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[merge] merged changes in QtPyLoT manually

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This commit is contained in:
Marcel Paffrath 2017-07-17 11:38:50 +02:00
commit 7f0ab4dd94
19 changed files with 196580 additions and 98416 deletions
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84
QtPyLoT.py
View File

@ -25,6 +25,7 @@ https://www.iconfinder.com/iconsets/flavour
import os
import sys
import platform
import argparse
import matplotlib
@ -41,7 +42,7 @@ from PySide.QtGui import QMainWindow, QInputDialog, QIcon, QFileDialog, \
QTreeView, QComboBox, QTabWidget, QPushButton, QGridLayout
import numpy as np
from obspy import UTCDateTime
from obspy.core.event import Magnitude
from obspy.core.event import Magnitude, Origin
from obspy.core.util import AttribDict
try:
@ -82,7 +83,13 @@ from pylot.core.util.map_projection import map_projection
from pylot.core.util.structure import DATASTRUCTURE
from pylot.core.util.thread import AutoPickThread, Thread
from pylot.core.util.version import get_git_version as _getVersionString
import icons_rc
if sys.version_info.major == 3:
import icons_rc_3 as icons_rc
elif sys.version_info.major == 2:
import icons_rc_2 as icons_rc
else:
raise ImportError('Could not determine python version.')
locateTool = dict(nll=nll)
@ -602,12 +609,10 @@ class MainWindow(QMainWindow):
def metadata(self):
return self._metadata
@metadata.setter
def metadata(self, value):
self._metadata = value
def updateFileMenu(self):
self.fileMenu.clear()
@ -711,7 +716,7 @@ class MainWindow(QMainWindow):
event = self.get_current_event()
data = Data(self, event)
try:
data_new = Data(self, evtdata=fname)
data_new = Data(self, evtdata=str(fname))
data += data_new
except ValueError:
qmb = QMessageBox(self, icon=QMessageBox.Question,
@ -857,11 +862,21 @@ class MainWindow(QMainWindow):
# get path from first event in list and split them
path = eventlist[0]
try:
system_name = platform.system()
if system_name in ["Linux", "Darwin"]:
dirs = {
'database': path.split('/')[-2],
'datapath': path.split('/')[-3],
'rootpath': '/' + os.path.join(*path.split('/')[:-3])
}
elif system_name == "Windows":
rootpath = path.split('/')[:-3]
rootpath[0] += '/'
dirs = {
'database': path.split('/')[-2],
'datapath': path.split('/')[-3],
'rootpath': os.path.join(*rootpath)
}
except Exception as e:
dirs = {
'database': '',
@ -1059,17 +1074,6 @@ class MainWindow(QMainWindow):
filename = 'PyLoT_' + eventname
outpath = os.path.join(directory, filename)
title = 'Save pick data ...'
#if not outformat:
# outformat = settings.value('output/Format')
# outformat = outformat[0:4]
#else:
# selected_filter = "NonLinLoc observation file (*.obs)"
# fname = outpath
#if outformat == '.obs':
# file_filter = "NonLinLoc observation file (*.obs)"
#elif outformat == '.cnv':
# file_filter = "VELEST observation file format (*.cnv)"
#elif outformat == '.xml':
file_filter = "(*.xml *.obs *.cnv)"
if dlgflag == 1:
@ -1078,12 +1082,11 @@ class MainWindow(QMainWindow):
outpath,
file_filter)
#fbasename, exform = os.path.splitext(fname)
try:
fbasename = fname
except:
fbasename = outpath
exform = ['.obs', '.xml', '.cnv']
#if not exform and selected_filter or not exform in OUTPUTFORMATS:
# exform = selected_filter.split('*')[1][:-1]
# return fname, exform
return fbasename, exform
settings = QSettings()
@ -1225,7 +1228,8 @@ class MainWindow(QMainWindow):
def okToContinue(self):
if self.dirty:
qmb = QMessageBox(self, icon=QMessageBox.Question, text='Do you wish to save changes in the current project?')
qmb = QMessageBox(self, icon=QMessageBox.Question,
text='Do you wish to save changes in the current project?')
qmb.setStandardButtons(QMessageBox.Save | QMessageBox.Discard | QMessageBox.Cancel)
qmb.setDefaultButton(QMessageBox.Save)
ret = qmb.exec_()
@ -1351,13 +1355,13 @@ class MainWindow(QMainWindow):
call modal plot thread method when finished.
'''
if load:
wfd_thread = Thread(self, self.loadWaveformData,
self.wfd_thread = Thread(self, self.loadWaveformData,
progressText='Reading data input...')
if load and plot:
wfd_thread.finished.connect(self.plotWaveformDataThread)
self.wfd_thread.finished.connect(self.plotWaveformDataThread)
if load:
wfd_thread.start()
self.wfd_thread.start()
if plot and not load:
self.plotWaveformDataThread()
@ -1519,7 +1523,8 @@ class MainWindow(QMainWindow):
# wfst += self.get_data().getWFData().select(component=alter_comp)
plotWidget = self.getPlotWidget()
self.adjustPlotHeight()
plots = plotWidget.plotWFData(wfdata=wfst, title=title, mapping=False, component=comp, nth_sample=int(nth_sample))
plots = plotWidget.plotWFData(wfdata=wfst, title=title, mapping=False, component=comp,
nth_sample=int(nth_sample))
return plots
def adjustPlotHeight(self):
@ -1920,8 +1925,10 @@ class MainWindow(QMainWindow):
dashed = QtCore.Qt.DashLine
dotted = QtCore.Qt.DotLine
phase_col = {
'P': (pg.mkPen('c'), pg.mkPen((0, 255, 255, 100), style=dashed), pg.mkPen('b', style=dashed), pg.mkPen('b', style=dotted)),
'S': (pg.mkPen('m'), pg.mkPen((255, 0, 255, 100), style=dashed), pg.mkPen('r', style=dashed), pg.mkPen('r', style=dotted))
'P': (pg.mkPen('c'), pg.mkPen((0, 255, 255, 100), style=dashed), pg.mkPen('b', style=dashed),
pg.mkPen('b', style=dotted)),
'S': (pg.mkPen('m'), pg.mkPen((255, 0, 255, 100), style=dashed), pg.mkPen('r', style=dashed),
pg.mkPen('r', style=dotted))
}
else:
phase_col = {
@ -1943,6 +1950,9 @@ class MainWindow(QMainWindow):
if picks['epp'] and picks['lpp']:
epp = picks['epp'] - stime
lpp = picks['lpp'] - stime
else:
epp = None
lpp = None
spe = picks['spe']
if not spe and epp and lpp:
@ -1956,7 +1966,8 @@ class MainWindow(QMainWindow):
pw.plot([lpp, lpp], ylims,
alpha=.25, pen=colors[0], name='LPP')
if spe:
spe_l = pg.PlotDataItem([mpp - spe, mpp - spe], ylims, pen=colors[1], name='{}-SPE'.format(phase))
spe_l = pg.PlotDataItem([mpp - spe, mpp - spe], ylims, pen=colors[1],
name='{}-SPE'.format(phase))
spe_r = pg.PlotDataItem([mpp + spe, mpp + spe], ylims, pen=colors[1])
pw.addItem(spe_l)
pw.addItem(spe_r)
@ -2151,6 +2162,7 @@ class MainWindow(QMainWindow):
'''
Build and initiate event table (3rd tab [index=2]) containing information of every event.
'''
def set_enabled(item, enabled=True, checkable=False):
# modify item flags depending on case needed
if enabled and not checkable:
@ -2352,10 +2364,12 @@ class MainWindow(QMainWindow):
# if not rest_flag:
# raise ProcessingError('Restitution of waveform data failed!')
if type == 'ML':
local_mag = LocalMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('sstop'), verbosity = True)
local_mag = LocalMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('sstop'),
verbosity=True)
return local_mag.updated_event()
elif type == 'Mw':
moment_mag = MomentMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('vp'), self.inputs.get('Qp'), self.inputs.get('rho'), verbosity = True)
moment_mag = MomentMagnitude(corr_wf, self.get_data().get_evt_data(), self.inputs.get('vp'),
self.inputs.get('Qp'), self.inputs.get('rho'), verbosity=True)
return moment_mag.updated_event()
else:
return None
@ -2558,6 +2572,7 @@ class Project(object):
'''
Pickable class containing information of a QtPyLoT project, like event lists and file locations.
'''
def __init__(self):
self.eventlist = []
self.location = None
@ -2610,13 +2625,17 @@ class Project(object):
print(e, datetime, filename)
continue
for event in self.eventlist:
if not event.origins:
continue
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)
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'))
@ -2704,6 +2723,7 @@ class getExistingDirectories(QFileDialog):
'''
File dialog with possibility to select multiple folders.
'''
def __init__(self, *args):
super(getExistingDirectories, self).__init__(*args)
self.setOption(self.DontUseNativeDialog, True)

0
icons_rc.py → icons_rc_2.py
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98097
icons_rc_3.py Normal file
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File diff suppressed because it is too large Load Diff

1
pylot/RELEASE-VERSION Normal file
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@ -0,0 +1 @@
b286-dirty

2
pylot/core/io/data.py
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@ -39,7 +39,7 @@ class Data(object):
elif isinstance(evtdata, dict):
evt = readPILOTEvent(**evtdata)
evtdata = evt
elif isinstance(evtdata, basestring):
elif isinstance(evtdata, str):
try:
cat = read_events(evtdata)
if len(cat) is not 1:

2
pylot/core/io/inputs.py
View File

@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
from pylot.core.util.errors import ParameterError
import default_parameters
from pylot.core.io import default_parameters
class PylotParameter(object):
'''

8
pylot/core/io/phases.py
View File

@ -253,8 +253,8 @@ def picks_from_picksdict(picks, creation_info=None):
lpp = phase['lpp']
pick.time_errors.lower_uncertainty = onset - epp
pick.time_errors.upper_uncertainty = lpp - onset
except KeyError as e:
warnings.warn(e.message, RuntimeWarning)
except (KeyError, TypeError) as e:
warnings.warn(str(e), RuntimeWarning)
try:
picker = phase['picker']
except KeyError as e:
@ -274,7 +274,7 @@ def picks_from_picksdict(picks, creation_info=None):
else:
pick.polarity = 'undecidable'
except KeyError as e:
if 'fm' in e.message: # no polarity information found for this phase
if 'fm' in str(e): # no polarity information found for this phase
pass
else:
raise e
@ -360,7 +360,7 @@ def reassess_pilot_event(root_dir, db_dir, event_id, out_dir=None, fn_param=None
default.get('nfac{0}'.format(phase)),
default.get('tsnrz' if phase == 'P' else 'tsnrh'),
Pick1=rel_pick,
iplot=None,
iplot=0,
verbosity=0)
if epp is None or lpp is None:
continue

6
pylot/core/pick/charfuns.py
View File

@ -307,7 +307,7 @@ class HOScf(CharacteristicFunction):
class ARZcf(CharacteristicFunction):
def calcCF(self, data):
print 'Calculating AR-prediction error from single trace ...'
print('Calculating AR-prediction error from single trace ...')
x = self.getDataArray(self.getCut())
xnp = x[0].data
nn = np.isnan(xnp)
@ -430,7 +430,7 @@ class ARZcf(CharacteristicFunction):
class ARHcf(CharacteristicFunction):
def calcCF(self, data):
print 'Calculating AR-prediction error from both horizontal traces ...'
print('Calculating AR-prediction error from both horizontal traces ...')
xnp = self.getDataArray(self.getCut())
n0 = np.isnan(xnp[0].data)
@ -567,7 +567,7 @@ class ARHcf(CharacteristicFunction):
class AR3Ccf(CharacteristicFunction):
def calcCF(self, data):
print 'Calculating AR-prediction error from all 3 components ...'
print('Calculating AR-prediction error from all 3 components ...')
xnp = self.getDataArray(self.getCut())
n0 = np.isnan(xnp[0].data)

2
pylot/core/pick/compare.py
View File

@ -480,7 +480,7 @@ def main():
Insheim = PDFstatistics(root_dir)
Insheim.curphase = 'p'
qdlist = Insheim.get('qdf', 0.2)
print qdlist
print(qdlist)
if __name__ == "__main__":

2
pylot/core/pick/picker.py
View File

@ -34,7 +34,7 @@ class AutoPicker(object):
warnings.simplefilter('ignore')
def __init__(self, cf, TSNR, PickWindow, iplot=None, aus=None, Tsmooth=None, Pick1=None, fig=None):
def __init__(self, cf, TSNR, PickWindow, iplot=0, aus=None, Tsmooth=None, Pick1=None, fig=None):
'''
:param: cf, characteristic function, on which the picking algorithm is applied
:type: `~pylot.core.pick.CharFuns.CharacteristicFunction` object

7
pylot/core/pick/utils.py
View File

@ -14,7 +14,7 @@ import numpy as np
from obspy.core import Stream, UTCDateTime
def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None):
'''
Function to derive earliest and latest possible pick after Diehl & Kissling (2009)
as reasonable uncertainties. Latest possible pick is based on noise level,
@ -144,7 +144,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, verbosity=1, fig=None):
return EPick, LPick, PickError
def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None, fig=None):
def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None):
'''
Function to derive first motion (polarity) of given phase onset Pick.
Calculation is based on zero crossings determined within time window pickwin
@ -357,7 +357,7 @@ def getSNR(X, TSNR, t1, tracenum=0):
assert isinstance(X, Stream), "%s is not a stream object" % str(X)
SNR = None
SNRdb = None
SNRdB = None
noiselevel = None
x = X[tracenum].data
@ -480,6 +480,7 @@ def getResolutionWindow(snr, extent):
'global': {'HRW': 40., 'MRW': 100., 'LRW': 200., 'VLRW': 300.}
}
if snr:
if snr < 1.5:
time_resolution = res_wins[extent]['VLRW']
elif snr < 2.:

4
pylot/core/pick/utils.py.orig
View File

@ -15,7 +15,7 @@ from obspy.core import Stream, UTCDateTime
import warnings
def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealthMode = False):
def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, stealthMode = False):
'''
Function to derive earliest and latest possible pick after Diehl & Kissling (2009)
as reasonable uncertainties. Latest possible pick is based on noise level,
@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=None, stealthMode = False):
return EPick, LPick, PickError
def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=None):
def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0):
'''
Function to derive first motion (polarity) of given phase onset Pick.
Calculation is based on zero crossings determined within time window pickwin

9
pylot/core/util/connection.py
View File

@ -1,13 +1,16 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import urllib2
try:
from urllib2 import urlopen
except:
from urllib.request import urlopen
def checkurl(url='https://ariadne.geophysik.rub.de/trac/PyLoT'):
try:
urllib2.urlopen(url, timeout=1)
urlopen(url, timeout=1)
return True
except urllib2.URLError:
except:
pass
return False

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

@ -4,7 +4,6 @@
import os
import glob
import sys
from obspy.io.xseed import Parser
import numpy as np
@ -170,7 +169,7 @@ def read_metadata(path_to_inventory):
invfile = list()
respfile = list()
# possible file extensions specified here:
inv = dict(dless=dlfile, xml=invfile, resp=respfile, dseed=dlfile)
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]

1
pylot/core/util/map_projection.py
View File

@ -19,6 +19,7 @@ class map_projection(QtGui.QWidget):
'''
QtGui.QWidget.__init__(self)
self._parent = parent
self.metadata = parent.metadata
self.parser = parent.metadata[1]
self.picks = None
self.picks_dict = None

10
pylot/core/util/pdf.py
View File

@ -59,7 +59,7 @@ def exp_parameter(te, tm, tl, eta):
return tm, sig1, sig2, a
def gauss_branches(k, (mu, sig1, sig2, a1, a2)):
def gauss_branches(k, param_tuple):
'''
function gauss_branches takes an axes x, a center value mu, two sigma
values sig1 and sig2 and two scaling factors a1 and a2 and return a
@ -79,6 +79,9 @@ def gauss_branches(k, (mu, sig1, sig2, a1, a2)):
:returns fun_vals: list with function values along axes x
'''
#python 3 workaround
mu, sig1, sig2, a1, a2 = param_tuple
def _func(k, mu, sig1, sig2, a1, a2):
if k < mu:
rval = a1 * 1 / (np.sqrt(2 * np.pi) * sig1) * np.exp(-((k - mu) / sig1) ** 2 / 2)
@ -93,7 +96,7 @@ def gauss_branches(k, (mu, sig1, sig2, a1, a2)):
return _func(k, mu, sig1, sig2, a1, a2)
def exp_branches(k, (mu, sig1, sig2, a)):
def exp_branches(k, param_tuple):
'''
function exp_branches takes an axes x, a center value mu, two sigma
values sig1 and sig2 and a scaling factor a and return a
@ -107,6 +110,9 @@ def exp_branches(k, (mu, sig1, sig2, a)):
:returns fun_vals: list with function values along axes x:
'''
#python 3 workaround
mu, sig1, sig2, a = param_tuple
def _func(k, mu, sig1, sig2, a):
mu = float(mu)
if k < mu:

12
pylot/core/util/utils.py
View File

@ -5,7 +5,7 @@ import hashlib
import numpy as np
from scipy.interpolate import splrep, splev
import os
import pwd
import platform
import re
import warnings
import subprocess
@ -258,7 +258,7 @@ def getLogin():
returns the actual user's login ID
:return: login ID
'''
return pwd.getpwuid(os.getuid())[0]
return os.getlogin()
def getOwner(fn):
@ -268,7 +268,15 @@ def getOwner(fn):
:type fn: str
:return: login ID of the file's owner
'''
system_name = platform.system()
if system_name in ["Linux", "Darwin"]:
import pwd
return pwd.getpwuid(os.stat(fn).st_uid).pw_name
elif system_name == "Windows":
import win32security
f = win32security.GetFileSecurity(fn, win32security.OWNER_SECURITY_INFORMATION)
(username, domain, sid_name_use) = win32security.LookupAccountSid(None, f.GetSecurityDescriptorOwner())
return username
def getPatternLine(fn, pattern):

40
pylot/core/util/widgets.py
View File

@ -6,6 +6,7 @@ Created on Wed Mar 19 11:27:35 2014
"""
import os
import sys
import getpass
import warnings
import copy
@ -47,7 +48,12 @@ from pylot.core.util.utils import prepTimeAxis, full_range, scaleWFData, \
demeanTrace, isSorted, findComboBoxIndex, clims
from autoPyLoT import autoPyLoT
from pylot.core.util.thread import Thread
import icons_rc
if sys.version_info.major == 3:
import icons_rc_3 as icons_rc
elif sys.version_info.major == 2:
import icons_rc_2 as icons_rc
else:
raise ImportError('Could not determine python version.')
if pg:
pg.setConfigOption('background', 'w')
@ -462,7 +468,7 @@ class WaveformWidgetPG(QtGui.QWidget):
def plotWFData(self, wfdata, title=None, zoomx=None, zoomy=None,
noiselevel=None, scaleddata=False, mapping=True,
component='*', nth_sample=1, iniPick=None):
component='*', nth_sample=1, iniPick=None, verbosity=0):
self.title = title
self.clearPlotDict()
wfstart, wfend = full_range(wfdata)
@ -509,6 +515,7 @@ class WaveformWidgetPG(QtGui.QWidget):
if n > nmax:
nmax = n
msg = 'plotting %s channel of station %s' % (channel, station)
if verbosity:
print(msg)
stime = trace.stats.starttime - wfstart
time_ax = prepTimeAxis(stime, trace)
@ -696,7 +703,7 @@ class WaveformWidget(FigureCanvas):
self.getAxes().set_ylim(lims)
def setYTickLabels(self, pos, labels):
self.getAxes().set_yticks(pos)
self.getAxes().set_yticks(list(pos))
self.getAxes().set_yticklabels(labels)
self.draw()
@ -865,7 +872,7 @@ class PickDlg(QDialog):
tip='Delete current picks.')
# create other widget elements
phaseitems = [None] + FILTERDEFAULTS.keys()
phaseitems = [None] + list(FILTERDEFAULTS.keys())
# create buttons for P and S filter and picking
self.p_button = QPushButton('P', self)
@ -945,7 +952,11 @@ class PickDlg(QDialog):
station_id = self.data.traces[0].get_id()
parser = self.parent().metadata[1]
station_coords = parser.get_coordinates(station_id)
source_origin = self.parent().get_current_event().origins[0]
origins = self.parent().get_current_event().origins
if origins:
source_origin = origins[0]
else:
raise ValueError('No source origin given.')
arrivals = self.model.get_travel_times_geo(source_origin.depth,
source_origin.latitude,
source_origin.longitude,
@ -1348,8 +1359,13 @@ class PickDlg(QDialog):
phase = self.currentPhase
filteroptions = self.getFilterOptions(phase[0]).parseFilterOptions()
if filteroptions:
try:
data.filter(**filteroptions)
wfdata.filter(**filteroptions)
except ValueError as e:
self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Information,
'Denied', 'setIniPickP: Could not filter waveform: {}'.format(e))
self.qmb.show()
result = getSNR(wfdata, (noise_win, gap_win, signal_win), ini_pick-stime_diff, itrace)
@ -1401,8 +1417,13 @@ class PickDlg(QDialog):
phase = self.currentPhase
filteroptions = self.getFilterOptions(phase).parseFilterOptions()
if filteroptions:
try:
data.filter(**filteroptions)
wfdata.filter(**filteroptions)
except ValueError as e:
self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Information,
'Denied', 'setIniPickS: Could not filter waveform: {}'.format(e))
self.qmb.show()
# determine SNR and noiselevel
result = getSNR(wfdata, (noise_win, gap_win, signal_win), ini_pick-stime_diff)
@ -1463,7 +1484,14 @@ class PickDlg(QDialog):
# copy and filter data for earliest and latest possible picks
wfdata = self.getWFData().copy().select(channel=channel)
if filteroptions:
try:
wfdata.filter(**filteroptions)
except ValueError as e:
self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Information,
'Denied', 'setPick: Could not filter waveform: {}'.format(e))
self.qmb.show()
# get earliest and latest possible pick and symmetric pick error
if wfdata[0].stats.channel[2] == 'Z' or wfdata[0].stats.channel[2] == '3':
@ -2736,7 +2764,7 @@ class InputsTab(PropTab):
from pylot.core.util.structure import DATASTRUCTURE
self.structureSelect.addItems(DATASTRUCTURE.keys())
self.structureSelect.addItems(list(DATASTRUCTURE.keys()))
dsind = findComboBoxIndex(self.structureSelect, curstructure)