skeletonizer.h

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// Copyright (C) 2005-2008 Washington University in St Louis, Baylor College of Medicine.  All rights reserved
// Author:        Sasakthi S. Abeysinghe (sasakthi@gmail.com)
// Description:   Performs skeletonization on a grayscale volume
 
#include "volume.h"
using namespace wustl_mm::SkeletonMaker;
 
#ifndef GRAYSKELETONCPP_VOLUME_SKELETONIZER_H
#define GRAYSKELETONCPP_VOLUME_SKELETONIZER_H
 
const int MAX_GAUSSIAN_FILTER_RADIUS = 10;
const int DEFAULT_SKELETON_DIRECTION_RADIUS = 3;
 
namespace wustl_mm {
        namespace GraySkeletonCPP {
 
                class VolumeSkeletonizer
                {
                public:
                        VolumeSkeletonizer(int pointRadius, int curveRadius, int surfaceRadius, int skeletonDirectionRadius=DEFAULT_SKELETON_DIRECTION_RADIUS);
                        ~VolumeSkeletonizer();
                        static Volume * PerformPureJuSkeletonization(Volume * imageVol, string outputPath, double threshold, int minCurveWidth, int minSurfaceWidth);
                        //Volume * PerformImmersionSkeletonizationAndPruning(Volume * sourceVol, Volume * preserveVol, double startGray, double endGray, double stepSize, int smoothingIterations, int smoothingRadius, int minCurveSize, int minSurfaceSize, int maxCurveHole, int maxSurfaceHole, string outputPath, bool doPruning, double pointThreshold, double curveThreshold, double surfaceThreshold);
                        static void CleanUpSkeleton(Volume * skeleton, int minNumVoxels = 4, float valueThreshold = 0.5); //Added for EMAN2
                        static void MarkSurfaces(Volume* skeleton); //Added for EMAN2
                        
                private:
                        static bool Are26Neighbors(Vec3<int> u, Vec3<int> v); //Added for EMAN2
                        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);
 
                        static const char THINNING_CLASS_SURFACE_PRESERVATION;
                        static const char THINNING_CLASS_CURVE_PRESERVATION_2D;
                        static const char THINNING_CLASS_CURVE_PRESERVATION;
                        static const char THINNING_CLASS_POINT_PRESERVATION;
                        static const char THINNING_CLASS_TOPOLOGY_PRESERVATION;
                        static const char PRUNING_CLASS_PRUNE_SURFACES;
                        static const char PRUNING_CLASS_PRUNE_CURVES;
                        static const char PRUNING_CLASS_PRUNE_POINTS;
 
                        //MathLib * math;
                        //NormalFinder * surfaceNormalFinder;
                        //ProbabilityDistribution3D gaussianFilterPointRadius;
                        //ProbabilityDistribution3D gaussianFilterCurveRadius;
                        //ProbabilityDistribution3D gaussianFilterSurfaceRadius;
                        //ProbabilityDistribution3D gaussianFilterMaxRadius;
                        //ProbabilityDistribution3D uniformFilterSkeletonDirectionRadius;
                        int pointRadius;
                        int curveRadius;
                        int surfaceRadius;
                        int skeletonDirectionRadius;
                };
        }
}
 
#endif