Matplotlib.Pyplot does not show output; No Error

Question

My platform is as follows

Centos 6.x (VirtualBox VM running on Win-7 host), Python 2.6.6, Matplotlib 1.3.1, Numpy 1.8.0, Scipy 0.14.0.dev-bb608ba

I am running the below histogram.py code

#!/usr/bin/env python

import numpy as np
import matplotlib.pyplot as plt

mu, sigma = 0, 1 # mean and standard deviation
f = np.random.normal(mu, sigma, 1000) # generate feature-vector with normal distribution

# plot the histogram - check the distribution
count, bins, ignored = plt.hist(f, 30, normed=True)

plt.plot(bins, 1/(sigma * np.sqrt(2 * np.pi)) *
                np.exp( - (bins - mu)**2 / (2 * sigma**2) ),
        linewidth=2, color='r')
plt.xlabel('Values')
plt.ylabel('Probability')
plt.title('Histogram')
plt.text(60, .025, r'$\mu=0,\ \sigma=1$')
plt.axis([-0.4, 0.3, 0, 5])
plt.grid(True)
plt.show()

But no output plot is appearing. I am receiving no error, so getting difficult to debug.

Following are the rc file-location and backend for my matplotlib installation

[hue@sandbox ~]$ python
Python 2.6.6 (r266:84292, Jul 10 2013, 22:48:45)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> matplotlib.matplotlib_fname()
'/usr/lib64/python2.6/site-packages/matplotlib-1.3.1-py2.6-linux-x86_64.egg/matplotlib/mpl-data/matplotlibrc'
>>> matplotlib.get_backend()
'agg'

Do I need to modify my 'agg' backend to 'Qt4Agg' or something else? Does it need me to modify the rc file?

Note: I checked my matplotlibrc file to have only backend : agg . Rest all parameters are commented.

As per below comments, I tried installing libpng but facing the below error:

pngfix.o: In function `zlib_reset':
/usr/lib/hue/libpng-1.6.6/contrib/tools/pngfix.c:2151: undefined reference to `inflateReset2'
collect2: ld returned 1 exit status

I have now successfully installed a stable and working duo of libpng-1.5.9/zlib-1.2.7 instead of the previous unstable versions libpng-1.6.6/zlib-1.2.8 and both the libs are successfully installed.

But despite having a working and stable libpng, I can't open the png file being generated by the python code (given above). Is there any specific configuration setting for VMs to open .png files? How exactly can .png files be opened on Linux VMs running on WIndows host?

Answer 1

The first step in debugging this is to replace plt.show() by plt.savefig('foo.png') . If it works, the problem is most probably with the backend:

>>> import matplotlib
>>> matplotlib.get_backend()
'Qt4Agg'

Try switching backends and see if that helps: How to switch backends in matplotlib / Python

If that does not help either, make sure you have all the dependencies ( http://matplotlib.org/users/installing.html ) --- I'd just reinstall from source. ( not pip install matplotlib )

Answer 2

I am having the exact same problem. However, this was my fix after a little bit of research:

sudo yum install PyQt4
sudo gedit file at mpl.matplotlib_fname()

Change the first and only uncommented setting (as default) at line 32:

backend : Qt4Agg

Answer 3

I once had a similar problem. I solved it by adding these lines imediately after import matplotlib.pyplot as plt and after every subsequent plt.show() :

plt.clf()
plt.cla()
plt.close()