#ifndef __itkTPGACLevelSetImageFilter_h
#define __itkTPGACLevelSetImageFilter_h
#include "itkGeodesicActiveContourLevelSetImageFilter.h"
namespace itk {
template <class TInputImage, class TFeatureImage, class TOutputPixelType = float >
class ITK_EXPORT TPGACLevelSetImageFilter : public GeodesicActiveContourLevelSetImageFilter< TInputImage, TFeatureImage, TOutputPixelType>
{
public:
typedef TPGACLevelSetImageFilter Self;
typedef GeodesicActiveContourLevelSetImageFilter<TInputImage, TFeatureImage, TOutputPixelType> Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
typedef TInputImage ImageType;
typedef typename ImageType::IndexType IndexType;
typedef typename Superclass::TimeStepType TimeStepType;
typedef typename Superclass::ValueType ValueType;
typedef typename Superclass::OutputImageType OutputImageType;
typedef typename Superclass::FeatureImageType FeatureImageType;
itkNewMacro(Self);
itkTypeMacro(TPGACLevelSetImageFilter, GeodesicActiveContourLevelSetImageFilter);
protected:
~TPGACLevelSetImageFilter() {}
TPGACLevelSetImageFilter();
virtual void PrintSelf(std::ostream &os, Indent indent) const;
TPGACLevelSetImageFilter(const Self &); // purposely not implemented
void operator=(const Self&); //purposely not implemented
inline virtual ValueType CalculateUpdateValue(const IndexType &idx, const TimeStepType &dt, const ValueType &value, const ValueType &change);
};
template <class TInputImage, class TFeatureImage, class TOutputType>
TPGACLevelSetImageFilter< TInputImage, TFeatureImage, TOutputType>
::TPGACLevelSetImageFilter()
: GeodesicActiveContourLevelSetImageFilter<TInputImage, TFeatureImage, TOutputType>()
{
// call parent constructor
}
template <class TInputImage, class TFeatureImage, class TOutputType>
void TPGACLevelSetImageFilter<TInputImage, TFeatureImage, TOutputType>
::PrintSelf(std::ostream &os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
}
// 6-neighbour table (including centre voxel, i.e. voxel 13)
static int nbh6Table[27][6] = {
{1, 3, 9, -1, -1, -1}, // 0
{0, 2, 4, 10, -1, -1}, // 1
{1, 5, 11, -1, -1, -1}, // 2
{0, 4, 6, 12, -1, -1}, // 3
{1, 3, 5, 7, 13, -1}, // 4
{2, 4, 8, 14, -1, -1}, // 5
{3, 7, 15, -1, -1, -1}, // 6
{4, 6, 8, 16, -1, -1}, // 7
{5, 7, 17, -1, -1, -1}, // 8
{0, 10, 12, 18, -1, -1}, // 9
{1, 9, 11, 13, 19, -1}, // 10
{2, 10, 14, 20, -1, -1}, // 11
{3, 9, 13, 15, 21, -1}, // 12
{4, 10, 12, 14, 16, 22}, // 13
{5, 11, 13, 17, 23, -1}, // 14
{6, 12, 16, 24, -1, -1}, // 15
{7, 13, 15, 17, 25, -1}, // 16
{8, 14, 16, 26, -1, -1}, // 17
{9, 19, 21, -1, -1, -1}, // 18
{10, 18, 20, 22, -1, -1}, // 19
{11, 19, 23, -1, -1, -1}, // 20
{12, 18, 22, 24, -1, -1}, // 21
{13, 19, 21, 23, 25, -1}, // 22
{14, 20, 22, 26, -1, -1}, // 23
{15, 21, 25, -1, -1, -1}, // 24
{16, 22, 24, 26, -1, -1}, // 25
{17, 23, 25, -1, -1, -1} // 26
};
// generated by gen26neighbourTable.py
// includes the centre voxel
static int nbh26Table[27][26] = {
{1, 3, 4, 9, 10, 12, 13, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 0
{0, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, -1, -1,-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 1
{1, 4, 5, 10, 11, 13, 14, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 2
{0, 1, 4, 6, 7, 9, 10, 12, 13, 15, 16, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 3
{0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 4
{1, 2, 4, 7, 8, 10, 11, 13, 14, 16, 17, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 5
{3, 4, 7, 12, 13, 15, 16, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 6
{3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 7
{4, 5, 7, 13, 14, 16, 17, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 8
{0, 1, 3, 4, 10, 12, 13, 18, 19, 21, 22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 9
{0, 1, 2, 3, 4, 5, 9, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 10
{1, 2, 4, 5, 10, 13, 14, 19, 20, 22, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 11
{0, 1, 3, 4, 6, 7, 9, 10, 13, 15, 16, 18, 19, 21, 22, 24, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 12
{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26}, // 13
{1, 2, 4, 5, 7, 8, 10, 11, 13, 16, 17, 19, 20, 22, 23, 25, 26, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 14
{3, 4, 6, 7, 12, 13, 16, 21, 22, 24, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 15
{3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 16
{4, 5, 7, 8, 13, 14, 16, 22, 23, 25, 26, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 17
{9, 10, 12, 13, 19, 21, 22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 18
{9, 10, 11, 12, 13, 14, 18, 20, 21, 22, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 19
{10, 11, 13, 14, 19, 22, 23, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 20
{9, 10, 12, 13, 15, 16, 18, 19, 22, 24, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 21
{9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 22
{10, 11, 13, 14, 16, 17, 19, 20, 22, 25, 26, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 23
{12, 13, 15, 16, 21, 22, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 24
{12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 26, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, // 25
{13, 14, 16, 17, 22, 23, 25, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1} // 26
};
static inline void fillLocal6Neighbours(int *srcNbh, int *dstNbh, int centre, int i0, int i1, int i2, int i3)
{
if (srcNbh[centre])
{
dstNbh[centre] = 1;
if (srcNbh[i0])
dstNbh[i0] = 1;
if (srcNbh[i1])
dstNbh[i1] = 1;
if (srcNbh[i2])
dstNbh[i2] = 1;
if (srcNbh[i3])
dstNbh[i3] = 1;
}
}
static void label6Neighbours(int *nbh, int *nbhlabels, int *nbhv, int curlabel, int idx)
{
// needs good initial value
int nbhIdx = 0;
// 6 neighbours max (also in the lookup table)
for (int i = 0; i < 6 && nbhIdx >= 0; i++)
{
nbhIdx = nbh6Table[idx][i];
// valid nbh index and the voxel exists and it hasn't been labeled
// yet
if (nbhIdx >= 0 && nbh[nbhIdx] && nbhlabels[nbhIdx] == 0)
{
// then label it
nbhlabels[nbhIdx] = curlabel;
// and record that it has been labeled, but needs to recursed
// we only do this if V doesn't have a value yet
if (nbhv[nbhIdx] == 0)
nbhv[nbhIdx] = 1;
}
}
}
static void label26Neighbours(int *nbh, int *nbhlabels, int *nbhv, int curlabel, int idx)
{
// needs good initial value
int nbhIdx = 0;
// 26 neighbours max (also in the lookup table)
for (int i = 0; i < 26 && nbhIdx >= 0; i++)
{
nbhIdx = nbh26Table[idx][i];
// valid nbh index and the voxel exists and it hasn't been labeled
// yet
if (nbhIdx >= 0 && nbh[nbhIdx] && nbhlabels[nbhIdx] == 0)
{
// then label it
nbhlabels[nbhIdx] = curlabel;
// and record that it has been labeled, but needs to recursed
// we only do this if V doesn't have a value yet
if (nbhv[nbhIdx] == 0)
nbhv[nbhIdx] = 1;
}
}
}
static inline int connectedComponents(int *nbh, int *nbhLabels, void (*labelNeighboursFunc)(int *, int *, int *, int, int) )
{
// create and init V struct
int nbhV[27];
memset(nbhV, 0, 27 * sizeof(int));
int curlabel = 1, assignedlabel = 0;
for (int i = 0; i < 27; i++)
{
// is there a voxel at this position, and has it not been labeled yet?
if (nbh[i] && nbhLabels[i] == 0)
{
// ON voxel not labeled yet
nbhLabels[i] = curlabel;
// this is to keep track of how many labels we've actually USED
assignedlabel = curlabel;
// mark it as being labeled
nbhV[i] = 1;
// now recurse through n26v finding ALL voxels of curlabel
// we continue doing this until there are no 1s, i.e. only
// 2s (neighbours examined) and 0s (no connected labels)
int onesFound;
do
{
onesFound = 0;
for (int j = 0; j < 27; j++)
{
if (nbhV[j] == 1)
{
onesFound = 1;
// this will label 6-neighbours and also flag the fact
// that they're labeled by setting a '1' in n26v
// neighbours that are already 2 will be left alone
labelNeighboursFunc(nbh, nbhLabels, nbhV, curlabel, j);
// now all neighbours of voxel j have also been labeled
nbhV[j] = 2;
}
} // for (int j = 0 ...
}
while (onesFound);
// if we find the next unlabeled thing, it has to be a new
// component by definition
curlabel++;
} // if (n26nbh[i] && n26labels[i] == 0) ...
} // for (int i = 0; i < 27 ...
return assignedlabel;
}
// you could also use epsilon from the levelset function
#define TPGAC_EPSILON 1e-5;
template <class TInputImage, class TFeatureImage, class TOutputType>
typename TPGACLevelSetImageFilter< TInputImage, TFeatureImage, TOutputType>::ValueType
TPGACLevelSetImageFilter<TInputImage, TFeatureImage, TOutputType>
::CalculateUpdateValue(const IndexType &idx, const TimeStepType &dt, const ValueType &value, const ValueType &change)
{
// * calculate new value
// * if new value has the same sign as current value, make the
// change
// * ELSE:
// * extract 3x3x3 neighbourhood of the current voxel
// * calculate N^2_6(x,X) and N^1_26(x,X')
// * count connected components (bail if more than 1)
// * if both 1, then x is simple point, allow change
// * if not (or bailed) x is not simple point
// * newValue = epsilon * sign(value) (epsilon small and positive)
ValueType temp_value = value + dt * change;
// sign is the same, we can return what we have
if (temp_value * value >= 0)
{
return temp_value;
}
// create a 3x3x3 nbh iterator over the output image
Size<3> radius = {1,1,1};
NeighborhoodIterator<OutputImageType>
nbhIterator(radius, this->GetOutput(),
this->GetOutput()->GetRequestedRegion());
// move the 3x3x3 nbh iterator over the current voxel
nbhIterator.SetLocation(idx);
// offset of centre pixel
//#define c 13
// transfer nbh to our interior/exterior nbh
int ieNbh[27];
for (int i = 0; i < 27; i++)
{
if (nbhIterator.GetPixel(i) >= 0)
{
// interior / inside / foreground
ieNbh[i] = 1;
}
else
{
// exterior / outside / background
ieNbh[i] = 0;
}
}
// N^2_6 == n26
// N^1_26 == n126
// now calculate N^2_6(interior) - we do this as straight-forward as
// possible for speed reasons
// first allocate and clear the nbh array
int n26nbh[27];
memset(n26nbh, 0, 27 * sizeof(int));
// if (ieNbh[4])
// {
// n26nbh[4] = 1;
// if (ieNbh[1]) n26nbh[1] = 1;
// if (ieNbh[3]) n26nbh[3] = 1;
// if (ieNbh[5]) n26nbh[5] = 1;
// if (ieNbh[7]) n26nbh[7] = 1;
// }
// then check the 6-neighbours of 4, i.e. 1, 3, 5, 7, but NOT the
// center voxel itself... that's explicitly excluded
fillLocal6Neighbours(ieNbh, n26nbh, 4, 1, 3, 5, 7);
fillLocal6Neighbours(ieNbh, n26nbh, 10, 1, 9, 11, 19);
fillLocal6Neighbours(ieNbh, n26nbh, 12, 3, 9, 15, 21);
fillLocal6Neighbours(ieNbh, n26nbh, 14, 5, 11, 17, 23);
fillLocal6Neighbours(ieNbh, n26nbh, 16, 7, 15, 17, 25);
fillLocal6Neighbours(ieNbh, n26nbh, 22, 19, 21, 23, 25);
// we should have a complete n^2_6(x,X) now...
// now determine number of connected components using
// fast method described in borgefors1997
int n26labels[27];
memset(n26labels, 0, 27 * sizeof(int));
int ncc6 = connectedComponents( n26nbh, n26labels, label6Neighbours);
if (ncc6 != 1)
{
// already T6(x,X) != 1, so we bail with epsilon * sign of old
// value... this saves us from the 26-neighbourhood background check
if (value < 0)
{
return -1 * TPGAC_EPSILON;
}
else
{
return TPGAC_EPSILON;
}
}
int n126nbh[27];
memset(n126nbh, 0, 27 * sizeof(int));
// we just invert ieNbh, because we're going to check the background
for (int i = 0; i < 27; i++)
{
n126nbh[i] = ! ieNbh[i];
}
// the centre voxel is NEVER used
n126nbh[13] = 0;
int n126labels[27];
memset(n126labels, 0, 27 * sizeof(int));
int ncc26 = connectedComponents(n126nbh, n126labels, label26Neighbours);
if (ncc26 != 1)
{
// T26(x,X') != 1, so we bail with epsilon * sign of old
// value...
if (value < 0)
{
return -1 * TPGAC_EPSILON;
}
else
{
return TPGAC_EPSILON;
}
}
// this means the voxel that is to be added is simple... we can just
// return the new value
return temp_value;
}
} // end namespace itk
//#if ITK_MANUAL_INSTANTIATION
//#include "itkTPGACLevelSetImageFilter.txx"
//#endif
#endif