Matplotlib Import Error : _backend_gdk.so:undefined symbol: PyArray_SetBaseObject

Question

I was trying to run the following code in OpenCV python.

#!/usr/bin/env python

import numpy as np
import time
import matplotlib
matplotlib.use('GTKAgg')
from matplotlib import pyplot as plt


def randomwalk(dims=(256, 256), n=20, sigma=5, alpha=0.95, seed=1):
    """ A simple random walk with memory """

    r, c = dims
    gen = np.random.RandomState(seed)
    pos = gen.rand(2, n) * ((r,), (c,))
    old_delta = gen.randn(2, n) * sigma

    while True:
        delta = (1. - alpha) * gen.randn(2, n) * sigma + alpha * old_delta
        pos += delta
        for ii in xrange(n):
            if not (0. <= pos[0, ii] < r):
                pos[0, ii] = abs(pos[0, ii] % r)
            if not (0. <= pos[1, ii] < c):
                pos[1, ii] = abs(pos[1, ii] % c)
        old_delta = delta
        yield pos


def run(niter=1000, doblit=True):
    """
    Display the simulation using matplotlib, optionally using blit for speed
    """

    fig, ax = plt.subplots(1, 1)
    ax.set_aspect('equal')
    ax.set_xlim(0, 255)
    ax.set_ylim(0, 255)
    ax.hold(True)
    rw = randomwalk()
    x, y = rw.next()

    plt.show(False)
    plt.draw()

    if doblit:
        # cache the background
        background = fig.canvas.copy_from_bbox(ax.bbox)

    points = ax.plot(x, y, 'o')[0]
    tic = time.time()

    for ii in xrange(niter):

        # update the xy data
        x, y = rw.next()
        points.set_data(x, y)

        if doblit:
            # restore background
            fig.canvas.restore_region(background)

            # redraw just the points
            ax.draw_artist(points)

            # fill in the axes rectangle
            fig.canvas.blit(ax.bbox)

        else:
            # redraw everything
            fig.canvas.draw()

    plt.close(fig)
    print "Blit = %s, average FPS: %.2f" % (
        str(doblit), niter / (time.time() - tic))

if __name__ == '__main__':
    run(doblit=False)
    run(doblit=True)

At first I got an error that said Import Error : No module named _backend_gdk. I searched a lot and tried various methods. Now, I get a different error.

Traceback (most recent call last):
  File "testblit.py", line 7, in <module>
    from matplotlib import pyplot as plt
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.5.dev1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 108, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.5.dev1-py2.7-linux-x86_64.egg/matplotlib/backends/__init__.py", line 32, in pylab_setup
    globals(),locals(),[backend_name],0)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.5.dev1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtkagg.py", line 14, in <module>
    from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK, FigureCanvasGTK,\
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.5.dev1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gtk.py", line 36, in <module>
    from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.5.dev1-py2.7-linux-x86_64.egg/matplotlib/backends/backend_gdk.py", line 33, in <module>
    from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
ImportError: /usr/local/lib/python2.7/dist-packages/matplotlib-1.5.dev1-py2.7-linux-x86_64.egg/matplotlib/backends/_backend_gdk.so: undefined symbol: PyArray_SetBaseObject

Any help to solve this problem would be appreciated. The code above is for real time plotting using blit that I found on stackoverflow.

Answer 1

在https://github.com/matplotlib/matplotlib/pull/5080应用此修复程序后，应使用numpy 1.7或更高版本或1.6进行编译。