segmentation/clitkExtractLymphStationsFilter.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 LymphStations part of a thorax CT.
  31     Need a set of Anatomical Features (AFDB)
  32   */
  33   //--------------------------------------------------------------------
  34
  35   template <class TImageType>
  36   class ITK_EXPORT ExtractLymphStationsFilter:
  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 ExtractLymphStationsFilter          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(ExtractLymphStationsFilter, 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     /** ImageDimension constants */
  74     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  75     FILTERBASE_INIT;
  76
  77     /** Main options (from ggo) */
  78     template <class ArgsInfoType>
  79     void SetArgsInfo(ArgsInfoType & argsinfo);
  80
  81     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  82     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  83     itkSetMacro(BackgroundValue, MaskImagePixelType);
  84     itkSetMacro(ForegroundValue, MaskImagePixelType);
  85
  86     // Station 7
  87     itkSetMacro(FuzzyThreshold, double);
  88     itkGetConstMacro(FuzzyThreshold, double);
  89     itkSetMacro(Station7Filename, std::string);
  90     itkGetConstMacro(Station7Filename, std::string);
  91
  92   protected:
  93     ExtractLymphStationsFilter();
  94     virtual ~ExtractLymphStationsFilter() {}
  95
  96     virtual void GenerateOutputInformation();
  97     virtual void GenerateInputRequestedRegion();
  98     virtual void GenerateData();
  99
 100     ImageConstPointer  m_Input;
 101     MaskImagePointer   m_Support;
 102     MaskImagePointer   m_Working_Support;
 103     MaskImagePointer   m_Output;
 104     MaskImagePixelType m_BackgroundValue;
 105     MaskImagePixelType m_ForegroundValue;
 106
 107     // Common
 108     MaskImagePointer m_Trachea;
 109
 110     // Station 7
 111     void ExtractStation_7();
 112     void ExtractStation_7_SI_Limits();
 113     void ExtractStation_7_RL_Limits();
 114     void ExtractStation_7_Posterior_Limits();
 115     std::string      m_Station7Filename;
 116     MaskImagePointer m_working_trachea;
 117     double           m_FuzzyThreshold;
 118     MaskImagePointer m_LeftBronchus;
 119     MaskImagePointer m_RightBronchus;
 120     MaskImagePointer m_Station7;
 121
 122     // Station 4RL
 123     void ExtractStation_4RL();
 124     void ExtractStation_4RL_SI_Limits();
 125     void ExtractStation_4RL_LR_Limits();
 126     MaskImagePointer m_Station4RL;
 127
 128   private:
 129     ExtractLymphStationsFilter(const Self&); //purposely not implemented
 130     void operator=(const Self&); //purposely not implemented
 131
 132   }; // end class
 133   //--------------------------------------------------------------------
 134
 135 } // end namespace clitk
 136 //--------------------------------------------------------------------
 137
 138 #ifndef ITK_MANUAL_INSTANTIATION
 139 #include "clitkExtractLymphStationsFilter.txx"
 140 #include "clitkExtractLymphStation_7.txx"
 141 #include "clitkExtractLymphStation_4RL.txx"
 142 #endif
 143
 144 #endif