wustl_mm::GraySkeletonCPP::VolumeSkeletonizer Class Reference

#include <skeletonizer.h>

Public Member Functions
	VolumeSkeletonizer (int pointRadius, int curveRadius, int surfaceRadius, int skeletonDirectionRadius=DEFAULT_SKELETON_DIRECTION_RADIUS)
	~VolumeSkeletonizer ()

Static Public Member Functions
static Volume *	PerformPureJuSkeletonization (Volume *imageVol, string outputPath, double threshold, int minCurveWidth, int minSurfaceWidth)
static void	CleanUpSkeleton (Volume *skeleton, int minNumVoxels=4, float valueThreshold=0.5)
static void	MarkSurfaces (Volume *skeleton)

Static Private Member Functions
static bool	Are26Neighbors (Vec3< int > u, Vec3< int > v)
static Volume *	GetJuSurfaceSkeleton (Volume *sourceVolume, Volume *preserve, double threshold)
static Volume *	GetJuCurveSkeleton (Volume *sourceVolume, Volume *preserve, double threshold, bool is3D)
static Volume *	GetJuTopologySkeleton (Volume *sourceVolume, Volume *preserve, double threshold)
static void	PruneCurves (Volume *sourceVolume, int pruneLength)
static void	PruneSurfaces (Volume *sourceVolume, int pruneLength)
static void	VoxelOr (Volume *sourceAndDestVolume1, Volume *sourceVolume2)
static Volume *	GetJuThinning (Volume *sourceVolume, Volume *preserve, double threshold, char thinningClass)

Private Attributes
int	pointRadius
int	curveRadius
int	surfaceRadius
int	skeletonDirectionRadius

Static Private Attributes
static const char	THINNING_CLASS_SURFACE_PRESERVATION = 4
static const char	THINNING_CLASS_CURVE_PRESERVATION_2D = 3
static const char	THINNING_CLASS_CURVE_PRESERVATION = 2
static const char	THINNING_CLASS_POINT_PRESERVATION = 1
static const char	THINNING_CLASS_TOPOLOGY_PRESERVATION = 0
static const char	PRUNING_CLASS_PRUNE_SURFACES = 5
static const char	PRUNING_CLASS_PRUNE_CURVES = 6
static const char	PRUNING_CLASS_PRUNE_POINTS = 7

Detailed Description

Definition at line 17 of file skeletonizer.h.

Constructor & Destructor Documentation

VolumeSkeletonizer()

VolumeSkeletonizer::VolumeSkeletonizer	(	int	pointRadius,
		int	curveRadius,
		int	surfaceRadius,
		int	skeletonDirectionRadius = DEFAULT_SKELETON_DIRECTION_RADIUS
	)

Definition at line 20 of file skeletonizer.cpp.

                                                                                                                                       {
//                      math = new MathLib();
//                      surfaceNormalFinder = new NormalFinder();
                        this->pointRadius = pointRadius;
                        this->curveRadius = curveRadius;
                        this->surfaceRadius = surfaceRadius;
                        this->skeletonDirectionRadius = skeletonDirectionRadius;
 
//                      gaussianFilterPointRadius.radius = pointRadius;
//                      math->GetBinomialDistribution(gaussianFilterPointRadius);
//
//                      gaussianFilterCurveRadius.radius = curveRadius;
//                      math->GetBinomialDistribution(gaussianFilterCurveRadius);
//
//                      gaussianFilterSurfaceRadius.radius = surfaceRadius;
//                      math->GetBinomialDistribution(gaussianFilterSurfaceRadius);
//
//                      gaussianFilterMaxRadius.radius = MAX_GAUSSIAN_FILTER_RADIUS;
//                      math->GetBinomialDistribution(gaussianFilterMaxRadius);
//
//                      uniformFilterSkeletonDirectionRadius.radius = skeletonDirectionRadius;
//                      math->GetUniformDistribution(uniformFilterSkeletonDirectionRadius);
                }

References curveRadius, pointRadius, skeletonDirectionRadius, and surfaceRadius.

~VolumeSkeletonizer()

VolumeSkeletonizer::~VolumeSkeletonizer

(

)

Definition at line 44 of file skeletonizer.cpp.

                                                        {
                        //delete math;
                        //delete surfaceNormalFinder;
                }

Member Function Documentation

Are26Neighbors()

bool VolumeSkeletonizer::Are26Neighbors ( Vec3< int >  u, Vec3< int >  v  )

staticprivate

Definition at line 54 of file skeletonizer.cpp.

                                                                                {
                        if ( u==v || abs(u[0]-v[0])>1 || abs(u[1]-v[1])>1 || abs(u[2]-v[2])>1) {
                                return false;
                        } else { 
                                return true;
                        }
                }

Referenced by CleanUpSkeleton().

CleanUpSkeleton()

void VolumeSkeletonizer::CleanUpSkeleton ( Volume *  skeleton, int  minNumVoxels = 4, float  valueThreshold = 0.5  )

static

Definition at line 94 of file skeletonizer.cpp.

                                                                                                                  {
                        
                        //Get the indices of voxels that are above the threshold, i.e. part of the skeleton
                        list< Vec3<int> > skel_indices;
                        Vec3<int> voxel_indices;
                        for (int k=0; k < skeleton->getSizeZ(); k++) {
                                for (int j=0; j < skeleton->getSizeY(); j++) {
                                        for (int i=0; i < skeleton->getSizeX(); i++) {
                                                if (skeleton->getDataAt(i,j,k) > valueThreshold) {
                                                        voxel_indices.set_value(i,j,k);
                                                        skel_indices.push_front(voxel_indices);
                                                }
                                        }
                                }
                        }
                        
                        vector< Vec3<int> > segment; //the coordinates for a set of connected skeleton voxels
                        list< Vec3<int> >::iterator itr;
                        
                        /*
                         1. Group the connected voxels together
                         2. Check the number of voxels in that group
                         3. If below the minimum number of voxels, remove them from the skeleton
                         4. Repeat until all the voxels in the skeleton have been grouped (possibly alone if not connected)
                        */
                        while (skel_indices.size() > 0) {
                                segment.clear();
                                segment.push_back(skel_indices.front());
                                skel_indices.pop_front();
                                // group connected voxels -- each member of segment neighbors at least one other member of segment
                                //For each voxel in segment, we test if each voxel in skel_indices is a neighbor
                                for (unsigned int seg_ix=0; seg_ix < segment.size(); seg_ix++) { 
                                        for (itr = skel_indices.begin(); itr != skel_indices.end(); itr++) {
                                                
                                                if (Are26Neighbors(segment[seg_ix], *itr)) {
                                                        segment.push_back(*itr);
                                                        skel_indices.erase(itr);
                                                }
                                        }
                                } //Now, a segment is complete
                                
 
                                //If the region of connected voxels is too small, remove them from the map
                                if (segment.size() < static_cast<unsigned int>(minNumVoxels)) {
                                        for (unsigned int ix=0; ix<segment.size(); ix++) {
                                                skeleton->setDataAt(segment[ix][0], segment[ix][1], segment[ix][2],0.0f);
                                        }
                                }
 
                        }
                }

References Are26Neighbors(), wustl_mm::SkeletonMaker::Volume::getDataAt(), wustl_mm::SkeletonMaker::Volume::getSizeX(), wustl_mm::SkeletonMaker::Volume::getSizeY(), wustl_mm::SkeletonMaker::Volume::getSizeZ(), EMAN::Vec3< Type >::set_value(), and wustl_mm::SkeletonMaker::Volume::setDataAt().

GetJuCurveSkeleton()

Volume * VolumeSkeletonizer::GetJuCurveSkeleton ( Volume *  sourceVolume, Volume *  preserve, double  threshold, bool  is3D  )

staticprivate

Definition at line 200 of file skeletonizer.cpp.

                                                                                                                                    {
                        char thinningClass = is3D ? THINNING_CLASS_CURVE_PRESERVATION : THINNING_CLASS_CURVE_PRESERVATION_2D;
                        return GetJuThinning(sourceVolume, preserve, threshold, thinningClass);
                }

References GetJuThinning(), THINNING_CLASS_CURVE_PRESERVATION, and THINNING_CLASS_CURVE_PRESERVATION_2D.

Referenced by PerformPureJuSkeletonization().

GetJuSurfaceSkeleton()

Volume * VolumeSkeletonizer::GetJuSurfaceSkeleton ( Volume *  sourceVolume, Volume *  preserve, double  threshold  )

staticprivate

Definition at line 205 of file skeletonizer.cpp.

                                                                                                                           {
                        return GetJuThinning(sourceVolume, preserve, threshold, THINNING_CLASS_SURFACE_PRESERVATION);
                }

References GetJuThinning(), and THINNING_CLASS_SURFACE_PRESERVATION.

Referenced by PerformPureJuSkeletonization().

GetJuThinning()

Volume * VolumeSkeletonizer::GetJuThinning ( Volume *  sourceVolume, Volume *  preserve, double  threshold, char  thinningClass  )

staticprivate

Definition at line 213 of file skeletonizer.cpp.

                                                                                                                                         {
                        Volume * thinnedVolume = new Volume(sourceVolume->getSizeX(), sourceVolume->getSizeY(), sourceVolume->getSizeZ(), 0, 0, 0, sourceVolume);
                        switch(thinningClass) {
                                case THINNING_CLASS_SURFACE_PRESERVATION :
                                        thinnedVolume->surfaceSkeletonPres((float)threshold, preserve);
                                        break;
                                case THINNING_CLASS_CURVE_PRESERVATION :
                                        thinnedVolume->curveSkeleton((float)threshold, preserve);
                                        break;
                                case THINNING_CLASS_CURVE_PRESERVATION_2D :
                                        thinnedVolume->curveSkeleton2D((float)threshold, preserve);
                                        break;
                                case THINNING_CLASS_TOPOLOGY_PRESERVATION :
                                        thinnedVolume->skeleton((float)threshold, preserve, preserve);
                        }
                        return thinnedVolume;
                }

References wustl_mm::SkeletonMaker::Volume::curveSkeleton(), wustl_mm::SkeletonMaker::Volume::curveSkeleton2D(), wustl_mm::SkeletonMaker::Volume::getSizeX(), wustl_mm::SkeletonMaker::Volume::getSizeY(), wustl_mm::SkeletonMaker::Volume::getSizeZ(), wustl_mm::SkeletonMaker::Volume::skeleton(), wustl_mm::SkeletonMaker::Volume::surfaceSkeletonPres(), THINNING_CLASS_CURVE_PRESERVATION, THINNING_CLASS_CURVE_PRESERVATION_2D, THINNING_CLASS_SURFACE_PRESERVATION, and THINNING_CLASS_TOPOLOGY_PRESERVATION.

Referenced by GetJuCurveSkeleton(), GetJuSurfaceSkeleton(), and GetJuTopologySkeleton().

GetJuTopologySkeleton()

Volume * VolumeSkeletonizer::GetJuTopologySkeleton ( Volume *  sourceVolume, Volume *  preserve, double  threshold  )

staticprivate

Definition at line 209 of file skeletonizer.cpp.

                                                                                                                            {
                        return GetJuThinning(sourceVolume, preserve, threshold, THINNING_CLASS_TOPOLOGY_PRESERVATION);
                }

References GetJuThinning(), and THINNING_CLASS_TOPOLOGY_PRESERVATION.

Referenced by PerformPureJuSkeletonization().

MarkSurfaces()

void VolumeSkeletonizer::MarkSurfaces ( Volume *  skeleton )

static

Definition at line 63 of file skeletonizer.cpp.

                                                                      {
 
                        int faceNeighbors[3][3][3] = {  {{1,0,0}, {1,0,1}, {0,0,1}},
                                                                                        {{1,0,0}, {1,1,0}, {0,1,0}},
                                                                                        {{0,1,0}, {0,1,1}, {0,0,1}} };
                        int indices[4];
                        bool faceFound;
 
                        for (int z = 0; z < skeleton->getSizeZ(); z++) {
                                for (int y = 0; y < skeleton->getSizeY(); y++) {
                                        for (int x = 0; x < skeleton->getSizeX(); x++) {
 
                                                indices[0] = skeleton->getIndex(x,y,z);
                                                for (int n = 0; n < 3; n++) {
                                                        faceFound = true;
                                                        for (int m = 0; m < 3; m++) {
                                                                indices[m+1] = skeleton->getIndex(x+faceNeighbors[n][m][0], y+faceNeighbors[n][m][1], z+faceNeighbors[n][m][2]);
                                                                faceFound = faceFound && (skeleton->getDataAt(indices[m+1]) > 0);
                                                        }
                                                        if (faceFound) {
                                                                for (int m = 0; m < 4; m++) {
                                                                        skeleton->setDataAt(indices[m], SURFACE_VAL);
                                                                }
                                                        }
                                                }
 
                                        }
                                }
                        }
                }

References wustl_mm::SkeletonMaker::Volume::getDataAt(), wustl_mm::SkeletonMaker::Volume::getIndex(), wustl_mm::SkeletonMaker::Volume::getSizeX(), wustl_mm::SkeletonMaker::Volume::getSizeY(), wustl_mm::SkeletonMaker::Volume::getSizeZ(), wustl_mm::SkeletonMaker::Volume::setDataAt(), SURFACE_VAL, x, and y.

PerformPureJuSkeletonization()

Volume * VolumeSkeletonizer::PerformPureJuSkeletonization ( Volume *  imageVol, string  outputPath, double  threshold, int  minCurveWidth, int  minSurfaceWidth  )

static

Definition at line 148 of file skeletonizer.cpp.

                                                                                                                                                             {
                        imageVol->pad(MAX_GAUSSIAN_FILTER_RADIUS, 0);
                        Volume * preservedVol = new Volume(imageVol->getSizeX(), imageVol->getSizeY(), imageVol->getSizeZ());
                        Volume * surfaceVol;
                        Volume * curveVol;
                        Volume * topologyVol;
                        //printf("\t\t\tUSING THRESHOLD : %f\n", threshold);
                        // Skeletonizing while preserving surface features curve features and topology
                        surfaceVol = GetJuSurfaceSkeleton(imageVol, preservedVol, threshold);
                        PruneSurfaces(surfaceVol, minSurfaceWidth);
                        VoxelOr(preservedVol, surfaceVol);
                        curveVol = VolumeSkeletonizer::GetJuCurveSkeleton(imageVol, preservedVol, threshold, true);
                        VolumeSkeletonizer::PruneCurves(curveVol, minCurveWidth);
                        VoxelOr(preservedVol, curveVol);
 
                        topologyVol = VolumeSkeletonizer::GetJuTopologySkeleton(imageVol, preservedVol, threshold);
 
                        //Code below by Ross as a test -- to replace GetJuTopologySkeleton return value
//                      int curveVolMax = curveVol->getVolumeData()->GetMaxIndex();
//                      int surfaceVolMax = curveVol->getVolumeData()->GetMaxIndex();
//                      int maximum = curveVolMax <= surfaceVolMax? curveVolMax : surfaceVolMax;
//                      if (curveVolMax != surfaceVolMax)
//                              cout << "Curve Skeleton: " << curveVolMax << '\n' << "Surface Skeleton" << surfaceVolMax << endl;
//                      topologyVol = new Volume(curveVol->getSizeX(), curveVol->getSizeY(), curveVol->getSizeZ());
//                      float val, cval, sval;
//                      for (int i = 0; i < maximum; i++)
//                      {
//                              cval = float(curveVol->getDataAt(i));
//                              sval = float(surfaceVol->getDataAt(i));
//                              if (cval && sval)
//                                      val = 100; //Something went wrong!
//                              else if (cval)
//                                      val = 1;
//                              else if (sval)
//                                      val = -1;
//                              else
//                                      val = 0;
//                              topologyVol->setDataAt(i, val);
//                      }
 
 
 
 
 
                        imageVol->pad(-MAX_GAUSSIAN_FILTER_RADIUS, 0);
                        topologyVol->pad(-MAX_GAUSSIAN_FILTER_RADIUS, 0);
                        delete preservedVol;
                        delete surfaceVol;
                        delete curveVol;
                        return topologyVol;
                }

References GetJuCurveSkeleton(), GetJuSurfaceSkeleton(), GetJuTopologySkeleton(), wustl_mm::SkeletonMaker::Volume::getSizeX(), wustl_mm::SkeletonMaker::Volume::getSizeY(), wustl_mm::SkeletonMaker::Volume::getSizeZ(), MAX_GAUSSIAN_FILTER_RADIUS, wustl_mm::SkeletonMaker::Volume::pad(), PruneCurves(), PruneSurfaces(), and VoxelOr().

PruneCurves()

void VolumeSkeletonizer::PruneCurves ( Volume *  sourceVolume, int  pruneLength  )

staticprivate

Definition at line 231 of file skeletonizer.cpp.

                                                                                           {
                        sourceVolume->erodeHelix(pruneLength);
                }

References wustl_mm::SkeletonMaker::Volume::erodeHelix().

Referenced by PerformPureJuSkeletonization().

PruneSurfaces()

void VolumeSkeletonizer::PruneSurfaces ( Volume *  sourceVolume, int  pruneLength  )

staticprivate

Definition at line 234 of file skeletonizer.cpp.

                                                                                             {
                        sourceVolume->erodeSheet(pruneLength);
                }

References wustl_mm::SkeletonMaker::Volume::erodeSheet().

Referenced by PerformPureJuSkeletonization().

VoxelOr()

void VolumeSkeletonizer::VoxelOr ( Volume *  sourceAndDestVolume1, Volume *  sourceVolume2  )

staticprivate

Definition at line 238 of file skeletonizer.cpp.

                                                                                                     {
                        if(sourceVolume2 != NULL) {
                                for(int x = 0; x < sourceAndDestVolume1->getSizeX(); x++) {
                                        for(int y = 0; y < sourceAndDestVolume1->getSizeY(); y++) {
                                                for(int z = 0; z < sourceAndDestVolume1->getSizeZ(); z++) {
                                                        sourceAndDestVolume1->setDataAt(x, y, z, max(sourceAndDestVolume1->getDataAt(x, y, z), sourceVolume2->getDataAt(x, y, z)));
                                                }
                                        }
                                }
                        }
                }

References wustl_mm::SkeletonMaker::Volume::getDataAt(), wustl_mm::SkeletonMaker::Volume::getSizeX(), wustl_mm::SkeletonMaker::Volume::getSizeY(), wustl_mm::SkeletonMaker::Volume::getSizeZ(), wustl_mm::SkeletonMaker::Volume::setDataAt(), x, and y.

Referenced by PerformPureJuSkeletonization().

Member Data Documentation

curveRadius

int wustl_mm::GraySkeletonCPP::VolumeSkeletonizer::curveRadius

private

Definition at line 54 of file skeletonizer.h.

Referenced by VolumeSkeletonizer().

pointRadius

int wustl_mm::GraySkeletonCPP::VolumeSkeletonizer::pointRadius

private

Definition at line 53 of file skeletonizer.h.

Referenced by VolumeSkeletonizer().

PRUNING_CLASS_PRUNE_CURVES

const char VolumeSkeletonizer::PRUNING_CLASS_PRUNE_CURVES = 6

staticprivate

Definition at line 43 of file skeletonizer.h.

PRUNING_CLASS_PRUNE_POINTS

const char VolumeSkeletonizer::PRUNING_CLASS_PRUNE_POINTS = 7

staticprivate

Definition at line 44 of file skeletonizer.h.

PRUNING_CLASS_PRUNE_SURFACES

const char VolumeSkeletonizer::PRUNING_CLASS_PRUNE_SURFACES = 5

staticprivate

Definition at line 42 of file skeletonizer.h.

skeletonDirectionRadius

int wustl_mm::GraySkeletonCPP::VolumeSkeletonizer::skeletonDirectionRadius

private

Definition at line 56 of file skeletonizer.h.

Referenced by VolumeSkeletonizer().

surfaceRadius

int wustl_mm::GraySkeletonCPP::VolumeSkeletonizer::surfaceRadius

private

Definition at line 55 of file skeletonizer.h.

Referenced by VolumeSkeletonizer().

THINNING_CLASS_CURVE_PRESERVATION

const char VolumeSkeletonizer::THINNING_CLASS_CURVE_PRESERVATION = 2

staticprivate

Definition at line 39 of file skeletonizer.h.

Referenced by GetJuCurveSkeleton(), and GetJuThinning().

THINNING_CLASS_CURVE_PRESERVATION_2D

const char VolumeSkeletonizer::THINNING_CLASS_CURVE_PRESERVATION_2D = 3

staticprivate

Definition at line 38 of file skeletonizer.h.

Referenced by GetJuCurveSkeleton(), and GetJuThinning().

THINNING_CLASS_POINT_PRESERVATION

const char VolumeSkeletonizer::THINNING_CLASS_POINT_PRESERVATION = 1

staticprivate

Definition at line 40 of file skeletonizer.h.

THINNING_CLASS_SURFACE_PRESERVATION

const char VolumeSkeletonizer::THINNING_CLASS_SURFACE_PRESERVATION = 4

staticprivate

Definition at line 37 of file skeletonizer.h.

Referenced by GetJuSurfaceSkeleton(), and GetJuThinning().

THINNING_CLASS_TOPOLOGY_PRESERVATION

const char VolumeSkeletonizer::THINNING_CLASS_TOPOLOGY_PRESERVATION = 0

staticprivate

Definition at line 41 of file skeletonizer.h.

Referenced by GetJuThinning(), and GetJuTopologySkeleton().

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The documentation for this class was generated from the following files:

• skeletonizer.h
• skeletonizer.cpp