[ITK] [ITK-users] Anti-alias filter
Tobias Gass
gass at vision.ee.ethz.ch
Thu Aug 14 07:32:06 EDT 2014
Dear all,
any further ideas on this one?
Thanks,
Tobias
2014-08-12 16:10 GMT+02:00 Tobias Gass <gass at vision.ee.ethz.ch>:
> Yes, this does result in the same problems as before.
>
>
> 2014-08-12 15:06 GMT+02:00 Bill Lorensen <bill.lorensen at gmail.com>:
>
> 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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>> >>>> >> >>>
>> >>>> >> >>>
>> >>>> >> >>>
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>> >>>>
>> >>>>
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>> >>>>
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>>
>>
>>
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>>
>
>
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