[ITK] Fwd: itk error: Inputs do not occupy the same physical space!

[Vishwanathan Shreyas]

Hi Brad,

"map_sync" here uses heavyweight independent processes. Also, the filter
fails on random files every time I run it. I ran it on a single core but it
was taking about 13 min for processing a single file, so I did not waste
time on running it as a single threaded function for any more files.
The platform I'm using is Windows Server 2012 standard.
Also, there is no problem with the data as I ran a script to check it.

Thanks,
Shreyas

On Tue, Jan 24, 2017 at 9:05 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> I am not familiar with “map_sync”. Is it from this class:
> https://ipython.org/ipython-doc/3/api/generated/IPython.para
> llel.client.view.html
> Does it use threads or heavy weight processes?
>
> If you run the filter with just the single threaded map function does it
> fail the same way? Which file does it fail on? If you just run it on that
> file does it still fail?
>
> We need to narrow down the problem to determine if it’s related to the way
> you are executing, or if perhaps N4 has a problem with your data. Perhaps
> it is some type of degenerate case, or there is a bug in the filter.
>
> Thanks,
> Brad
>
> On Jan 24, 2017, at 12:44 AM, Vishwanathan Shreyas <
> shreyas122011 at gmail.com> wrote:
>
> SimpleITK on python gives me a weird bug, after running successfully a few
> times. I'm using the MICCAI BRATS database. Here's my code:
>
> def N43D(fl):
>
>     im = SimpleITK.ReadImage(fl)
>
>     msk = SimpleITK.BinaryThreshold(im, 0, 0)
>
>     msk = SimpleITK.BinaryNot(msk)
>
>     msk = SimpleITK.Cast(msk, SimpleITK.sitkUInt8)
>
>     im = SimpleITK.Cast(im, SimpleITK.sitkFloat32)
>
>     im_n4 = SimpleITK.N4BiasFieldCorrection(im, msk)
>
>     SimpleITK.WriteImage(im_n4, os.path.splitext(fl)[0]+'_n4.mha', useCompression=True)
>
>
>
> Also, I'm using multiple cores for a list of files:
>
> dview.map_sync(N43D, fl)
>
>
>
> The program runs fine for about 40 files. Then I get this error on all my
> engines:
>
> [0:apply]:
> RuntimeErrorTraceback (most recent call last)<string> in <module>()<ipython-input-56-03a02a993653> in N43D(fl)
> c:\users\shreyas_v\anaconda2\lib\site-packages\SimpleITK\SimpleITK.pyc in N4BiasFieldCorrection(*args, **kwargs)
>   43368
>   43369     """> 43370     return _SimpleITK.N4BiasFieldCorrection(*args, **kwargs)  43371 class NaryAddImageFilter(ImageFilter_3):  43372     """RuntimeError: Exception thrown in SimpleITK N4BiasFieldCorrection: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageToImageFilter.hxx:248:
> itk::ERROR: SubtractImageFilter(00000000065D8220): Inputs do not occupy the same physical space!
> InputImage Origin: [0.0000000e+000, -2.3900000e+002, 0.0000000e+000], InputImage_1 Origin: [-5.9750000e+001, -5.9750000e+001, -3.8500000e+001]
>     Tolerance: 1.0000000e-006
> InputImage Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000], InputImage_1 Spacing: [5.9750000e+001, 5.9750000e+001, 3.8500000e+001]
>     Tolerance: 1.0000000e-006
>
>
> Has anyone faced this issue before?
>
> Regards,
> Shreyas
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