@@ -4794,8 +4929,8 @@ class InputsTab(PropTab):
         self.tstopBox = QSpinBox()
         for spinbox in [self.tstartBox, self.tstopBox]:
             spinbox.setRange(-99999, 99999)
-        self.tstartBox.setValue(float(settings.value('tstart')) if get_None(settings.value('tstart')) else 0)
-        self.tstopBox.setValue(float(settings.value('tstop')) if get_None(settings.value('tstop')) else 1e6)
+        self.tstartBox.setValue(float(settings.value('tstart')) if get_none(settings.value('tstart')) else 0)
+        self.tstopBox.setValue(float(settings.value('tstop')) if get_none(settings.value('tstop')) else 1e6)
         self.cuttimesLayout.addWidget(self.tstartBox, 10)
         self.cuttimesLayout.addWidget(QLabel('[s] and'), 0)
         self.cuttimesLayout.addWidget(self.tstopBox, 10)
@@ -4854,12 +4989,7 @@ class InputsTab(PropTab):
         else:
             index = 2
         datapath = para.get('datapath') if not para.get('datapath') is None else ''
-        rootpath = para.get('rootpath') if not para.get('rootpath') is None else ''
-        database = para.get('database') if not para.get('database') is None else ''
-        if isinstance(database, int):
-            database = str(database)
-        path = os.path.join(os.path.expanduser('~'), rootpath, datapath, database)
-        values = {"data/dataRoot": self.dataDirEdit.setText("%s" % path),
+        values = {"data/dataRoot": self.dataDirEdit.setText("%s" % datapath),
                   "user/FullName": self.fullNameEdit.text(),
                   "data/Structure": self.structureSelect.setCurrentIndex(index),
                   "tstart": self.tstartBox.setValue(0),
@@ -5791,7 +5921,7 @@ class ChooseWaveFormWindow(QWidget):
         #self.currentSpectro = self.traces[
         #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
         #self.currentSpectro.show()
-        applyFFT()
+        self.applyFFT()
 
     def applyFFT(self, trace):
         tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']

pylot/correlation/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+#

pylot/correlation/parameters_adriaarray.yaml

@@ -0,0 +1,95 @@
+#############################  correlation parameters  #####################################
+# min_corr_stacking: minimum correlation coefficient for building beam trace
+# min_corr_export: minimum correlation coefficient for pick export
+# min_stack: minimum number of stations for building beam trace
+# t_before: correlation window before pick
+# t_after: correlation window after pick#
+# cc_maxlag: maximum shift for initial correlation
+# cc_maxlag2: maximum shift for second (final) correlation (also for calculating pick uncertainty)
+# initial_pick_outlier_threshold: (hopefully) threshold for excluding large outliers of initial (AIC) picks
+# export_threshold: automatically exclude all onsets which deviate more than this threshold from corrected taup onsets
+# min_picks_export: minimum number of correlated picks for export
+# min_picks_autopylot: minimum number of reference auto picks to continue with event
+# check_RMS: do RMS check to search for restitution errors (very experimental)
+# use_taupy_onsets: use taupy onsets as reference picks instead of external picks
+# station_list: use the following stations as reference for stacking
+# use_stacked_trace: use existing stacked trace if found (spare re-computation)
+# data_dir: obspyDMT data subdirectory (e.g. 'raw', 'processed')
+# pickfile_extension: use quakeML files (PyLoT output) with the following extension, e.g. '_autopylot' for pickfiles
+#                     such as 'PyLoT_20170501_141822_autopylot.xml'
+# dt_stacking: time shift for stacking (e.g. [0, 250] for 0 and 250 seconds shift)
+# filter_options: filter for first correlation (rough)
+# filter_options_final: filter for second correlation (fine)
+# filter_type: e.g. 'bandpass'
+# sampfreq: sampling frequency of the data
+
+logging: info
+pick_phases: ['P', 'S']
+
+# P-phase
+P:
+  min_corr_stacking: 0.8
+  min_corr_export: 0.6
+  min_stack: 20
+  t_before: 30.
+  t_after: 50.
+  cc_maxlag: 50.
+  cc_maxlag2: 5.
+  initial_pick_outlier_threshold: 30.
+  export_threshold: 2.5
+  min_picks_export: 100
+  min_picks_autopylot: 50
+  check_RMS: True
+  use_taupy_onsets: False
+  station_list: ['HU.MORH', 'HU.TIH',  'OX.FUSE', 'OX.BAD']
+  use_stacked_trace: False
+  data_dir: 'processed'
+  pickfile_extension: '_autopylot'
+  dt_stacking: [250, 250]
+
+  # filter for first correlation (rough)
+  filter_options:
+    freqmax: 0.5
+    freqmin: 0.03
+  # filter for second correlation (fine)
+  filter_options_final:
+    freqmax: 0.5
+    freqmin: 0.03
+
+  filter_type: bandpass
+  sampfreq: 20.0
+
+# S-phase
+S:
+  min_corr_stacking: 0.7
+  min_corr_export: 0.6
+  min_stack: 20
+  t_before: 60.
+  t_after: 60.
+  cc_maxlag: 100.
+  cc_maxlag2: 25.
+  initial_pick_outlier_threshold: 30.
+  export_threshold: 5.0
+  min_picks_export: 200
+  min_picks_autopylot: 50
+  check_RMS: True
+  use_taupy_onsets: False
+  station_list: ['HU.MORH','HU.TIH',  'OX.FUSE', 'OX.BAD']
+  use_stacked_trace: False
+  data_dir: 'processed'
+  pickfile_extension: '_autopylot'
+  dt_stacking: [250, 250]
+
+  # filter for first correlation (rough)
+  filter_options:
+    freqmax: 0.1
+    freqmin: 0.01
+
+  # filter for second correlation (fine)
+  filter_options_final:
+    freqmax: 0.2
+    freqmin: 0.01
+
+  filter_type: bandpass
+  sampfreq: 20.0
+

pylot/correlation/submit_pick_corr_correction.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+#ulimit -s 8192
+#ulimit -v $(ulimit -v | awk '{printf("%d",$1*0.95)}')
+#ulimit -v
+
+#655360
+
+source /opt/anaconda3/etc/profile.d/conda.sh
+conda activate pylot_311
+NSLOTS=20
+
+#qsub -l low -cwd -l "os=*stretch" -pe smp 40 submit_pick_corr_correction.sh
+#$ -l low
+#$ -l h_vmem=6G
+#$ -cwd
+#$ -pe smp 20
+#$ -N corr_pick
+
+
+export PYTHONPATH="$PYTHONPATH:/home/marcel/git/pylot_tools/"
+export PYTHONPATH="$PYTHONPATH:/home/marcel/git/"
+export PYTHONPATH="$PYTHONPATH:/home/marcel/git/pylot/"
+
+#export MKL_NUM_THREADS=${NSLOTS:=1}
+#export NUMEXPR_NUM_THREADS=${NSLOTS:=1}
+#export OMP_NUM_THREADS=${NSLOTS:=1}
+
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M5.8-6.0' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 0 -istop 100
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M5.8-6.0' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 100 -istop 200
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M6.0-6.5' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 0 -istop 100
+#python pick_correlation_correction.py '/data/AlpArray_Data/dmt_database_mantle_M5.8-6.0' '/home/marcel/.pylot/pylot_alparray_mantle_corr_stack_0.03-0.5.in' -pd -n ${NSLOTS:=1} -istart 100 -istop 200
+#python pick_correlation_correction.py 'H:\sciebo\dmt_database' 'H:\Sciebo\dmt_database\pylot_alparray_mantle_corr_S_0.01-0.2.in' -pd -n 4 -t
+
+pylot_infile='/home/marcel/.pylot/pylot_alparray_syn_fwi_mk6_it3.in'
+#pylot_infile='/home/marcel/.pylot/pylot_adriaarray_corr_P_and_S.in'
+
+# THIS SCRIPT SHOLD BE CALLED BY "submit_to_grid_engine.py" using the following line:
+python pick_correlation_correction.py $1 $pylot_infile -pd -n ${NSLOTS:=1} -istart $2 --params 'parameters_fwi_mk6_it3.yaml'
+#--event_blacklist eventlist.txt

pylot/correlation/submit_to_grid_engine.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+
+import subprocess
+
+fnames = [
+    ('/data/AlpArray_Data/dmt_database_synth_model_mk6_it3_no_rotation', 0),
+          ]
+
+#fnames = [('/data/AlpArray_Data/dmt_database_mantle_0.01-0.2_SKS-phase', 0),
+#          ('/data/AlpArray_Data/dmt_database_mantle_0.01-0.2_S-phase', 0),]
+
+####
+script_location = '/home/marcel/VersionCtrl/git/code_base/correlation_picker/submit_pick_corr_correction.sh'
+####
+
+for fnin, istart in fnames:
+    input_cmds = f'qsub -q low.q@minos15,low.q@minos14,low.q@minos13,low.q@minos12,low.q@minos11 {script_location} {fnin} {istart}'
+
+    print(input_cmds)
+    print(subprocess.check_output(input_cmds.split()))
+
+
+

pylot/correlation/utils.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import glob
+import json
+
+from obspy import read_events
+
+from pylot.core.util.dataprocessing import Metadata
+from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
+
+
+def get_event_obspy_dmt(eventdir):
+    event_pkl_file = os.path.join(eventdir, 'info', 'event.pkl')
+    if not os.path.exists(event_pkl_file):
+        raise IOError('Could not find event path for event: {}'.format(eventdir))
+    event = qml_from_obspyDMT(event_pkl_file)
+    return event
+
+
+def get_event_pylot(eventdir, extension=''):
+    event_id = get_event_id(eventdir)
+    filename = os.path.join(eventdir, 'PyLoT_{}{}.xml'.format(event_id, extension))
+    if not os.path.isfile(filename):
+        return
+    cat = read_events(filename)
+    return cat[0]
+
+
+def get_event_id(eventdir):
+    event_id = os.path.split(eventdir)[-1]
+    return event_id
+
+
+def get_picks(eventdir, extension=''):
+    event_id = get_event_id(eventdir)
+    filename = 'PyLoT_{}{}.xml'
+    filename = filename.format(event_id, extension)
+    fpath = os.path.join(eventdir, filename)
+    fpaths = glob.glob(fpath)
+    if len(fpaths) == 1:
+        cat = read_events(fpaths[0])
+        picks = cat[0].picks
+        return picks
+    elif len(fpaths) == 0:
+        print('get_picks: File not found: {}'.format(fpath))
+        return
+    print(f'WARNING: Ambiguous pick file specification. Found the following pick files {fpaths}\nFilemask: {fpath}')
+    return
+
+
+def write_json(object, fname):
+    with open(fname, 'w') as outfile:
+        json.dump(object, outfile, sort_keys=True, indent=4)
+
+
+def get_metadata(eventdir):
+    metadata_path = os.path.join(eventdir, 'resp')
+    metadata = Metadata(inventory=metadata_path, verbosity=0)
+    return metadata

requirements.txt

@@ -1,12 +1,7 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: win-64
-cartopy=0.20.2
-matplotlib-base=3.3.4
-numpy=1.22.3
-obspy=1.3.0
-pyqtgraph=0.12.4
-pyside2=5.13.2
-python=3.8.12
-qt=5.12.9
-scipy=1.8.0
+Cartopy==0.23.0
+joblib==1.4.2
+obspy==1.4.1
+pyaml==24.7.0
+pyqtgraph==0.13.7
+PySide2==5.15.8
+pytest==8.3.2

tests/test_autopicker/pylot_alparray_mantle_corr_stack_0.03-0.5.in

@@ -0,0 +1,99 @@
+%This is a parameter input file for PyLoT/autoPyLoT.
+%All main and special settings regarding data handling
+%and picking are to be set here!
+%Parameters are optimized for %extent data sets!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#main settings#
+dmt_database_test                                  #datapath#       %data path
+20171010_063224.a                                  #eventID#        %event ID for single event processing (* for all events found in database)
+                                                   #invdir#         %full path to  inventory or dataless-seed file                                                       
+PILOT                                              #datastructure#  %choose data structure                                                                               
+True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#NLLoc settings#
+None                                               #nllocbin#       %path to NLLoc executable                                                                            
+None                                               #nllocroot#      %root of NLLoc-processing directory                                                                  
+None                                               #phasefile#      %name of autoPyLoT-output phase file for NLLoc                                                       
+None                                               #ctrfile#        %name of autoPyLoT-output control file for NLLoc                                                     
+ttime                                              #ttpatter#       %pattern of NLLoc ttimes from grid                                                                   
+AUTOLOC_nlloc                                      #outpatter#      %pattern of NLLoc-output file                                                                        
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#parameters for seismic moment estimation#
+3530.0                                             #vp#             %average P-wave velocity                                                                             
+2500.0                                             #rho#            %average rock density [kg/m^3]                                                                       
+300.0 0.8                                          #Qp#             %quality factor for P waves (Qp*f^a); list(Qp, a)                                                    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#settings local magnitude#
+1.0 1.0 1.0                                        #WAscaling#      %Scaling relation (log(Ao)+Alog(r)+Br+C) of Wood-Anderson amplitude Ao [nm]                           If zeros are set, original Richter magnitude is calculated!
+1.0 1.0                                            #magscaling#     %Scaling relation for derived local magnitude [a*Ml+b].                            If zeros are set, no scaling of network magnitude is applied!
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#filter settings#
+0.03 0.03                                          #minfreq#        %Lower filter frequency [P, S]                                                                       
+0.5 0.5                                            #maxfreq#        %Upper filter frequency [P, S]                                                                       
+4 4                                                #filter_order#   %filter order [P, S]                                                                                 
+bandpass bandpass                                  #filter_type#    %filter type (bandpass, bandstop, lowpass, highpass) [P, S]                                          
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+#common settings picker#
+global                                             #extent#         %extent of array ("local", "regional" or "global")                                                   
+-100.0                                             #pstart#         %start time [s] for calculating CF for P-picking (if TauPy: seconds relative to estimated onset)     
+50.0                                               #pstop#          %end time [s] for calculating CF for P-picking (if TauPy: seconds relative to estimated onset)       
+-50.0                                              #sstart#         %start time [s] relative to P-onset for calculating CF for S-picking                                 
+50.0                                               #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
+True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
+ak135                                              #taup_model#     %Define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6
+P,Pdiff,S,SKS                                      #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
+0.03 0.5                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
+0.01 0.5                                           #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
+0.03 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     
+0.01 0.5                                           #bph2#           %lower/upper corner freq. of second band pass filter z-comp. [Hz]                                    
+#special settings for calculating CF#
+%!!Edit the following only if you know what you are doing!!%
+#Z-component#
+HOS                                                #algoP#          %choose algorithm for P-onset determination (HOS, ARZ, or AR3)                                       
+300.0                                              #tlta#           %for HOS-/AR-AIC-picker, length of LTA window [s]                                                    
+4                                                  #hosorder#       %for HOS-picker, order of Higher Order Statistics                                                    
+2                                                  #Parorder#       %for AR-picker, order of AR process of Z-component                                                   
+16.0                                               #tdet1z#         %for AR-picker, length of AR determination window [s] for Z-component, 1st pick                      
+10.0                                               #tpred1z#        %for AR-picker, length of AR prediction window [s] for Z-component, 1st pick                         
+12.0                                               #tdet2z#         %for AR-picker, length of AR determination window [s] for Z-component, 2nd pick                      
+6.0                                                #tpred2z#        %for AR-picker, length of AR prediction window [s] for Z-component, 2nd pick                         
+0.001                                              #addnoise#       %add noise to seismogram for stable AR prediction                                                    
+60.0 5.0 20.0 12.0                                 #tsnrz#          %for HOS/AR, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]     
+50.0                                               #pickwinP#       %for initial AIC pick, length of P-pick window [s]                                                   
+30.0                                               #Precalcwin#     %for HOS/AR, window length [s] for recalculation of CF (relative to 1st pick)                        
+2.0                                                #aictsmooth#     %for HOS/AR, take average of samples for smoothing of AIC-function [s]                               
+2.0                                                #tsmoothP#       %for HOS/AR, take average of samples in this time window for smoothing CF [s]                        
+0.006                                              #ausP#           %for HOS/AR, artificial uplift of samples (aus) of CF (P)                                            
+2.0                                                #nfacP#          %for HOS/AR, noise factor for noise level determination (P)                                          
+#H-components#
+ARH                                                #algoS#          %choose algorithm for S-onset determination (ARH or AR3)                                             
+12.0                                               #tdet1h#         %for HOS/AR, length of AR-determination window [s], H-components, 1st pick                           
+6.0                                                #tpred1h#        %for HOS/AR, length of AR-prediction window [s], H-components, 1st pick                              
+8.0                                                #tdet2h#         %for HOS/AR, length of AR-determinaton window [s], H-components, 2nd pick                            
+4.0                                                #tpred2h#        %for HOS/AR, length of AR-prediction window [s], H-components, 2nd pick                              
+4                                                  #Sarorder#       %for AR-picker, order of AR process of H-components                                                  
+100.0                                              #Srecalcwin#     %for AR-picker, window length [s] for recalculation of CF (2nd pick) (H)                             
+195.0                                              #pickwinS#       %for initial AIC pick, length of S-pick window [s]                                                   
+60.0 10.0 30.0 12.0                                #tsnrh#          %for ARH/AR3, window lengths for SNR-and slope estimation [tnoise, tsafetey, tsignal, tslope] [s]    
+22.0                                               #aictsmoothS#    %for AIC-picker, take average of samples in this time window for smoothing of AIC-function [s]       
+20.0                                               #tsmoothS#       %for AR-picker, take average of samples for smoothing CF [s] (S)                                     
+0.001                                              #ausS#           %for HOS/AR, artificial uplift of samples (aus) of CF (S)                                            
+2.0                                                #nfacS#          %for AR-picker, noise factor for noise level determination (S)                                       
+#first-motion picker#
+1                                                  #minfmweight#    %minimum required P weight for first-motion determination                                            
+3.0                                                #minFMSNR#       %miniumum required SNR for first-motion determination                                                
+10.0                                               #fmpickwin#      %pick window [s] around P onset for calculating zero crossings                                       
+#quality assessment#
+0.1 0.2 0.4 0.8                                    #timeerrorsP#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for P                           
+4.0 8.0 16.0 32.0                                  #timeerrorsS#    %discrete time errors [s] corresponding to picking weights [0 1 2 3] for S                           
+0.005                                              #minAICPslope#   %below this slope [counts/s] the initial P pick is rejected                                          
+1.1                                                #minAICPSNR#     %below this SNR the initial P pick is rejected                                                       
+0.002                                              #minAICSslope#   %below this slope [counts/s] the initial S pick is rejected                                          
+1.3                                                #minAICSSNR#     %below this SNR the initial S pick is rejected                                                       
+20.0                                               #minsiglength#   %length of signal part for which amplitudes must exceed noiselevel [s]                               
+1.0                                                #noisefactor#    %noiselevel*noisefactor=threshold                                                                    
+10.0                                               #minpercent#     %required percentage of amplitudes exceeding threshold                                               
+0.1                                                #zfac#           %P-amplitude must exceed at least zfac times RMS-S amplitude                                         
+100.0                                              #mdttolerance#   %maximum allowed deviation of P picks from median [s]                                                
+50.0                                               #wdttolerance#   %maximum allowed deviation from Wadati-diagram                                                       
+25.0                                               #jackfactor#     %pick is removed if the variance of the subgroup with the pick removed is larger than the mean variance of all subgroups times safety factor

tests/test_autopicker/test_autopylot.py

@@ -0,0 +1,67 @@
+import os
+import pytest
+
+from obspy import read_events
+
+from autoPyLoT import autoPyLoT
+
+
+class TestAutopickerGlobal():
+    def init(self):
+        self.params_infile = 'pylot_alparray_mantle_corr_stack_0.03-0.5.in'
+        self.test_event_dir = 'dmt_database_test'
+        self.fname_outfile_xml = os.path.join(
+            self.test_event_dir, '20171010_063224.a', 'PyLoT_20171010_063224.a_autopylot.xml'
+        )
+
+        # check if the input files exist
+        if not os.path.isfile(self.params_infile):
+            print(f'Test input file {os.path.abspath(self.params_infile)} not found.')
+            return False
+
+        if not os.path.exists(self.test_event_dir):
+            print(
+                f'Test event directory not found at location "{os.path.abspath(self.test_event_dir)}". '
+                f'Make sure to load it from the website first.'
+            )
+            return False
+
+        return True
+
+    def test_autopicker(self):
+        assert self.init(), 'Initialization failed due to missing input files.'
+        # check for output file in test directory and remove it if necessary
+        if os.path.isfile(self.fname_outfile_xml):
+            os.remove(self.fname_outfile_xml)
+        autoPyLoT(inputfile=self.params_infile, eventid='20171010_063224.a', obspyDMT_wfpath='processed')
+
+        # test for different known output files if they are identical or not
+        compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_autopylot.xml', True)
+        compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_saved_from_GUI.xml', True)
+        compare_pickfiles(self.fname_outfile_xml, 'PyLoT_20171010_063224.a_corrected_taup_times_0.03-0.5_P.xml', False)
+
+
+def compare_pickfiles(pickfile1: str, pickfile2: str, samefile: bool = True) -> None:
+    """
+    Compare the pick times and errors from two pick files.
+
+    Parameters:
+        pickfile1 (str): The path to the first pick file.
+        pickfile2 (str): The path to the second pick file.
+        samefile (bool): A flag indicating whether the two files are expected to be the same. Defaults to True.
+
+    Returns:
+        None
+    """
+    cat1 = read_events(pickfile1)
+    cat2 = read_events(pickfile2)
+    picks1 = sorted(cat1[0].picks, key=lambda pick: str(pick.waveform_id))
+    picks2 = sorted(cat2[0].picks, key=lambda pick: str(pick.waveform_id))
+    pick_times1 = [pick.time for pick in picks1]
+    pick_times2 = [pick.time for pick in picks2]
+    pick_terrs1 = [pick.time_errors for pick in picks1]
+    pick_terrs2 = [pick.time_errors for pick in picks2]
+
+    # check if times and errors are identical or not depending on the samefile flag
+    assert (pick_times1 == pick_times2) is samefile, 'Pick times error'
+    assert (pick_terrs1 == pick_terrs2) is samefile, 'Pick time errors errors'

tests/test_autopickstation/autoPyLoT_global_taupy_false.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/home/darius                                       #rootpath#       %project path                                                                                        
-alparray                                           #datapath#       %data path                                                                                           
-waveforms_used                                     #database#       %name of data base                                                                                   
-e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in database)                           
+/home/darius/alparray/waveforms_used               #datapath#       %data path
+e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
 /home/darius/alparray/metadata                     #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -43,6 +41,7 @@ global                                             #extent#         %extent of a
 875.0                                              #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
 False                                              #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
 IASP91                                             #taup_model#     %define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6
+P,Pdiff,S,Sdiff                                    #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 0.01 0.1                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
 0.001 0.5                                          #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
 0.01 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

tests/test_autopickstation/autoPyLoT_global_taupy_true.in

@@ -4,10 +4,8 @@
 %Parameters are optimized for %extent data sets!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #main settings#
-/home/darius                                       #rootpath#       %project path                                                                                        
-alparray                                           #datapath#       %data path                                                                                           
-waveforms_used                                     #database#       %name of data base                                                                                   
-e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in database)                           
+/home/darius/alparray/waveforms_used               #datapath#       %data path
+e0093.173.16                                       #eventID#        %event ID for single event processing (* for all events found in datapath)
 /home/darius/alparray/metadata                     #invdir#         %full path to  inventory or dataless-seed file                                                       
 PILOT                                              #datastructure#  %choose data structure                                                                               
 True                                               #apverbose#      %choose 'True' or 'False' for terminal output                                                        
@@ -43,6 +41,7 @@ global                                             #extent#         %extent of a
 875.0                                              #sstop#          %end time [s] after P-onset for calculating CF for S-picking                                         
 True                                               #use_taup#       %use estimated traveltimes from TauPy for calculating windows for CF                                 
 IASP91                                             #taup_model#     %define TauPy model for traveltime estimation. Possible values: 1066a, 1066b, ak135, ak135f, herrin, iasp91, jb, prem, pwdk, sp6
+P,Pdiff,S,Sdiff                                    #taup_phases#    %Specify possible phases for TauPy (comma separated). See Obspy TauPy documentation for possible values.
 0.01 0.1                                           #bpz1#           %lower/upper corner freq. of first band pass filter Z-comp. [Hz]                                     
 0.001 0.5                                          #bpz2#           %lower/upper corner freq. of second band pass filter Z-comp. [Hz]                                    
 0.01 0.5                                           #bph1#           %lower/upper corner freq. of first band pass filter H-comp. [Hz]                                     

tests/test_autopickstation/test_autopickstation.py

@@ -1,6 +1,7 @@
 import os
 import sys
 import unittest
+import pytest
 
 import obspy
 from obspy import UTCDateTime
@@ -105,7 +106,6 @@ class TestAutopickStation(unittest.TestCase):
         # show complete diff when difference in results dictionaries are found
         self.maxDiff = None
 
-    # @skip("Works")
     def test_autopickstation_taupy_disabled_gra1(self):
         expected = {
             'P': {'picker': 'auto', 'snrdb': 15.405649120980094, 'weight': 0, 'Mo': None, 'marked': [], 'Mw': None,
@@ -121,8 +121,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra1, pickparam=self.pickparam_taupy_disabled,
                                               metadata=(None, None))
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA1', station)
 
     def test_autopickstation_taupy_enabled_gra1(self):
@@ -140,8 +140,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra1, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA1', station)
 
     def test_autopickstation_taupy_disabled_gra2(self):
@@ -157,8 +157,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra2, pickparam=self.pickparam_taupy_disabled,
                                               metadata=(None, None))
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA2', station)
 
     def test_autopickstation_taupy_enabled_gra2(self):
@@ -175,8 +175,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.gra2, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA2', station)
 
     def test_autopickstation_taupy_disabled_ech(self):
@@ -190,8 +190,8 @@ class TestAutopickStation(unittest.TestCase):
                           'fm': None, 'spe': None, 'channel': u'LHE'}}
         with HidePrints():
             result, station = autopickstation(wfstream=self.ech, pickparam=self.pickparam_taupy_disabled)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('ECH', station)
 
     def test_autopickstation_taupy_enabled_ech(self):
@@ -208,8 +208,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.ech, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('ECH', station)
 
     def test_autopickstation_taupy_disabled_fiesa(self):
@@ -224,8 +224,8 @@ class TestAutopickStation(unittest.TestCase):
                           'fm': None, 'spe': None, 'channel': u'LHE'}}
         with HidePrints():
             result, station = autopickstation(wfstream=self.fiesa, pickparam=self.pickparam_taupy_disabled)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('FIESA', station)
 
     def test_autopickstation_taupy_enabled_fiesa(self):
@@ -242,8 +242,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.fiesa, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertDictContainsSubset(expected=expected['P'], actual=result['P'])
-        self.assertDictContainsSubset(expected=expected['S'], actual=result['S'])
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('FIESA', station)
 
     def test_autopickstation_gra1_z_comp_missing(self):
@@ -272,7 +272,8 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=wfstream, pickparam=self.pickparam_taupy_disabled,
                                               metadata=(None, None))
-        self.assertEqual(expected, result)
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
         self.assertEqual('GRA1', station)
 
     def test_autopickstation_a106_taupy_enabled(self):
@@ -290,7 +291,9 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.a106, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertEqual(expected, result)
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
+
 
     def test_autopickstation_station_missing_in_metadata(self):
         """This station is not in the metadata, but Taupy is enabled. Taupy should exit cleanly and modify the starttime
@@ -311,8 +314,37 @@ class TestAutopickStation(unittest.TestCase):
         with HidePrints():
             result, station = autopickstation(wfstream=self.a005a, pickparam=self.pickparam_taupy_enabled,
                                               metadata=self.metadata, origin=self.origin)
-        self.assertEqual(expected, result)
+        compare_dicts(expected=expected['P'], result=result['P'], hint='P-')
+        compare_dicts(expected=expected['S'], result=result['S'], hint='S-')
 
 
+def run_dict_comparison(result, expected):
+    for key, expected_value in expected.items():
+        if isinstance(expected_value, dict):
+            run_dict_comparison(result[key], expected[key])
+        else:
+            res = result[key]
+            if isinstance(res, UTCDateTime) and isinstance(expected_value, UTCDateTime):
+                res = res.timestamp
+                expected_value = expected_value.timestamp
+            assert expected_value == pytest.approx(res), f'{key}: {expected_value} != {res}'
+
+
+def compare_dicts(result, expected, hint=''):
+    try:
+        run_dict_comparison(result, expected)
+    except AssertionError:
+        raise AssertionError(f'{hint}Dictionaries not equal.'
+                             f'\n\n<<Expected>>\n{pretty_print_dict(expected)}'
+                             f'\n\n<<Result>>\n{pretty_print_dict(result)}')
+
+
+def pretty_print_dict(dct):
+    retstr = ''
+    for key, value in sorted(dct.items(), key=lambda x: x[0]):
+        retstr += f"{key} : {value}\n"
+
+    return retstr
+
 if __name__ == '__main__':
     unittest.main()

tests/test_pick_correlation_correction/test_pick_correlation_correction.py

@@ -0,0 +1,76 @@
+import pytest
+from obspy import read, Trace, UTCDateTime
+
+from pylot.correlation.pick_correlation_correction import XCorrPickCorrection
+
+
+class TestXCorrPickCorrection():
+    def setup(self):
+        self.make_test_traces()
+        self.make_test_picks()
+        self.t_before = 2.
+        self.t_after = 2.
+        self.cc_maxlag = 0.5
+
+    def make_test_traces(self):
+        # take first trace of test Stream from obspy
+        tr1 = read()[0]
+        # filter trace
+        tr1.filter('bandpass', freqmin=1, freqmax=20)
+        # make a copy and shift the copy by 0.1 s
+        tr2 = tr1.copy()
+        tr2.stats.starttime += 0.1
+
+        self.trace1 = tr1
+        self.trace2 = tr2
+
+    def make_test_picks(self):
+        # create an artificial reference pick on reference trace (trace1) and another one on the 0.1 s shifted trace
+        self.tpick1 = UTCDateTime('2009-08-24T00:20:07.7')
+        # shift the second pick by 0.2 s, the correction should be around 0.1 s now
+        self.tpick2 = self.tpick1 + 0.2
+
+    def test_slice_trace_okay(self):
+
+        self.setup()
+        xcpc = XCorrPickCorrection(UTCDateTime(), Trace(), UTCDateTime(), Trace(),
+                                   t_before=self.t_before, t_after=self.t_after, cc_maxlag=self.cc_maxlag)
+
+        test_trace = self.trace1
+        pick_time = self.tpick2
+
+        sliced_trace = xcpc.slice_trace(test_trace, pick_time)
+        assert ((sliced_trace.stats.starttime == pick_time - self.t_before - self.cc_maxlag / 2)
+                and (sliced_trace.stats.endtime == pick_time + self.t_after + self.cc_maxlag / 2))
+
+    def test_slice_trace_fails(self):
+        self.setup()
+
+        test_trace = self.trace1
+        pick_time = self.tpick1
+
+        with pytest.raises(ValueError):
+            xcpc = XCorrPickCorrection(UTCDateTime(), Trace(), UTCDateTime(), Trace(),
+                                       t_before=self.t_before + 20, t_after=self.t_after, cc_maxlag=self.cc_maxlag)
+            xcpc.slice_trace(test_trace, pick_time)
+
+        with pytest.raises(ValueError):
+            xcpc = XCorrPickCorrection(UTCDateTime(), Trace(), UTCDateTime(), Trace(),
+                                       t_before=self.t_before, t_after=self.t_after + 50, cc_maxlag=self.cc_maxlag)
+            xcpc.slice_trace(test_trace, pick_time)
+
+    def test_cross_correlation(self):
+        self.setup()
+
+        # create XCorrPickCorrection object
+        xcpc = XCorrPickCorrection(self.tpick1, self.trace1, self.tpick2, self.trace2, t_before=self.t_before,
+                                   t_after=self.t_after, cc_maxlag=self.cc_maxlag)
+
+        # execute correlation
+        correction, cc_max, uncert, fwfm = xcpc.cross_correlation(False, '', '')
+
+        # define awaited test result
+        test_result = (-0.09983091718314982, 0.9578431835689154, 0.0015285160561610929, 0.03625786256084631)
+
+        # check results
+        assert pytest.approx(test_result, rel=1e-6) == (correction, cc_max, uncert, fwfm)