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 > > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > 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: > http://www.itk.org/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html 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: http://www.itk.org/mailman/listinfo/insight-developers
