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 // vtk
  27 #include <vtkPolyData.h>
  28
  29 namespace clitk {
  30
  31   //--------------------------------------------------------------------
  32   /*
  33     Try to extract the LymphStations part of a thorax CT.
  34     Need a set of Anatomical Features (AFDB)
  35   */
  36   //--------------------------------------------------------------------
  37
  38   template <class TImageType>
  39   class ITK_EXPORT ExtractLymphStationsFilter:
  40     public virtual clitk::FilterBase,
  41     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  42     public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
  43   {
  44
  45   public:
  46     /** Standard class typedefs. */
  47     typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
  48     typedef ExtractLymphStationsFilter          Self;
  49     typedef itk::SmartPointer<Self>             Pointer;
  50     typedef itk::SmartPointer<const Self>       ConstPointer;
  51
  52     /** Method for creation through the object factory. */
  53     itkNewMacro(Self);
  54
  55     /** Run-time type information (and related methods). */
  56     itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter);
  57
  58     /** Some convenient typedefs. */
  59     typedef TImageType                       ImageType;
  60     typedef typename ImageType::ConstPointer ImageConstPointer;
  61     typedef typename ImageType::Pointer      ImagePointer;
  62     typedef typename ImageType::RegionType   ImageRegionType;
  63     typedef typename ImageType::PixelType    ImagePixelType;
  64     typedef typename ImageType::SizeType     ImageSizeType;
  65     typedef typename ImageType::IndexType    ImageIndexType;
  66     typedef typename ImageType::PointType    ImagePointType;
  67
  68     typedef uchar MaskImagePixelType;
  69     typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
  70     typedef typename MaskImageType::Pointer      MaskImagePointer;
  71     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  72     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  73     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  74     typedef typename MaskImageType::PointType    MaskImagePointType;
  75
  76     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
  77     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
  78     typedef typename MaskSliceType::PointType    MaskSlicePointType;
  79
  80     /** ImageDimension constants */
  81     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  82     FILTERBASE_INIT;
  83
  84     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  85     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  86     itkSetMacro(BackgroundValue, MaskImagePixelType);
  87     itkSetMacro(ForegroundValue, MaskImagePixelType);
  88
  89     // Station 8
  90     itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
  91     itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
  92     itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
  93     itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
  94     itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
  95     itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
  96     itkSetMacro(InjectedThresholdForS8, double);
  97     itkGetConstMacro(InjectedThresholdForS8, double);
  98
  99     // Station 7
 100
 101     // All stations
 102     bool GetComputeStation(std::string s);
 103     void AddComputeStation(std::string station) ;
 104     void SetFuzzyThreshold(std::string station, std::string tag, double value);
 105     double GetFuzzyThreshold(std::string station, std::string tag);
 106
 107   protected:
 108     ExtractLymphStationsFilter();
 109     virtual ~ExtractLymphStationsFilter() {}
 110
 111     virtual void GenerateOutputInformation();
 112     virtual void GenerateInputRequestedRegion();
 113     virtual void GenerateData();
 114
 115     ImageConstPointer  m_Input;
 116     MaskImagePointer   m_Mediastinum;
 117     MaskImagePointer   m_Working_Support;
 118     std::map<std::string, MaskImagePointer> m_ListOfStations;
 119     MaskImagePixelType m_BackgroundValue;
 120     MaskImagePixelType m_ForegroundValue;
 121     std::map<std::string, bool> m_ComputeStationMap;
 122
 123     bool CheckForStation(std::string station);
 124     void Remove_Structures(std::string station, std::string s);
 125
 126     // Global parameters
 127     typedef std::map<std::string, double> FuzzyThresholdByStructureType;
 128     std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
 129
 130     // Station 8
 131     double m_DistanceMaxToAnteriorPartOfTheSpine;
 132     double m_DiaphragmInferiorLimit;
 133     double m_CarinaZ;
 134     double m_OriginOfRightMiddleLobeBronchusZ;
 135     double m_InjectedThresholdForS8;
 136     MaskImagePointer m_Esophagus;
 137     MaskImagePointType m_EsophagusDiltationForAnt;
 138     MaskImagePointType m_EsophagusDiltationForRight;
 139     MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
 140     void ExtractStation_8();
 141     void ExtractStation_8_SetDefaultValues();
 142     void ExtractStation_8_SI_Limits();
 143     void ExtractStation_8_Post_Limits();
 144     void ExtractStation_8_Ant_Sup_Limits();
 145     void ExtractStation_8_Ant_Inf_Limits();
 146     void ExtractStation_8_Ant_Injected_Limits();
 147     void ExtractStation_8_LR_1_Limits();
 148     void ExtractStation_8_LR_2_Limits();
 149     void ExtractStation_8_Single_CCL_Limits();
 150     void ExtractStation_8_LR_Limits();
 151     void ExtractStation_8_Remove_Structures();
 152     void ExtractStation_8_LR_Limits_old();
 153     void ExtractStation_8_LR_Limits_old2();
 154
 155     // Station 3P
 156     void ExtractStation_3P();
 157     void ExtractStation_3P_SetDefaultValues();
 158     void ExtractStation_3P_SI_Limits();
 159     void ExtractStation_3P_Remove_Structures();
 160     void ExtractStation_3P_Ant_Limits();
 161     void ExtractStation_3P_Post_Limits();
 162     void ExtractStation_3P_LR_sup_Limits();
 163     void ExtractStation_3P_LR_sup_Limits_2();
 164     void ExtractStation_3P_LR_inf_Limits();
 165
 166     // Station 2RL
 167     void ExtractStation_2RL();
 168     void ExtractStation_2RL_SetDefaultValues();
 169     void ExtractStation_2RL_SI_Limits();
 170     void ExtractStation_2RL_Ant_Limits();
 171     void ExtractStation_2RL_Ant_Limits2();
 172     void ExtractStation_2RL_Post_Limits();
 173     void ExtractStation_2RL_LR_Limits();
 174     void ExtractStation_2RL_Remove_Structures();
 175     void ExtractStation_2RL_SeparateRL();
 176     vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
 177
 178     // Station 3A
 179     void ExtractStation_3A();
 180     void ExtractStation_3A_SetDefaultValues();
 181     void ExtractStation_3A_SI_Limits();
 182     void ExtractStation_3A_Ant_Limits();
 183     void ExtractStation_3A_Post_Limits();
 184
 185     // Station 7
 186     void ExtractStation_7();
 187     void ExtractStation_7_SetDefaultValues();
 188     void ExtractStation_7_SI_Limits();
 189     void ExtractStation_7_RL_Limits();
 190     void ExtractStation_7_Posterior_Limits();
 191     void ExtractStation_7_Remove_Structures();
 192     MaskImagePointer m_Working_Trachea;
 193     MaskImagePointer m_LeftBronchus;
 194     MaskImagePointer m_RightBronchus;
 195     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
 196     ListOfPointsType  m_RightMostInLeftBronchus;
 197     ListOfPointsType  m_AntMostInLeftBronchus;
 198     ListOfPointsType  m_PostMostInLeftBronchus;
 199     ListOfPointsType  m_LeftMostInRightBronchus;
 200     ListOfPointsType  m_AntMostInRightBronchus;
 201     ListOfPointsType  m_PostMostInRightBronchus;
 202
 203     void FindExtremaPointsInBronchus(MaskImagePointer input,
 204                                      int direction,
 205                                      double distance_max_from_center_point,
 206                                      ListOfPointsType & LR,
 207                                      ListOfPointsType & Ant,
 208                                      ListOfPointsType & Post);
 209     // Station 4RL
 210     void ExtractStation_4RL();
 211     void ExtractStation_4RL_SI_Limits();
 212     void ExtractStation_4RL_LR_Limits();
 213     void ExtractStation_4RL_AP_Limits();
 214     MaskImagePointer m_RightSupport;
 215     MaskImagePointer m_LeftSupport;
 216
 217   private:
 218     ExtractLymphStationsFilter(const Self&); //purposely not implemented
 219     void operator=(const Self&); //purposely not implemented
 220
 221   }; // end class
 222   //--------------------------------------------------------------------
 223
 224 } // end namespace clitk
 225 //--------------------------------------------------------------------
 226
 227 #ifndef ITK_MANUAL_INSTANTIATION
 228 #include "clitkExtractLymphStationsFilter.txx"
 229 #include "clitkExtractLymphStation_8.txx"
 230 #include "clitkExtractLymphStation_3P.txx"
 231 #include "clitkExtractLymphStation_2RL.txx"
 232 #include "clitkExtractLymphStation_3A.txx"
 233 #include "clitkExtractLymphStation_7.txx"
 234 #include "clitkExtractLymphStation_4RL.txx"
 235 #endif
 236
 237 #endif