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

Fri Sep 16 12:00:15 EDT 2016

Pysurfer isn't running headless- it's using x2go, which is based upon the
nx protocol, a technology that improves the ability of X11 to function over
a network connection. Therefore, I don't think that Xvfb is related.
xvfbwrapper might be usable as a workaround, however.

As I mentioned in my last post, I traced the offending method back to
mayavi.  I've opened an issue related to this here
<https://github.com/enthought/mayavi/issues/440>.

Kirstie- if you'd be willing to refer your sysadmin to this thread I think
that would be great, as I would be interested in hearing what theories or
potential fixes he/she might have for this issue as well.

--John

On Fri, Sep 16, 2016 at 5:43 AM, JB Poline <jbpoline at gmail.com> wrote:

> That's a cool idea and package - thanks for pointing to this !
>
> On 16 September 2016 at 02:40, Ariel Rokem <arokem at gmail.com> wrote:
>
>>
>> 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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