[cctbxbb] Deprecation warning?

[Graeme.Winter at diamond.ac.uk]

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,  <Graeme.Winter at diamond.ac.uk> 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 at 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
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb


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