[Neuroimaging] [PySurfer] Brain's save_image method produces images with only background color

[Ariel Rokem]

On Thu, Sep 15, 2016 at 1:33 PM, Kirstie Whitaker <kw401 at cam.ac.uk> wrote:

> Hi John,
>
> I'm travelling at the moment but I've had problems with pysurfer showing
> beautiful brains on the screen but only saving a black box to file. It
> happened right after our systems admin updated a few things but I haven't
> been able to get a clear list from him of what changed except: everything
> should work.
>
> My point with this email is please do share back what you learn.....even
> if it ends up being not a pysurfer problem. At the moment my workaround is
> to move everything I do to a different cluster that works!! Non efficient
> to say the least!
>
> Thank you
> Kirstie
>
> Sent from my iPhone, please excuse any typos or excessive brevity
>
> On 15 Sep 2016, at 12:44, John Pellman <pellman.john at gmail.com> wrote:
>
> I've had at this a little bit more and my current suspicion is that this
> behavior is the result of an interaction between our remote desktop service
> (x2go) and Mayavi.
>
> I created a an identical Miniconda environment for Pysurfer on both our
> server and my laptop and ran the following code to test this theory:
>
> # The Basic Visualization demo from the Pysurfer gallery.
>> from surfer import Brain
>>
>> print(__doc__)
>>
>> """
>> Define the three important variables.
>> Note that these are the first three positional arguments
>> in tksurfer (and pysurfer for that matter).
>> """
>> subject_id = 'fsaverage'
>> hemi = 'lh'
>> surface = 'inflated'
>>
>> """
>> Call the Brain object constructor with these
>> parameters to initialize the visualization session.
>> """
>> brain = Brain(subject_id, hemi, surface)
>>
>> # Save an image out to /tmp
>> print 'Saving out an image to /tmp using Brain.save_image.'
>> brain.save_image('/tmp/brain.png')
>>
>> # Looking at just the screenshot method of pysurfer's Brain object.
>> # This is called by save_image and is fed into scipy.misc.imsave.
>> # If the boolean expression evaluated here is true, then only a black
>> # background is being fed into scipy's misc.imsave method for evaluation.
>> x = brain.screenshot()
>> print 'Test pysurfer\'s Brain.screenshot.'
>> if sum(x.flatten()==0)!=len(x.flatten()):
>>     print 'Pass'
>> else:
>>     print 'Fail'
>>
>> # Looking at the Mayavi mlab.screenshot method.
>> # This is called by screenshot_single, which is called by Brain's
>> screenshot.
>> # If the boolean expression evaluated here is true, then only a black
>> # background is being fed into Brain.screenshot()
>> from mayavi import mlab
>> x = mlab.screenshot(brain.brain_matrix[0,0]._f, 'rgb', False)
>> print 'Test mayavi\'s mlab.screenshot'
>> if sum(x.flatten()==0)!=len(x.flatten()):
>>     print 'Pass'
>> else:
>>     print 'Fail'
>>
>
> On the server through an x2go session both Brain.screenshot and
> mlab.screenshot failed to produce a non-blank image, while on my laptop's
> local environment both of these methods did produce the desired output
> (i.e., there were some nonzero outputs).
>
> Since this doesn't seem to be an error with pysurfer in particular, I'm
> going to proceed to see if anyone using Mayavi with x2go or nx has
> encountered similar issues by querying their forums / issue pages.  I just
> wanted to leave this here if someone else encounters the same issue in the
> future.
>
> A shot in the dark: Could it be something to do with running headless?
Maybe running this under XVFB (e.g. through xvfbwrapper
<https://pypi.python.org/pypi/xvfbwrapper>) would help?

Ariel


> --John
>
> On Tue, Sep 13, 2016 at 1:24 PM, John Pellman <pellman.john at gmail.com>
> wrote:
>
>> It looks like it might be related to the following issue described at
>> StackOverflow:
>>
>> http://stackoverflow.com/questions/16543634/mayavi-mlab-save
>> fig-gives-an-empty-image
>>
>> On Mon, Sep 12, 2016 at 2:00 PM, John Pellman <pellman.john at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I'm encountering a peculiar Pysurfer error on our server and I was
>>> wondering if anyone has encountered anything similar or might have some
>>> insight into how I can tackle it.  Basically, when our researchers try to
>>> save a png image using Brain.save_image() or Brain.save_imageset() the
>>> images produced only contain the background color (as you may have inferred
>>> from the subject line).  I've traced this back to Scipy method
>>> (scipy.misc.imsave), but it looks like this would only output an empty png
>>> if the image passed in were completely zeroed out.  Our setup uses the
>>> following versions of pysurfer/its dependencies:
>>>
>>> Numpy: 1.10.0.dev0+1fe98ff
>>> Scipy: 0.17.0.dev0+f2f6e48
>>> Ipython: 3.1.0
>>> nibabel: 2.0.0
>>> Mayavi: 4.4.2
>>> matplotlib: 1.4.3
>>> PIL: 1.1.7
>>> Pysurfer: 0.5
>>>
>>> This setup is running within a Miniconda environment using Python
>>> 2.7.11.  I'm uncertain if this is related, but running the example code
>>> here <http://pysurfer.github.io/examples/plot_basics.html> produces the
>>> following warning:
>>>
>>> *(ipython:20765): Gdk-WARNING **:
>>> /build/buildd/gtk+2.0-2.24.27/gdk/x11/gdkdrawable-x11.c:952 drawable is not
>>> a pixmap or window*
>>>
>>> Any insight would be greatly appreciated.
>>>
>>> Best,
>>> John Pellman
>>>
>>
>>
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