segmentation/clitkExtractAirwaysTreeInfoFilter.h

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 #ifndef CLITKEXTRACTAIRWAYTREEINFOSFILTER_H
  20 #define CLITKEXTRACTAIRWAYTREEINFOSFILTER_H
  21
  22 // clitk
  23 #include "clitkFilterBase.h"
  24 #include "clitkDecomposeAndReconstructImageFilter.h"
  25 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
  26 #include "clitkSegmentationUtils.h"
  27 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
  28 #include "tree.hh"
  29
  30 // itk
  31 #include "itkStatisticsImageFilter.h"
  32
  33 namespace clitk {
  34
  35   //--------------------------------------------------------------------
  36   /*
  37     From a trachea binary image, compute the skeleton and track the
  38     path to find the carena.
  39   */
  40   //--------------------------------------------------------------------
  41
  42
  43
  44   class Bifurcation
  45   {
  46   public:
  47     typedef itk::Index<3> IndexType;
  48     typedef itk::Point<double, 3> PointType;
  49     typedef double PixelType;
  50     Bifurcation(IndexType _index, PixelType _l, PixelType _l1, PixelType _l2) {
  51       index = _index;
  52       _l = l;
  53       _l1 = l1;
  54       _l2 = l2;
  55     }
  56
  57     IndexType index;
  58     PointType point;
  59     double weight;
  60     PixelType l;
  61     PixelType l1;
  62     PixelType l2;
  63     typedef itk::Index<3> NodeType;
  64     typedef tree<NodeType> TreeType;
  65     typedef TreeType::iterator TreeIterator;
  66     TreeIterator treeIter;
  67   };
  68   //--------------------------------------------------------------------
  69
  70
  71   //--------------------------------------------------------------------
  72   template <class TImageType>
  73   class ITK_EXPORT ExtractAirwaysTreeInfoFilter:
  74     public virtual clitk::FilterBase,
  75     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  76     public itk::ImageToImageFilter<TImageType, TImageType>
  77   {
  78
  79   public:
  80     /** Standard class typedefs. */
  81     typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
  82     typedef ExtractAirwaysTreeInfoFilter         Self;
  83     typedef itk::SmartPointer<Self>             Pointer;
  84     typedef itk::SmartPointer<const Self>       ConstPointer;
  85
  86     /** Method for creation through the object factory. */
  87     itkNewMacro(Self);
  88
  89     /** Run-time type information (and related methods). */
  90     itkTypeMacro(ExtractAirwaysTreeInfoFilter, ImageToImageFilter);
  91     FILTERBASE_INIT;
  92
  93     /** Some convenient typedefs */
  94     typedef TImageType                       ImageType;
  95     typedef typename ImageType::ConstPointer ImageConstPointer;
  96     typedef typename ImageType::Pointer      ImagePointer;
  97     typedef typename ImageType::RegionType   ImageRegionType;
  98     typedef typename ImageType::PixelType    ImagePixelType;
  99     typedef typename ImageType::SizeType     ImageSizeType;
 100     typedef typename ImageType::IndexType    ImageIndexType;
 101     typedef typename ImageType::PointType    ImagePointType;
 102
 103     typedef Bifurcation BifurcationType;
 104     typedef ImageIndexType NodeType;
 105     typedef tree<NodeType> TreeType;
 106     typedef typename TreeType::iterator TreeIterator;
 107
 108     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
 109     typedef int InternalPixelType;
 110     typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
 111     typedef typename InternalImageType::Pointer                      InternalImagePointer;
 112     typedef typename InternalImageType::IndexType                    InternalIndexType;
 113     typedef LabelizeParameters<InternalPixelType>                    LabelParamType;
 114
 115     // Data Structures for trees
 116     struct FullTreeNodeType {
 117       ImageIndexType index;
 118       ImagePointType point;
 119       double weight;
 120     };
 121     struct StructuralTreeNodeType {
 122       ImageIndexType index;
 123       ImagePointType point;
 124       double weight;
 125     };
 126     typedef tree<FullTreeNodeType> FullTreeType;
 127     typedef tree<StructuralTreeNodeType> StructuralTreeType;
 128     FullTreeType mFullSkeletonTree;
 129     StructuralTreeType mStructuralSkeletonTree;
 130
 131     /** Connect inputs */
 132     void SetInput(const ImageType * image);
 133
 134     // Background / Foreground
 135     itkGetConstMacro(BackgroundValue, ImagePixelType);
 136     itkGetConstMacro(ForegroundValue, ImagePixelType);
 137
 138     // Get results
 139     itkGetConstMacro(FirstTracheaPoint, ImagePointType);
 140     itkGetConstMacro(CarinaPoint, ImagePointType);
 141
 142   protected:
 143     ExtractAirwaysTreeInfoFilter();
 144     virtual ~ExtractAirwaysTreeInfoFilter() {}
 145
 146     // Main members
 147     ImageConstPointer input;
 148     ImagePointer skeleton;
 149     ImagePointer working_input;
 150
 151     // Global options
 152     itkSetMacro(BackgroundValue, ImagePixelType);
 153     itkSetMacro(ForegroundValue, ImagePixelType);
 154     ImagePixelType m_BackgroundValue;
 155     ImagePixelType m_ForegroundValue;
 156
 157     // Results
 158     ImagePointType m_FirstTracheaPoint;
 159     ImagePointType m_CarinaPoint;
 160
 161     virtual void GenerateOutputInformation();
 162     virtual void GenerateData();
 163
 164     TreeType m_SkeletonTree;
 165     void TrackFromThisIndex2(ImageIndexType index, ImagePointer skeleton,
 166                              ImagePixelType label,
 167                              typename FullTreeType::iterator currentNode,
 168                              typename StructuralTreeType::iterator currentSNode);
 169     void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
 170                             ImagePointer skeleton,
 171                             ImageIndexType index,
 172                             ImagePixelType label,
 173                             TreeIterator currentNode);
 174   private:
 175     ExtractAirwaysTreeInfoFilter(const Self&); //purposely not implemented
 176     void operator=(const Self&); //purposely not implemented
 177
 178   }; // end class
 179   //--------------------------------------------------------------------
 180
 181 } // end namespace clitk
 182 //--------------------------------------------------------------------
 183
 184 #ifndef ITK_MANUAL_INSTANTIATION
 185 #include "clitkExtractAirwaysTreeInfoFilter.txx"
 186 #endif
 187
 188 #endif