segmentation/clitkExtractAirwayTreeInfoFilter.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
  28 // itk
  29 #include "itkStatisticsImageFilter.h"
  30
  31 namespace clitk {
  32
  33   //--------------------------------------------------------------------
  34   /*
  35     From a trachea binary image, compute the skeleton and track the
  36     path to find the carena.
  37   */
  38   //--------------------------------------------------------------------
  39
  40
  41   //--------------------------------------------------------------------
  42   template<class IndexType, class PixelType>
  43   class Bifurcation
  44   {
  45   public:
  46     Bifurcation(IndexType _index, PixelType _l, PixelType _l1, PixelType _l2) {
  47       index = _index;
  48       _l = l;
  49       _l1 = l1;
  50       _l2 = l2;
  51     }
  52     IndexType index;
  53     PixelType l;
  54     PixelType l1;
  55     PixelType l2;
  56   };
  57   //--------------------------------------------------------------------
  58
  59
  60   //--------------------------------------------------------------------
  61   template <class TImageType>
  62   class ITK_EXPORT ExtractAirwayTreeInfoFilter:
  63     public clitk::FilterBase,
  64     public itk::ImageToImageFilter<TImageType, TImageType>
  65   {
  66
  67   public:
  68     /** Standard class typedefs. */
  69     typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
  70     typedef ExtractAirwayTreeInfoFilter         Self;
  71     typedef itk::SmartPointer<Self>             Pointer;
  72     typedef itk::SmartPointer<const Self>       ConstPointer;
  73
  74     /** Method for creation through the object factory. */
  75     itkNewMacro(Self);
  76
  77     /** Run-time type information (and related methods). */
  78     itkTypeMacro(ExtractAirwayTreeInfoFilter, ImageToImageFilter);
  79     FILTERBASE_INIT;
  80
  81     /** Some convenient typedefs */
  82     typedef TImageType                       ImageType;
  83     typedef typename ImageType::ConstPointer ImageConstPointer;
  84     typedef typename ImageType::Pointer      ImagePointer;
  85     typedef typename ImageType::RegionType   ImageRegionType;
  86     typedef typename ImageType::PixelType    ImagePixelType;
  87     typedef typename ImageType::SizeType     ImageSizeType;
  88     typedef typename ImageType::IndexType    ImageIndexType;
  89     typedef typename ImageType::PointType    ImagePointType;
  90
  91     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  92     typedef int InternalPixelType;
  93     typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
  94     typedef typename InternalImageType::Pointer                      InternalImagePointer;
  95     typedef typename InternalImageType::IndexType                    InternalIndexType;
  96     typedef LabelizeParameters<InternalPixelType>                    LabelParamType;
  97
  98     /** Connect inputs */
  99     void SetInput(const ImageType * image);
 100
 101     // Set all options at a time
 102     template<class ArgsInfoType>
 103       void SetArgsInfo(ArgsInfoType arg);
 104
 105     // Background / Foreground
 106     itkGetConstMacro(BackgroundValue, ImagePixelType);
 107     itkGetConstMacro(ForegroundValue, ImagePixelType);
 108
 109     // Get results
 110     itkGetConstMacro(FirstTracheaPoint, ImagePointType);
 111
 112   protected:
 113     ExtractAirwayTreeInfoFilter();
 114     virtual ~ExtractAirwayTreeInfoFilter() {}
 115
 116     // Main members
 117     ImageConstPointer input;
 118     ImagePointer skeleton;
 119     ImagePointer working_input;
 120
 121     // Global options
 122     itkSetMacro(BackgroundValue, ImagePixelType);
 123     itkSetMacro(ForegroundValue, ImagePixelType);
 124     ImagePixelType m_BackgroundValue;
 125     ImagePixelType m_ForegroundValue;
 126
 127     // Results
 128     ImagePointType m_FirstTracheaPoint;
 129
 130     virtual void GenerateOutputInformation();
 131     virtual void GenerateData();
 132
 133     typedef Bifurcation<ImageIndexType,ImagePixelType> BifurcationType;
 134     void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations,
 135                             ImagePointer skeleton,
 136                             ImageIndexType index,
 137                             ImagePixelType label);
 138   private:
 139     ExtractAirwayTreeInfoFilter(const Self&); //purposely not implemented
 140     void operator=(const Self&); //purposely not implemented
 141
 142   }; // end class
 143   //--------------------------------------------------------------------
 144
 145 } // end namespace clitk
 146 //--------------------------------------------------------------------
 147
 148 #ifndef ITK_MANUAL_INSTANTIATION
 149 #include "clitkExtractAirwayTreeInfoFilter.txx"
 150 #endif
 151
 152 #endif