[Insight-developers] denoising filter

[Bradley Lowekamp]

Nick,

I just ran into this problem too this morning. I am glad you looked into the problem further than I did.

I was wrapping it for SimpleITK. I was setting up the filter with the defaults matching:

http://review.source.kitware.com/#/c/8803/1/Code/BasicFilters/json/PatchBasedDenoisingImageFilter.json

And I was testing it with the following 3D image:

http://itk.org/gitweb?p=SimpleITKData.git;a=blob;f=Input/RA-Short.nrrd;h=fca085049470a826324a4f2c93af2fd65fbaed52;hb=HEAD

With the following meta information:
  Size: [64, 64, 64]
  Spacing: [0.755874, 0.755874, 0.755874]
  Origin: [0.283453, 0.283453, 0.283453]
  Direction: 
1 0 0
0 1 0
0 0 1


I get the same error with the defaults as you did, when I run the filter with the defaults

And then if I change the patchRadius:

python: sitk.PatchBasedDenoising( img, patchRadius=8 )
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/home/blowekamp/src/SimpleITK/Testing/Data/Input/<ipython console> in <module>()

/home/blowekamp/build/SimpleITK/SimpleITK-build/Wrapping/SimpleITK.pyc in PatchBasedDenoising(*args, **kwargs)
   5767         double fractionPixelsForSigmaUpdate=1.0) -> Image
   5768     """
-> 5769   return _SimpleITK.PatchBasedDenoising(*args, **kwargs)
   5770 class MaximumProjectionImageFilter(_object):
   5771     """

RuntimeError: Exception thrown in SimpleITK PatchBasedDenoising: /home/blowekamp/build/SimpleITK/ITK-prefix/include/ITK-4.3/itkPatchBasedDenoisingImageFilter.hxx:641:
itk::ERROR: PatchBasedDenoisingImageFilter(0x3086ee0): Center pixel's weight (0.685381) must be equal to 1.0

Thanks,
Brad

On Dec 6, 2012, at 12:07 PM, Nicholas Tustison <ntustison at gmail.com> wrote:

> Hi Kris,
> 
> Today I finally got a chance to look at your denoising work (I'm ashamed
> that I was at Penn for with Suyash for some time but I never asked him 
> about it).  Anyway, I have a couple questions and I was hoping you could
> help me try to run your denoising work on some of my MRI.   I took the test 
> that you wrote and modified it only so that I could use it as a stand-alone
> program.  I also verified that my version worked with the test images.  
> However, when I tried to use it on my image (stats below)
> 
> Image information
>  Size:          [256, 256, 20]
>  Origin:        [-232.879, -135.656, 240.706]
>  SpatialExtent: [498.047, 498.047, 190]
>  Center:        [16.1448, 113.368, 335.706]
>  Spacing:       [1.95312, 1.95312, 10]
>  Index:         [0, 0, 0]
>  Direction:     
> 1 0 0
> 0 1 0
> 0 0 1
> 
> using the following parameters
> 
> patchRadius = 4 
> noiseModel = gaussian 
> fidelityWeight = 0.0 
> numberOfIterations = 1 
> sigmaMultiplicationFactor = 2
> 
> it gave me the following error
> 
> Line: 634
> Description: itk::ERROR: PatchBasedDenoisingImageFilter(0x7fbffb0f5e10): Center pixel's weight (0) must be equal to 1.0 
> 
> After investigating this section of the code, I noticed that the physicalWeightsImage
> (after writing it to an image file) consists of what looked like a weighted 2-D disc.  
> Based on my reading of the comments, should this be more of a 3-D weighted sphere?  
> If so, I made some changes in the code to actually get a weighted sphere thinking 
> that might be solve the problem but I still got the same error.  However, if I increase
> the radius to 8, it seems to get past that error without issue.  Is there a general rule
> for determining a minimal radius for this filter?
> 
> Thanks for your help,
> Nick
> 
> 
> 
> 
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