Animation module errors out when using Python3

[aignas]

I used the double pendulum example and it did not work with the latest version of Matplotlib and Py3k on Arch Linux. However, it worked with Python2.7. I was using

#! /usr/bin/env python3

as my shebang in the script.

The exact script which I used is here: https://gist.github.com/gns-ank/5347084#file-double_pendulum-py

The error log:

Traceback (most recent call last):
  File "./double_pendulum_animated.py", line 88, in <module>
    ani.save('double_pendulum.mp4', fps=15)
  File "/usr/lib/python3.3/site-packages/matplotlib/animation.py", line 616, in save
    writer.grab_frame()
  File "/usr/lib/python3.3/site-packages/matplotlib/animation.py", line 200, in grab_frame
    dpi=self.dpi)
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 1371, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/python3.3/site-packages/matplotlib/backend_bases.py", line 2101, in print_figure
    self.figure.dpi = origDPI
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 375, in _set_dpi
    self.dpi_scale_trans.clear().scale(dpi, dpi)
  File "/usr/lib/python3.3/site-packages/matplotlib/transforms.py", line 1751, in clear
    self._mtx = np.identity(3)
  File "/usr/lib/python3.3/site-packages/numpy/core/numeric.py", line 1913, in identity
    from numpy import eye
  File "<frozen importlib._bootstrap>", line 1609, in _handle_fromlist
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte

Press ENTER or type command to continue

[mdboom]

Hmm... I can't reproduce with matplotlib 1.2.1, python 3.3 and numpy 1.7 on a Fedora box.

The traceback leads us into numpy, of course, so perhaps therein lies the bug. Can you open up a Python 3 interpreter and type:

import numpy
numpy.identity(3)

[aignas]

I get the following:

Python 3.3.1 (default, Apr  6 2013, 19:03:55) 
[GCC 4.8.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.identity(3)
array([[ 1.,  0.,  0.],
       [ 0.,  1.,  0.],
       [ 0.,  0.,  1.]])
>>>

I have numpy 1.7.0, mpl 1.2.1.

[mdboom]

Interesting. There's definitely something fishy going on. Maybe try to use the Python debugger to see what's going on here. This is not in matplotlib, but in code that is trying to import numpy.eye -- Something corrupted about your __pycache__ files, perhaps?

File "<frozen importlib._bootstrap>", line 1609, in _handle_fromlist
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte

[aignas]

How should I check for corrupted 'pycache' files?

[mdboom]

I'm not sure -- did you perhaps compile numpy and/or matplotlib with an earlier version of Python and then are now opening them with Python 3.3.1?

File "<frozen importlib._bootstrap>", line 1609, in _handle_fromlist

That line number 1609 doesn't make much sense with the version of _bootstrap.py in Python 3.3.1, since there doesn't seem to be any decoding happening on that line (and fromlist is just a regular list):

File "<frozen importlib._bootstrap>", line 1609, in _handle_fromlist

So perhaps you're somehow getting an older version of _bootstrap.py than the one that comes with Python 3.3.1?

I think the only way to really figure this out (as there's a lot of redflags here that something is usual about your environment), is to start this up in the debugger:

python3 -m pdb double_pendulum_animated.py

and when it fails, start poking around and seeing where this non UTF-8 data is coming from that it's trying (and failing) to decode.

If you haven't already done so, I'd try creating a new Python 3.3.1 environment and install everything (numpy, matplotlib etc) fresh into it after clearing the build directories.

[vlsd]

I am having the exact same issue while trying to run some older code after an update. Any new info on this? Also, @gns-ank are you by chance running Arch Linux? I have a nagging feeling that this is a packaging bug.

Also, extra info: the error only happens when calling animation.save(); this might be a video codec problem. Using plt.show() or anything like that works without a snag. Any advice?

[wackywendell]

I am also having the same issue, also on Arch Linux. By "same issue" I mean that if I run the same example code, I get the same error and traceback. I have tried recompiling matplotlib in its own directory to no avail.

However, I have noticed that with my own code, I get a very different traceback (but the same error):

Traceback (most recent call last):
  File "src/2Danimation.py", line 71, in <module>
    ani.save('test.mp4', fps=3, writer=writer)#, extra_args=['-vcodec', 'libx264'])
  File "/usr/lib/python3.3/site-packages/matplotlib/animation.py", line 616, in save
    writer.grab_frame()
  File "/usr/lib/python3.3/site-packages/matplotlib/animation.py", line 200, in grab_frame
    dpi=self.dpi)
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 1371, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/python3.3/site-packages/matplotlib/backend_bases.py", line 2057, in print_figure
    bbox_inches = self.figure.get_tightbbox(renderer)
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 1500, in get_tightbbox
    for ax in self.axes:
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 367, in _get_axes
    return self._axstack.as_list()
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 73, in as_list
    ia_list = [a for k, a in self._elements]
  File "/usr/lib/python3.3/site-packages/matplotlib/figure.py", line 73, in <listcomp>
    ia_list = [a for k, a in self._elements]
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte

So... I don't know where this error is coming from, but it looks to me like the from numpy import eye is a red herring...

[trwaters]

This problem frustrated me after I made the effort to setup a virtualenv for python3.3 on both my mac and linux boxes. I ended up abandoning that altogether in favor of the environment used to do these types of animations,
http://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/
This guy, Jake, uses anaconda, found here https://store.continuum.io/
It is a complete scientific computing package similar to an EPD install, which uses python 2.7 and matplotlib 1.2.1
(I heard of anaconda through Jake's course advertisement on scientific computing in python, worth a look:
https://github.com/jakevdp/2013_fall_ASTR599
You will still probably need ffmpeg, as I didn't check to see if anaconda has a codec already. I got ffmpeg for my mac running Lion using sudo port install ffmpeg (which supposedly depends on lame, so first do sudo port install lame to be safe) and for Ubuntu using this PPA
https://launchpad.net/~jon-severinsson/+archive/ffmpeg

It would still be nice to see the problem resolved for Python 3 however.

[mdboom]

It appears that the original bug is actually a bug in Numpy -- not it happens within importing numpy.eye. I'm going to close this, but feel free to reopen if I'm wrong on further investigation.

[vlsd]

@mdboom do you happen to know the corresponding bug in numpy or does that need to be filed?

[astrojuanlu]

@mdboom @vlsd I run into this too and I also wonder which is the corresponding NumPy bug, I'm running recent versions.

[mdboom]

Re-reading this thread, it's possible it's not a bug in Numpy. @Juanlu001 -- can you provide the full traceback and exactly which version of matplotlib, Numpy, and Python you are running, on which platform, and how you set up the environment?

[astrojuanlu]

Sure:

The code is https://gist.github.com/Juanlu001/7674552 (swapping comments in lines 36 and 37 to run animation.save)

$ uname -a
Linux nebulae 3.12.1-1-ARCH #1 SMP PREEMPT Thu Nov 21 08:18:42 CET 2013 x86_64 GNU/Linux
$ python --version
Python 3.3.2
$ python -c "import numpy; print(numpy.version.version)"
1.8.0
$ python -c "import matplotlib; print(matplotlib.__version__)"
1.3.1
$ python mathgif.py 
Traceback (most recent call last):
  File "mathgif.py", line 69, in <module>
    main(traj, cline, size=(WIDTH, HEIGHT), nframes=NFRAMES, npoints=NPOINTS)
  File "mathgif.py", line 37, in main
    anim.save("mathgif.mp4", fps=10)
  File "/home/juanlu/.local/lib/python3.3/site-packages/matplotlib/animation.py", line 719, in save
    writer.grab_frame(**savefig_kwargs)
  File "/home/juanlu/.local/lib/python3.3/site-packages/matplotlib/animation.py", line 205, in grab_frame
    dpi=self.dpi, **savefig_kwargs)
  File "/home/juanlu/.local/lib/python3.3/site-packages/matplotlib/figure.py", line 1422, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/home/juanlu/.local/lib/python3.3/site-packages/matplotlib/backend_bases.py", line 2225, in print_figure
    self.figure.dpi = origDPI
  File "/home/juanlu/.local/lib/python3.3/site-packages/matplotlib/figure.py", line 385, in _set_dpi
    self.dpi_scale_trans.clear().scale(dpi, dpi)
  File "/home/juanlu/.local/lib/python3.3/site-packages/matplotlib/transforms.py", line 1786, in clear
    self._mtx = np.identity(3)
  File "/home/juanlu/.local/lib/python3.3/site-packages/numpy/core/numeric.py", line 2053, in identity
    from numpy import eye
  File "<frozen importlib._bootstrap>", line 1612, in _handle_fromlist
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte

[felixonmars]

Well, I tried a lot and still can't figure out with the problem. I've tried to rebuild both numpy and matplotlib against current python (3.3.3) too.

Here are something from pdb:

(Pdb) args
module = <module 'numpy' from '/usr/lib/python3.3/site-packages/numpy/__init__.py'>
fromlist = ('eye',)
import_ = <built-in function __import__>