nightly/itkShortestPathImageFilter_8h_source.html

/*============================================================================


The Medical Imaging Interaction Toolkit (MITK)


Copyright (c) German Cancer Research Center (DKFZ)

All rights reserved.


Use of this source code is governed by a 3-clause BSD license that can be

found in the LICENSE file.


============================================================================*/

#ifndef __itkShortestPathImageFilter_h

#define __itkShortestPathImageFilter_h


#include "itkImageToImageFilter.h"

#include "itkShortestPathCostFunction.h"

#include "itkShortestPathNode.h"

#include <itkImageRegionIteratorWithIndex.h>


#include <itkMacro.h>


// ------- INFORMATION ----------

// void SetInput( ItkImage ) // Compulsory

// void SetStartIndex (const IndexType & StartIndex); // Compulsory

// void SetEndIndex(const IndexType & EndIndex); // Compulsory

// void SetFullNeighborsMode(bool) // Optional (default=false), if false N4, if true N26

// void SetActivateTimeOut(bool) // Optional (default=false), for debug issues: after 30s algorithms terminates. You can

// have a look at the VectorOrderImage to see how far it came

// void SetMakeOutputImage(bool) // Optional (default=true), Generate an outputimage of the path. You can also get the

// path directoy with GetVectorPath()

// void SetCalcAllDistances(bool) // Optional (default=false), Calculate Distances over the whole image. CAREFUL,

// algorithm time extends a lot. Necessary for GetDistanceImage

// void SetStoreVectorOrder(bool) // Optional (default=false), Stores in which order the pixels were checked. Necessary

// for GetVectorOrderImage

// void AddEndIndex(const IndexType & EndIndex) //Optional. By calling this function you can add several endpoints! The

// algorithm will look for several shortest Pathes. From Start to all Endpoints.

//

// std::vector< itk::Index<3> > GetVectorPath(); // returns the shortest path as vector

// std::vector< std::vector< itk::Index<3> > GetMultipleVectorPathe(); // returns a vector of shortest Pathes (which are

// vectors of points)

// GetDistanceImage // Returns the distance image

// GetVectorOrderIMage // Returns the Vector Order image

//

// EXAMPLE USE

// pleae see qmitkmitralvalvesegmentation4dtee bundle


namespace itk

{

  template <class TInputImageType, class TOutputImageType>

  class ShortestPathImageFilter : public ImageToImageFilter<TInputImageType, TOutputImageType>

  {

  public:

    // Standard Typedefs

    typedef ShortestPathImageFilter Self;

    typedef ImageToImageFilter<TInputImageType, TOutputImageType> Superclass;

    typedef SmartPointer<Self> Pointer;

    typedef SmartPointer<const Self> ConstPointer;


    // Typdefs for metric

    typedef ShortestPathCostFunction<TInputImageType> CostFunctionType;

    typedef typename CostFunctionType::Pointer CostFunctionTypePointer;


    // More typdefs for convenience

    typedef TInputImageType InputImageType;

    typedef typename TInputImageType::Pointer InputImagePointer;

    typedef typename TInputImageType::PixelType InputImagePixelType;

    typedef typename TInputImageType::SizeType InputImageSizeType;

    typedef typename TInputImageType::IndexType IndexType;

    typedef typename itk::ImageRegionIteratorWithIndex<InputImageType> InputImageIteratorType;


    typedef TOutputImageType OutputImageType;

    typedef typename TOutputImageType::Pointer OutputImagePointer;

    typedef typename TOutputImageType::PixelType OutputImagePixelType;

    typedef typename TOutputImageType::IndexType OutputImageIndexType;

    typedef ImageRegionIteratorWithIndex<OutputImageType> OutputImageIteratorType;

    typedef itk::ShapedNeighborhoodIterator<TInputImageType> itkShapedNeighborhoodIteratorType;


    // New Macro for smartpointer instantiation

    itkFactorylessNewMacro(Self);

    itkCloneMacro(Self);


    // Run-time type information

    itkTypeMacro(ShortestPathImageFilter, ImageToImageFilter);


    // Display

    void PrintSelf(std::ostream &os, Indent indent) const override;


    // Compare function for A_STAR

    struct CompareNodeStar

    {

      bool operator()(ShortestPathNode *a, ShortestPathNode *b) { return (a->distAndEst > b->distAndEst); }

    };


    // \brief Set Starpoint for ShortestPath Calculation

    void SetStartIndex(const IndexType &StartIndex);


    // \brief Adds Endpoint for multiple ShortestPath Calculation

    void AddEndIndex(const IndexType &index);


    // \brief Set Endpoint for ShortestPath Calculation

    void SetEndIndex(const IndexType &EndIndex);


    // \brief Set FullNeighborsMode. false = no diagonal neighbors, in 2D this means N4 Neigborhood. true = would be N8

    // in 2D

    itkSetMacro(FullNeighborsMode, bool);

    itkGetMacro(FullNeighborsMode, bool);


    // \brief Set Graph_fullNeighbors. false = no diagonal neighbors, in 2D this means N4 Neigborhood. true = would be

    // N8 in 2D

    itkSetMacro(Graph_fullNeighbors, bool);


    // \brief (default=true), Produce output image, which shows the shortest path. But you can also get the shortest

    // Path directly as vector with the function GetVectorPath

    itkSetMacro(MakeOutputImage, bool);

    itkGetMacro(MakeOutputImage, bool);


    // \brief (default=false), Store an Vector of Order, so you can call getVectorOrderImage after update

    itkSetMacro(StoreVectorOrder, bool);

    itkGetMacro(StoreVectorOrder, bool);


    // \brief (default=false), // Calculate all Distances to all pixels, so you can call getDistanceImage after update

    // (warning algo will take a long time)

    itkSetMacro(CalcAllDistances, bool);

    itkGetMacro(CalcAllDistances, bool);


    // \brief (default=false), for debug issues: after 30s algorithms terminates. You can have a look at the

    // VectorOrderImage to see how far it came

    itkSetMacro(ActivateTimeOut, bool);

    itkGetMacro(ActivateTimeOut, bool);


    // \brief returns shortest Path as vector

    std::vector<IndexType> GetVectorPath();


    // \brief returns Multiple shortest Paths. You can call this function, when u performed a multiple shortest path

    // search (one start, several ends)

    std::vector<std::vector<IndexType>> GetMultipleVectorPaths();


    // \brief returns the vector order image. It shows in which order the pixels were checked. good for debugging. Be

    // sure to have m_StoreVectorOrder=true

    OutputImagePointer GetVectorOrderImage();


    // \brief returns the distance image. It shows the distances from the startpoint to all other pixels. Be sure to

    // have m_CalcAllDistances=true

    OutputImagePointer GetDistanceImage();


    // \brief Fill m_VectorPath

    void MakeShortestPathVector();


    // \brief cleans up the filter

    void CleanUp();


    itkSetObjectMacro(CostFunction,

                      CostFunctionType); // itkSetObjectMacro = set function that uses pointer as parameter

    itkGetObjectMacro(CostFunction, CostFunctionType);


    void SetUseCostFunction(bool doUseCostFunction) { m_useCostFunction = doUseCostFunction; };

    bool GetUseCostFunction() { return m_useCostFunction; };


  protected:

    std::vector<IndexType>

      m_endPoints; // if you fill this vector, the algo will not rest until all endPoints have been reached

    std::vector<IndexType> m_endPointsClosed;


    ShortestPathNode *m_Nodes; // main list that contains all nodes

    NodeNumType m_Graph_NumberOfNodes;

    NodeNumType m_Graph_StartNode;

    NodeNumType m_Graph_EndNode;

    bool m_Graph_fullNeighbors;

    bool m_useCostFunction;

    std::vector<ShortestPathNode *> m_Graph_DiscoveredNodeList;

    ShortestPathImageFilter(Self &); // intentionally not implemented

    void operator=(const Self &);    // intentionally not implemented

    const static int BACKGROUND = 0;

    const static int FOREGROUND = 255;

    bool m_FullNeighborsMode;


    bool m_MakeOutputImage;

    bool m_StoreVectorOrder; // Store an Vector of Order, so you can call getVectorOrderImage after update

    bool m_CalcAllDistances; // Calculate all Distances, so you can call getDistanceImage after update (warning algo

                             // will take a long time)


    bool multipleEndPoints;


    bool m_ActivateTimeOut; // if true, then i search max. 30 secs. then abort


    bool m_Initialized;


    CostFunctionTypePointer m_CostFunction;

    IndexType m_StartIndex, m_EndIndex;

    std::vector<IndexType> m_VectorPath;

    std::vector<std::vector<IndexType>> m_MultipleVectorPaths;


    std::vector<NodeNumType> m_VectorOrder;


    ShortestPathImageFilter();


    ~ShortestPathImageFilter() override;


    // \brief Create all the outputs

    void MakeOutputs();


    // \brief Generate Data

    void GenerateData() override;


    // \brief gets the estimate costs from pixel a to target.

    double getEstimatedCostsToTarget(const IndexType &a);


    typename InputImageType::Pointer m_magnitudeImage;


    // \brief Convert a indexnumber of a node in m_Nodes to image coordinates

    typename TInputImageType::IndexType NodeToCoord(NodeNumType);


    // \brief Convert image coordinate to a indexnumber of a node in m_Nodes

    unsigned int CoordToNode(IndexType);


    // \brief Returns the neighbors of a node

    std::vector<ShortestPathNode *> GetNeighbors(NodeNumType nodeNum, bool FullNeighbors);


    // \brief Check if coords are in bounds of image

    bool CoordIsInBounds(IndexType);


    // \brief Initializes the graph

    void InitGraph();


    // \brief Start ShortestPathSearch

    void StartShortestPathSearch();

  };


} // end of namespace itk


#include "itkShortestPathImageFilter.txx"


#endif