[Insight-users] How to create/draw a sphere surface image mask with 26|6 connectivity?

[Luis Ibanez]

Hi Lynx,


1) You are right , this code may be generating only
    face connected contours (6-connected in 3D).
    Converting it to 26-connected surfaces may not
    be a trivial task, but it is worth looking into it.

    Would you like to give it a try ?


2) The concept of SpatialObjects in ITK is similar to
     the vtkImplicit functions, but it is not fully equivalent.
     SpatialObjects were designed with the goal of
     representing anatomical structures in mind.


3)  You right, these examples were written with the
     intention of being included in a future version of
     the ITK Software Guide.  The current version of
     the guide precedes the creation of these examples.


4)  The lack of progress reporting from the
      SpatialObjectToImageFilter looks like a bug.

      Could you please file a bug report here?
      http://public.kitware.com/Bug


   Thanks


            Luis


----------------------------------------------------------------------
On Mon, Feb 15, 2010 at 2:47 AM,  <lynx.abraxas at freenet.de> wrote:
> On 13/02/10 15:34:32, Luis Ibanez wrote:
>> You could use the following set of classes
>>
>>
>>     1) itkEllipseSpatialObject
>>     2) itkSpatialObjectToImageFilter
>>     3) itkSimpleContourExtractorImageFilter
>>
>>
>> With (1) you can create a Sphere of the proper size,
>> With (2) you can rasterize that sphere into a binary image mask
>> With (3) you can extract the contour of the binary image mask
>>
>>
>> The filter (3) allows you to select the "thickness" of
>> the contour. You do this by adjusting the value of the
>> neighborhood "Radius" parameter.
>>
>
> Thanks  a lot Luis for Your quick and helpful answer. With that I could create
> the attached test porgram.
>
> Looking at the results slice by slice I wonder if the result is really just 26
> connective.  With  that I mean: Does the result have no additional voxels that
> would not be necessary to assure 26 connectivity?
> How could I create a sphere mask that  has  exactly  only  6  connectivity?  I
> thought  of a thickness below 1 but SimpleContourExtractorImageFilter does not
> allow that.
>
>
> I'm not sure if I understand SpatialObject correctly. Are they  some  how  the
> correspondence to vtk impicit functions?
>
>> You will find source code guiding examples in
>>
>>   Insight/Examples/Filtering/
>>          SpatialObjectToImage1.cxx
>>          SpatialObjectToImage2.cxx
>>          SpatialObjectToImage3.cxx
>
> When  searching  the  docs  about  this  I  didn't  find these examples in the
> userguide altough they seem to be written for it.
>
>> Anti-aliased versions could be produced in several
>> different ways, depending on what you plan to do
>> with the resulting contour.
>>
>> Some of the options for anti-aliased versions are:
>>
>> A)  Take the aliased contour and pass it as input
>>       to the itk::AntiAliasBinaryImageFilter
>>
>> B) Use either one of the following distance map filters:
>>
>>         * SignedDanielssonDistanceMapImageFilter
>>         * SignedMaurerDistanceMapImageFilter
>
> This is a really cool way to do it.
>
> Thanks again
> Lynx
>
> PS: I don't get a progress report from SpatialObjectToImageFilter.
>
> ____________________________________
>
> #include <itkImageFileReader.h>
> #include <itkImageFileWriter.h>
>
> #include <itkEllipseSpatialObject.h>
> #include <itkSpatialObjectToImageFilter.h>
> #include <itkSimpleContourExtractorImageFilter.h>
> #include "itkFilterWatcher2.h"
>
> int main( int argc, char * argv[] )
>    {
>    if( argc != 5 )
>        {
>        std::cerr << "Usage: " << argv[0];
>        std::cerr << " outputImage";
>        std::cerr << " resolution";
>        std::cerr << " radius";
>        std::cerr << " thickness";
>        std::cerr << std::endl;
>        return EXIT_FAILURE;
>        }
>
>    typedef  unsigned char OutputPixelType;
>
>    const unsigned int Dimension = 3;
>
>    typedef itk::Image<OutputPixelType,  Dimension>   OutputImageType;
>    typedef itk::EllipseSpatialObject< Dimension >   EllipseType;
>    EllipseType::Pointer ellipse    = EllipseType::New();
>
>    ellipse->SetRadius(atof(argv[3]));
>    //ellipse->SetDefaultInsideValue(255);
>    //ellipse->SetDefaultOutsideValue(0);
>
>    typedef itk::SpatialObjectToImageFilter<EllipseType, OutputImageType> SpatialObjectToImageFilterType;
>    SpatialObjectToImageFilterType::Pointer filter= SpatialObjectToImageFilterType::New();
>    FilterWatcher watcher(filter, "filter");
>
>    int d= atoi(argv[2]);
>    OutputImageType::SizeType size;
>    size[ 0 ] = d;
>    size[ 1 ] = d;
>    size[ 2 ] = d;
>    filter->SetSize( size );
>
> //     OutputImageType::SpacingType spacing;
> //     spacing[0] =  2 / size[0]; //use twice the radius;)
> //     spacing[1] =  2 / size[1];
> //     spacing[2] =  2 / size[2];
> //     filter->SetSpacing( spacing );
>    filter->SetInsideValue(255);
>    filter->SetOutsideValue(0);
>
>    double o= ((d - 1)/2.); //minus 1 probably because of counting starting at 0
>    double O[3]={-o, -o, -o};
>    filter->SetOrigin(O);
>    filter->SetInput(ellipse);
>    std::cout << "origin: " << o + 1 << std::endl;
>
>    filter->Update();
>
>    typedef itk::SimpleContourExtractorImageFilter<OutputImageType, OutputImageType> SimpleContourExtractorImageFilterType;
>    SimpleContourExtractorImageFilterType::Pointer extractor= SimpleContourExtractorImageFilterType::New();
>
>    extractor->SetInputBackgroundValue(0);
>    extractor->SetInputForegroundValue(255);
>    extractor->SetOutputBackgroundValue(0);
>    extractor->SetOutputForegroundValue(255);
>
>    OutputImageType::SizeType radius;
>    radius[ 0 ] = atoi(argv[4]);
>    radius[ 1 ] = atoi(argv[4]);
>    radius[ 2 ] = atoi(argv[4]);
>    extractor->SetRadius(radius);
>
>    extractor->SetInput(filter->GetOutput());
>
>    typedef itk::ImageFileWriter<OutputImageType>  WriterType;
>    WriterType::Pointer writer = WriterType::New();
>
>    writer->SetFileName(argv[1]);
>    //writer->SetInput(filter->GetOutput());
>    writer->SetInput(extractor->GetOutput());
>
>    try
>        {
>        writer->Update();
>        }
>    catch( itk::ExceptionObject & excp )
>        {
>        std::cerr << excp << std::endl;
>        return EXIT_FAILURE;
>        }
>
>    return EXIT_SUCCESS;
>    }
>
>
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