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 "clitkStructuresExtractionFilter.h"
  24
  25 // vtk
  26 #include <vtkPolyData.h>
  27
  28 namespace clitk {
  29
  30   //--------------------------------------------------------------------
  31   /*
  32     Try to extract the LymphStations part of a thorax CT.
  33     Need a set of Anatomical Features (AFDB)
  34   */
  35   //--------------------------------------------------------------------
  36
  37   template <class TImageType>
  38   class ITK_EXPORT ExtractLymphStationsFilter:
  39     public clitk::StructuresExtractionFilter<TImageType>
  40   {
  41
  42   public:
  43     /** Standard class typedefs. */
  44     typedef clitk::StructuresExtractionFilter<TImageType> 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     typedef typename MaskSliceType::PointType    MaskSlicePointType;
  76     typedef typename MaskSliceType::RegionType   MaskSliceRegionType;
  77     typedef typename MaskSliceType::SizeType     MaskSliceSizeType;
  78     typedef typename MaskSliceType::IndexType    MaskSliceIndexType;
  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(EsophagusDiltationForAnt, MaskImagePointType);
  91     itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
  92     itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
  93     itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
  94     itkSetMacro(InjectedThresholdForS8, double);
  95     itkGetConstMacro(InjectedThresholdForS8, double);
  96
  97     // Station 7
  98     itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
  99     itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
 100     itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
 101
 102     // All stations
 103     bool GetComputeStation(std::string s);
 104     void AddComputeStation(std::string station) ;
 105     void SetFuzzyThreshold(std::string station, std::string tag, double value);
 106     double GetFuzzyThreshold(std::string station, std::string tag);
 107     void SetThreshold(std::string station, std::string tag, double value);
 108     double GetThreshold(std::string station, std::string tag);
 109     itkGetConstMacro(ComputeStationsSupportsFlag, bool);
 110     itkSetMacro(ComputeStationsSupportsFlag, bool);
 111     itkBooleanMacro(ComputeStationsSupportsFlag);
 112
 113   protected:
 114     ExtractLymphStationsFilter();
 115     virtual ~ExtractLymphStationsFilter() {}
 116
 117     virtual void GenerateOutputInformation();
 118     virtual void GenerateInputRequestedRegion();
 119     virtual void GenerateData();
 120
 121     // To avoid repeat "this->"
 122     AnatomicalFeatureDatabase * GetAFDB() { return clitk::FilterWithAnatomicalFeatureDatabaseManagement::GetAFDB(); }
 123     void WriteAFDB() { clitk::FilterWithAnatomicalFeatureDatabaseManagement::WriteAFDB(); }
 124     void LoadAFDB() {  clitk::FilterWithAnatomicalFeatureDatabaseManagement::LoadAFDB(); }
 125     void StartNewStep(std::string s) { clitk::FilterBase::StartNewStep(s); }
 126     void StartSubStep() { clitk::FilterBase::StartSubStep(); }
 127     template<class TInternalImageType>
 128       void StopCurrentStep(typename TInternalImageType::Pointer p, std::string txt="") { clitk::FilterBase::StopCurrentStep<TInternalImageType>(p, txt); }
 129     void StopCurrentStep() {clitk::FilterBase::StopCurrentStep(); }
 130     void StopSubStep() {clitk::FilterBase::StopSubStep(); }
 131
 132     ImageConstPointer  m_Input;
 133     MaskImagePointer   m_Mediastinum;
 134     MaskImagePointer   m_Working_Support;
 135     std::map<std::string, MaskImagePointer> m_ListOfStations;
 136     std::map<std::string, MaskImagePointer> m_ListOfSupports;
 137     MaskImagePixelType m_BackgroundValue;
 138     MaskImagePixelType m_ForegroundValue;
 139     std::map<std::string, bool> m_ComputeStationMap;
 140
 141     bool CheckForStation(std::string station);
 142     void Remove_Structures(std::string station, std::string s);
 143
 144     // Functions common to several stations
 145     double FindCarina();
 146     double FindApexOfTheChest();
 147     double FindSuperiorBorderOfAorticArch();
 148     double FindInferiorBorderOfAorticArch();
 149     void FindLeftAndRightBronchi();
 150     void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
 151     MaskImagePointer FindAntPostVesselsOLD();
 152     MaskImagePointer FindAntPostVessels2();
 153
 154     // Global parameters
 155     typedef std::map<std::string, double> FuzzyThresholdByStructureType;
 156     std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
 157     typedef std::map<std::string, double> ThresholdByStructureType;
 158     std::map<std::string, ThresholdByStructureType> m_Threshold;
 159
 160     // Station's supports
 161     void ExtractStationSupports();
 162     void Support_SupInf_S1RL();
 163     void Support_LeftRight_S1R_S1L();
 164     void Support_SupInf_S2R_S2L();
 165     void Support_LeftRight_S2R_S2L();
 166     void Support_SupInf_S4R_S4L();
 167     void Support_LeftRight_S4R_S4L();
 168     void Support_Post_S1S2S4();
 169     void Support_S3P();
 170     void Support_S3A();
 171     void Support_S5();
 172     void Support_S6();
 173
 174     MaskImagePointer LimitsWithTrachea(MaskImageType * input,
 175                                        int extremaDirection, int lineDirection,
 176                                        double offset, double maxSupPosition);
 177     MaskImagePointer LimitsWithTrachea(MaskImageType * input,
 178                                        int extremaDirection, int lineDirection,
 179                                        double offset);
 180     // Station 8
 181     double m_DiaphragmInferiorLimit;
 182     double m_OriginOfRightMiddleLobeBronchusZ;
 183     double m_InjectedThresholdForS8;
 184     MaskImagePointer m_Esophagus;
 185     MaskImagePointType m_EsophagusDiltationForAnt;
 186     MaskImagePointType m_EsophagusDiltationForRight;
 187
 188     void ExtractStation_8();
 189     void ExtractStation_8_SetDefaultValues();
 190     void ExtractStation_8_SI_Limits();
 191     void ExtractStation_8_Ant_Limits();
 192     void ExtractStation_8_Left_Sup_Limits();
 193     void ExtractStation_8_Left_Inf_Limits();
 194     void ExtractStation_8_Single_CCL_Limits();
 195     void ExtractStation_8_Remove_Structures();
 196
 197     // Station 3P
 198     void ExtractStation_3P();
 199     void ExtractStation_3P_SetDefaultValues();
 200     void ExtractStation_3P_LR_inf_Limits();
 201     void ExtractStation_3P_LR_sup_Limits_2();
 202     void ExtractStation_3P_Remove_Structures();
 203     void ExtractStation_3P_LR_sup_Limits();
 204
 205     // Station 3A
 206     void ExtractStation_3A();
 207     void ExtractStation_3A_SetDefaultValues();
 208     void ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support();
 209     void ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support();
 210     void ExtractStation_3A_AntPost_Superiorly();
 211     void ExtractStation_3A_Remove_Structures();
 212
 213     // Station 2RL
 214     void ExtractStation_2RL();
 215     void ExtractStation_2RL_SetDefaultValues();
 216     void ExtractStation_2RL_Ant_Limits(std::string s);
 217     void ExtractStation_2RL_Remove_Structures(std::string s);
 218     void ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split();
 219     vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
 220
 221     // Station 1RL
 222     void ExtractStation_1RL();
 223     void ExtractStation_1RL_SetDefaultValues();
 224     void ExtractStation_1RL_Ant_Limits();
 225     void ExtractStation_1RL_Post_Limits();
 226
 227     // Station 4RL
 228     void ExtractStation_4RL_SetDefaultValues();
 229     void ExtractStation_4RL();
 230     void ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint);
 231
 232     // Station 5
 233     void ExtractStation_5_SetDefaultValues();
 234     void ExtractStation_5();
 235     void ExtractStation_5_Limits_AscendingAorta_Ant();
 236
 237     // Station 6
 238     void ExtractStation_6_SetDefaultValues();
 239     void ExtractStation_6();
 240
 241
 242     // Station 7
 243     void ExtractStation_7();
 244     void ExtractStation_7_SetDefaultValues();
 245     void ExtractStation_7_SI_Limits();
 246     void ExtractStation_7_RL_Interior_Limits();
 247
 248     void ExtractStation_7_RL_Limits_OLD();
 249     void ExtractStation_7_Posterior_Limits();
 250     void ExtractStation_7_Remove_Structures();
 251     bool m_S7_UseMostInferiorPartOnlyFlag;
 252     bool m_ComputeStationsSupportsFlag;
 253     MaskImagePointer m_Working_Trachea;
 254     MaskImagePointer m_LeftBronchus;
 255     MaskImagePointer m_RightBronchus;
 256     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
 257     ListOfPointsType  m_RightMostInLeftBronchus;
 258     ListOfPointsType  m_AntMostInLeftBronchus;
 259     ListOfPointsType  m_PostMostInLeftBronchus;
 260     ListOfPointsType  m_LeftMostInRightBronchus;
 261     ListOfPointsType  m_AntMostInRightBronchus;
 262     ListOfPointsType  m_PostMostInRightBronchus;
 263
 264     void FindExtremaPointsInBronchus(MaskImagePointer input,
 265                                      int direction,
 266                                      double distance_max_from_center_point,
 267                                      ListOfPointsType & LR,
 268                                      ListOfPointsType & Ant,
 269                                      ListOfPointsType & Post);
 270   private:
 271     ExtractLymphStationsFilter(const Self&); //purposely not implemented
 272     void operator=(const Self&); //purposely not implemented
 273
 274   }; // end class
 275   //--------------------------------------------------------------------
 276
 277 } // end namespace clitk
 278 //--------------------------------------------------------------------
 279
 280 #ifndef ITK_MANUAL_INSTANTIATION
 281 #include "clitkExtractLymphStationsFilter.txx"
 282 #include "clitkExtractLymphStation_Supports.txx"
 283 #include "clitkExtractLymphStation_3P.txx"
 284 #include "clitkExtractLymphStation_2RL.txx"
 285 #include "clitkExtractLymphStation_3A.txx"
 286 #include "clitkExtractLymphStation_4RL.txx"
 287 #include "clitkExtractLymphStation_1RL.txx"
 288 #include "clitkExtractLymphStation_5.txx"
 289 #include "clitkExtractLymphStation_6.txx"
 290
 291 #include "clitkExtractLymphStation_8.txx"
 292 #include "clitkExtractLymphStation_7.txx"
 293 #endif
 294
 295 #endif