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Edit: workaround at the end of this post.

I was trying to run some of the examples provided here and here.

One of these examples was:

from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

u = np.linspace(0, 2 * np.pi, 100)
v = np.linspace(0, np.pi, 100)

x = 10 * np.outer(np.cos(u), np.sin(v))
y = 10 * np.outer(np.sin(u), np.sin(v))
z = 10 * np.outer(np.ones(np.size(u)), np.cos(v))
ax.plot_surface(x, y, z,  rstride=4, cstride=4, color='b')

plt.show()

This gave me the following error: 

/usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.py:842: MatplotlibDeprecationWarning: The set_scale function was deprecated in version 1.3.
  self.zaxis.set_scale('linear')
Traceback (most recent call last):
  File "/mnt/hgfs/MCLS/postprocessing/surface3d_demo2.py", line 6, in <module>
    ax = fig.add_subplot(111, projection='3d')
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.4.x-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 958, in add_subplot
    a = subplot_class_factory(projection_class)(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.4.x-py2.7-linux-x86_64.egg/matplotlib/axes/_subplots.py", line 78, in __init__
    self._axes_class.__init__(self, fig, self.figbox, **kwargs)
  File "/usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.py", line 78, in __init__
    *args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.4.x-py2.7-linux-x86_64.egg/matplotlib/axes/_base.py", line 436, in __init__
    self.cla()
  File "/usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.py", line 847, in cla
    Axes.cla(self)
  File "/usr/local/lib/python2.7/dist-packages/matplotlib-1.4.x-py2.7-linux-x86_64.egg/matplotlib/axes/_base.py", line 897, in cla
    self.grid(self._gridOn, which=rcParams['axes.grid.which'])
  File "/usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.py", line 1057, in grid
    self._draw_grid = maxes._string_to_bool(b)
AttributeError: 'module' object has no attribute '_string_to_bool'

The error is originated from: ax = fig.add_subplot(111, projection='3d')

I tried to check and upgrade matplotlib. Running python -c 'import matplotlib; print matplotlib.__version__' gave me 1.4.x.

I dived in the underlying code and found this:

def grid(self, b=True, **kwargs):
'''
Set / unset 3D grid.

.. note::
    Currently, this function does not behave the same as
    :meth:`matplotlib.axes.Axes.grid`, but it is intended to
    eventually support that behavior.

.. versionchanged :: 1.1.0
    This function was changed, but not tested. Please report any bugs.
'''
# TODO: Operate on each axes separately
if len(kwargs) :
    b = True
self._draw_grid = maxes._string_to_bool(b)

Can anyone give me a suggestion where to go further?

Edit: I have found a workaround for this problem. As can be seen from the last error message something went wrong in the _string_to_bool function. Simply add the following line

from matplotlib.cbook import _string_to_bool

on top of 

/usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.py

I still get an error message, but at least I get some output.

Raghav RV
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Hennep
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  • How did you install mpl? It looks like you are sourcing files from inside /usr/lib which on most systems is controlled by the OS package manager, but I know of no one who ships 1.4.x. – tacaswell Aug 19 '14 at 23:11
  • https://github.com/matplotlib/matplotlib/blob/master/lib/mpl_toolkits/mplot3d/axes3d.py#L1262 is the only place in `axes3d.py` where that function is used and was last touched in 2013. I suspect the actual problem is that you install is borked. – tacaswell Aug 19 '14 at 23:15
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    @tcaswell I forgot how I did install mpl previously. Now I have reinstalled the mpl_toolkit using `sudo apt-get install python-mpltoolkits.basemap`. After removing the mpl_toolkits using `sudo apt-get purge --auto-remove python-mpltoolkits.basemap` and manually removing the mpl_toolkits folder. This new installation works without any problems. Thanks for your help! – Hennep Aug 21 '14 at 10:16

6 Answers6

11

For me, (Ubuntu 14.04, using the system Python) the problem was solved by removing the apt package python-matplotlib (prompted by this bug report). A newer matplotlib was also installed in /usr by pip; I think some newer pip packages were somehow getting modules from the older apt packages.

This was after trying meyerson's pip install --upgrade --ignore-installed matplotlib[mplot3d] command, which did result in NumPy being recompiled (and, I suppose, Matplotlib being reinstalled), but didn't solve the problem.

It's also interesting to note that I only had the problem when running the script in question (a batch of unittests) at the command line, but not when running in the LiClipse test runner (which uses a different, explicitly changeable, PYTHONPATH order. I regret I did not try changing this order to see if I could reproduce the problem in Eclipse.

tsbertalan
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  • ``sudo apt-get remove python-matplotlib`` solved the problem for me either. – niekas May 20 '15 at 11:47
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    This also worked for me. I had also previously installed python-matplotlib which left some files behind that the new version picked up on. A post in [this](https://github.com/matplotlib/matplotlib/issues/4064) bug report thread sheds light on what was breaking in my case and probably most or all others with this problem: _In older release the toolkits were stored in a seperate folder mpl_toolkits which have since been moved into the matplotlib folder. Thus this version is not overwritten when installing a new version of matplotlib and wrongly picked up when importing the toolkits._ – toes Jun 12 '15 at 00:59
8

I had the exact problem, here is how I had it solved (in my case):

1) rename (or delete) the folder mplot3d (so matplotlib thinks it's not there):

/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/mpl_toolkits/mplot3d-old

2) update matplotlib with specifiying mplot3d:

pip install --upgrade matplotlib[mplot3d]
Aziz Alto
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    Actually, step 1) was necessary for me - it seems that it was just necessary to add the extra `mplot3d` requirement inside the virtualenv that overrides the system one. Works splendidly :) – metakermit Jan 26 '15 at 10:36
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    I believe a force install / upgrade + ignore-isntalled is an equivalent to this solution `pip install --upgrade --ignore-installed matplotlib[mplot3d]` – meyerson Jan 28 '15 at 20:57
  • didn't work for me. I use Ubuntu and python on virtualenv with --system-site-packages (for other packages with binaries to work correctly). – Valentas May 13 '15 at 15:18
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    Did not work for me. `UnknownExtra: matplotlib 1.4.3 has no such extra feature 'mplot3d'` – moonkey Jul 08 '15 at 17:32
  • @metakermit Yes, I have the same issue and changing the name of the outdated folder solves the problem. Actually, I upgraded my matplotlib via pip to version 1.5 and it seems that Python confuses about the paths – lenhhoxung Nov 17 '15 at 16:08
3

For me the iamaziz answer did not work, and the issue occurs on Ubuntu 14.04 using virtualenv with --system-site-packages and matplotlib, pandas installed via pip. I found that moving the line

 from mpl_toolkits.mplot3d import Axes3D

before the import of pandas solves the problem.

Valentas
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2

Adding to @Hennep's workaround:

Add following line to file

/usr/lib/pymodules/python2.7/mpl_toolkits/mplot3d/axes3d.py

from matplotlib.cbook import _string_to_bool

And then change the code to

def grid(self, b=True, **kwargs):
'''Set / unset 3D grid.

.. note::
Currently, this function does not behave the same as
:meth:`matplotlib.axes.Axes.grid`, but it is intended to
eventually support that behavior.

.. versionchanged :: 1.1.0
This function was changed, but not tested. Please report any bugs.
'''
# TODO: Operate on each axes separately
if len(kwargs) :
    b = True
self._draw_grid = _string_to_bool(b)

Remove the word maxes from the function and everything is working fine for me if I did this.

Kirubaharan J
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1

I was able to get things working in OS X 10.10.2 using a very similar workaround to those posted here. None of the specific workarounds posted here worked in my case, but they got me on the right track to solve the issue. All the mplot3d stuff was working on my linux box, not on my mac. I use homebrew on the OS X side. I was getting errors in cbook, specifically the _string_to_bool error. There were calls made in cbook.py, axes3d.py, and axes.py. All I did for a workaround was track down the axes3d.py, axes.py and cbook.py files on my linux box, and replace those files on my OS X machine, after that everything worked perfectly and I was able to use mplot3. Homebrew uses a lot of symlinks, so be aware of that, I like to back up the original files and replace them there, not at the link level. Brew might also scatter files around a bit, here's where they were on my machine:

/Library/Python/2.7/site-packages/matplotlib-override/matplotlib/axes.py

/usr/local/Cellar/matplotlib/1.4.2/lib/python2.7/site-packages/mpl_toolkits/mplot3d/axes3d.py

/usr/local/Cellar/matplotlib/1.4.2/lib/python2.7/site-packages/matplotlib/cbook.py

on the linux side (symlinked from /usr/lib/pymodules/python2.7): /usr/share/pyshared/matplotlib/axes.py

/usr/share/pyshared/matplotlib/cbook.py

/usr/share/pyshared/mpl_toolkits/mplot3d/axes3d.py

Just back up, replace with files from your linux box, and give it a shot, worked for me.

If you do not have a version running on linux you might just be able to pull axes.py, axes3d.py and cbook.py from github, which has matplotlibs .py files posted.

cason
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1

In my case I was importing seaborn and pandas along with Axes3D. Importing both seaborn and pandas after Axes3D removed the error.

deerishi
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