Ok, there are 2 problems going on. The first is that the patch
weights are not appropriately 3D sphere. The second is that the
resampling of the patch weights results in a max patch weight < 1 for
non-integer resampling values. But I think the resampling should
really be reconsidered a bit more. If the image spacing is
0.5,0.5,0.5 I'm not sure that resampling really needs to happen. The
point is really to make the patch weights capture the relative
anisotropy. Thus if the image spacing is 1,1,0.5 then maybe in that
case it makes sense to resample the patch weights in the z direction
to cover the same amount of physical space. I'm including Suyash on
this message to see what he thinks is the best way to handle this.
I haven't looked at your code changes yet, as I first wanted to
understand better what was happening. I'll take a look there next.
-Kris
On Dec 6, 2012, at 12:24 PM, Nicholas Tustison wrote:
Thanks Kris and Brad for your responses. Since it's easier to
look at code, I thought I'd post the changes I had to make.
http://review.source.kitware.com/#/c/8833/
Kris, if I read the code correctly, it seems to me that the physical
weighting image shouldn't be affected at all by anisotropic voxels
in the input image. Am I reading that right? The size of the
physical
weighting image seems only affected by the patch radius with
isotropic spacing equal to 1. When I write that image to disk using
my patch, I get an isotropic weighting distance function. Otherwise
I get a flat disk where the weighting in the z? direction seems to be
close to 0. Before we get to the issue that both Brad and I are
having of the thrown exception, perhaps we can clarify this issue.
Is that okay?
Thanks again for your help with this, Kris,
Nick
On Dec 6, 2012, at 1:08 PM, Bradley Lowekamp
<[email protected]> wrote:
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
<[email protected]> 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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Kitware offers ITK Training Courses, for more information visit:
http://kitware.com/products/protraining.php
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
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