[Insight-users] BinaryThinningImageFilter
and BinaryPruningImageFiler
Luis Ibanez
luis.ibanez at kitware.com
Mon Dec 6 14:40:41 EST 2004
Hi Robert,
Thanks for posting the corrections to these two filters.
Unfortunately the diffs didn't come too well through the email.
Could you please resend us the files (not just the diffs) so
we can test them and commit the changes to CVS ?
Thanks a lot,
Luis
----------------------------------------
Uitert, Robert Van (NIH/CC/DRD) wrote:
> Hi,
>
> We had problems getting the BinaryThinningImageFilter and
> BinaryPruningImageFilter to work properly. The BinaryThinningImageFilter
> was outputting one of the edges of the binary region rather than a skeleton
> and the BinaryPruningImageFilter was not pruning the image at all. Below
> we've included a diff between the cvs version and our working versions of
> the .txx files of these filters. We would be glad to commit these back into
> the itk repository.
>
> Also on
> http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html
> the documentation states that :
> "This filter computes one pixel wide edges of the input image.
> The input is assumed to be a binary image. The filter will produce a
> skeleton of the object"
> those two lines contradict each other. The first should be:
> "This filter computes one pixel wide skeleton of the input image."
>
> For the itkBinaryPruningImageFilter, we decided to stop the pruning before
> all desired iterations are completed, iff in the previous iteration there
> were only 2 voxels eliminated. This is logical, as in this case the skeleton
> has already been reduced to a single line.
>
>
> Robert Van Uitert and Ingmar Bitter
> Diagnostic Radiology Department
> Clinical Center
> National Institutes of Health
>
>
>
> Index: itkBinaryThinningImageFilter.txx
> ===================================================================
> RCS file:
> /cvsroot/Insight/Insight/Code/Algorithms/itkBinaryThinningImageFilter.txx,v
> retrieving revision 1.2
> diff -r1.2 itkBinaryThinningImageFilter.txx
> 115a116
>
>> std::vector< std::vector<int> > structureElements(8);
>
> 117,124c118,216
> < typename NeighborhoodIteratorType::OffsetType offset1 = {{-1,-1}};
> < typename NeighborhoodIteratorType::OffsetType offset2 = {{-1,0}};
> < typename NeighborhoodIteratorType::OffsetType offset3 = {{-1,1 }};
> < typename NeighborhoodIteratorType::OffsetType offset4 = {{0,1}};
> < typename NeighborhoodIteratorType::OffsetType offset5 = {{1,1}};
> < typename NeighborhoodIteratorType::OffsetType offset6 = {{1,0}};
> < typename NeighborhoodIteratorType::OffsetType offset7 = {{1,-1}};
> < typename NeighborhoodIteratorType::OffsetType offset8 = {{0,-1}};
> ---
>
>> std::vector<typename NeighborhoodIteratorType::OffsetType> offset(8);
>> typename NeighborhoodIteratorType::OffsetType offset0 = {{-1,-1}};
>> offset[0] = offset0;
>> typename NeighborhoodIteratorType::OffsetType offset1 = {{-1,0}};
>> offset[1] = offset1;
>> typename NeighborhoodIteratorType::OffsetType offset2 = {{-1,1}};
>> offset[2] = offset2;
>> typename NeighborhoodIteratorType::OffsetType offset3 = {{0,1}};
>> offset[3] = offset3;
>> typename NeighborhoodIteratorType::OffsetType offset4 = {{1,1}};
>> offset[4] = offset4;
>> typename NeighborhoodIteratorType::OffsetType offset5 = {{1,0}};
>> offset[5] = offset5;
>> typename NeighborhoodIteratorType::OffsetType offset6 = {{1,-1}};
>> offset[6] = offset6;
>> typename NeighborhoodIteratorType::OffsetType offset7 = {{0,-1}};
>> offset[7] = offset7;
>>
>> // 3 4 5
>> // 2 6
>> // 1 8 7
>>
>> structureElements[0].push_back(1);
>> structureElements[0].push_back(2);
>> structureElements[0].push_back(0);
>> structureElements[0].push_back(0);
>> structureElements[0].push_back(0);
>> structureElements[0].push_back(2);
>> structureElements[0].push_back(1);
>> structureElements[0].push_back(1);
>>
>> structureElements[1].push_back(1);
>> structureElements[1].push_back(1);
>> structureElements[1].push_back(2);
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(2);
>> structureElements[1].push_back(1);
>>
>> structureElements[2].push_back(1);
>> structureElements[2].push_back(1);
>> structureElements[2].push_back(1);
>> structureElements[2].push_back(2);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(2);
>>
>> structureElements[3].push_back(2);
>> structureElements[3].push_back(1);
>> structureElements[3].push_back(1);
>> structureElements[3].push_back(1);
>> structureElements[3].push_back(2);
>> structureElements[3].push_back(0);
>> structureElements[3].push_back(0);
>> structureElements[3].push_back(0);
>>
>> structureElements[4].push_back(0);
>> structureElements[4].push_back(2);
>> structureElements[4].push_back(1);
>> structureElements[4].push_back(1);
>> structureElements[4].push_back(1);
>> structureElements[4].push_back(2);
>> structureElements[4].push_back(0);
>> structureElements[4].push_back(0);
>>
>> structureElements[5].push_back(0);
>> structureElements[5].push_back(0);
>> structureElements[5].push_back(2);
>> structureElements[5].push_back(1);
>> structureElements[5].push_back(1);
>> structureElements[5].push_back(1);
>> structureElements[5].push_back(2);
>> structureElements[5].push_back(0);
>>
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(2);
>> structureElements[6].push_back(1);
>> structureElements[6].push_back(1);
>> structureElements[6].push_back(1);
>> structureElements[6].push_back(2);
>>
>> structureElements[7].push_back(2);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(2);
>> structureElements[7].push_back(1);
>> structureElements[7].push_back(1);
>> structureElements[7].push_back(1);
>>
>>
>> bool somethingGotDeleted(true);
>> while(somethingGotDeleted)
>> {
>> somethingGotDeleted = false;
>
> 126,133c218
> <
> <
> < int count = 1;
> < while(count)
> < {
> < count = 0;
> < ot.GoToBegin();
> < while( ! ot.IsAtEnd() )
> ---
>
>> for (int structrureElem=0; structrureElem<structureElements.size();
>
> ++structrureElem)
> 135,166c220,239
> < if (ot.GetCenterPixel())
> < {
> < PixelType genus;
> < genus = ot.GetPixel(offset1) + ot.GetPixel(offset2);
> < genus += ot.GetPixel(offset3) + ot.GetPixel(offset4);
> < genus += ot.GetPixel(offset5) + ot.GetPixel(offset6);
> < genus += ot.GetPixel(offset7) + ot.GetPixel(offset8);
> < if (genus != 1)
> < {
> < genus += ot.GetPixel(offset8) * ot.GetPixel(offset1) *
> ot.GetPixel(offset2);
> < genus += ot.GetPixel(offset2) * ot.GetPixel(offset3) *
> ot.GetPixel(offset4);
> < genus += ot.GetPixel(offset4) * ot.GetPixel(offset5) *
> ot.GetPixel(offset6);
> < genus += ot.GetPixel(offset6) * ot.GetPixel(offset7) *
> ot.GetPixel(offset8);
> < genus -= ot.GetPixel(offset1) * ot.GetPixel(offset2);
> < genus -= ot.GetPixel(offset2) * ot.GetPixel(offset3);
> < genus -= ot.GetPixel(offset3) * ot.GetPixel(offset4);
> < genus -= ot.GetPixel(offset4) * ot.GetPixel(offset5);
> < genus -= ot.GetPixel(offset5) * ot.GetPixel(offset6);
> < genus -= ot.GetPixel(offset6) * ot.GetPixel(offset7);
> < genus -= ot.GetPixel(offset7) * ot.GetPixel(offset8);
> < genus -= ot.GetPixel(offset8) * ot.GetPixel(offset1);
> < genus -= ot.GetPixel(offset8) * ot.GetPixel(offset2);
> < genus -= ot.GetPixel(offset2) * ot.GetPixel(offset4);
> < genus -= ot.GetPixel(offset4) * ot.GetPixel(offset6);
> < genus -= ot.GetPixel(offset6) * ot.GetPixel(offset8);
> < --genus;
> <
> < if ( genus == 0 )
> < {
> < ot.SetCenterPixel( genus );
> < ++count;
> < }
> ---
>
>> for (ot.GoToBegin(); ! ot.IsAtEnd(); ++ot)
>> {
>> if (ot.GetCenterPixel())
>> {
>> bool matches(true);
>> for (int k=0; matches && k<8; ++k)
>> {
>> int n = structureElements[structrureElem][k];
>> if (n<2)
>> {
>> int pixelOnOff = int(ot.GetPixel(offset[k]) > 0);
>> matches = (n == pixelOnOff);
>> }
>> }
>> if (matches)
>> {
>> ot.SetCenterPixel( PixelType(0) );
>> somethingGotDeleted = true;
>> }
>> }
>
> 168,170d240
> < }
> <
> < ++ot;
> 171a242,250
>
>>
>> // swap order to eliminate bias
>> for(int i=0; i<4; i++)
>> {
>> int num0 = drand48()*3.9999;
>> structureElements[num0*2].swap(structureElements[i*2]);
>> structureElements[num0*2+1].swap(structureElements[i*2+1]);
>> }
>> }
>
> 173d251
> < }
>
>
> Index: itkBinaryPruningImageFilter.txx
> ===================================================================
> RCS file:
> /cvsroot/Insight/Insight/Code/Algorithms/itkBinaryPruningImageFilter.txx,v
> retrieving revision 1.4
> diff -r1.4 itkBinaryPruningImageFilter.txx
> 118,125d117
> < typename NeighborhoodIteratorType::OffsetType offset1 = {{-1,-1}};
> < typename NeighborhoodIteratorType::OffsetType offset2 = {{-1,0}};
> < typename NeighborhoodIteratorType::OffsetType offset3 = {{-1,1 }};
> < typename NeighborhoodIteratorType::OffsetType offset4 = {{0,1}};
> < typename NeighborhoodIteratorType::OffsetType offset5 = {{1,1}};
> < typename NeighborhoodIteratorType::OffsetType offset6 = {{1,0}};
> < typename NeighborhoodIteratorType::OffsetType offset7 = {{1,-1}};
> < typename NeighborhoodIteratorType::OffsetType offset8 = {{0,-1}};
> 126a119
>
>> std::vector< std::vector<int> > structureElements(9);
>
> 128,147c121,227
> <
> < unsigned int count = 0;
> < while(count < m_Iteration)
> < {
> < ot.GoToBegin();
> < while( ! ot.IsAtEnd() )
> < {
> < if (ot.GetCenterPixel())
> < {
> < PixelType genus;
> < genus = ot.GetPixel(offset1) + ot.GetPixel(offset2);
> < genus += ot.GetPixel(offset3) + ot.GetPixel(offset4);
> < genus += ot.GetPixel(offset5) + ot.GetPixel(offset6);
> < genus += ot.GetPixel(offset7) + ot.GetPixel(offset8);
> < if (genus < 2)
> < {
> < genus = 0;
> < ot.SetCenterPixel( genus );
> < }
> < }
> ---
>
>> std::vector<typename NeighborhoodIteratorType::OffsetType> offset(8);
>> typename NeighborhoodIteratorType::OffsetType offset0 = {{-1,-1}};
>> offset[0] = offset0;
>> typename NeighborhoodIteratorType::OffsetType offset1 = {{-1,0}};
>> offset[1] = offset1;
>> typename NeighborhoodIteratorType::OffsetType offset2 = {{-1,1}};
>> offset[2] = offset2;
>> typename NeighborhoodIteratorType::OffsetType offset3 = {{0,1}};
>> offset[3] = offset3;
>> typename NeighborhoodIteratorType::OffsetType offset4 = {{1,1}};
>> offset[4] = offset4;
>> typename NeighborhoodIteratorType::OffsetType offset5 = {{1,0}};
>> offset[5] = offset5;
>> typename NeighborhoodIteratorType::OffsetType offset6 = {{1,-1}};
>> offset[6] = offset6;
>> typename NeighborhoodIteratorType::OffsetType offset7 = {{0,-1}};
>> offset[7] = offset7;
>>
>> // 3 4 5
>> // 2 6
>> // 1 8 7
>>
>> structureElements[0].push_back(2); // o o o
>> structureElements[0].push_back(0); // o o
>> structureElements[0].push_back(0); // x 1 x
>> structureElements[0].push_back(0);
>> structureElements[0].push_back(0);
>> structureElements[0].push_back(0);
>> structureElements[0].push_back(2);
>> structureElements[0].push_back(1);
>>
>> structureElements[1].push_back(1); // o o o
>> structureElements[1].push_back(2); // x o
>> structureElements[1].push_back(0); // 1 x o
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(0);
>> structureElements[1].push_back(2);
>>
>> structureElements[2].push_back(2);
>> structureElements[2].push_back(1);
>> structureElements[2].push_back(2);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(0);
>> structureElements[2].push_back(0);
>>
>> structureElements[3].push_back(0);
>> structureElements[3].push_back(2);
>> structureElements[3].push_back(1);
>> structureElements[3].push_back(2);
>> structureElements[3].push_back(0);
>> structureElements[3].push_back(0);
>> structureElements[3].push_back(0);
>> structureElements[3].push_back(0);
>>
>> structureElements[4].push_back(0);
>> structureElements[4].push_back(0);
>> structureElements[4].push_back(2);
>> structureElements[4].push_back(1);
>> structureElements[4].push_back(2);
>> structureElements[4].push_back(0);
>> structureElements[4].push_back(0);
>> structureElements[4].push_back(0);
>>
>> structureElements[5].push_back(0);
>> structureElements[5].push_back(0);
>> structureElements[5].push_back(0);
>> structureElements[5].push_back(2);
>> structureElements[5].push_back(1);
>> structureElements[5].push_back(2);
>> structureElements[5].push_back(0);
>> structureElements[5].push_back(0);
>>
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(0);
>> structureElements[6].push_back(2);
>> structureElements[6].push_back(1);
>> structureElements[6].push_back(2);
>> structureElements[6].push_back(0);
>>
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(0);
>> structureElements[7].push_back(2);
>> structureElements[7].push_back(1);
>> structureElements[7].push_back(2);
>>
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>> structureElements[8].push_back(0);
>>
>> int numGotDeleted = 3;
>> for (int iteration = 0; numGotDeleted > 2 && iteration < m_Iteration;
>
> ++iteration )
>
>> {
>> numGotDeleted = 0;
>
> 149c229,259
> < ++ot;
> ---
>
>> for (int structrureElem=0; structrureElem<structureElements.size();
>
> ++structrureElem)
>
>> {
>> for (ot.GoToBegin(); ! ot.IsAtEnd(); ++ot)
>> {
>> if (ot.GetCenterPixel())
>> {
>> bool matches(true);
>> for (int k=0; matches && k<8; ++k)
>> {
>> int n = structureElements[structrureElem][k];
>> if (n<2)
>> {
>> int pixelOnOff = int(ot.GetPixel(offset[k]) > 0);
>> matches = (n == pixelOnOff);
>> }
>> }
>> if (matches)
>> {
>> ot.SetCenterPixel( PixelType(0) );
>> ++numGotDeleted;
>> }
>> }
>> }
>> }
>>
>> // swap order to eliminate bias
>> for(int i=0; i<9; i++)
>> {
>> int num0 = drand48()*8.9999;
>> structureElements[num0].swap(structureElements[i]);
>> }
>
> 151,152c261
> < ++count;
> < }
> ---
>
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