foldgraphattributes.h

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#ifndef AIMS_FOLDGRAPH_FOLDGRAPHATTRIBUTES
#define AIMS_FOLDGRAPH_FOLDGRAPHATTRIBUTES

#include <aims/data/data.h>
#include <aims/mesh/mesher.h>

class Graph;

namespace aims
{
  class AffineTransformation3d;
  template <typename T> class BucketMap;

  class FoldGraphAttributes
  {
  public:
    FoldGraphAttributes( const AimsData<int16_t> & skel, Graph & graph, 
                         const AffineTransformation3d *talairachAffineTransformation3d = 0,
                         int16_t inside = 0, int16_t outside = 11, 
                         bool withmeshes = true,
                         const std::vector<int> & graphversion
                             = std::vector<int>() );
    void cleanup();
    void doAll();

    void makeMeshes();
    void makeGlobalAttributes();
    void makeSimpleSurfaceAttributes();
    void makeJunctionAttributes();
    void makePliDePassageAttributes();
    void makeCorticalRelationAttributes();
    void makeSummaryGlobalAttributes();

    AimsData<int16_t> &getDepth();
    const AimsData<int16_t> &getDepth() const;
    AimsData<int16_t> &getNDepth();
    const AimsData<int16_t> &getNDepth() const;
    AimsData<float> &getBrainDepth();
    AimsData<float> &getBrainDepthGradX();
    AimsData<float> &getBrainDepthGradY();
    AimsData<float> &getBrainDepthGradZ();
    const AimsData<float> &getBrainDepth() const;
    const AimsData<float> &getBrainDepthGradX() const;
    const AimsData<float> &getBrainDepthGradY() const;
    const AimsData<float> &getBrainDepthGradZ() const;
    AimsData<float> &getDilatedDepth();
    AimsData<float> &getDilatedDepthGradX();
    AimsData<float> &getDilatedDepthGradY();
    AimsData<float> &getDilatedDepthGradZ();
    const AimsData<float> &getDilatedDepth() const;
    const AimsData<float> &getDilatedDepthGradX() const;
    const AimsData<float> &getDilatedDepthGradY() const;
    const AimsData<float> &getDilatedDepthGradZ() const;
    float getDepthfactor() const;
    void prepareDepthMap();
    void prepareBrainDepthMap();
    AimsData<int16_t> rebuildCorticalRelations();
    std::vector<int> graphVersion() const;
    void thickness( const BucketMap<float> & midinterfaceDistances,
                    const carto::VolumeRef<int16_t> voronoi );
    void greyAndCSFVolumes( const carto::VolumeRef<int16_t> gw,
                            const carto::VolumeRef<int16_t> voronoi );
    void setMaxThreads( int mt );
    int maxThreads() const { return _maxthreads; }
    Mesher & mesher() { return _mesher; }

  private:
    class DistanceMapThreadContext;
    friend class DistanceMapThreadContext;

    void prepareNativeDepthMap();
    void prepareNormalizedDepthMap( const AimsData<int16_t> & th );
    void prepareDilatedDepthMap( const AimsData<int16_t> & th );
    void prepareGradientX();
    void prepareGradientY();
    void prepareGradientZ();
    void prepareBrainGradientX();
    void prepareBrainGradientY();
    void prepareBrainGradientZ();

    AimsData<int16_t>   _skel;
    Graph               & _graph;
    int16_t             _inside;
    int16_t             _outside;
    const AffineTransformation3d        *_motion;
    AimsData<int16_t>   _depth;
    AimsData<int16_t>   _ndepth;
    AimsData<float>     _braindepthmap;
    AimsData<float>     _braindepthmap_gradX;
    AimsData<float>     _braindepthmap_gradY;
    AimsData<float>     _braindepthmap_gradZ;
    AimsData<float>     _dilated_depthmap;
    AimsData<float>     _dilated_depthmap_gradX;
    AimsData<float>     _dilated_depthmap_gradY;
    AimsData<float>     _dilated_depthmap_gradZ;
    bool                _domeshes;
    std::vector<int>    _graphversion;
    int                 _maxthreads;
    Mesher              _mesher;
  };

}

#endif