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(OutputFolder, std::string);
  92     itkSetMacro(OutputFolder, std::string);
  93
  94     itkGetConstMacro(Threshold, ImagePixelType);
  95     itkSetMacro(Threshold, ImagePixelType);
  96
  97   protected:
  98     ExtractMediastinalVesselsFilter();
  99     virtual ~ExtractMediastinalVesselsFilter() {}
 100
 101     virtual void GenerateOutputInformation();
 102     virtual void GenerateInputRequestedRegion();
 103     virtual void GenerateData();
 104
 105     std::string        m_OutputFolder;
 106     ImagePointer       m_Input;
 107     MaskImagePointer   m_Working_Support;
 108     MaskImagePointer   m_Mediastinum;
 109     MaskImagePointer   m_Mask;
 110     MaskImagePixelType m_BackgroundValue;
 111     MaskImagePixelType m_ForegroundValue;
 112     MaskImagePixelType m_TemporaryForegroundValue;
 113     ImagePixelType     m_Threshold;
 114
 115     std::vector<MaskSlicePointer> m_slice_recon;
 116
 117     void CropSupInf();
 118     //void SearchBrachioCephalicArtery(int & BCA_first_slice, LabelType & BCA_first_label);
 119     void TrackBifurcationFromPoint(MaskImagePointer & recon,
 120                                    std::vector<MaskSlicePointer> & slices_recon,
 121                                    MaskImagePointType BCA_p,
 122                                    LabelType newLabel,
 123                                    std::vector<MaskImagePointType> & bif);
 124
 125   private:
 126     ExtractMediastinalVesselsFilter(const Self&); //purposely not implemented
 127     void operator=(const Self&); //purposely not implemented
 128
 129   }; // end class
 130   //--------------------------------------------------------------------
 131
 132 } // end namespace clitk
 133 //--------------------------------------------------------------------
 134
 135 #ifndef ITK_MANUAL_INSTANTIATION
 136 #include "clitkExtractMediastinalVesselsFilter.txx"
 137 #endif
 138
 139 #endif