[change] corrected for required versions

[update] raising PickingFailedException when CF cannot be calculated due to missing signal (too short waveform)

README.md

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

autoPyLoT.py

@@ -28,7 +28,7 @@ from pylot.core.util.dataprocessing import restitute_data, Metadata
 from pylot.core.util.defaults import SEPARATOR
 from pylot.core.util.event import Event
 from pylot.core.util.structure import DATASTRUCTURE
-from pylot.core.util.utils import get_None, trim_station_components, check4gapsAndRemove, check4doubled, \
+from pylot.core.util.utils import get_none, trim_station_components, check4gapsAndRemove, check4doubled, \
     check4rotated
 from pylot.core.util.version import get_git_version as _getVersionString
 
@@ -91,9 +91,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                                                               sp=sp_info)
     print(splash)
 
-    parameter = get_None(parameter)
-    inputfile = get_None(inputfile)
-    eventid = get_None(eventid)
+    parameter = get_none(parameter)
+    inputfile = get_none(inputfile)
+    eventid = get_none(eventid)
 
     fig_dict = None
     fig_dict_wadatijack = None
@@ -119,13 +119,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
             obspyDMT_wfpath = input_dict['obspyDMT_wfpath']
 
     if not parameter:
-        if inputfile:
-            parameter = PylotParameter(inputfile)
-            # iplot = parameter['iplot']
-        else:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
+        if not inputfile:
+            print('Using default input parameter')
+        parameter = PylotParameter(inputfile)
     else:
         if not type(parameter) == PylotParameter:
             print('Wrong input type for parameter: {}'.format(type(parameter)))
@@ -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')
@@ -247,7 +243,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 pylot_event = Event(eventpath)  # event should be path to event directory
                 data.setEvtData(pylot_event)
             if fnames == 'None':
-                data.setWFData(glob.glob(os.path.join(datapath, event_datapath, '*')))
+                data.set_wf_data(glob.glob(os.path.join(datapath, event_datapath, '*')))
                 # the following is necessary because within
                 # multiple event processing no event ID is provided
                 # in autopylot.in
@@ -262,7 +258,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                                                       now.minute)
                     parameter.setParam(eventID=eventID)
             else:
-                data.setWFData(fnames)
+                data.set_wf_data(fnames)
 
                 eventpath = events[0]
                 # now = datetime.datetime.now()
@@ -272,7 +268,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                 #                               now.hour,
                 #                               now.minute)
                 parameter.setParam(eventID=eventid)
-            wfdat = data.getWFData()  # all available streams
+            wfdat = data.get_wf_data()  # all available streams
             if not station == 'all':
                 wfdat = wfdat.select(station=station)
                 if not wfdat:

autopylot.sh

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

pylot.yml

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

pylot/core/analysis/magnitude.py

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

pylot/core/io/data.py

@@ -1,624 +1,69 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import copy
 import os
+from dataclasses import dataclass, field
+from typing import List, Union
 
-from PySide2.QtWidgets import QMessageBox
-from obspy import read_events
-from obspy.core import read, Stream, UTCDateTime
-from obspy.core.event import Event as ObsPyEvent
-from obspy.io.sac import SacIOError
+from obspy import UTCDateTime
 
-import pylot.core.loc.focmec as focmec
-import pylot.core.loc.hypodd as hypodd
-import pylot.core.loc.velest as velest
-from pylot.core.io.phases import readPILOTEvent, picks_from_picksdict, \
-    picksdict_from_pilot, merge_picks, PylotParameter
-from pylot.core.util.errors import FormatError, OverwriteError
-from pylot.core.util.event import Event
-from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
-from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
-    check4gapsAndMerge, trim_station_components
+from pylot.core.io.event import EventData
+from pylot.core.io.waveformdata import WaveformData
+from pylot.core.util.dataprocessing import Metadata
 
-
-class Data(object):
-    """
-    Data container with attributes wfdata holding ~obspy.core.stream.
-
-    :type parent: PySide2.QtWidgets.QWidget object, optional
-    :param parent: A PySide2.QtWidgets.QWidget object utilized when
-    called by a GUI to display a PySide2.QtWidgets.QMessageBox instead of printing
-    to standard out.
-    :type evtdata: ~obspy.core.event.Event object, optional
-    :param evtdata ~obspy.core.event.Event object containing all derived or
-    loaded event. Container object holding, e.g. phase arrivals, etc.
-    """
+@dataclass
+class Data:
+    event_data: EventData = field(default_factory=EventData)
+    waveform_data: WaveformData = field(default_factory=WaveformData)
+    metadata: Metadata = field(default_factory=Metadata)
+    _parent: Union[None, 'QtWidgets.QWidget'] = None
 
     def __init__(self, parent=None, evtdata=None):
         self._parent = parent
-        if self.getParent():
-            self.comp = parent.getComponent()
-        else:
-            self.comp = 'Z'
-            self.wfdata = Stream()
-        self._new = False
-        if isinstance(evtdata, ObsPyEvent) or isinstance(evtdata, Event):
-            pass
-        elif isinstance(evtdata, dict):
-            evt = readPILOTEvent(**evtdata)
-            evtdata = evt
-        elif isinstance(evtdata, str):
-            try:
-                cat = read_events(evtdata)
-                if len(cat) != 1:
-                    raise ValueError('ambiguous event information for file: '
-                                     '{file}'.format(file=evtdata))
-                evtdata = cat[0]
-            except TypeError as e:
-                if 'Unknown format for file' in e.message:
-                    if 'PHASES' in evtdata:
-                        picks = picksdict_from_pilot(evtdata)
-                        evtdata = ObsPyEvent()
-                        evtdata.picks = picks_from_picksdict(picks)
-                    elif 'LOC' in evtdata:
-                        raise NotImplementedError('PILOT location information '
-                                                  'read support not yet '
-                                                  'implemeted.')
-                    elif 'event.pkl' in evtdata:
-                        evtdata = qml_from_obspyDMT(evtdata)
-                    else:
-                        raise e
-                else:
-                    raise e
-        else:  # create an empty Event object
-            self.setNew()
-            evtdata = ObsPyEvent()
-            evtdata.picks = []
-        self.evtdata = evtdata
-        self.wforiginal = None
-        self.cuttimes = None
-        self.dirty = False
-        self.processed = None
+        self.event_data = EventData(evtdata)
+        self.waveform_data = WaveformData()
 
     def __str__(self):
-        return str(self.wfdata)
+        return str(self.waveform_data.wfdata)
 
     def __add__(self, other):
-        assert isinstance(other, Data), "operands must be of same type 'Data'"
-        rs_id = self.get_evt_data().get('resource_id')
-        rs_id_other = other.get_evt_data().get('resource_id')
-        if other.isNew() and not self.isNew():
-            picks_to_add = other.get_evt_data().picks
-            old_picks = self.get_evt_data().picks
-            wf_ids_old = [pick.waveform_id for pick in old_picks]
-            for new_pick in picks_to_add:
-                wf_id = new_pick.waveform_id
-                if wf_id in wf_ids_old:
-                    for old_pick in old_picks:
-                        comparison = [old_pick.waveform_id == new_pick.waveform_id,
-                                      old_pick.phase_hint == new_pick.phase_hint,
-                                      old_pick.method_id == new_pick.method_id]
-                        if all(comparison):
-                            del (old_pick)
-                old_picks.append(new_pick)
-        elif not other.isNew() and self.isNew():
-            new = other + self
-            self.evtdata = new.get_evt_data()
-        elif self.isNew() and other.isNew():
+        if not isinstance(other, Data):
+            raise TypeError("Operands must be of type 'Data'")
+        if self.event_data.is_new() and other.event_data.is_new():
             pass
-        elif rs_id == rs_id_other:
-            other.setNew()
+        elif other.event_data.is_new():
+            new_picks = other.event_data.evtdata.picks
+            old_picks = self.event_data.evtdata.picks
+            old_picks.extend([pick for pick in new_picks if pick not in old_picks])
+        elif self.event_data.is_new():
+            return other + self
+        elif self.event_data.get_id() == other.event_data.get_id():
+            other.event_data.set_new()
             return self + other
         else:
-            raise ValueError("both Data objects have differing "
-                             "unique Event identifiers")
+            raise ValueError("Both Data objects have differing unique Event identifiers")
         return self
 
-    def getPicksStr(self):
-        """
-        Return picks in event data
-        :return: picks seperated by newlines
-        :rtype: str
-        """
-        picks_str = ''
-        for pick in self.get_evt_data().picks:
-            picks_str += str(pick) + '\n'
-        return picks_str
-
-    def getParent(self):
-        """
-        Get PySide.QtGui.QWidget parent object
-        """
+    def get_parent(self):
         return self._parent
 
-    def isNew(self):
-        return self._new
+    def filter_wf_data(self, **kwargs):
+        self.waveform_data.wfdata.detrend('linear')
+        self.waveform_data.wfdata.taper(0.02, type='cosine')
+        self.waveform_data.wfdata.filter(**kwargs)
+        self.waveform_data.dirty = True
 
-    def setNew(self):
-        self._new = True
+    def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
+        return self.waveform_data.load_waveforms(fnames, fnames_alt, check_rotated, metadata, tstart, tstop)
 
-    def getCutTimes(self):
-        """
-        Returns earliest start and latest end of all waveform data
-        :return: minimum start time and maximum end time as a tuple
-        :rtype: (UTCDateTime, UTCDateTime)
-        """
-        if self.cuttimes is None:
-            self.updateCutTimes()
-        return self.cuttimes
+    def reset_wf_data(self):
+        self.waveform_data.reset()
 
-    def updateCutTimes(self):
-        """
-        Update cuttimes to contain earliest start and latest end time
-        of all waveform data
-        :rtype: None
-        """
-        self.cuttimes = full_range(self.getWFData())
+    def get_wf_data(self):
+        return self.waveform_data.wfdata
 
-    def getEventFileName(self):
-        ID = self.getID()
-        # handle forbidden filenames especially on windows systems
-        return fnConstructor(str(ID))
-
-    def checkEvent(self, event, fcheck, forceOverwrite=False):
-        """
-        Check information in supplied event and own event and replace with own
-        information if no other information are given or forced by forceOverwrite
-        :param event: Event that supplies information for comparison
-        :type event: pylot.core.util.event.Event
-        :param fcheck: check and delete existing information
-        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
-        :type fcheck: str, [str]
-        :param forceOverwrite: Set to true to force overwrite own information. If false,
-        supplied information from event is only used if there is no own information in that
-        category (given in fcheck: manual, auto, origin, magnitude)
-        :type forceOverwrite: bool
-        :return:
-        :rtype: None
-        """
-        if 'origin' in fcheck:
-            self.replaceOrigin(event, forceOverwrite)
-        if 'magnitude' in fcheck:
-            self.replaceMagnitude(event, forceOverwrite)
-        if 'auto' in fcheck:
-            self.replacePicks(event, 'auto')
-        if 'manual' in fcheck:
-            self.replacePicks(event, 'manual')
-
-    def replaceOrigin(self, event, forceOverwrite=False):
-        """
-        Replace own origin with the one supplied in event if own origin is not
-        existing or forced by forceOverwrite = True
-        :param event: Event that supplies information for comparison
-        :type event: pylot.core.util.event.Event
-        :param forceOverwrite: always replace own information with supplied one if true
-        :type forceOverwrite: bool
-        :return:
-        :rtype: None
-        """
-        if self.get_evt_data().origins or forceOverwrite:
-            if event.origins:
-                print("Found origin, replace it by new origin.")
-            event.origins = self.get_evt_data().origins
-
-    def replaceMagnitude(self, event, forceOverwrite=False):
-        """
-        Replace own magnitude with the one supplied in event if own magnitude is not
-        existing or forced by forceOverwrite = True
-        :param event: Event that supplies information for comparison
-        :type event: pylot.core.util.event.Event
-        :param forceOverwrite: always replace own information with supplied one if true
-        :type forceOverwrite: bool
-        :return:
-        :rtype: None
-        """
-        if self.get_evt_data().magnitudes or forceOverwrite:
-            if event.magnitudes:
-                print("Found magnitude, replace it by new magnitude")
-            event.magnitudes = self.get_evt_data().magnitudes
-
-    def replacePicks(self, event, picktype):
-        """
-        Replace picks in event with own picks
-        :param event: Event that supplies information for comparison
-        :type event: pylot.core.util.event.Event
-        :param picktype: 'auto' or 'manual' picks
-        :type picktype: str
-        :return:
-        :rtype: None
-        """
-        checkflag = 1
-        picks = event.picks
-        # remove existing picks
-        for j, pick in reversed(list(enumerate(picks))):
-            try:
-                if picktype in str(pick.method_id.id):
-                    picks.pop(j)
-                    checkflag = 2
-            except AttributeError as e:
-                msg = '{}'.format(e)
-                print(e)
-                checkflag = 0
-        if checkflag > 0:
-            if checkflag == 1:
-                print("Write new %s picks to catalog." % picktype)
-            if checkflag == 2:
-                print("Found %s pick(s), remove them and append new picks to catalog." % picktype)
-
-            # append new picks
-            for pick in self.get_evt_data().picks:
-                if picktype in str(pick.method_id.id):
-                    picks.append(pick)
-
-    def exportEvent(self, fnout, fnext='.xml', fcheck='auto', upperErrors=None):
-        """
-        Export event to file
-        :param fnout: basename of file
-        :param fnext: file extensions xml, cnv, obs, focmec, or/and pha
-        :param fcheck: check and delete existing information
-        can be a str or a list of strings of ['manual', 'auto', 'origin', 'magnitude']
-        """
-        from pylot.core.util.defaults import OUTPUTFORMATS
-
-        if not type(fcheck) == list:
-            fcheck = [fcheck]
-
-        try:
-            evtformat = OUTPUTFORMATS[fnext]
-        except KeyError as e:
-            errmsg = '{0}; selected file extension {1} not ' \
-                     'supported'.format(e, fnext)
-            raise FormatError(errmsg)
-
-        if hasattr(self.get_evt_data(), 'notes'):
-            try:
-                with open(os.path.join(os.path.dirname(fnout), 'notes.txt'), 'w') as notes_file:
-                    notes_file.write(self.get_evt_data().notes)
-            except Exception as e:
-                print('Warning: Could not save notes.txt: ', str(e))
-
-        # check for already existing xml-file
-        if fnext == '.xml':
-            if os.path.isfile(fnout + fnext):
-                print("xml-file already exists! Check content ...")
-                cat = read_events(fnout + fnext)
-                if len(cat) > 1:
-                    raise IOError('Ambigious event information in file {}'.format(fnout + fnext))
-                if len(cat) < 1:
-                    raise IOError('No event information in file {}'.format(fnout + fnext))
-                event = cat[0]
-                if not event.resource_id == self.get_evt_data().resource_id:
-                    QMessageBox.warning(self, 'Warning', 'Different resource IDs!')
-                    return
-                self.checkEvent(event, fcheck)
-                self.setEvtData(event)
-
-            self.get_evt_data().write(fnout + fnext, format=evtformat)
-
-        # try exporting event
-        else:
-            evtdata_org = self.get_evt_data()
-            picks = evtdata_org.picks
-            eventpath = evtdata_org.path
-            picks_copy = copy.deepcopy(picks)
-            evtdata_copy = Event(eventpath)
-            evtdata_copy.picks = picks_copy
-
-            # check for stations picked automatically as well as manually
-            # Prefer manual picks!
-            for i in range(len(picks)):
-                if picks[i].method_id == 'manual':
-                    mstation = picks[i].waveform_id.station_code
-                    mstation_ext = mstation + '_'
-                    for k in range(len(picks_copy)):
-                        if ((picks_copy[k].waveform_id.station_code == mstation) or
-                            (picks_copy[k].waveform_id.station_code == mstation_ext)) and \
-                                (picks_copy[k].method_id == 'auto'):
-                            del picks_copy[k]
-                            break
-            lendiff = len(picks) - len(picks_copy)
-            if lendiff != 0:
-                print("Manual as well as automatic picks available. Prefered the {} manual ones!".format(lendiff))
-
-            if upperErrors:
-                # check for pick uncertainties exceeding adjusted upper errors
-                # Picks with larger uncertainties will not be saved in output file!
-                for j in range(len(picks)):
-                    for i in range(len(picks_copy)):
-                        if picks_copy[i].phase_hint[0] == 'P':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]) or \
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
-                                print("Uncertainty exceeds or equal adjusted upper time error!")
-                                print("Adjusted uncertainty: {}".format(upperErrors[0]))
-                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
-                                print("{1} P-Pick of station {0} will not be saved in outputfile".format(
-                                    picks_copy[i].waveform_id.station_code,
-                                    picks_copy[i].method_id))
-                                print("#")
-                                del picks_copy[i]
-                                break
-                        if picks_copy[i].phase_hint[0] == 'S':
-                            if (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]) or \
-                                    (picks_copy[i].time_errors['uncertainty'] is None):
-                                print("Uncertainty exceeds or equal adjusted upper time error!")
-                                print("Adjusted uncertainty: {}".format(upperErrors[1]))
-                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
-                                print("{1} S-Pick of station {0} will not be saved in outputfile".format(
-                                    picks_copy[i].waveform_id.station_code,
-                                    picks_copy[i].method_id))
-                                print("#")
-                                del picks_copy[i]
-                                break
-
-            if fnext == '.obs':
-                try:
-                    evtdata_copy.write(fnout + fnext, format=evtformat)
-                    # write header afterwards
-                    evid = str(evtdata_org.resource_id).split('/')[1]
-                    header = '# EQEVENT:  Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' % evid
-                    nllocfile = open(fnout + fnext)
-                    l = nllocfile.readlines()
-                    # Adding A0/Generic Amplitude to .obs file
-                    # l2 = []
-                    # for li in l:
-                    #    for amp in evtdata_org.amplitudes:
-                    #        if amp.waveform_id.station_code == li[0:5].strip():
-                    #            li = li[0:64] + '{:0.2e}'.format(amp.generic_amplitude) + li[73:-1] + '\n'
-                    #            l2.append(li)
-                    # l = l2
-                    nllocfile.close()
-                    l.insert(0, header)
-                    nllocfile = open(fnout + fnext, 'w')
-                    nllocfile.write("".join(l))
-                    nllocfile.close()
-                except KeyError as e:
-                    raise KeyError('''{0} export format
-                                     not implemented: {1}'''.format(evtformat, e))
-            if fnext == '.cnv':
-                try:
-                    velest.export(picks_copy, fnout + fnext, eventinfo=self.get_evt_data())
-                except KeyError as e:
-                    raise KeyError('''{0} export format
-                                     not implemented: {1}'''.format(evtformat, e))
-            if fnext == '_focmec.in':
-                try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
-                    focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
-                except KeyError as e:
-                    raise KeyError('''{0} export format
-                                     not implemented: {1}'''.format(evtformat, e))
-            if fnext == '.pha':
-                try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
-                    hypodd.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))
-
-    def getComp(self):
-        """
-        Get component (ZNE)
-        """
-        return self.comp
-
-    def getID(self):
-        """
-        Get unique resource id
-        """
-        try:
-            return self.evtdata.get('resource_id').id
-        except:
-            return None
-
-    def filterWFData(self, kwargs):
-        """
-        Filter waveform data
-        :param kwargs: arguments to pass through to filter function
-        """
-        data = self.getWFData()
-        data.detrend('linear')
-        data.taper(0.02, type='cosine')
-        data.filter(**kwargs)
-        self.dirty = True
-
-    def setWFData(self, fnames, fnames_syn=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
-        :type fnames: list
-        """
-        self.wfdata = Stream()
-        self.wforiginal = None
-        self.wfsyn = Stream()
-        if tstart == tstop:
-            tstart = tstop = None
-        self.tstart = tstart
-        self.tstop = tstop
-
-        # if obspy_dmt:
-        #     wfdir = 'raw'
-        #     self.processed = False
-        #     for fname in fnames:
-        #         if fname.endswith('processed'):
-        #             wfdir = 'processed'
-        #             self.processed = True
-        #             break
-        #     for fpath in fnames:
-        #         if fpath.endswith(wfdir):
-        #             wffnames = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
-        #         if 'syngine' in fpath.split('/')[-1]:
-        #             wffnames_syn = [os.path.join(fpath, fname) for fname in os.listdir(fpath)]
-        # else:
-        #     wffnames = fnames
-        if fnames is not None:
-            self.appendWFData(fnames)
-            if fnames_syn is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
-        else:
-            return False
-
-        # various pre-processing steps:
-        # remove possible underscores in station names
-        # self.wfdata = remove_underscores(self.wfdata)
-        # check for gaps and merge
-        self.wfdata = check4gapsAndMerge(self.wfdata)
-        # check for stations with rotated components
-        if checkRotated and metadata is not None:
-            self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
-        # trim station components to same start value
-        trim_station_components(self.wfdata, trim_start=True, trim_end=False)
-
-        # make a copy of original data
-        self.wforiginal = self.getWFData().copy()
-        self.dirty = False
-        return True
-
-    def appendWFData(self, fnames, synthetic=False):
-        """
-        Read waveform data from fnames and append it to current wf data
-        :param fnames: waveform data to append
-        :type fnames: list
-        """
-        assert isinstance(fnames, list), "input parameter 'fnames' is " \
-                                         "supposed to be of type 'list' " \
-                                         "but is actually" \
-                                         " {0}".format(type(fnames))
-        if self.dirty:
-            self.resetWFData()
-
-        real_or_syn_data = {True: self.wfsyn,
-                            False: self.wfdata}
-
-        warnmsg = ''
-        for fname in set(fnames):
-            try:
-                real_or_syn_data[synthetic] += 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)
-                except Exception as e:
-                    try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
-                                                            endtime=self.tstop)
-                    except Exception as e:
-                        warnmsg += '{0}\n{1}\n'.format(fname, e)
-            except SacIOError as se:
-                warnmsg += '{0}\n{1}\n'.format(fname, se)
-        if warnmsg:
-            warnmsg = 'WARNING in appendWFData: unable to read waveform data\n' + warnmsg
-            print(warnmsg)
-
-    def getWFData(self):
-        return self.wfdata
-
-    def getOriginalWFData(self):
-        return self.wforiginal
-
-    def getSynWFData(self):
-        return self.wfsyn
-
-    def resetWFData(self):
-        """
-        Set waveform data to original waveform data
-        """
-        if self.getOriginalWFData():
-            self.wfdata = self.getOriginalWFData().copy()
-        else:
-            self.wfdata = Stream()
-        self.dirty = False
-
-    def resetPicks(self):
-        """
-        Clear all picks from event
-        """
-        self.get_evt_data().picks = []
-
-    def get_evt_data(self):
-        return self.evtdata
-
-    def setEvtData(self, event):
-        self.evtdata = event
-
-    def applyEVTData(self, data, typ='pick'):
-        """
-        Either takes an `obspy.core.event.Event` object and applies all new
-        information on the event to the actual data if typ is 'event or
-        creates ObsPy pick objects and append it to the picks list from the
-        PyLoT dictionary contain all picks if type is pick
-        :param data: data to apply, either picks or complete event
-        :type data:
-        :param typ: which event data to apply, 'pick' or 'event'
-        :type typ: str
-        :param authority_id: (currently unused)
-        :type: str
-        :raise OverwriteError:
-        """
-
-        def applyPicks(picks):
-            """
-            Creates ObsPy pick objects and append it to the picks list from the
-            PyLoT dictionary contain all picks.
-            :param picks:
-            :raise OverwriteError: raises an OverwriteError if the picks list is
-             not empty. The GUI will then ask for a decision.
-            """
-            # firstonset = find_firstonset(picks)
-            # check for automatic picks
-            print("Writing phases to ObsPy-quakeml file")
-            for key in picks:
-                if not picks[key].get('P'):
-                    continue
-                if picks[key]['P']['picker'] == 'auto':
-                    print("Existing auto-picks will be overwritten in pick-dictionary!")
-                    picks = picks_from_picksdict(picks)
-                    break
-                else:
-                    if self.get_evt_data().picks:
-                        raise OverwriteError('Existing picks would be overwritten!')
-                    else:
-                        picks = picks_from_picksdict(picks)
-                        break
-            self.get_evt_data().picks = picks
-            # if 'smi:local' in self.getID() and firstonset:
-            #     fonset_str = firstonset.strftime('%Y_%m_%d_%H_%M_%S')
-            #     ID = ResourceIdentifier('event/' + fonset_str)
-            #     ID.convertIDToQuakeMLURI(authority_id=authority_id)
-            #     self.get_evt_data().resource_id = ID
-
-        def applyEvent(event):
-            """
-            takes an `obspy.core.event.Event` object and applies all new
-            information on the event to the actual data
-            :param event:
-            """
-            if event is None:
-                print("applyEvent: Received None")
-                return
-            if self.isNew():
-                self.setEvtData(event)
-            else:
-                # prevent overwriting original pick information
-                event_old = self.get_evt_data()
-                if not event_old.resource_id == event.resource_id:
-                    print("WARNING: Missmatch in event resource id's: {} and {}".format(
-                        event_old.resource_id,
-                        event.resource_id))
-                else:
-                    picks = copy.deepcopy(event_old.picks)
-                    event = merge_picks(event, picks)
-                # apply event information from location
-                event_old.update(event)
-
-        applydata = {'pick': applyPicks,
-                     'event': applyEvent}
-
-        applydata[typ](data)
-        self._new = False
+    def rotate_wf_data(self):
+        self.waveform_data.rotate_zne(self.metadata)
 
 
 class GenericDataStructure(object):
@@ -803,22 +248,6 @@ class PilotDataStructure(GenericDataStructure):
         self.setExpandFields(['root', 'database'])
 
 
-class ObspyDMTdataStructure(GenericDataStructure):
-    """
-    Object containing the data access information for the old PILOT data
-    structure.
-    """
-
-    def __init__(self, **fields):
-        if not fields:
-            fields = {'database': '',
-                      'root': ''}
-
-        GenericDataStructure.__init__(self, **fields)
-
-        self.setExpandFields(['root', 'database'])
-
-
 class SeiscompDataStructure(GenericDataStructure):
     """
     Dictionary containing the data access information for an SDS data archive:

pylot/core/io/event.py

@@ -0,0 +1,106 @@
+import copy
+from dataclasses import dataclass
+from typing import Union
+
+from obspy import read_events
+from obspy.core.event import Event as ObsPyEvent
+
+
+@dataclass
+class EventData:
+    evtdata: Union[ObsPyEvent, None] = None
+    _new: bool = False
+
+    def __init__(self, evtdata=None):
+        self.set_event_data(evtdata)
+
+    def set_event_data(self, evtdata):
+        if isinstance(evtdata, ObsPyEvent):
+            self.evtdata = evtdata
+        elif isinstance(evtdata, dict):
+            self.evtdata = self.read_pilot_event(**evtdata)
+        elif isinstance(evtdata, str):
+            self.evtdata = self.read_event_file(evtdata)
+        else:
+            self.set_new()
+            self.evtdata = ObsPyEvent(picks=[])
+
+    def read_event_file(self, evtdata: str) -> ObsPyEvent:
+        try:
+            cat = read_events(evtdata)
+            if len(cat) != 1:
+                raise ValueError(f'ambiguous event information for file: {evtdata}')
+            return cat[0]
+        except TypeError as e:
+            self.handle_event_file_error(e, evtdata)
+
+    def handle_event_file_error(self, e: TypeError, evtdata: str):
+        if 'Unknown format for file' in str(e):
+            if 'PHASES' in evtdata:
+                picks = self.picksdict_from_pilot(evtdata)
+                evtdata = ObsPyEvent(picks=self.picks_from_picksdict(picks))
+            elif 'LOC' in evtdata:
+                raise NotImplementedError('PILOT location information read support not yet implemented.')
+            elif 'event.pkl' in evtdata:
+                evtdata = self.qml_from_obspy_dmt(evtdata)
+            else:
+                raise e
+        else:
+            raise e
+
+    def set_new(self):
+        self._new = True
+
+    def is_new(self) -> bool:
+        return self._new
+
+    def get_picks_str(self) -> str:
+        return '\n'.join(str(pick) for pick in self.evtdata.picks)
+
+    def replace_origin(self, event: ObsPyEvent, force_overwrite: bool = False):
+        if self.evtdata.origins or force_overwrite:
+            event.origins = self.evtdata.origins
+
+    def replace_magnitude(self, event: ObsPyEvent, force_overwrite: bool = False):
+        if self.evtdata.magnitudes or force_overwrite:
+            event.magnitudes = self.evtdata.magnitudes
+
+    def replace_picks(self, event: ObsPyEvent, picktype: str):
+        checkflag = 1
+        picks = event.picks
+        for j, pick in reversed(list(enumerate(picks))):
+            if picktype in str(pick.method_id.id):
+                picks.pop(j)
+                checkflag = 2
+
+        if checkflag > 0:
+            for pick in self.evtdata.picks:
+                if picktype in str(pick.method_id.id):
+                    picks.append(pick)
+
+    def get_id(self) -> Union[str, None]:
+        try:
+            return self.evtdata.resource_id.id
+        except:
+            return None
+
+    def apply_event_data(self, data, typ='pick'):
+        if typ == 'pick':
+            self.apply_picks(data)
+        elif typ == 'event':
+            self.apply_event(data)
+
+    def apply_picks(self, picks):
+        self.evtdata.picks = picks
+
+    def apply_event(self, event: ObsPyEvent):
+        if self.is_new():
+            self.evtdata = event
+        else:
+            old_event = self.evtdata
+            if old_event.resource_id == event.resource_id:
+                picks = copy.deepcopy(old_event.picks)
+                event = self.merge_picks(event, picks)
+                old_event.update(event)
+            else:
+                print(f"WARNING: Mismatch in event resource id's: {old_event.resource_id} and {event.resource_id}")

pylot/core/io/getEventListFromXML.py

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

pylot/core/io/getQualitiesfromxml.py

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

pylot/core/io/location.py

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

pylot/core/io/project.py

@@ -0,0 +1,177 @@
+import os
+
+from pylot.core.util.event import Event
+
+
+class Project(object):
+    '''
+    Pickable class containing information of a PyLoT project, like event lists and file locations.
+    '''
+
+    # TODO: remove rootpath
+    def __init__(self):
+        self.eventlist = []
+        self.location = None
+        self.rootpath = None
+        self.datapath = None
+        self.dirty = False
+        self.parameter = None
+        self._table = None
+
+    def add_eventlist(self, eventlist):
+        '''
+        Add events from an eventlist containing paths to event directories.
+        Will skip existing paths.
+        '''
+        if len(eventlist) == 0:
+            return
+        for item in eventlist:
+            event = Event(item)
+            event.rootpath = self.parameter['rootpath']
+            event.database = self.parameter['database']
+            event.datapath = self.parameter['datapath']
+            if not event.path in self.getPaths():
+                self.eventlist.append(event)
+                self.setDirty()
+            else:
+                print('Skipping event with path {}. Already part of project.'.format(event.path))
+        self.eventlist.sort(key=lambda x: x.pylot_id)
+        self.search_eventfile_info()
+
+    def remove_event(self, event):
+        self.eventlist.remove(event)
+
+    def remove_event_by_id(self, eventID):
+        for event in self.eventlist:
+            if eventID in str(event.resource_id):
+                self.remove_event(event)
+                break
+
+    def read_eventfile_info(self, filename, separator=','):
+        '''
+        Try to read event information from file (:param:filename) comparing specific event datetimes.
+        File structure (each row): event, date, time, magnitude, latitude, longitude, depth
+        separated by :param:separator each.
+        '''
+        with open(filename, 'r') as infile:
+            for line in infile.readlines():
+                eventID, date, time, mag, lat, lon, depth = line.split(separator)[:7]
+                # skip first line
+                try:
+                    day, month, year = date.split('/')
+                except:
+                    continue
+                year = int(year)
+                # hardcoded, if year only consists of 2 digits (e.g. 16 instead of 2016)
+                if year < 100:
+                    year += 2000
+                datetime = '{}-{}-{}T{}'.format(year, month, day, time)
+                try:
+                    datetime = UTCDateTime(datetime)
+                except Exception as e:
+                    print(e, datetime, filename)
+                    continue
+                for event in self.eventlist:
+                    if eventID in str(event.resource_id) or eventID in event.origins:
+                        if event.origins:
+                            origin = event.origins[0]  # should have only one origin
+                            if origin.time == datetime:
+                                origin.latitude = float(lat)
+                                origin.longitude = float(lon)
+                                origin.depth = float(depth)
+                            else:
+                                continue
+                        elif not event.origins:
+                            origin = Origin(resource_id=event.resource_id,
+                                            time=datetime, latitude=float(lat),
+                                            longitude=float(lon), depth=float(depth))
+                            event.origins.append(origin)
+                        event.magnitudes.append(Magnitude(resource_id=event.resource_id,
+                                                          mag=float(mag),
+                                                          mag_type='M'))
+                        break
+
+    def search_eventfile_info(self):
+        '''
+        Search all datapaths in rootpath for filenames with given file extension fext
+        and try to read event info from it
+        '''
+        datapaths = []
+        fext = '.csv'
+        for event in self.eventlist:
+            if not event.datapath in datapaths:
+                datapaths.append(event.datapath)
+        for datapath in datapaths:
+            # datapath = os.path.join(self.rootpath, datapath)
+            if os.path.isdir(datapath):
+                for filename in os.listdir(datapath):
+                    filename = os.path.join(datapath, filename)
+                    if os.path.isfile(filename) and filename.endswith(fext):
+                        try:
+                            self.read_eventfile_info(filename)
+                        except Exception as e:
+                            print('Failed on reading eventfile info from file {}: {}'.format(filename, e))
+            else:
+                print("Directory %s does not exist!" % datapath)
+
+    def getPaths(self):
+        '''
+        Returns paths (eventlist) of all events saved in the project.
+        '''
+        paths = []
+        for event in self.eventlist:
+            paths.append(event.path)
+        return paths
+
+    def setDirty(self, value=True):
+        self.dirty = value
+
+    def getEventFromPath(self, path):
+        '''
+        Search for an event in the project by event path.
+        '''
+        for event in self.eventlist:
+            if event.path == path:
+                return event
+
+    def save(self, filename=None):
+        '''
+        Save PyLoT Project to a file.
+        Can be loaded by using project.load(filename).
+        '''
+        try:
+            import pickle
+        except ImportError:
+            import _pickle as pickle
+
+        if filename:
+            self.location = filename
+        else:
+            filename = self.location
+
+        table = self._table  # MP: see below
+        try:
+            outfile = open(filename, 'wb')
+            self._table = []  # MP: Workaround as long as table cannot be saved as part of project
+            pickle.dump(self, outfile, protocol=pickle.HIGHEST_PROTOCOL)
+            self.setDirty(False)
+            self._table = table  # MP: see above
+            return True
+        except Exception as e:
+            print('Could not pickle PyLoT project. Reason: {}'.format(e))
+            self.setDirty()
+            self._table = table  # MP: see above
+            return False
+
+    @staticmethod
+    def load(filename):
+        '''
+        Load project from filename.
+        '''
+        import pickle
+        infile = open(filename, 'rb')
+        project = pickle.load(infile)
+        infile.close()
+        project.location = filename
+        print('Loaded %s' % filename)
+        return project

pylot/core/io/utils.py

@@ -0,0 +1,13 @@
+import os
+from typing import List
+
+
+def validate_filenames(filenames: List[str]) -> List[str]:
+    """
+    validate a list of filenames for file abundance
+    :param filenames: list of possible filenames
+    :type filenames: List[str]
+    :return: list of valid filenames
+    :rtype: List[str]
+    """
+    return [fn for fn in filenames if os.path.isfile(fn)]

pylot/core/io/waveformdata.py

@@ -0,0 +1,123 @@
+import logging
+from dataclasses import dataclass, field
+from typing import Union, List
+
+from obspy import Stream, read
+from obspy.io.sac import SacIOError
+
+from pylot.core.io.utils import validate_filenames
+from pylot.core.util.dataprocessing import Metadata
+from pylot.core.util.utils import get_stations, check_for_nan, check4rotated
+
+
+@dataclass
+class WaveformData:
+    wfdata: Stream = field(default_factory=Stream)
+    wforiginal: Union[Stream, None] = None
+    wf_alt: Stream = field(default_factory=Stream)
+    dirty: bool = False
+
+    def load_waveforms(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
+        fn_list = validate_filenames(fnames)
+        if not fn_list:
+            logging.warning('No valid filenames given for loading waveforms')
+        else:
+            self.clear()
+            self.add_waveforms(fn_list)
+
+        if fnames_alt is None:
+            pass
+        else:
+            alt_fn_list = validate_filenames(fnames_alt)
+            if not alt_fn_list:
+                logging.warning('No valid alternative filenames given for loading waveforms')
+            else:
+                self.add_waveforms(alt_fn_list, alternative=True)
+
+        if not fn_list and not alt_fn_list:
+            logging.error('No filenames or alternative filenames given for loading waveforms')
+            return False
+
+        self.merge()
+        self.replace_nan()
+        if not check_rotated or not metadata:
+            pass
+        else:
+            self.rotate_zne()
+        self.trim_station_traces()
+        self.wforiginal = self.wfdata.copy()
+        self.dirty = False
+        return True
+
+    def add_waveforms(self, fnames: List[str], alternative: bool = False):
+        data_stream = self.wf_alt if alternative else self.wfdata
+        warnmsg = ''
+        for fname in set(fnames):
+            try:
+                data_stream += read(fname)
+            except TypeError:
+                try:
+                    data_stream += read(fname, format='GSE2')
+                except Exception as e:
+                    try:
+                        data_stream += read(fname, format='SEGY')
+                    except Exception as e:
+                        warnmsg += f'{fname}\n{e}\n'
+            except SacIOError as se:
+                warnmsg += f'{fname}\n{se}\n'
+
+        if warnmsg:
+            print(f'WARNING in add_waveforms: unable to read waveform data\n{warnmsg}')
+
+    def clear(self):
+        self.wfdata = Stream()
+        self.wforiginal = None
+        self.wf_alt = Stream()
+
+    def reset(self):
+        """
+        Resets the waveform data to its original state.
+        """
+        if self.wforiginal:
+            self.wfdata = self.wforiginal.copy()
+        else:
+            self.wfdata = Stream()
+        self.dirty = False
+
+    def merge(self):
+        """
+        check for gaps in Stream and merge if gaps are found
+        """
+        gaps = self.wfdata.get_gaps()
+        if gaps:
+            merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
+            self.wfdata.merge(method=1)
+            logging.info('Merged the following stations because of gaps:')
+            for station in merged:
+                logging.info(station)
+
+    def replace_nan(self):
+        """
+        Replace all NaNs in data with 0. (in place)
+        """
+        self.wfdata = check_for_nan(self.wfdata)
+
+    def rotate_zne(self, metadata: Metadata = None):
+        """
+        Check all traces in stream for rotation. If a trace is not in ZNE rotation (last symbol of channel code is numeric) and the trace
+        is in the metadata with azimuth and dip, rotate it to classical ZNE orientation.
+        Rotating the traces requires them to be of the same length, so, all traces will be trimmed to a common length as a
+        side effect.
+        """
+
+        self.wfdata = check4rotated(self.wfdata, metadata)
+
+    def trim_station_traces(self):
+        """
+        trim data stream to common time window
+        """
+
+        for station in get_stations(self.wfdata):
+            station_traces = self.wfdata.select(station=station)
+            station_traces.trim(starttime=max([trace.stats.starttime for trace in station_traces]),
+                                endtime=min([trace.stats.endtime for trace in station_traces]))

pylot/core/loc/focmec.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, parameter, eventinfo):
     :type eventinfo:  list object
     '''
     # write phases to FOCMEC-phase file
-    writephases(picks, 'FOCMEC', fnout, parameter, eventinfo)
+    write_phases(picks, 'FOCMEC', fnout, parameter, eventinfo)

pylot/core/loc/hash.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, parameter, eventinfo):
     :type eventinfo:  list object
     '''
     # write phases to HASH-phase file
-    writephases(picks, 'HASH', fnout, parameter, eventinfo)
+    write_phases(picks, 'HASH', fnout, parameter, eventinfo)

pylot/core/loc/hypo71.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -22,4 +22,4 @@ def export(picks, fnout, parameter):
     :type parameter:  object
     '''
     # write phases to HYPO71-phase file
-    writephases(picks, 'HYPO71', fnout, parameter)
+    write_phases(picks, 'HYPO71', fnout, parameter)

pylot/core/loc/hypodd.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, parameter, eventinfo):
     :type eventinfo:  list object
     '''
     # write phases to hypoDD-phase file
-    writephases(picks, 'HYPODD', fnout, parameter, eventinfo)
+    write_phases(picks, 'HYPODD', fnout, parameter, eventinfo)

pylot/core/loc/hyposat.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -22,4 +22,4 @@ def export(picks, fnout, parameter):
     :type parameter:  object
     '''
     # write phases to HYPOSAT-phase file
-    writephases(picks, 'HYPOSAT', fnout, parameter)
+    write_phases(picks, 'HYPOSAT', fnout, parameter)

pylot/core/loc/nll.py

@@ -7,7 +7,7 @@ import subprocess
 
 from obspy import read_events
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.gui import which
 from pylot.core.util.utils import getPatternLine, runProgram
 from pylot.core.util.version import get_git_version as _getVersionString
@@ -34,7 +34,7 @@ def export(picks, fnout, parameter):
     :type parameter:  object
     '''
     # write phases to NLLoc-phase file
-    writephases(picks, 'NLLoc', fnout, parameter)
+    write_phases(picks, 'NLLoc', fnout, parameter)
 
 
 def modify_inputs(ctrfn, root, nllocoutn, phasefn, tttn):
@@ -82,8 +82,8 @@ def locate(fnin, parameter=None):
     :param fnin: external program name
     :return: None
     """
-    exe_path = which('NLLoc', parameter)
-    if exe_path is None:
+    exe_path = os.path.join(parameter['nllocbin'], 'NLLoc')
+    if not os.path.isfile(exe_path):
         raise NLLocError('NonLinLoc executable not found; check your '
                          'environment variables')
 

pylot/core/loc/velest.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from pylot.core.io.phases import writephases
+from pylot.core.io.phases import write_phases
 from pylot.core.util.version import get_git_version as _getVersionString
 
 __version__ = _getVersionString()
@@ -25,4 +25,4 @@ def export(picks, fnout, eventinfo, parameter=None):
     :type parameter:  object
     '''
     # write phases to VELEST-phase file
-    writephases(picks, 'VELEST', fnout, parameter, eventinfo)
+    write_phases(picks, 'VELEST', fnout, parameter, eventinfo)

pylot/core/pick/autopick.py

@@ -20,9 +20,9 @@ from pylot.core.pick.charfuns import CharacteristicFunction
 from pylot.core.pick.charfuns import HOScf, AICcf, ARZcf, ARHcf, AR3Ccf
 from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
-    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class
+    getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
 from pylot.core.util.utils import getPatternLine, gen_Pool, \
-    get_Bool, identifyPhaseID, get_None, correct_iplot
+    get_bool, identifyPhaseID, get_none, correct_iplot
 
 
 def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
@@ -232,20 +232,6 @@ class PickingContainer:
         self.Sflag = 0
 
 
-class MissingTraceException(ValueError):
-    """
-    Used to indicate missing traces in a obspy.core.stream.Stream object
-    """
-    pass
-
-
-class PickingFailedException(Exception):
-    """
-    Raised when picking fails due to missing values etc.
-    """
-    pass
-
-
 class AutopickStation(object):
 
     def __init__(self, wfstream, pickparam, verbose, iplot=0, fig_dict=None, metadata=None, origin=None):
@@ -272,7 +258,7 @@ class AutopickStation(object):
         self.pickparams = copy.deepcopy(pickparam)
         self.verbose = verbose
         self.iplot = correct_iplot(iplot)
-        self.fig_dict = get_None(fig_dict)
+        self.fig_dict = get_none(fig_dict)
         self.metadata = metadata
         self.origin = origin
 
@@ -429,7 +415,7 @@ class AutopickStation(object):
             if station_coords is None:
                 exit_taupy()
                 raise AttributeError('Warning: Could not find station in metadata')
-            # TODO raise when metadata.get_coordinates returns None
+            # TODO: raise when metadata.get_coordinates returns None
             source_origin = origin[0]
             model = TauPyModel(taup_model)
             taup_phases = self.pickparams['taup_phases']
@@ -471,11 +457,13 @@ class AutopickStation(object):
             """If taupy failed to calculate theoretical starttimes, picking continues.
             For this a clean exit is required, since the P starttime is no longer relative to the theoretic onset but
             to the vertical trace starttime, eg. it can't be < 0."""
+            # TODO here the pickparams is modified, instead of a copy
             if self.pickparams["pstart"] < 0:
-                # TODO here the pickparams is modified, instead of a copy
                 self.pickparams["pstart"] = 0
+            if self.pickparams["sstart"] < 0:
+                self.pickparams["sstart"] = 0
 
-        if self.pickparams["use_taup"] is False:
+        if get_bool(self.pickparams["use_taup"]) is False:
             # correct user mistake where a relative cuttime is selected (pstart < 0) but use of taupy is disabled/ has
             # not the required parameters
             exit_taupy()
@@ -499,6 +487,20 @@ class AutopickStation(object):
         self.pickparams["pstart"] = max(self.pickparams["pstart"], 0)
         self.pickparams["pstop"] = min(self.pickparams["pstop"], len(self.ztrace) * self.ztrace.stats.delta)
 
+        if self.horizontal_traces_exist():
+            # for the two horizontal components take earliest and latest time to make sure that the s onset is not clipped
+            # if start and endtime of horizontal traces differ, the s windowsize will automatically increase
+            trace_s_start = min([self.etrace.stats.starttime, self.ntrace.stats.starttime])
+            # modifiy sstart and sstop relative to estimated first S arrival (relative to station time axis)
+            self.pickparams["sstart"] += (self.origin[0].time + estFirstS) - trace_s_start
+            self.pickparams["sstop"] += (self.origin[0].time + estFirstS) - trace_s_start
+            print('autopick: CF calculation times respectively:'
+                  ' sstart: {} s, sstop: {} s'.format(self.pickparams["sstart"], self.pickparams["sstop"]))
+            # make sure pstart and pstop are inside the starttime/endtime of horizontal traces
+            self.pickparams["sstart"] = max(self.pickparams["sstart"], 0)
+            self.pickparams["sstop"] = min(self.pickparams["sstop"], len(self.ntrace) * self.ntrace.stats.delta,
+                                           len(self.etrace) * self.etrace.stats.delta)
+
     def autopickstation(self):
         """
         Main function of autopickstation, which calculates P and S picks and returns them in a dictionary.
@@ -508,6 +510,17 @@ class AutopickStation(object):
         station's value is the station name on which the picks were calculated.
         :rtype: dict
         """
+
+        if get_bool(self.pickparams['use_taup']) is True and self.origin is not None:
+            try:
+                # modify pstart, pstop, sstart, sstop to be around theoretical onset if taupy should be used,
+                # else do nothing
+                self.modify_starttimes_taupy()
+            except AttributeError as ae:
+                print(ae)
+            except MissingTraceException as mte:
+                print(mte)
+
         try:
             self.pick_p_phase()
         except MissingTraceException as mte:
@@ -515,13 +528,15 @@ class AutopickStation(object):
         except PickingFailedException as pfe:
             print(pfe)
 
-        if self.horizontal_traces_exist() and self.p_results.weight is not None and self.p_results.weight < 4:
-            try:
-                self.pick_s_phase()
-            except MissingTraceException as mte:
-                print(mte)
-            except PickingFailedException as pfe:
-                print(pfe)
+        if self.horizontal_traces_exist():
+            if (self.p_results.weight is not None and self.p_results.weight < 4) or \
+                    get_bool(self.pickparams.get('use_taup')):
+                try:
+                    self.pick_s_phase()
+                except MissingTraceException as mte:
+                    print(mte)
+                except PickingFailedException as pfe:
+                    print(pfe)
 
         self.plot_pick_results()
         self.finish_picking()
@@ -631,7 +646,7 @@ class AutopickStation(object):
             ax1.set_ylim([-1.5, 1.5])
             ax1.set_ylabel('Normalized Counts')
 
-            if self.horizontal_traces_exist() and self.s_data.Sflag == 1:
+            if self.horizontal_traces_exist():# and self.s_data.Sflag == 1:
                 # plot E trace
                 ax2 = fig.add_subplot(3, 1, 2, sharex=ax1)
                 th1data = np.linspace(0, self.etrace.stats.endtime - self.etrace.stats.starttime,
@@ -661,13 +676,14 @@ class AutopickStation(object):
                         ax2.plot([self.s_results.lpp, self.s_results.lpp], [-1.1, 1.1], 'g--', label='lpp')
                         ax2.plot([self.s_results.epp, self.s_results.epp], [-1.1, 1.1], 'g--', label='epp')
                         title = '{channel}, S weight={sweight}, SNR={snr:7.2}, SNR[dB]={snrdb:7.2}'
-                        ax2.set_title(title.format(channel=self.etrace.stats.channel,
-                                                   sweight=self.s_results.weight,
-                                                   snr=self.s_results.snr,
-                                                   snrdb=self.s_results.snrdb))
+                        ax2.set_title(title.format(channel=str(self.etrace.stats.channel),
+                                                   sweight=str(self.s_results.weight),
+                                                   snr=str(self.s_results.snr),
+                                                   snrdb=str(self.s_results.snrdb)))
                     else:
                         title = '{channel}, S weight={sweight}, SNR=None, SNR[dB]=None'
-                        ax2.set_title(title.format(channel=self.etrace.stats.channel, sweight=self.s_results.weight))
+                        ax2.set_title(title.format(channel=str(self.etrace.stats.channel),
+                                                   sweight=str(self.s_results.weight)))
                 ax2.legend(loc=1)
                 ax2.set_yticks([])
                 ax2.set_ylim([-1.5, 1.5])
@@ -795,15 +811,6 @@ class AutopickStation(object):
         # save filtered trace in instance for later plotting
         self.tr_filt_z_bpz2 = tr_filt
 
-        if get_Bool(self.pickparams['use_taup']) is True and self.origin is not None:
-            try:
-                # modify pstart, pstop to be around theoretical onset if taupy should be used, else does nothing
-                self.modify_starttimes_taupy()
-            except AttributeError as ae:
-                print(ae)
-            except MissingTraceException as mte:
-                print(mte)
-
         Lc = self.pickparams['pstop'] - self.pickparams['pstart']
 
         Lwf = self.ztrace.stats.endtime - self.ztrace.stats.starttime
@@ -915,7 +922,7 @@ class AutopickStation(object):
             "minFMSNR"]:
             # if SNR is high enough, try to determine first motion of onset
             self.set_current_figure('fm_picker')
-            self.p_results.fm = fmpicker(self.zstream, z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
+            self.p_results.fm = fmpicker(self.zstream.copy(), z_copy, self.pickparams["fmpickwin"], self.p_results.mpp,
                                          self.iplot, self.current_figure, self.current_linecolor)
         msg = "autopickstation: P-weight: {}, SNR: {}, SNR[dB]: {}, Polarity: {}"
         msg = msg.format(self.p_results.weight, self.p_results.snr, self.p_results.snrdb, self.p_results.fm)
@@ -1127,9 +1134,11 @@ class AutopickStation(object):
                   ''.format(self.s_results.weight, self.s_results.snr, self.s_results.snrdb))
 
     def pick_s_phase(self):
-
-        # determine time window for calculating CF after P onset
-        cuttimesh = self._calculate_cuttimes(type='S', iteration=1)
+        if get_bool(self.pickparams.get('use_taup')) is True:
+            cuttimesh = (self.pickparams.get('sstart'), self.pickparams.get('sstop'))
+        else:
+            # determine time window for calculating CF after P onset
+            cuttimesh = self._calculate_cuttimes(type='S', iteration=1)
 
         # calculate autoregressive CF
         self.arhcf1 = self._calculate_autoregressive_cf_s_pick(cuttimesh)

pylot/core/pick/charfuns.py

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

pylot/core/pick/picker.py

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

pylot/core/pick/utils.py

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

pylot/core/util/array_map.py

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

pylot/core/util/dataprocessing.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import glob
+import logging
 import os
 import sys
 
@@ -189,7 +190,11 @@ class Metadata(object):
         metadata = self.get_metadata(seed_id, time)
         if not metadata:
             return
-        return metadata['data'].get_coordinates(seed_id, time)
+        try:
+            return metadata['data'].get_coordinates(seed_id, time)
+        # no specific exception defined in obspy inventory
+        except Exception as e:
+            logging.warning(f'Could not get metadata for {seed_id}')
 
     def get_all_coordinates(self):
         def stat_info_from_parser(parser):
@@ -271,7 +276,7 @@ class Metadata(object):
                     continue
             invtype, robj = self._read_metadata_file(os.path.join(path_to_inventory, fname))
             try:
-                robj.get_coordinates(station_seed_id)
+                # robj.get_coordinates(station_seed_id)  # TODO: Commented out, failed with Parser, is this needed?
                 self.inventory_files[fname] = {'invtype': invtype,
                                                'data': robj}
                 if station_seed_id in self.seed_ids.keys():
@@ -333,19 +338,6 @@ class Metadata(object):
         return inv, exc
 
 
-def time_from_header(header):
-    """
-    Function takes in the second line from a .gse file and takes out the date and time from that line.
-    :param header: second line from .gse file
-    :type header: string
-    :return: a list of integers of form [year, month, day, hour, minute, second, microsecond]
-    """
-    timeline = header.split(' ')
-    time = timeline[1].split('/') + timeline[2].split(':')
-    time = time[:-1] + time[-1].split('.')
-    return [int(t) for t in time]
-
-
 def check_time(datetime):
     """
     Function takes in date and time as list and validates it's values by trying to make an UTCDateTime object from it
@@ -383,167 +375,6 @@ def check_time(datetime):
         return False
 
 
-# TODO: change root to datapath
-def get_file_list(root_dir):
-    """
-    Function uses a directorie to get all the *.gse files from it.
-    :param root_dir: a directorie leading to the .gse files
-    :type root_dir: string
-    :return: returns a list of filenames (without path to them)
-    """
-    file_list = glob.glob1(root_dir, '*.gse')
-    return file_list
-
-
-def checks_station_second(datetime, file):
-    """
-    Function uses the given list to check if the parameter 'second' is set to 60 by mistake
-     and sets the time correctly if so. Can only correct time if no date change would be necessary.
-    :param datetime: [year, month, day, hour, minute, second, microsecond]
-    :return: returns the input with the correct value for second
-    """
-    if datetime[5] == 60:
-        if datetime[4] == 59:
-            if datetime[3] == 23:
-                err_msg = 'Date should be next day. ' \
-                          'File not changed: {0}'.format(file)
-                raise ValueError(err_msg)
-            else:
-                datetime[3] += 1
-                datetime[4] = 0
-                datetime[5] = 0
-        else:
-            datetime[4] += 1
-            datetime[5] = 0
-    return datetime
-
-
-def make_time_line(line, datetime):
-    """
-    Function takes in the original line from a .gse file and a list of date and
-    time values to make a new line with corrected date and time.
-    :param line: second line from .gse file.
-    :type line: string
-    :param datetime: list of integers [year, month, day, hour, minute, second, microsecond]
-    :type datetime: list
-    :return: returns a string to write it into a file.
-    """
-    ins_form = '{0:02d}:{1:02d}:{2:02d}.{3:03d}'
-    insertion = ins_form.format(int(datetime[3]),
-                                int(datetime[4]),
-                                int(datetime[5]),
-                                int(datetime[6] * 1e-3))
-    newline = line[:16] + insertion + line[28:]
-    return newline
-
-
-def evt_head_check(root_dir, out_dir=None):
-    """
-    A function to make sure that an arbitrary number of .gse files have correct values in their header.
-    :param root_dir: a directory leading to the .gse files.
-    :type root_dir: string
-    :param out_dir: a directory to store the new files somwhere els.
-    :return: returns nothing
-    """
-    if not out_dir:
-        print('WARNING files are going to be overwritten!')
-        inp = str(input('Continue? [y/N]'))
-        if not inp == 'y':
-            sys.exit()
-    filelist = get_file_list(root_dir)
-    nfiles = 0
-    for file in filelist:
-        infile = open(os.path.join(root_dir, file), 'r')
-        lines = infile.readlines()
-        infile.close()
-        datetime = time_from_header(lines[1])
-        if check_time(datetime):
-            continue
-        else:
-            nfiles += 1
-            datetime = checks_station_second(datetime, file)
-            print('writing ' + file)
-            # write File
-            lines[1] = make_time_line(lines[1], datetime)
-            if not out_dir:
-                out = open(os.path.join(root_dir, file), 'w')
-                out.writelines(lines)
-                out.close()
-            else:
-                out = open(os.path.join(out_dir, file), 'w')
-                out.writelines(lines)
-                out.close()
-    print(nfiles)
-
-
-def read_metadata(path_to_inventory):
-    """
-    take path_to_inventory and return either the corresponding list of files
-    found or the Parser object for a network dataless seed volume to prevent
-    read overhead for large dataless seed volumes
-    :param path_to_inventory:
-    :return: tuple containing a either list of files or `obspy.io.xseed.Parser`
-    object and the inventory type found
-    :rtype: tuple
-    """
-    dlfile = list()
-    invfile = list()
-    respfile = list()
-    # possible file extensions specified here:
-    inv = dict(dless=dlfile, xml=invfile, resp=respfile, dseed=dlfile[:])
-    if os.path.isfile(path_to_inventory):
-        ext = os.path.splitext(path_to_inventory)[1].split('.')[1]
-        inv[ext] += [path_to_inventory]
-    else:
-        for ext in inv.keys():
-            inv[ext] += glob.glob1(path_to_inventory, '*.{0}'.format(ext))
-
-    invtype = key_for_set_value(inv)
-
-    if invtype is None:
-        print("Neither dataless-SEED file, inventory-xml file nor "
-              "RESP-file found!")
-        print("!!WRONG CALCULATION OF SOURCE PARAMETERS!!")
-        robj = None,
-    elif invtype == 'dless':  # prevent multiple read of large dlsv
-        print("Reading metadata information from dataless-SEED file ...")
-        if len(inv[invtype]) == 1:
-            fullpath_inv = os.path.join(path_to_inventory, inv[invtype][0])
-            robj = Parser(fullpath_inv)
-        else:
-            robj = inv[invtype]
-    else:
-        print("Reading metadata information from inventory-xml file ...")
-        robj = read_inventory(inv[invtype])
-    return invtype, robj
-
-
-# idea to optimize read_metadata
-# def read_metadata_new(path_to_inventory):
-#     metadata_objects = []
-#     # read multiple files from directory
-#     if os.path.isdir(path_to_inventory):
-#         fnames = os.listdir(path_to_inventory)
-#     # read single file
-#     elif os.path.isfile(path_to_inventory):
-#         fnames = [path_to_inventory]
-#     else:
-#         print("Neither dataless-SEED file, inventory-xml file nor "
-#               "RESP-file found!")
-#         print("!!WRONG CALCULATION OF SOURCE PARAMETERS!!")
-#         fnames = []
-#
-#     for fname in fnames:
-#         path_to_inventory_filename = os.path.join(path_to_inventory, fname)
-#         try:
-#             ftype, robj = read_metadata_file(path_to_inventory_filename)
-#             metadata_objects.append((ftype, robj))
-#         except Exception as e:
-#             print('Could not read metadata file {} '
-#                   'because of the following Exception: {}'.format(path_to_inventory_filename, e))
-#     return metadata_objects
-
-
 def restitute_trace(input_tuple):
     def no_metadata(tr, seed_id):
         print('no metadata file found '

pylot/core/util/defaults.py

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

pylot/core/util/generate_array_maps.py

@@ -20,7 +20,7 @@ import matplotlib
 matplotlib.use('Qt5Agg')
 sys.path.append(os.path.join('/'.join(sys.argv[0].split('/')[:-1]), '../../..'))
 
-from PyLoT import Project
+from pylot.core.io.project import Project
 from pylot.core.util.dataprocessing import Metadata
 from pylot.core.util.array_map import Array_map
 
@@ -42,7 +42,7 @@ def main(project_file_path, manual=False, auto=True, file_format='png', f_ext=''
         for item in input_list:
             array_map_worker(item)
     else:
-        pool = multiprocessing.Pool(ncores)
+        pool = multiprocessing.Pool(ncores, maxtasksperchild=1000)
         pool.map(array_map_worker, input_list)
         pool.close()
         pool.join()

pylot/core/util/gui.py

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

pylot/core/util/structure.py

@@ -6,7 +6,7 @@ Created on Wed Jan 26 17:47:25 2015
 @author: sebastianw
 """
 
-from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure, ObspyDMTdataStructure
+from pylot.core.io.data import SeiscompDataStructure, PilotDataStructure
 
 DATASTRUCTURE = {'PILOT': PilotDataStructure, 'SeisComP': SeiscompDataStructure,
-                 'obspyDMT': ObspyDMTdataStructure, None: PilotDataStructure}
+                 'obspyDMT': PilotDataStructure, None: PilotDataStructure}

pylot/core/util/thread.py

@@ -41,7 +41,8 @@ class Thread(QThread):
             exctype, value = sys.exc_info()[:2]
             self._executedErrorInfo = '{} {} {}'. \
                 format(exctype, value, traceback.format_exc())
-        sys.stdout = self.old_stdout
+        if self.redirect_stdout:
+            sys.stdout = self.old_stdout
 
     def showProgressbar(self):
         if self.progressText:
@@ -159,7 +160,7 @@ class MultiThread(QThread):
         try:
             if not self.ncores:
                 self.ncores = multiprocessing.cpu_count()
-            pool = multiprocessing.Pool(self.ncores)
+            pool = multiprocessing.Pool(self.ncores, maxtasksperchild=1000)
             self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
             # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
             pool.close()

pylot/core/util/utils.py

@@ -1,12 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
+import glob
 import hashlib
+import logging
 import os
 import platform
 import re
 import subprocess
 import warnings
+from functools import lru_cache
 
 import numpy as np
 from obspy import UTCDateTime, read
@@ -18,6 +20,10 @@ from pylot.core.io.inputs import PylotParameter, FilterOptions
 from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
 from pylot.styles import style_settings
 
+Rgba: Type[tuple] = Tuple[int, int, int, int]
+Mplrgba: Type[tuple] = Tuple[float, float, float, float]
+Mplrgbastr: Type[tuple] = Tuple[str, str, str, str]
+
 
 def _pickle_method(m):
     if m.im_self is None:
@@ -37,15 +43,14 @@ def getAutoFilteroptions(phase, parameter):
     return filteroptions
 
 
-def readDefaultFilterInformation(fname):
+def readDefaultFilterInformation():
     """
     Read default filter information from pylot.in file
-    :param fname: path to pylot.in file
-    :type fname: str
     :return: dictionary containing the defailt filter information
     :rtype: dict
     """
-    pparam = PylotParameter(fname)
+    pparam = PylotParameter()
+    pparam.reset_defaults()
     return readFilterInformation(pparam)
 
 
@@ -82,25 +87,6 @@ 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
@@ -166,11 +152,11 @@ def clims(lim1, lim2):
     """
     takes two pairs of limits and returns one pair of common limts
     :param lim1: limit 1
-    :type lim1: int
+    :type lim1: List[int]
     :param lim2: limit 2
-    :type lim2: int
+    :type lim2: List[int]
     :return: new upper and lower limit common to both given limits
-    :rtype: [int, int]
+    :rtype: List[int]
 
     >>> clims([0, 4], [1, 3])
     [0, 4]
@@ -302,7 +288,7 @@ def fnConstructor(s):
     if type(s) is str:
         s = s.split(':')[-1]
     else:
-        s = getHash(UTCDateTime())
+        s = get_hash(UTCDateTime())
 
     badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
     badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
@@ -314,32 +300,77 @@ def fnConstructor(s):
     return fn
 
 
-def get_None(value):
+def get_none(value):
     """
     Convert "None" to None
     :param value:
-    :type value: str, bool
+    :type value: str, NoneType
     :return:
-    :rtype: bool
+    :rtype: type(value) or NoneType
+
+    >>> st = read()
+    >>> print(get_none(st))
+    3 Trace(s) in Stream:
+    BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    >>> get_none('Stream')
+    'Stream'
+    >>> get_none(0)
+    0
+    >>> get_none(0.)
+    0.0
+    >>> print(get_none('None'))
+    None
+    >>> print(get_none(None))
+    None
     """
-    if value == 'None':
+    if value is None or (type(value) is str and value == 'None'):
         return None
     else:
         return value
 
 
-def get_Bool(value):
+def get_bool(value):
     """
-    Convert string representations of bools to their true boolean value
+    Convert string representations of bools to their true boolean value. Return value if it cannot be identified as bool.
     :param value:
-    :type value: str, bool
+    :type value: str, bool, int, float
     :return: true boolean value
     :rtype: bool
+
+    >>> get_bool(True)
+    True
+    >>> get_bool(False)
+    False
+    >>> get_bool(0)
+    False
+    >>> get_bool(0.)
+    False
+    >>> get_bool(0.1)
+    True
+    >>> get_bool(2)
+    True
+    >>> get_bool(-1)
+    False
+    >>> get_bool(-0.3)
+    False
+    >>> get_bool(None)
+    None
+    >>> get_bool('Stream')
+    'Stream'
     """
-    if value in ['True', 'true']:
+    if type(value) == bool:
+        return value
+    elif value in ['True', 'true']:
         return True
     elif value in ['False', 'false']:
         return False
+    elif isinstance(value, float) or isinstance(value, int):
+        if value > 0. or value > 0:
+            return True
+        else:
+            return False
     else:
         return value
 
@@ -353,8 +384,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
-    1920
+    >>> four_digits(75)
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -436,36 +467,53 @@ def backtransformFilterString(st):
     return st
 
 
-def getHash(time):
+def get_hash(time):
     """
     takes a time object and returns the corresponding SHA1 hash of the formatted date string
     :param time: time object for which a hash should be calculated
     :type time: `~obspy.core.utcdatetime.UTCDateTime`
     :return: SHA1 hash
     :rtype: str
+
+    >>> time = UTCDateTime(0)
+    >>> get_hash(time)
+    '7627cce3b1b58dd21b005dac008b34d18317dd15'
+    >>> get_hash(0)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'time' is not an ObsPy UTCDateTime object
     """
+    assert isinstance(time, UTCDateTime), '\'time\' is not an ObsPy UTCDateTime object'
     hg = hashlib.sha1()
-    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f').encode('utf-8'))
     return hg.hexdigest()
 
 
-def getLogin():
+def get_login():
     """
-    returns the actual user's login ID
-    :return: login ID
+    returns the actual user's name
+    :return: login name
     :rtype: str
     """
     import getpass
     return getpass.getuser()
 
 
-def getOwner(fn):
+def get_owner(fn):
     """
     takes a filename and return the login ID of the actual owner of the file
     :param fn: filename of the file tested
     :type fn: str
     :return: login ID of the file's owner
     :rtype: str
+
+    >>> import tempfile
+    >>> with tempfile.NamedTemporaryFile() as tmpfile:
+    ...     tmpfile.write(b'') and True
+    ...     tmpfile.flush()
+    ...     get_owner(tmpfile.name) == os.path.expanduser('~').split('/')[-1]
+    0
+    True
     """
     system_name = platform.system()
     if system_name in ["Linux", "Darwin"]:
@@ -511,6 +559,11 @@ def is_executable(fn):
     :param fn: path to the file to be tested
     :return: True or False
     :rtype: bool
+
+    >>> is_executable('/bin/ls')
+    True
+    >>> is_executable('/var/log/system.log')
+    False
     """
     return os.path.isfile(fn) and os.access(fn, os.X_OK)
 
@@ -537,24 +590,36 @@ def isSorted(iterable):
     >>> isSorted([2,3,1,4])
     False
     """
-    assert isIterable(iterable), 'object is not iterable; object: {' \
-                                 '}'.format(iterable)
+    assert is_iterable(iterable), "object is not iterable; object: {}".format(iterable)
     if type(iterable) is str:
         iterable = [s for s in iterable]
     return sorted(iterable) == iterable
 
 
-def isIterable(obj):
+def is_iterable(obj):
     """
     takes a python object and returns True is the object is iterable and
     False otherwise
     :param obj: a python object
-    :type obj: object
+    :type obj: obj
     :return: True of False
     :rtype: bool
+
+    >>> is_iterable(1)
+    False
+    >>> is_iterable(True)
+    False
+    >>> is_iterable(0.)
+    False
+    >>> is_iterable((0,1,3,4))
+    True
+    >>> is_iterable([1])
+    True
+    >>> is_iterable('a')
+    True
     """
     try:
-        iterator = iter(obj)
+        iter(obj)
     except TypeError as te:
         return False
     return True
@@ -563,13 +628,19 @@ def isIterable(obj):
 def key_for_set_value(d):
     """
     takes a dictionary and returns the first key for which's value the
-    boolean is True
+    boolean representation is True
     :param d: dictionary containing values
     :type d: dict
     :return: key to the first non-False value found; None if no value's
     boolean equals True
-    :rtype:
+    :rtype: bool or NoneType
+
+    >>> key_for_set_value({'one': 0, 'two': 1})
+    'two'
+    >>> print(key_for_set_value({1: 0, 2: False}))
+    None
     """
+    assert type(d) is dict, "Function only defined for inputs of type 'dict'."
     r = None
     for k, v in d.items():
         if v:
@@ -577,32 +648,53 @@ def key_for_set_value(d):
     return r
 
 
-def prepTimeAxis(stime, trace, verbosity=0):
+def prep_time_axis(offset, trace, verbosity=0):
     """
-    takes a starttime and a trace object and returns a valid time axis for
+    takes an offset and a trace object and returns a valid time axis for
     plotting
-    :param stime: start time of the actual seismogram as UTCDateTime
-    :type stime: `~obspy.core.utcdatetime.UTCDateTime`
+    :param offset: offset of the actual seismogram on plotting axis
+    :type offset: float or int
     :param trace: seismic trace object
     :type trace: `~obspy.core.trace.Trace`
     :param verbosity: if != 0, debug output will be written to console
     :type verbosity: int
     :return: valid numpy array with time stamps for plotting
     :rtype: `~numpy.ndarray`
+
+    >>> tr = read()[0]
+    >>> prep_time_axis(0., tr)
+    array([0.00000000e+00, 1.00033344e-02, 2.00066689e-02, ...,
+           2.99799933e+01, 2.99899967e+01, 3.00000000e+01])
+    >>> prep_time_axis(22.5, tr)
+    array([22.5       , 22.51000333, 22.52000667, ..., 52.47999333,
+           52.48999667, 52.5       ])
+    >>> prep_time_axis(tr.stats.starttime, tr)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'offset' is not of type 'float' or 'int'; type: <class 'obspy.core.utcdatetime.UTCDateTime'>
+    >>> tr.stats.npts -= 1
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033356e-02, 2.00066711e-02, ...,
+           2.99699933e+01, 2.99799967e+01, 2.99900000e+01])
+    >>> tr.stats.npts += 2
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033333e-02, 2.00066667e-02, ...,
+           2.99899933e+01, 2.99999967e+01, 3.00100000e+01])
     """
+    assert isinstance(offset, (float, int)), "'offset' is not of type 'float' or 'int'; type: {}".format(type(offset))
     nsamp = trace.stats.npts
     srate = trace.stats.sampling_rate
     tincr = trace.stats.delta
-    etime = stime + nsamp / srate
-    time_ax = np.linspace(stime, etime, nsamp)
+    etime = offset + nsamp / srate
+    time_ax = np.linspace(offset, etime, nsamp)
     if len(time_ax) < nsamp:
         if verbosity:
             print('elongate time axes by one datum')
-        time_ax = np.arange(stime, etime + tincr, tincr)
+        time_ax = np.arange(offset, etime + tincr, tincr)
     elif len(time_ax) > nsamp:
         if verbosity:
             print('shorten time axes by one datum')
-        time_ax = np.arange(stime, etime - tincr, tincr)
+        time_ax = np.arange(offset, etime - tincr, tincr)
     if len(time_ax) != nsamp:
         print('Station {0}, {1} samples of data \n '
               '{2} length of time vector \n'
@@ -618,13 +710,13 @@ def find_horizontals(data):
     :param data: waveform data
     :type data: `obspy.core.stream.Stream`
     :return: components list
-    :rtype: list
+    :rtype: List(str)
 
     ..example::
 
     >>> st = read()
     >>> find_horizontals(st)
-    [u'N', u'E']
+    ['N', 'E']
     """
     rval = []
     for tr in data:
@@ -635,7 +727,7 @@ def find_horizontals(data):
     return rval
 
 
-def pick_color(picktype, phase, quality=0):
+def pick_color(picktype: Literal['manual', 'automatic'], phase: Literal['P', 'S'], quality: int = 0) -> Rgba:
     """
     Create pick color by modifying the base color by the quality.
 
@@ -648,7 +740,7 @@ def pick_color(picktype, phase, quality=0):
     :param quality: quality of pick. Decides the new intensity of the modifier color
     :type quality: int
     :return: tuple containing modified rgba color values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     min_quality = 3
     bpc = base_phase_colors(picktype, phase)  # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
@@ -704,17 +796,17 @@ def pick_linestyle_plt(picktype, key):
     return linestyles[picktype][key]
 
 
-def modify_rgba(rgba, modifier, intensity):
+def modify_rgba(rgba: Rgba, modifier: Literal['r', 'g', 'b'], intensity: float) -> Rgba:
     """
     Modify rgba color by adding the given intensity to the modifier color
     :param rgba: tuple containing rgba values
-    :type rgba: (int, int, int, int)
-    :param modifier: which color should be modified, eg. 'r', 'g', 'b'
-    :type modifier: str
+    :type rgba: Rgba
+    :param modifier: which color should be modified; options: 'r', 'g', 'b'
+    :type modifier: Literal['r', 'g', 'b']
     :param intensity: intensity to be added to selected color
     :type intensity: float
     :return: tuple containing rgba values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     rgba = list(rgba)
     index = {'r': 0,
@@ -748,18 +840,20 @@ def transform_colors_mpl_str(colors, no_alpha=False):
     Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
     :param colors: tuple of rgba color values ranging from [0, 255]
     :type colors: (float, float, float, float)
-    :param no_alpha: Wether to return a alpha value in the matplotlib color string
+    :param no_alpha: Whether to return an alpha value in the matplotlib color string
     :type no_alpha: bool
     :return: String containing r, g, b values and alpha value if no_alpha is False (default)
     :rtype: str
+
+    >>> transform_colors_mpl_str((255., 255., 255., 255.), True)
+    '(1.0, 1.0, 1.0)'
+    >>> transform_colors_mpl_str((255., 255., 255., 255.))
+    '(1.0, 1.0, 1.0, 1.0)'
     """
-    colors = list(colors)
-    colors_mpl = tuple([color / 255. for color in colors])
     if no_alpha:
-        colors_mpl = '({}, {}, {})'.format(*colors_mpl)
+        return '({}, {}, {})'.format(*transform_colors_mpl(colors))
     else:
-        colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
-    return colors_mpl
+        return '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
 
 
 def transform_colors_mpl(colors):
@@ -769,27 +863,16 @@ 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
@@ -897,13 +980,53 @@ def check4doubled(data):
     return data
 
 
+def check_for_nan(data, nan_value=0.):
+    """
+    Replace all NaNs in data with nan_value (in place)
+    :param data: stream of seismic data
+    :type data: `~obspy.core.stream.Stream`
+    :param nan_value: value which all NaNs are set to
+    :type nan_value: float, int
+    :return: None
+    """
+    if not data:
+        return
+    for trace in data:
+        np.nan_to_num(trace.data, copy=False, nan=nan_value)
+
+
+def get_pylot_eventfile_with_extension(event, fext):
+    if hasattr(event, 'path'):
+        eventpath = event.path
+    else:
+        logging.warning('No attribute path found for event.')
+        return
+    eventname = event.pylot_id #path.split('/')[-1]  # or event.pylot_id
+    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
+    if os.path.isfile(filename):
+        return filename
+
+
+def get_possible_pylot_eventfile_extensions(event, fext):
+    if hasattr(event, 'path'):
+        eventpath = event.path
+    else:
+        logging.warning('No attribute path found for event.')
+        return []
+    eventname = event.pylot_id
+    filename = os.path.join(eventpath, 'PyLoT_' + eventname + fext)
+    filenames = glob.glob(filename)
+    extensions = [os.path.split(path)[-1].split('PyLoT_' + eventname)[-1] for path in filenames]
+    return extensions
+
+
 def get_stations(data):
     """
-    Get list of all station names in data stream
+    Get list of all station names in data-stream
     :param data: stream containing seismic traces
     :type data: `~obspy.core.stream.Stream`
     :return: list of all station names in data, no duplicates
-    :rtype: list of str
+    :rtype: List(str)
     """
     stations = []
     for tr in data:
@@ -930,66 +1053,87 @@ 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
-        :type wfstream: `~obspy.core.stream.Stream`
+        :param wfs_in: stream containing seismic traces of a station
+        :type wfs_in: `~obspy.core.stream.Stream`
         :param metadata: tuple containing metadata type string and metadata parser object
         :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
         :return: stream object with traditionally oriented traces (ZNE)
         :rtype: `~obspy.core.stream.Stream`
         """
 
-        # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
-        orientations = [trace_id[-1] for trace_id in trace_ids]
-        rotation_required = [orientation.isnumeric() for orientation in orientations]
-        if any(rotation_required):
-            t_start = full_range(wfstream)
-            try:
-                azimuts = []
-                dips = []
-                for tr_id in trace_ids:
-                    azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
-                    dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
-            except (KeyError, TypeError) as e:
-                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
-                return wfstream
-            if len(wfstream) < 3:
-                print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
-                return wfstream
-            # to rotate all traces must have same length, so trim them
-            wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
-            try:
-                z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
-                                     wfstream[1], azimuts[1], dips[1],
-                                     wfstream[2], azimuts[2], dips[2])
-                print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
-                # replace old data with rotated data, change the channel code to ZNE
-                z_index = dips.index(min(
-                    dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
-                wfstream[z_index].data = z
-                wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
-                del trace_ids[z_index]
-                for trace_id in trace_ids:
-                    coordinates = metadata.get_coordinates(trace_id, t_start)
-                    dip, az = coordinates['dip'], coordinates['azimuth']
-                    trace = wfstream.select(id=trace_id)[0]
-                    if az > 315 or az <= 45 or az > 135 and az <= 225:
-                        trace.data = n
-                        trace.stats.channel = trace.stats.channel[0:-1] + 'N'
-                    elif az > 45 and az <= 135 or az > 225 and az <= 315:
-                        trace.data = e
-                        trace.stats.channel = trace.stats.channel[0:-1] + 'E'
-            except (ValueError) as e:
-                print(e)
-                return wfstream
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
 
-        return wfstream
+        # check if any traces in this station need to be rotated
+        trace_ids = [trace.id for trace in wfs_in]
+        if not rotation_required(trace_ids):
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            return wfs_in
+
+        # check metadata quality
+        t_start = full_range(wfs_in)
+        try:
+            azimuths = []
+            dips = []
+            for tr_id in trace_ids:
+                azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
+        except (KeyError, TypeError) as err:
+            logging.error(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
+                  f"available in metadata. Stream remains unchanged.")
+            return wfs_in
+        except Exception as err:
+            print(f"Unexpected {err=}, {type(err)=}")
+            raise
+
+        # to rotate all traces must have same length, so trim them
+        wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
+        try:
+            z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
+                                 wfs_out[1], azimuths[1], dips[1],
+                                 wfs_out[2], azimuths[2], dips[2])
+            print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
+            # replace old data with rotated data, change the channel code to ZNE
+            z_index = dips.index(min(
+                dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90
+            # being vertical)
+            wfs_out[z_index].data = z
+            wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
+            del trace_ids[z_index]
+            for trace_id in trace_ids:
+                coordinates = metadata.get_coordinates(trace_id, t_start)
+                dip, az = coordinates['dip'], coordinates['azimuth']
+                trace = wfs_out.select(id=trace_id)[0]
+                if az > 315 or az <= 45 or 135 < az <= 225:
+                    trace.data = n
+                    trace.stats.channel = trace.stats.channel[0:-1] + 'N'
+                elif 45 < az <= 135 or 225 < az <= 315:
+                    trace.data = e
+                    trace.stats.channel = trace.stats.channel[0:-1] + 'E'
+        except ValueError as err:
+            print(f"{err=} Rotation failed. Stream remains unchanged.")
+            return wfs_in
+
+        return wfs_out
 
     if metadata is None:
         if verbosity:
@@ -1003,38 +1147,6 @@ 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
@@ -1169,7 +1281,7 @@ def correct_iplot(iplot):
     try:
         iplot = int(iplot)
     except ValueError:
-        if get_Bool(iplot):
+        if get_bool(iplot):
             iplot = 2
         else:
             iplot = 0

requirements.txt

@@ -1,12 +1,9 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: win-64
-cartopy=0.20.2
-matplotlib-base=3.3.4
-numpy=1.22.3
-obspy=1.3.0
-pyqtgraph=0.12.4
-pyside2=5.13.2
-python=3.8.12
-qt=5.12.9
-scipy=1.8.0
+cartopy>=0.20.2
+numpy<2
+obspy>=1.3.0
+pyqtgraph>=0.12.4
+pyside2>=5.13.2
+scipy>=1.8.0

tests/test_get_qualities_from_xml.py

@@ -5,7 +5,7 @@ from pylot.core.io.phases import getQualitiesfromxml
 
 class TestQualityFromXML(unittest.TestCase):
     def setUp(self):
-        self.xmlpaths = ['PyLoT_e0019.048.13.xml']
+        self.path = '.'
         self.ErrorsP = [0.02, 0.04, 0.08, 0.16]
         self.ErrorsS = [0.04, 0.08, 0.16, 0.32]
         self.test0_result = [[0.0136956521739, 0.0126, 0.0101612903226, 0.00734848484849, 0.0135069444444,
@@ -23,10 +23,10 @@ class TestQualityFromXML(unittest.TestCase):
                             [92.0, 4.0, 4.0, 0, 0]
 
     def test_result_plotflag0(self):
-        self.assertEqual(getQualitiesfromxml(self.xmlpaths, self.ErrorsP, self.ErrorsS, 0), self.test0_result)
+        self.assertEqual(getQualitiesfromxml(self.path, self.ErrorsP, self.ErrorsS, 0), self.test0_result)
 
     def test_result_plotflag1(self):
-        self.assertEqual(getQualitiesfromxml(self.xmlpaths, self.ErrorsP, self.ErrorsS, 1), self.test1_result)
+        self.assertEqual(getQualitiesfromxml(self.path, self.ErrorsP, self.ErrorsS, 1), self.test1_result)
 
 
 if __name__ == '__main__':