segmentation/clitkExtractMediastinalVesselsFilter.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 CLITKEXTRACTLYMPHSTATIONSFILTER_H
  20 #define CLITKEXTRACTLYMPHSTATIONSFILTER_H
  21
  22 // clitk
  23 #include "clitkFilterBase.h"
  24 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
  25
  26 namespace clitk {
  27
  28   //--------------------------------------------------------------------
  29   /*
  30     Try to extract the some Mediastinal Vessels in a thorax CT.
  31     Need a set of Anatomical Features (AFDB)
  32   */
  33   //--------------------------------------------------------------------
  34
  35   template <class TImageType>
  36   class ITK_EXPORT ExtractMediastinalVesselsFilter:
  37     public virtual clitk::FilterBase,
  38     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  39     public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
  40   {
  41
  42   public:
  43     /** Standard class typedefs. */
  44     typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
  45     typedef ExtractMediastinalVesselsFilter          Self;
  46     typedef itk::SmartPointer<Self>             Pointer;
  47     typedef itk::SmartPointer<const Self>       ConstPointer;
  48
  49     /** Method for creation through the object factory. */
  50     itkNewMacro(Self);
  51
  52     /** Run-time type information (and related methods). */
  53     itkTypeMacro(ExtractMediastinalVesselsFilter, ImageToImageFilter);
  54
  55     /** Some convenient typedefs. */
  56     typedef TImageType                       ImageType;
  57     typedef typename ImageType::ConstPointer ImageConstPointer;
  58     typedef typename ImageType::Pointer      ImagePointer;
  59     typedef typename ImageType::RegionType   ImageRegionType;
  60     typedef typename ImageType::PixelType    ImagePixelType;
  61     typedef typename ImageType::SizeType     ImageSizeType;
  62     typedef typename ImageType::IndexType    ImageIndexType;
  63     typedef typename ImageType::PointType    ImagePointType;
  64
  65     typedef uchar MaskImagePixelType;
  66     typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
  67     typedef typename MaskImageType::Pointer      MaskImagePointer;
  68     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  69     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  70     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  71     typedef typename MaskImageType::PointType    MaskImagePointType;
  72
  73     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
  74     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
  75     typedef typename MaskSliceType::PointType    MaskSlicePointType;
  76
  77     typedef long LabelType;
  78     /** ImageDimension constants */
  79     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  80     FILTERBASE_INIT;
  81
  82     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  83     itkSetMacro(BackgroundValue, MaskImagePixelType);
  84
  85     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  86     itkSetMacro(ForegroundValue, MaskImagePixelType);
  87
  88     itkGetConstMacro(TemporaryForegroundValue, MaskImagePixelType);
  89     itkSetMacro(TemporaryForegroundValue, MaskImagePixelType);
  90
  91     itkGetConstMacro(ThresholdHigh, ImagePixelType);
  92     itkSetMacro(ThresholdHigh, ImagePixelType);
  93
  94     itkGetConstMacro(ThresholdLow, ImagePixelType);
  95     itkSetMacro(ThresholdLow, ImagePixelType);
  96
  97     itkGetConstMacro(ErosionRadius, int);
  98     itkSetMacro(ErosionRadius, int);
  99
 100     itkGetConstMacro(DilatationRadius, int);
 101     itkSetMacro(DilatationRadius, int);
 102
 103     itkGetConstMacro(MaxDistancePostToCarina, double);
 104     itkSetMacro(MaxDistancePostToCarina, double);
 105     itkGetConstMacro(MaxDistanceAntToCarina, double);
 106     itkSetMacro(MaxDistanceAntToCarina, double);
 107     itkGetConstMacro(MaxDistanceLeftToCarina, double);
 108     itkSetMacro(MaxDistanceLeftToCarina, double);
 109     itkGetConstMacro(MaxDistanceRightToCarina, double);
 110     itkSetMacro(MaxDistanceRightToCarina, double);
 111
 112     itkSetMacro(DebugFlag, bool);
 113     itkGetConstMacro(DebugFlag, bool);
 114     itkBooleanMacro(DebugFlag);
 115
 116     itkSetMacro(SoughtVesselSeedName, std::string);
 117     itkGetConstMacro(SoughtVesselSeedName, std::string);
 118
 119     itkSetMacro(SoughtVesselName, std::string);
 120     itkGetConstMacro(SoughtVesselName, std::string);
 121
 122     itkSetMacro(OutputFilename, std::string);
 123     itkGetConstMacro(OutputFilename, std::string);
 124
 125     itkSetMacro(MaxNumberOfFoundBifurcation, int);
 126     itkGetConstMacro(MaxNumberOfFoundBifurcation, int);
 127
 128     itkSetMacro(FinalOpeningRadius, int);
 129     itkGetConstMacro(FinalOpeningRadius, int);
 130
 131   protected:
 132     ExtractMediastinalVesselsFilter();
 133     virtual ~ExtractMediastinalVesselsFilter() {}
 134
 135     virtual void GenerateOutputInformation();
 136     virtual void GenerateInputRequestedRegion();
 137     virtual void GenerateData();
 138
 139     bool               m_DebugFlag;
 140     ImagePointer       m_Input;
 141     MaskImagePointer   m_Working_Support;
 142     MaskImagePointer   m_Mediastinum;
 143     MaskImagePointer   m_Mask;
 144     MaskImagePixelType m_BackgroundValue;
 145     MaskImagePixelType m_ForegroundValue;
 146     MaskImagePixelType m_TemporaryForegroundValue;
 147     ImagePixelType     m_ThresholdHigh;
 148     ImagePixelType     m_ThresholdLow;
 149     int                m_ErosionRadius;
 150     int                m_DilatationRadius;
 151     double             m_MaxDistancePostToCarina;
 152     double             m_MaxDistanceAntToCarina;
 153     double             m_MaxDistanceLeftToCarina;
 154     double             m_MaxDistanceRightToCarina;
 155     int                m_MaxNumberOfFoundBifurcation;
 156     int                m_FinalOpeningRadius;
 157
 158     std::vector<MaskSlicePointer> m_slice_recon;
 159     std::vector<MaskSlicePointer> m_slice_recon2;
 160
 161     // Resulting structures
 162     MaskImageType::Pointer m_SoughtVessel;
 163     std::string m_SoughtVesselSeedName;
 164     std::string m_SoughtVesselName;
 165     std::string m_OutputFilename;
 166
 167     void CropInputImage();
 168     void TrackBifurcationFromPoint(MaskImagePointer & recon,
 169                                    std::vector<MaskSlicePointer> & slices_recon,
 170                                    MaskImagePointType point3D,
 171                                    MaskImagePointType pointMaxSlice,
 172                                    LabelType newLabel,
 173                                    std::vector<MaskImagePointType> & bif);
 174
 175     void TrackVesselsFromPoint(MaskImagePointer & recon,
 176                                std::vector<MaskSlicePointer> & slices_recon,
 177                                MaskImagePointType point3D,
 178                                MaskImagePointType pointMaxSlice,
 179                                LabelType newLabel);
 180
 181   private:
 182     ExtractMediastinalVesselsFilter(const Self&); //purposely not implemented
 183     void operator=(const Self&); //purposely not implemented
 184
 185   }; // end class
 186   //--------------------------------------------------------------------
 187
 188 } // end namespace clitk
 189 //--------------------------------------------------------------------
 190
 191 #ifndef ITK_MANUAL_INSTANTIATION
 192 #include "clitkExtractMediastinalVesselsFilter.txx"
 193 #endif
 194
 195 #endif