[Insight-users] Sparse image for building distance field

[Dan Mueller]

Hi Sergiy,

You might also be interested in the following Insight Journal article:
    http://www.insight-journal.org/browse/publication/646

It is quite old, so I doubt it will compile with the latest ITK without
modifications...

HTH

Cheers, Dan


On 22 March 2013 23:16, Sergiy Tkachuk <sergtk.job at gmail.com> wrote:

> Hello all,
>
> I want to build distance field for the object.
> My object is very sparsed and I want to build distance field for it and
> not to allocate memory for every voxel in the grid.
> Number of voxel in 3d grid is about 10^10 (more precisely: 2000x2000x2000)
> Number of voxel in object itself is about 10^6.
>
> I tried to play with itk::SignedMaurerDistanceMapImageFilter creating
> image 5x5x5 in sandbox:
>
>
>     const unsigned int Dimension = 3;
>     typedef char InputPixelType;
>     typedef float OutputPixelType;
>
>     typedef itk::Image<InputPixelType, Dimension> InputImageType;
>     typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
>
>     InputImageType::Pointer image = InputImageType::New();
>
>     InputImageType::SizeType size;
>     size[0] = 5;
>     size[1] = 5;
>     size[2] = 5;
>
>     InputImageType::IndexType start;
>     start.Fill(0);
>
>     InputImageType::RegionType region;
>     region.SetIndex(start);
>     region.SetSize(size);
>
>     image->SetRegions(region);
>     image->Allocate();
>
>     image->FillBuffer(0);
>
>     InputImageType::IndexType index;
>
>     // initialize
>     InputImageType::IndexType gapIndex;
>     gapIndex[0] = gapIndex[1] = gapIndex[2] = 2;
>     for (index[0] = 0; index[0] < size[0]; ++index[0])
>         for (index[1] = 0; index[1] < size[1]; ++index[1])
>             for (index[2] = 0; index[2] < size[2]; ++index[2]) {
>                 if (index == gapIndex) continue;
>                 image->SetPixel(index, 1);
>             }
>
>     // Define the distance map filter and apply it to the image
>     typedef itk::SignedMaurerDistanceMapImageFilter<InputImageType,
> OutputImageType> DistanceFilterType;
>     DistanceFilterType::Pointer distanceFilter = DistanceFilterType::New();
>     distanceFilter->SetInput(image);
>     distanceFilter->SetBackgroundValue(0);
>     distanceFilter->SetSquaredDistance(false);
>     distanceFilter->Update();
>
>     // Output distance field values
>     for (int x = 1; x < size[0]-1; ++x)
>     {
>         for (int y = 1; y < size[1]-1; ++y)
>         {
>             for (int z = 1; z < size[2]-1; ++z)
>             {
>                 InputImageType::IndexType ind;
>                 ind[0] = x;
>                 ind[1] = y;
>                 ind[2] = z;
>
>                 float value = distanceFilter->GetOutput()->GetPixel(ind);
>                 std::cout << x << " " << y << " " << z << " -> " << value
> << std::endl;
>             }
>         }
>     }
>
>
> The code works fine.
> But it requires memory for every voxel of grid, and this is not acceptable
> for 10^10 voxels.
>
> Is it possible to use some kind of sparse structure to build distance
> field?
>
> I read about itk::SparseImage, but it seems this structure is sparse
> concerning value only, but indices are allocated for the whole grid. Am I
> undestood correctly? If no, I will be glad if somebody point out where I am
> mistaken. Thanks.
>
> If itk::SparseImage is not sutable in my case, is it possible to implement
> custom Image format for input to itk::SignedMaurerDistanceMapImageFilter?
> If so, are the any useful guidelines to achieve this?
> For now it is not clear for me how to correctly derive my Image type from
> DataObject and handle regions - I don't need full power of ITK filter
> pipeline, just to call itk::SignedMaurerDistanceMapImageFilter - possibly
> this helps me to simplify custom image implementation.
>
> Any ideas could be helpful for me!
>
> Thanks in advance,
> Sergiy
>
>
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