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://oncora1.lyon.fnclcc.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     IndexType index;
  57     PointType point;
  58     PixelType l;
  59     PixelType l1;
  60     PixelType l2;
  61     typedef itk::Index<3> NodeType;
  62     typedef tree<NodeType> TreeType;
  63     typedef TreeType::iterator TreeIterator;
  64     TreeIterator treeIter;
  65   };
  66   //--------------------------------------------------------------------
  67
  68
  69   //--------------------------------------------------------------------
  70   template <class TImageType>
  71   class ITK_EXPORT ExtractAirwaysTreeInfoFilter:
  72     public virtual clitk::FilterBase,
  73     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  74     public itk::ImageToImageFilter<TImageType, TImageType>
  75   {
  76
  77   public:
  78     /** Standard class typedefs. */
  79     typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
  80     typedef ExtractAirwaysTreeInfoFilter         Self;
  81     typedef itk::SmartPointer<Self>             Pointer;
  82     typedef itk::SmartPointer<const Self>       ConstPointer;
  83
  84     /** Method for creation through the object factory. */
  85     itkNewMacro(Self);
  86
  87     /** Run-time type information (and related methods). */
  88     itkTypeMacro(ExtractAirwaysTreeInfoFilter, ImageToImageFilter);
  89     FILTERBASE_INIT;
  90
  91     /** Some convenient typedefs */
  92     typedef TImageType                       ImageType;
  93     typedef typename ImageType::ConstPointer ImageConstPointer;
  94     typedef typename ImageType::Pointer      ImagePointer;
  95     typedef typename ImageType::RegionType   ImageRegionType;
  96     typedef typename ImageType::PixelType    ImagePixelType;
  97     typedef typename ImageType::SizeType     ImageSizeType;
  98     typedef typename ImageType::IndexType    ImageIndexType;
  99     typedef typename ImageType::PointType    ImagePointType;
 100
 101     typedef Bifurcation BifurcationType;
 102     typedef ImageIndexType NodeType;
 103     typedef tree<NodeType> TreeType;
 104     typedef typename TreeType::iterator TreeIterator;
 105
 106     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
 107     typedef int InternalPixelType;
 108     typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
 109     typedef typename InternalImageType::Pointer                      InternalImagePointer;
 110     typedef typename InternalImageType::IndexType                    InternalIndexType;
 111     typedef LabelizeParameters<InternalPixelType>                    LabelParamType;
 112
 113     /** Connect inputs */
 114     void SetInput(const ImageType * image);
 115
 116     // Set all options at a time
 117     template<class ArgsInfoType>
 118       void SetArgsInfo(ArgsInfoType arg);
 119
 120     // Background / Foreground
 121     itkGetConstMacro(BackgroundValue, ImagePixelType);
 122     itkGetConstMacro(ForegroundValue, ImagePixelType);
 123
 124     // Get results
 125     itkGetConstMacro(FirstTracheaPoint, ImagePointType);
 126     itkGetConstMacro(CarinaPoint, ImagePointType);
 127
 128   protected:
 129     ExtractAirwaysTreeInfoFilter();
 130     virtual ~ExtractAirwaysTreeInfoFilter() {}
 131
 132     // Main members
 133     ImageConstPointer input;
 134     ImagePointer skeleton;
 135     ImagePointer working_input;
 136
 137     // Global options
 138     itkSetMacro(BackgroundValue, ImagePixelType);
 139     itkSetMacro(ForegroundValue, ImagePixelType);
 140     ImagePixelType m_BackgroundValue;
 141     ImagePixelType m_ForegroundValue;
 142
 143     // Results
 144     ImagePointType m_FirstTracheaPoint;
 145     ImagePointType m_CarinaPoint;
 146
 147     virtual void GenerateOutputInformation();
 148     virtual void GenerateData();
 149
 150     TreeType m_SkeletonTree;
 151     void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
 152                             ImagePointer skeleton,
 153                             ImageIndexType index,
 154                             ImagePixelType label,
 155                             TreeIterator currentNode);
 156   private:
 157     ExtractAirwaysTreeInfoFilter(const Self&); //purposely not implemented
 158     void operator=(const Self&); //purposely not implemented
 159
 160   }; // end class
 161   //--------------------------------------------------------------------
 162
 163 } // end namespace clitk
 164 //--------------------------------------------------------------------
 165
 166 #ifndef ITK_MANUAL_INSTANTIATION
 167 #include "clitkExtractAirwaysTreeInfoFilter.txx"
 168 #endif
 169
 170 #endif