[ITK-users] Anti-alias filter
Bill Lorensen
bill.lorensen at gmail.com
Tue Aug 12 09:06:22 EDT 2014
Have you tried:
UseImageSpacingOn();
On Tue, Aug 12, 2014 at 8:47 AM, Tobias Gass <gass at vision.ee.ethz.ch> wrote:
> Further update: when manually increasing the spacing of the input image
> (without resampling, thus not changing the size), the filter works well.
> This probably indicates numerical instability depending on image spacing
> somewhere in the code, which would probably be great if it could be fixed.
>
> Best,
> Tobias
>
>
> 2014-08-12 14:33 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
>
>> 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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>>>> >> >>> >
>>>> >> >>>
>>>> >> >>>
>>>> >> >>>
>>>> >> >>> --
>>>> >> >>> Unpaid intern in BillsBasement at noware dot com
>>>> >> >>
>>>> >> >>
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> > --
>>>> >> > Unpaid intern in BillsBasement at noware dot com
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >> Unpaid intern in BillsBasement at noware dot com
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Unpaid intern in BillsBasement at noware dot com
>>>> _____________________________________
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>>>
>>
>
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