From 554afc5a813089b8985c255475551bb737cc735a Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Mon, 10 Apr 2023 18:35:58 +0200
Subject: [PATCH 01/31] bugfix: update check4rotate

---
 pylot/core/util/utils.py | 126 +++++++++++++++++++++++----------------
 1 file changed, 73 insertions(+), 53 deletions(-)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 0557db83..bb64fdda 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -167,11 +167,11 @@ 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]
@@ -539,8 +539,7 @@ def isSorted(iterable):
     >>> isSorted([2,3,1,4])
     False
     """
-    assert isIterable(iterable), 'object is not iterable; object: {' \
-                                 '}'.format(iterable)
+    assert isIterable(iterable), "object is not iterable; object: {}".format(iterable)
     if type(iterable) is str:
         iterable = [s for s in iterable]
     return sorted(iterable) == iterable
@@ -551,7 +550,7 @@ def isIterable(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
     """
@@ -959,66 +958,87 @@ 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`
         """
 
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
+        
         # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
-        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
+        trace_ids = [trace.id for trace in wfs_in]
+        if not rotation_required(trace_ids):
+            print(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            return wfs_in
 
-        return wfstream
+        # 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:
+            print(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:
-- 
2.45.2


From 221743fe20f6fdcb4d631fea7df1518162dab799 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Mon, 10 Apr 2023 19:14:23 +0200
Subject: [PATCH 02/31] bugfix: correct erroneous and add new doctests

---
 PyLoT.py                   | 15 +--------
 pylot/core/pick/utils.py   |  4 +--
 pylot/core/util/utils.py   | 64 +++++++++++++++++++++++++++++---------
 pylot/core/util/widgets.py | 40 ++----------------------
 4 files changed, 55 insertions(+), 68 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 6e881d77..ac6ff10c 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -496,6 +496,7 @@ class MainWindow(QMainWindow):
                                                       icon=eventlist_xml_icon,
                                                       tip='Create an Eventlist from a XML File')
         self.eventlist_xml_action.setEnabled(False)
+
         printAction = self.createAction(self, "&Print event ...",
                                         self.show_event_information, QKeySequence.Print,
                                         print_icon,
@@ -1403,8 +1404,6 @@ class MainWindow(QMainWindow):
 
         for id, event in enumerate(self.project.eventlist):
             event_path = event.path
-            #phaseErrors = {'P': self._inputs['timeerrorsP'],
-            #               'S': self._inputs['timeerrorsS']}
 
             man_au_picks = {'manual': event.pylot_picks,
                             'auto': event.pylot_autopicks}
@@ -1473,7 +1472,6 @@ class MainWindow(QMainWindow):
 
             for picktype, item_np in [('manual', item_nmp), ('auto', item_nap)]:
                 npicks_str = f"{npicks[picktype]['P']}|{npicks[picktype]['S']}"
-                #npicks_str += f"({npicks_total[picktype]['P']}/{npicks_total[picktype]['S']})"
                 item_np.setText(npicks_str)
 
             item_ref = QStandardItem()  # str(event_ref))
@@ -1718,8 +1716,6 @@ class MainWindow(QMainWindow):
             for tr in self.get_data().wfdata.select(component=ch).traces:
                 traces[tr.stats.station][ch] = tr
 
-        names.sort()
-        a = self.get_current_event()
 
         print (self.get_data().wfdata.traces[0])
 
@@ -1729,14 +1725,6 @@ class MainWindow(QMainWindow):
         self.tabs.setCurrentIndex(3)
         figCanvas = test.makeSpecFig(direction=self.dispComponent, height = height, width = width, parent = self.tabs.widget)
         return figCanvas
-        #self.spectro_layout.addWidget()
-        # self.get_data().wfdata.spectrogram()
-        # self.tabs.addTab(figCanvas, 'Spectrogram')
-        # self.tabs[3] = figCanvas
-        # self.refreshTabs()
-        # test.show()
-
-
 
     def compareMulti(self):
         if not self.compareoptions:
@@ -1896,7 +1884,6 @@ class MainWindow(QMainWindow):
         # which will read in data input twice. Therefore current tab is changed to 0
         # in loadProject before calling this function.
         self.fill_eventbox()
-        #print(f'{self.get_current_event()=}')
         plotted = False
         if self.tabs.currentIndex() == 2:
             self.init_event_table()
diff --git a/pylot/core/pick/utils.py b/pylot/core/pick/utils.py
index e2bb8e7a..def27b8a 100644
--- a/pylot/core/pick/utils.py
+++ b/pylot/core/pick/utils.py
@@ -275,7 +275,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P1 = np.polyfit(xslope1, xraw[islope1], 1)
                 datafit1 = np.polyval(P1, xslope1)
-            except Exception as e:
+            except ValueError as e:
                 print("fmpicker: Problems with data fit! {}".format(e))
                 print("Skip first motion determination!")
                 return FM
@@ -321,7 +321,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P2 = np.polyfit(xslope2, xfilt[islope2], 1)
                 datafit2 = np.polyval(P2, xslope2)
-            except Exception as e:
+            except ValueError as e:
                 emsg = 'fmpicker: polyfit failed: {}'.format(e)
                 print(emsg)
                 return FM
diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index bb64fdda..7cd53465 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -333,18 +333,37 @@ def get_bool(value):
     """
     Convert string representations of bools to their true boolean value
     :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
     """
-    if type(value) is bool:
+    if type(value) == bool:
         return value
     elif value in ['True', 'true']:
         return True
     elif value in ['False', 'false']:
         return False
+    elif value > 0. or value > 0:
+        return True
     else:
-        return bool(value)
+        return False
 
 def four_digits(year):
     """
@@ -355,8 +374,8 @@ 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)
@@ -513,6 +532,11 @@ 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)
 
@@ -619,13 +643,13 @@ 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:
@@ -819,6 +843,19 @@ def trim_station_components(data, trim_start=True, trim_end=True):
     return data
 
 
+def merge_stream(stream):
+    gaps = stream.get_gaps()
+    if gaps:
+        # list of merged stations (seed_ids)
+        merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
+        stream.merge(method=1)
+        print('Merged the following stations because of gaps:')
+        for merged_station in merged:
+            print(merged_station)
+
+    return stream, gaps
+
+
 def check4gapsAndRemove(data):
     """
     check for gaps in Stream and remove them
@@ -839,12 +876,12 @@ def check4gapsAndRemove(data):
     return data
 
 
-def check_for_gaps_and_merge(data):
+def check4gapsAndMerge(data):
     """
     check for gaps in Stream and merge if gaps are found
     :param data: stream of seismic data
     :type data: `~obspy.core.stream.Stream`
-    :return: data stream, gaps returned from obspy get_gaps
+    :return: data stream
     :rtype: `~obspy.core.stream.Stream`
     """
     gaps = data.get_gaps()
@@ -855,7 +892,7 @@ def check_for_gaps_and_merge(data):
         for merged_station in merged:
             print(merged_station)
 
-    return data, gaps
+    return data
 
 
 def check4doubled(data):
@@ -927,11 +964,11 @@ def get_possible_pylot_eventfile_extensions(event, fext):
 
 def get_stations(data):
     """
-    Get list of all station names in data stream
+    Get list of all station names in data-stream
     :param data: stream containing seismic traces
     :type data: `~obspy.core.stream.Stream`
     :return: list of all station names in data, no duplicates
-    :rtype: list of str
+    :rtype: List(str)
     """
     stations = []
     for tr in data:
@@ -987,7 +1024,7 @@ def check4rotated(data, metadata=None, verbosity=1):
         if len(wfs_in) < 3:
             print(f"Stream {wfs_in=}, has not enough components to rotate.")
             return wfs_in
-        
+
         # check if any traces in this station need to be rotated
         trace_ids = [trace.id for trace in wfs_in]
         if not rotation_required(trace_ids):
@@ -1155,7 +1192,6 @@ def identifyPhase(phase):
         return False
 
 
-@lru_cache
 def identifyPhaseID(phase):
     """
     Returns phase id (capital P or S)
diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index a9a3e6f4..297d47e3 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -897,8 +897,6 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         else:
             st_select = wfdata
 
-        # st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice
-
         # list containing tuples of network, station, channel (for sorting)
         nslc = []
         for trace in st_select:
@@ -5788,10 +5786,7 @@ class ChooseWaveFormWindow(QWidget):
     def submit(self):
         matplotlib.pyplot.close(self.currentSpectro)
         t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        #self.currentSpectro = self.traces[
-        #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
-        #self.currentSpectro.show()
-        applyFFT()
+        self.applyFFT()
 
     def applyFFT(self, trace):
         tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
@@ -5886,21 +5881,6 @@ class SpectrogramTab(QWidget):
                           colors='m', linestyles='dashed',
                           linewidth=2)
 
-            # Different axis settings for visual improvements
-            # axis[i].set_xlim(left=0, right=end - start)
-            # axis[i].spines['top'].set_visible(False)
-            # axis[i].spines['right'].set_visible(False)
-            # # axis[i].spines['left'].set_visible(False)
-
-            # axis[i].tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
-            # if not (len(self.traces) == i - 1):
-                # axis[i].spines['bottom'].set_visible(False)
-            # axis[i].set_yticks([])
-            # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
-
-            #ax.axhline(n, color="0.5", lw=0.5)
-
-
             grams.append(tra.spectrogram(show=False, axes=axis[i]))
             i+=1
 
@@ -5909,24 +5889,8 @@ class SpectrogramTab(QWidget):
         fC = FigureCanvas(figure)
         return fC
 
-    #for t in self.traces:
-       # tra = self.traces[t]['Z']
-       # transformed = abs(np.fft.rfft(tra.data))
-       # axis[i].plot(transformed, label=t)
-       # # axis[i].tick_params(labelbottom=False)
-       # axis[i].spines['top'].set_visible(False)
-       # axis[i].spines['right'].set_visible(False)
-       # axis[i].spines['left'].set_visible(False)
-       # if not (len(self.traces) == i - 1):
-       #     axis[i].spines['bottom'].set_visible(False)
-       # axis[i].set_yticks([])
-       # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
-       # # axis[i].axis('off')
-       # i += 1
-       # # self.applyFFTs(t)
-
 
 if __name__ == '__main__':
     import doctest
 
-    doctest.testmod()
+    doctest.testmod()
\ No newline at end of file
-- 
2.45.2


From 7fbc3bc5ae4cba7601978075afa17fbfbe49cf08 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Wed, 12 Apr 2023 20:32:44 +0200
Subject: [PATCH 03/31] bugfix: add new tests and refactor get_none

---
 autoPyLoT.py                |  10 +-
 pylot/core/pick/autopick.py |   4 +-
 pylot/core/pick/utils.py    |  14 +--
 pylot/core/util/utils.py    |  25 +++-
 pylot/core/util/widgets.py  | 238 +++++-------------------------------
 5 files changed, 66 insertions(+), 225 deletions(-)

diff --git a/autoPyLoT.py b/autoPyLoT.py
index 00da0797..0a801286 100755
--- a/autoPyLoT.py
+++ b/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
@@ -154,7 +154,7 @@ 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')
diff --git a/pylot/core/pick/autopick.py b/pylot/core/pick/autopick.py
index 6cca5691..70f71658 100644
--- a/pylot/core/pick/autopick.py
+++ b/pylot/core/pick/autopick.py
@@ -22,7 +22,7 @@ from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
     getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
 from pylot.core.util.utils import getPatternLine, gen_Pool, \
-    get_bool, identifyPhaseID, get_None, correct_iplot
+    get_bool, identifyPhaseID, get_none, correct_iplot
 
 
 def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
@@ -258,7 +258,7 @@ class AutopickStation(object):
         self.pickparams = copy.deepcopy(pickparam)
         self.verbose = verbose
         self.iplot = correct_iplot(iplot)
-        self.fig_dict = get_None(fig_dict)
+        self.fig_dict = get_none(fig_dict)
         self.metadata = metadata
         self.origin = origin
 
diff --git a/pylot/core/pick/utils.py b/pylot/core/pick/utils.py
index def27b8a..196ac2ee 100644
--- a/pylot/core/pick/utils.py
+++ b/pylot/core/pick/utils.py
@@ -15,7 +15,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 from scipy.signal import argrelmax
 
-from pylot.core.util.utils import get_bool, get_None, SetChannelComponents
+from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
     PickError = symmetrize_error(diffti_te, diffti_tl)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -344,7 +344,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
         print("fmpicker: Found polarity %s" % FM)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
             returnflag = 0
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -1213,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
             t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
                             trace.stats.npts)
             if i == 0:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax1 = fig.add_subplot(3, 1, i + 1)
                 ax = ax1
                 ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
             else:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
@@ -1494,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
     # set initial quality to 4 (worst) and change only if one condition is hit
     quality = 4
 
-    if get_None(uncertainty) is None:
+    if get_none(uncertainty) is None:
         return quality
 
     if uncertainty <= Errors[0]:
diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 7cd53465..9b80655d 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -315,15 +315,32 @@ def fnConstructor(s):
     return fn
 
 
-def get_None(value):
+def get_none(value):
     """
     Convert "None" to None
     :param value:
-    :type value: str, bool
+    :type value: str, NoneType
     :return:
-    :rtype: bool
+    :rtype: type(value) or NoneType
+
+    >>> st = read()
+    >>> print(get_none(st))
+    3 Trace(s) in Stream:
+    BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    >>> get_none('Stream')
+    'Stream'
+    >>> get_none(0)
+    0
+    >>> get_none(0.)
+    0.0
+    >>> print(get_none('None'))
+    None
+    >>> print(get_none(None))
+    None
     """
-    if value == 'None':
+    if value is None or (type(value) is str and value == 'None'):
         return None
     else:
         return value
diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index 297d47e3..c0c97c62 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -53,7 +53,7 @@ from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorte
     pick_linestyle_plt, pick_color_plt, \
     check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
-    identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
+    identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
     station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
@@ -860,26 +860,13 @@ class WaveformWidgetPG(QtWidgets.QWidget):
     def clearPlotDict(self):
         self.plotdict = dict()
 
-    def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
-                   component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
-        def station_sort(nslc):
-            """Try to sort after station integer in case of a line array (e.g. active seismics)"""
-            try:
-                rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
-                return rval
-            except ValueError as e:
-                # this is the standard case for seismological stations
-                pass
-            except Exception as e:
-                print(f'Sorting by station integer failed with unknown exception: {e}')
-
-            # fallback to default sorting
-            return sorted(nslc)
-
+    def plotWFData(self, wfdata, wfsyn=None, title=None, zoomx=None, zoomy=None,
+                   noiselevel=None, scaleddata=False, mapping=True,
+                   component='*', nth_sample=1, iniPick=None, verbosity=0,
+                   method='normal', gain=1.):
         if not wfdata:
             print('Nothing to plot.')
             return
-
         self.title = title
         self.clearPlotDict()
         self.wfstart, self.wfend = full_range(wfdata)
@@ -897,12 +884,14 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         else:
             st_select = wfdata
 
+        st_select, gaps = merge_stream(st_select)
+
         # list containing tuples of network, station, channel (for sorting)
         nslc = []
         for trace in st_select:
             nslc.append(
                 trace.get_id())  # (trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
-        nslc = station_sort(nslc)
+        nslc.sort()
         nslc.reverse()
         plots = []
 
@@ -966,7 +955,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         self.ylabel = ''
         self.setXLims([0, self.wfend - self.wfstart])
         self.setYLims([0.5, nmax + 0.5])
-        return plots
+        return plots, gaps
 
     def minMax(self, trace, time_ax):
         '''
@@ -988,7 +977,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         min_ = data.min(axis=1)
         max_ = data.max(axis=1)
         if remaining_samples:
-            extreme_values = np.empty((npixel + 1, 2), dtype=float)
+            extreme_values = np.empty((npixel + 1, 2), dtype=np.float)
             extreme_values[:-1, 0] = min_
             extreme_values[:-1, 1] = max_
             extreme_values[-1, 0] = \
@@ -996,7 +985,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
             extreme_values[-1, 1] = \
                 trace.data[-remaining_samples:].max()
         else:
-            extreme_values = np.empty((npixel, 2), dtype=float)
+            extreme_values = np.empty((npixel, 2), dtype=np.float)
             extreme_values[:, 0] = min_
             extreme_values[:, 1] = max_
         data = extreme_values.flatten()
@@ -1566,114 +1555,6 @@ class PylotCanvas(FigureCanvas):
         self.draw()
 
 
-class SearchFileByExtensionDialog(QtWidgets.QDialog):
-    def __init__(self, parent=None, label='Text: ', default_text='.xml', events=None):
-        super(SearchFileByExtensionDialog, self).__init__(parent)
-        self.events = events
-        self.filepaths = []
-        self.file_extensions = []
-        self.default_text = default_text
-        self.label = label
-        self.setButtons()
-        self.setupUi()
-        self.connectSignals()
-        self.showPaths()
-        self.refreshSelectionBox()
-        self.refresh_timer = QTimer(self)
-        self.refresh_timer.timeout.connect(self.showPaths)
-        self.refresh_timer.start(10000)
-
-        self.resize(800, 450)
-
-
-    def setupUi(self):
-        self.main_layout = QtWidgets.QVBoxLayout()
-        self.header_layout = QtWidgets.QHBoxLayout()
-        #
-        self.setLayout(self.main_layout)
-
-        # widgets inside the dialog
-        self.textLabel = QtWidgets.QLabel(self.label)
-        self.comboBox = QtWidgets.QComboBox()
-        self.comboBox.addItem(self.default_text)
-        self.comboBox.setEditable(True)
-
-        # optional search button, currently disabled. List refreshed when text changes
-        self.searchButton = QtWidgets.QPushButton('Search')
-        self.searchButton.setVisible(False)
-
-        self.tableWidget = QtWidgets.QTableWidget()
-        tableWidget = self.tableWidget
-        tableWidget.setColumnCount(3)
-        tableWidget.setRowCount(len(self.events))
-        tableWidget.setHorizontalHeaderLabels(('Event ID', 'Filename', 'Last modified'))
-        tableWidget.setEditTriggers(tableWidget.NoEditTriggers)
-        tableWidget.setSortingEnabled(True)
-        header = tableWidget.horizontalHeader()
-        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
-        header.setStretchLastSection(True)
-
-        self.statusText = QtWidgets.QLabel()
-
-        self.header_layout.addWidget(self.textLabel)
-        self.header_layout.addWidget(self.comboBox)
-        self.header_layout.addWidget(self.searchButton)
-
-        self.main_layout.addLayout(self.header_layout)
-        self.main_layout.addWidget(self.tableWidget)
-        self.main_layout.addWidget(self.statusText)
-        self.main_layout.addWidget(self._buttonbox)
-
-    def showPaths(self):
-        self.filepaths = []
-        fext = self.comboBox.currentText()
-        self.tableWidget.clearContents()
-        for index, event in enumerate(self.events):
-            filename = get_pylot_eventfile_with_extension(event, fext)
-            self.tableWidget.setItem(index, 0, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
-            if filename:
-                self.filepaths.append(filename)
-                ts = int(os.path.getmtime(filename))
-
-                # create QTableWidgetItems of filepath and last modification time
-                fname_item = QtWidgets.QTableWidgetItem(f'{os.path.split(filename)[-1]}')
-                ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
-                self.tableWidget.setItem(index, 1, fname_item)
-                self.tableWidget.setItem(index, 2, ts_item)
-
-        # TODO: Idea -> only refresh if table contents changed. Use selection to load only a subset of files
-        if len(self.filepaths) > 0:
-            status_text = f'Found {len(self.filepaths)} eventfiles. Do you want to load them?'
-        else:
-            status_text = 'Did not find any files for specified file mask.'
-        self.statusText.setText(status_text)
-
-    def refreshSelectionBox(self):
-        fext = self.comboBox.currentText()
-        self.file_extensions = [fext]
-
-        for event in self.events:
-            extensions = get_possible_pylot_eventfile_extensions(event, '*.xml')
-            for ext in extensions:
-                if not ext in self.file_extensions:
-                    self.file_extensions.append(ext)
-
-        self.comboBox.clear()
-        for ext in sorted(self.file_extensions):
-            self.comboBox.addItem(ext)
-
-    def setButtons(self):
-        self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
-                                           QDialogButtonBox.Cancel)
-
-    def connectSignals(self):
-        self._buttonbox.accepted.connect(self.accept)
-        self._buttonbox.rejected.connect(self.reject)
-        self.comboBox.editTextChanged.connect(self.showPaths)
-        self.searchButton.clicked.connect(self.showPaths)
-
-
-
 class SingleTextLineDialog(QtWidgets.QDialog):
     def __init__(self, parent=None, label='Text: ', default_text='.xml'):
         super(SingleTextLineDialog, self).__init__(parent)
@@ -1905,7 +1786,7 @@ class PickDlg(QDialog):
 
         # init expected picks using obspy Taup
         try:
-            if self.metadata and model != "None":
+            if self.metadata and model is not None:
                 self.model = TauPyModel(model)
                 self.get_arrivals()
                 self.drawArrivals()
@@ -2632,9 +2513,7 @@ class PickDlg(QDialog):
         data.normalize()
         if not data:
             QtWidgets.QMessageBox.warning(self, 'No channel to plot',
-                                          'No channel to plot for phase: {}. '
-                                          'Make sure to select the correct channels for P and S '
-                                          'in the menu in the top panel.'.format(phase))
+                                          'No channel to plot for phase: {}.'.format(phase))
             self.leave_picking_mode()
             return
 
@@ -2774,7 +2653,7 @@ class PickDlg(QDialog):
             minFMSNR = parameter.get('minFMSNR')
             quality = get_quality_class(spe, parameter.get('timeerrorsP'))
             if quality <= minFMweight and snr >= minFMSNR:
-                FM = fmpicker(self.getWFData().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
+                FM = fmpicker(self.getWFData().select(channel=channel), wfdata, parameter.get('fmpickwin'),
                               pick - stime_diff)
 
         # save pick times for actual phase
@@ -3687,9 +3566,8 @@ class TuneAutopicker(QWidget):
             # wfdat = remove_underscores(wfdat)
             # rotate misaligned stations to ZNE
             # check for gaps and doubled channels
-            wfdat, _ = check_for_gaps_and_merge(wfdat)
-            # check for nans
-            check_for_nan(wfdat)
+            wfdat, gaps = merge_stream(wfdat)
+            # check4gaps(wfdat)
             check4doubled(wfdat)
             wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
             # trim station components to same start value
@@ -3733,14 +3611,14 @@ class TuneAutopicker(QWidget):
         self.listWidget.scrollToBottom()
 
     def get_current_event(self):
-        path = self.get_current_event_fp()
+        path = self.eventBox.currentText()
         return self.parent().project.getEventFromPath(path)
 
     def get_current_event_name(self):
-        return self.eventBox.currentText().split('/')[-1].rstrip('*')
+        return self.eventBox.currentText().split('/')[-1].split('*')[0]
 
     def get_current_event_fp(self):
-        return self.eventBox.currentText().rstrip('*')
+        return self.eventBox.currentText().split('*')[0]
 
     def get_current_event_picks(self, station):
         event = self.get_current_event()
@@ -3844,7 +3722,6 @@ class TuneAutopicker(QWidget):
         st = self.data.getWFData()
         tr = st.select(station=self.get_current_station())[0]
         starttime = tr.stats.starttime
-        # create two lists with figure names and subindices (for subplots) to get the correct axes
         p_axes = [
             ('mainFig', 0),
             ('aicFig', 0),
@@ -4792,8 +4669,8 @@ class InputsTab(PropTab):
         self.tstopBox = QSpinBox()
         for spinbox in [self.tstartBox, self.tstopBox]:
             spinbox.setRange(-99999, 99999)
-        self.tstartBox.setValue(float(settings.value('tstart')) if get_None(settings.value('tstart')) else 0)
-        self.tstopBox.setValue(float(settings.value('tstop')) if get_None(settings.value('tstop')) else 1e6)
+        self.tstartBox.setValue(float(settings.value('tstart')) if get_none(settings.value('tstart')) else 0)
+        self.tstopBox.setValue(float(settings.value('tstop')) if get_none(settings.value('tstop')) else 1e6)
         self.cuttimesLayout.addWidget(self.tstartBox, 10)
         self.cuttimesLayout.addWidget(QLabel('[s] and'), 0)
         self.cuttimesLayout.addWidget(self.tstopBox, 10)
@@ -5786,20 +5663,9 @@ class ChooseWaveFormWindow(QWidget):
     def submit(self):
         matplotlib.pyplot.close(self.currentSpectro)
         t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        self.applyFFT()
-
-    def applyFFT(self, trace):
-        tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
-        transformed = abs(np.fft.rfft(tra.data))
-        print ( transformed )
-        matplotlib.pyplot.plot ( transformed )
-        matplotlib.pyplot.show()
-
-    def applyFFTs(self, tra):
-        transformed = abs(np.fft.rfft(tra.data))
-        print ( transformed )
-        matplotlib.pyplot.plot ( transformed )
-        matplotlib.pyplot.show()
+        self.currentSpectro = self.traces[
+            self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
+        self.currentSpectro.show()
 
     def submitN(self):
         matplotlib.pyplot.close(self.currentSpectro)
@@ -5815,6 +5681,13 @@ class ChooseWaveFormWindow(QWidget):
             self.chooseBoxTraces.currentText()[3:]]['E'].spectrogram(show=False, title=t)
         self.currentSpectro.show()
 
+    def submitZ(self):
+        matplotlib.pyplot.close(self.currentSpectro)
+        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
+        self.currentSpectro = self.traces[
+            self.chooseBoxTraces.currentText()[3:]]['Z'].spectrogram(show=False, title=t)
+        self.currentSpectro.show()
+
     # Creates a QComboBox and adds all traces provided
     def createComboBoxTraces(self):
         if len(self.wFs) <= 0:
@@ -5841,55 +5714,6 @@ class ChooseWaveFormWindow(QWidget):
         pass
 
 
-class SpectrogramTab(QWidget):
-    def __init__(self, traces, wfdata, parent=None):
-        super(SpectrogramTab, self).__init__(parent)
-        self.setupUi()
-        self.traces = traces
-        self.wfdata = wfdata
-
-    def setupUi(self):
-        pass
-    def makeSpecFig(self, direction = 'Z', height = 0, width = 0, parent = None):
-
-        i = 0
-        grams = []
-        figure, axis = matplotlib.pyplot.subplots(len(self.traces), sharex=True)
-
-        start, end = full_range(self.wfdata)
-
-        if height != 0 and width != 0:
-            figure.figsize = (width, height)
-            figure.set_figwidth = width
-            figure.set_figheight = height
-
-        #figure.tight_layout()
-
-        for t in self.traces:
-            tra = self.traces[t][direction]
-            #print(start, end)
-
-            # Set Title
-            if i == 0:
-                if direction == 'Z':
-                    figure.suptitle("section: vertical components")
-                elif direction == 'E':
-                    figure.suptitle("section: east-west components")
-                elif direction == 'N':
-                    figure.suptitle("section: north-south components")
-                axis[i].vlines(0, axis[i].get_ylim()[0], axis[i].get_ylim()[1],
-                          colors='m', linestyles='dashed',
-                          linewidth=2)
-
-            grams.append(tra.spectrogram(show=False, axes=axis[i]))
-            i+=1
-
-        #figure.setXLims([0, end - start])
-        figure.set_tight_layout(True)
-        fC = FigureCanvas(figure)
-        return fC
-
-
 if __name__ == '__main__':
     import doctest
 
-- 
2.45.2


From eb15382b5fe68cbef55529fb67f11e693bd8ccb2 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Wed, 12 Apr 2023 21:22:58 +0200
Subject: [PATCH 04/31] bugfix: refactor get_owner and get_hash; add tests

---
 pylot/core/io/location.py |  4 ++--
 pylot/core/io/phases.py   |  6 +++---
 pylot/core/util/utils.py  | 25 +++++++++++++++++++++----
 3 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/pylot/core/io/location.py b/pylot/core/io/location.py
index 6fa2bbac..0fc5130d 100644
--- a/pylot/core/io/location.py
+++ b/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 getLogin, get_hash
 
 
 def create_amplitude(pickID, amp, unit, category, cinfo):
@@ -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:
diff --git a/pylot/core/io/phases.py b/pylot/core/io/phases.py
index 97e3e4c1..34dd1677 100644
--- a/pylot/core/io/phases.py
+++ b/pylot/core/io/phases.py
@@ -16,7 +16,7 @@ from pylot.core.io.inputs import PylotParameter
 from pylot.core.io.location import create_event, \
     create_magnitude
 from pylot.core.pick.utils import select_for_phase, get_quality_class
-from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
+from pylot.core.util.utils import get_owner, full_range, four_digits, transformFilterString4Export, \
     backtransformFilterString, loopIdentifyPhase, identifyPhase
 
 
@@ -58,7 +58,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if phasfn is not None and os.path.isfile(phasfn):
         phases = sio.loadmat(phasfn)
         phasctime = UTCDateTime(os.path.getmtime(phasfn))
-        phasauthor = getOwner(phasfn)
+        phasauthor = get_owner(phasfn)
     else:
         phases = None
         phasctime = None
@@ -66,7 +66,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if locfn is not None and os.path.isfile(locfn):
         loc = sio.loadmat(locfn)
         locctime = UTCDateTime(os.path.getmtime(locfn))
-        locauthor = getOwner(locfn)
+        locauthor = get_owner(locfn)
     else:
         loc = None
         locctime = None
diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 9b80655d..64b86807 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -303,7 +303,7 @@ 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)(\.|$)')
@@ -474,16 +474,25 @@ 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()
 
 
@@ -497,13 +506,21 @@ def getLogin():
     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"]:
-- 
2.45.2


From f043401cc055f782d527a0d323448745bb759cee Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sun, 16 Apr 2023 09:50:42 +0200
Subject: [PATCH 05/31] bugfix: rename is_iterable and add doc tests

---
 pylot/core/util/utils.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 64b86807..dea7ee69 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -597,13 +597,13 @@ 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
@@ -611,9 +611,22 @@ def isIterable(obj):
     :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
-- 
2.45.2


From fb32d5e0c5a7682ce9298061b6e71f0a3add468b Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sun, 16 Apr 2023 09:58:51 +0200
Subject: [PATCH 06/31] bugfix: add tests to key_for_set_value

---
 pylot/core/util/utils.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index dea7ee69..e111f065 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -635,13 +635,19 @@ def is_iterable(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:
-- 
2.45.2


From 2bbb84190c1314affe954aed186e9b90be40db80 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sun, 23 Apr 2023 21:37:20 +0200
Subject: [PATCH 07/31] feat: add type hints and tests for plot utils

---
 pylot/core/util/utils.py   | 76 +++++++++++++++++++++++++++-----------
 pylot/core/util/widgets.py | 12 +++---
 2 files changed, 60 insertions(+), 28 deletions(-)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index e111f065..5807a856 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -20,6 +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:
@@ -121,7 +125,7 @@ def gen_Pool(ncores=0):
 
     print('gen_Pool: Generated multiprocessing Pool with {} cores\n'.format(ncores))
 
-    pool = multiprocessing.Pool(ncores, maxtasksperchild=100)
+    pool = multiprocessing.Pool(ncores)
     return pool
 
 
@@ -382,6 +386,7 @@ def get_bool(value):
     else:
         return False
 
+
 def four_digits(year):
     """
     takes a two digit year integer and returns the correct four digit equivalent
@@ -655,32 +660,53 @@ 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'
@@ -713,7 +739,7 @@ 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.
 
@@ -726,7 +752,7 @@ 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)}
@@ -782,17 +808,17 @@ 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,
@@ -826,18 +852,20 @@ 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):
@@ -847,6 +875,10 @@ 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])
diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index c0c97c62..f3b9d33a 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -49,7 +49,7 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
 from pylot.core.pick.compare import Comparison
 from pylot.core.pick.autopick import fmpicker
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
-from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
+from pylot.core.util.utils import prep_time_axis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
     pick_linestyle_plt, pick_color_plt, \
     check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
@@ -923,10 +923,10 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
             stime = trace.stats.starttime - self.wfstart
-            time_ax = prepTimeAxis(stime, trace)
+            time_ax = prep_time_axis(stime, trace)
             if st_syn:
                 stime_syn = trace_syn.stats.starttime - self.wfstart
-                time_ax_syn = prepTimeAxis(stime_syn, trace_syn)
+                time_ax_syn = prep_time_axis(stime_syn, trace_syn)
 
             if method == 'fast':
                 trace.data, time_ax = self.minMax(trace, time_ax)
@@ -1409,7 +1409,7 @@ class PylotCanvas(FigureCanvas):
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
             stime = trace.stats.starttime - wfstart
-            time_ax = prepTimeAxis(stime, trace)
+            time_ax = prep_time_axis(stime, trace)
             if time_ax is not None:
                 if scaleToChannel:
                     st_scale = wfdata.select(channel=scaleToChannel)
@@ -1447,7 +1447,7 @@ class PylotCanvas(FigureCanvas):
                 if not scaleddata:
                     trace.detrend('constant')
                     trace.normalize(np.max(np.abs(trace.data)) * 2)
-                time_ax = prepTimeAxis(stime, trace)
+                time_ax = prep_time_axis(stime, trace)
                 times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
                 p_data = compare_stream[0].data
                 # #normalize
@@ -2548,7 +2548,7 @@ class PickDlg(QDialog):
 
         # prepare plotting of data
         for trace in data:
-            t = prepTimeAxis(trace.stats.starttime - stime, trace)
+            t = prep_time_axis(trace.stats.starttime - stime, trace)
             inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
             trace = demeanTrace(trace, inoise)
             # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
-- 
2.45.2


From e3dd4a4e28284e5ba06f4ecc7cb0fbd7450bf4c7 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sun, 23 Apr 2023 22:05:11 +0200
Subject: [PATCH 08/31] bugfix: remove unused functions; correct for wrong
 formatting (PEP)

---
 PyLoT.py                  |  4 +--
 pylot/core/io/location.py |  4 +--
 pylot/core/util/utils.py  | 72 ++-------------------------------------
 3 files changed, 7 insertions(+), 73 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index ac6ff10c..2c2a2a48 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -72,7 +72,7 @@ from pylot.core.util.errors import DatastructureError, \
     OverwriteError
 from pylot.core.util.connection import checkurl
 from pylot.core.util.dataprocessing import Metadata, restitute_data
-from pylot.core.util.utils import fnConstructor, getLogin, \
+from pylot.core.util.utils import fnConstructor, get_login, \
     full_range, readFilterInformation, pick_color_plt, \
     pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
     transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
@@ -196,7 +196,7 @@ class MainWindow(QMainWindow):
                 if settings.value("user/FullName", None) is None:
                     fulluser = QInputDialog.getText(self, "Enter Name:", "Full name")
                     settings.setValue("user/FullName", fulluser)
-                    settings.setValue("user/Login", getLogin())
+                    settings.setValue("user/Login", get_login())
                 if settings.value("agency_id", None) is None:
                     agency = QInputDialog.getText(self,
                                                   "Enter authority/institution name:",
diff --git a/pylot/core/io/location.py b/pylot/core/io/location.py
index 0fc5130d..3ef79519 100644
--- a/pylot/core/io/location.py
+++ b/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, get_hash
+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,
diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 5807a856..50d7b867 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -87,25 +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
@@ -501,10 +482,10 @@ def get_hash(time):
     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
@@ -885,21 +866,6 @@ def transform_colors_mpl(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
@@ -1174,38 +1140,6 @@ 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
-- 
2.45.2


From 0fb0b0f11cf044263f29a2f56d6310a311e8dedd Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Fri, 7 Jun 2024 13:07:42 +0200
Subject: [PATCH 09/31] [bugfix] re-implement ability of get_bool to return
 unidentifiable input

---
 pylot/core/util/utils.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index 50d7b867..ffd9a077 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -333,7 +333,7 @@ def get_none(value):
 
 def get_bool(value):
     """
-    Convert string representations of bools to their true boolean value
+    Convert string representations of bools to their true boolean value. Return value if it cannot be identified as bool.
     :param value:
     :type value: str, bool, int, float
     :return: true boolean value
@@ -355,6 +355,8 @@ def get_bool(value):
     False
     >>> get_bool(-0.3)
     False
+    >>> get_bool(None)
+    None
     """
     if type(value) == bool:
         return value
@@ -362,10 +364,13 @@ def get_bool(value):
         return True
     elif value in ['False', 'false']:
         return False
-    elif value > 0. or value > 0:
-        return True
+    elif isinstance(value, float) or isinstance(value, int):
+        if value > 0. or value > 0:
+            return True
+        else:
+            return False
     else:
-        return False
+        return value
 
 
 def four_digits(year):
-- 
2.45.2


From ad62284e0e4feb7bf9a650bbdd64f6536fc92062 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Fri, 7 Jun 2024 13:09:34 +0200
Subject: [PATCH 10/31] [update] improve pickfile selection, give the ability
 to select only specific files

---
 PyLoT.py                   |  11 +-
 pylot/core/util/widgets.py | 318 +++++++++++++++++++++++++++++++++----
 2 files changed, 294 insertions(+), 35 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 2c2a2a48..919780f5 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -1011,13 +1011,12 @@ class MainWindow(QMainWindow):
                                           events=events)
         if not sld.exec_():
             return
-        fext = sld.comboBox.currentText()
-        # fext = '.xml'
+        filenames = sld.getChecked()
         for event in events:
-            filename = get_pylot_eventfile_with_extension(event, fext)
-            if filename:
-                self.load_data(filename, draw=False, event=event, overwrite=True)
-                refresh = True
+            for filename in filenames:
+                if os.path.isfile(filename) and event.pylot_id in filename:
+                    self.load_data(filename, draw=False, event=event, overwrite=True)
+                    refresh = True
         if not refresh:
             return
         if self.get_current_event().pylot_picks:
diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index f3b9d33a..3b0d0105 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -7,6 +7,7 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
+import glob
 import multiprocessing
 import os
 import subprocess
@@ -16,6 +17,7 @@ import traceback
 
 import matplotlib
 import numpy as np
+from pylot.core.io.phases import getQualitiesfromxml
 
 matplotlib.use('QT5Agg')
 
@@ -860,13 +862,26 @@ class WaveformWidgetPG(QtWidgets.QWidget):
     def clearPlotDict(self):
         self.plotdict = dict()
 
-    def plotWFData(self, wfdata, wfsyn=None, title=None, zoomx=None, zoomy=None,
-                   noiselevel=None, scaleddata=False, mapping=True,
-                   component='*', nth_sample=1, iniPick=None, verbosity=0,
-                   method='normal', gain=1.):
+    def plotWFData(self, wfdata, wfsyn=None, title=None, scaleddata=False, mapping=True,
+                   component='*', nth_sample=1, verbosity=0, method='normal', gain=1., shift_syn=0.2):
+        def station_sort(nslc):
+            """Try to sort after station integer in case of a line array (e.g. active seismics)"""
+            try:
+                rval = sorted(nslc, key=lambda x: int(x.split('.')[1]))
+                return rval
+            except ValueError as e:
+                # this is the standard case for seismological stations
+                pass
+            except Exception as e:
+                print(f'Sorting by station integer failed with unknown exception: {e}')
+
+            # fallback to default sorting
+            return sorted(nslc)
+
         if not wfdata:
             print('Nothing to plot.')
             return
+
         self.title = title
         self.clearPlotDict()
         self.wfstart, self.wfend = full_range(wfdata)
@@ -884,14 +899,14 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         else:
             st_select = wfdata
 
-        st_select, gaps = merge_stream(st_select)
+        # st_select, gaps = check_for_gaps_and_merge(st_select) #MP MP commented because probably done twice
 
         # list containing tuples of network, station, channel (for sorting)
         nslc = []
         for trace in st_select:
             nslc.append(
                 trace.get_id())  # (trace.stats.network, trace.stats.station, trace.stats.location trace.stats.channel))
-        nslc.sort()
+        nslc = station_sort(nslc)
         nslc.reverse()
         plots = []
 
@@ -955,7 +970,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         self.ylabel = ''
         self.setXLims([0, self.wfend - self.wfstart])
         self.setYLims([0.5, nmax + 0.5])
-        return plots, gaps
+        return plots
 
     def minMax(self, trace, time_ax):
         '''
@@ -977,7 +992,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         min_ = data.min(axis=1)
         max_ = data.max(axis=1)
         if remaining_samples:
-            extreme_values = np.empty((npixel + 1, 2), dtype=np.float)
+            extreme_values = np.empty((npixel + 1, 2), dtype=float)
             extreme_values[:-1, 0] = min_
             extreme_values[:-1, 1] = max_
             extreme_values[-1, 0] = \
@@ -985,7 +1000,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
             extreme_values[-1, 1] = \
                 trace.data[-remaining_samples:].max()
         else:
-            extreme_values = np.empty((npixel, 2), dtype=np.float)
+            extreme_values = np.empty((npixel, 2), dtype=float)
             extreme_values[:, 0] = min_
             extreme_values[:, 1] = max_
         data = extreme_values.flatten()
@@ -1555,6 +1570,160 @@ class PylotCanvas(FigureCanvas):
         self.draw()
 
 
+class SearchFileByExtensionDialog(QtWidgets.QDialog):
+    def __init__(self, parent=None, label='Text: ', default_text='.xml', events=None):
+        super(SearchFileByExtensionDialog, self).__init__(parent)
+        self.events = events
+        self.filepaths = []
+        self.file_extensions = []
+        self.check_all_state = True
+        self.default_text = default_text
+        self.label = label
+        self.setButtons()
+        self.setupUi()
+        self.connectSignals()
+        self.showPaths()
+        self.refreshSelectionBox()
+        # self.refresh_timer = QTimer(self)
+        # self.refresh_timer.timeout.connect(self.showPaths)
+        # self.refresh_timer.start(10000)
+
+        self.resize(800, 450)
+
+    def setupUi(self):
+        ncol = 4
+        self.main_layout = QtWidgets.QVBoxLayout()
+        self.header_layout = QtWidgets.QHBoxLayout()
+        self.footer_layout = QtWidgets.QHBoxLayout()
+        #
+        self.setLayout(self.main_layout)
+
+        # widgets inside the dialog
+        self.textLabel = QtWidgets.QLabel(self.label)
+        self.comboBox = QtWidgets.QComboBox()
+        self.comboBox.addItem(self.default_text)
+        self.comboBox.setEditable(True)
+
+        # optional search button, currently disabled. List refreshed when text changes
+        self.searchButton = QtWidgets.QPushButton('Search')
+        self.searchButton.setVisible(False)
+
+        # check/uncheck button for table
+        self.checkAllButton = QtWidgets.QPushButton('Check/Uncheck all')
+
+        # table
+        self.tableWidget = QtWidgets.QTableWidget()
+        tableWidget = self.tableWidget
+        tableWidget.setColumnCount(ncol)
+        tableWidget.setRowCount(len(self.events))
+        tableWidget.setHorizontalHeaderLabels(('', 'Event ID', 'Filename', 'Last modified'))
+        tableWidget.setEditTriggers(tableWidget.NoEditTriggers)
+        tableWidget.setSortingEnabled(True)
+        header = tableWidget.horizontalHeader()
+        header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
+        header.setStretchLastSection(True)
+
+        self.statusText = QtWidgets.QLabel()
+
+        self.header_layout.addWidget(self.textLabel)
+        self.header_layout.addWidget(self.comboBox)
+        self.header_layout.addWidget(self.searchButton)
+
+        self.footer_layout.addWidget(self.checkAllButton)
+        self.footer_layout.addWidget(self.statusText)
+        self.footer_layout.setStretch(0, 0)
+
+        self.main_layout.addLayout(self.header_layout)
+        self.main_layout.addWidget(self.tableWidget)
+        self.main_layout.addLayout(self.footer_layout)
+        self.main_layout.addWidget(self._buttonbox)
+
+    def showPaths(self):
+        self.filepaths = []
+        fext = self.comboBox.currentText()
+        self.tableWidget.clearContents()
+        for index, event in enumerate(self.events):
+            filename = get_pylot_eventfile_with_extension(event, fext)
+            pf_selected_item = QtWidgets.QTableWidgetItem()
+            if filename:
+                pf_selected_item.setCheckState(QtCore.Qt.Checked)
+            #check_state = QtCore.Qt.Checked if filename else QtCore.Qt.Unchecked
+            #pf_selected_item.setCheckState(check_state)
+            self.tableWidget.setItem(index, 0, pf_selected_item)
+            self.tableWidget.setItem(index, 1, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
+            if filename:
+                self.filepaths.append(filename)
+                ts = int(os.path.getmtime(filename))
+
+                # create QTableWidgetItems of filepath and last modification time
+                fname_item = QtWidgets.QTableWidgetItem(f'{os.path.split(filename)[-1]}')
+                fname_item.setData(3, filename)
+                ts_item = QtWidgets.QTableWidgetItem(f'{datetime.datetime.fromtimestamp(ts)}')
+                self.tableWidget.setItem(index, 2, fname_item)
+                self.tableWidget.setItem(index, 3, ts_item)
+
+        self.update_status()
+
+    def refreshSelectionBox(self):
+        fext = self.comboBox.currentText()
+        self.file_extensions = [fext]
+
+        for event in self.events:
+            extensions = get_possible_pylot_eventfile_extensions(event, '*.xml')
+            for ext in extensions:
+                if not ext in self.file_extensions:
+                    self.file_extensions.append(ext)
+
+        self.comboBox.clear()
+        for ext in sorted(self.file_extensions):
+            self.comboBox.addItem(ext)
+
+    def setButtons(self):
+        self._buttonbox = QDialogButtonBox(QDialogButtonBox.Ok |
+                                           QDialogButtonBox.Cancel)
+
+    def toggleCheckAll(self):
+        self.check_all_state = not self.check_all_state
+        self.checkAll(self.check_all_state)
+
+    def checkAll(self, state):
+        state = QtCore.Qt.Checked if state else QtCore.Qt.Unchecked
+        for row_ind in range(self.tableWidget.rowCount()):
+            item = self.tableWidget.item(row_ind, 0)
+            item.setCheckState(state)
+
+    def getChecked(self):
+        filepaths = []
+        for row_ind in range(self.tableWidget.rowCount()):
+            item_check = self.tableWidget.item(row_ind, 0)
+            if item_check.checkState() == QtCore.Qt.Checked:
+                item_fname = self.tableWidget.item(row_ind, 2)
+                filepath = item_fname.data(3)
+                filepaths.append(filepath)
+        return filepaths
+
+    def update_status(self, row=None, col=None):
+        if col is not None and col != 0:
+            return
+        filepaths = self.getChecked()
+        if len(filepaths) > 0:
+            status_text = f'Found {len(filepaths)} eventfiles. Do you want to load them?'
+        else:
+            status_text = 'Did not find any files for specified file mask.'
+        self.statusText.setText(status_text)
+
+
+    def connectSignals(self):
+        self._buttonbox.accepted.connect(self.accept)
+        self._buttonbox.rejected.connect(self.reject)
+        self.comboBox.editTextChanged.connect(self.showPaths)
+        self.searchButton.clicked.connect(self.showPaths)
+        self.checkAllButton.clicked.connect(self.toggleCheckAll)
+        self.checkAllButton.clicked.connect(self.update_status)
+        self.tableWidget.cellClicked.connect(self.update_status)
+
+
+
 class SingleTextLineDialog(QtWidgets.QDialog):
     def __init__(self, parent=None, label='Text: ', default_text='.xml'):
         super(SingleTextLineDialog, self).__init__(parent)
@@ -1786,7 +1955,7 @@ class PickDlg(QDialog):
 
         # init expected picks using obspy Taup
         try:
-            if self.metadata and model is not None:
+            if self.metadata and model != "None":
                 self.model = TauPyModel(model)
                 self.get_arrivals()
                 self.drawArrivals()
@@ -2146,7 +2315,7 @@ class PickDlg(QDialog):
 
                 # create action and add to menu
                 # phase name transferred using lambda function
-                slot = lambda phase=phase, phaseID=phaseID: phaseSelect[phaseID](phase)
+                slot = lambda ph=phase, phID=phaseID: phaseSelect[phID](ph)
                 picksAction = createAction(parent=self, text=phase,
                                            slot=slot,
                                            shortcut=shortcut)
@@ -2513,7 +2682,9 @@ class PickDlg(QDialog):
         data.normalize()
         if not data:
             QtWidgets.QMessageBox.warning(self, 'No channel to plot',
-                                          'No channel to plot for phase: {}.'.format(phase))
+                                          'No channel to plot for phase: {}. '
+                                          'Make sure to select the correct channels for P and S '
+                                          'in the menu in the top panel.'.format(phase))
             self.leave_picking_mode()
             return
 
@@ -2653,7 +2824,7 @@ class PickDlg(QDialog):
             minFMSNR = parameter.get('minFMSNR')
             quality = get_quality_class(spe, parameter.get('timeerrorsP'))
             if quality <= minFMweight and snr >= minFMSNR:
-                FM = fmpicker(self.getWFData().select(channel=channel), wfdata, parameter.get('fmpickwin'),
+                FM = fmpicker(self.getWFData().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
                               pick - stime_diff)
 
         # save pick times for actual phase
@@ -3566,8 +3737,9 @@ class TuneAutopicker(QWidget):
             # wfdat = remove_underscores(wfdat)
             # rotate misaligned stations to ZNE
             # check for gaps and doubled channels
-            wfdat, gaps = merge_stream(wfdat)
-            # check4gaps(wfdat)
+            wfdat, _ = check_for_gaps_and_merge(wfdat)
+            # check for nans
+            check_for_nan(wfdat)
             check4doubled(wfdat)
             wfdat = check4rotated(wfdat, self.parent().metadata, verbosity=0)
             # trim station components to same start value
@@ -3611,14 +3783,14 @@ class TuneAutopicker(QWidget):
         self.listWidget.scrollToBottom()
 
     def get_current_event(self):
-        path = self.eventBox.currentText()
+        path = self.get_current_event_fp()
         return self.parent().project.getEventFromPath(path)
 
     def get_current_event_name(self):
-        return self.eventBox.currentText().split('/')[-1].split('*')[0]
+        return self.eventBox.currentText().split('/')[-1].rstrip('*')
 
     def get_current_event_fp(self):
-        return self.eventBox.currentText().split('*')[0]
+        return self.eventBox.currentText().rstrip('*')
 
     def get_current_event_picks(self, station):
         event = self.get_current_event()
@@ -3722,6 +3894,7 @@ class TuneAutopicker(QWidget):
         st = self.data.getWFData()
         tr = st.select(station=self.get_current_station())[0]
         starttime = tr.stats.starttime
+        # create two lists with figure names and subindices (for subplots) to get the correct axes
         p_axes = [
             ('mainFig', 0),
             ('aicFig', 0),
@@ -5663,9 +5836,23 @@ class ChooseWaveFormWindow(QWidget):
     def submit(self):
         matplotlib.pyplot.close(self.currentSpectro)
         t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        self.currentSpectro = self.traces[
-            self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
-        self.currentSpectro.show()
+        #self.currentSpectro = self.traces[
+        #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
+        #self.currentSpectro.show()
+        self.applyFFT()
+
+    def applyFFT(self, trace):
+        tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']
+        transformed = abs(np.fft.rfft(tra.data))
+        print ( transformed )
+        matplotlib.pyplot.plot ( transformed )
+        matplotlib.pyplot.show()
+
+    def applyFFTs(self, tra):
+        transformed = abs(np.fft.rfft(tra.data))
+        print ( transformed )
+        matplotlib.pyplot.plot ( transformed )
+        matplotlib.pyplot.show()
 
     def submitN(self):
         matplotlib.pyplot.close(self.currentSpectro)
@@ -5681,13 +5868,6 @@ class ChooseWaveFormWindow(QWidget):
             self.chooseBoxTraces.currentText()[3:]]['E'].spectrogram(show=False, title=t)
         self.currentSpectro.show()
 
-    def submitZ(self):
-        matplotlib.pyplot.close(self.currentSpectro)
-        t = self.chooseBoxTraces.currentText() + " " + self.chooseBoxComponent.currentText()
-        self.currentSpectro = self.traces[
-            self.chooseBoxTraces.currentText()[3:]]['Z'].spectrogram(show=False, title=t)
-        self.currentSpectro.show()
-
     # Creates a QComboBox and adds all traces provided
     def createComboBoxTraces(self):
         if len(self.wFs) <= 0:
@@ -5714,7 +5894,87 @@ class ChooseWaveFormWindow(QWidget):
         pass
 
 
+class SpectrogramTab(QWidget):
+    def __init__(self, traces, wfdata, parent=None):
+        super(SpectrogramTab, self).__init__(parent)
+        self.setupUi()
+        self.traces = traces
+        self.wfdata = wfdata
+
+    def setupUi(self):
+        pass
+    def makeSpecFig(self, direction = 'Z', height = 0, width = 0, parent = None):
+
+        i = 0
+        grams = []
+        figure, axis = matplotlib.pyplot.subplots(len(self.traces), sharex=True)
+
+        start, end = full_range(self.wfdata)
+
+        if height != 0 and width != 0:
+            figure.figsize = (width, height)
+            figure.set_figwidth = width
+            figure.set_figheight = height
+
+        #figure.tight_layout()
+
+        for t in self.traces:
+            tra = self.traces[t][direction]
+            #print(start, end)
+
+            # Set Title
+            if i == 0:
+                if direction == 'Z':
+                    figure.suptitle("section: vertical components")
+                elif direction == 'E':
+                    figure.suptitle("section: east-west components")
+                elif direction == 'N':
+                    figure.suptitle("section: north-south components")
+                axis[i].vlines(0, axis[i].get_ylim()[0], axis[i].get_ylim()[1],
+                          colors='m', linestyles='dashed',
+                          linewidth=2)
+
+            # Different axis settings for visual improvements
+            # axis[i].set_xlim(left=0, right=end - start)
+            # axis[i].spines['top'].set_visible(False)
+            # axis[i].spines['right'].set_visible(False)
+            # # axis[i].spines['left'].set_visible(False)
+
+            # axis[i].tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
+            # if not (len(self.traces) == i - 1):
+                # axis[i].spines['bottom'].set_visible(False)
+            # axis[i].set_yticks([])
+            # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
+
+            #ax.axhline(n, color="0.5", lw=0.5)
+
+
+            grams.append(tra.spectrogram(show=False, axes=axis[i]))
+            i+=1
+
+        #figure.setXLims([0, end - start])
+        figure.set_tight_layout(True)
+        fC = FigureCanvas(figure)
+        return fC
+
+    #for t in self.traces:
+       # tra = self.traces[t]['Z']
+       # transformed = abs(np.fft.rfft(tra.data))
+       # axis[i].plot(transformed, label=t)
+       # # axis[i].tick_params(labelbottom=False)
+       # axis[i].spines['top'].set_visible(False)
+       # axis[i].spines['right'].set_visible(False)
+       # axis[i].spines['left'].set_visible(False)
+       # if not (len(self.traces) == i - 1):
+       #     axis[i].spines['bottom'].set_visible(False)
+       # axis[i].set_yticks([])
+       # axis[i].set_ylabel(t, loc='center', rotation='horizontal')
+       # # axis[i].axis('off')
+       # i += 1
+       # # self.applyFFTs(t)
+
+
 if __name__ == '__main__':
     import doctest
 
-    doctest.testmod()
\ No newline at end of file
+    doctest.testmod()
-- 
2.45.2


From 356988e71dce873af781d5b7334c58235ed438a9 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Fri, 7 Jun 2024 14:32:57 +0200
Subject: [PATCH 11/31] [update] further improved Pickfile selection dialog,
 now providing methods "overwrite" or "merge"

---
 PyLoT.py                   | 16 ++++++++++------
 pylot/core/util/widgets.py | 36 +++++++++++++++++++++++++++---------
 2 files changed, 37 insertions(+), 15 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 919780f5..8762abda 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -1011,11 +1011,12 @@ class MainWindow(QMainWindow):
                                           events=events)
         if not sld.exec_():
             return
+
         filenames = sld.getChecked()
         for event in events:
             for filename in filenames:
                 if os.path.isfile(filename) and event.pylot_id in filename:
-                    self.load_data(filename, draw=False, event=event, overwrite=True)
+                    self.load_data(filename, draw=False, event=event, ask_user=True, merge_strategy=sld.merge_strategy)
                     refresh = True
         if not refresh:
             return
@@ -1024,8 +1025,8 @@ class MainWindow(QMainWindow):
         self.fill_eventbox()
         self.setDirty(True)
 
-    def load_data(self, fname=None, loc=False, draw=True, event=None, overwrite=False):
-        if not overwrite:
+    def load_data(self, fname=None, loc=False, draw=True, event=None, ask_user=False, merge_strategy='Overwrite'):
+        if not ask_user:
             if not self.okToContinue():
                 return
         if fname is None:
@@ -1039,9 +1040,12 @@ class MainWindow(QMainWindow):
         data = Data(self, event)
         try:
             data_new = Data(self, evtdata=str(fname))
-            # MP MP commented because adding several picks might cause inconsistencies
-            data = data_new
-            # data += data_new
+            if merge_strategy == 'Overwrite':
+                data = data_new
+            elif merge_strategy == 'Merge':
+                data += data_new
+            else:
+                raise NotImplementedError(f'Unknown merge strategy: {merge_strategy}')
         except ValueError:
             qmb = QMessageBox(self, icon=QMessageBox.Question,
                               text='Warning: Missmatch in event identifiers {} and {}. Continue?'.format(
diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index 3b0d0105..77d6ebf5 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -1577,6 +1577,7 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.filepaths = []
         self.file_extensions = []
         self.check_all_state = True
+        self.merge_strategy = None
         self.default_text = default_text
         self.label = label
         self.setButtons()
@@ -1611,6 +1612,15 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         # check/uncheck button for table
         self.checkAllButton = QtWidgets.QPushButton('Check/Uncheck all')
 
+        # radiobutton for merge selection
+        self.mergeRadioButtonGroup = QtWidgets.QButtonGroup()
+        self.merge_button = QtWidgets.QRadioButton('Merge')
+        self.overwrite_button = QtWidgets.QRadioButton('Overwrite')
+        self.mergeRadioButtonGroup.addButton(self.merge_button)
+        self.mergeRadioButtonGroup.addButton(self.overwrite_button)
+        self.merge_button.setChecked(True)
+        self.merge_strategy = self.merge_button.text()
+
         # table
         self.tableWidget = QtWidgets.QTableWidget()
         tableWidget = self.tableWidget
@@ -1631,7 +1641,11 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
 
         self.footer_layout.addWidget(self.checkAllButton)
         self.footer_layout.addWidget(self.statusText)
+        self.footer_layout.addWidget(self.merge_button)
+        self.footer_layout.addWidget(self.overwrite_button)
+
         self.footer_layout.setStretch(0, 0)
+        self.footer_layout.setStretch(1, 1)
 
         self.main_layout.addLayout(self.header_layout)
         self.main_layout.addWidget(self.tableWidget)
@@ -1645,10 +1659,8 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         for index, event in enumerate(self.events):
             filename = get_pylot_eventfile_with_extension(event, fext)
             pf_selected_item = QtWidgets.QTableWidgetItem()
-            if filename:
-                pf_selected_item.setCheckState(QtCore.Qt.Checked)
-            #check_state = QtCore.Qt.Checked if filename else QtCore.Qt.Unchecked
-            #pf_selected_item.setCheckState(check_state)
+            check_state = QtCore.Qt.Checked if filename else QtCore.Qt.Unchecked
+            pf_selected_item.setCheckState(check_state)
             self.tableWidget.setItem(index, 0, pf_selected_item)
             self.tableWidget.setItem(index, 1, QtWidgets.QTableWidgetItem(f'{event.pylot_id}'))
             if filename:
@@ -1698,8 +1710,9 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
             item_check = self.tableWidget.item(row_ind, 0)
             if item_check.checkState() == QtCore.Qt.Checked:
                 item_fname = self.tableWidget.item(row_ind, 2)
-                filepath = item_fname.data(3)
-                filepaths.append(filepath)
+                if item_fname:
+                    filepath = item_fname.data(3)
+                    filepaths.append(filepath)
         return filepaths
 
     def update_status(self, row=None, col=None):
@@ -1707,11 +1720,15 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
             return
         filepaths = self.getChecked()
         if len(filepaths) > 0:
-            status_text = f'Found {len(filepaths)} eventfiles. Do you want to load them?'
+            status_text = f"Found {len(filepaths)} eventfile{'s' if len(filepaths) > 1 else ''}. Do you want to load them?"
         else:
-            status_text = 'Did not find any files for specified file mask.'
+            status_text = 'Did not find/select any files for specified file mask.'
         self.statusText.setText(status_text)
 
+    def update_merge_strategy(self):
+        for button in (self.merge_button, self.overwrite_button):
+            if button.isChecked():
+                self.merge_strategy = button.text()
 
     def connectSignals(self):
         self._buttonbox.accepted.connect(self.accept)
@@ -1721,7 +1738,8 @@ class SearchFileByExtensionDialog(QtWidgets.QDialog):
         self.checkAllButton.clicked.connect(self.toggleCheckAll)
         self.checkAllButton.clicked.connect(self.update_status)
         self.tableWidget.cellClicked.connect(self.update_status)
-
+        self.merge_button.clicked.connect(self.update_merge_strategy)
+        self.overwrite_button.clicked.connect(self.update_merge_strategy)
 
 
 class SingleTextLineDialog(QtWidgets.QDialog):
-- 
2.45.2


From c021ca19d78a646668dbc74d8ce1901bd11328b4 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Fri, 7 Jun 2024 14:34:27 +0200
Subject: [PATCH 12/31] [minor] switch default cmap for array_map to 'viridis'

---
 pylot/core/util/array_map.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pylot/core/util/array_map.py b/pylot/core/util/array_map.py
index 3407ba8a..0c5dcb5d 100644
--- a/pylot/core/util/array_map.py
+++ b/pylot/core/util/array_map.py
@@ -124,8 +124,8 @@ class Array_map(QtWidgets.QWidget):
         self.cmaps_box = QtWidgets.QComboBox()
         self.cmaps_box.setMaxVisibleItems(20)
         [self.cmaps_box.addItem(map_name) for map_name in sorted(plt.colormaps())]
-        # try to set to hsv as default
-        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)
-- 
2.45.2


From db976e5ea9ac886ec5c32c658cab30698ddc88dd Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Fri, 7 Jun 2024 15:01:36 +0200
Subject: [PATCH 13/31] [bugfix] removing redundancy and wrong bullsh..
 try-except code

---
 PyLoT.py                |  9 +++------
 autoPyLoT.py            | 10 +++-------
 pylot/core/io/data.py   | 11 +++++------
 pylot/core/io/phases.py | 36 +++++++++++++++++-------------------
 4 files changed, 28 insertions(+), 38 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 8762abda..0c07a316 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -25,6 +25,7 @@ https://www.iconfinder.com/iconsets/flavour
 
 import argparse
 import json
+import logging
 import os
 import platform
 import shutil
@@ -113,11 +114,7 @@ class MainWindow(QMainWindow):
     def __init__(self, parent=None, infile=None, reset_qsettings=False):
         super(MainWindow, self).__init__(parent)
 
-        # check for default pylot.in-file
-        if not infile:
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-        if os.path.isfile(infile) is False:
+        if infile and os.path.isfile(infile) is False:
             infile = QFileDialog().getOpenFileName(caption='Choose PyLoT-input file')[0]
 
             if not os.path.exists(infile):
@@ -253,7 +250,7 @@ class MainWindow(QMainWindow):
             self._inputs.reset_defaults()
             # check for default pylot.in-file
             infile = os.path.join(pylot_config_dir, '.pylot.in')
-            print('Using default input file {}'.format(infile))
+            logging.warning('Using default input file {}'.format(infile))
             self._inputs.export2File(infile)
         self.infile = infile
 
diff --git a/autoPyLoT.py b/autoPyLoT.py
index 0a801286..506025c5 100755
--- a/autoPyLoT.py
+++ b/autoPyLoT.py
@@ -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)))
diff --git a/pylot/core/io/data.py b/pylot/core/io/data.py
index b085d181..16107ace 100644
--- a/pylot/core/io/data.py
+++ b/pylot/core/io/data.py
@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import copy
+import logging
 import os
 
 from PySide2.QtWidgets import QMessageBox
@@ -408,18 +409,16 @@ class Data(object):
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '_focmec.in':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                     focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
                                      not implemented: {1}'''.format(evtformat, e))
             if fnext == '.pha':
                 try:
-                    infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-                    print('Using default input file {}'.format(infile))
-                    parameter = PylotParameter(infile)
+                    parameter = PylotParameter()
+                    logging.warning('Using default input parameter')
                     hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
                 except KeyError as e:
                     raise KeyError('''{0} export format
diff --git a/pylot/core/io/phases.py b/pylot/core/io/phases.py
index 34dd1677..3c50d131 100644
--- a/pylot/core/io/phases.py
+++ b/pylot/core/io/phases.py
@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 import glob
+import logging
 import os
 import warnings
 
@@ -217,7 +218,7 @@ def picksdict_from_obs(fn):
     return picks
 
 
-def picksdict_from_picks(evt):
+def picksdict_from_picks(evt, parameter=None):
     """
     Takes an Event object and return the pick dictionary commonly used within
     PyLoT
@@ -230,6 +231,7 @@ def picksdict_from_picks(evt):
         'auto': {}
     }
     for pick in evt.picks:
+        errors = None
         phase = {}
         station = pick.waveform_id.station_code
         if pick.waveform_id.channel_code is None:
@@ -273,32 +275,28 @@ def picksdict_from_picks(evt):
         phase['epp'] = epp
         phase['lpp'] = lpp
         phase['spe'] = spe
-        try:
-            phase['weight'] = weight
-        except:
-            # get onset weight from uncertainty
-            infile = os.path.join(os.path.expanduser('~'), '.pylot', 'pylot.in')
-            print('Using default input file {}'.format(infile))
-            parameter = PylotParameter(infile)
+        weight = phase.get('weight')
+        if not weight:
+            if not parameter:
+                logging.warning('Using ')
+                logging.warning('Using default input parameter')
+                parameter = PylotParameter()
             pick.phase_hint = identifyPhase(pick.phase_hint)
             if pick.phase_hint == 'P':
                 errors = parameter['timeerrorsP']
             elif pick.phase_hint == 'S':
                 errors = parameter['timeerrorsS']
-            weight = get_quality_class(spe, errors)
-            phase['weight'] = weight
+            if errors:
+                weight = get_quality_class(spe, errors)
+                phase['weight'] = weight
         phase['channel'] = channel
         phase['network'] = network
         phase['picker'] = pick_method
-        try:
-            if pick.polarity == 'positive':
-                phase['fm'] = 'U'
-            elif pick.polarity == 'negative':
-                phase['fm'] = 'D'
-            else:
-                phase['fm'] = 'N'
-        except:
-            print("No FM info available!")
+        if pick.polarity == 'positive':
+            phase['fm'] = 'U'
+        elif pick.polarity == 'negative':
+            phase['fm'] = 'D'
+        else:
             phase['fm'] = 'N'
         phase['filter_id'] = filter_id if filter_id is not None else ''
 
-- 
2.45.2


From 0a5f5f08175736b53c4caa369e5e67be3c530bb6 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Fri, 7 Jun 2024 15:56:05 +0200
Subject: [PATCH 14/31] [minor] removed unneeded imports

---
 PyLoT.py                 | 21 +++++++++++++++++----
 pylot/core/util/utils.py |  4 ++--
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 0c07a316..739b7100 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -493,7 +493,6 @@ class MainWindow(QMainWindow):
                                                       icon=eventlist_xml_icon,
                                                       tip='Create an Eventlist from a XML File')
         self.eventlist_xml_action.setEnabled(False)
-
         printAction = self.createAction(self, "&Print event ...",
                                         self.show_event_information, QKeySequence.Print,
                                         print_icon,
@@ -1404,6 +1403,8 @@ class MainWindow(QMainWindow):
 
         for id, event in enumerate(self.project.eventlist):
             event_path = event.path
+            #phaseErrors = {'P': self._inputs['timeerrorsP'],
+            #               'S': self._inputs['timeerrorsS']}
 
             man_au_picks = {'manual': event.pylot_picks,
                             'auto': event.pylot_autopicks}
@@ -1472,6 +1473,7 @@ class MainWindow(QMainWindow):
 
             for picktype, item_np in [('manual', item_nmp), ('auto', item_nap)]:
                 npicks_str = f"{npicks[picktype]['P']}|{npicks[picktype]['S']}"
+                #npicks_str += f"({npicks_total[picktype]['P']}/{npicks_total[picktype]['S']})"
                 item_np.setText(npicks_str)
 
             item_ref = QStandardItem()  # str(event_ref))
@@ -1716,6 +1718,8 @@ class MainWindow(QMainWindow):
             for tr in self.get_data().wfdata.select(component=ch).traces:
                 traces[tr.stats.station][ch] = tr
 
+        names.sort()
+        a = self.get_current_event()
 
         print (self.get_data().wfdata.traces[0])
 
@@ -1725,6 +1729,14 @@ class MainWindow(QMainWindow):
         self.tabs.setCurrentIndex(3)
         figCanvas = test.makeSpecFig(direction=self.dispComponent, height = height, width = width, parent = self.tabs.widget)
         return figCanvas
+        #self.spectro_layout.addWidget()
+        # self.get_data().wfdata.spectrogram()
+        # self.tabs.addTab(figCanvas, 'Spectrogram')
+        # self.tabs[3] = figCanvas
+        # self.refreshTabs()
+        # test.show()
+
+
 
     def compareMulti(self):
         if not self.compareoptions:
@@ -1884,6 +1896,7 @@ class MainWindow(QMainWindow):
         # which will read in data input twice. Therefore current tab is changed to 0
         # in loadProject before calling this function.
         self.fill_eventbox()
+        #print(f'{self.get_current_event()=}')
         plotted = False
         if self.tabs.currentIndex() == 2:
             self.init_event_table()
@@ -1977,8 +1990,8 @@ class MainWindow(QMainWindow):
 
         if len(curr_event.origins) > 0:
             origin_time = curr_event.origins[0].time
-            tstart = settings.value('tstart') if get_None(settings.value('tstart')) else 0
-            tstop = settings.value('tstop') if get_None(settings.value('tstop')) else 0
+            tstart = settings.value('tstart') if get_none(settings.value('tstart')) else 0
+            tstop = settings.value('tstop') if get_none(settings.value('tstop')) else 0
             tstart = origin_time + float(tstart)
             tstop = origin_time + float(tstop)
         else:
@@ -2293,7 +2306,7 @@ class MainWindow(QMainWindow):
         # wfst += self.get_data().getWFData().select(component=alter_comp)
         plotWidget = self.getPlotWidget()
         self.adjustPlotHeight()
-        if get_bool(settings.value('large_dataset')):
+        if get_bool(settings.value('large_dataset')) == True:
             self.plot_method = 'fast'
         else:
             self.plot_method = 'normal'
diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index ffd9a077..ff85a0ef 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -1084,7 +1084,7 @@ def check4rotated(data, metadata=None, verbosity=1):
         # 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):
-            print(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            logging.debug(f"Stream does not need any rotation: Traces are {trace_ids=}")
             return wfs_in
 
         # check metadata quality
@@ -1096,7 +1096,7 @@ def check4rotated(data, metadata=None, verbosity=1):
                 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:
-            print(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
+            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:
-- 
2.45.2


From d02f74ab1016727c49285a68667b5f526a8c8c57 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Wed, 12 Jun 2024 13:44:02 +0200
Subject: [PATCH 15/31] [bugfix] added missing Parameter object in call for
 picksdict_from_picks

---
 PyLoT.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/PyLoT.py b/PyLoT.py
index 739b7100..71ca3cea 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -2999,10 +2999,16 @@ class MainWindow(QMainWindow):
             event = self.get_current_event()
         event.pylot_picks = {}
         event.pylot_autopicks = {}
-        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data())
+        picksdict = picksdict_from_picks(evt=self.get_data().get_evt_data(), parameter=self.getParameter())
         event.addPicks(picksdict['manual'])
         event.addAutopicks(picksdict['auto'])
 
+    def getParameter(self):
+        if hasattr(self.project, 'parameter') and isinstance(self.project.parameter, PylotParameter):
+            return self.project.parameter
+        else:
+            return self._inputs
+
     def drawPicks(self, station=None, picktype=None, stime=None):
         # if picktype not specified, draw both
         if not stime:
-- 
2.45.2


From 7393201b90972f9e8987a04a71f679d22e3edaa5 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Wed, 12 Jun 2024 16:11:53 +0200
Subject: [PATCH 16/31] [minor] inform if station coordinates were not found in
 metadata

---
 pylot/core/util/widgets.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index 77d6ebf5..9136b1d4 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -2218,10 +2218,12 @@ class PickDlg(QDialog):
         station_id = trace.get_id()
         starttime = trace.stats.starttime
         station_coords = self.metadata.get_coordinates(station_id, starttime)
+        if not station_coords:
+            print('get_arrivals: No station coordinates found. Return!')
+            return
         origins = self.pylot_event.origins
         if phases == ['None', 'None']:
-            print("get_arrivals: Creation info (manual or auto) not available!")
-            print("Return!")
+            print("get_arrivals: Creation info (manual or auto) not available! Return!")
             return
         if origins:
             source_origin = origins[0]
-- 
2.45.2


From 70d5c2d621d210e1d263fc1b79ae259e898b3f71 Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Tue, 30 Jan 2024 17:00:42 +0100
Subject: [PATCH 17/31] [minor] mpl.figure.canvas.draw -> draw_idle

---
 pylot/core/util/widgets.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index 9136b1d4..988b3aa2 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -1150,12 +1150,12 @@ class PylotCanvas(FigureCanvas):
         ax.set_xlim(self.cur_xlim)
         ax.set_ylim(self.cur_ylim)
         self.refreshPickDlgText()
-        ax.figure.canvas.draw()
+        ax.figure.canvas.draw_idle()
 
     def panRelease(self, gui_event):
         self.press = None
         self.press_rel = None
-        self.figure.canvas.draw()
+        self.figure.canvas.draw_idle()
 
     def panZoom(self, gui_event, threshold=2., factor=1.1):
         if not gui_event.x and not gui_event.y:
@@ -3947,7 +3947,7 @@ class TuneAutopicker(QWidget):
             self.plot_manual_pick_to_ax(ax=ax, picks=picks, phase='S',
                                         starttime=starttime, quality=qualitySpick)
         for canvas in self.parent().canvas_dict.values():
-            canvas.draw()
+            canvas.draw_idle()
 
     def plot_manual_pick_to_ax(self, ax, picks, phase, starttime, quality):
         mpp = picks[phase]['mpp'] - starttime
-- 
2.45.2


From 6b7f297d7a439ebece458df07e42ec8b8967202c Mon Sep 17 00:00:00 2001
From: Marcel <marcel.paffrath@rub.de>
Date: Tue, 30 Jan 2024 17:01:56 +0100
Subject: [PATCH 18/31] [update] adding possibility to display other waveform
 data (e.g. denoised/synthetic) together with genuine data for comparison

---
 PyLoT.py                     | 38 ++++++++++++++++++++++++------------
 pylot/core/io/data.py        | 29 ++++++++++++++-------------
 pylot/core/util/array_map.py | 10 ++++++----
 3 files changed, 47 insertions(+), 30 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 71ca3cea..1624aaaa 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -178,6 +178,7 @@ class MainWindow(QMainWindow):
         self.autodata = Data(self)
 
         self.fnames = None
+        self.fnames_comp = None
         self._stime = None
 
         # track deleted picks for logging
@@ -1129,16 +1130,19 @@ class MainWindow(QMainWindow):
             else:
                 return
 
-    def getWFFnames_from_eventbox(self, eventbox=None):
+    def getWFFnames_from_eventbox(self, eventbox: str = None, subpath: str = None) -> list:
         '''
         Return waveform filenames from event in eventbox.
         '''
         # TODO: add dataStructure class for obspyDMT here, this is just a workaround!
         eventpath = self.get_current_event_path(eventbox)
-        basepath = eventpath.split(os.path.basename(eventpath))[0]
+        if subpath:
+            eventpath = os.path.join(eventpath, subpath)
+        if not os.path.isdir(eventpath):
+            return []
         if self.dataStructure:
             if not eventpath:
-                return
+                return []
             fnames = [os.path.join(eventpath, f) for f in os.listdir(eventpath)]
         else:
             raise DatastructureError('not specified')
@@ -1960,13 +1964,20 @@ class MainWindow(QMainWindow):
 
     def prepareLoadWaveformData(self):
         self.fnames = self.getWFFnames_from_eventbox()
-        self.fnames_syn = []
+        self.fnames_comp = []
+        fnames_comp = self.getWFFnames_from_eventbox(subpath='compare')
+        self.dataPlot.activateCompareOptions(bool(fnames_comp))
+        if fnames_comp:
+            if self.dataPlot.comp_checkbox.isChecked():
+                self.fnames_comp = fnames_comp
+
         eventpath = self.get_current_event_path()
         basepath = eventpath.split(os.path.basename(eventpath))[0]
         self.obspy_dmt = check_obspydmt_structure(basepath)
         self.dataPlot.activateObspyDMToptions(self.obspy_dmt)
         if self.obspy_dmt:
             self.prepareObspyDMT_data(eventpath)
+            self.dataPlot.activateCompareOptions(True)
 
     def loadWaveformData(self):
         '''
@@ -1999,7 +2010,7 @@ class MainWindow(QMainWindow):
             tstop = None
 
         self.data.setWFData(self.fnames,
-                            self.fnames_syn,
+                            self.fnames_comp,
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
@@ -2007,7 +2018,7 @@ class MainWindow(QMainWindow):
 
     def prepareObspyDMT_data(self, eventpath):
         qcbox_processed = self.dataPlot.qcombo_processed
-        qcheckb_syn = self.dataPlot.syn_checkbox
+        qcheckb_syn = self.dataPlot.comp_checkbox
         qcbox_processed.setEnabled(False)
         qcheckb_syn.setEnabled(False)
         for fpath in os.listdir(eventpath):
@@ -2015,8 +2026,8 @@ class MainWindow(QMainWindow):
             if 'syngine' in fpath:
                 eventpath_syn = os.path.join(eventpath, fpath)
                 qcheckb_syn.setEnabled(True)
-                if self.dataPlot.syn_checkbox.isChecked():
-                    self.fnames_syn = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
+                if self.dataPlot.comp_checkbox.isChecked():
+                    self.fnames_comp = [os.path.join(eventpath_syn, filename) for filename in os.listdir(eventpath_syn)]
             if 'processed' in fpath:
                 qcbox_processed.setEnabled(True)
         if qcbox_processed.isEnabled():
@@ -2297,7 +2308,7 @@ class MainWindow(QMainWindow):
         comp = self.getComponent()
         title = 'section: {0} components'.format(zne_text[comp])
         wfst = self.get_data().getWFData()
-        wfsyn = self.get_data().getSynWFData()
+        wfsyn = self.get_data().getAltWFdata()
         if self.filterActionP.isChecked() and filter:
             self.filterWaveformData(plot=False, phase='P')
         elif self.filterActionS.isChecked() and filter:
@@ -2609,18 +2620,21 @@ class MainWindow(QMainWindow):
             print("Warning! No network, station, and location info available!")
             return
         self.update_status('picking on station {0}'.format(station))
-        data = self.get_data().getOriginalWFData().copy()
+        wfdata = self.get_data().getOriginalWFData().copy()
+        wfdata_comp = self.get_data().getAltWFdata().copy()
         event = self.get_current_event()
         wftype = self.dataPlot.qcombo_processed.currentText() if self.obspy_dmt else None
         pickDlg = PickDlg(self, parameter=self._inputs,
-                          data=data.select(station=station),
+                          data=wfdata.select(station=station),
+                          data_compare=wfdata_comp.select(station=station),
                           station=station, network=network,
                           location=location,
                           picks=self.getPicksOnStation(station, 'manual'),
                           autopicks=self.getPicksOnStation(station, 'auto'),
                           metadata=self.metadata, event=event,
                           model=self.inputs.get('taup_model'),
-                          filteroptions=self.filteroptions, wftype=wftype)
+                          filteroptions=self.filteroptions, wftype=wftype,
+                          show_comp_data=self.dataPlot.comp_checkbox.isChecked())
         if self.filterActionP.isChecked():
             pickDlg.currentPhase = "P"
             pickDlg.filterWFData()
diff --git a/pylot/core/io/data.py b/pylot/core/io/data.py
index 16107ace..13eb9fb6 100644
--- a/pylot/core/io/data.py
+++ b/pylot/core/io/data.py
@@ -450,10 +450,11 @@ class Data(object):
         data.filter(**kwargs)
         self.dirty = True
 
-    def setWFData(self, fnames, fnames_syn=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
+    def setWFData(self, fnames, fnames_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
         """
         Clear current waveform data and set given waveform data
         :param fnames: waveform data names to append
+        :param fnames_alt: alternative data to show (e.g. synthetic/processed)
         :type fnames: list
         """
         def check_fname_exists(filenames: list) -> list:
@@ -463,14 +464,14 @@ class Data(object):
 
         self.wfdata = Stream()
         self.wforiginal = None
-        self.wfsyn = Stream()
+        self.wf_alt = Stream()
         if tstart == tstop:
             tstart = tstop = None
         self.tstart = tstart
         self.tstop = tstop
 
         fnames = check_fname_exists(fnames)
-        fnames_syn = check_fname_exists(fnames_syn)
+        fnames_alt = check_fname_exists(fnames_alt)
         # if obspy_dmt:
         #     wfdir = 'raw'
         #     self.processed = False
@@ -488,8 +489,8 @@ class Data(object):
         #     wffnames = fnames
         if fnames is not None:
             self.appendWFData(fnames)
-            if fnames_syn is not None:
-                self.appendWFData(fnames_syn, synthetic=True)
+            if fnames_alt is not None:
+                self.appendWFData(fnames_alt, alternative=True)
         else:
             return False
 
@@ -511,7 +512,7 @@ class Data(object):
         self.dirty = False
         return True
 
-    def appendWFData(self, fnames, synthetic=False):
+    def appendWFData(self, fnames, alternative=False):
         """
         Read waveform data from fnames and append it to current wf data
         :param fnames: waveform data to append
@@ -524,20 +525,20 @@ class Data(object):
         if self.dirty:
             self.resetWFData()
 
-        real_or_syn_data = {True: self.wfsyn,
-                            False: self.wfdata}
+        orig_or_alternative_data = {True: self.wf_alt,
+                                    False: self.wfdata}
 
         warnmsg = ''
         for fname in set(fnames):
             try:
-                real_or_syn_data[synthetic] += read(fname, starttime=self.tstart, endtime=self.tstop)
+                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
             except TypeError:
                 try:
-                    real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
+                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                 except Exception as e:
                     try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
-                                                            endtime=self.tstop)
+                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
+                                                                      endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
             except SacIOError as se:
@@ -552,8 +553,8 @@ class Data(object):
     def getOriginalWFData(self):
         return self.wforiginal
 
-    def getSynWFData(self):
-        return self.wfsyn
+    def getAltWFdata(self):
+        return self.wf_alt
 
     def resetWFData(self):
         """
diff --git a/pylot/core/util/array_map.py b/pylot/core/util/array_map.py
index 0c5dcb5d..afc00eaf 100644
--- a/pylot/core/util/array_map.py
+++ b/pylot/core/util/array_map.py
@@ -474,17 +474,19 @@ class Array_map(QtWidgets.QWidget):
                                                                   transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        data = self._parent.get_data().getWFData()
+        wfdata = self._parent.get_data().getWFData()
+        wfdata_comp = self._parent.get_data().getWFDataComp()
         for index in ind:
             network, station = self._station_onpick_ids[index].split('.')[:2]
             pyl_mw = self._parent
             try:
-                data = data.select(station=station)
-                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,
-- 
2.45.2


From 8eb958c91b28be2a448156f328797616bed5eb71 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Tue, 16 Jul 2024 12:08:00 +0200
Subject: [PATCH 19/31] change: add docu and test case

---
 pylot/core/util/utils.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pylot/core/util/utils.py b/pylot/core/util/utils.py
index ff85a0ef..0c74ddfe 100644
--- a/pylot/core/util/utils.py
+++ b/pylot/core/util/utils.py
@@ -357,6 +357,8 @@ def get_bool(value):
     False
     >>> get_bool(None)
     None
+    >>> get_bool('Stream')
+    'Stream'
     """
     if type(value) == bool:
         return value
-- 
2.45.2


From 59f2c4b46f68ee66d7d5e8172e31a70bd5cbb722 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Tue, 16 Jul 2024 14:49:32 +0200
Subject: [PATCH 20/31] refactor: remove unused code; restructure writephases

---
 pylot/core/io/phases.py | 775 +++++++---------------------------------
 1 file changed, 122 insertions(+), 653 deletions(-)

diff --git a/pylot/core/io/phases.py b/pylot/core/io/phases.py
index 3c50d131..542f8f6a 100644
--- a/pylot/core/io/phases.py
+++ b/pylot/core/io/phases.py
@@ -21,25 +21,6 @@ from pylot.core.util.utils import get_owner, full_range, four_digits, transformF
     backtransformFilterString, loopIdentifyPhase, identifyPhase
 
 
-def add_amplitudes(event, amplitudes):
-    amplitude_list = []
-    for pick in event.picks:
-        try:
-            a0 = amplitudes[pick.waveform_id.station_code]
-            amplitude = ope.Amplitude(generic_amplitude=a0 * 1e-3)
-            amplitude.unit = 'm'
-            amplitude.category = 'point'
-            amplitude.waveform_id = pick.waveform_id
-            amplitude.magnitude_hint = 'ML'
-            amplitude.pick_id = pick.resource_id
-            amplitude.type = 'AML'
-            amplitude_list.append(amplitude)
-        except KeyError:
-            continue
-    event.amplitudes = amplitude_list
-    return event
-
-
 def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     """
     readPILOTEvent - function
@@ -193,31 +174,6 @@ def convert_pilot_times(time_array):
     return UTCDateTime(*times)
 
 
-def picksdict_from_obs(fn):
-    """
-    create pick dictionary from obs file
-    :param fn: filename
-    :type fn:
-    :return:
-    :rtype:
-    """
-    picks = dict()
-    station_name = str()
-    for line in open(fn, 'r'):
-        if line.startswith('#'):
-            continue
-        else:
-            phase_line = line.split()
-            if not station_name == phase_line[0]:
-                phase = dict()
-            station_name = phase_line[0]
-            phase_name = phase_line[4].upper()
-            pick = UTCDateTime(phase_line[6] + phase_line[7] + phase_line[8])
-            phase[phase_name] = dict(mpp=pick, fm=phase_line[5])
-            picks[station_name] = phase
-    return picks
-
-
 def picksdict_from_picks(evt, parameter=None):
     """
     Takes an Event object and return the pick dictionary commonly used within
@@ -373,636 +329,149 @@ def picks_from_picksdict(picks, creation_info=None):
     return picks_list
 
 
-def reassess_pilot_db(root_dir, db_dir, out_dir=None, fn_param=None, verbosity=0):
-    # TODO: change root to datapath
-    db_root = os.path.join(root_dir, db_dir)
-    evt_list = glob.glob1(db_root, 'e????.???.??')
-
-    for evt in evt_list:
-        if verbosity > 0:
-            print('Reassessing event {0}'.format(evt))
-        reassess_pilot_event(root_dir, db_dir, evt, out_dir, fn_param, verbosity)
-
-
-def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None, verbosity=0):
-    from obspy import read
-
-    from pylot.core.io.inputs import PylotParameter
-    from pylot.core.pick.utils import earllatepicker
-    # TODO: change root to datapath
-
-    default = PylotParameter(fn_param, verbosity)
-
-    search_base = os.path.join(root_dir, db_dir, event_id)
-    phases_file = glob.glob(os.path.join(search_base, 'PHASES.mat'))
-    if not phases_file:
-        return
-    if verbosity > 1:
-        print('Opening PILOT phases file: {fn}'.format(fn=phases_file[0]))
-    picks_dict = picksdict_from_pilot(phases_file[0])
-    if verbosity > 0:
-        print('Dictionary read from PHASES.mat:\n{0}'.format(picks_dict))
-    datacheck = list()
-    info = None
-    for station in picks_dict.keys():
-        fn_pattern = os.path.join(search_base, '{0}*'.format(station))
-        try:
-            st = read(fn_pattern)
-        except TypeError as e:
-            if 'Unknown format for file' in e.message:
-                try:
-                    st = read(fn_pattern, format='GSE2')
-                except ValueError as e:
-                    if e.message == 'second must be in 0..59':
-                        info = 'A known Error was raised. Please find the list of corrupted files and double-check these files.'
-                        datacheck.append(fn_pattern + ' (time info)\n')
-                        continue
-                    else:
-                        raise ValueError(e.message)
-                except Exception as e:
-                    if 'No file matching file pattern:' in e.message:
-                        if verbosity > 0:
-                            warnings.warn('no waveform data found for station {station}'.format(station=station),
-                                          RuntimeWarning)
-                        datacheck.append(fn_pattern + ' (no data)\n')
-                        continue
-                    else:
-                        raise e
-            else:
-                raise e
-        for phase in picks_dict[station].keys():
-            try:
-                mpp = picks_dict[station][phase]['mpp']
-            except KeyError as e:
-                print(e.message, station)
-                continue
-            sel_st = select_for_phase(st, phase)
-            if not sel_st:
-                msg = 'no waveform data found for station {station}'.format(station=station)
-                warnings.warn(msg, RuntimeWarning)
-                continue
-            stime, etime = full_range(sel_st)
-            rel_pick = mpp - stime
-            epp, lpp, spe = earllatepicker(sel_st,
-                                           default.get('nfac{0}'.format(phase)),
-                                           default.get('tsnrz' if phase == 'P' else 'tsnrh'),
-                                           Pick1=rel_pick,
-                                           iplot=0,
-                                           verbosity=0)
-            if epp is None or lpp is None:
-                continue
-            epp = stime + epp
-            lpp = stime + lpp
-            min_diff = 3 * st[0].stats.delta
-            if lpp - mpp < min_diff:
-                lpp = mpp + min_diff
-            if mpp - epp < min_diff:
-                epp = mpp - min_diff
-            picks_dict[station][phase] = dict(epp=epp, mpp=mpp, lpp=lpp, spe=spe)
-    if datacheck:
-        if info:
-            if verbosity > 0:
-                print(info + ': {0}'.format(search_base))
-        fncheck = open(os.path.join(search_base, 'datacheck_list'), 'w')
-        fncheck.writelines(datacheck)
-        fncheck.close()
-        del datacheck
-    # create Event object for export
-    evt = ope.Event(resource_id=event_id)
-    evt.picks = picks_from_picksdict(picks_dict)
-    # write phase information to file
-    if not out_dir:
-        fnout_prefix = os.path.join(root_dir, db_dir, event_id, 'PyLoT_{0}.'.format(event_id))
-    else:
-        out_dir = os.path.join(out_dir, db_dir)
-        if not os.path.isdir(out_dir):
-            os.makedirs(out_dir)
-        fnout_prefix = os.path.join(out_dir, 'PyLoT_{0}.'.format(event_id))
-    evt.write(fnout_prefix + 'xml', format='QUAKEML')
-
-
 def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
     """
-    Function of methods to write phases to the following standard file
-    formats used for locating earthquakes:
+    Writes earthquake phase data to different file formats.
 
-    HYPO71, NLLoc, VELEST, HYPOSAT, FOCMEC, and hypoDD
-
-    :param arrivals:dictionary containing all phase information including
-     station ID, phase, first motion, weight (uncertainty), ...
+    :param arrivals: Dictionary containing phase information (station ID, phase, first motion, weight, etc.)
     :type arrivals: dict
-
-    :param fformat: chosen file format (location routine),
-    choose between NLLoc, HYPO71, HYPOSAT, VELEST,
-    HYPOINVERSE, FOCMEC, and hypoDD
+    :param fformat: File format to write to (e.g., 'NLLoc', 'HYPO71', 'HYPOSAT', 'VELEST', 'HYPODD', 'FOCMEC')
     :type fformat: str
-
-    :param filename: full path and name of phase file
-    :type filename:  string
-
-    :param parameter: all input information
-    :type parameter:  object
-
-    :param eventinfo: optional, needed for VELEST-cnv file
-            and FOCMEC- and HASH-input files 
-    :type eventinfo: `obspy.core.event.Event` object
+    :param filename: Path and name of the output phase file
+    :type filename: str
+    :param parameter: Additional parameters for writing the phase data
+    :type parameter: object
+    :param eventinfo: Event information needed for specific formats like VELEST, FOCMEC, and HASH
+    :type eventinfo: obspy.core.event.Event
     """
-    if fformat == 'NLLoc':
-        print("Writing phases to %s for NLLoc" % filename)
-        fid = open("%s" % filename, 'w')
-        # write header
-        fid.write('# EQEVENT: %s Label: EQ%s  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n' %
-                  (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        for key in arrivals:
-            # P onsets
-            if 'P' in arrivals[key]:
-                try:
-                    fm = arrivals[key]['P']['fm']
-                except KeyError as e:
-                    print(e)
-                    fm = None
-                if fm is None:
-                    fm = '?'
-                onset = arrivals[key]['P']['mpp']
-                year = onset.year
-                month = onset.month
-                day = onset.day
-                hh = onset.hour
-                mm = onset.minute
-                ss = onset.second
-                ms = onset.microsecond
-                ss_ms = ss + ms / 1000000.0
-                pweight = 1  # use pick
-                try:
-                    if arrivals[key]['P']['weight'] >= 4:
-                        pweight = 0  # do not use pick
-                        print("Station {}: Uncertain pick, do not use it!".format(key))
-                except KeyError as e:
-                    print(e.message + '; no weight set during processing')
-                fid.write('%s ? ? ? P   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
-                                                                                           fm,
-                                                                                           year,
-                                                                                           month,
-                                                                                           day,
-                                                                                           hh,
-                                                                                           mm,
-                                                                                           ss_ms,
-                                                                                           pweight))
-            # S onsets
-            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
-                fm = '?'
-                onset = arrivals[key]['S']['mpp']
-                year = onset.year
-                month = onset.month
-                day = onset.day
-                hh = onset.hour
-                mm = onset.minute
-                ss = onset.second
-                ms = onset.microsecond
-                ss_ms = ss + ms / 1000000.0
-                sweight = 1  # use pick
-                try:
-                    if arrivals[key]['S']['weight'] >= 4:
-                        sweight = 0  # do not use pick
-                except KeyError as e:
-                    print(str(e) + '; no weight set during processing')
-                Ao = arrivals[key]['S']['Ao']  # peak-to-peak amplitude
-                if Ao == None:
-                    Ao = 0.0
-                # fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
-                fid.write('%s ? ? ? S   %s %d%02d%02d %02d%02d %7.4f GAU 0 %9.2f 0 0 %d \n' % (key,
-                                                                                               fm,
-                                                                                               year,
-                                                                                               month,
-                                                                                               day,
-                                                                                               hh,
-                                                                                               mm,
-                                                                                               ss_ms,
-                                                                                               Ao,
-                                                                                               sweight))
 
-        fid.close()
-    elif fformat == 'HYPO71':
-        print("Writing phases to %s for HYPO71" % filename)
-        fid = open("%s" % filename, 'w')
-        # write header
-        fid.write('                                                                %s\n' %
-                  parameter.get('eventID'))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        for key in arrivals:
-            if arrivals[key]['P']['weight'] < 4:
-                stat = key
-                if len(stat) > 4:  # HYPO71 handles only 4-string station IDs
-                    stat = stat[1:5]
-                Ponset = arrivals[key]['P']['mpp']
-                Sonset = arrivals[key]['S']['mpp']
-                pweight = arrivals[key]['P']['weight']
-                sweight = arrivals[key]['S']['weight']
-                fm = arrivals[key]['P']['fm']
-                if fm is None:
-                    fm = '-'
-                Ao = arrivals[key]['S']['Ao']
-                if Ao is None:
-                    Ao = ''
-                else:
-                    Ao = str('%7.2f' % Ao)
-                year = Ponset.year
-                if year >= 2000:
-                    year = year - 2000
-                else:
-                    year = year - 1900
-                month = Ponset.month
-                day = Ponset.day
-                hh = Ponset.hour
-                mm = Ponset.minute
-                ss = Ponset.second
-                ms = Ponset.microsecond
-                ss_ms = ss + ms / 1000000.0
-                if pweight < 2:
-                    pstr = 'I'
-                elif pweight >= 2:
-                    pstr = 'E'
-                if arrivals[key]['S']['weight'] < 4:
-                    Sss = Sonset.second
-                    Sms = Sonset.microsecond
-                    Sss_ms = Sss + Sms / 1000000.0
-                    Sss_ms = str('%5.02f' % Sss_ms)
-                    if sweight < 2:
-                        sstr = 'I'
-                    elif sweight >= 2:
-                        sstr = 'E'
-                    fid.write('%-4s%sP%s%d %02d%02d%02d%02d%02d%5.2f       %s%sS %d   %s\n' % (stat,
-                                                                                               pstr,
-                                                                                               fm,
-                                                                                               pweight,
-                                                                                               year,
-                                                                                               month,
-                                                                                               day,
-                                                                                               hh,
-                                                                                               mm,
-                                                                                               ss_ms,
-                                                                                               Sss_ms,
-                                                                                               sstr,
-                                                                                               sweight,
-                                                                                               Ao))
-                else:
-                    fid.write('%-4s%sP%s%d %02d%02d%02d%02d%02d%5.2f                  %s\n' % (stat,
-                                                                                               pstr,
-                                                                                               fm,
-                                                                                               pweight,
-                                                                                               year,
-                                                                                               month,
-                                                                                               day,
-                                                                                               hh,
-                                                                                               mm,
-                                                                                               ss_ms,
-                                                                                               Ao))
+    def write_nlloc():
+        with open(filename, 'w') as fid:
+            fid.write('# EQEVENT: {} Label: EQ{}  Loc:  X 0.00  Y 0.00  Z 10.00  OT 0.00 \n'.format(
+                parameter.get('database'), parameter.get('eventID')))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value:
+                        fm = value[phase].get('fm', '?')
+                        onset = value[phase]['mpp']
+                        ss_ms = onset.second + onset.microsecond / 1000000.0
+                        weight = 1 if value[phase].get('weight', 0) < 4 else 0
+                        amp = value[phase].get('Ao', 0.0) if phase == 'S' else ''
+                        fid.write('{} ? ? ? {}   {}{}{} {}{} {:7.4f} GAU 0 {} 0 0 {}\n'.format(
+                            key, phase, fm, onset.year, onset.month, onset.day, onset.hour, onset.minute, ss_ms, amp,
+                            weight))
 
-        fid.close()
+    def write_hypo71():
+        with open(filename, 'w') as fid:
+            fid.write(
+                '                                                                {}\n'.format(parameter.get('eventID')))
+            for key, value in arrivals.items():
+                if value['P'].get('weight', 0) < 4:
+                    stat = key[:4]
+                    Ponset = value['P']['mpp']
+                    Sonset = value.get('S', {}).get('mpp')
+                    pweight = value['P'].get('weight', 0)
+                    sweight = value.get('S', {}).get('weight', 0)
+                    fm = value['P'].get('fm', '-')
+                    Ao = value.get('S', {}).get('Ao', '')
+                    year = Ponset.year - 2000 if Ponset.year >= 2000 else Ponset.year - 1900
+                    ss_ms = Ponset.second + Ponset.microsecond / 1000000.0
+                    if Sonset:
+                        Sss_ms = Sonset.second + Sonset.microsecond / 1000000.0
+                        fid.write('{}P{}{}{} {}{}{}{}{} {:5.2f}       {}{}S {}   {}\n'.format(
+                            stat, 'I' if pweight < 2 else 'E', fm, pweight, year, Ponset.month, Ponset.day,
+                            Ponset.hour, Ponset.minute, ss_ms, Sss_ms, 'I' if sweight < 2 else 'E', sweight, Ao))
+                    else:
+                        fid.write('{}P{}{}{} {}{}{}{}{} {:5.2f}                  {}\n'.format(
+                            stat, 'I' if pweight < 2 else 'E', fm, pweight, year, Ponset.month, Ponset.day,
+                            Ponset.hour, Ponset.minute, ss_ms, Ao))
 
-    elif fformat == 'HYPOSAT':
-        print("Writing phases to %s for HYPOSAT" % filename)
-        fid = open("%s" % filename, 'w')
-        # write header
-        fid.write('%s, event %s \n' % (parameter.get('database'), parameter.get('eventID')))
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        for key in arrivals:
-            # P onsets
-            if 'P' in  arrivals[key] and arrivals[key]['P']['mpp'] is not None:
-                if arrivals[key]['P']['weight'] < 4:
-                    Ponset = arrivals[key]['P']['mpp']
-                    pyear = Ponset.year
-                    pmonth = Ponset.month
-                    pday = Ponset.day
-                    phh = Ponset.hour
-                    pmm = Ponset.minute
-                    pss = Ponset.second
-                    pms = Ponset.microsecond
-                    Pss = pss + pms / 1000000.0
-                    # use symmetrized picking error as std
-                    # (read the HYPOSAT manual)
-                    pstd = arrivals[key]['P']['spe']
-                    if pstd is None:
-                        errorsP = parameter.get('timeerrorsP')
-                        if arrivals[key]['P']['weight'] == 0:
-                            pstd = errorsP[0]
-                        elif arrivals[key]['P']['weight'] == 1:
-                            pstd = errorsP[1]
-                        elif arrivals[key]['P']['weight'] == 2:
-                            pstd = errorsP[2]
-                        elif arrivals[key]['P']['weight'] == 3:
-                            psrd = errorsP[3]
-                        else:
-                            pstd = errorsP[4]
-                    fid.write('%-5s P1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
-                              % (key, pyear, pmonth, pday, phh, pmm, Pss, pstd))
-            # S onsets
-            if 'S' in arrivals[key] and arrivals[key]['S']['mpp'] is not None:
-                if arrivals[key]['S']['weight'] < 4:
-                    Sonset = arrivals[key]['S']['mpp']
-                    syear = Sonset.year
-                    smonth = Sonset.month
-                    sday = Sonset.day
-                    shh = Sonset.hour
-                    smm = Sonset.minute
-                    sss = Sonset.second
-                    sms = Sonset.microsecond
-                    Sss = sss + sms / 1000000.0
-                    sstd = arrivals[key]['S']['spe']
-                    if pstd is None:
-                        errorsS = parameter.get('timeerrorsS')
-                        if arrivals[key]['S']['weight'] == 0:
-                            pstd = errorsS[0]
-                        elif arrivals[key]['S']['weight'] == 1:
-                            pstd = errorsS[1]
-                        elif arrivals[key]['S']['weight'] == 2:
-                            pstd = errorsS[2]
-                        elif arrivals[key]['S']['weight'] == 3:
-                            psrd = errorsS[3]
-                        else:
-                            pstd = errorsP[4]
-                    fid.write('%-5s S1       %4.0f %02d %02d %02d %02d %05.02f   %5.3f -999.   0.00 -999.  0.00\n'
-                              % (key, syear, smonth, sday, shh, smm, Sss, sstd))
-        fid.close()
+    def write_hyposat():
+        with open(filename, 'w') as fid:
+            fid.write('{}, event {} \n'.format(parameter.get('database'), parameter.get('eventID')))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value and value[phase].get('weight', 0) < 4:
+                        onset = value[phase]['mpp']
+                        ss_ms = onset.second + onset.microsecond / 1000000.0
+                        std = value[phase].get('spe', parameter.get('timeerrorsP')[value[phase].get('weight', 0)])
+                        fid.write(
+                            '{:<5} {}1       {:4} {:02} {:02} {:02} {:02} {:05.02f}   {:5.3f} -999.   0.00 -999.  0.00\n'.format(
+                                key, phase, onset.year, onset.month, onset.day, onset.hour, onset.minute, ss_ms, std))
 
-    elif fformat == 'VELEST':
-        print("Writing phases to %s for VELEST" % filename)
-        fid = open("%s" % filename, 'w')
-        # get informations needed in cnv-file
-        # check, whether latitude is N or S and longitude is E or W
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
+    def write_velest():
+        if not eventinfo:
             print("No source origin calculated yet, thus no cnv-file creation possible!")
             return
-        if eventsource['latitude'] < 0:
-            cns = 'S'
-        else:
-            cns = 'N'
-        if eventsource['longitude'] < 0:
-            cew = 'W'
-        else:
-            cew = 'E'
-        # get last two integers of origin year
-        stime = eventsource['time']
-        if stime.year - 2000 >= 0:
-            syear = stime.year - 2000
-        else:
-            syear = stime.year - 1900
-        ifx = 0  # default value, see VELEST manual, pp. 22-23
-        # write header
-        fid.write('%s%02d%02d %02d%02d %05.2f %7.4f%c %8.4f%c %7.2f %6.2f     %02.0f  0.0 0.03  1.0  1.0\n' % (
-            syear, stime.month, stime.day, stime.hour, stime.minute, stime.second, eventsource['latitude'],
-            cns, eventsource['longitude'], cew, eventsource['depth'], eventinfo.magnitudes[0]['mag'], ifx))
-        n = 0
-        # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
-            # convert pick object (PyLoT) into dictionary
-            evt = ope.Event(resource_id=eventinfo['resource_id'])
-            evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
-        # prefer manual picks
-        usedarrivals = chooseArrivals(arrivals)
-        for key in usedarrivals:
-            # P onsets
-            if 'P' in usedarrivals[key]:
-                if usedarrivals[key]['P']['weight'] < 4:
-                    n += 1
-                    stat = key
-                    if len(stat) > 4:  # VELEST handles only 4-string station IDs
-                        stat = stat[1:5]
-                    Ponset = usedarrivals[key]['P']['mpp']
-                    Pweight = usedarrivals[key]['P']['weight']
-                    Prt = Ponset - stime  # onset time relative to source time
-                    if n % 6 != 0:
-                        fid.write('%-4sP%d%6.2f' % (stat, Pweight, Prt))
-                    else:
-                        fid.write('%-4sP%d%6.2f\n' % (stat, Pweight, Prt))
-                        # S onsets
-            if 'S' in usedarrivals[key]:
-                if usedarrivals[key]['S']['weight'] < 4:
-                    n += 1
-                    stat = key
-                    if len(stat) > 4:  # VELEST handles only 4-string station IDs
-                        stat = stat[1:5]
-                    Sonset = usedarrivals[key]['S']['mpp']
-                    Sweight = usedarrivals[key]['S']['weight']
-                    Srt = Ponset - stime  # onset time relative to source time
-                    if n % 6 != 0:
-                        fid.write('%-4sS%d%6.2f' % (stat, Sweight, Srt))
-                    else:
-                        fid.write('%-4sS%d%6.2f\n' % (stat, Sweight, Srt))
-        fid.close()
+        with open(filename, 'w') as fid:
+            origin = eventinfo.origins[0]
+            lat_dir = 'S' if origin.latitude < 0 else 'N'
+            lon_dir = 'W' if origin.longitude < 0 else 'E'
+            year = origin.time.year - 2000 if origin.time.year >= 2000 else origin.time.year - 1900
+            fid.write(
+                '{}{}{} {}{} {} {:05.2f} {:7.4f}{} {:8.4f}{} {:7.2f} {:6.2f}     {:02.0f}  0.0 0.03  1.0  1.0\n'.format(
+                    year, origin.time.month, origin.time.day, origin.time.hour, origin.time.minute, origin.time.second,
+                    origin.latitude, lat_dir, origin.longitude, lon_dir, origin.depth, eventinfo.magnitudes[0].mag, 0))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value and value[phase].get('weight', 0) < 4:
+                        onset = value[phase]['mpp']
+                        rt = (onset - origin.time).total_seconds()
+                        fid.write('{:<4}{}{}{:6.2f}\n'.format(key[:4], phase, value[phase].get('weight', 0), rt))
 
-    elif fformat == 'HYPODD':
-        print("Writing phases to %s for hypoDD" % filename)
-        fid = open("%s" % filename, 'w')
-        # get event information needed for hypoDD-phase file
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
+    def write_hypodd():
+        if not eventinfo:
             print("No source origin calculated yet, thus no hypoDD-infile creation possible!")
             return
-        stime = eventsource['time']
-        try:
-            event = eventinfo['pylot_id']
-            hddID = event.split('.')[0][1:5]
-        except:
-            print("Error 1111111!")
-            hddID = "00000"
-            # write header
-        fid.write('# %d  %d %d %d %d %5.2f %7.4f +%6.4f %7.4f %4.2f 0.1 0.5 %4.2f      %s\n' % (
-            stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
-            eventsource['latitude'], eventsource['longitude'], eventsource['depth'] / 1000,
-            eventinfo.magnitudes[0]['mag'], eventsource['quality']['standard_error'], hddID))
-        # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
-            # convert pick object (PyLoT) into dictionary
-            evt = ope.Event(resource_id=eventinfo['resource_id'])
-            evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
-        # prefer manual picks
-        usedarrivals = chooseArrivals(arrivals)
-        for key in usedarrivals:
-            if 'P' in usedarrivals[key]:
-                # P onsets
-                if usedarrivals[key]['P']['weight'] < 4:
-                    Ponset = usedarrivals[key]['P']['mpp']
-                    Prt = Ponset - stime  # onset time relative to source time
-                    fid.write('%s    %6.3f  1  P\n' % (key, Prt))
-            if 'S' in usedarrivals[key]:
-                # S onsets
-                if usedarrivals[key]['S']['weight'] < 4:
-                    Sonset = usedarrivals[key]['S']['mpp']
-                    Srt = Sonset - stime  # onset time relative to source time
-                    fid.write('%-5s    %6.3f  1  S\n' % (key, Srt))
+        with open(filename, 'w') as fid:
+            origin = eventinfo.origins[0]
+            stime = origin.time
+            fid.write('# {}  {} {} {} {} {} {:7.4f} +{:6.4f} {:7.4f} {:4.2f} 0.1 0.5 {:4.2f}      {}\n'.format(
+                stime.year, stime.month, stime.day, stime.hour, stime.minute, stime.second,
+                origin.latitude, origin.longitude, origin.depth / 1000, eventinfo.magnitudes[0].mag,
+                origin.quality.standard_error, "00000"))
+            for key, value in arrivals.items():
+                for phase in ['P', 'S']:
+                    if phase in value and value[phase].get('weight', 0) < 4:
+                        onset = value[phase]['mpp']
+                        rt = (onset - stime).total_seconds()
+                        fid.write('{}    {:6.3f}  1  {}\n'.format(key, rt, phase))
 
-        fid.close()
-
-    elif fformat == 'FOCMEC':
-        print("Writing phases to %s for FOCMEC" % filename)
-        fid = open("%s" % filename, 'w')
-        # get event information needed for FOCMEC-input file
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
+    def write_focmec():
+        if not eventinfo:
             print("No source origin calculated yet, thus no FOCMEC-infile creation possible!")
             return
-        stime = eventsource['time']
-
-        # avoid printing '*' in focmec-input file
-        if parameter.get('eventid') == '*' or parameter.get('eventid') is None:
-            evID = 'e0000'
-        else:
-            evID = parameter.get('eventid')
-
-        # write header line including event information
-        fid.write('%s %d%02d%02d%02d%02d%02.0f %7.4f %6.4f %3.1f %3.1f\n' % (evID,
-                                                                             stime.year, stime.month, stime.day,
-                                                                             stime.hour, stime.minute, stime.second,
-                                                                             eventsource['latitude'],
-                                                                             eventsource['longitude'],
-                                                                             eventsource['depth'] / 1000,
-                                                                             eventinfo.magnitudes[0]['mag']))
-        picks = eventinfo.picks
-        # check whether arrivals are dictionaries (autoPyLoT) or pick object (PyLoT)
-        if isinstance(arrivals, dict) == False:
-            # convert pick object (PyLoT) into dictionary
-            evt = ope.Event(resource_id=eventinfo['resource_id'])
-            evt.picks = arrivals
-            arrivals = picksdict_from_picks(evt)
-        # check for automatic and manual picks
-        # prefer manual picks
-        usedarrivals = chooseArrivals(arrivals)
-        for key in usedarrivals:
-            if 'P' in usedarrivals[key]:
-                if usedarrivals[key]['P']['weight'] < 4 and usedarrivals[key]['P']['fm'] is not None:
-                    stat = key
-                    for i in range(len(picks)):
-                        station = picks[i].waveform_id.station_code
-                        if station == stat:
-                            # get resource ID
-                            resid_picks = picks[i].get('resource_id')
-                            # find same ID in eventinfo
-                            # there it is the pick_id!!
-                            for j in range(len(eventinfo.origins[0].arrivals)):
-                                resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
-                                if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
-                                    if len(stat) > 4:  # FOCMEC handles only 4-string station IDs
-                                        stat = stat[1:5]
-                                    az = eventinfo.origins[0].arrivals[j].get('azimuth')
-                                    inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
-                                    fid.write('%-4s  %6.2f  %6.2f%s \n' % (stat,
-                                                                           az,
-                                                                           inz,
-                                                                           usedarrivals[key]['P']['fm']))
+        with open(filename, 'w') as fid:
+            origin = eventinfo.origins[0]
+            stime = origin.time
+            fid.write('{} {}{:02d}{:02d}{:02d}{:02d}{:02.0f} {:7.4f} {:6.4f} {:3.1f} {:3.1f}\n'.format(
+                parameter.get('eventid', 'e0000'), stime.year, stime.month, stime.day, stime.hour, stime.minute,
+                stime.second, origin.latitude, origin.longitude, origin.depth / 1000, eventinfo.magnitudes[0].mag))
+            for key, value in arrivals.items():
+                if 'P' in value and value['P'].get('weight', 0) < 4 and value['P'].get('fm'):
+                    for pick in eventinfo.picks:
+                        if pick.waveform_id.station_code == key:
+                            for arrival in origin.arrivals:
+                                if arrival.pick_id == pick.resource_id and arrival.phase == 'P':
+                                    stat = key[:4]
+                                    az = arrival.azimuth
+                                    inz = arrival.takeoff_angle
+                                    fid.write('{:<4}  {:6.2f}  {:6.2f}{}\n'.format(stat, az, inz, value['P']['fm']))
                                     break
 
-        fid.close()
+    if fformat == 'NLLoc':
+        write_nlloc()
+    elif fformat == 'HYPO71':
+        write_hypo71()
+    elif fformat == 'HYPOSAT':
+        write_hyposat()
+    elif fformat == 'VELEST':
+        write_velest()
+    elif fformat == 'HYPODD':
+        write_hypodd()
+    elif fformat == 'FOCMEC':
+        write_focmec()
 
-    elif fformat == 'HASH':
-        # two different input files for 
-        # HASH-driver 1 and 2 (see HASH manual!)
-        filename1 = filename + 'drv1' + '.phase'
-        filename2 = filename + 'drv2' + '.phase'
-        print("Writing phases to %s for HASH for HASH-driver 1" % filename1)
-        fid1 = open("%s" % filename1, 'w')
-        print("Writing phases to %s for HASH for HASH-driver 2" % filename2)
-        fid2 = open("%s" % filename2, 'w')
-        # get event information needed for HASH-input file
-        try:
-            eventsource = eventinfo.origins[0]
-        except:
-            print("No source origin calculated yet, thus no cnv-file creation possible!")
-            return
-        eventsource = eventinfo.origins[0]
-        event = parameter.get('eventID')
-        hashID = event.split('.')[0][1:5]
-        latdeg = eventsource['latitude']
-        latmin = eventsource['latitude'] * 60 / 10000
-        londeg = eventsource['longitude']
-        lonmin = eventsource['longitude'] * 60 / 10000
-        erh = 1 / 2 * (eventsource.origin_uncertainty['min_horizontal_uncertainty'] +
-                       eventsource.origin_uncertainty['max_horizontal_uncertainty']) / 1000
-        erz = eventsource.depth_errors['uncertainty']
-        stime = eventsource['time']
-        if stime.year - 2000 >= 0:
-            syear = stime.year - 2000
-        else:
-            syear = stime.year - 1900
-        picks = eventinfo.picks
-        # write header line including event information
-        # for HASH-driver 1
-        fid1.write('%s%02d%02d%02d%02d%5.2f%2dN%5.2f%3dE%5.2f%6.3f%4.2f%5.2f%5.2f%s\n' % (syear,
-                                                                                          stime.month, stime.day,
-                                                                                          stime.hour, stime.minute,
-                                                                                          stime.second,
-                                                                                          latdeg, latmin, londeg,
-                                                                                          lonmin, eventsource['depth'],
-                                                                                          eventinfo.magnitudes[0][
-                                                                                              'mag'], erh, erz,
-                                                                                          hashID))
-        # write header line including event information
-        # for HASH-driver 2
-        fid2.write(
-            '%d%02d%02d%02d%02d%5.2f%dN%5.2f%3dE%6.2f%5.2f    %d                                          %5.2f %5.2f                                        %4.2f      %s \n' % (
-                syear, stime.month, stime.day,
-                stime.hour, stime.minute, stime.second,
-                latdeg, latmin, londeg, lonmin,
-                eventsource['depth'],
-                eventsource['quality']['used_phase_count'],
-                erh, erz, eventinfo.magnitudes[0]['mag'],
-                hashID))
-        # Prefer Manual Picks over automatic ones if possible
-        arrivals = chooseArrivals(arrivals)  # MP MP what is chooseArrivals? It is not defined anywhere
-        # write phase lines
-        for key in arrivals:
-            if 'P' in arrivals[key]:
-                if arrivals[key]['P']['weight'] < 4 and arrivals[key]['P']['fm'] is not None:
-                    stat = key
-                    ccode = arrivals[key]['P']['channel']
-                    ncode = arrivals[key]['P']['network']
-
-                    if arrivals[key]['P']['weight'] < 2:
-                        Pqual = 'I'
-                    else:
-                        Pqual = 'E'
-
-                    for i in range(len(picks)):
-                        station = picks[i].waveform_id.station_code
-                        if station == stat:
-                            # get resource ID
-                            resid_picks = picks[i].get('resource_id')
-                            # find same ID in eventinfo
-                            # there it is the pick_id!!
-                            for j in range(len(eventinfo.origins[0].arrivals)):
-                                resid_eventinfo = eventinfo.origins[0].arrivals[j].get('pick_id')
-                                if resid_eventinfo == resid_picks and eventinfo.origins[0].arrivals[j].phase == 'P':
-                                    if len(stat) > 4:  # HASH handles only 4-string station IDs
-                                        stat = stat[1:5]
-                                    az = eventinfo.origins[0].arrivals[j].get('azimuth')
-                                    inz = eventinfo.origins[0].arrivals[j].get('takeoff_angle')
-                                    dist = eventinfo.origins[0].arrivals[j].get('distance')
-                                    # write phase line for HASH-driver 1
-                                    fid1.write(
-                                        '%-4s%sP%s%d                   0                                   %3.1f          %03d %03d   2     1   %s\n' % (
-                                            stat, Pqual, arrivals[key]['P']['fm'], arrivals[key]['P']['weight'],
-                                            dist, inz, az, ccode))
-                                    # write phase line for HASH-driver 2
-                                    fid2.write('%-4s %s   %s %s %s                    \n' % (
-                                        stat,
-                                        ncode,
-                                        ccode,
-                                        Pqual,
-                                        arrivals[key]['P']['fm']))
-                                    break
-
-        fid1.write('                                    %s' % hashID)
-        fid1.close()
-        fid2.close()
 
 
 def chooseArrivals(arrivals):
-- 
2.45.2


From c8f9c1c33a5a6297bdd8b0fb5657b31ea5e399a6 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Wed, 17 Jul 2024 13:29:10 +0200
Subject: [PATCH 21/31] refactor: rename writephases; add write hash to
 write_phases

---
 pylot/core/io/phases.py   | 85 +++++++++++++++++++++++++++++++++++++--
 pylot/core/loc/focmec.py  |  4 +-
 pylot/core/loc/hash.py    |  4 +-
 pylot/core/loc/hypo71.py  |  4 +-
 pylot/core/loc/hypodd.py  |  4 +-
 pylot/core/loc/hyposat.py |  4 +-
 pylot/core/loc/nll.py     |  4 +-
 pylot/core/loc/velest.py  |  4 +-
 8 files changed, 96 insertions(+), 17 deletions(-)

diff --git a/pylot/core/io/phases.py b/pylot/core/io/phases.py
index 542f8f6a..1aa4ee89 100644
--- a/pylot/core/io/phases.py
+++ b/pylot/core/io/phases.py
@@ -329,7 +329,7 @@ def picks_from_picksdict(picks, creation_info=None):
     return picks_list
 
 
-def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
+def write_phases(arrivals, fformat, filename, parameter=None, eventinfo=None):
     """
     Writes earthquake phase data to different file formats.
 
@@ -459,6 +459,84 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                                     fid.write('{:<4}  {:6.2f}  {:6.2f}{}\n'.format(stat, az, inz, value['P']['fm']))
                                     break
 
+    def write_hash():
+        # Define filenames for HASH driver 1 and 2
+        filename1 = f"{filename}drv1.phase"
+        filename2 = f"{filename}drv2.phase"
+
+        print(f"Writing phases to {filename1} for HASH-driver 1")
+        print(f"Writing phases to {filename2} for HASH-driver 2")
+
+        # Open files for writing
+        with open(filename1, 'w') as fid1, open(filename2, 'w') as fid2:
+            # Get event information needed for HASH-input file
+            try:
+                eventsource = eventinfo.origins[0]
+            except IndexError:
+                print("No source origin calculated yet, thus no cnv-file creation possible!")
+                return
+
+            event = parameter.get('eventID')
+            hashID = event.split('.')[0][1:5]
+            latdeg = eventsource['latitude']
+            latmin = (eventsource['latitude'] * 60) / 10000
+            londeg = eventsource['longitude']
+            lonmin = (eventsource['longitude'] * 60) / 10000
+
+            erh = (eventsource.origin_uncertainty['min_horizontal_uncertainty'] +
+                   eventsource.origin_uncertainty['max_horizontal_uncertainty']) / 2000
+            erz = eventsource.depth_errors['uncertainty']
+
+            stime = eventsource['time']
+            syear = stime.year % 100  # Calculate two-digit year
+
+            picks = eventinfo.picks
+
+            # Write header line including event information for HASH-driver 1
+            fid1.write(f"{syear:02d}{stime.month:02d}{stime.day:02d}{stime.hour:02d}{stime.minute:02d}"
+                       f"{stime.second:05.2f}{latdeg:2d}N{latmin:05.2f}{londeg:3d}E{lonmin:05.2f}"
+                       f"{eventsource['depth']:6.2f}{eventinfo.magnitudes[0]['mag']:4.2f}{erh:5.2f}{erz:5.2f}{hashID}\n")
+
+            # Write header line including event information for HASH-driver 2
+            fid2.write(f"{syear:02d}{stime.month:02d}{stime.day:02d}{stime.hour:02d}{stime.minute:02d}"
+                       f"{stime.second:05.2f}{latdeg}N{latmin:05.2f}{londeg}E{lonmin:6.2f}{eventsource['depth']:5.2f}"
+                       f"{eventsource['quality']['used_phase_count']:3d}{erh:5.2f}{erz:5.2f}"
+                       f"{eventinfo.magnitudes[0]['mag']:4.2f}{hashID}\n")
+
+            # Write phase lines
+            for key, arrival in arrivals.items():
+                if 'P' in arrival and arrival['P']['weight'] < 4 and arrival['P']['fm'] is not None:
+                    stat = key
+                    ccode = arrival['P']['channel']
+                    ncode = arrival['P']['network']
+                    Pqual = 'I' if arrival['P']['weight'] < 2 else 'E'
+
+                    for pick in picks:
+                        if pick.waveform_id.station_code == stat:
+                            resid_picks = pick.get('resource_id')
+                            for origin_arrival in eventinfo.origins[0].arrivals:
+                                if (origin_arrival.get('pick_id') == resid_picks and
+                                        origin_arrival.phase == 'P'):
+                                    if len(stat) > 4:  # HASH handles only 4-character station IDs
+                                        stat = stat[1:5]
+
+                                    az = origin_arrival.get('azimuth')
+                                    inz = origin_arrival.get('takeoff_angle')
+                                    dist = origin_arrival.get('distance')
+
+                                    # Write phase line for HASH-driver 1
+                                    fid1.write(f"{stat:<4}{Pqual}P{arrival['P']['fm']}{arrival['P']['weight']:d}"
+                                               f"{dist:3.1f}{inz:03d}{az:03d}{ccode}\n")
+
+                                    # Write phase line for HASH-driver 2
+                                    fid2.write(f"{stat:<4} {ncode} {ccode} {Pqual} {arrival['P']['fm']}\n")
+                                    break
+
+            fid1.write(f"{'':<36}{hashID}")
+
+    # Prefer Manual Picks over automatic ones if possible
+    arrivals = chooseArrivals(arrivals)  # Function not defined, assumed to exist
+
     if fformat == 'NLLoc':
         write_nlloc()
     elif fformat == 'HYPO71':
@@ -471,7 +549,8 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
         write_hypodd()
     elif fformat == 'FOCMEC':
         write_focmec()
-
+    elif fformat == 'HASH':
+        write_hash()
 
 
 def chooseArrivals(arrivals):
@@ -591,7 +670,7 @@ def getQualitiesfromxml(path, errorsP, errorsS, plotflag=1, figure=None, verbosi
                 mstation = pick.waveform_id.station_code
                 mstation_ext = mstation + '_'
                 for mpick in arrivals_copy:
-                    phase = identifyPhase(loopIdentifyPhase(pick.phase_hint)) # MP MP catch if this fails?
+                    phase = identifyPhase(loopIdentifyPhase(pick.phase_hint))  # MP MP catch if this fails?
                     if ((mpick.waveform_id.station_code == mstation) or
                         (mpick.waveform_id.station_code == mstation_ext)) and \
                             (mpick.method_id.id.split('/')[1] == 'auto') and \
diff --git a/pylot/core/loc/focmec.py b/pylot/core/loc/focmec.py
index 2df845cf..29cb7496 100644
--- a/pylot/core/loc/focmec.py
+++ b/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)
diff --git a/pylot/core/loc/hash.py b/pylot/core/loc/hash.py
index 5ba18faa..d39e5076 100644
--- a/pylot/core/loc/hash.py
+++ b/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)
diff --git a/pylot/core/loc/hypo71.py b/pylot/core/loc/hypo71.py
index 430e2c14..e96c7bc3 100644
--- a/pylot/core/loc/hypo71.py
+++ b/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)
diff --git a/pylot/core/loc/hypodd.py b/pylot/core/loc/hypodd.py
index c194ed90..7fe2a744 100644
--- a/pylot/core/loc/hypodd.py
+++ b/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)
diff --git a/pylot/core/loc/hyposat.py b/pylot/core/loc/hyposat.py
index e9c05a87..49cbe098 100644
--- a/pylot/core/loc/hyposat.py
+++ b/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)
diff --git a/pylot/core/loc/nll.py b/pylot/core/loc/nll.py
index 658bb368..ad3eb571 100644
--- a/pylot/core/loc/nll.py
+++ b/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):
diff --git a/pylot/core/loc/velest.py b/pylot/core/loc/velest.py
index 8dd5d88f..040bacab 100644
--- a/pylot/core/loc/velest.py
+++ b/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)
-- 
2.45.2


From ef69fc429fd4cdbc5ce254562f39ca49ea6f21dd Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Wed, 17 Jul 2024 14:05:04 +0200
Subject: [PATCH 22/31] refactor: removed unused code

---
 PyLoT.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 1624aaaa..46745c52 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -1553,11 +1553,6 @@ class MainWindow(QMainWindow):
             fname = str(action.data().toString())
         return fname
 
-    def getEventFileName(self, type='manual'):
-        if self.get_fnames(type) is None:
-            self.set_fname(self.get_data().getEventFileName(), type)
-        return self.get_fnames(type)
-
     def saveData(self, event=None, directory=None, outformats=['.xml', '.cnv', '.obs', '_focmec.in', '.pha']):
         '''
         Save event data to directory with specified output formats.
-- 
2.45.2


From c4aeab0d8968df3ce9c2b12d5436c5fbb4cb3f98 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Wed, 17 Jul 2024 14:06:13 +0200
Subject: [PATCH 23/31] suggestion: add new dataclasses; remove unused code

---
 pylot/core/io/data.py | 414 ++++++++++++++++++------------------------
 1 file changed, 172 insertions(+), 242 deletions(-)

diff --git a/pylot/core/io/data.py b/pylot/core/io/data.py
index 13eb9fb6..6259c6d7 100644
--- a/pylot/core/io/data.py
+++ b/pylot/core/io/data.py
@@ -4,13 +4,16 @@
 import copy
 import logging
 import os
+import fnmatch
+from dataclasses import dataclass, field
+from typing import List
 
 from PySide2.QtWidgets import QMessageBox
-from obspy import read_events
-from obspy.core import read, Stream, UTCDateTime
+from obspy import read, read_events, Stream, Catalog, UTCDateTime
 from obspy.core.event import Event as ObsPyEvent
 from obspy.io.sac import SacIOError
 
+
 import pylot.core.loc.focmec as focmec
 import pylot.core.loc.hypodd as hypodd
 import pylot.core.loc.velest as velest
@@ -139,29 +142,6 @@ class Data(object):
     def setNew(self):
         self._new = True
 
-    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 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 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
@@ -252,184 +232,6 @@ class Data(object):
                 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))
-
-
-            no_uncertainties_p = []
-            no_uncertainties_s = []
-            if upperErrors:
-                # check for pick uncertainties exceeding adjusted upper errors
-                # Picks with larger uncertainties will not be saved in output file!
-                for j in range(len(picks)):
-                    for i in range(len(picks_copy)):
-                        if picks_copy[i].phase_hint[0] == 'P':
-                            # Skipping pick if no upper_uncertainty is found and warning user
-                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
-                                #print("{1} P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
-                                 #   picks_copy[i].waveform_id.station_code,
-                                  #  picks_copy[i].method_id))
-                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_p:
-                                    no_uncertainties_p.append(picks_copy[i].waveform_id.station_code)
-                                continue
-
-                            #print ("checking for upper_uncertainty")
-                            if  (picks_copy[i].time_errors['uncertainty'] is None) or \
-                                    (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[0]):
-                                print("Uncertainty exceeds or equal adjusted upper time error!")
-                                print("Adjusted uncertainty: {}".format(upperErrors[0]))
-                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
-                                print("{1} P-Pick of station {0} will not be saved in outputfile".format(
-                                    picks_copy[i].waveform_id.station_code,
-                                    picks_copy[i].method_id))
-                                del picks_copy[i]
-                                break
-                        if picks_copy[i].phase_hint[0] == 'S':
-
-                            # Skipping pick if no upper_uncertainty is found and warning user
-                            if picks_copy[i].time_errors['upper_uncertainty'] is None:
-                                #print("{1} S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(
-                                    #picks_copy[i].waveform_id.station_code,
-                                    #picks_copy[i].method_id))
-                                if not picks_copy[i].waveform_id.station_code in no_uncertainties_s:
-                                    no_uncertainties_s.append(picks_copy[i].waveform_id.station_code)
-                                continue
-
-
-                            if (picks_copy[i].time_errors['uncertainty'] is None) or \
-                                (picks_copy[i].time_errors['upper_uncertainty'] >= upperErrors[1]):
-                                print("Uncertainty exceeds or equal adjusted upper time error!")
-                                print("Adjusted uncertainty: {}".format(upperErrors[1]))
-                                print("Pick uncertainty: {}".format(picks_copy[i].time_errors['uncertainty']))
-                                print("{1} S-Pick of station {0} will not be saved in outputfile".format(
-                                    picks_copy[i].waveform_id.station_code,
-                                    picks_copy[i].method_id))
-                                del picks_copy[i]
-                                break
-            for s in no_uncertainties_p:
-                print("P-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
-            for s in no_uncertainties_s:
-                print("S-Pick of station {0} does not have upper_uncertainty and cant be checked".format(s))
-
-            if fnext == '.obs':
-                try:
-                    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:
-                    parameter = PylotParameter()
-                    logging.warning('Using default input parameter')
-                    focmec.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
-                except KeyError as e:
-                    raise KeyError('''{0} export format
-                                     not implemented: {1}'''.format(evtformat, e))
-            if fnext == '.pha':
-                try:
-                    parameter = PylotParameter()
-                    logging.warning('Using default input parameter')
-                    hypodd.export(picks_copy, fnout + fnext, parameter, eventinfo=self.get_evt_data())
-                except KeyError as e:
-                    raise KeyError('''{0} export format
-                                     not implemented: {1}'''.format(evtformat, e))
-
-    def getComp(self):
-        """
-        Get component (ZNE)
-        """
-        return self.comp
-
     def getID(self):
         """
         Get unique resource id
@@ -470,23 +272,10 @@ class Data(object):
         self.tstart = tstart
         self.tstop = tstop
 
+        # remove directories
         fnames = check_fname_exists(fnames)
         fnames_alt = check_fname_exists(fnames_alt)
-        # if obspy_dmt:
-        #     wfdir = 'raw'
-        #     self.processed = False
-        #     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_alt is not None:
@@ -494,9 +283,6 @@ class Data(object):
         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, _ = check_for_gaps_and_merge(self.wfdata)
         # check for nans
@@ -618,11 +404,6 @@ class Data(object):
                         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):
             """
@@ -654,6 +435,171 @@ class Data(object):
         applydata[typ](data)
         self._new = False
 
+@dataclass
+class SeismicEventData:
+    event_id: str = ""
+    catalog: Catalog = field(default_factory=Catalog)
+
+    def find_event_files(self, directory: str, extensions: List[str]) -> List[str]:
+        """
+        Browse the directory to find event files with specified extensions.
+
+        Parameters:
+        directory (str): The directory path to search for event files.
+        extensions (List[str]): List of file extensions to search for.
+
+        Returns:
+        List[str]: List of file paths that match the given extensions.
+
+        Example:
+        >>> sed = SeismicEventData()
+        >>> sed.find_event_files('test_directory', ['.xml', '.quakeml']) # doctest: +SKIP
+        ['test_directory/event1.xml', 'test_directory/event2.quakeml']
+        """
+        matches = []
+        for root, _, files in os.walk(directory):
+            for ext in extensions:
+                for filename in fnmatch.filter(files, f'*{ext}'):
+                    matches.append(os.path.join(root, filename))
+        return matches
+
+    def read_event_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
+        """
+        Read a seismic event from the first found file in the directory with specified format.
+
+        Parameters:
+        directory (str): The directory path to search for event files.
+        extensions (List[str]): List of file extensions to search for.
+        format (str): The format to read the event file.
+
+        Example:
+        >>> sed = SeismicEventData()
+        >>> sed.read_event_from_directory('test_directory', ['.xml', '.quakeml'], 'QUAKEML') # doctest: +SKIP
+        """
+        event_files = self.find_event_files(directory, extensions)
+        if event_files:
+            self.read_event(event_files[0], format)
+        else:
+            raise FileNotFoundError(f"No event files found in directory {directory} with extensions {extensions}.")
+
+    def read_event(self, file_path: str, format: str) -> None:
+        """
+        Read a seismic event from a file with specified format.
+
+        Parameters:
+        file_path (str): The path to the event file.
+        format (str): The format to read the event file.
+
+        Example:
+        >>> sed = SeismicEventData()
+        >>> sed.read_event('test_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
+        """
+        if os.path.exists(file_path):
+            self.catalog = read_events(file_path, format=format)
+            self.event_id = self.catalog[0].resource_id.id.split('/')[-1] if self.catalog else ""
+        else:
+            raise FileNotFoundError(f"File {file_path} does not exist.")
+
+    def write_event(self, file_path: str, format: str) -> None:
+        """
+        Write the seismic event to a file with specified format.
+
+        Parameters:
+        file_path (str): The path to the output file.
+        format (str): The format to write the event file.
+
+        Example:
+        >>> sed = SeismicEventData(event_id='12345')
+        >>> sed.write_event('output_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
+        """
+        self.catalog.write(file_path, format=format)
+
+@dataclass
+class WaveformData:
+    stream: Stream = field(default_factory=Stream)
+
+    def find_waveform_files(self, directory: str, extensions: List[str]) -> List[str]:
+        """
+        Browse the directory to find waveform files with specified extensions.
+
+        Parameters:
+        directory (str): The directory path to search for waveform files.
+        extensions (List[str]): List of file extensions to search for.
+
+        Returns:
+        List[str]: List of file paths that match the given extensions.
+
+        Example:
+        >>> wd = WaveformData()
+        >>> wd.find_waveform_files('test_directory', ['.mseed']) # doctest: +SKIP
+        ['test_directory/waveform1.mseed']
+        """
+        matches = []
+        for root, _, files in os.walk(directory):
+            for ext in extensions:
+                for filename in fnmatch.filter(files, f'*{ext}'):
+                    matches.append(os.path.join(root, filename))
+        return matches
+
+    def read_waveform_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
+        """
+        Read waveform data from the first found file in the directory with specified format.
+
+        Parameters:
+        directory (str): The directory path to search for waveform files.
+        extensions (List[str]): List of file extensions to search for.
+        format (str): The format to read the waveform file.
+
+        Example:
+        >>> wd = WaveformData()
+        >>> wd.read_waveform_from_directory('test_directory', ['.mseed'], 'MSEED') # doctest: +SKIP
+        """
+        waveform_files = self.find_waveform_files(directory, extensions)
+        if waveform_files:
+            self.read_waveform(waveform_files[0], format)
+        else:
+            raise FileNotFoundError(f"No waveform files found in directory {directory} with extensions {extensions}.")
+
+    def read_waveform(self, file_path: str, format: str) -> None:
+        """
+        Read waveform data from a file with specified format.
+
+        Parameters:
+        file_path (str): The path to the waveform file.
+        format (str): The format to read the waveform file.
+
+        Example:
+        >>> wd = WaveformData()
+        >>> wd.read_waveform('test_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
+        """
+        if os.path.exists(file_path):
+            self.stream = read(file_path, format=format)
+        else:
+            raise FileNotFoundError(f"File {file_path} does not exist.")
+
+    def write_waveform(self, file_path: str, format: str) -> None:
+        """
+        Write the waveform data to a file with specified format.
+
+        Parameters:
+        file_path (str): The path to the output file.
+        format (str): The format to write the waveform file.
+
+        Example:
+        >>> wd = WaveformData()
+        >>> wd.write_waveform('output_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
+        """
+        self.stream.write(file_path, format=format)
+
+# Example usage:
+# seismic_event = SeismicEventData()
+# seismic_event.read_event_from_directory("path_to_directory", extensions=[".xml", ".quakeml"], format="QUAKEML")
+# seismic_event.write_event("output_event_file.xml", format="QUAKEML")
+
+# waveform_data = WaveformData()
+# waveform_data.read_waveform_from_directory("path_to_directory", extensions=[".mseed"], format="MSEED")
+# waveform_data.write_waveform("output_waveform_file.mseed", format="MSEED")
+
 
 class GenericDataStructure(object):
     """
@@ -837,22 +783,6 @@ 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:
-- 
2.45.2


From 8dd5789b0cd71943c497f56fca2b28cd912d929d Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Wed, 17 Jul 2024 14:07:05 +0200
Subject: [PATCH 24/31] refactor: remove unnecessary additional declaration

---
 pylot/core/util/structure.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pylot/core/util/structure.py b/pylot/core/util/structure.py
index dd6cffd9..571f5dab 100644
--- a/pylot/core/util/structure.py
+++ b/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}
-- 
2.45.2


From 50cabb0038be120492a4fd9b39dcc17570d51ae1 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sat, 20 Jul 2024 10:23:40 +0200
Subject: [PATCH 25/31] refactor: remove unused code; rewrite too complex
 functions

---
 PyLoT.py | 537 ++++++++++++++++++++-----------------------------------
 1 file changed, 196 insertions(+), 341 deletions(-)

diff --git a/PyLoT.py b/PyLoT.py
index 46745c52..59e66551 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -108,6 +108,7 @@ locateTool = dict(nll=nll)
 
 
 class MainWindow(QMainWindow):
+    _metadata: Metadata
     __version__ = _getVersionString()
     closing = Signal()
 
@@ -241,20 +242,6 @@ class MainWindow(QMainWindow):
 
         self.loc = False
 
-    def init_config_files(self, infile):
-        pylot_config_dir = os.path.join(os.path.expanduser('~'), '.pylot')
-        if not os.path.exists(pylot_config_dir):
-            os.mkdir(pylot_config_dir)
-
-        self._inputs = PylotParameter(infile)
-        if not infile:
-            self._inputs.reset_defaults()
-            # check for default pylot.in-file
-            infile = os.path.join(pylot_config_dir, '.pylot.in')
-            logging.warning('Using default input file {}'.format(infile))
-            self._inputs.export2File(infile)
-        self.infile = infile
-
     def setupUi(self, use_logwidget=False):
         try:
             self.startTime = min(
@@ -911,7 +898,7 @@ class MainWindow(QMainWindow):
         return self._metadata
 
     @metadata.setter
-    def metadata(self, value):
+    def metadata(self, value: Metadata):
         self._metadata = value
 
     def updateFilteroptions(self):
@@ -1069,9 +1056,6 @@ class MainWindow(QMainWindow):
                 self.refreshEvents()
             self.setDirty(True)
 
-    def add_recentfile(self, event):
-        self.recentfiles.insert(0, event)
-
     def set_button_border_color(self, button, color=None):
         '''
         Set background color of a button.
@@ -1180,104 +1164,117 @@ class MainWindow(QMainWindow):
     def getLastEvent(self):
         return self.recentfiles[0]
 
-    def add_events(self):
+    def add_events(self) -> None:
         '''
         Creates and adds events by user selection of event folders to GUI.
         '''
         if not self.project:
             self.createNewProject()
-        ed = GetExistingDirectories(self, 'Select event directories...')
-        if ed.exec_():
-            eventlist = [event for event in ed.selectedFiles() if not event.endswith('EVENTS-INFO')]
-            basepath = eventlist[0].split(os.path.basename(eventlist[0]))[0]
-            # small hack: if a file "eventlist.txt" is found in the basepath use only those events specified inside
-            eventlist_file = os.path.join(basepath, 'eventlist.txt')
-            if os.path.isfile(eventlist_file):
-                with open(eventlist_file, 'r') as infile:
-                    eventlist_subset = [os.path.join(basepath, filename.split('\n')[0]) for filename in
-                                        infile.readlines()]
-                    msg = 'Found file "eventlist.txt" in database path. WILL ONLY USE SELECTED EVENTS out of {} events ' \
-                          'contained in this subset'
-                    print(msg.format(len(eventlist_subset)))
-                    eventlist = [eventname for eventname in eventlist if eventname in eventlist_subset]
-            if check_obspydmt_structure(basepath):
-                print('Recognized obspyDMT structure in selected files. Setting Datastructure to ObspyDMT')
-                self.dataStructure = DATASTRUCTURE['obspyDMT']()
-                eventlist = check_all_obspy(eventlist)
-            else:
-                print('Setting Datastructure to PILOT')
-                self.dataStructure = DATASTRUCTURE['PILOT']()
-                eventlist = check_all_pylot(eventlist)
-            if not eventlist:
-                print('No events found! Expected structure for event folders: [eEVID.DOY.YR],\n'
-                      ' e.g. eventID=1, doy=2, yr=2016: e0001.002.16 or obspyDMT database')
-                return
-        else:
-            return
-        if not self.project:
-            print('No project found.')
+
+        eventlist, basepath = self.get_event_directories()
+        if not eventlist:
             return
 
-        # get path from first event in list and split them
-        path = eventlist[0]
+        eventlist = self.set_data_structure(basepath, eventlist)
+        if not eventlist:
+            self.show_no_events_message()
+            return
+
+        dirs = self.initialize_directory_structure(eventlist[0])
+        if not dirs:
+            return
+
+        self.update_project_settings(dirs)
+
+        self.project.add_eventlist(eventlist)
+        self.init_events()
+        self.setDirty(True)
+
+    def get_event_directories(self):
+        ed = GetExistingDirectories(self, 'Select event directories...')
+        if not ed.exec_():
+            return None, None
+
+        eventlist = [event for event in ed.selectedFiles() if not event.endswith('EVENTS-INFO')]
+        basepath = eventlist[0].split(os.path.basename(eventlist[0]))[0]
+        eventlist = self.filter_eventlist_with_file(eventlist, basepath)
+        return eventlist, basepath
+
+    def filter_eventlist_with_file(self, eventlist, basepath):
+        eventlist_file = os.path.join(basepath, 'eventlist.txt')
+        if os.path.isfile(eventlist_file):
+            with open(eventlist_file, 'r') as infile:
+                eventlist_subset = [os.path.join(basepath, filename.strip()) for filename in infile]
+                print(
+                    f'Found file "eventlist.txt" in database path. WILL ONLY USE SELECTED EVENTS out of {len(eventlist_subset)} events contained in this subset')
+                eventlist = [eventname for eventname in eventlist if eventname in eventlist_subset]
+        return eventlist
+
+    def set_data_structure(self, basepath, eventlist):
+        if check_obspydmt_structure(basepath):
+            print('Recognized obspyDMT structure in selected files. Setting Datastructure to ObspyDMT')
+            self.dataStructure = DATASTRUCTURE['obspyDMT']()
+            eventlist = check_all_obspy(eventlist)
+        else:
+            print('Setting Datastructure to PILOT')
+            self.dataStructure = DATASTRUCTURE['PILOT']()
+            eventlist = check_all_pylot(eventlist)
+        return eventlist
+
+    def show_no_events_message(self):
+        print('No events found! Expected structure for event folders: [eEVID.DOY.YR],\n'
+              ' e.g. eventID=1, doy=2, yr=2016: e0001.002.16 or obspyDMT database')
+
+    def initialize_directory_structure(self, path):
         try:
             system_name = platform.system()
             if system_name in ["Linux", "Darwin"]:
                 dirs = {
                     'database': path.split('/')[-2],
-                    'datapath': os.path.split(path)[0],  # path.split('/')[-3],
+                    'datapath': os.path.split(path)[0],
                     'rootpath': '/' + os.path.join(*path.split('/')[:-3])
                 }
             elif system_name == "Windows":
                 rootpath = path.split('/')[:-3]
                 rootpath[0] += '/'
                 dirs = {
-                    # TODO: Arrange path to meet Win standards
                     'database': path.split('/')[-2],
                     'datapath': path.split('/')[-3],
                     'rootpath': os.path.join(*rootpath)
                 }
         except Exception as e:
-            dirs = {
-                'database': '',
-                'datapath': '',
-                'rootpath': ''
-            }
-            print('Warning: Could not automatically init folder structure. ({})'.format(e))
+            print(f'Warning: Could not automatically init folder structure. ({e})')
+            return None
 
+        self.save_directory_settings(dirs['datapath'])
+        return dirs
+
+    def save_directory_settings(self, datapath):
         settings = QSettings()
-        settings.setValue("data/dataRoot", dirs['datapath'])  # d irs['rootpath'])
+        settings.setValue("data/dataRoot", datapath)
         settings.sync()
 
+    def update_project_settings(self, dirs):
         if not self.project.eventlist:
-            # init parameter object
-            self.setParameter(show=False)
-            # hide all parameter (show all needed parameter later)
+            self.set_parameter(show=False)
             self.paraBox.hide_parameter()
-            for directory in dirs.keys():
-                # set parameter
-                box = self.paraBox.boxes[directory]
-                self.paraBox.setValue(box, dirs[directory])
-                # show needed parameter in box
-                self.paraBox.show_parameter(directory)
-            dirs_box = self.paraBox.get_groupbox_dialog('Directories')
-            if not dirs_box.exec_():
+            self.update_paraBox(dirs)
+            if not self.paraBox.get_groupbox_dialog('Directories').exec_():
                 return
             self.project.rootpath = dirs['rootpath']
             self.project.datapath = dirs['datapath']
         else:
-            if hasattr(self.project, 'datapath'):
-                if not self.project.datapath == dirs['datapath']:
-                    QMessageBox.warning(self, "PyLoT Warning",
-                                        'Datapath missmatch to current project!')
-                    return
-            else:
-                self.project.rootpath = dirs['rootpath']
-                self.project.datapath = dirs['datapath']
+            if hasattr(self.project, 'datapath') and self.project.datapath != dirs['datapath']:
+                QMessageBox.warning(self, "PyLoT Warning", 'Datapath mismatch to current project!')
+                return
+            self.project.rootpath = dirs['rootpath']
+            self.project.datapath = dirs['datapath']
 
-        self.project.add_eventlist(eventlist)
-        self.init_events()
-        self.setDirty(True)
+    def update_paraBox(self, dirs):
+        for directory, path in dirs.items():
+            box = self.paraBox.boxes[directory]
+            self.paraBox.setValue(box, path)
+            self.paraBox.show_parameter(directory)
 
     def remove_event(self, event):
         qmb = QMessageBox(self, icon=QMessageBox.Question,
@@ -1297,11 +1294,6 @@ class MainWindow(QMainWindow):
         '''
         qcb = QComboBox()
         palette = qcb.palette()
-        # change highlight color:
-        # palette.setBrush(QtGui.QPalette.Inactive, QtGui.QPalette.Highlight,
-        #                  QtGui.QBrush(QtGui.QColor(0,0,127,127)))
-        # palette.setBrush(QtGui.QPalette.Active, QtGui.QPalette.Highlight,
-        #                  QtGui.QBrush(QtGui.QColor(0,0,127,127)))
         qcb.setPalette(palette)
         return qcb
 
@@ -1376,15 +1368,40 @@ class MainWindow(QMainWindow):
         :type: str
         '''
 
-        # if pick widget is open, refresh tooltips as well
+        self.refresh_tooltips()
+
+        if not eventBox:
+            eventBox = self.eventBox
+        self.setup_eventBox(eventBox)
+
+        current_event = self.get_current_event()
+        eventBox.clear()
+        model = eventBox.model()
+
+        plmax = self.get_max_path_length()
+        index = eventBox.currentIndex()
+
+        for id, event in enumerate(self.project.eventlist):
+            event_data = self.collect_event_data(event, plmax)
+            itemlist = self.create_event_items(event_data)
+            self.setItemColor(itemlist, id, event, current_event)
+
+            if event.isTestEvent() and select_events == 'ref' or self.isEmpty(event.path):
+                self.disable_items(itemlist)
+
+            model.appendRow(itemlist)
+            self.validate_event_path(event.path, id)
+
+        eventBox.setCurrentIndex(index)
+        self.refreshRefTestButtons()
+
+    def refresh_tooltips(self):
         if self.apw:
             self.apw.refresh_tooltips()
         if hasattr(self, 'cmpw'):
             self.cmpw.refresh_tooltips()
 
-        if not eventBox:
-            eventBox = self.eventBox
-        index = eventBox.currentIndex()
+    def setup_eventBox(self, eventBox):
         tv = QtWidgets.QTableView()
         header = tv.horizontalHeader()
         header.setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
@@ -1392,136 +1409,107 @@ class MainWindow(QMainWindow):
         header.hide()
         tv.verticalHeader().hide()
         tv.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
-
-        current_event = self.get_current_event()
-
         eventBox.setView(tv)
-        eventBox.clear()
-        model = eventBox.model()
-        plmax = 0
-        # set maximum length of path string
-        for event in self.project.eventlist:
-            pl = len(event.path)
-            if pl > plmax:
-                plmax = pl
 
-        for id, event in enumerate(self.project.eventlist):
-            event_path = event.path
-            #phaseErrors = {'P': self._inputs['timeerrorsP'],
-            #               'S': self._inputs['timeerrorsS']}
+    def get_max_path_length(self):
+        return max(len(event.path) for event in self.project.eventlist)
 
-            man_au_picks = {'manual': event.pylot_picks,
-                            'auto': event.pylot_autopicks}
-            npicks = {'manual': {'P': 0, 'S': 0},
-                      'auto': {'P': 0, 'S': 0}}
-            npicks_total = {'manual': {'P': 0, 'S': 0},
-                            'auto': {'P': 0, 'S': 0}}
+    def collect_event_data(self, event, plmax):
+        data = {
+            'path': event.path,
+            'picks': self.get_picks(event),
+            'is_ref': event.isRefEvent(),
+            'is_test': event.isTestEvent(),
+            'time': None,
+            'lat': None,
+            'lon': None,
+            'depth': None,
+            'localmag': None,
+            'momentmag': None,
+            'notes': event.notes,
+            'dirty': event.dirty,
+            'plmax': plmax,
+        }
 
-            for ma in man_au_picks.keys():
-                if man_au_picks[ma]:
-                    for picks in man_au_picks[ma].values():
-                        for phasename, pick in picks.items():
-                            if not type(pick) in [dict, AttribDict]:
-                                continue
+        if event.origins:
+            origin = event.origins[0]
+            data['time'] = origin.time + 0  # add 0 to avoid exception for time = 0s
+            data['lat'] = origin.latitude
+            data['lon'] = origin.longitude
+            data['depth'] = origin.depth
+
+        if event.magnitudes:
+            data['momentmag'] = '{:.1f}'.format(event.magnitudes[0].mag)
+            data['localmag'] = '{:.1f}'.format(event.magnitudes[1].mag) if len(event.magnitudes) > 1 else ' '
+
+        return data
+
+    def get_picks(self, event):
+        man_au_picks = {'manual': event.pylot_picks, 'auto': event.pylot_autopicks}
+        npicks = {'manual': {'P': 0, 'S': 0}, 'auto': {'P': 0, 'S': 0}}
+        npicks_total = {'manual': {'P': 0, 'S': 0}, 'auto': {'P': 0, 'S': 0}}
+
+        for ma, picks in man_au_picks.items():
+            if picks:
+                for pick_values in picks.values():
+                    for phasename, pick in pick_values.items():
+                        if isinstance(pick, (dict, AttribDict)):
                             phase_ID = identifyPhaseID(phasename)
-                            if not phase_ID in npicks[ma].keys():
-                                continue
-                            if pick.get('spe'):
-                                npicks[ma][phase_ID] += 1
-                            npicks_total[ma][phase_ID] += 1
+                            if phase_ID in npicks[ma]:
+                                if pick.get('spe'):
+                                    npicks[ma][phase_ID] += 1
+                                npicks_total[ma][phase_ID] += 1
 
-            event_ref = event.isRefEvent()
-            event_test = event.isTestEvent()
+        return npicks, npicks_total
 
-            time = lat = lon = depth = localmag = None
-            if len(event.origins) == 1:
-                origin = event.origins[0]
-                time = origin.time + 0  # add 0 because there was an exception for time = 0s
-                lat = origin.latitude
-                lon = origin.longitude
-                depth = origin.depth
-            if len(event.magnitudes):  # if magnitude information exists, i.e., event.magnitudes has at least 1 entry
-                moment_magnitude = event.magnitudes[0]
-                momentmag = '%4.1f' % moment_magnitude.mag
-                if len(event.magnitudes) > 1:
-                    local_magnitude = event.magnitudes[1]
-                    localmag = '%4.1f' % local_magnitude.mag
-                else:
-                    localmag = ' '
+    def create_event_items(self, data):
+        items = [
+            self.create_standard_item(data['path'], data['plmax'],
+                                      icon=self.style().standardIcon(QStyle.SP_DirOpenIcon)),
+            self.create_standard_item(data['time'].strftime("%Y-%m-%d %H:%M:%S") if data['time'] else ''),
+            self.create_standard_item(data['lat']),
+            self.create_standard_item(data['lon']),
+            self.create_standard_item(data['depth']),
+            self.create_standard_item(data['localmag']),
+            self.create_standard_item(data['momentmag']),
+            self.create_pick_item(data['picks'][0]['manual']),
+            self.create_pick_item(data['picks'][0]['auto']),
+            self.create_ref_test_item(data['is_ref'], 'ref'),
+            self.create_ref_test_item(data['is_test'], 'test'),
+            self.create_standard_item(data['notes'])
+        ]
 
-            else:
-                momentmag = ' '
-                localmag = ' '
+        for item in items:
+            item.setTextAlignment(Qt.AlignCenter)
+            if data['dirty'] and item == items[0]:
+                item.setText(f"{item.text()}*")
 
-            # text = '{path:{plen}} | manual: [{p:3d}] | auto: [{a:3d}]'
-            # text = text.format(path=event_path,
-            #                    plen=plmax,
-            #                    p=event_npicks,
-            #                    a=event_nautopicks)
+        return items
 
-            event_str = '{path:{plen}}'.format(path=event_path, plen=plmax)
-            if event.dirty:
-                event_str += '*'
-            item_path = QStandardItem(event_str)
-            item_time = QStandardItem('{}'.format(time.strftime("%Y-%m-%d %H:%M:%S") if time else ''))
-            item_lat = QStandardItem('{}'.format(lat))
-            item_lon = QStandardItem('{}'.format(lon))
-            item_depth = QStandardItem('{}'.format(depth))
-            item_localmag = QStandardItem('{}'.format(localmag))
-            item_momentmag = QStandardItem('{}'.format(momentmag))
+    def create_standard_item(self, text, max_length=None, icon=None):
+        item = QStandardItem(f"{text:{max_length}}" if max_length else str(text))
+        if icon:
+            item.setIcon(icon)
+        return item
 
-            item_nmp = QStandardItem()
-            item_nap = QStandardItem()
-            item_nmp.setIcon(self.manupicksicon_small)
-            item_nap.setIcon(self.autopicksicon_small)
+    def create_pick_item(self, picks):
+        item = QStandardItem()
+        item.setText(f"{picks['P']}|{picks['S']}")
+        return item
 
-            for picktype, item_np in [('manual', item_nmp), ('auto', item_nap)]:
-                npicks_str = f"{npicks[picktype]['P']}|{npicks[picktype]['S']}"
-                #npicks_str += f"({npicks_total[picktype]['P']}/{npicks_total[picktype]['S']})"
-                item_np.setText(npicks_str)
+    def create_ref_test_item(self, condition, color_key):
+        item = QStandardItem()
+        if condition:
+            item.setBackground(self._ref_test_colors[color_key])
+        return item
 
-            item_ref = QStandardItem()  # str(event_ref))
-            item_test = QStandardItem()  # str(event_test))
-            if event_ref:
-                item_ref.setBackground(self._ref_test_colors['ref'])
-            if event_test:
-                item_test.setBackground(self._ref_test_colors['test'])
-            item_notes = QStandardItem(event.notes)
+    def disable_items(self, items):
+        for item in items:
+            item.setEnabled(False)
 
-            openIcon = self.style().standardIcon(QStyle.SP_DirOpenIcon)
-            item_path.setIcon(openIcon)
-            # if ref: set different color e.g.
-            # if event_ref:
-            #     item.setBackground(self._colors['ref'])
-            # if event_test:
-            #     itemt.setBackground(self._colors['test'])
-            # item.setForeground(QtGui.QColor('black'))
-            # font = item.font()
-            # font.setPointSize(10)
-            # item.setFont(font)
-            # item2.setForeground(QtGui.QColor('black'))
-            # item2.setFont(font)
-            itemlist = [item_path, item_time, item_lat, item_lon, item_depth,
-                        item_localmag, item_momentmag, item_nmp, item_nap, item_ref, item_test, item_notes]
-            for item in itemlist:
-                item.setTextAlignment(Qt.AlignCenter)
-            if event_test and select_events == 'ref' or self.isEmpty(event_path):
-                for item in itemlist:
-                    item.setEnabled(False)
-
-            # item color
-            self.setItemColor(itemlist, id, event, current_event)
-
-            model.appendRow(itemlist)
-            if not event.path == self.eventBox.itemText(id).split('*')[0].strip():
-                message = ('Path missmatch creating eventbox.\n'
-                           '{} unequal {}.'
-                           .format(event.path, self.eventBox.itemText(id)))
-                raise ValueError(message)
-                # not working with obspy events
-                # eventBox.setItemData(id, event)
-        eventBox.setCurrentIndex(index)
-        self.refreshRefTestButtons()
+    def validate_event_path(self, path, id):
+        if path != self.eventBox.itemText(id).split('*')[0].strip():
+            raise ValueError(f"Path mismatch creating eventbox. {path} unequal {self.eventBox.itemText(id)}")
 
     def isEmpty(self, event_path):
         wf_stat = {True: 'processed',
@@ -1978,14 +1966,6 @@ class MainWindow(QMainWindow):
         '''
         Load waveform data corresponding to current selected event.
         '''
-        # if self.fnames and self.okToContinue():
-        #     self.setDirty(True)
-        #     ans = self.data.setWFData(self.fnames)
-        # elif self.fnames is None and self.okToContinue():
-        #     ans = self.data.setWFData(self.getWFFnames())
-        # else:
-        #     ans = False
-
         settings = QSettings()
         # process application events to wait for event items to appear in event box
         QApplication.processEvents()
@@ -2033,21 +2013,6 @@ class MainWindow(QMainWindow):
         eventpath_dmt = os.path.join(eventpath, wftype)
         self.fnames = [os.path.join(eventpath_dmt, filename) for filename in os.listdir(eventpath_dmt)]
 
-    # def setWFstatus(self):
-    #     '''
-    #     show status of current data, can be either 'raw' or 'processed'
-    #     :param status:
-    #     :return:
-    #     '''
-    #     status = self.data.processed
-    #     wf_stat_color = {True: 'green',
-    #                      False: 'black',
-    #                      None: None}
-    #     wf_stat = {True: 'processed',
-    #                False: 'raw',
-    #                None: None}
-    #     self.dataPlot.setQCboxItem(wf_stat[status])
-
     def check_plot_quantity(self):
         """
         Check the amount of samples to be plotted and ask user to reduce the amount if it is too large.
@@ -2067,24 +2032,6 @@ class MainWindow(QMainWindow):
             self.update_status('Dataset is very large. Using fast plotting method (MIN/MAX)', 10000)
         settings.sync()
         return True
-        # nth_sample_new = int(np.ceil(npts/npts_max))
-        # message = "You are about to plot a huge dataset with {npts} datapoints. With a current setting of " \
-        #           "nth_sample = {nth_sample} a total of {npts2plot} points will be plotted which is more " \
-        #           "than the maximum setting of {npts_max}. " \
-        #           "PyLoT recommends to raise nth_sample from {nth_sample} to {nth_sample_new}. Do you want "\
-        #           "to change nth_sample to {nth_sample_new} now?"
-        #
-        # ans = QMessageBox.question(self, self.tr("Optimize plot performance..."),
-        #                            self.tr(message.format(npts=npts,
-        #                                                   nth_sample=nth_sample,
-        #                                                   npts_max=npts_max,
-        #                                                   nth_sample_new=nth_sample_new,
-        #                                                   npts2plot=npts2plot)),
-        #                            QMessageBox.Yes | QMessageBox.No,
-        #                            QMessageBox.Yes)
-        # if ans == QMessageBox.Yes:
-        #     settings.setValue("nth_sample", nth_sample_new)
-        #     settings.sync()
 
     def get_npts_to_plot(self):
         if not hasattr(self.data, 'wfdata'):
@@ -2334,20 +2281,14 @@ class MainWindow(QMainWindow):
     def plotZ(self):
         self.setComponent('Z')
         self.plotWaveformDataThread()
-        # self.drawPicks()
-        # self.draw()
 
     def plotN(self):
         self.setComponent('N')
         self.plotWaveformDataThread()
-        # self.drawPicks()
-        # self.draw()
 
     def plotE(self):
         self.setComponent('E')
         self.plotWaveformDataThread()
-        # self.drawPicks()
-        # self.draw()
 
     def pushFilterWF(self, param_args):
         self.get_data().filterWFData(param_args)
@@ -2393,8 +2334,6 @@ class MainWindow(QMainWindow):
                 self.get_data().resetWFData()
             if plot:
                 self.plotWaveformDataThread(filter=False)
-                # self.drawPicks()
-                # self.draw()
 
     def getAutoFilteroptions(self, phase):
         return getAutoFilteroptions(phase, self._inputs)
@@ -2426,20 +2365,8 @@ class MainWindow(QMainWindow):
 
     def getFilterOptions(self):
         return self.filteroptions
-        # try:
-        #     return self.filteroptions[self.getSeismicPhase()]
-        # except AttributeError as e:
-        #     print(e)
-        #     return FilterOptions(None, None, None)
 
-    def getFilters(self):
-        return self.filteroptions
-
-    def setFilterOptions(self, filterOptions):  # , seismicPhase=None):
-        # if seismicPhase is None:
-        #     self.getFilterOptions()[self.getSeismicPhase()] = filterOptions
-        # else:
-        #     self.getFilterOptions()[seismicPhase] = filterOptions
+    def setFilterOptions(self, filterOptions):
         self.filterOptions = filterOptions
         filterP = filterOptions['P']
         filterS = filterOptions['S']
@@ -2468,28 +2395,6 @@ class MainWindow(QMainWindow):
 
         self.checkFilterOptions()
 
-    # def updateFilterOptions(self):
-    #     try:
-    #         settings = QSettings()
-    #         if settings.value("filterdefaults",
-    #                           None) is None and not self.getFilters():
-    #             for key, value in FILTERDEFAULTS.items():
-    #                 self.setFilterOptions(FilterOptions(**value), key)
-    #         elif settings.value("filterdefaults", None) is not None:
-    #             for key, value in settings.value("filterdefaults"):
-    #                 self.setFilterOptions(FilterOptions(**value), key)
-    #     except Exception as e:
-    #         self.update_status('Error ...')
-    #         emsg = QErrorMessage(self)
-    #         emsg.showMessage('Error: {0}'.format(e))
-    #     else:
-    #         self.update_status('Filter loaded ... '
-    #                            '[{0}: {1} Hz]'.format(
-    #             self.getFilterOptions().getFilterType(),
-    #             self.getFilterOptions().getFreq()))
-    #     if self.filterActionP.isChecked() or self.filterActionS.isChecked():
-    #         self.filterWaveformData()
-
     def getSeismicPhase(self):
         return self.seismicPhase
 
@@ -2515,11 +2420,6 @@ class MainWindow(QMainWindow):
     def alterPhase(self):
         pass
 
-    def setSeismicPhase(self, phase):
-        self.seismicPhase = self.seismicPhaseButtonGroup.getValue()
-        self.update_status('Seismic phase changed to '
-                           '{0}'.format(self.getSeismicPhase()))
-
     def scrollPlot(self, gui_event):
         '''
         Function connected to mouse wheel scrolling inside WFdataPlot.
@@ -2935,11 +2835,6 @@ class MainWindow(QMainWindow):
         automanu[type](station=station, pick=picks)
         return rval
 
-    def deletePicks(self, station, deleted_pick, type):
-        deleted_pick['station'] = station
-        self.addPicks(station, {}, type=type)
-        self.log_deleted_picks([deleted_pick])
-
     def log_deleted_picks(self, deleted_picks, event_path=None):
         '''
         Log deleted picks to list self.deleted_picks
@@ -3075,10 +2970,6 @@ class MainWindow(QMainWindow):
                 elif phaseID == 'S':
                     quality = getQualityFromUncertainty(picks['spe'], self._inputs['timeerrorsS'])
 
-                # quality = getPickQuality(self.get_data().getWFData(),
-                #                          stat_picks, self._inputs, phaseID,
-                #                          compclass)
-
                 if not picks['mpp']: continue
 
                 mpp = picks['mpp'] - stime
@@ -3628,19 +3519,6 @@ class MainWindow(QMainWindow):
     def check4Loc(self):
         return self.picksNum() >= 4
 
-    # def check4Comparison(self):
-    #     mpicks = self.getPicks()
-    #     apicks = self.getPicks('auto')
-    #     for station, phases in mpicks.items():
-    #         try:
-    #             aphases = apicks[station]
-    #             for phase in phases.keys():
-    #                 if phase in aphases.keys():
-    #                     return True
-    #         except KeyError:
-    #             continue
-    #     return False
-
     def picksNum(self, type='manual'):
         num = 0
         for phases in self.getPicks(type).values():
@@ -3681,16 +3559,6 @@ class MainWindow(QMainWindow):
     def show_event_information(self):
         pass
 
-    def createNewEvent(self):
-        if self.okToContinue():
-            new = NewEventDlg()
-            if new.exec_() != QDialog.Rejected:
-                evtpar = new.getValues()
-                cinfo = create_creation_info(agency_id=self.agency)
-                event = create_event(evtpar['origintime'], cinfo)
-                self.data = Data(self, evtdata=event)
-                self.setDirty(True)
-
     def createNewProject(self):
         '''
         Create new project file.
@@ -3834,16 +3702,6 @@ class MainWindow(QMainWindow):
         self.dirty = value
         self.fill_eventbox()
 
-    def closeEvent(self, event):
-        if self.okToContinue():
-            if hasattr(self, 'logwidget'):
-                self.logwidget.close()
-            event.accept()
-        else:
-            event.ignore()
-            # self.closing.emit()
-            # QMainWindow.closeEvent(self, event)
-
     def setParameter(self, checked=0, show=True):
         if checked: pass  # dummy argument to receive trigger signal (checked) if called by QAction
         if not self.paraBox:
@@ -4095,8 +3953,6 @@ def create_window():
     app.setOrganizationDomain("rub.de")
     app.setApplicationName("PyLoT")
     app.references = set()
-    # app.references.add(window)
-    # window.show()
     return app, app_created
 
 
@@ -4104,7 +3960,6 @@ def main(project_filename=None, pylot_infile=None, reset_qsettings=False):
 
     # create the Qt application
     pylot_app, app_created = create_window()
-    # pylot_app = QApplication(sys.argv)
     pixmap = QPixmap(":/splash/splash.png")
     splash = QSplashScreen(pixmap)
     splash.show()
-- 
2.45.2


From 29a1e4ebe6bc193d3031d2cd006c6351176d37e2 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sat, 20 Jul 2024 10:30:18 +0200
Subject: [PATCH 26/31] refactor: move Project definition to individual file

---
 PyLoT.py                               | 183 +------------------------
 pylot/core/io/project.py               | 177 ++++++++++++++++++++++++
 pylot/core/util/generate_array_maps.py |   2 +-
 3 files changed, 180 insertions(+), 182 deletions(-)
 create mode 100644 pylot/core/io/project.py

diff --git a/PyLoT.py b/PyLoT.py
index 59e66551..334a5652 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -25,7 +25,6 @@ https://www.iconfinder.com/iconsets/flavour
 
 import argparse
 import json
-import logging
 import os
 import platform
 import shutil
@@ -48,7 +47,6 @@ from PySide2.QtWidgets import QMainWindow, QInputDialog, QFileDialog, \
     QTreeView, QComboBox, QTabWidget, QPushButton, QGridLayout, QTableWidgetItem, QTableWidget
 import numpy as np
 from obspy import UTCDateTime, Stream
-from obspy.core.event import Magnitude, Origin
 from obspy.core.util import AttribDict
 
 from pylot.core.util.obspyDMT_interface import check_obspydmt_structure
@@ -68,6 +66,7 @@ from autoPyLoT import autoPyLoT
 from pylot.core.pick.compare import Comparison
 from pylot.core.pick.utils import getQualityFromUncertainty
 from pylot.core.io.phases import picksdict_from_picks
+from pylot.core.io.project import Project
 import pylot.core.loc.nll as nll
 from pylot.core.util.errors import DatastructureError, \
     OverwriteError
@@ -79,10 +78,7 @@ from pylot.core.util.utils import fnConstructor, get_login, \
     transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
     check_all_pylot, get_bool, get_None, get_pylot_eventfile_with_extension
 from pylot.core.util.gui import make_pen
-from pylot.core.util.event import Event
-from pylot.core.io.location import create_creation_info, create_event
-from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
-    PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
+from pylot.core.util.widgets import FilterOptionsDialog, PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog, LogWidget, PickQualitiesFromXml, \
     SourceSpecWindow, ChooseWaveFormWindow, SpectrogramTab, SearchFileByExtensionDialog
@@ -3751,181 +3747,6 @@ class MainWindow(QMainWindow):
             form = HelpForm(self, ':/help.html')
         form.show()
 
-
-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
-
-
 class GetExistingDirectories(QFileDialog):
     '''
     File dialog with possibility to select multiple folders.
diff --git a/pylot/core/io/project.py b/pylot/core/io/project.py
new file mode 100644
index 00000000..764b004a
--- /dev/null
+++ b/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
diff --git a/pylot/core/util/generate_array_maps.py b/pylot/core/util/generate_array_maps.py
index 0e7a9d64..69d3bb59 100755
--- a/pylot/core/util/generate_array_maps.py
+++ b/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
 
-- 
2.45.2


From b15cfe2e1da32945dbcdb8e3eb209903b6b1db39 Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Tue, 23 Jul 2024 13:42:45 +0200
Subject: [PATCH 27/31] bugfix: corrected for ValueError

---
 PyLoT.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/PyLoT.py b/PyLoT.py
index 334a5652..a6d902d8 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -1408,7 +1408,10 @@ class MainWindow(QMainWindow):
         eventBox.setView(tv)
 
     def get_max_path_length(self):
-        return max(len(event.path) for event in self.project.eventlist)
+        if self.project.eventlist:
+            return max(len(event.path) for event in self.project.eventlist)
+        else:
+            return None
 
     def collect_event_data(self, event, plmax):
         data = {
-- 
2.45.2


From 63dac0fff692484f7e057c49a2961491dcc3347e Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Tue, 23 Jul 2024 15:17:00 +0200
Subject: [PATCH 28/31] refactor: restructure data objects

---
 pylot/core/io/data.py         | 612 ++--------------------------------
 pylot/core/io/event.py        | 106 ++++++
 pylot/core/io/waveformdata.py | 243 ++++++++++++++
 3 files changed, 383 insertions(+), 578 deletions(-)
 create mode 100644 pylot/core/io/event.py
 create mode 100644 pylot/core/io/waveformdata.py

diff --git a/pylot/core/io/data.py b/pylot/core/io/data.py
index 6259c6d7..1172568e 100644
--- a/pylot/core/io/data.py
+++ b/pylot/core/io/data.py
@@ -1,605 +1,61 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import copy
-import logging
 import os
-import fnmatch
 from dataclasses import dataclass, field
-from typing import List
+from typing import List, Union
 
-from PySide2.QtWidgets import QMessageBox
-from obspy import read, read_events, Stream, Catalog, UTCDateTime
-from obspy.core.event import Event as ObsPyEvent
-from obspy.io.sac import SacIOError
+from obspy import UTCDateTime
 
+from pylot.core.io.event import EventData
+from pylot.core.io.waveformdata import WaveformData
 
-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, \
-    check_for_gaps_and_merge, trim_station_components, check_for_nan
-
-
-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)
+    _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 '
-                                                  'implemented.')
-                    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 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 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_alt=None, checkRotated=False, metadata=None, tstart=0, tstop=0):
-        """
-        Clear current waveform data and set given waveform data
-        :param fnames: waveform data names to append
-        :param fnames_alt: alternative data to show (e.g. synthetic/processed)
-        :type fnames: list
-        """
-        def check_fname_exists(filenames: list) -> list:
-            if filenames:
-                filenames = [fn for fn in filenames if os.path.isfile(fn)]
-            return filenames
-
-        self.wfdata = Stream()
-        self.wforiginal = None
-        self.wf_alt = Stream()
-        if tstart == tstop:
-            tstart = tstop = None
-        self.tstart = tstart
-        self.tstop = tstop
-
-        # remove directories
-        fnames = check_fname_exists(fnames)
-        fnames_alt = check_fname_exists(fnames_alt)
-
-        if fnames is not None:
-            self.appendWFData(fnames)
-            if fnames_alt is not None:
-                self.appendWFData(fnames_alt, alternative=True)
-        else:
-            return False
-
-        # check for gaps and merge
-        self.wfdata, _ = check_for_gaps_and_merge(self.wfdata)
-        # check for nans
-        check_for_nan(self.wfdata)
-        # check for stations with rotated components
-        if checkRotated and metadata is not None:
-            self.wfdata = check4rotated(self.wfdata, metadata, verbosity=0)
-        # 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, alternative=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()
-
-        orig_or_alternative_data = {True: self.wf_alt,
-                                    False: self.wfdata}
-
-        warnmsg = ''
-        for fname in set(fnames):
-            try:
-                orig_or_alternative_data[alternative] += read(fname, starttime=self.tstart, endtime=self.tstop)
-            except TypeError:
-                try:
-                    orig_or_alternative_data[alternative] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
-                except Exception as e:
-                    try:
-                        orig_or_alternative_data[alternative] += read(fname, format='SEGY', starttime=self.tstart,
-                                                                      endtime=self.tstop)
-                    except Exception as e:
-                        warnmsg += '{0}\n{1}\n'.format(fname, e)
-            except SacIOError as se:
-                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 getAltWFdata(self):
-        return self.wf_alt
-
-    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
-
-        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
-
-@dataclass
-class SeismicEventData:
-    event_id: str = ""
-    catalog: Catalog = field(default_factory=Catalog)
-
-    def find_event_files(self, directory: str, extensions: List[str]) -> List[str]:
-        """
-        Browse the directory to find event files with specified extensions.
-
-        Parameters:
-        directory (str): The directory path to search for event files.
-        extensions (List[str]): List of file extensions to search for.
-
-        Returns:
-        List[str]: List of file paths that match the given extensions.
-
-        Example:
-        >>> sed = SeismicEventData()
-        >>> sed.find_event_files('test_directory', ['.xml', '.quakeml']) # doctest: +SKIP
-        ['test_directory/event1.xml', 'test_directory/event2.quakeml']
-        """
-        matches = []
-        for root, _, files in os.walk(directory):
-            for ext in extensions:
-                for filename in fnmatch.filter(files, f'*{ext}'):
-                    matches.append(os.path.join(root, filename))
-        return matches
-
-    def read_event_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
-        """
-        Read a seismic event from the first found file in the directory with specified format.
-
-        Parameters:
-        directory (str): The directory path to search for event files.
-        extensions (List[str]): List of file extensions to search for.
-        format (str): The format to read the event file.
-
-        Example:
-        >>> sed = SeismicEventData()
-        >>> sed.read_event_from_directory('test_directory', ['.xml', '.quakeml'], 'QUAKEML') # doctest: +SKIP
-        """
-        event_files = self.find_event_files(directory, extensions)
-        if event_files:
-            self.read_event(event_files[0], format)
-        else:
-            raise FileNotFoundError(f"No event files found in directory {directory} with extensions {extensions}.")
-
-    def read_event(self, file_path: str, format: str) -> None:
-        """
-        Read a seismic event from a file with specified format.
-
-        Parameters:
-        file_path (str): The path to the event file.
-        format (str): The format to read the event file.
-
-        Example:
-        >>> sed = SeismicEventData()
-        >>> sed.read_event('test_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
-        """
-        if os.path.exists(file_path):
-            self.catalog = read_events(file_path, format=format)
-            self.event_id = self.catalog[0].resource_id.id.split('/')[-1] if self.catalog else ""
-        else:
-            raise FileNotFoundError(f"File {file_path} does not exist.")
-
-    def write_event(self, file_path: str, format: str) -> None:
-        """
-        Write the seismic event to a file with specified format.
-
-        Parameters:
-        file_path (str): The path to the output file.
-        format (str): The format to write the event file.
-
-        Example:
-        >>> sed = SeismicEventData(event_id='12345')
-        >>> sed.write_event('output_directory/event1.xml', 'QUAKEML') # doctest: +SKIP
-        """
-        self.catalog.write(file_path, format=format)
-
-@dataclass
-class WaveformData:
-    stream: Stream = field(default_factory=Stream)
-
-    def find_waveform_files(self, directory: str, extensions: List[str]) -> List[str]:
-        """
-        Browse the directory to find waveform files with specified extensions.
-
-        Parameters:
-        directory (str): The directory path to search for waveform files.
-        extensions (List[str]): List of file extensions to search for.
-
-        Returns:
-        List[str]: List of file paths that match the given extensions.
-
-        Example:
-        >>> wd = WaveformData()
-        >>> wd.find_waveform_files('test_directory', ['.mseed']) # doctest: +SKIP
-        ['test_directory/waveform1.mseed']
-        """
-        matches = []
-        for root, _, files in os.walk(directory):
-            for ext in extensions:
-                for filename in fnmatch.filter(files, f'*{ext}'):
-                    matches.append(os.path.join(root, filename))
-        return matches
-
-    def read_waveform_from_directory(self, directory: str, extensions: List[str], format: str) -> None:
-        """
-        Read waveform data from the first found file in the directory with specified format.
-
-        Parameters:
-        directory (str): The directory path to search for waveform files.
-        extensions (List[str]): List of file extensions to search for.
-        format (str): The format to read the waveform file.
-
-        Example:
-        >>> wd = WaveformData()
-        >>> wd.read_waveform_from_directory('test_directory', ['.mseed'], 'MSEED') # doctest: +SKIP
-        """
-        waveform_files = self.find_waveform_files(directory, extensions)
-        if waveform_files:
-            self.read_waveform(waveform_files[0], format)
-        else:
-            raise FileNotFoundError(f"No waveform files found in directory {directory} with extensions {extensions}.")
-
-    def read_waveform(self, file_path: str, format: str) -> None:
-        """
-        Read waveform data from a file with specified format.
-
-        Parameters:
-        file_path (str): The path to the waveform file.
-        format (str): The format to read the waveform file.
-
-        Example:
-        >>> wd = WaveformData()
-        >>> wd.read_waveform('test_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
-        """
-        if os.path.exists(file_path):
-            self.stream = read(file_path, format=format)
-        else:
-            raise FileNotFoundError(f"File {file_path} does not exist.")
-
-    def write_waveform(self, file_path: str, format: str) -> None:
-        """
-        Write the waveform data to a file with specified format.
-
-        Parameters:
-        file_path (str): The path to the output file.
-        format (str): The format to write the waveform file.
-
-        Example:
-        >>> wd = WaveformData()
-        >>> wd.write_waveform('output_directory/waveform1.mseed', 'MSEED') # doctest: +SKIP
-        """
-        self.stream.write(file_path, format=format)
-
-# Example usage:
-# seismic_event = SeismicEventData()
-# seismic_event.read_event_from_directory("path_to_directory", extensions=[".xml", ".quakeml"], format="QUAKEML")
-# seismic_event.write_event("output_event_file.xml", format="QUAKEML")
-
-# waveform_data = WaveformData()
-# waveform_data.read_waveform_from_directory("path_to_directory", extensions=[".mseed"], format="MSEED")
-# waveform_data.write_waveform("output_waveform_file.mseed", format="MSEED")
+    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.set_wf_data(fnames, fnames_alt, check_rotated, metadata, tstart, tstop)
 
+    def reset_wf_data(self):
+        self.waveform_data.reset_wf_data()
 
 class GenericDataStructure(object):
     """
diff --git a/pylot/core/io/event.py b/pylot/core/io/event.py
new file mode 100644
index 00000000..2f7a669b
--- /dev/null
+++ b/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}")
diff --git a/pylot/core/io/waveformdata.py b/pylot/core/io/waveformdata.py
new file mode 100644
index 00000000..7ecfff42
--- /dev/null
+++ b/pylot/core/io/waveformdata.py
@@ -0,0 +1,243 @@
+import logging
+import os
+from dataclasses import dataclass, field
+from typing import Union, List
+
+import numpy as np
+from obspy import Stream, read
+from obspy.io.sac import SacIOError
+from obspy.signal.rotate import rotate2zne
+
+from pylot.core.util.utils import full_range, get_stations
+
+
+@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 set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
+        self.clear_data()
+        fnames = self.check_fname_exists(fnames)
+        fnames_alt = self.check_fname_exists(fnames_alt)
+
+        if fnames:
+            self.append_wf_data(fnames)
+            if fnames_alt:
+                self.append_wf_data(fnames_alt, alternative=True)
+            self.wfdata, _ = self.check_for_gaps_and_merge(self.wfdata)
+            self.check_for_nan(self.wfdata)
+            if check_rotated and metadata:
+                self.wfdata = self.check4rotated(self.wfdata, metadata, verbosity=0)
+            self.trim_station_components(self.wfdata, trim_start=True, trim_end=False)
+            self.wforiginal = self.wfdata.copy()
+            self.dirty = False
+            return True
+        return False
+
+    def append_wf_data(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 appendWFData: unable to read waveform data\n{warnmsg}')
+
+    def clear_data(self):
+        self.wfdata = Stream()
+        self.wforiginal = None
+        self.wf_alt = Stream()
+
+    def reset_wf_data(self):
+        if self.wforiginal:
+            self.wfdata = self.wforiginal.copy()
+        else:
+            self.wfdata = Stream()
+        self.dirty = False
+
+    def check_fname_exists(self, filenames: List[str]) -> List[str]:
+        return [fn for fn in filenames if os.path.isfile(fn)]
+
+    def check_for_gaps_and_merge(self, stream):
+        """
+        check for gaps in Stream and merge if gaps are found
+        :param stream: stream of seismic data
+        :type stream: `~obspy.core.stream.Stream`
+        :return: data stream, gaps returned from obspy get_gaps
+        :rtype: `~obspy.core.stream.Stream`
+        """
+        gaps = stream.get_gaps()
+        if gaps:
+            merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
+            stream.merge(method=1)
+            print('Merged the following stations because of gaps:')
+            for merged_station in merged:
+                print(merged_station)
+
+        return stream, gaps
+
+    def check_for_nan(self, stream):
+        """
+        Replace all NaNs in data with nan_value (in place)
+        :param stream: stream of seismic data
+        :type stream: `~obspy.core.stream.Stream`
+        :param nan_value: value which all NaNs are set to
+        :type nan_value: float, int
+        :return: None
+        """
+        if not stream:
+            return
+        for trace in stream:
+            np.nan_to_num(trace.data, copy=False, nan=0.)
+
+
+    def check4rotated(self, stream, metadata=None, verbosity=1):
+        """
+        Check all traces in data. 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.
+        :param stream: stream object containing seismic traces
+        :type stream: `~obspy.core.stream.Stream`
+        :param metadata: tuple containing metadata type string and metadata parser object
+        :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
+        :param verbosity: if 0 print no information at runtime
+        :type verbosity: int
+        :return: stream object with traditionally oriented traces (ZNE) for stations that had misaligned traces (123) before
+        :rtype: `~obspy.core.stream.Stream`
+        """
+
+        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 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`
+            """
+
+            if len(wfs_in) < 3:
+                print(f"Stream {wfs_in=}, has not enough components to rotate.")
+                return wfs_in
+
+            # check if any traces in this station need to be rotated
+            trace_ids = [trace.id for trace in 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 = self.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:
+                msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
+                print(msg)
+            return stream
+        stations = get_stations(stream)
+        for station in stations:  # loop through all stations and rotate data if neccessary
+            wf_station = stream.select(station=station)
+            rotate_components(wf_station, metadata)
+        return stream
+
+    def trim_station_components(stream, 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
+        :param stream: stream of seismic data
+        :type stream: `~obspy.core.stream.Stream`
+        :param trim_start: trim start of stream
+        :type trim_start: bool
+        :param trim_end: trim end of stream
+        :type trim_end: bool
+        :return: data stream
+        :rtype: `~obspy.core.stream.Stream`
+        """
+        starttime = {False: None}
+        endtime = {False: None}
+
+        stations = get_stations(stream)
+
+        print('trim_station_components: Will trim stream for trim_start: {} and for '
+              'trim_end: {}.'.format(trim_start, trim_end))
+        for station in stations:
+            wf_station = stream.select(station=station)
+            starttime[True] = max([trace.stats.starttime for trace in wf_station])
+            endtime[True] = min([trace.stats.endtime for trace in wf_station])
+            wf_station.trim(starttime=starttime[trim_start], endtime=endtime[trim_end])
+
+        return stream
-- 
2.45.2


From 76d4ec290c0e67ad195cd831699098b67f1cd3ad Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sat, 27 Jul 2024 13:58:06 +0200
Subject: [PATCH 29/31] refactor: restructure data objects

---
 PyLoT.py                      |  34 +--
 autoPyLoT.py                  |   6 +-
 pylot/core/io/data.py         |  13 +-
 pylot/core/io/utils.py        |  13 +
 pylot/core/io/waveformdata.py | 236 +++++-------------
 pylot/core/util/array_map.py  |   4 +-
 pylot/core/util/widgets.py    | 445 +++++++++++++++++++---------------
 7 files changed, 352 insertions(+), 399 deletions(-)
 create mode 100644 pylot/core/io/utils.py

diff --git a/PyLoT.py b/PyLoT.py
index a6d902d8..8ce799bb 100755
--- a/PyLoT.py
+++ b/PyLoT.py
@@ -1773,7 +1773,7 @@ class MainWindow(QMainWindow):
 
     def getStime(self):
         if self.get_data():
-            return full_range(self.get_data().getWFData())[0]
+            return full_range(self.get_data().get_wf_data())[0]
 
     def addActions(self, target, actions):
         for action in actions:
@@ -1983,7 +1983,7 @@ class MainWindow(QMainWindow):
             tstart = None
             tstop = None
 
-        self.data.setWFData(self.fnames,
+        self.data.set_wf_data(self.fnames,
                             self.fnames_comp,
                             checkRotated=True,
                             metadata=self.metadata,
@@ -2035,7 +2035,7 @@ class MainWindow(QMainWindow):
     def get_npts_to_plot(self):
         if not hasattr(self.data, 'wfdata'):
             return 0
-        return sum(trace.stats.npts for trace in self.data.getWFData())
+        return sum(trace.stats.npts for trace in self.data.get_wf_data())
 
     def connectWFplotEvents(self):
         '''
@@ -2248,14 +2248,14 @@ class MainWindow(QMainWindow):
         zne_text = {'Z': 'vertical', 'N': 'north-south', 'E': 'east-west'}
         comp = self.getComponent()
         title = 'section: {0} components'.format(zne_text[comp])
-        wfst = self.get_data().getWFData()
+        wfst = self.get_data().get_wf_data()
         wfsyn = self.get_data().getAltWFdata()
         if self.filterActionP.isChecked() and filter:
             self.filterWaveformData(plot=False, phase='P')
         elif self.filterActionS.isChecked() and filter:
             self.filterWaveformData(plot=False, phase='S')
-        # wfst = self.get_data().getWFData().select(component=comp)
-        # wfst += self.get_data().getWFData().select(component=alter_comp)
+        # wfst = self.get_data().get_wf_data().select(component=comp)
+        # wfst += self.get_data().get_wf_data().select(component=alter_comp)
         plotWidget = self.getPlotWidget()
         self.adjustPlotHeight()
         if get_bool(settings.value('large_dataset')) == True:
@@ -2270,7 +2270,7 @@ class MainWindow(QMainWindow):
     def adjustPlotHeight(self):
         if self.pg:
             return
-        height_need = len(self.data.getWFData()) * self.height_factor
+        height_need = len(self.data.get_wf_data()) * self.height_factor
         plotWidget = self.getPlotWidget()
         if self.tabs.widget(0).frameSize().height() < height_need:
             plotWidget.setMinimumHeight(height_need)
@@ -2290,24 +2290,24 @@ class MainWindow(QMainWindow):
         self.plotWaveformDataThread()
 
     def pushFilterWF(self, param_args):
-        self.get_data().filterWFData(param_args)
+        self.get_data().filter_wf_data(param_args)
 
     def filterP(self):
         self.filterActionS.setChecked(False)
         if self.filterActionP.isChecked():
             self.filterWaveformData(phase='P')
         else:
-            self.resetWFData()
+            self.reset_wf_data()
 
     def filterS(self):
         self.filterActionP.setChecked(False)
         if self.filterActionS.isChecked():
             self.filterWaveformData(phase='S')
         else:
-            self.resetWFData()
+            self.reset_wf_data()
 
-    def resetWFData(self):
-        self.get_data().resetWFData()
+    def reset_wf_data(self):
+        self.get_data().reset_wf_data()
         self.plotWaveformDataThread()
 
     def filterWaveformData(self, plot=True, phase=None):
@@ -2326,11 +2326,11 @@ class MainWindow(QMainWindow):
                     kwargs = self.getFilterOptions()[phase].parseFilterOptions()
                     self.pushFilterWF(kwargs)
                 else:
-                    self.get_data().resetWFData()
+                    self.get_data().reset_wf_data()
             elif self.filterActionP.isChecked() or self.filterActionS.isChecked():
                 self.adjustFilterOptions()
             else:
-                self.get_data().resetWFData()
+                self.get_data().reset_wf_data()
             if plot:
                 self.plotWaveformDataThread(filter=False)
 
@@ -2531,10 +2531,10 @@ class MainWindow(QMainWindow):
                           show_comp_data=self.dataPlot.comp_checkbox.isChecked())
         if self.filterActionP.isChecked():
             pickDlg.currentPhase = "P"
-            pickDlg.filterWFData()
+            pickDlg.filter_wf_data()
         elif self.filterActionS.isChecked():
             pickDlg.currentPhase = "S"
-            pickDlg.filterWFData()
+            pickDlg.filter_wf_data()
         pickDlg.nextStation.setChecked(self.nextStation)
         pickDlg.nextStation.stateChanged.connect(self.toggle_next_station)
         if pickDlg.exec_():
@@ -3478,7 +3478,7 @@ class MainWindow(QMainWindow):
         if not self.metadata:
             return None
 
-        wf_copy = self.get_data().getWFData().copy()
+        wf_copy = self.get_data().get_wf_data().copy()
 
         wf_select = Stream()
         # restitute only picked traces
diff --git a/autoPyLoT.py b/autoPyLoT.py
index 506025c5..cc86a786 100755
--- a/autoPyLoT.py
+++ b/autoPyLoT.py
@@ -243,7 +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
@@ -258,7 +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()
@@ -268,7 +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:
diff --git a/pylot/core/io/data.py b/pylot/core/io/data.py
index 1172568e..26a2e72a 100644
--- a/pylot/core/io/data.py
+++ b/pylot/core/io/data.py
@@ -9,11 +9,13 @@ from obspy import UTCDateTime
 
 from pylot.core.io.event import EventData
 from pylot.core.io.waveformdata import WaveformData
+from pylot.core.util.dataprocessing import Metadata
 
 @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):
@@ -52,10 +54,17 @@ class Data:
         self.waveform_data.dirty = 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.set_wf_data(fnames, fnames_alt, check_rotated, metadata, tstart, tstop)
+        return self.waveform_data.load_waveforms(fnames, fnames_alt, check_rotated, metadata, tstart, tstop)
 
     def reset_wf_data(self):
-        self.waveform_data.reset_wf_data()
+        self.waveform_data.reset()
+
+    def get_wf_data(self):
+        return self.waveform_data.wfdata
+
+    def rotate_wf_data(self):
+        self.waveform_data.rotate_zne(self.metadata)
+
 
 class GenericDataStructure(object):
     """
diff --git a/pylot/core/io/utils.py b/pylot/core/io/utils.py
new file mode 100644
index 00000000..109ee8a2
--- /dev/null
+++ b/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)]
\ No newline at end of file
diff --git a/pylot/core/io/waveformdata.py b/pylot/core/io/waveformdata.py
index 7ecfff42..c2b0078c 100644
--- a/pylot/core/io/waveformdata.py
+++ b/pylot/core/io/waveformdata.py
@@ -1,14 +1,13 @@
 import logging
-import os
 from dataclasses import dataclass, field
 from typing import Union, List
 
-import numpy as np
 from obspy import Stream, read
 from obspy.io.sac import SacIOError
-from obspy.signal.rotate import rotate2zne
 
-from pylot.core.util.utils import full_range, get_stations
+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
@@ -18,26 +17,39 @@ class WaveformData:
     wf_alt: Stream = field(default_factory=Stream)
     dirty: bool = False
 
-    def set_wf_data(self, fnames: List[str], fnames_alt: List[str] = None, check_rotated=False, metadata=None, tstart=0, tstop=0):
-        self.clear_data()
-        fnames = self.check_fname_exists(fnames)
-        fnames_alt = self.check_fname_exists(fnames_alt)
+    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:
-            self.append_wf_data(fnames)
-            if fnames_alt:
-                self.append_wf_data(fnames_alt, alternative=True)
-            self.wfdata, _ = self.check_for_gaps_and_merge(self.wfdata)
-            self.check_for_nan(self.wfdata)
-            if check_rotated and metadata:
-                self.wfdata = self.check4rotated(self.wfdata, metadata, verbosity=0)
-            self.trim_station_components(self.wfdata, trim_start=True, trim_end=False)
-            self.wforiginal = self.wfdata.copy()
-            self.dirty = False
-            return True
-        return False
+        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)
 
-    def append_wf_data(self, fnames: List[str], alternative: bool = False):
+        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):
@@ -55,189 +67,57 @@ class WaveformData:
                 warnmsg += f'{fname}\n{se}\n'
 
         if warnmsg:
-            print(f'WARNING in appendWFData: unable to read waveform data\n{warnmsg}')
+            print(f'WARNING in add_waveforms: unable to read waveform data\n{warnmsg}')
 
-    def clear_data(self):
+    def clear(self):
         self.wfdata = Stream()
         self.wforiginal = None
         self.wf_alt = Stream()
 
-    def reset_wf_data(self):
+    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 check_fname_exists(self, filenames: List[str]) -> List[str]:
-        return [fn for fn in filenames if os.path.isfile(fn)]
-
-    def check_for_gaps_and_merge(self, stream):
+    def merge(self):
         """
         check for gaps in Stream and merge if gaps are found
-        :param stream: stream of seismic data
-        :type stream: `~obspy.core.stream.Stream`
-        :return: data stream, gaps returned from obspy get_gaps
-        :rtype: `~obspy.core.stream.Stream`
         """
-        gaps = stream.get_gaps()
+        gaps = self.wfdata.get_gaps()
         if gaps:
             merged = ['{}.{}.{}.{}'.format(*gap[:4]) for gap in gaps]
-            stream.merge(method=1)
-            print('Merged the following stations because of gaps:')
-            for merged_station in merged:
-                print(merged_station)
+            self.wfdata.merge(method=1)
+            logging.info('Merged the following stations because of gaps:')
+            for station in merged:
+                logging.info(station)
 
-        return stream, gaps
-
-    def check_for_nan(self, stream):
+    def replace_nan(self):
         """
-        Replace all NaNs in data with nan_value (in place)
-        :param stream: stream of seismic data
-        :type stream: `~obspy.core.stream.Stream`
-        :param nan_value: value which all NaNs are set to
-        :type nan_value: float, int
-        :return: None
+        Replace all NaNs in data with 0. (in place)
         """
-        if not stream:
-            return
-        for trace in stream:
-            np.nan_to_num(trace.data, copy=False, nan=0.)
+        self.wfdata = check_for_nan(self.wfdata)
 
-
-    def check4rotated(self, stream, metadata=None, verbosity=1):
+    def rotate_zne(self, metadata: Metadata = None):
         """
-        Check all traces in data. If a trace is not in ZNE rotation (last symbol of channel code is numeric) and the trace
+        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.
-        :param stream: stream object containing seismic traces
-        :type stream: `~obspy.core.stream.Stream`
-        :param metadata: tuple containing metadata type string and metadata parser object
-        :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
-        :param verbosity: if 0 print no information at runtime
-        :type verbosity: int
-        :return: stream object with traditionally oriented traces (ZNE) for stations that had misaligned traces (123) before
-        :rtype: `~obspy.core.stream.Stream`
         """
 
-        def rotation_required(trace_ids):
-            """
-            Derive if any rotation is required from the orientation code of the input.
+        self.wfdata = check4rotated(self.wfdata, metadata)
 
-            :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 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`
-            """
-
-            if len(wfs_in) < 3:
-                print(f"Stream {wfs_in=}, has not enough components to rotate.")
-                return wfs_in
-
-            # check if any traces in this station need to be rotated
-            trace_ids = [trace.id for trace in 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 = self.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:
-                msg = 'Warning: could not rotate traces since no metadata was given\nset Inventory file!'
-                print(msg)
-            return stream
-        stations = get_stations(stream)
-        for station in stations:  # loop through all stations and rotate data if neccessary
-            wf_station = stream.select(station=station)
-            rotate_components(wf_station, metadata)
-        return stream
-
-    def trim_station_components(stream, trim_start=True, trim_end=True):
+    def trim_station_traces(self):
         """
-        cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
-        :param stream: stream of seismic data
-        :type stream: `~obspy.core.stream.Stream`
-        :param trim_start: trim start of stream
-        :type trim_start: bool
-        :param trim_end: trim end of stream
-        :type trim_end: bool
-        :return: data stream
-        :rtype: `~obspy.core.stream.Stream`
+        trim data stream to common time window
         """
-        starttime = {False: None}
-        endtime = {False: None}
 
-        stations = get_stations(stream)
-
-        print('trim_station_components: Will trim stream for trim_start: {} and for '
-              'trim_end: {}.'.format(trim_start, trim_end))
-        for station in stations:
-            wf_station = stream.select(station=station)
-            starttime[True] = max([trace.stats.starttime for trace in wf_station])
-            endtime[True] = min([trace.stats.endtime for trace in wf_station])
-            wf_station.trim(starttime=starttime[trim_start], endtime=endtime[trim_end])
-
-        return stream
+        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]))
diff --git a/pylot/core/util/array_map.py b/pylot/core/util/array_map.py
index afc00eaf..ea8d0c00 100644
--- a/pylot/core/util/array_map.py
+++ b/pylot/core/util/array_map.py
@@ -474,8 +474,8 @@ class Array_map(QtWidgets.QWidget):
                                                                   transform=ccrs.PlateCarree(), label='deleted'))
 
     def openPickDlg(self, ind):
-        wfdata = self._parent.get_data().getWFData()
-        wfdata_comp = self._parent.get_data().getWFDataComp()
+        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
diff --git a/pylot/core/util/widgets.py b/pylot/core/util/widgets.py
index 988b3aa2..7ef01394 100644
--- a/pylot/core/util/widgets.py
+++ b/pylot/core/util/widgets.py
@@ -140,18 +140,6 @@ class LogWidget(QtWidgets.QWidget):
         self.stderr.append(60 * '#' + '\n\n')
 
 
-def getDataType(parent):
-    type = QInputDialog().getItem(parent, "Select phases type", "Type:",
-                                  ["manual", "automatic"])
-
-    if type[0].startswith('auto'):
-        type = 'auto'
-    else:
-        type = type[0]
-
-    return type
-
-
 def plot_pdf(_axes, x, y, annotation, bbox_props, xlabel=None, ylabel=None,
              title=None):
     # try method or data
@@ -795,7 +783,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
 
     def connect_signals(self):
         self.qcombo_processed.activated.connect(self.parent().newWF)
-        self.syn_checkbox.clicked.connect(self.parent().newWF)
+        self.comp_checkbox.clicked.connect(self.parent().newWF)
 
     def init_labels(self):
         self.label_layout.addWidget(self.status_label)
@@ -806,13 +794,13 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         # use widgets as placeholder, so that child widgets keep position when others are hidden
         mid_layout = QHBoxLayout()
         right_layout = QHBoxLayout()
-        mid_layout.addWidget(self.syn_checkbox)
+        mid_layout.addWidget(self.comp_checkbox)
         right_layout.addWidget(self.qcombo_processed)
         mid_widget.setLayout(mid_layout)
         right_widget.setLayout(right_layout)
         self.label_layout.addWidget(mid_widget)
         self.label_layout.addWidget(right_widget)
-        self.syn_checkbox.setLayoutDirection(Qt.RightToLeft)
+        self.comp_checkbox.setLayoutDirection(Qt.RightToLeft)
         self.label_layout.setStretch(0, 4)
         self.label_layout.setStretch(1, 0)
         self.label_layout.setStretch(2, 0)
@@ -827,7 +815,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
             label = QtWidgets.QLabel()
             self.perm_labels.append(label)
         self.qcombo_processed = QtWidgets.QComboBox()
-        self.syn_checkbox = QtWidgets.QCheckBox('synthetics')
+        self.comp_checkbox = QtWidgets.QCheckBox('Load comparison data')
         self.addQCboxItem('processed', 'green')
         self.addQCboxItem('raw', 'black')
         # self.perm_qcbox_right.setAlignment(2)
@@ -836,9 +824,11 @@ class WaveformWidgetPG(QtWidgets.QWidget):
     def getPlotDict(self):
         return self.plotdict
 
-    def activateObspyDMToptions(self, activate):
-        self.syn_checkbox.setVisible(activate)
-        self.qcombo_processed.setVisible(activate)
+    def activateObspyDMToptions(self, activate: bool) -> None:
+        self.qcombo_processed.setEnabled(activate)
+
+    def activateCompareOptions(self, activate: bool) -> None:
+        self.comp_checkbox.setEnabled(activate)
 
     def setPermText(self, number, text=None, color='black'):
         if not 0 <= number < len(self.perm_labels):
@@ -961,7 +951,7 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                     [time for index, time in enumerate(time_ax_syn) if not index % nth_sample] if st_syn else [])
                 trace.data = np.array(
                     [datum * gain + n for index, datum in enumerate(trace.data) if not index % nth_sample])
-                trace_syn.data = np.array([datum + n for index, datum in enumerate(trace_syn.data)
+                trace_syn.data = np.array([datum + n + shift_syn for index, datum in enumerate(trace_syn.data)
                                            if not index % nth_sample] if st_syn else [])
                 plots.append((times, trace.data,
                               times_syn, trace_syn.data))
@@ -1007,15 +997,6 @@ class WaveformWidgetPG(QtWidgets.QWidget):
         time_ax = np.linspace(time_ax[0], time_ax[-1], num=len(data))
         return data, time_ax
 
-    # def getAxes(self):
-    #     return self.axes
-
-    # def getXLims(self):
-    #     return self.getAxes().get_xlim()
-
-    # def getYLims(self):
-    #     return self.getAxes().get_ylim()
-
     def setXLims(self, lims):
         vb = self.plotWidget.getPlotItem().getViewBox()
         vb.setXRange(float(lims[0]), float(lims[1]), padding=0)
@@ -1169,8 +1150,6 @@ class PylotCanvas(FigureCanvas):
                 break
         if not ax_check: return
 
-        # self.updateCurrentLimits() #maybe put this down to else:
-
         # calculate delta (relative values in axis)
         old_x, old_y = self.press_rel
         xdiff = gui_event.x - old_x
@@ -1373,110 +1352,145 @@ class PylotCanvas(FigureCanvas):
             plot_positions[channel] = plot_pos
         return plot_positions
 
-    def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None,
+    def plotWFData(self, wfdata, wfdata_compare=None, title=None, zoomx=None, zoomy=None,
                    noiselevel=None, scaleddata=False, mapping=True,
                    component='*', nth_sample=1, iniPick=None, verbosity=0,
                    plot_additional=False, additional_channel=None, scaleToChannel=None,
                    snr=None):
+        ax = self.prepare_plot()
+        self.clearPlotDict()
+
+        wfstart, wfend = self.get_wf_range(wfdata)
+        compclass = self.get_comp_class()
+        plot_streams = self.get_plot_streams(wfdata, wfdata_compare, component, compclass)
+
+        st_main = plot_streams['wfdata']['data']
+        if mapping:
+            plot_positions = self.calcPlotPositions(st_main, compclass)
+
+        nslc = self.get_sorted_nslc(st_main)
+        nmax = self.plot_traces(ax, plot_streams, nslc, wfstart, mapping, plot_positions,
+                                scaleToChannel, noiselevel, scaleddata, nth_sample, verbosity)
+
+        if plot_additional and additional_channel:
+            self.plot_additional_trace(ax, wfdata, additional_channel, scaleToChannel,
+                                       scaleddata, nth_sample, wfstart)
+
+        self.finalize_plot(ax, wfstart, wfend, nmax, zoomx, zoomy, iniPick, title, snr)
+
+    def prepare_plot(self):
         ax = self.axes[0]
         ax.cla()
+        return ax
 
-        self.clearPlotDict()
-        wfstart, wfend = full_range(wfdata)
-        nmax = 0
+    def get_wf_range(self, wfdata):
+        return full_range(wfdata)
 
+    def get_comp_class(self):
         settings = QSettings()
-        compclass = SetChannelComponents.from_qsettings(settings)
+        return SetChannelComponents.from_qsettings(settings)
 
-        if not component == '*':
-            alter_comp = compclass.getCompPosition(component)
-            # alter_comp = str(alter_comp[0])
-
-            st_select = wfdata.select(component=component)
-            st_select += wfdata.select(component=alter_comp)
-        else:
-            st_select = wfdata
-
-        if mapping:
-            plot_positions = self.calcPlotPositions(st_select, compclass)
-
-        # list containing tuples of network, station, channel and plot position (for sorting)
-        nslc = []
-        for plot_pos, trace in enumerate(st_select):
-            if not trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
-                print('Warning: Unrecognized channel {}'.format(trace.stats.channel))
-                continue
-            nslc.append(trace.get_id())
-        nslc.sort()
-        nslc.reverse()
+    def get_plot_streams(self, wfdata, wfdata_compare, component, compclass):
+        def get_wf_dict(data=Stream(), linecolor='k', offset=0., **plot_kwargs):
+            return dict(data=data, linecolor=linecolor, offset=offset, plot_kwargs=plot_kwargs)
 
         linecolor = (0., 0., 0., 1.) if not self.style else self.style['linecolor']['rgba_mpl']
+        plot_streams = {
+            'wfdata': get_wf_dict(linecolor=linecolor, linewidth=0.7),
+            'wfdata_comp': get_wf_dict(offset=0.1, linecolor='b', alpha=0.7, linewidth=0.5)
+        }
 
+        if component != '*':
+            alter_comp = compclass.getCompPosition(component)
+            plot_streams['wfdata']['data'] = wfdata.select(component=component) + wfdata.select(component=alter_comp)
+            if wfdata_compare:
+                plot_streams['wfdata_comp']['data'] = wfdata_compare.select(
+                    component=component) + wfdata_compare.select(component=alter_comp)
+        else:
+            plot_streams['wfdata']['data'] = wfdata
+            if wfdata_compare:
+                plot_streams['wfdata_comp']['data'] = wfdata_compare
+
+        return plot_streams
+
+    def get_sorted_nslc(self, st_main):
+        nslc = [trace.get_id() for trace in st_main if trace.stats.channel[-1] in ['Z', 'N', 'E', '1', '2', '3']]
+        nslc.sort(reverse=True)
+        return nslc
+
+    def plot_traces(self, ax, plot_streams, nslc, wfstart, mapping, plot_positions, scaleToChannel, noiselevel,
+                    scaleddata, nth_sample, verbosity):
+        nmax = 0
         for n, seed_id in enumerate(nslc):
             network, station, location, channel = seed_id.split('.')
-            st = st_select.select(id=seed_id)
-            trace = st[0].copy()
-            if mapping:
-                n = plot_positions[trace.stats.channel]
-            if n > nmax:
-                nmax = n
-            if verbosity:
-                msg = 'plotting %s channel of station %s' % (channel, station)
-                print(msg)
-            stime = trace.stats.starttime - wfstart
-            time_ax = prep_time_axis(stime, trace)
-            if time_ax is not None:
-                if scaleToChannel:
-                    st_scale = wfdata.select(channel=scaleToChannel)
-                    if st_scale:
-                        tr = st_scale[0]
-                        trace.detrend('constant')
-                        trace.normalize(np.max(np.abs(tr.data)) * 2)
-                        scaleddata = True
-                if not scaleddata:
-                    trace.detrend('constant')
-                    trace.normalize(np.max(np.abs(trace.data)) * 2)
-
-                times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
-                data = [datum + n for index, datum in enumerate(trace.data) if not index % nth_sample]
-                ax.axhline(n, color="0.5", lw=0.5)
-                ax.plot(times, data, color=linecolor, linewidth=0.7)
-                if noiselevel is not None:
-                    for level in [-noiselevel[channel], noiselevel[channel]]:
-                        ax.plot([time_ax[0], time_ax[-1]],
-                                [n + level, n + level],
-                                color=linecolor,
-                                linestyle='dashed')
+            for wf_name, wf_dict in plot_streams.items():
+                st_select = wf_dict.get('data')
+                if not st_select:
+                    continue
+                trace = st_select.select(id=seed_id)[0].copy()
+                if mapping:
+                    n = plot_positions[trace.stats.channel]
+                if n > nmax:
+                    nmax = n
+                if verbosity:
+                    print(f'plotting {channel} channel of station {station}')
+                time_ax = prep_time_axis(trace.stats.starttime - wfstart, trace)
+                self.plot_trace(ax, trace, time_ax, wf_dict, n, scaleToChannel, noiselevel, scaleddata, nth_sample)
                 self.setPlotDict(n, seed_id)
-        if plot_additional and additional_channel:
-            compare_stream = wfdata.select(channel=additional_channel)
-            if compare_stream:
-                trace = compare_stream[0]
-                if scaleToChannel:
-                    st_scale = wfdata.select(channel=scaleToChannel)
-                    if st_scale:
-                        tr = st_scale[0]
-                        trace.detrend('constant')
-                        trace.normalize(np.max(np.abs(tr.data)) * 2)
-                        scaleddata = True
-                if not scaleddata:
-                    trace.detrend('constant')
-                    trace.normalize(np.max(np.abs(trace.data)) * 2)
-                time_ax = prep_time_axis(stime, trace)
-                times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
-                p_data = compare_stream[0].data
-                # #normalize
-                # p_max = max(abs(p_data))
-                # p_data /= p_max
-                for index in range(3):
-                    ax.plot(times, p_data, color='red', alpha=0.5, linewidth=0.7)
-                    p_data += 1
+        return nmax
 
+    def plot_trace(self, ax, trace, time_ax, wf_dict, n, scaleToChannel, noiselevel, scaleddata, nth_sample):
+        if time_ax is not None:
+            if scaleToChannel:
+                self.scale_trace(trace, scaleToChannel)
+                scaleddata = True
+            if not scaleddata:
+                trace.detrend('constant')
+                trace.normalize(np.max(np.abs(trace.data)) * 2)
+            offset = wf_dict.get('offset')
+
+            times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
+            data = [datum + n + offset for index, datum in enumerate(trace.data) if not index % nth_sample]
+            ax.axhline(n, color="0.5", lw=0.5)
+            ax.plot(times, data, color=wf_dict.get('linecolor'), **wf_dict.get('plot_kwargs'))
+            if noiselevel is not None:
+                self.plot_noise_level(ax, time_ax, noiselevel, channel, n, wf_dict.get('linecolor'))
+
+    def scale_trace(self, trace, scaleToChannel):
+        st_scale = wfdata.select(channel=scaleToChannel)
+        if st_scale:
+            tr = st_scale[0]
+            trace.detrend('constant')
+            trace.normalize(np.max(np.abs(tr.data)) * 2)
+
+    def plot_noise_level(self, ax, time_ax, noiselevel, channel, n, linecolor):
+        for level in [-noiselevel[channel], noiselevel[channel]]:
+            ax.plot([time_ax[0], time_ax[-1]], [n + level, n + level], color=linecolor, linestyle='dashed')
+
+    def plot_additional_trace(self, ax, wfdata, additional_channel, scaleToChannel, scaleddata, nth_sample, wfstart):
+        compare_stream = wfdata.select(channel=additional_channel)
+        if compare_stream:
+            trace = compare_stream[0]
+            if scaleToChannel:
+                self.scale_trace(trace, scaleToChannel)
+                scaleddata = True
+            if not scaleddata:
+                trace.detrend('constant')
+                trace.normalize(np.max(np.abs(trace.data)) * 2)
+            time_ax = prep_time_axis(trace.stats.starttime - wfstart, trace)
+            self.plot_additional_data(ax, trace, time_ax, nth_sample)
+
+    def plot_additional_data(self, ax, trace, time_ax, nth_sample):
+        times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
+        p_data = trace.data
+        for index in range(3):
+            ax.plot(times, p_data, color='red', alpha=0.5, linewidth=0.7)
+            p_data += 1
+
+    def finalize_plot(self, ax, wfstart, wfend, nmax, zoomx, zoomy, iniPick, title, snr):
         if iniPick:
-            ax.vlines(iniPick, ax.get_ylim()[0], ax.get_ylim()[1],
-                      colors='m', linestyles='dashed',
-                      linewidth=2)
-        xlabel = 'seconds since {0}'.format(wfstart)
+            ax.vlines(iniPick, ax.get_ylim()[0], ax.get_ylim()[1], colors='m', linestyles='dashed', linewidth=2)
+        xlabel = f'seconds since {wfstart}'
         ylabel = ''
         self.updateWidget(xlabel, ylabel, title)
         self.setXLims(ax, [0, wfend - wfstart])
@@ -1486,15 +1500,14 @@ class PylotCanvas(FigureCanvas):
         if zoomy is not None:
             self.setYLims(ax, zoomy)
         if snr is not None:
-            if snr < 2:
-                warning = 'LOW SNR'
-                if snr < 1.5:
-                    warning = 'VERY LOW SNR'
-                ax.text(0.1, 0.9, 'WARNING - {}'.format(warning), ha='center', va='center', transform=ax.transAxes,
-                        color='red')
-
+            self.plot_snr_warning(ax, snr)
         self.draw()
 
+    def plot_snr_warning(self, ax, snr):
+        if snr < 2:
+            warning = 'LOW SNR' if snr >= 1.5 else 'VERY LOW SNR'
+            ax.text(0.1, 0.9, f'WARNING - {warning}', ha='center', va='center', transform=ax.transAxes, color='red')
+
     @staticmethod
     def getXLims(ax):
         return ax.get_xlim()
@@ -1846,8 +1859,8 @@ class PhaseDefaults(QtWidgets.QDialog):
 class PickDlg(QDialog):
     update_picks = QtCore.Signal(dict)
 
-    def __init__(self, parent=None, data=None, station=None, network=None, location=None, picks=None,
-                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None,
+    def __init__(self, parent=None, data=None, data_compare=None, station=None, network=None, location=None, picks=None,
+                 autopicks=None, rotate=False, parameter=None, embedded=False, metadata=None, show_comp_data=False,
                  event=None, filteroptions=None, model=None, wftype=None):
         super(PickDlg, self).__init__(parent, Qt.Window)
         self.orig_parent = parent
@@ -1856,6 +1869,7 @@ class PickDlg(QDialog):
         # initialize attributes
         self.parameter = parameter
         self._embedded = embedded
+        self.showCompData = show_comp_data
         self.station = station
         self.network = network
         self.location = location
@@ -1894,11 +1908,32 @@ class PickDlg(QDialog):
         else:
             self.filteroptions = FILTERDEFAULTS
         self.pick_block = False
+
+        # set attribute holding data
+        if data is None or not data:
+            try:
+                data = parent.get_data().get_wf_data().copy()
+                self.data = data.select(station=station)
+            except AttributeError as e:
+                errmsg = 'You either have to put in a data or an appropriate ' \
+                         'parent (PyLoT MainWindow) object: {0}'.format(e)
+                raise Exception(errmsg)
+        else:
+            self.data = data
+        self.data_compare = data_compare
+
         self.nextStation = QtWidgets.QCheckBox('Continue with next station ')
 
         # comparison channel
-        self.compareChannel = QtWidgets.QComboBox()
-        self.compareChannel.activated.connect(self.resetPlot)
+        self.referenceChannel = QtWidgets.QComboBox()
+        self.referenceChannel.activated.connect(self.resetPlot)
+
+        # comparison channel
+        self.compareCB = QtWidgets.QCheckBox()
+        self.compareCB.setChecked(self.showCompData)
+        self.compareCB.clicked.connect(self.switchCompData)
+        self.compareCB.clicked.connect(self.resetPlot)
+        self.compareCB.setVisible(bool(self.data_compare))
 
         # scale channel
         self.scaleChannel = QtWidgets.QComboBox()
@@ -1911,19 +1946,7 @@ class PickDlg(QDialog):
         self.cur_xlim = None
         self.cur_ylim = None
 
-        # set attribute holding data
-        if data is None or not data:
-            try:
-                data = parent.get_data().getWFData().copy()
-                self.data = data.select(station=station)
-            except AttributeError as e:
-                errmsg = 'You either have to put in a data or an appropriate ' \
-                         'parent (PyLoT MainWindow) object: {0}'.format(e)
-                raise Exception(errmsg)
-        else:
-            self.data = data
-
-        self.stime, self.etime = full_range(self.getWFData())
+        self.stime, self.etime = full_range(self.get_wf_data())
 
         # initialize plotting widget
         self.multicompfig = PylotCanvas(parent=self, multicursor=True)
@@ -1934,12 +1957,12 @@ class PickDlg(QDialog):
         self.setupUi()
 
         # fill compare and scale channels
-        self.compareChannel.addItem('-', None)
+        self.referenceChannel.addItem('-', None)
         self.scaleChannel.addItem('individual', None)
 
-        for trace in self.getWFData():
+        for trace in self.get_wf_data():
             channel = trace.stats.channel
-            self.compareChannel.addItem(channel, trace)
+            self.referenceChannel.addItem(channel, trace)
             if not channel[-1] in ['Z', 'N', 'E', '1', '2', '3']:
                 print('Skipping unknown channel for scaling: {}'.format(channel))
                 continue
@@ -1956,7 +1979,7 @@ class PickDlg(QDialog):
         if self.wftype is not None:
             title += ' | ({})'.format(self.wftype)
 
-        self.multicompfig.plotWFData(wfdata=self.getWFData(),
+        self.multicompfig.plotWFData(wfdata=self.get_wf_data(), wfdata_compare=self.get_wf_dataComp(),
                                      title=title)
 
         self.multicompfig.setZoomBorders2content()
@@ -2132,8 +2155,11 @@ class PickDlg(QDialog):
         _dialtoolbar.addWidget(est_label)
         _dialtoolbar.addWidget(self.plot_arrivals_button)
         _dialtoolbar.addSeparator()
-        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare to channel: '))
-        _dialtoolbar.addWidget(self.compareChannel)
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Plot reference channel: '))
+        _dialtoolbar.addWidget(self.referenceChannel)
+        _dialtoolbar.addSeparator()
+        _dialtoolbar.addWidget(QtWidgets.QLabel('Compare: '))
+        _dialtoolbar.addWidget(self.compareCB)
         _dialtoolbar.addSeparator()
         _dialtoolbar.addWidget(QtWidgets.QLabel('Scaling: '))
         _dialtoolbar.addWidget(self.scaleChannel)
@@ -2470,7 +2496,7 @@ class PickDlg(QDialog):
     def activatePicking(self):
         self.leave_rename_phase()
         self.renamePhaseAction.setEnabled(False)
-        self.compareChannel.setEnabled(False)
+        self.referenceChannel.setEnabled(False)
         self.scaleChannel.setEnabled(False)
         phase = self.currentPhase
         phaseID = self.getPhaseID(phase)
@@ -2488,7 +2514,7 @@ class PickDlg(QDialog):
         if self.autoFilterAction.isChecked():
             for filteraction in [self.filterActionP, self.filterActionS]:
                 filteraction.setChecked(False)
-            self.filterWFData()
+            self.filter_wf_data()
             self.draw()
         else:
             self.draw()
@@ -2502,7 +2528,7 @@ class PickDlg(QDialog):
         self.disconnectPressEvent()
         self.multicompfig.connectEvents()
         self.renamePhaseAction.setEnabled(True)
-        self.compareChannel.setEnabled(True)
+        self.referenceChannel.setEnabled(True)
         self.scaleChannel.setEnabled(True)
         self.connect_pick_delete()
         self.draw()
@@ -2572,9 +2598,15 @@ class PickDlg(QDialog):
     def getGlobalLimits(self, ax, axis):
         return self.multicompfig.getGlobalLimits(ax, axis)
 
-    def getWFData(self):
+    def get_wf_data(self):
         return self.data
 
+    def get_wf_dataComp(self):
+        if self.showCompData:
+            return self.data_compare
+        else:
+            return Stream()
+
     def selectWFData(self, channel):
         component = channel[-1].upper()
         wfdata = Stream()
@@ -2584,17 +2616,17 @@ class PickDlg(QDialog):
                 return tr
 
         if component == 'E' or component == 'N':
-            for trace in self.getWFData():
+            for trace in self.get_wf_data():
                 trace = selectTrace(trace, 'NE')
                 if trace:
                     wfdata.append(trace)
         elif component == '1' or component == '2':
-            for trace in self.getWFData():
+            for trace in self.get_wf_data():
                 trace = selectTrace(trace, '12')
                 if trace:
                     wfdata.append(trace)
         else:
-            wfdata = self.getWFData().select(component=component)
+            wfdata = self.get_wf_data().select(component=component)
         return wfdata
 
     def getPicks(self, picktype='manual'):
@@ -2696,11 +2728,16 @@ class PickDlg(QDialog):
 
         stime = self.getStartTime()
 
-        # copy data for plotting
-        data = self.getWFData().copy()
-        data = self.getPickPhases(data, phase)
-        data.normalize()
-        if not data:
+        # copy wfdata for plotting
+        wfdata = self.get_wf_data().copy()
+        wfdata_comp = self.get_wf_dataComp().copy()
+        wfdata = self.getPickPhases(wfdata, phase)
+        wfdata_comp = self.getPickPhases(wfdata_comp, phase)
+        for wfd in [wfdata, wfdata_comp]:
+            if wfd:
+                wfd.normalize()
+
+        if not wfdata:
             QtWidgets.QMessageBox.warning(self, 'No channel to plot',
                                           'No channel to plot for phase: {}. '
                                           'Make sure to select the correct channels for P and S '
@@ -2708,14 +2745,16 @@ class PickDlg(QDialog):
             self.leave_picking_mode()
             return
 
-        # filter data and trace on which is picked prior to determination of SNR
+        # filter wfdata and trace on which is picked prior to determination of SNR
         filterphase = self.currentFilterPhase()
         if filterphase:
             filteroptions = self.getFilterOptions(filterphase).parseFilterOptions()
             try:
-                data.detrend('linear')
-                data.filter(**filteroptions)
-                # wfdata.filter(**filteroptions)# MP MP removed filtering of original data
+                for wfd in [wfdata, wfdata_comp]:
+                    if wfd:
+                        wfd.detrend('linear')
+                        wfd.filter(**filteroptions)
+                # wfdata.filter(**filteroptions)# MP MP removed filtering of original wfdata
             except ValueError as e:
                 self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Information,
                                                  'Denied',
@@ -2725,8 +2764,8 @@ class PickDlg(QDialog):
         snr = []
         noiselevels = {}
         # determine SNR and noiselevel
-        for trace in data.traces:
-            st = data.select(channel=trace.stats.channel)
+        for trace in wfdata.traces:
+            st = wfdata.select(channel=trace.stats.channel)
             stime_diff = trace.stats.starttime - stime
             result = getSNR(st, (noise_win, gap_win, signal_win), ini_pick - stime_diff)
             snr.append(result[0])
@@ -2737,23 +2776,25 @@ class PickDlg(QDialog):
                 noiselevel = nfac
             noiselevels[trace.stats.channel] = noiselevel
 
-        # prepare plotting of data
-        for trace in data:
-            t = prep_time_axis(trace.stats.starttime - stime, trace)
-            inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
-            trace = demeanTrace(trace, inoise)
-            # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
-            channel = trace.stats.channel
-            noiselevel = noiselevels[channel]
-            noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
-            trace.data *= noiseScaleFactor
-            noiselevels[channel] *= noiseScaleFactor
+        # prepare plotting of wfdata
+        for wfd in [wfdata, wfdata_comp]:
+            if wfd:
+                for trace in wfd:
+                    t = prep_time_axis(trace.stats.starttime - stime, trace)
+                    inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
+                    trace = demeanTrace(trace, inoise)
+                    # upscale trace wfdata in a way that each trace is vertically zoomed to noiselevel*factor
+                    channel = trace.stats.channel
+                    noiselevel = noiselevels[channel]
+                    noiseScaleFactor = self.calcNoiseScaleFactor(noiselevel, zoomfactor=5.)
+                    trace.data *= noiseScaleFactor
+                    noiselevels[channel] *= noiseScaleFactor
 
         mean_snr = np.mean(snr)
         x_res = getResolutionWindow(mean_snr, parameter.get('extent'))
 
         xlims = [ini_pick - x_res, ini_pick + x_res]
-        ylims = list(np.array([-.5, .5]) + [0, len(data) - 1])
+        ylims = list(np.array([-.5, .5]) + [0, len(wfdata) - 1])
 
         title = self.getStation() + ' picking mode'
         title += ' | SNR: {}'.format(mean_snr)
@@ -2761,9 +2802,10 @@ class PickDlg(QDialog):
             filtops_str = transformFilteroptions2String(filteroptions)
             title += ' | Filteroptions: {}'.format(filtops_str)
 
-        plot_additional = bool(self.compareChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data,
+        plot_additional = bool(self.referenceChannel.currentText())
+        additional_channel = self.referenceChannel.currentText()
+        self.multicompfig.plotWFData(wfdata=wfdata,
+                                     wfdata_compare=wfdata_comp,
                                      title=title,
                                      zoomx=xlims,
                                      zoomy=ylims,
@@ -2797,7 +2839,7 @@ class PickDlg(QDialog):
             filteroptions = None
 
         # copy and filter data for earliest and latest possible picks
-        wfdata = self.getWFData().copy().select(channel=channel)
+        wfdata = self.get_wf_data().copy().select(channel=channel)
         if filteroptions:
             try:
                 wfdata.detrend('linear')
@@ -2844,7 +2886,7 @@ class PickDlg(QDialog):
             minFMSNR = parameter.get('minFMSNR')
             quality = get_quality_class(spe, parameter.get('timeerrorsP'))
             if quality <= minFMweight and snr >= minFMSNR:
-                FM = fmpicker(self.getWFData().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
+                FM = fmpicker(self.get_wf_data().select(channel=channel).copy(), wfdata.copy(), parameter.get('fmpickwin'),
                               pick - stime_diff)
 
         # save pick times for actual phase
@@ -3136,7 +3178,7 @@ class PickDlg(QDialog):
     def togglePickBlocker(self):
         return not self.pick_block
 
-    def filterWFData(self, phase=None):
+    def filter_wf_data(self, phase=None):
         if not phase:
             phase = self.currentPhase
             if self.getPhaseID(phase) == 'P':
@@ -3154,7 +3196,8 @@ class PickDlg(QDialog):
         self.cur_xlim = self.multicompfig.axes[0].get_xlim()
         self.cur_ylim = self.multicompfig.axes[0].get_ylim()
         # self.multicompfig.updateCurrentLimits()
-        data = self.getWFData().copy()
+        wfdata = self.get_wf_data().copy()
+        wfdata_comp = self.get_wf_dataComp().copy()
         title = self.getStation()
         if filter:
             filtoptions = None
@@ -3162,19 +3205,22 @@ class PickDlg(QDialog):
                 filtoptions = self.getFilterOptions(self.getPhaseID(phase), gui_filter=True).parseFilterOptions()
 
             if filtoptions is not None:
-                data.detrend('linear')
-                data.taper(0.02, type='cosine')
-                data.filter(**filtoptions)
+                for wfd in [wfdata, wfdata_comp]:
+                    if wfd:
+                        wfd.detrend('linear')
+                        wfd.taper(0.02, type='cosine')
+                        wfd.filter(**filtoptions)
                 filtops_str = transformFilteroptions2String(filtoptions)
                 title += ' | Filteroptions: {}'.format(filtops_str)
 
         if self.wftype is not None:
             title += ' | ({})'.format(self.wftype)
 
-        plot_additional = bool(self.compareChannel.currentText())
-        additional_channel = self.compareChannel.currentText()
+        plot_additional = bool(self.referenceChannel.currentText())
+        additional_channel = self.referenceChannel.currentText()
         scale_channel = self.scaleChannel.currentText()
-        self.multicompfig.plotWFData(wfdata=data, title=title,
+        self.multicompfig.plotWFData(wfdata=wfdata, wfdata_compare=wfdata_comp,
+                                     title=title,
                                      zoomx=self.getXLims(),
                                      zoomy=self.getYLims(),
                                      plot_additional=plot_additional,
@@ -3188,14 +3234,14 @@ class PickDlg(QDialog):
     def filterP(self):
         self.filterActionS.setChecked(False)
         if self.filterActionP.isChecked():
-            self.filterWFData('P')
+            self.filter_wf_data('P')
         else:
             self.refreshPlot()
 
     def filterS(self):
         self.filterActionP.setChecked(False)
         if self.filterActionS.isChecked():
-            self.filterWFData('S')
+            self.filter_wf_data('S')
         else:
             self.refreshPlot()
 
@@ -3247,11 +3293,14 @@ class PickDlg(QDialog):
         self.resetZoom()
         self.refreshPlot()
 
+    def switchCompData(self):
+        self.showCompData = self.compareCB.isChecked()
+
     def refreshPlot(self):
         if self.autoFilterAction.isChecked():
             self.filterActionP.setChecked(False)
             self.filterActionS.setChecked(False)
-        # data = self.getWFData().copy()
+        # data = self.get_wf_data().copy()
         # title = self.getStation()
         filter = False
         phase = None
@@ -3751,8 +3800,8 @@ class TuneAutopicker(QWidget):
         fnames = self.station_ids[self.get_current_station_id()]
         if not fnames == self.fnames:
             self.fnames = fnames
-            self.data.setWFData(fnames)
-            wfdat = self.data.getWFData()  # all available streams
+            self.data.set_wf_data(fnames)
+            wfdat = self.data.get_wf_data()  # all available streams
             # remove possible underscores in station names
             # wfdat = remove_underscores(wfdat)
             # rotate misaligned stations to ZNE
@@ -3857,12 +3906,14 @@ class TuneAutopicker(QWidget):
             network = None
             location = None
 
-        wfdata = self.data.getWFData()
+        wfdata = self.data.get_wf_data()
+        wfdata_comp = self.data.get_wf_dataComp()
         metadata = self.parent().metadata
         event = self.get_current_event()
         filteroptions = self.parent().filteroptions
         wftype = self.wftype if self.obspy_dmt else ''
         self.pickDlg = PickDlg(self.parent(), data=wfdata.select(station=station).copy(),
+                               data_comp=wfdata_comp.select(station=station).copy(),
                                station=station, network=network,
                                location=location, parameter=self.parameter,
                                picks=self.get_current_event_picks(station),
@@ -3911,7 +3962,7 @@ class TuneAutopicker(QWidget):
         for plotitem in self._manual_pick_plots:
             self.clear_plotitem(plotitem)
         self._manual_pick_plots = []
-        st = self.data.getWFData()
+        st = self.data.get_wf_data()
         tr = st.select(station=self.get_current_station())[0]
         starttime = tr.stats.starttime
         # create two lists with figure names and subindices (for subplots) to get the correct axes
-- 
2.45.2


From c0c3cbbd7bc3b7744df56c86b7d156470ab9c75f Mon Sep 17 00:00:00 2001
From: Sebastian Wehling-Benatelli <sebastian.wehling@rub.de>
Date: Sun, 18 Aug 2024 14:00:00 +0200
Subject: [PATCH 30/31] refactor: remove unused methods

---
 pylot/core/util/dataprocessing.py | 174 ------------------------------
 1 file changed, 174 deletions(-)

diff --git a/pylot/core/util/dataprocessing.py b/pylot/core/util/dataprocessing.py
index 09d2ba13..0c1cf1d1 100644
--- a/pylot/core/util/dataprocessing.py
+++ b/pylot/core/util/dataprocessing.py
@@ -338,19 +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
@@ -388,167 +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 '
-- 
2.45.2


From e434bda9935c0da38ea36d82dc3485597568b2a0 Mon Sep 17 00:00:00 2001
From: Wehling-Benatelli <sebastian.wehling-benatelli@cgi.com>
Date: Thu, 29 Aug 2024 16:10:13 +0200
Subject: [PATCH 31/31] [change] corrected for required versions

---
 requirements.txt | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index b5e3fe81..a80fadd8 100644
--- a/requirements.txt
+++ b/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
\ No newline at end of file
+cartopy>=0.20.2
+numpy<2
+obspy>=1.3.0
+pyqtgraph>=0.12.4
+pyside2>=5.13.2
+scipy>=1.8.0
\ No newline at end of file
-- 
2.45.2