[ITK] [ITK-users] Memory leak in Python wrapped Image GetPixel method?

[Paavolainen, Lassi]

In case it makes any difference, I can see the same issue with freshly installed another computer. Though both have pretty much the same environment (updated Ubuntu 14.04, Python 2.7.6). The freshly installed machine is using ITK 4.7.1, but as said I can see the same problem with ITK 4.6 and 3.20.

Would be nice to hear if anyone with similar setup is able to reproduce the issue.

Lassi

________________________________________
From: Insight-users [insight-users-bounces at itk.org] on behalf of Paavolainen, Lassi [lassi.paavolainen at jyu.fi]
Sent: Monday, March 09, 2015 21:59
To: Matt McCormick
Cc: insight-users at itk.org
Subject: Re: [ITK-users] Memory leak in Python wrapped Image GetPixel method?

Hi Matt,

Seems its an issue with local environment. Here is also for the list what I replied to Gaetan:
"This is interesting. I'm using ITK 4.6.1 with swig that comes with it. I now tested with 3.20 that has been built long time ago with swig 1.9 (if I remember correctly). The same thing. So the conclusion is that it must be something local as I'm sure I've done something similar over the years many times.

Next is to try to find out what on my environment causes this."

To add to that, I ran 30 iterations using valgrind. Here is the report:
==8603== HEAP SUMMARY:
==8603==     in use at exit: 478,066,856 bytes in 483,719 blocks
==8603==   total heap usage: 657,312 allocs, 173,593 frees, 787,087,705 bytes allocated
==8603==
==8603== LEAK SUMMARY:
==8603==    definitely lost: 0 bytes in 0 blocks
==8603==    indirectly lost: 0 bytes in 0 blocks
==8603==      possibly lost: 20,224 bytes in 34 blocks
==8603==    still reachable: 478,046,632 bytes in 483,685 blocks
==8603==         suppressed: 0 bytes in 0 blocks

So almost 500 MB is in heap but still reachable when the program exits.

Lassi

________________________________________
From: Matt McCormick [matt.mccormick at kitware.com]
Sent: Monday, March 09, 2015 20:22
To: Paavolainen, Lassi
Cc: insight-users at itk.org; Gaëtan Lehmann; Michka Popoff
Subject: Re: [ITK-users] Memory leak in Python wrapped Image GetPixel method?

Hi Lassi,

Thanks for investigating and reporting the issue!

I have created an issue in the Issue Tracker to keep track of it:

  https://issues.itk.org/jira/browse/ITK-3352

Matt

On Mon, Mar 9, 2015 at 6:11 AM, Paavolainen, Lassi
<lassi.paavolainen at jyu.fi> wrote:
> Hi,
>
> I noticed that GetPixel method in itk.Image object eats memory in Python wrapped code. I think I've seen some Python wrapping memory issues years ago but nothing as simple as this. Here is a simple test script:
> import sys
> import itk
> reader = itk.ImageFileReader.IUC2.New()
> reader.SetFileName(sys.argv[1])
> reader.Update()
> img = reader.GetOutput()
> size = img.GetLargestPossibleRegion().GetSize()
> for i in range(100):
>         for x in range(size[0]):
>                 for y in range(size[1]):
>                         value = img.GetPixel((x,y))
>         print "Done with iteration %d"%(i+1)
>
> When I run it with 1 MB image, it end up taking 1.5 GB of memory. After spending lots of time on debugging a bigger bunch of code I realized that the GetPixel method was to blame. Can anyone reproduce it? I'm using ITK 4.6.1
>
> Cheers,
> Lassi
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Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

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