[ITK-users] Anti-alias filter
Tobias Gass
gass at vision.ee.ethz.ch
Tue Aug 12 08:33:14 EDT 2014
Update: meanwhile I also tried cropping the image to investigate the impact
of the overall size (#voxels) of the image. It appears to not have an
effect, the same artifacts occur when processing a significantly smaller
region (1/2 size).
2014-08-12 10:44 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
> Hi,
>
> changing the PixelType did not yield any change. However, I did some
> further tests which seem to point at image spacing or total size to be the
> culprit. My original image is fairly high-res, with 0.25mm in-plane
> resolution and 0.75mm slice thickness and 512x512x409 voxel size. I tried
> resampling the image to different isotropic resolutions (0.25, 0.3, 0.34,
> 0.35, 0.4, 0.5, 0.75, 1)mm isotropic spacing. For all spacings down to
> 0.35mm, the AA filter converged nicely and the output looks as I'd expect
> it. Lower than 0.35mm spacing, and it fails in the way I described (from
> this spacing on the #vox is equal or greater than the #voxels in my
> original image).
>
> Any idea what might cause this, or what to further investigate?
>
> Thanks,
> Tobias
>
>
> 2014-08-11 22:17 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>
> Paraview should do the right thing.
>>
>> On Mon, Aug 11, 2014 at 3:38 PM, Tobias Gass <gass at vision.ee.ethz.ch>
>> wrote:
>> > I will try that tomorrow morning (living in GMT+1). I used paraview to
>> > extract the isosurface, but also looked at the output of the AA-filter
>> > directly (which looked fuzzy). I can also post an image of that
>> tomorrow.
>> >
>> > Thanks for your help!
>> > Tobias
>> >
>> >
>> > 2014-08-11 21:22 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>> >
>> >> How are you extracting the final isosurface?
>> >>
>> >> On Mon, Aug 11, 2014 at 3:22 PM, Bill Lorensen <
>> bill.lorensen at gmail.com>
>> >> wrote:
>> >> > If you change
>> >> > typedef short PixelType;
>> >> > to
>> >> > typedef double PixelType;
>> >> >
>> >> > do the results change.
>> >> >
>> >> >
>> >> > On Mon, Aug 11, 2014 at 2:47 PM, Tobias Gass <gass at vision.ee.ethz.ch
>> >
>> >> > wrote:
>> >> >>
>> >> >>> Can you post your code. The results do not look correct.
>> >> >>
>> >> >>
>> >> >> Sure. The {write,read}Image functions are just convenient wrappers
>> for
>> >> >> the
>> >> >> respective ITK tools.
>> >> >>
>> >> >>
>> >> >> #include <stdio.h>
>> >> >>
>> >> >> #include <iostream>
>> >> >>
>> >> >> #include "argstream.h"
>> >> >>
>> >> >> #include "ImageUtils.h"
>> >> >>
>> >> >> #include "itkAntiAliasBinaryImageFilter.h"
>> >> >>
>> >> >> using namespace std;
>> >> >>
>> >> >> using namespace itk;
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> int main(int argc, char ** argv)
>> >> >>
>> >> >> {
>> >> >>
>> >> >>
>> >> >> feenableexcept(FE_INVALID|FE_DIVBYZERO|FE_OVERFLOW);
>> >> >>
>> >> >> typedef short PixelType;
>> >> >>
>> >> >> typedef double OutputPixelType;
>> >> >>
>> >> >> const unsigned int D=3;
>> >> >>
>> >> >> typedef Image<PixelType,D> ImageType;
>> >> >>
>> >> >>
>> >> >>
>> >> >> typedef ImageType::Pointer ImagePointerType;
>> >> >>
>> >> >>
>> >> >>
>> >> >> typedef Image<OutputPixelType,D> OutputImageType;
>> >> >>
>> >> >> typedef OutputImageType::Pointer OutputImagePointerType;
>> >> >>
>> >> >>
>> >> >>
>> >> >> argstream * as=new argstream(argc,argv);
>> >> >>
>> >> >> string inFile, outFile;
>> >> >>
>> >> >> double thresh=0.0;
>> >> >>
>> >> >> (*as) >> parameter ("in", inFile, " filename...", true);
>> >> >>
>> >> >> (*as) >> parameter ("out", outFile, " filename...", true);
>> >> >>
>> >> >>
>> >> >> (*as) >> help();
>> >> >>
>> >> >> as->defaultErrorHandling();
>> >> >>
>> >> >>
>> >> >> ImagePointerType img = ImageUtils<ImageType>::readImage(inFile);
>> >> >>
>> >> >>
>> >> >> typedef itk::AntiAliasBinaryImageFilter <ImageType,
>> >> >> OutputImageType>
>> >> >>
>> >> >> AntiAliasBinaryImageFilterType;
>> >> >>
>> >> >>
>> >> >>
>> >> >> AntiAliasBinaryImageFilterType::Pointer antiAliasFilter
>> >> >>
>> >> >> = AntiAliasBinaryImageFilterType::New ();
>> >> >>
>> >> >> antiAliasFilter->SetInput(img);
>> >> >>
>> >> >> antiAliasFilter->SetNumberOfIterations(5);
>> >> >>
>> >> >> antiAliasFilter->SetMaximumRMSError(0.02);
>> >> >>
>> >> >>
>> >> >> antiAliasFilter->Update();
>> >> >>
>> >> >>
>> >> >> // For increased code coverage. Does nothing.
>> >> >>
>> >> >> antiAliasFilter->GetMaximumRMSError();
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> antiAliasFilter->Update();
>> >> >>
>> >> >>
>> >> >> std::cout << "Maximum RMS change value threshold was: 0.02 " <<
>> >> >> std::endl;
>> >> >>
>> >> >> std::cout << "Last RMS change value was: " <<
>> >> >> antiAliasFilter->GetRMSChange() << std::endl;
>> >> >>
>> >> >>
>> >> >> std::cout<< antiAliasFilter->GetElapsedIterations() <<endl;
>> >> >>
>> >> >>
>> >> >> std::cout<<antiAliasFilter->GetLowerBinaryValue()<<" "<<
>> >> >> antiAliasFilter->GetUpperBinaryValue()<<std::endl;
>> >> >>
>> >> >>
>> >> >> OutputImagePointerType out=antiAliasFilter->GetOutput();
>> >> >>
>> >> >>
>> >> >> ImageUtils<OutputImageType>::writeImage(outFile,out);
>> >> >>
>> >> >>
>> >> >> return 1;
>> >> >>
>> >> >> }
>> >> >>
>> >> >>
>> >> >> I tried different values for maxIter (1,2,3,4,5,10,100,1000) and
>> >> >> maxRMSError
>> >> >> (0.02 0.07 0.08 0.8), and the best visual results are achieved after
>> >> >> one
>> >> >> iteration where RMSE changes by about 0.08. This increases for all
>> >> >> following
>> >> >> iterations, which have an RMSE-change of about 0.25 for all number
>> of
>> >> >> iterations tested. All this is using ITK 4.5 pulled from the GIT
>> >> >> repository
>> >> >> a while ago, running on an intel i7 on Debian.
>> >> >>
>> >> >> Thanks a lot!
>> >> >> Tobias
>> >> >>
>> >> >>>
>> >> >>>
>> >> >>> On Mon, Aug 11, 2014 at 12:18 PM, Tobias Gass <
>> gass at vision.ee.ethz.ch>
>> >> >>> wrote:
>> >> >>> > Dear all,
>> >> >>> >
>> >> >>> > I'm having problems using the anti-alias filter, which I want to
>> use
>> >> >>> > in
>> >> >>> > order to smooth a binary segmentation volume. I'm using
>> essentially
>> >> >>> > the
>> >> >>> > example code from the repository, which for my input file seems
>> to
>> >> >>> > start
>> >> >>> > oscillating after 2 iterations, leading to weird 'pointy'
>> artifacts
>> >> >>> > on
>> >> >>> > the
>> >> >>> > surface as can be seen from the attached screenshot (AA filter
>> >> >>> > output is
>> >> >>> > on
>> >> >>> > the left, input on the right).
>> >> >>> >
>> >> >>> > Is there any parameter to set/implement which could improve the
>> >> >>> > behavior
>> >> >>> > of
>> >> >>> > this filter? I'm assuming that my input is reasonable, or is this
>> >> >>> > something
>> >> >>> > the filter is expected to have problems with? It is notable that
>> >> >>> > such
>> >> >>> > errors
>> >> >>> > seem to mainly appear in 'flat' regions of the volume, and are
>> not
>> >> >>> > apparent
>> >> >>> > in the curved shaft of the bone.
>> >> >>> >
>> >> >>> > Any help, or pointers to further resources are appreciated,
>> >> >>> > thanks,
>> >> >>> > Tobias
>> >> >>> >
>> >> >>> > _____________________________________
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>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> --
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>> >> >>
>> >> >>
>> >> >
>> >> >
>> >> >
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>> >>
>> >>
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>>
>>
>>
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