[update] WIP: adding tests for autopylot (global)

[refactor] minor

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
@@ -72,11 +73,11 @@ 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
@@ -84,7 +85,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, 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 infile and os.path.isfile(infile) is False:
-        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:
             infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]
 
             if not os.path.exists(infile):
@@ -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
@@ -196,7 +194,7 @@ class MainWindow(QMainWindow):
                 if settings.value("user/FullName", None) is None:
                     fulluser = QInputDialog.getText(self, "Enter Name:", "Full name")
                     settings.setValue("user/FullName", fulluser)
-                    settings.setValue("user/Login", getLogin())
+                    settings.setValue("user/Login", get_login())
                 if settings.value("agency_id", None) is None:
                     agency = QInputDialog.getText(self,
                                                   "Enter authority/institution name:",
@@ -253,7 +251,7 @@ 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
 
@@ -1010,12 +1008,12 @@ 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)
+            for filename in filenames:
-            if filename:
+                if os.path.isfile(filename) and event.pylot_id in filename:
-                self.load_data(filename, draw=False, event=event, overwrite=True)
+                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
                     refresh = True
         if not refresh:
             return
@@ -1024,8 +1022,8 @@ class MainWindow(QMainWindow):
         self.fill_eventbox()
         self.setDirty(True)
 
-    def load_data(self, fname=None, loc=False, draw=True, event=None, overwrite=False):
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
-        if not overwrite:
+        if not ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1039,9 +1037,12 @@ class MainWindow(QMainWindow):
         data = Data(self, event)
         try:
             data_new = Data(self, evtdata=str(fname))
-            # MP MP commented because adding several picks might cause inconsistencies
+            if merge_strategy == 'Overwrite':
                 data = data_new
-            # data += data_new
+            elif merge_strategy == 'Merge':
+                data += data_new
+            else:
+                raise NotImplementedError(f'Unknown merge strategy: {merge_strategy}')
         except ValueError:
             qmb = QMessageBox(self, icon=QMessageBox.Question,
                               text='Warning: Missmatch in event identifiers {} and {}. Continue?'.format(
@@ -1129,16 +1130,19 @@ class MainWindow(QMainWindow):
             else:
                 return
 
-    def getWFFnames_from_eventbox(self, eventbox=None):
+    def getWFFnames_from_eventbox(self, eventbox: str = None, subpath: str = None) -> list:
         '''
         Return waveform filenames from event in eventbox.
         '''
         # TODO: add dataStructure class for obspyDMT here, this is just a workaround!
         eventpath = self.get_current_event_path(eventbox)
-        basepath = eventpath.split(os.path.basename(eventpath))[0]
+        if subpath:
+            eventpath = os.path.join(eventpath, subpath)
+        if not os.path.isdir(eventpath):
+            return []
         if self.dataStructure:
             if not eventpath:
-                return
+                return []
             fnames = [os.path.join(eventpath, f) for f in os.listdir(eventpath)]
         else:
             raise DatastructureError('not specified')
@@ -1960,13 +1964,20 @@ class MainWindow(QMainWindow):
 
     def prepareLoadWaveformData(self):
         self.fnames = self.getWFFnames_from_eventbox()
-        self.fnames_syn = []
+        self.fnames_comp = []
+        fnames_comp = self.getWFFnames_from_eventbox(subpath='compare')
+        self.dataPlot.activateCompareOptions(bool(fnames_comp))
+        if fnames_comp:
+            if self.dataPlot.comp_checkbox.isChecked():
+                self.fnames_comp = fnames_comp
+
         eventpath = self.get_current_event_path()
         basepath = eventpath.split(os.path.basename(eventpath))[0]
         self.obspy_dmt = check_obspydmt_structure(basepath)
         self.dataPlot.activateObspyDMToptions(self.obspy_dmt)
         if self.obspy_dmt:
             self.prepareObspyDMT_data(eventpath)
+            self.dataPlot.activateCompareOptions(True)
 
     def loadWaveformData(self):
         '''
@@ -1990,8 +2001,8 @@ class MainWindow(QMainWindow):
 
         if len(curr_event.origins) > 0:
             origin_time = curr_event.origins[0].time
-            tstart = settings.value('tstart') if get_None(settings.value('tstart')) else 0
+            tstart = settings.value('tstart') if get_none(settings.value('tstart')) else 0
-            tstop = settings.value('tstop') if get_None(settings.value('tstop')) else 0
+            tstop = settings.value('tstop') if get_none(settings.value('tstop')) else 0
             tstart = origin_time + float(tstart)
             tstop = origin_time + float(tstop)
         else:
@@ -1999,7 +2010,7 @@ class MainWindow(QMainWindow):
             tstop = None
 
         self.data.setWFData(self.fnames,
-                            self.fnames_syn,
+                            self.fnames_comp,
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
@@ -2007,7 +2018,7 @@ class MainWindow(QMainWindow):
 
     def prepareObspyDMT_data(self, eventpath):
         qcbox_processed = self.dataPlot.qcombo_processed
-        qcheckb_syn = self.dataPlot.syn_checkbox
+        qcheckb_syn = self.dataPlot.comp_checkbox
         qcbox_processed.setEnabled(False)
         qcheckb_syn.setEnabled(False)
         for fpath in os.listdir(eventpath):
@@ -2015,8 +2026,8 @@ class MainWindow(QMainWindow):
             if 'syngine' in fpath:
                 eventpath_syn = os.path.join(eventpath, fpath)
                 qcheckb_syn.setEnabled(True)
-                if self.dataPlot.syn_checkbox.isChecked():
+                if self.dataPlot.comp_checkbox.isChecked():
-                    self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                    self.fnames_comp = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
             if 'processed' in fpath:
                 qcbox_processed.setEnabled(True)
         if qcbox_processed.isEnabled():
@@ -2186,6 +2197,7 @@ class MainWindow(QMainWindow):
         if event.pylot_autopicks:
             self.drawPicks(picktype='auto')
         if event.pylot_picks or event.pylot_autopicks:
+            if not self._inputs.get('extent') == 'global':
                 self.locateEventAction.setEnabled(True)
             self.qualities_action.setEnabled(True)
             self.eventlist_xml_action.setEnabled(True)
@@ -2297,7 +2309,7 @@ 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 +2318,7 @@ 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'
@@ -2609,18 +2621,20 @@ 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 +3013,16 @@ class MainWindow(QMainWindow):
             event = self.get_current_event()
         event.pylot_picks = {}
         event.pylot_autopicks = {}
-        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data())
+        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data(), parameter=self.getParameter())
         event.addPicks(picksdict['manual'])
         event.addAutopicks(picksdict['auto'])
 
+    def getParameter(self):
+        if hasattr(self.project, 'parameter') and isinstance(self.project.parameter, PylotParameter):
+            return self.project.parameter
+        else:
+            return self._inputs
+
     def drawPicks(self, station=None, picktype=None, stime=None):
         # if picktype not specified, draw both
         if not stime:

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
 
@@ -27,28 +27,30 @@ 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:
 
@@ -108,4 +110,4 @@ Others: A. Bruestle, T. Meier, W. Friederich
 
 [ObsPy]: http://github.com/obspy/obspy/wiki
 
-April 2022
+August 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)
+    parameter = get_none(parameter)
-    inputfile = get_None(inputfile)
+    inputfile = get_none(inputfile)
-    eventid = get_None(eventid)
+    eventid = get_none(eventid)
 
     fig_dict = None
     fig_dict_wadatijack = None
@@ -119,13 +119,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
             obspyDMT_wfpath = input_dict['obspyDMT_wfpath']
 
     if not parameter:
-        if inputfile:
+        if not inputfile:
+            print('Using default input parameter')
         parameter = PylotParameter(inputfile)
-            # iplot = parameter['iplot']
-        else:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
     else:
         if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
@@ -154,7 +150,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         datastructure.setExpandFields(exf)
 
         # check if default location routine NLLoc is available and all stations are used
-        if get_None(parameter['nllocbin']) and station == 'all':
+        if get_none(parameter['nllocbin']) and station == 'all':
             locflag = 1
             # get NLLoc-root path
             nllocroot = parameter.get('nllocroot')

pylot.yml

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

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')
+                    parameter = PylotParameter()
-                    print('Using default input file {}'.format(infile))
+                    logging.warning('Using default input parameter')
-                    parameter = PylotParameter(infile)
                     focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.pha':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                    parameter = PylotParameter()
-                    print('Using default input file {}'.format(infile))
+                    logging.warning('Using default input parameter')
-                    parameter = PylotParameter(infile)
                     hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
@@ -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:
+            if fnames_alt is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
+                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
@@ -525,19 +527,19 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        real_or_syn_data = {True: self.wfsyn,
+        orig_or_alternative_data = {True: self.wf_alt,
                                     False: self.wfdata}
 
         warnmsg = ''
         for fname in set(fnames):
             try:
-                real_or_syn_data[synthetic] += read(fname, starttime=self.tstart, endtime=self.tstop)
+                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
             except TypeError:
                 try:
-                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
+                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                 except Exception as e:
                     try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
+                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
                                                                       endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
@@ -553,8 +555,8 @@ class Data(object):
     def getOriginalWFData(self):
         return self.wforiginal
 
-    def getSynWFData(self):
+    def getAltWFdata(self):
-        return self.wfsyn
+        return self.wf_alt
 
     def resetWFData(self):
         """

pylot/core/io/default_parameters.py

@@ -511,7 +511,7 @@ 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,

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:
@@ -273,33 +275,29 @@ def picksdict_from_picks(evt):
         phase['epp'] = epp
         phase['lpp'] = lpp
         phase['spe'] = spe
-        try:
+        weight = phase.get('weight')
-            phase['weight'] = weight
+        if not weight:
-        except:
+            if not parameter:
-            # get onset weight from uncertainty
+                logging.warning('Using ')
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
+                logging.warning('Using default input parameter')
-            print('Using default input file {}'.format(infile))
+                parameter = PylotParameter()
-            parameter = PylotParameter(infile)
             pick.phase_hint = identifyPhase(pick.phase_hint)
             if pick.phase_hint == 'P':
                 errors = parameter['timeerrorsP']
             elif pick.phase_hint == 'S':
                 errors = parameter['timeerrorsS']
+            if errors:
                 weight = get_quality_class(spe, errors)
                 phase['weight'] = weight
         phase['channel'] = channel
         phase['network'] = network
         phase['picker'] = pick_method
-        try:
         if pick.polarity == 'positive':
             phase['fm'] = 'U'
         elif pick.polarity == 'negative':
             phase['fm'] = 'D'
         else:
             phase['fm'] = 'N'
-        except:
-            print("No FM info available!")
-            phase['fm'] = 'N'
         phase['filter_id'] = filter_id if filter_id is not None else ''
 
         onsets[pick.phase_hint] = phase.copy()

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):
@@ -258,7 +258,7 @@ class AutopickStation(object):
         self.pickparams = copy.deepcopy(pickparam)
         self.verbose = verbose
         self.iplot = correct_iplot(iplot)
-        self.fig_dict = get_None(fig_dict)
+        self.fig_dict = get_none(fig_dict)
         self.metadata = metadata
         self.origin = origin
 

pylot/core/pick/utils.py

@@ -15,7 +15,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 from scipy.signal import argrelmax
 
-from pylot.core.util.utils import get_bool, get_None, SetChannelComponents
+from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -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
@@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
             returnflag = 0
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -1213,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
             t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
                             trace.stats.npts)
             if i == 0:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax1 = fig.add_subplot(3, 1, i + 1)
                 ax = ax1
                 ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
             else:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
@@ -1494,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
     # set initial quality to 4 (worst) and change only if one condition is hit
     quality = 4
 
-    if get_None(uncertainty) is None:
+    if get_none(uncertainty) is None:
         return quality
 
     if uncertainty <= Errors[0]:

pylot/core/util/array_map.py

@@ -124,8 +124,8 @@ class Array_map(QtWidgets.QWidget):
         self.cmaps_box = QtWidgets.QComboBox()
         self.cmaps_box.setMaxVisibleItems(20)
         [self.cmaps_box.addItem(map_name) for map_name in sorted(plt.colormaps())]
-        # try to set to hsv as default
+        # try to set to viridis as default
-        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('hsv'))
+        self.cmaps_box.setCurrentIndex(self.cmaps_box.findText('viridis'))
 
         self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
@@ -474,21 +474,22 @@ class Array_map(QtWidgets.QWidget):
                                                                   transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        data = self._parent.get_data().getWFData()
+        wfdata = self._parent.get_data().getWFData()
+        wfdata_comp = self._parent.get_data().getAltWFdata()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
             pyl_mw = self._parent
             try:
-                data = data.select(station=station)
+                wfdata = wfdata.select(station=station)
-                if not data:
+                wfdata_comp = wfdata_comp.select(station=station)
+                if not wfdata:
                     self._warn('No data for station {}'.format(station))
                     return
                 pickDlg = PickDlg(self._parent, parameter=self.parameter,
-                                  data=data, network=network, station=station,
+                                  data=wfdata.copy(), data_compare=wfdata_comp.copy(), network=network, station=station,
                                   picks=self._parent.get_current_event().getPick(station),
                                   autopicks=self._parent.get_current_event().getAutopick(station),
                                   filteroptions=self._parent.filteroptions, metadata=self.metadata,
-                                  model=self.parameter.get('taup_model'),
                                   event=pyl_mw.get_current_event())
             except Exception as e:
                 message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)

pylot/core/util/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 bool(value)
+            return False
+    else:
+        return value
+
 
 def four_digits(year):
     """
@@ -355,8 +383,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
+    >>> four_digits(75)
-    1920
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -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
+    returns the actual user's name
-    :return: login ID
+    :return: login name
     :rtype: str
     """
     import getpass
     return getpass.getuser()
 
 
-def getOwner(fn):
+def get_owner(fn):
     """
     takes a filename and return the login ID of the actual owner of the file
     :param fn: filename of the file tested
     :type fn: str
     :return: login ID of the file's owner
     :rtype: str
+
+    >>> import tempfile
+    >>> with tempfile.NamedTemporaryFile() as tmpfile:
+    ...     tmpfile.write(b'') and True
+    ...     tmpfile.flush()
+    ...     get_owner(tmpfile.name) == os.path.expanduser('~').split('/')[-1]
+    0
+    True
     """
     system_name = platform.system()
     if system_name in ["Linux", "Darwin"]:
@@ -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: {' \
+    assert is_iterable(iterable), "object is not iterable; object: {}".format(iterable)
-                                 '}'.format(iterable)
     if type(iterable) is str:
         iterable = [s for s in iterable]
     return sorted(iterable) == iterable
 
 
-def isIterable(obj):
+def is_iterable(obj):
     """
     takes a python object and returns True is the object is iterable and
     False otherwise
     :param obj: a python object
-    :type obj: object
+    :type obj: obj
     :return: True of False
     :rtype: bool
+
+    >>> is_iterable(1)
+    False
+    >>> is_iterable(True)
+    False
+    >>> is_iterable(0.)
+    False
+    >>> is_iterable((0,1,3,4))
+    True
+    >>> is_iterable([1])
+    True
+    >>> is_iterable('a')
+    True
     """
     try:
-        iterator = iter(obj)
+        iter(obj)
     except TypeError as te:
         return False
     return True
@@ -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
+    :param offset: offset of the actual seismogram on plotting axis
-    :type stime: `~obspy.core.utcdatetime.UTCDateTime`
+    :type offset: float or int
     :param trace: seismic trace object
     :type trace: `~obspy.core.trace.Trace`
     :param verbosity: if != 0, debug output will be written to console
     :type verbosity: int
     :return: valid numpy array with time stamps for plotting
     :rtype: `~numpy.ndarray`
+
+    >>> tr = read()[0]
+    >>> prep_time_axis(0., tr)
+    array([0.00000000e+00, 1.00033344e-02, 2.00066689e-02, ...,
+           2.99799933e+01, 2.99899967e+01, 3.00000000e+01])
+    >>> prep_time_axis(22.5, tr)
+    array([22.5       , 22.51000333, 22.52000667, ..., 52.47999333,
+           52.48999667, 52.5       ])
+    >>> prep_time_axis(tr.stats.starttime, tr)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'offset' is not of type 'float' or 'int'; type: <class 'obspy.core.utcdatetime.UTCDateTime'>
+    >>> tr.stats.npts -= 1
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033356e-02, 2.00066711e-02, ...,
+           2.99699933e+01, 2.99799967e+01, 2.99900000e+01])
+    >>> tr.stats.npts += 2
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033333e-02, 2.00066667e-02, ...,
+           2.99899933e+01, 2.99999967e+01, 3.00100000e+01])
     """
+    assert isinstance(offset, (float, int)), "'offset' is not of type 'float' or 'int'; type: {}".format(type(offset))
     nsamp = trace.stats.npts
     srate = trace.stats.sampling_rate
     tincr = trace.stats.delta
-    etime = stime + nsamp / srate
+    etime = offset + nsamp / srate
-    time_ax = np.linspace(stime, etime, nsamp)
+    time_ax = np.linspace(offset, etime, nsamp)
     if len(time_ax) < nsamp:
         if verbosity:
             print('elongate time axes by one datum')
-        time_ax = np.arange(stime, etime + tincr, tincr)
+        time_ax = np.arange(offset, etime + tincr, tincr)
     elif len(time_ax) > nsamp:
         if verbosity:
             print('shorten time axes by one datum')
-        time_ax = np.arange(stime, etime - tincr, tincr)
+        time_ax = np.arange(offset, etime - tincr, tincr)
     if len(time_ax) != nsamp:
         print('Station {0}, {1} samples of data \n '
               '{2} length of time vector \n'
@@ -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)
+    :type rgba: Rgba
-    :param modifier: which color should be modified, eg. 'r', 'g', 'b'
+    :param modifier: which color should be modified; options: 'r', 'g', 'b'
-    :type modifier: str
+    :type modifier: Literal['r', 'g', 'b']
     :param intensity: intensity to be added to selected color
     :type intensity: float
     :return: tuple containing rgba values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     rgba = list(rgba)
     index = {'r': 0,
@@ -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 '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
-    return colors_mpl
 
 
 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 +1039,87 @@ def check4rotated(data, metadata=None, verbosity=1):
     :rtype: `~obspy.core.stream.Stream`
     """
 
-    def rotate_components(wfstream, metadata=None):
+    def rotation_required(trace_ids):
+        """
+        Derive if any rotation is required from the orientation code of the input.
+
+        :param trace_ids: string identifier of waveform data trace
+        :type trace_ids: List(str)
+        :return: boolean representing if rotation is necessary for any of the traces
+        :rtype: bool
+        """
+        orientations = [trace_id[-1] for trace_id in trace_ids]
+        return any([orientation.isnumeric() for orientation in orientations])
+
+    def rotate_components(wfs_in, metadata=None):
         """
         Rotate components if orientation code is numeric (= non traditional orientation).
 
         Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
         Returns unrotated traces of no metadata is provided
-        :param wfstream: stream containing seismic traces of a station
+        :param wfs_in: stream containing seismic traces of a station
-        :type wfstream: `~obspy.core.stream.Stream`
+        :type wfs_in: `~obspy.core.stream.Stream`
         :param metadata: tuple containing metadata type string and metadata parser object
         :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
         :return: stream object with traditionally oriented traces (ZNE)
         :rtype: `~obspy.core.stream.Stream`
         """
 
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
+
         # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
+        trace_ids = [trace.id for trace in wfs_in]
-        orientations = [trace_id[-1] for trace_id in trace_ids]
+        if not rotation_required(trace_ids):
-        rotation_required = [orientation.isnumeric() for orientation in orientations]
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
-        if any(rotation_required):
+            return wfs_in
-            t_start = full_range(wfstream)
+
+        # check metadata quality
+        t_start = full_range(wfs_in)
         try:
-                azimuts = []
+            azimuths = []
             dips = []
             for tr_id in trace_ids:
-                    azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
                 dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
-            except (KeyError, TypeError) as e:
+        except (KeyError, TypeError) as err:
-                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
+            logging.error(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
-                return wfstream
+                  f"available in metadata. Stream remains unchanged.")
-            if len(wfstream) < 3:
+            return wfs_in
-                print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
+        except Exception as err:
-                return wfstream
+            print(f"Unexpected {err=}, {type(err)=}")
+            raise
+
         # to rotate all traces must have same length, so trim them
-            wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
+        wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
         try:
-                z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
+            z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
-                                     wfstream[1], azimuts[1], dips[1],
+                                 wfs_out[1], azimuths[1], dips[1],
-                                     wfstream[2], azimuts[2], dips[2])
+                                 wfs_out[2], azimuths[2], dips[2])
             print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
             # replace old data with rotated data, change the channel code to ZNE
             z_index = dips.index(min(
-                    dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
+                dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90
-                wfstream[z_index].data = z
+            # being vertical)
-                wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
+            wfs_out[z_index].data = z
+            wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
             del trace_ids[z_index]
             for trace_id in trace_ids:
                 coordinates = metadata.get_coordinates(trace_id, t_start)
                 dip, az = coordinates['dip'], coordinates['azimuth']
-                    trace = wfstream.select(id=trace_id)[0]
+                trace = wfs_out.select(id=trace_id)[0]
-                    if az > 315 or az <= 45 or az > 135 and az <= 225:
+                if az > 315 or az <= 45 or 135 < az <= 225:
                     trace.data = n
                     trace.stats.channel = trace.stats.channel[0:-1] + 'N'
-                    elif az > 45 and az <= 135 or az > 225 and az <= 315:
+                elif 45 < az <= 135 or 225 < az <= 315:
                     trace.data = e
                     trace.stats.channel = trace.stats.channel[0:-1] + 'E'
-            except (ValueError) as e:
+        except ValueError as err:
-                print(e)
+            print(f"{err=} Rotation failed. Stream remains unchanged.")
-                return wfstream
+            return wfs_in
 
-        return wfstream
+        return wfs_out
 
     if metadata is None:
         if verbosity:
@@ -1032,38 +1133,6 @@ def check4rotated(data, metadata=None, verbosity=1):
     return data
 
 
-def scaleWFData(data, factor=None, components='all'):
-    """
-    produce scaled waveforms from given waveform data and a scaling factor,
-    waveform may be selected by their components name
-    :param data: waveform data to be scaled
-    :type data: `~obspy.core.stream.Stream` object
-    :param factor: scaling factor
-    :type factor: float
-    :param components: components labels for the traces in data to be scaled by
-     the scaling factor (optional, default: 'all')
-    :type components: tuple
-    :return:  scaled waveform data
-    :rtype: `~obspy.core.stream.Stream` object
-    """
-    if components != 'all':
-        for comp in components:
-            if factor is None:
-                max_val = np.max(np.abs(data.select(component=comp)[0].data))
-                data.select(component=comp)[0].data /= 2 * max_val
-            else:
-                data.select(component=comp)[0].data /= 2 * factor
-    else:
-        for tr in data:
-            if factor is None:
-                max_val = float(np.max(np.abs(tr.data)))
-                tr.data /= 2 * max_val
-            else:
-                tr.data /= 2 * factor
-
-    return data
-
-
 def runProgram(cmd, parameter=None):
     """
     run an external program specified by cmd with parameters input returning the

pylot/core/util/widgets.py

@@ -7,6 +7,7 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
+import glob
 import multiprocessing
 import os
 import subprocess
@@ -16,6 +17,7 @@ import traceback
 
 import matplotlib
 import numpy as np
+from pylot.core.io.phases import getQualitiesfromxml
 
 matplotlib.use('QT5Agg')
 
@@ -49,11 +51,11 @@ 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 +795,7 @@ 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 +806,13 @@ 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 +827,7 @@ 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 +836,11 @@ class WaveformWidgetPG(QtWidgets.QWidget):
     def getPlotDict(self):
         return self.plotdict
 
-    def activateObspyDMToptions(self, activate):
+    def activateObspyDMToptions(self, activate: bool) -> None:
-        self.syn_checkbox.setVisible(activate)
+        self.qcombo_processed.setEnabled(activate)
-        self.qcombo_processed.setVisible(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 +940,10 @@ 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 +963,7 @@ 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 +1152,12 @@ 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 +1375,15 @@ 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 +1394,33 @@ 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)
+            plot_streams['wfdata']['data'] = wfdata.select(component=component)
-            st_select += wfdata.select(component=alter_comp)
+            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
@@ -1408,10 +1428,12 @@ 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('.')
+            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:
@@ -1422,7 +1444,7 @@ class PylotCanvas(FigureCanvas):
                     msg = 'plotting %s channel of station %s' % (channel, station)
                     print(msg)
                 stime = trace.stats.starttime - wfstart
-            time_ax = prepTimeAxis(stime, trace)
+                time_ax = prep_time_axis(stime, trace)
                 if time_ax is not None:
                     if scaleToChannel:
                         st_scale = wfdata.select(channel=scaleToChannel)
@@ -1435,15 +1457,17 @@ class PylotCanvas(FigureCanvas):
                         trace.detrend('constant')
                         trace.normalize(np.max(np.abs(trace.data)) * 2)
 
+                    offset = wf_dict.get('offset')
+
                     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]
+                    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=linecolor, linewidth=0.7)
+                    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=linecolor,
+                                    color=wf_dict.get('linecolor'),
                                     linestyle='dashed')
                     self.setPlotDict(n, seed_id)
         if plot_additional and additional_channel:
@@ -1460,7 +1484,7 @@ 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 +1598,8 @@ 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 +1607,17 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.connectSignals()
         self.showPaths()
         self.refreshSelectionBox()
-        self.refresh_timer = QTimer(self)
+        # self.refresh_timer = QTimer(self)
-        self.refresh_timer.timeout.connect(self.showPaths)
+        # self.refresh_timer.timeout.connect(self.showPaths)
-        self.refresh_timer.start(10000)
+        # 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 +1631,24 @@ 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 +1661,17 @@ 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 +1680,23 @@ 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, fname_item)
-                self.tableWidget.setItem(index, 2, ts_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
+        self.update_status()
-        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)
 
     def refreshSelectionBox(self):
         fext = self.comboBox.currentText()
@@ -1668,12 +1716,52 @@ 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 +1868,18 @@ 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,
+    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,
+                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
-                 event=None, filteroptions=None, model=None, wftype=None):
+                 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 +1918,6 @@ 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 +1930,31 @@ 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 +1967,12 @@ 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 +1989,7 @@ 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 +2165,11 @@ class PickDlg(QDialog):
         _dialtoolbar.addWidget(est_label)
         _dialtoolbar.addWidget(self.plot_arrivals_button)
         _dialtoolbar.addSeparator()
-        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare to channel: '))
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Plot reference channel: '))
-        _dialtoolbar.addWidget(self.compareChannel)
+        _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 +2254,12 @@ 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("get_arrivals: Creation info (manual or auto) not available! Return!")
-            print("Return!")
             return
         if origins:
             source_origin = origins[0]
@@ -2166,8 +2270,8 @@ class PickDlg(QDialog):
         arrivals = func[plot](source_origin.depth,
                               source_origin.latitude,
                               source_origin.longitude,
-                              station_coords['latitude'],
+                              station_coords.get('latitude'),
-                              station_coords['longitude'],
+                              station_coords.get('longitude'),
                               phases)
         self.arrivals = arrivals
 
@@ -2267,7 +2371,7 @@ 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 +2506,7 @@ 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 +2538,7 @@ 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 +2611,12 @@ 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 +2738,16 @@ class PickDlg(QDialog):
 
         stime = self.getStartTime()
 
-        # copy data for plotting
+        # copy wfdata for plotting
-        data = self.getWFData().copy()
+        wfdata = self.getWFData().copy()
-        data = self.getPickPhases(data, phase)
+        wfdata_comp = self.getWFDataComp().copy()
-        data.normalize()
+        wfdata = self.getPickPhases(wfdata, phase)
-        if not data:
+        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 +2755,16 @@ 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')
+                for wfd in [wfdata, wfdata_comp]:
-                data.filter(**filteroptions)
+                    if wfd:
-                # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
+                        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 +2774,8 @@ class PickDlg(QDialog):
         snr = []
         noiselevels = {}
         # determine SNR and noiselevel
-        for trace in data.traces:
+        for trace in wfdata.traces:
-            st = data.select(channel=trace.stats.channel)
+            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])
@@ -2669,12 +2786,14 @@ class PickDlg(QDialog):
                 noiselevel = nfac
             noiselevels[trace.stats.channel] = noiselevel
 
-        # prepare plotting of data
+        # prepare plotting of wfdata
-        for trace in data:
+        for wfd in [wfdata, wfdata_comp]:
-            t = prepTimeAxis(trace.stats.starttime - stime, trace)
+            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 data in a way that each trace is vertically zoomed to noiselevel*factor
+                    # 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.)
@@ -2685,7 +2804,7 @@ class PickDlg(QDialog):
         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 +2812,10 @@ class PickDlg(QDialog):
             filtops_str = transformFilteroptions2String(filteroptions)
             title += ' | Filteroptions: {}'.format(filtops_str)
 
-        plot_additional = bool(self.compareChannel.currentText())
+        plot_additional = bool(self.referenceChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
+        additional_channel = self.referenceChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data,
+        self.multicompfig.plotWFData(wfdata=wfdata,
+                                     wfdata_compare=wfdata_comp,
                                      title=title,
                                      zoomx=xlims,
                                      zoomy=ylims,
@@ -3086,7 +3206,8 @@ 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 +3215,22 @@ class PickDlg(QDialog):
                 filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()
 
             if filtoptions is not None:
-                data.detrend('linear')
+                for wfd in [wfdata, wfdata_comp]:
-                data.taper(0.02, type='cosine')
+                    if wfd:
-                data.filter(**filtoptions)
+                        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())
+        plot_additional = bool(self.referenceChannel.currentText())
-        additional_channel = self.compareChannel.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 +3303,9 @@ 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)
@@ -3790,11 +3917,13 @@ 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 +4008,7 @@ 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
@@ -4794,8 +4923,8 @@ 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.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.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)
@@ -5791,7 +5920,7 @@ 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 +1,90 @@
+#############################  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 autopicks 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'
+
+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:
+Cartopy==0.23.0
-# $ conda create --name <env> --file <this file>
+joblib==1.4.2
-# platform: win-64
+obspy==1.4.1
-cartopy=0.20.2
+pyaml==24.7.0
-matplotlib-base=3.3.4
+pyqtgraph==0.13.7
-numpy=1.22.3
+PySide2==5.15.8
-obspy=1.3.0
+pytest==8.3.2
-pyqtgraph=0.12.4
-pyside2=5.13.2
-python=3.8.12
-qt=5.12.9
-scipy=1.8.0

tests/test_autopicker/pylot_alparray_mantle_corr_stack_0.03-0.5.in

@@ -0,0 +1,101 @@
+%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#
+                                                   #rootpath#       %project path                                                                                        
+                                                   #datapath#       %data path                                                                                           
+                                                   #database#       %name of data base                                                                                   
+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 +1,27 @@
+import os
+import pytest
+
+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'
+
+        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.'
+        #autoPyLoT(inputfile=self.params_infile, eventid='20171010_063224.a')

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)