Segfault using matplotlib with PyQt

Question

Can anyone hint at why the following code (taken from here) segfaults on exit?

"""
This demo demonstrates how to embed a matplotlib (mpl) plot 
into a PyQt4 GUI application, including:

* Using the navigation toolbar
* Adding data to the plot
* Dynamically modifying the plot's properties
* Processing mpl events
* Saving the plot to a file from a menu

The main goal is to serve as a basis for developing rich PyQt GUI
applications featuring mpl plots (using the mpl OO API).

Eli Bendersky ([email protected])
License: this code is in the public domain
Last modified: 19.01.2009
"""
import sys, os, random
from PyQt4.QtCore import *
from PyQt4.QtGui import *

import matplotlib
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar
from matplotlib.figure import Figure


class AppForm(QMainWindow):
    def __init__(self, parent=None):
        QMainWindow.__init__(self, parent)
        self.setWindowTitle('Demo: PyQt with matplotlib')

        self.create_menu()
        self.create_main_frame()
        self.create_status_bar()

        self.textbox.setText('1 2 3 4')
        self.on_draw()

    def save_plot(self):
        file_choices = "PNG (*.png)|*.png"

        path = unicode(QFileDialog.getSaveFileName(self, 
                        'Save file', '', 
                        file_choices))
        if path:
            self.canvas.print_figure(path, dpi=self.dpi)
            self.statusBar().showMessage('Saved to %s' % path, 2000)

    def on_about(self):
        msg = """ A demo of using PyQt with matplotlib:

         * Use the matplotlib navigation bar
         * Add values to the text box and press Enter (or click "Draw")
         * Show or hide the grid
         * Drag the slider to modify the width of the bars
         * Save the plot to a file using the File menu
         * Click on a bar to receive an informative message
        """
        QMessageBox.about(self, "About the demo", msg.strip())

    def on_pick(self, event):
        # The event received here is of the type
        # matplotlib.backend_bases.PickEvent
        #
        # It carries lots of information, of which we're using
        # only a small amount here.
        # 
        box_points = event.artist.get_bbox().get_points()
        msg = "You've clicked on a bar with coords:\n %s" % box_points

        QMessageBox.information(self, "Click!", msg)

    def on_draw(self):
        """ Redraws the figure
        """
        str = unicode(self.textbox.text())
        self.data = map(int, str.split())

        x = range(len(self.data))

        # clear the axes and redraw the plot anew
        #
        self.axes.clear()        
        self.axes.grid(self.grid_cb.isChecked())

        self.axes.bar(
            left=x, 
            height=self.data, 
            width=self.slider.value() / 100.0, 
            align='center', 
            alpha=0.44,
            picker=5)

        self.canvas.draw()

    def create_main_frame(self):
        self.main_frame = QWidget()

        # Create the mpl Figure and FigCanvas objects. 
        # 5x4 inches, 100 dots-per-inch
        #
        self.dpi = 100
        self.fig = Figure((5.0, 4.0), dpi=self.dpi)
        self.canvas = FigureCanvas(self.fig)
        self.canvas.setParent(self.main_frame)

        # Since we have only one plot, we can use add_axes 
        # instead of add_subplot, but then the subplot
        # configuration tool in the navigation toolbar wouldn't
        # work.
        #
        self.axes = self.fig.add_subplot(111)

        # Bind the 'pick' event for clicking on one of the bars
        #
        self.canvas.mpl_connect('pick_event', self.on_pick)

        # Create the navigation toolbar, tied to the canvas
        #
        self.mpl_toolbar = NavigationToolbar(self.canvas, self.main_frame)

        # Other GUI controls
        # 
        self.textbox = QLineEdit()
        self.textbox.setMinimumWidth(200)
        self.connect(self.textbox, SIGNAL('editingFinished ()'), self.on_draw)

        self.draw_button = QPushButton("&Draw")
        self.connect(self.draw_button, SIGNAL('clicked()'), self.on_draw)

        self.grid_cb = QCheckBox("Show &Grid")
        self.grid_cb.setChecked(False)
        self.connect(self.grid_cb, SIGNAL('stateChanged(int)'), self.on_draw)

        slider_label = QLabel('Bar width (%):')
        self.slider = QSlider(Qt.Horizontal)
        self.slider.setRange(1, 100)
        self.slider.setValue(20)
        self.slider.setTracking(True)
        self.slider.setTickPosition(QSlider.TicksBothSides)
        self.connect(self.slider, SIGNAL('valueChanged(int)'), self.on_draw)

        #
        # Layout with box sizers
        # 
        hbox = QHBoxLayout()

        for w in [  self.textbox, self.draw_button, self.grid_cb,
                    slider_label, self.slider]:
            hbox.addWidget(w)
            hbox.setAlignment(w, Qt.AlignVCenter)

        vbox = QVBoxLayout()
        vbox.addWidget(self.canvas)
        vbox.addWidget(self.mpl_toolbar)
        vbox.addLayout(hbox)

        self.main_frame.setLayout(vbox)
        self.setCentralWidget(self.main_frame)

    def create_status_bar(self):
        self.status_text = QLabel("This is a demo")
        self.statusBar().addWidget(self.status_text, 1)

    def create_menu(self):        
        self.file_menu = self.menuBar().addMenu("&File")

        load_file_action = self.create_action("&Save plot",
            shortcut="Ctrl+S", slot=self.save_plot, 
            tip="Save the plot")
        quit_action = self.create_action("&Quit", slot=self.close, 
            shortcut="Ctrl+Q", tip="Close the application")

        self.add_actions(self.file_menu, 
            (load_file_action, None, quit_action))

        self.help_menu = self.menuBar().addMenu("&Help")
        about_action = self.create_action("&About", 
            shortcut='F1', slot=self.on_about, 
            tip='About the demo')

        self.add_actions(self.help_menu, (about_action,))

    def add_actions(self, target, actions):
        for action in actions:
            if action is None:
                target.addSeparator()
            else:
                target.addAction(action)

    def create_action(  self, text, slot=None, shortcut=None, 
                        icon=None, tip=None, checkable=False, 
                        signal="triggered()"):
        action = QAction(text, self)
        if icon is not None:
            action.setIcon(QIcon(":/%s.png" % icon))
        if shortcut is not None:
            action.setShortcut(shortcut)
        if tip is not None:
            action.setToolTip(tip)
            action.setStatusTip(tip)
        if slot is not None:
            self.connect(action, SIGNAL(signal), slot)
        if checkable:
            action.setCheckable(True)
        return action


if __name__ == "__main__":
    app = QApplication(sys.argv)
    form = AppForm()
    form.show()
    app.exec_()

Aside from the segfault on exiting, it works fine otherwise.

Version info:

misha@misha-desktop:~/co/python/resampling$ python
Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) 
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> matplotlib.__version__
'0.99.1.1'
misha@misha-desktop:~/co/python/resampling$ qmake-qt4 -v
QMake version 2.01a
Using Qt version 4.6.2 in /usr/lib
misha@misha-desktop:~/co/python/resampling$ pyuic4 --version
Python User Interface Compiler 4.7.2 for Qt version 4.6.2

misha, this sample keeps working fine for me, and I didn't get user reports with similar problems. Can you figure out where the segfault is coming from, i.e. Python, matplotlib's DLLs or PyQt's DLLs? — Eli Bendersky
– Eli Bendersky, Commented Apr 24, 2011 at 12:37
@Eli I tried running it through gdb, but strangely, it exits normally. If I run it outside the debug environment, I get a segfault on exit (always). Any ideas? Also, thanks for providing the sample, it saved me a lot of time. — mpenkov
– mpenkov, Commented Apr 26, 2011 at 3:14
try to examine the core-dump with gdb - you can do that even without running through it. I would then open a bug to the relevant project, because a bug it must be - no Python implementation or library can have a segfault as a result of running pure Python code — Eli Bendersky
– Eli Bendersky, Commented Apr 26, 2011 at 3:58
The code works for me. Win XP, Python 2.6.4, matplotlib 0.99.3, Qt 4.6.2 — Jesse Aldridge
– Jesse Aldridge, Commented Jun 25, 2011 at 19:32
segmentation fault . ubuntu 10.10, python 2.6.5, matplotlib 0.99.1.1, qt 4.6 — linjunhalida
– linjunhalida, Commented Sep 16, 2011 at 8:06

David K. Hess · Accepted Answer · 2011-11-29 13:15:07Z

1

The QApplication object is being garbage collected before the Form during exit. Make this change to your code:

if __name__ == "__main__":
    app = QApplication(sys.argv)
    form = AppForm()
    form.show()
    app.exec_()
    del form

and the segfault goes away. It appears something in PyQt or matplotlib depends on the QApplication object still existing when resources are being released on exit.

edited Nov 29, 2011 at 13:15

answered Nov 28, 2011 at 3:05

David K. Hess

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4 Comments

mpenkov Over a year ago

Nice try, but it still segfaults on my side. I've updated the source code of my answer. Thanks for the idea, though.

David K. Hess Over a year ago

That's really odd. I have the exact same environment as you and it stopped segfaulting for me when I made that change.

David K. Hess Over a year ago

Well, if you make the change exactly as I indicate, the segfault does go away. If however, you make the change as you did (which should be equivalent) the segfault is still there. Go figure.

David K. Hess Over a year ago

Did you try my last edit above? I've run that one many times and cannot get it to segfault.

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