Hi Nat, Interesting, here is the offending code def plot_shoebox(shoebox): ''' Render a shoebox as a sequence of png images using matplotlib. ''' frame, slow, fast = shoebox.accessor().all() max_value = 100 for j in range(frame): from scitbx.array_family import flex import numpy import matplotlib from matplotlib import pyplot grid = flex.grid((slow, fast)) slice = flex.double(grid) for s in range(slow): for f in range(fast): if shoebox[(j, s, f)] < 0: slice[(s, f)] = max_value else: slice[(s, f)] = shoebox[(j, s, f)] image = numpy.reshape(slice.as_numpy_array(), (slow, fast)) pyplot.imshow(image, cmap = matplotlib.cm.Greys, vmax = max_value, interpolation = 'nearest', norm = None, filternorm = 0.0) pyplot.savefig('frame%02d.png' % (j)) i.e. pretty similar to your example, and the error Graemes-MacBook-Pro:cube graeme$ cctbx.python cube.py /Users/graeme/svn/cctbx_plus/base/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_wx.py:1382: wxPyDeprecationWarning: Using deprecated class PySimpleApp. wxapp = wx.PySimpleApp() That said, I am using a home-brewed cctbx.python which should correspond to the cctbx plus build - I used the same script to make it as you guys use to make the python base. I will add the deprecation-avoiding code you include below with a loud warning that really this should not be needed. Thanks, Graeme On 7 Aug 2012, at 18:49, Nathaniel Echols wrote:

On Tue, Aug 7, 2012 at 3:04 AM, wrote:

...

Is there a way to avoid this?

Using matplotlib.pyplot.

/Users/graeme/svn/cctbx_plus/base/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/backends/backend_wx.py:1382: wxPyDeprecationWarning: Using deprecated class PySimpleApp. wxapp = wx.PySimpleApp()

You can do this:

import warnings warnings.filterwarnings("ignore", category=DeprecationWarning)

But that's somewhat dangerous. How are you starting pyplot? I don't get this error when I try something trivial like this:

nat@clover:~> phenix.wxpython

...

...

...

import matplotlib.pyplot as plt f = plt.figure() p = plt.plot([1,2,3],[4,5,6]) plt.show()

But if I do this, I get the same warning:

...

...

...

import wx app = wx.PySimpleApp() __main__:1: wxPyDeprecationWarning: Using deprecated class.

So I suspect matplotlib is suppressing the warning somehow. Alternately, it looks as though if a wx.App instance has already been created, matplotlib will use that instead.

-Nat _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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On Wed, Aug 8, 2012 at 3:52 AM, wrote:

Interestingly I added this

import warnings warnings.filterwarnings("ignore", category=DeprecationWarning)

and it did not make the warnings go away… even though I tried both where I import matplotlib and also in the top of the main() routine.

That seems odd to me - any ideas?

I guess my assumption about the inheritance of wxPyDeprecationWarning was incorrect - at any rate, this seems to work: warnings.filterwarnings("ignore", category=wx.wxPyDeprecationWarning) -Nat