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     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
  74     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
  75
  76     /** ImageDimension constants */
  77     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  78     FILTERBASE_INIT;
  79
  80     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  81     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  82     itkSetMacro(BackgroundValue, MaskImagePixelType);
  83     itkSetMacro(ForegroundValue, MaskImagePixelType);
  84
  85     // Station 8
  86     itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
  87     itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
  88     itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
  89     itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
  90     itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
  91     itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
  92     itkSetMacro(FuzzyThresholdForS8, double);
  93     itkGetConstMacro(FuzzyThresholdForS8, double);
  94
  95     itkSetMacro(InjectedThresholdForS8, double);
  96     itkGetConstMacro(InjectedThresholdForS8, double);
  97
  98     // Station 7
  99     void SetFuzzyThresholdForS7(std::string tag, double value);
 100     double GetFuzzyThresholdForS7(std::string tag);
 101
 102     // All stations
 103     bool GetComputeStation(std::string s);
 104     void AddComputeStation(std::string station) ;
 105
 106   protected:
 107     ExtractLymphStationsFilter();
 108     virtual ~ExtractLymphStationsFilter() {}
 109
 110     virtual void GenerateOutputInformation();
 111     virtual void GenerateInputRequestedRegion();
 112     virtual void GenerateData();
 113
 114     ImageConstPointer  m_Input;
 115     MaskImagePointer   m_Mediastinum;
 116     MaskImagePointer   m_Working_Support;
 117     std::map<std::string, MaskImagePointer> m_ListOfStations;
 118     MaskImagePixelType m_BackgroundValue;
 119     MaskImagePixelType m_ForegroundValue;
 120     std::map<std::string, bool> m_ComputeStationMap;
 121
 122     bool CheckForStation(std::string station);
 123     void Remove_Structures(std::string s);
 124
 125     // Station 8
 126     double m_DistanceMaxToAnteriorPartOfTheSpine;
 127     double m_DiaphragmInferiorLimit;
 128     double m_CarinaZ;
 129     double m_OriginOfRightMiddleLobeBronchusZ;
 130     double m_FuzzyThresholdForS8;
 131     double m_InjectedThresholdForS8;
 132     MaskImagePointer m_Esophagus;
 133     MaskImagePointType m_EsophagusDiltationForAnt;
 134     MaskImagePointType m_EsophagusDiltationForRight;
 135     MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
 136     void ExtractStation_8();
 137     void ExtractStation_8_SetDefaultValues();
 138     void ExtractStation_8_SI_Limits();
 139     void ExtractStation_8_Post_Limits();
 140     void ExtractStation_8_Ant_Sup_Limits();
 141     void ExtractStation_8_Ant_Inf_Limits();
 142     void ExtractStation_8_Ant_Injected_Limits();
 143     void ExtractStation_8_LR_1_Limits();
 144     void ExtractStation_8_LR_2_Limits();
 145     void ExtractStation_8_Single_CCL_Limits();
 146     void ExtractStation_8_LR_Limits();
 147     void ExtractStation_8_Remove_Structures();
 148     void ExtractStation_8_LR_Limits_old();
 149     void ExtractStation_8_LR_Limits_old2();
 150
 151     // Station 3P
 152     void ExtractStation_3P();
 153     void ExtractStation_3P_SetDefaultValues();
 154     void ExtractStation_3P_SI_Limits();
 155     void ExtractStation_3P_Remove_Structures();
 156     void ExtractStation_3P_Ant_Limits();
 157     void ExtractStation_3P_Post_Limits();
 158     void ExtractStation_3P_LR_sup_Limits();
 159     void ExtractStation_3P_LR_sup_Limits_2();
 160     void ExtractStation_3P_LR_inf_Limits();
 161
 162     // Station 3A
 163     void ExtractStation_3A();
 164     void ExtractStation_3A_SetDefaultValues();
 165     void ExtractStation_3A_SI_Limits();
 166     void ExtractStation_3A_Ant_Limits();
 167
 168     // Station 7
 169     void ExtractStation_7();
 170     void ExtractStation_7_SetDefaultValues();
 171     void ExtractStation_7_SI_Limits();
 172     void ExtractStation_7_RL_Limits();
 173     void ExtractStation_7_Posterior_Limits();
 174     void ExtractStation_7_Remove_Structures();
 175     MaskImagePointer m_Working_Trachea;
 176     std::map<std::string, double> m_FuzzyThresholdForS7;
 177     MaskImagePointer m_LeftBronchus;
 178     MaskImagePointer m_RightBronchus;
 179     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
 180     ListOfPointsType  m_RightMostInLeftBronchus;
 181     ListOfPointsType  m_AntMostInLeftBronchus;
 182     ListOfPointsType  m_PostMostInLeftBronchus;
 183     ListOfPointsType  m_LeftMostInRightBronchus;
 184     ListOfPointsType  m_AntMostInRightBronchus;
 185     ListOfPointsType  m_PostMostInRightBronchus;
 186
 187     void FindExtremaPointsInBronchus(MaskImagePointer input,
 188                                      int direction,
 189                                      double distance_max_from_center_point,
 190                                      ListOfPointsType & LR,
 191                                      ListOfPointsType & Ant,
 192                                      ListOfPointsType & Post);
 193     // Station 4RL
 194     void ExtractStation_4RL();
 195     void ExtractStation_4RL_SI_Limits();
 196     void ExtractStation_4RL_LR_Limits();
 197     void ExtractStation_4RL_AP_Limits();
 198     MaskImagePointer m_RightSupport;
 199     MaskImagePointer m_LeftSupport;
 200
 201   private:
 202     ExtractLymphStationsFilter(const Self&); //purposely not implemented
 203     void operator=(const Self&); //purposely not implemented
 204
 205   }; // end class
 206   //--------------------------------------------------------------------
 207
 208 } // end namespace clitk
 209 //--------------------------------------------------------------------
 210
 211 #ifndef ITK_MANUAL_INSTANTIATION
 212 #include "clitkExtractLymphStationsFilter.txx"
 213 #include "clitkExtractLymphStation_8.txx"
 214 #include "clitkExtractLymphStation_3P.txx"
 215 #include "clitkExtractLymphStation_3A.txx"
 216 #include "clitkExtractLymphStation_7.txx"
 217 #include "clitkExtractLymphStation_4RL.txx"
 218 #endif
 219
 220 #endif