Merge remote-tracking branch 'origin/develop' into feature/port-to-python-3.9.0

Aiming also to avoid deprecations and outdated versions of dependencies.

README.md

@@ -66,27 +66,41 @@ PyLoT has been tested on Mac OSX (10.11), Debian Linux 8 and on Windows 10.
 
 #### Features:
 
-- event organisation in project files and waveform visualisation
+- centralize all functionalities of PyLoT and control them from within the main GUI
-- consistent manual phase picking through predefined SNR dependant zoom level
+- handling multiple events inside GUI with project files (save and load work progress)
-- consistent automatic phase picking routines using Higher Order Statistics, AIC and Autoregression
+- GUI based adjustments of pick parameters and I/O
-- interactive tuning of auto-pick parameters
+- interactive tuning of parameters from within the GUI
-- uniform uncertainty estimation from waveform's properties for automatic and manual picks
+- call automatic picking algorithm from within the GUI
-- pdf representation and comparison of picks taking the uncertainty intrinsically into account 
+- comparison of automatic with manual picks for multiple events using clear differentiation of manual picks into 'tune' and 'test-set' (beta)
-- Richter and moment magnitude estimation
+- manual picking of different (user defined) phase types
-- location determination with external installation of [NonLinLoc](http://alomax.free.fr/nlloc/index.html)
+- phase onset estimation with ObsPy TauPy
+- interactive zoom/scale functionalities in all plots (mousewheel, pan, pan-zoom)
+- array map to visualize stations and control onsets (beta feature, switch to manual picks not implemented)
 
-#### Known issues:
+##### Platform support:
+- Python 3 support
+- Windows support
 
-- Sometimes an error might occur when using Qt
+##### Performance:
+- multiprocessing for automatic picking and restitution of multiple stations
+- use pyqtgraph library for better performance on main waveform plot
 
-We hope to solve these with the next release.
+##### Visualization:
+- pick uncertainty (quality classes) visualization with gradients
+- pick color unification for all plots
+- new icons and stylesheets
+
+#### Known Issues:
+- some Qt related errors might occur at runtime
+- filter toggle not working in pickDlg
+- PyLoT data structure requires at least three parent directories for waveform data directory
 
 ## Staff
 
 Original author(s): L. Kueperkoch, S. Wehling-Benatelli, M. Bischoff (PILOT)
 
-Developer(s): S. Wehling-Benatelli, L. Kueperkoch, K. Olbert, M. Bischoff,
+Developer(s): S. Wehling-Benatelli, L. Kueperkoch, M. Paffrath, K. Olbert,
-              C. Wollin, M. Rische, M. Paffrath
+M. Bischoff, C. Wollin, M. Rische
 
 Others: A. Bruestle, T. Meier, W. Friederich
 

autoPyLoT.py

@@ -18,7 +18,7 @@ import pylot.core.loc.hypodd as hypodd
 import pylot.core.loc.hyposat as hyposat
 import pylot.core.loc.nll as nll
 import pylot.core.loc.velest as velest
-# from PySide.QtGui import QWidget, QInputDialog
+# from PySide2.QtWidgets import QWidget, QInputDialog
 from pylot.core.analysis.magnitude import MomentMagnitude, LocalMagnitude
 from pylot.core.io.data import Data
 from pylot.core.io.inputs import PylotParameter

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
@@ -26,9 +26,9 @@ class Data(object):
     """
     Data container with attributes wfdata holding ~obspy.core.stream.
 
-    :type parent: PySide.QtGui.QWidget object, optional
+    :type parent: PySide2.QtWidgets.QWidget object, optional
-    :param parent: A PySide.QtGui.QWidget object utilized when
+    :param parent: A PySide2.QtWidgets.QWidget object utilized when
-    called by a GUI to display a PySide.QtGui.QMessageBox instead of printing
+    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
@@ -128,7 +128,7 @@ class Data(object):
 
     def getParent(self):
         """
-        Get PySide.QtGui.QWidget parent object
+        Get PySide2.QtWidgets.QWidget parent object
         """
         return self._parent
 

pylot/core/util/array_map.py

@@ -6,7 +6,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import obspy
 import traceback
-from PySide import QtGui
+from PySide2 import QtWidgets
 from matplotlib.figure import Figure
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from mpl_toolkits.basemap import Basemap
@@ -18,7 +18,7 @@ from pylot.core.pick.utils import get_quality_class
 plt.interactive(False)
 
 
-class Array_map(QtGui.QWidget):
+class Array_map(QtWidgets.QWidget):
     def __init__(self, parent, metadata, parameter=None, figure=None, annotate=True, pointsize=25.,
                  linewidth=1.5, width=5e6, height=2e6):
         '''
@@ -27,7 +27,7 @@ class Array_map(QtGui.QWidget):
         :param parameter: object of PyLoT parameter class
         :param figure:
         '''
-        QtGui.QWidget.__init__(self)
+        QtWidgets.QWidget.__init__(self)
         assert (parameter != None or parent != None), 'either parent or parameter has to be set'
         self._parent = parent
         self.metadata = metadata
@@ -224,43 +224,43 @@ class Array_map(QtGui.QWidget):
         if not self.figure:
             self.figure = Figure()
 
-        self.status_label = QtGui.QLabel()
+        self.status_label = QtWidgets.QLabel()
 
         self.main_ax = self.figure.add_subplot(111)
         #self.main_ax.set_facecolor('0.7')
         self.canvas = PylotCanvas(self.figure, parent=self._parent, multicursor=True,
                                   panZoomX=False, panZoomY=False)
 
-        self.main_box = QtGui.QVBoxLayout()
+        self.main_box = QtWidgets.QVBoxLayout()
         self.setLayout(self.main_box)
 
-        self.top_row = QtGui.QHBoxLayout()
+        self.top_row = QtWidgets.QHBoxLayout()
         self.main_box.addLayout(self.top_row, 1)
 
-        self.comboBox_phase = QtGui.QComboBox()
+        self.comboBox_phase = QtWidgets.QComboBox()
         self.comboBox_phase.insertItem(0, 'P')
         self.comboBox_phase.insertItem(1, 'S')
 
-        self.comboBox_am = QtGui.QComboBox()
+        self.comboBox_am = QtWidgets.QComboBox()
         self.comboBox_am.insertItem(0, 'hybrid (prefer manual)')
         self.comboBox_am.insertItem(1, 'manual')
         self.comboBox_am.insertItem(2, 'auto')
 
-        self.annotations_box = QtGui.QCheckBox('Annotate')
+        self.annotations_box = QtWidgets.QCheckBox('Annotate')
         self.annotations_box.setChecked(True)
-        self.auto_refresh_box = QtGui.QCheckBox('Automatic refresh')
+        self.auto_refresh_box = QtWidgets.QCheckBox('Automatic refresh')
         self.auto_refresh_box.setChecked(True)
-        self.refresh_button = QtGui.QPushButton('Refresh')
+        self.refresh_button = QtWidgets.QPushButton('Refresh')
-        self.cmaps_box = QtGui.QComboBox()
+        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'))
 
-        self.top_row.addWidget(QtGui.QLabel('Select a phase: '))
+        self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
         self.top_row.addWidget(self.comboBox_phase)
         self.top_row.setStretch(1, 1)  # set stretch of item 1 to 1
-        self.top_row.addWidget(QtGui.QLabel('Pick type: '))
+        self.top_row.addWidget(QtWidgets.QLabel('Pick type: '))
         self.top_row.addWidget(self.comboBox_am)
         self.top_row.setStretch(3, 1)  # set stretch of item 1 to 1
         self.top_row.addWidget(self.cmaps_box)
@@ -633,6 +633,6 @@ class Array_map(QtGui.QWidget):
             map.ax.figure.canvas.draw()
 
     def _warn(self, message):
-        self.qmb = QtGui.QMessageBox(QtGui.QMessageBox.Icon.Warning,
+        self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Warning,
                                      'Warning', message)
         self.qmb.show()

pylot/core/util/map_projection.py

@@ -0,0 +1,364 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import matplotlib.pyplot as plt
+import numpy as np
+import obspy
+from PySide2 import QtWidgets
+from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
+import cartopy
+import cartopy.feature as cpf
+from pylot.core.util.widgets import PickDlg
+from scipy.interpolate import griddata
+
+plt.interactive(False)
+
+
+class map_projection(QtWidgets.QWidget):
+    def __init__(self, parent, figure=None):
+        '''
+
+        :param: picked, can be False, auto, manual
+        :value: str
+        '''
+        QtWidgets.QWidget.__init__(self)
+        self._parent = parent
+        self.metadata = parent.metadata
+        self.parser = parent.metadata[1]
+        self.picks = None
+        self.picks_dict = None
+        self.eventLoc = None
+        self.figure = figure
+        self.init_graphics()
+        self.init_stations()
+        self.init_basemap()
+        self.init_map()
+        # self.show()
+
+    def init_map(self):
+        self.init_lat_lon_dimensions()
+        self.init_lat_lon_grid()
+        self.connectSignals()
+        self.draw_everything()
+
+    def onpick(self, event):
+        ind = event.ind
+        button = event.mouseevent.button
+        if ind == [] or not button == 1:
+            return
+        data = self._parent.get_data().getWFData()
+        for index in ind:
+            station = str(self.station_names[index].split('.')[-1])
+            try:
+                pickDlg = PickDlg(self, parameter=self._parent._inputs,
+                                  data=data.select(station=station),
+                                  station=station,
+                                  picks=self._parent.get_current_event().getPick(station),
+                                  autopicks=self._parent.get_current_event().getAutopick(station))
+            except Exception as e:
+                message = 'Could not generate Plot for station {st}.\n {er}'.format(st=station, er=e)
+                self._warn(message)
+                print(message, e)
+                return
+            pyl_mw = self._parent
+            try:
+                if pickDlg.exec_():
+                    pyl_mw.setDirty(True)
+                    pyl_mw.update_status('picks accepted ({0})'.format(station))
+                    replot = pyl_mw.get_current_event().setPick(station, pickDlg.getPicks())
+                    self._refresh_drawings()
+                    if replot:
+                        pyl_mw.plotWaveformData()
+                        pyl_mw.drawPicks()
+                        pyl_mw.draw()
+                    else:
+                        pyl_mw.drawPicks(station)
+                        pyl_mw.draw()
+                else:
+                    pyl_mw.update_status('picks discarded ({0})'.format(station))
+            except Exception as e:
+                message = 'Could not save picks for station {st}.\n{er}'.format(st=station, er=e)
+                self._warn(message)
+                print(message, e)
+
+    def connectSignals(self):
+        self.comboBox_phase.currentIndexChanged.connect(self._refresh_drawings)
+        self.zoom_id = self.main_ax.figure.canvas.mpl_connect('scroll_event', self.zoom)
+
+    def init_graphics(self):
+        if not self.figure:
+            if not hasattr(self._parent, 'am_figure'):
+                self.figure = plt.figure()
+                self.toolbar = NavigationToolbar(self.figure.canvas, self)
+            else:
+                self.figure = self._parent.am_figure
+                self.toolbar = self._parent.am_toolbar
+
+        self.main_ax = self.figure.add_subplot(111)
+        self.canvas = self.figure.canvas
+
+        self.main_box = QtWidgets.QVBoxLayout()
+        self.setLayout(self.main_box)
+
+        self.top_row = QtWidgets.QHBoxLayout()
+        self.main_box.addLayout(self.top_row)
+
+        self.comboBox_phase = QtWidgets.QComboBox()
+        self.comboBox_phase.insertItem(0, 'P')
+        self.comboBox_phase.insertItem(1, 'S')
+
+        self.comboBox_am = QtWidgets.QComboBox()
+        self.comboBox_am.insertItem(0, 'auto')
+        self.comboBox_am.insertItem(1, 'manual')
+
+        self.top_row.addWidget(QtWidgets.QLabel('Select a phase: '))
+        self.top_row.addWidget(self.comboBox_phase)
+        self.top_row.setStretch(1, 1)  # set stretch of item 1 to 1
+
+        self.main_box.addWidget(self.canvas)
+        self.main_box.addWidget(self.toolbar)
+
+    def init_stations(self):
+        def get_station_names_lat_lon(parser):
+            station_names = []
+            lat = []
+            lon = []
+            for station in parser.stations:
+                station_name = station[0].station_call_letters
+                network = station[0].network_code
+                if not station_name in station_names:
+                    station_names.append(network + '.' + station_name)
+                    lat.append(station[0].latitude)
+                    lon.append(station[0].longitude)
+            return station_names, lat, lon
+
+        station_names, lat, lon = get_station_names_lat_lon(self.parser)
+        self.station_names = station_names
+        self.lat = lat
+        self.lon = lon
+
+    def init_picks(self):
+        phase = self.comboBox_phase.currentText()
+
+        def get_picks(station_names):
+            picks = []
+            for station in station_names:
+                try:
+                    station = station.split('.')[-1]
+                    picks.append(self.picks_dict[station][phase]['mpp'])
+                except:
+                    picks.append(np.nan)
+            return picks
+
+        def get_picks_rel(picks):
+            picks_rel = []
+            picks_utc = []
+            for pick in picks:
+                if type(pick) is obspy.core.utcdatetime.UTCDateTime:
+                    picks_utc.append(pick)
+            minp = min(picks_utc)
+            for pick in picks:
+                if type(pick) is obspy.core.utcdatetime.UTCDateTime:
+                    pick -= minp
+                picks_rel.append(pick)
+            return picks_rel
+
+        self.picks = get_picks(self.station_names)
+        self.picks_rel = get_picks_rel(self.picks)
+
+    def init_picks_active(self):
+        def remove_nan_picks(picks):
+            picks_no_nan = []
+            for pick in picks:
+                if not np.isnan(pick):
+                    picks_no_nan.append(pick)
+            return picks_no_nan
+
+        self.picks_no_nan = remove_nan_picks(self.picks_rel)
+
+    def init_stations_active(self):
+        def remove_nan_lat_lon(picks, lat, lon):
+            lat_no_nan = []
+            lon_no_nan = []
+            for index, pick in enumerate(picks):
+                if not np.isnan(pick):
+                    lat_no_nan.append(lat[index])
+                    lon_no_nan.append(lon[index])
+            return lat_no_nan, lon_no_nan
+
+        self.lat_no_nan, self.lon_no_nan = remove_nan_lat_lon(self.picks_rel, self.lat, self.lon)
+
+    def init_lat_lon_dimensions(self):
+        def get_lon_lat_dim(lon, lat):
+            londim = max(lon) - min(lon)
+            latdim = max(lat) - min(lat)
+            return londim, latdim
+
+        self.londim, self.latdim = get_lon_lat_dim(self.lon, self.lat)
+
+    def init_basemap(self, resolution='l'):
+        ax = self.main_ax(projection=cartopy.crs.PlateCarree())
+
+        ax.add_feature(cpf.LAND)
+        ax.add_feature(cpf.OCEAN)
+        ax.add_feature(cpf.COASTLINE)
+        ax.add_feature(cpf.BORDERS, linestyle=':')
+        ax.add_feature(cpf.LAKES, alpha=0.5)
+        ax.add_feature(cpf.RIVERS)
+
+        ax.set_extent([min(self.lon), max(self.lon), min(self.lat), max(self.lat)])
+        self.figure.tight_layout()
+
+    def init_lat_lon_grid(self):
+        def get_lat_lon_axis(lat, lon):
+            steplat = (max(lat) - min(lat)) / 250
+            steplon = (max(lon) - min(lon)) / 250
+
+            lataxis = np.arange(min(lat), max(lat), steplat)
+            lonaxis = np.arange(min(lon), max(lon), steplon)
+            return lataxis, lonaxis
+
+        def get_lat_lon_grid(lataxis, lonaxis):
+            longrid, latgrid = np.meshgrid(lonaxis, lataxis)
+            return latgrid, longrid
+
+        self.lataxis, self.lonaxis = get_lat_lon_axis(self.lat, self.lon)
+        self.latgrid, self.longrid = get_lat_lon_grid(self.lataxis, self.lonaxis)
+
+    def init_picksgrid(self):
+        self.picksgrid_no_nan = griddata((self.lat_no_nan, self.lon_no_nan),
+                                         self.picks_no_nan, (self.latgrid, self.longrid),
+                                         method='linear')  ##################
+
+    def draw_contour_filled(self, nlevel='50'):
+        levels = np.linspace(min(self.picks_no_nan), max(self.picks_no_nan), nlevel)
+        self.contourf = self.main_ax.contourf(self.longrid, self.latgrid, self.picksgrid_no_nan,
+                                              levels, latlon=True, zorder=9, alpha=0.5)
+
+    def scatter_all_stations(self):
+        self.sc = self.main_ax.scatter(self.lon, self.lat, s=50, facecolor='none', latlon=True,
+                                       zorder=10, picker=True, edgecolor='m', label='Not Picked')
+        self.cid = self.canvas.mpl_connect('pick_event', self.onpick)
+        if self.eventLoc:
+            lat, lon = self.eventLoc
+            self.sc_event = self.main_ax.scatter(lon, lat, s=100, facecolor='red',
+                                                 latlon=True, zorder=11, label='Event (might be outside map region)')
+
+    def scatter_picked_stations(self):
+        lon = self.lon_no_nan
+        lat = self.lat_no_nan
+
+        # workaround because of an issue with latlon transformation of arrays with len <3
+        if len(lon) <= 2 and len(lat) <= 2:
+            self.sc_picked = self.main_ax.scatter(lon[0], lat[0], s=50, facecolor='white',
+                                                  c=self.picks_no_nan[0], latlon=True, zorder=11, label='Picked')
+        if len(lon) == 2 and len(lat) == 2:
+            self.sc_picked = self.main_ax.scatter(lon[1], lat[1], s=50, facecolor='white',
+                                                  c=self.picks_no_nan[1], latlon=True, zorder=11)
+        else:
+            self.sc_picked = self.main_ax.scatter(lon, lat, s=50, facecolor='white',
+                                                  c=self.picks_no_nan, latlon=True, zorder=11, label='Picked')
+
+    def annotate_ax(self):
+        self.annotations = []
+        for index, name in enumerate(self.station_names):
+            self.annotations.append(self.main_ax.annotate(' %s' % name, xy=(self.x[index], self.y[index]),
+                                                          fontsize='x-small', color='white', zorder=12))
+        self.legend = self.main_ax.legend(loc=1)
+
+    def add_cbar(self, label):
+        cbar = self.main_ax.figure.colorbar(self.sc_picked, fraction=0.025)
+        cbar.set_label(label)
+        return cbar
+
+    def refresh_drawings(self, picks=None):
+        self.picks_dict = picks
+        self._refresh_drawings()
+
+    def _refresh_drawings(self):
+        self.remove_drawings()
+        self.draw_everything()
+
+    def draw_everything(self):
+        if self.picks_dict:
+            self.init_picks()
+            self.init_picks_active()
+            self.init_stations_active()
+            if len(self.picks_no_nan) >= 3:
+                self.init_picksgrid()
+                self.draw_contour_filled()
+        self.scatter_all_stations()
+        if self.picks_dict:
+            self.scatter_picked_stations()
+            self.cbar = self.add_cbar(label='Time relative to first onset [s]')
+            self.comboBox_phase.setEnabled(True)
+        else:
+            self.comboBox_phase.setEnabled(False)
+        self.annotate_ax()
+        self.canvas.draw()
+
+    def remove_drawings(self):
+        if hasattr(self, 'sc_picked'):
+            self.sc_picked.remove()
+            del (self.sc_picked)
+        if hasattr(self, 'sc_event'):
+            self.sc_event.remove()
+            del (self.sc_event)
+        if hasattr(self, 'cbar'):
+            self.cbar.remove()
+            del (self.cbar)
+        if hasattr(self, 'contourf'):
+            self.remove_contourf()
+            del (self.contourf)
+        if hasattr(self, 'cid'):
+            self.canvas.mpl_disconnect(self.cid)
+            del (self.cid)
+        try:
+            self.sc.remove()
+        except Exception as e:
+            print('Warning: could not remove station scatter plot.\nReason: {}'.format(e))
+        try:
+            self.legend.remove()
+        except Exception as e:
+            print('Warning: could not remove legend. Reason: {}'.format(e))
+        self.canvas.draw()
+
+    def remove_contourf(self):
+        for item in self.contourf.collections:
+            item.remove()
+
+    def remove_annotations(self):
+        for annotation in self.annotations:
+            annotation.remove()
+
+    def zoom(self, event):
+        map = self.main_ax
+        xlim = map.ax.get_xlim()
+        ylim = map.ax.get_ylim()
+        x, y = event.xdata, event.ydata
+        zoom = {'up': 1. / 2.,
+                'down': 2.}
+
+        if not event.xdata or not event.ydata:
+            return
+
+        if event.button in zoom:
+            factor = zoom[event.button]
+            xdiff = (xlim[1] - xlim[0]) * factor
+            xl = x - 0.5 * xdiff
+            xr = x + 0.5 * xdiff
+            ydiff = (ylim[1] - ylim[0]) * factor
+            yb = y - 0.5 * ydiff
+            yt = y + 0.5 * ydiff
+
+            if xl < map.xmin or yb < map.ymin or xr > map.xmax or yt > map.ymax:
+                xl, xr = map.xmin, map.xmax
+                yb, yt = map.ymin, map.ymax
+            map.ax.set_xlim(xl, xr)
+            map.ax.set_ylim(yb, yt)
+            map.ax.figure.canvas.draw()
+
+    def _warn(self, message):
+        self.qmb = QtWidgets.QMessageBox(QtWidgets.QMessageBox.Icon.Warning,
+                                     'Warning', message)
+        self.qmb.show()

pylot/core/util/thread.py

@@ -1,11 +1,8 @@
 # -*- coding: utf-8 -*-
+import sys, os, traceback
 import multiprocessing
-import os
+from PySide2.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
-import sys
+from PySide2.QtWidgets import QDialog, QProgressBar, QLabel, QHBoxLayout, QPushButton
-import traceback
-
-from PySide.QtCore import QThread, Signal, Qt, Slot, QRunnable, QObject
-from PySide.QtGui import QDialog, QProgressBar, QLabel, QHBoxLayout
 
 
 class Thread(QThread):
@@ -27,7 +24,7 @@ class Thread(QThread):
         if self.redirect_stdout:
             sys.stdout = self
         try:
-            if self.arg is not None:
+            if self.arg:
                 self.data = self.func(self.arg)
             else:
                 self.data = self.func()
@@ -36,20 +33,31 @@ class Thread(QThread):
             self._executed = False
             self._executedError = e
             traceback.print_exc()
-            exctype, value = sys.exc_info()[:2]
+            exctype, value = sys.exc_info ()[:2]
-            self._executedErrorInfo = '{} {} {}'. \
+            self._executedErrorInfo = '{} {} {}'.\
                 format(exctype, value, traceback.format_exc())
         sys.stdout = sys.__stdout__
 
     def showProgressbar(self):
         if self.progressText:
-            # # generate widget if not given in init
-            # if not self.pb_widget:
-            #     self.pb_widget = ProgressBarWidget(self.parent())
-            #     self.pb_widget.setWindowFlags(Qt.SplashScreen)
-            #     self.pb_widget.setModal(True)
 
-            self.pb_widget.label.setText(self.progressText)
+            # generate widget if not given in init
+            if not self.pb_widget:
+                self.pb_widget = QDialog(self.parent())
+                self.pb_widget.setWindowFlags(Qt.SplashScreen)
+                self.pb_widget.setModal(True)
+
+            # add button
+            delete_button = QPushButton('X')
+            delete_button.clicked.connect(self.exit)
+            hl = QHBoxLayout()
+            pb = QProgressBar()
+            pb.setRange(0, 0)
+            hl.addWidget(pb)
+            hl.addWidget(QLabel(self.progressText))
+            if self.abortButton:
+                hl.addWidget(delete_button)
+            self.pb_widget.setLayout(hl)
             self.pb_widget.show()
 
     def hideProgressbar(self):
@@ -67,7 +75,6 @@ class Worker(QRunnable):
     '''
     Worker class to be run by MultiThread(QThread).
     '''
-
     def __init__(self, fun, args,
                  progressText=None,
                  pb_widget=None,
@@ -75,7 +82,7 @@ class Worker(QRunnable):
         super(Worker, self).__init__()
         self.fun = fun
         self.args = args
-        # self.kwargs = kwargs
+        #self.kwargs = kwargs
         self.signals = WorkerSignals()
         self.progressText = progressText
         self.pb_widget = pb_widget
@@ -89,9 +96,9 @@ class Worker(QRunnable):
         try:
             result = self.fun(self.args)
         except:
-            exctype, value = sys.exc_info()[:2]
+            exctype, value = sys.exc_info ()[:2]
             print(exctype, value, traceback.format_exc())
-            self.signals.error.emit((exctype, value, traceback.format_exc()))
+            self.signals.error.emit ((exctype, value, traceback.format_exc ()))
         else:
             self.signals.result.emit(result)
         finally:
@@ -133,13 +140,13 @@ class MultiThread(QThread):
 
     def run(self):
         if self.redirect_stdout:
-            sys.stdout = self
+             sys.stdout = self
         try:
             if not self.ncores:
                 self.ncores = multiprocessing.cpu_count()
             pool = multiprocessing.Pool(self.ncores)
             self.data = pool.map_async(self.func, self.args, callback=self.emitDone)
-            # self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
+            #self.data = pool.apply_async(self.func, self.shotlist, callback=self.emitDone) #emit each time returned
             pool.close()
             self._executed = True
         except Exception as e: