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     typedef typename MaskSliceType::RegionType   MaskSliceRegionType;
  80     typedef typename MaskSliceType::SizeType     MaskSliceSizeType;
  81     typedef typename MaskSliceType::IndexType    MaskSliceIndexType;
  82
  83     /** ImageDimension constants */
  84     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  85     FILTERBASE_INIT;
  86
  87     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  88     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  89     itkSetMacro(BackgroundValue, MaskImagePixelType);
  90     itkSetMacro(ForegroundValue, MaskImagePixelType);
  91
  92     // Station 8
  93     // itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
  94     //itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
  95     itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
  96     itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
  97     itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
  98     itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
  99     itkSetMacro(InjectedThresholdForS8, double);
 100     itkGetConstMacro(InjectedThresholdForS8, double);
 101
 102     // Station 7
 103     itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
 104     itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
 105     itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
 106
 107     // All stations
 108     bool GetComputeStation(std::string s);
 109     void AddComputeStation(std::string station) ;
 110     void SetFuzzyThreshold(std::string station, std::string tag, double value);
 111     double GetFuzzyThreshold(std::string station, std::string tag);
 112     void SetThreshold(std::string station, std::string tag, double value);
 113     double GetThreshold(std::string station, std::string tag);
 114     itkGetConstMacro(ComputeStationsSupportsFlag, bool);
 115     itkSetMacro(ComputeStationsSupportsFlag, bool);
 116     itkBooleanMacro(ComputeStationsSupportsFlag);
 117
 118   protected:
 119     ExtractLymphStationsFilter();
 120     virtual ~ExtractLymphStationsFilter() {}
 121
 122     virtual void GenerateOutputInformation();
 123     virtual void GenerateInputRequestedRegion();
 124     virtual void GenerateData();
 125
 126     ImageConstPointer  m_Input;
 127     MaskImagePointer   m_Mediastinum;
 128     MaskImagePointer   m_Working_Support;
 129     std::map<std::string, MaskImagePointer> m_ListOfStations;
 130     std::map<std::string, MaskImagePointer> m_ListOfSupports;
 131     MaskImagePixelType m_BackgroundValue;
 132     MaskImagePixelType m_ForegroundValue;
 133     std::map<std::string, bool> m_ComputeStationMap;
 134
 135     bool CheckForStation(std::string station);
 136     void Remove_Structures(std::string station, std::string s);
 137
 138     // Functions common to several stations
 139     double FindCarina();
 140     double FindApexOfTheChest();
 141     double FindSuperiorBorderOfAorticArch();
 142     double FindInferiorBorderOfAorticArch();
 143     void FindLeftAndRightBronchi();
 144     void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
 145     MaskImagePointer FindAntPostVessels();
 146     MaskImagePointer FindAntPostVessels2();
 147
 148     // Global parameters
 149     typedef std::map<std::string, double> FuzzyThresholdByStructureType;
 150     std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
 151     typedef std::map<std::string, double> ThresholdByStructureType;
 152     std::map<std::string, ThresholdByStructureType> m_Threshold;
 153
 154     // Station's supports
 155     void ExtractStationSupports();
 156     void Support_SupInf_S1RL();
 157     void Support_LeftRight_S1R_S1L();
 158     void Support_SupInf_S2R_S2L();
 159     void Support_LeftRight_S2R_S2L();
 160     void Support_SupInf_S4R_S4L();
 161     void Support_LeftRight_S4R_S4L();
 162     void Support_Post_S1S2S4();
 163     void Support_S3P();
 164     void Support_S3A();
 165     void Support_S5();
 166     void Support_S6();
 167
 168     MaskImagePointer LimitsWithTrachea(MaskImageType * input,
 169                                        int extremaDirection, int lineDirection,
 170                                        double offset, double maxSupPosition);
 171     MaskImagePointer LimitsWithTrachea(MaskImageType * input,
 172                                        int extremaDirection, int lineDirection,
 173                                        double offset);
 174
 175     // Station 8
 176     // double m_DistanceMaxToAnteriorPartOfTheSpine;
 177     double m_DiaphragmInferiorLimit;
 178     double m_OriginOfRightMiddleLobeBronchusZ;
 179     double m_InjectedThresholdForS8;
 180     MaskImagePointer m_Esophagus;
 181     MaskImagePointType m_EsophagusDiltationForAnt;
 182     MaskImagePointType m_EsophagusDiltationForRight;
 183
 184     void ExtractStation_8();
 185     void ExtractStation_8_SetDefaultValues();
 186     void ExtractStation_8_SI_Limits();
 187     void ExtractStation_8_Ant_Limits();
 188     void ExtractStation_8_Left_Sup_Limits();
 189     void ExtractStation_8_Left_Inf_Limits();
 190     void ExtractStation_8_Single_CCL_Limits();
 191     void ExtractStation_8_Remove_Structures();
 192
 193     // Station 3P
 194     void ExtractStation_3P();
 195     void ExtractStation_3P_SetDefaultValues();
 196     void ExtractStation_3P_LR_inf_Limits();
 197     void ExtractStation_3P_LR_sup_Limits_2();
 198     void ExtractStation_3P_Remove_Structures();
 199     void ExtractStation_3P_LR_sup_Limits();
 200
 201     // Station 3A
 202     void ExtractStation_3A();
 203     void ExtractStation_3A_SetDefaultValues();
 204     void ExtractStation_3A_AntPost_S5();
 205     void ExtractStation_3A_AntPost_S6();
 206     void ExtractStation_3A_AntPost_Superiorly();
 207     void ExtractStation_3A_Remove_Structures();
 208     void ExtractStation_3A_PostToBones();
 209
 210     // Station 2RL
 211     void ExtractStation_2RL();
 212     void ExtractStation_2RL_SetDefaultValues();
 213     void ExtractStation_2RL_SI_Limits();
 214     void ExtractStation_2RL_Ant_Limits();
 215     void ExtractStation_2RL_Ant_Limits2();
 216     void ExtractStation_2RL_Post_Limits();
 217     void ExtractStation_2RL_LR_Limits();
 218     void ExtractStation_2RL_Remove_Structures();
 219     void ExtractStation_2RL_SeparateRL();
 220     vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
 221
 222     // Station 7
 223     void ExtractStation_7();
 224     void ExtractStation_7_SetDefaultValues();
 225     void ExtractStation_7_SI_Limits();
 226     void ExtractStation_7_RL_Interior_Limits();
 227
 228
 229     void ExtractStation_7_RL_Limits_OLD();
 230     void ExtractStation_7_Posterior_Limits();
 231     void ExtractStation_7_Remove_Structures();
 232     bool m_S7_UseMostInferiorPartOnlyFlag;
 233     bool m_ComputeStationsSupportsFlag;
 234     MaskImagePointer m_Working_Trachea;
 235     MaskImagePointer m_LeftBronchus;
 236     MaskImagePointer m_RightBronchus;
 237     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
 238     ListOfPointsType  m_RightMostInLeftBronchus;
 239     ListOfPointsType  m_AntMostInLeftBronchus;
 240     ListOfPointsType  m_PostMostInLeftBronchus;
 241     ListOfPointsType  m_LeftMostInRightBronchus;
 242     ListOfPointsType  m_AntMostInRightBronchus;
 243     ListOfPointsType  m_PostMostInRightBronchus;
 244
 245     void FindExtremaPointsInBronchus(MaskImagePointer input,
 246                                      int direction,
 247                                      double distance_max_from_center_point,
 248                                      ListOfPointsType & LR,
 249                                      ListOfPointsType & Ant,
 250                                      ListOfPointsType & Post);
 251     // Station 4RL
 252     void ExtractStation_4RL();
 253     void ExtractStation_4RL_SI_Limits();
 254     void ExtractStation_4RL_LR_Limits();
 255     void ExtractStation_4RL_AP_Limits();
 256     MaskImagePointer m_RightSupport;
 257     MaskImagePointer m_LeftSupport;
 258
 259   private:
 260     ExtractLymphStationsFilter(const Self&); //purposely not implemented
 261     void operator=(const Self&); //purposely not implemented
 262
 263   }; // end class
 264   //--------------------------------------------------------------------
 265
 266 } // end namespace clitk
 267 //--------------------------------------------------------------------
 268
 269 #ifndef ITK_MANUAL_INSTANTIATION
 270 #include "clitkExtractLymphStationsFilter.txx"
 271 #include "clitkExtractLymphStation_Supports.txx"
 272 #include "clitkExtractLymphStation_8.txx"
 273 #include "clitkExtractLymphStation_3P.txx"
 274 #include "clitkExtractLymphStation_2RL.txx"
 275 #include "clitkExtractLymphStation_3A.txx"
 276 #include "clitkExtractLymphStation_7.txx"
 277 #include "clitkExtractLymphStation_4RL.txx"
 278 #endif
 279
 280 #endif