.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9 (pylot)" project-jdk-type="Python SDK" />
+</project>

.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/pylot.iml" filepath="$PROJECT_DIR$/.idea/pylot.iml" />
+    </modules>
+  </component>
+</project>

.idea/pylot.iml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.9 (pylot)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</module>

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>

PyLoT.py

@@ -35,18 +35,17 @@ import traceback
 import json
 from datetime import datetime
 
-matplotlib.use('Qt4Agg')
-matplotlib.rcParams['backend.qt4'] = 'PySide'
+matplotlib.use('Qt5Agg')
 matplotlib.rcParams['savefig.dpi'] = 300
 
-
-from PySide import QtGui, QtCore
-from PySide.QtCore import QCoreApplication, QSettings, Signal, QFile, \
+from PySide2 import QtGui, QtCore, QtWidgets
+from PySide2.QtCore import QCoreApplication, QSettings, Signal, QFile, \
     QFileInfo, Qt, QSize
-from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
-    QWidget, QHBoxLayout, QVBoxLayout, QStyle, QKeySequence, QLabel, QFrame, QAction, \
-    QDialog, QApplication, QPixmap, QMessageBox, QSplashScreen, \
-    QActionGroup, QListWidget, QListView, QAbstractItemView, \
+from PySide2.QtGui import QIcon, QKeySequence, QPixmap
+from PySide2.QtWidgets import QMainWindow, QInputDialog, QFileDialog, \
+    QWidget, QHBoxLayout, QVBoxLayout, QStyle, QLabel, QFrame, QAction, \
+    QDialog, QErrorMessage, QApplication, QMessageBox, QSplashScreen, \
+    QActionGroup, QListWidget, QLineEdit, QListView, QAbstractItemView, \
     QTreeView, QComboBox, QTabWidget, QPushButton, QGridLayout
 import numpy as np
 from obspy import UTCDateTime, Stream
@@ -58,9 +57,10 @@ from pylot.core.util.obspyDMT_interface import check_obspydmt_structure
 import pyqtgraph as pg
 
 try:
-    from matplotlib.backends.backend_qt4agg import FigureCanvas
+    from matplotlib.backends.backend_qt5agg import FigureCanvas
 except ImportError:
-    from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+    from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
 from matplotlib.figure import Figure
 
 from pylot.core.analysis.magnitude import LocalMagnitude, MomentMagnitude
@@ -87,7 +87,7 @@ from pylot.core.util.widgets import FilterOptionsDialog, NewEventDlg, \
     PylotCanvas, WaveformWidgetPG, PropertiesDlg, HelpForm, createAction, PickDlg, \
     ComparisonWidget, TuneAutopicker, PylotParaBox, AutoPickDlg, CanvasWidget, AutoPickWidget, \
     CompareEventsWidget, ProgressBarWidget, AddMetadataWidget, SingleTextLineDialog
-from pylot.core.util.array_map import Array_map
+#from pylot.core.util.array_map import Array_map
 from pylot.core.util.structure import DATASTRUCTURE
 from pylot.core.util.thread import Thread, Worker
 from pylot.core.util.version import get_git_version as _getVersionString
@@ -581,7 +581,6 @@ class MainWindow(QMainWindow):
         self.autoPickMenu = self.pickMenu.addMenu(self.autopicksicon_small, 'Automatic picking')
         self.autoPickMenu.setEnabled(False)
 
-
         autoPickActions = (self.auto_pick, self.auto_pick_local, self.auto_pick_sge)
 
         self.helpMenu = self.menuBar().addMenu('&Help')
@@ -714,7 +713,6 @@ class MainWindow(QMainWindow):
 
         self.setCentralWidget(_widget)
 
-
     def init_wfWidget(self):
         xlab = self.startTime.strftime('seconds since %Y/%m/%d %H:%M:%S (%Z)')
         plottitle = None  # "Overview: {0} components ".format(self.getComponent())
@@ -760,7 +758,6 @@ class MainWindow(QMainWindow):
         if event.key() == QtCore.Qt.Key.Key_R:
             self.reset_gain()
 
-
     def keyReleaseEvent(self, event):
         if event.key() == QtCore.Qt.Key.Key_Control:
             self._ctrl = False
@@ -780,7 +777,7 @@ class MainWindow(QMainWindow):
     def modify_gain(self, direction, factor):
         assert (direction in ['+', '-']), 'unknown direction'
         if self._ctrl:
-            factor = factor**3
+            factor = factor ** 3
         if direction == '+':
             self.gain *= factor
         elif direction == '-':
@@ -932,7 +929,6 @@ class MainWindow(QMainWindow):
 
             self.recentProjectsMenu.addAction(action)
 
-
     @property
     def inputs(self):
         return self._inputs
@@ -970,7 +966,7 @@ class MainWindow(QMainWindow):
         if not sld.exec_():
             return
         fext = sld.lineEdit.text()
-        #fext = '.xml'
+        # fext = '.xml'
         for event in events:
             path = event.path
             eventname = path.split('/')[-1]  # or event.pylot_id
@@ -1002,7 +998,7 @@ class MainWindow(QMainWindow):
             data_new = Data(self, evtdata=str(fname))
             # MP MP commented because adding several picks might cause inconsistencies
             data = data_new
-            #data += data_new
+            # data += data_new
         except ValueError:
             qmb = QMessageBox(self, icon=QMessageBox.Question,
                               text='Warning: Missmatch in event identifiers {} and {}. Continue?'.format(
@@ -1151,7 +1147,8 @@ class MainWindow(QMainWindow):
             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()]
+                    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)))
@@ -1393,7 +1390,7 @@ class MainWindow(QMainWindow):
                 moment_magnitude = event.magnitudes[0]
                 local_magnitude = event.magnitudes[1]
                 localmag = '%4.1f' % local_magnitude.mag
-                momentmag = '%4.1f'% moment_magnitude.mag
+                momentmag = '%4.1f' % moment_magnitude.mag
 
             # text = '{path:{plen}} | manual: [{p:3d}] | auto: [{a:3d}]'
             # text = text.format(path=event_path,
@@ -1505,6 +1502,7 @@ class MainWindow(QMainWindow):
             event = self.get_current_event()
         if not type(outformats) == list:
             outformats = [outformats]
+
         def getSavePath(event, directory, outformats):
             if not directory:
                 title = 'Save event data as {} to directory ...'.format(outformats)
@@ -1881,7 +1879,7 @@ class MainWindow(QMainWindow):
                             checkRotated=True,
                             metadata=self.metadata,
                             tstart=tstart,
-                            tstop=tstop,)
+                            tstop=tstop, )
 
     def prepareObspyDMT_data(self, eventpath):
         qcbox_processed = self.dataPlot.qcombo_processed
@@ -2077,7 +2075,7 @@ class MainWindow(QMainWindow):
         if self.obspy_dmt:
             invpath = os.path.join(self.get_current_event_path(), 'resp')
             if not invpath in self.metadata.inventories:
-                self.metadata.add_inventory(invpath, obspy_dmt_inv = True)
+                self.metadata.add_inventory(invpath, obspy_dmt_inv=True)
             # check if directory is empty
             if os.listdir(invpath):
                 self.init_map_button.setEnabled(True)
@@ -2643,9 +2641,9 @@ class MainWindow(QMainWindow):
             # init event selection options for autopick
             self.pickoptions = [('current event', self.get_current_event, None),
                                 ('tune events', self.get_ref_events, self._style['ref']['rgba']),
-                                ('test events', self.get_test_events, self._style['test']['rgba']),]
-                                #('all (picked) events', self.get_manu_picked_events, None),
-                                #('all events', self.get_all_events, None)]
+                                ('test events', self.get_test_events, self._style['test']['rgba']), ]
+            # ('all (picked) events', self.get_manu_picked_events, None),
+            # ('all events', self.get_all_events, None)]
 
             self.listWidget = QListWidget()
             self.setDirty(True)
@@ -2870,7 +2868,6 @@ class MainWindow(QMainWindow):
         else:
             event.addAutopicks(picksdict['auto'])
 
-
     def drawPicks(self, station=None, picktype=None, stime=None):
         # if picktype not specified, draw both
         if not stime:
@@ -3363,7 +3360,7 @@ class MainWindow(QMainWindow):
                 event, time, lat, lon, depth, mag, nmp, nap, tune, test, notes = row
                 row_str = ''
                 for index in range(len(row)):
-                    row_str += '{}'+'{}'.format(separator)
+                    row_str += '{}' + '{}'.format(separator)
 
                 row_str = row_str.format(event.text(), time.text(), lat.text(), lon.text(), depth.text(), mag.text(),
                                          nmp.text(), nap.text(), bool(tune.checkState()), bool(test.checkState()),
@@ -3392,7 +3389,6 @@ class MainWindow(QMainWindow):
         if event == current_event:
             set_background_color(item_list, QtGui.QColor(*(0, 143, 143, 255)))
 
-
     def set_metadata(self):
         self.project.inventories = self.metadata.inventories
         if self.metadata.inventories:
@@ -3404,7 +3400,7 @@ class MainWindow(QMainWindow):
             self.init_map_button.setEnabled(False)
             self.initMapAction.setEnabled(False)
             self.inventory_label.setText("No inventory set...")
-            #self.setDirty(False)
+            # self.setDirty(False)
 
     def add_metadata(self):
         self.add_metadata_widget = AddMetadataWidget(self, metadata=self.metadata)
@@ -3697,7 +3693,6 @@ class MainWindow(QMainWindow):
         self.plotWaveformDataThread()
         self.refreshTabs()
 
-
     def PyLoTprefs(self):
         if not self._props:
             self._props = PropertiesDlg(self, infile=self.infile,

icons.qrc

@@ -29,7 +29,6 @@
         <file>icons/map.png</file>
         <file>icons/openloc.png</file>
         <file>icons/compare_button.png</file>
-        <file>icons/pick_qualities_button.png</file>
         <file>icons/locate_button.png</file>
         <file>icons/Matlab_PILOT_icon.png</file>
         <file>icons/printer.png</file>

pylot/core/analysis/magnitude.py

@@ -223,7 +223,7 @@ class LocalMagnitude(Magnitude):
                  in 'Z3']
         # checking horizontal count and calculating power_sum accordingly
         if len(power) == 1:
-                print ('WARNING: Only one horizontal found for station {0}.'.format(st[0].stats.station))
+            print('WARNING: Only one horizontal found for station {0}.'.format(st[0].stats.station))
             power_sum = power[0]
         elif len(power) == 2:
             power_sum = power[0] + power[1]
@@ -589,13 +589,13 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
 
         # fft
         fny = freq / 2
-        #l = len(xdat) / freq
+        # l = len(xdat) / freq
         # number of fft bins after Bath
-        #n = freq * l
+        # n = freq * l
         # find next power of 2 of data length
         m = pow(2, np.ceil(np.log(len(xdat)) / np.log(2)))
         N = min(int(np.power(m, 2)), 16384)
-        #N = int(np.power(m, 2))
+        # N = int(np.power(m, 2))
         y = dt * np.fft.fft(xdat, N)
         Y = abs(y[: N / 2])
         L = (N - 1) / freq

pylot/core/io/data.py

@@ -8,7 +8,7 @@ from obspy.core import read, Stream, UTCDateTime
 from obspy.core.event import Event as ObsPyEvent
 from obspy.io.sac import SacIOError
 
-from PySide.QtGui import QMessageBox
+from PySide2.QtWidgets import QMessageBox
 
 import pylot.core.loc.velest as velest
 import pylot.core.loc.focmec as focmec
@@ -21,6 +21,7 @@ from pylot.core.util.obspyDMT_interface import qml_from_obspyDMT
 from pylot.core.util.utils import fnConstructor, full_range, check4rotated, \
     check4gapsAndMerge, trim_station_components
 
+
 class Data(object):
     """
     Data container with attributes wfdata holding ~obspy.core.stream.
@@ -47,7 +48,7 @@ class Data(object):
         elif isinstance(evtdata, dict):
             evt = readPILOTEvent(**evtdata)
             evtdata = evt
-        elif type(evtdata) in [str, unicode]:
+        elif type(evtdata) == str:
             try:
                 cat = read_events(evtdata)
                 if len(cat) is not 1:
@@ -99,7 +100,7 @@ class Data(object):
                                       old_pick.phase_hint == new_pick.phase_hint,
                                       old_pick.method_id == new_pick.method_id]
                         if all(comparison):
-                            del(old_pick)
+                            del (old_pick)
                 old_picks.append(new_pick)
         elif not other.isNew() and self.isNew():
             new = other + self
@@ -288,6 +289,7 @@ class Data(object):
                 self.checkEvent(event, fcheck)
                 self.setEvtData(event)
 
+
             self.get_evt_data().write(fnout + fnext, format=evtformat)
 
         # try exporting event
@@ -489,7 +491,8 @@ class Data(object):
                     real_or_syn_data[synthetic] += read(fname, format='GSE2', starttime=self.tstart, endtime=self.tstop)
                 except Exception as e:
                     try:
-                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart, endtime=self.tstop)
+                        real_or_syn_data[synthetic] += read(fname, format='SEGY', starttime=self.tstart,
+                                                            endtime=self.tstop)
                     except Exception as e:
                         warnmsg += '{0}\n{1}\n'.format(fname, e)
             except SacIOError as se:

pylot/core/io/phases.py

@@ -252,7 +252,7 @@ def picksdict_from_picks(evt):
         if picker == 'None':
             picker = 'manual'
         try:
-            #onsets = picksdict[picker][station]
+            # onsets = picksdict[picker][station]
             onsets = picksdict[station]
         except KeyError as e:
             # print(e)
@@ -573,7 +573,7 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
                 except KeyError as e:
                     print(str(e) + '; no weight set during processing')
                 Ao = arrivals[key]['S']['Ao']  # peak-to-peak amplitude
-                #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 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,

pylot/core/util/array_map.py

@@ -6,7 +6,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 import obspy
 import traceback
-from PySide import QtGui
+#from PySide2 import QtGui
+from PySide2 import QtWidgets as QtGui
 from matplotlib.figure import Figure
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from mpl_toolkits.basemap import Basemap

pylot/core/util/thread.py

@@ -4,8 +4,8 @@ import os
 import sys
 import traceback
 
-from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
-from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout
+from PySide2.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
+from PySide2.QtWidgets import QDialog, QProgressBar, QLabel, QHBoxLayout
 
 
 class Thread(QThread):

pylot/core/util/widgets.py

@@ -17,27 +17,28 @@ import sys
 import time
 import traceback
 
-matplotlib.use('QT4Agg')
+matplotlib.use('QT5Agg')
 
 from matplotlib.figure import Figure
 
 try:
-    from matplotlib.backends.backend_qt4agg import FigureCanvas
+    from matplotlib.backends.backend_qt5agg import FigureCanvas
 except ImportError:
-    from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
-from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT
+    from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT
 from matplotlib.widgets import MultiCursor
 from obspy import read
 
-from PySide import QtCore, QtGui
-from PySide.QtGui import QAction, QApplication, QCheckBox, QComboBox, \
+from PySide2 import QtCore, QtGui
+from PySide2.QtGui import QIcon, QPixmap, QKeySequence
+from PySide2.QtWidgets import QAction, QApplication, QCheckBox, QComboBox, \
     QDateTimeEdit, QDialog, QDialogButtonBox, QDoubleSpinBox, QGroupBox, \
-    QGridLayout, QFormLayout, QIcon, QLabel, QLineEdit, QMessageBox, \
-    QPixmap, QSpinBox, QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
-    QPushButton, QFileDialog, QInputDialog, QKeySequence
-from PySide.QtCore import QSettings, Qt, QUrl, Signal
-from PySide.QtWebKit import QWebView
-from obspy import Stream, Trace, UTCDateTime
+    QGridLayout, QFormLayout, QLabel, QLineEdit, QMessageBox, \
+    QSpinBox, QTabWidget, QToolBar, QVBoxLayout, QHBoxLayout, QWidget, \
+    QPushButton, QFileDialog, QInputDialog
+from PySide2.QtCore import QSettings, Qt, QUrl, Signal, Slot
+from PySide2.QtWebEngineWidgets import QWebEngineView as QWebView
+from obspy import Stream, UTCDateTime
 from obspy.core.util import AttribDict
 from obspy.taup import TauPyModel
 from obspy.taup.utils import get_phase_names