marcel/pylot
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Code Issues 7 Pull Requests 1 Releases Wiki Activity

[fix] made PyLoT start again #7

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sebastianw wants to merge 3 commits from feature/python-3-compatibility into develop
pull from: feature/python-3-compatibility
merge into: marcel:develop
Conversation 0 Commits 3 Files Changed 14 +108789 -109233
14 changed files with 108789 additions and 109233 deletions
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Showing only changes of commit cf70c65e83 - Show all commits

6
.idea/inspectionProfiles/profiles_settings.xml Normal file
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@ -0,0 +1,6 @@
<component name="InspectionProjectProfileManager">
<settings>
<option name="USE_PROJECT_PROFILE" value="false" />
<version value="1.0" />
</settings>
</component>

4
.idea/misc.xml Normal file
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@ -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>

8
.idea/modules.xml Normal file
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@ -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>

12
.idea/pylot.iml Normal file
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@ -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>

6
.idea/vcs.xml Normal file
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@ -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>

83
PyLoT.py
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@ -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
@ -418,9 +418,9 @@ class MainWindow(QMainWindow):
None, paraIcon,
"Modify Parameter")
self.deleteAutopicksAction = self.createAction(self, "Delete Autopicks",
self.deleteAllAutopicks,
None, deleteIcon,
"Delete all automatic picks from Project.")
self.deleteAllAutopicks,
None, deleteIcon,
"Delete all automatic picks from Project.")
self.filterActionP = createAction(parent=self, text='Apply P Filter',
slot=self.filterP,
icon=self.filter_icon_p,
@ -551,7 +551,7 @@ class MainWindow(QMainWindow):
shortcut='Alt+Ctrl+L',
icon=locate_icon,
tip='Locate the event using '
'the displayed manual arrivals.')
'the displayed manual arrivals.')
self.locateEventAction.setEnabled(False)
locationToolActions = (self.locateEventAction,)
@ -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)
@ -2479,7 +2477,7 @@ class MainWindow(QMainWindow):
if not seed_id:
seed_id = self.getTraceID(wfID)
try:
network, station, location = seed_id.split('.')[:3]
network, station, location = seed_id.split('.')[:3]
except:
print("Warning! No network, station, and location info available!")
return
@ -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)
@ -2843,7 +2841,7 @@ class MainWindow(QMainWindow):
def safetyCopy(self, event_path):
fpath = self.get_deleted_picks_fpath(event_path)
fpath_new = fpath.split('.json')[0] + '_copy_{}.json'.format(datetime.now()).replace(' ', '_')
fpath_new = fpath.split('.json')[0] + '_copy_{}.json'.format(datetime.now()).replace(' ', '_')
shutil.move(fpath, fpath_new)
def load_deleted_picks(self, event_path):
@ -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:
@ -2923,7 +2920,7 @@ class MainWindow(QMainWindow):
phaseID = self.getPhaseID(phase)
# get quality classes
if phaseID == 'P':
if phaseID == 'P':
quality = getQualityFromUncertainty(picks['spe'], self._inputs['timeerrorsP'])
elif phaseID == 'S':
quality = getQualityFromUncertainty(picks['spe'], self._inputs['timeerrorsS'])
@ -3297,7 +3294,7 @@ class MainWindow(QMainWindow):
item_test.setCheckState(QtCore.Qt.Unchecked)
row = [item_delete, item_path, item_time, item_lat, item_lon, item_depth, item_localmag,
item_momentmag, item_nmp, item_nap, item_ref, item_test, item_notes]
item_momentmag, item_nmp, item_nap, item_ref, item_test, item_notes]
self.project._table.append(row)
self.setItemColor(row, index, event, current_event)
@ -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)
@ -3652,7 +3648,7 @@ class MainWindow(QMainWindow):
else:
self.dataPlot.setPermText(1)
self.dataPlot.setPermText(0, '| Number of traces: {} | Gain: {}'.format(len(self.getPlotWidget().getPlotDict()),
self.gain))
self.gain))
def _setDirty(self):
self.setDirty(True)
@ -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,
@ -3766,10 +3761,10 @@ class Project(object):
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.
'''
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]

1
icons.qrc
View File

@ -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>

217791
icons_rc_3.py
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File diff suppressed because it is too large Load Diff

22
pylot/core/analysis/magnitude.py
View File

@ -223,13 +223,13 @@ 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))
power_sum = power[0]
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]
power_sum = power[0] + power[1]
else:
raise ValueError('Wood-Anderson aomplitude defintion only valid for'
' up to two horizontals: {0} given'.format(len(power)))
raise ValueError('Wood-Anderson aomplitude defintion only valid for'
' up to two horizontals: {0} given'.format(len(power)))
sqH = np.sqrt(power_sum)
@ -324,7 +324,7 @@ class LocalMagnitude(Magnitude):
if self.verbose:
print(
"Local Magnitude for station {0}: ML = {1:3.1f}".format(
station, magnitude.mag))
station, magnitude.mag))
magnitude.origin_id = self.origin_id
magnitude.waveform_id = pick.waveform_id
magnitude.amplitude_id = amplitude.resource_id
@ -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
@ -638,8 +638,8 @@ def calcsourcespec(wfstream, onset, vp, delta, azimuth, incidence,
w0 = np.median([w01, w02])
Fc = np.median([fc1, fc2])
if verbosity:
print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
w0, Fc))
print("calcsourcespec: Using w0-value = %e m/Hz and fc = %f Hz" % (
w0, Fc))
if iplot >= 1:
f1 = plt.figure()
tLdat = np.arange(0, len(Ldat) * dt, dt)

13
pylot/core/io/data.py
View File

@ -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
@ -111,7 +112,7 @@ class Data(object):
return self + other
else:
raise ValueError("both Data objects have differing "
"unique Event identifiers")
"unique Event identifiers")
return self
def getPicksStr(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:

24
pylot/core/io/phases.py
View File

@ -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)
@ -572,18 +572,18 @@ def writephases(arrivals, fformat, filename, parameter=None, eventinfo=None):
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
#fid.write('%s ? ? ? S %s %d%02d%02d %02d%02d %7.4f GAU 0 0 0 0 %d \n' % (key,
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 %9.2f 0 0 %d \n' % (key,
fm,
year,
month,
day,
hh,
mm,
ss_ms,
Ao,
sweight))
fm,
year,
month,
day,
hh,
mm,
ss_ms,
Ao,
sweight))
fid.close()
elif fformat == 'HYPO71':

3
pylot/core/util/array_map.py
View File

@ -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

4
pylot/core/util/thread.py
View File

@ -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):

25
pylot/core/util/widgets.py
View File

@ -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