[Insight-users] 1D Convolution with Gaussian Kernel using

Nicholas Tustison ntustison at gmail.com
Thu Nov 17 12:50:16 EST 2011 

Hi Antonio,

Instead of using the ConvolutionImageFilter, you might want to explore 
existing functionality in combining the GaussianOperator with the 
NeighborhoodOperatorImageFilter.

  typedef itk::NeighborhoodOperatorImageFilter<ImageType, ImageType> SmootherType;
  typename SmootherType::Pointer smoother = SmootherType::New();

  typedef GaussianOperator<PixelType, ImageDimension> GaussianType;
  GaussianType gaussian;
  gaussian.SetVariance( variance );
  gaussian.SetDirection( 0 );

  gaussian.SetMaximumError( 0.001 );
  gaussian.SetMaximumKernelWidth( inputImage->GetRequestedRegion().GetSize()[0] );
  gaussian.CreateDirectional();

  smoother->SetOperator( gaussian );
  smoother->SetInput( inputImage );
  smoother->Update();

  smoothImage = smoother->GetOutput();

However, in case you want to keep your image, you can use GaussianImageSource
to create  2-D image which has size Nx1 and then that image should plug right into
the ConvolutionImageFilter.  I just did it right now with my code and it seemed
to work as expected.

Nick



On Nov 17, 2011, at 4:42 AM, Antonio Gómez Barquero wrote:

> 
> 
> Hi!
> 
> You were right, now it compiles, but I only have some numbers in the first
> 20 positions, after that everything is 0, so is wrong, also it takes around
> 15 seconds to perform the calculation which is a crazy thing!.
> 
> I prefer to generate the Gaussian myself and after that translate it into an
> image ( kernel in this case) because I am doing work also with Matlab, and I
> would like to use the same Gaussian. 
> 
> But I think I am missing something in the body of the iteration , something
> that performs the convolution itself or maybe the point of doing the
> convolution in x-axis in 1D....
> 
>   while(!imageIterator.IsAtEnd()) 
>    {
>    //imageIterator.Set??
> 
>    ++imageIterator; //operator++  increments the iterator one position in
> the positive direction
> 
>    }
> 
> 
> Also, the perfect final would be to have a Kernel of 25 pixels ( the same I
> have originally in my Matlab program), and then performing the convolution
> in each row of the x-direction of the image...I think that must be a
> way...so I follow reading the ITK manual and let's see I found something.
> 
> Any Tip or idea or help will be highly appreciated!
> 
> Antonio
> 
> -----Mensaje original-----
> De: Cory Quammen [mailto:cquammen at cs.unc.edu] 
> Enviado el: miércoles, 16 de noviembre de 2011 17:28
> Para: Antonio Gómez Barquero
> CC: insight-users at itk.org
> Asunto: Re: [Insight-users] 1D Convolution with Gaussian Kernel using
> 
> Antonio,
> 
> It looks like you are defining your kernel to be 256x256, not 256x1.
> You probably want to call
> 
> size[0] = width;
> size[1] = 1;
> 
> instead of
> 
> size.Fill(width);
> 
> You might want to consider using the GaussianImageSource
> (http://www.itk.org/Doxygen/html/classitk_1_1GaussianImageSource.html)
> to generate your Gaussian.
> 
> Hope that helps,
> Cory
> 
> 2011/11/16 Antonio Gómez Barquero <agb1 at alu.upct.es>:
>> SORRY, the last e-mail was icomplete, here is ok:
>> 
>> 
>> 
>> My goal is to calculate the calculation in each row of a 2D-image ( in 
>> the
>> x-direction)
>> 
>> After following the tip from Cory I am trying to use the 
>> ‘ConvolutionImageFilter’, and make a kernel with the Gaussian values I 
>> calculate before.
>> 
>> I took a look to this example
>> (http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/ConvolutionImage
>> Filter) and my question is how to include the values of the Gaussian 
>> filter to the kernel, I tried wit the code below and it compiles, but 
>> it seems the execution has no end when I update the convolutionFilter… 
>> Because of that I think that I am doing something wrong. My code is 
>> below and is not so much, if some can give some help I would 
>> appreciate that really a lot !!!!.
>> 
>> 
>> 
>>       typedef itk::ConvolutionImageFilter <ImageType> ConvFilterType;
>> 
>> 
>> 
>>       ImageType::Pointer kernel = ImageType::New();
>> 
>>       CreateKernel(kernel, Gaussian , 256);
>> 
>> 
>> 
>>       //Convolve image with kernel
>> 
>>       ConvFilterType::Pointer convolutionFilter = 
>> ConvFilterType::New();
>> 
>>       convolutionFilter->SetInput(Li_itk);
>> 
>>       convolutionFilter->SetImageKernelInput(kernel);
>> 
>>       convolutionFilter->Update();
>> 
>> 
>> 
>> void Reg_image_v2::CreateKernel(Reg_image_v2::ImageType::Pointer 
>> kernel, double *Gaussian, unsigned int width) {
>> 
>> 
>> 
>>       ImageType::IndexType start;
>> 
>>       start.Fill(0);
>> 
>>       ImageType::SizeType size;
>> 
>>       size.Fill(width);
>> 
>>       ImageType::RegionType region;
>> 
>>       region.SetSize(size);
>> 
>>       region.SetIndex(start);
>> 
>>       kernel->SetRegions(region);
>> 
>>       kernel->Allocate();
>> 
>> 
>> 
>>       ImageType::IndexType pixelIndex;
>> 
>>       for (int i = 0 ; i < width ; i ++){
>> 
>>             pixelIndex[0] = i ;
>> 
>>             pixelIndex[1] = 0 ;
>> 
>>             kernel->SetPixel(pixelIndex,Gaussian[i]);
>> 
>>       }
>> 
>>       itk::ImageRegionIterator<ImageType> imageIterator(kernel, 
>> region);
>> 
>>    while(!imageIterator.IsAtEnd())
>> 
>>     {
>> 
>>     //imageIterator.Set??
>> 
>>     ++imageIterator; //operator++  increments the iterator one 
>> position in the positive direction
>> 
>>     }
>> 
>> 
>> 
>> 
>> 
>> } // end createKernel
>> 
>> 
>> 
>> 
>> 
>> Antonio Gómez Barquero
>> 
>> 
>> 
>> Ingeniero de Telecomunicaciones -Becario Investigador asociado a 
>> Actividades de I+D+I
>> 
>> GTTS ( Grupo de Tratamiento y Teoría de la Señal)[ 
>> http://gtts.upct.es/]
>> 
>> UPCT (Universidad Politécnica de Cartagena)[ http://www.upct.es/]
>> 
>> 
>> 
>> _____________________________________
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>> 
> 
> 
> 
> --
> Cory Quammen
> Research Associate
> Department of Computer Science
> The University of North Carolina at Chapel Hill
> 
> _____________________________________
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> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
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