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 #include "clitkLabelImageOverlapMeasureFilter.h"
  25
  26 // vtk
  27 #include <vtkPolyData.h>
  28
  29 namespace clitk {
  30
  31   class SupportLimitsType {
  32   public:
  33     std::string station_limit;
  34     std::string station;
  35     std::string structure_limit;
  36     std::string structure;
  37     double offset;
  38     void Read(istream & is) {
  39       is >> station_limit;
  40       is >> station;
  41       is >> structure_limit;
  42       is >> structure;
  43       std::string s;
  44       is >> s;
  45       offset = atof(s.c_str());
  46     }
  47   };
  48
  49   //--------------------------------------------------------------------
  50   /*
  51     Try to extract the LymphStations part of a thorax CT.
  52     Need a set of Anatomical Features (AFDB)
  53   */
  54   //--------------------------------------------------------------------
  55
  56   template <class TImageType>
  57   class ITK_EXPORT ExtractLymphStationsFilter:
  58     public clitk::StructuresExtractionFilter<TImageType>
  59   {
  60
  61   public:
  62     /** Standard class typedefs. */
  63     typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
  64     typedef ExtractLymphStationsFilter          Self;
  65     typedef itk::SmartPointer<Self>             Pointer;
  66     typedef itk::SmartPointer<const Self>       ConstPointer;
  67
  68     /** Method for creation through the object factory. */
  69     itkNewMacro(Self);
  70
  71     /** Run-time type information (and related methods). */
  72     itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter);
  73
  74     /** Some convenient typedefs. */
  75     typedef TImageType                       ImageType;
  76     typedef typename ImageType::ConstPointer ImageConstPointer;
  77     typedef typename ImageType::Pointer      ImagePointer;
  78     typedef typename ImageType::RegionType   ImageRegionType;
  79     typedef typename ImageType::PixelType    ImagePixelType;
  80     typedef typename ImageType::SizeType     ImageSizeType;
  81     typedef typename ImageType::IndexType    ImageIndexType;
  82     typedef typename ImageType::PointType    ImagePointType;
  83
  84     typedef uchar MaskImagePixelType;
  85     typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
  86     typedef typename MaskImageType::Pointer      MaskImagePointer;
  87     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  88     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  89     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  90     typedef typename MaskImageType::PointType    MaskImagePointType;
  91
  92     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
  93     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
  94     typedef typename MaskSliceType::PointType    MaskSlicePointType;
  95     typedef typename MaskSliceType::RegionType   MaskSliceRegionType;
  96     typedef typename MaskSliceType::SizeType     MaskSliceSizeType;
  97     typedef typename MaskSliceType::IndexType    MaskSliceIndexType;
  98
  99     /** ImageDimension constants */
 100     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
 101     FILTERBASE_INIT;
 102
 103     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
 104     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
 105     itkSetMacro(BackgroundValue, MaskImagePixelType);
 106     itkSetMacro(ForegroundValue, MaskImagePixelType);
 107
 108     // Station 8
 109     itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
 110     itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
 111     itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
 112     itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
 113     itkSetMacro(InjectedThresholdForS8, double);
 114     itkGetConstMacro(InjectedThresholdForS8, double);
 115
 116     // Station 7
 117     itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
 118     itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
 119     itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
 120
 121     // All stations
 122     bool GetComputeStation(std::string s);
 123     void AddComputeStation(std::string station) ;
 124     void SetFuzzyThreshold(std::string station, std::string tag, double value);
 125     double GetFuzzyThreshold(std::string station, std::string tag);
 126     void SetThreshold(std::string station, std::string tag, double value);
 127     double GetThreshold(std::string station, std::string tag);
 128     itkGetConstMacro(ForceSupportsFlag, bool);
 129     itkSetMacro(ForceSupportsFlag, bool);
 130     itkBooleanMacro(ForceSupportsFlag);
 131
 132     itkGetConstMacro(CheckSupportFlag, bool);
 133     itkSetMacro(CheckSupportFlag, bool);
 134     itkBooleanMacro(CheckSupportFlag);
 135
 136     itkGetConstMacro(SupportLimitsFilename, std::string);
 137     itkSetMacro(SupportLimitsFilename, std::string);
 138
 139   protected:
 140     ExtractLymphStationsFilter();
 141     virtual ~ExtractLymphStationsFilter() {}
 142
 143     virtual void GenerateOutputInformation();
 144     virtual void GenerateInputRequestedRegion();
 145     virtual void GenerateData();
 146
 147     // To avoid repeat "this->"
 148     AnatomicalFeatureDatabase * GetAFDB() { return clitk::FilterWithAnatomicalFeatureDatabaseManagement::GetAFDB(); }
 149     void WriteAFDB() { clitk::FilterWithAnatomicalFeatureDatabaseManagement::WriteAFDB(); }
 150     void LoadAFDB() {  clitk::FilterWithAnatomicalFeatureDatabaseManagement::LoadAFDB(); }
 151     void StartNewStep(std::string s) { clitk::FilterBase::StartNewStep(s); }
 152     void StartSubStep() { clitk::FilterBase::StartSubStep(); }
 153     template<class TInternalImageType>
 154       void StopCurrentStep(typename TInternalImageType::Pointer p, std::string txt="") { clitk::FilterBase::StopCurrentStep<TInternalImageType>(p, txt); }
 155     void StopCurrentStep() {clitk::FilterBase::StopCurrentStep(); }
 156     void StopSubStep() {clitk::FilterBase::StopSubStep(); }
 157
 158     ImageConstPointer  m_Input;
 159     MaskImagePointer   m_Mediastinum;
 160     MaskImagePointer   m_Working_Support;
 161     std::map<std::string, MaskImagePointer> m_ListOfStations;
 162     std::map<std::string, MaskImagePointer> m_ListOfSupports;
 163     MaskImagePixelType m_BackgroundValue;
 164     MaskImagePixelType m_ForegroundValue;
 165     std::map<std::string, bool> m_ComputeStationMap;
 166     std::string m_SupportLimitsFilename;
 167     std::vector<SupportLimitsType> m_ListOfSupportLimits;
 168
 169     bool CheckForStation(std::string station);
 170     void Remove_Structures(std::string station, std::string s);
 171     void WriteImageSupport(std::string support);
 172     void WriteImageStation(std::string station);
 173     void ComputeOverlapWithRef(std::string station);
 174     void Support_SI_Limit(const std::string station_limit, const std::string station,
 175                           const std::string structure_limit, const std::string structure,
 176                           const double offset);
 177     void ReadSupportLimits(std::string filename);
 178
 179     // Functions common to several stations
 180     double FindCarina();
 181     double FindApexOfTheChest();
 182     double FindSuperiorBorderOfAorticArch();
 183     double FindInferiorBorderOfAorticArch();
 184     void FindLeftAndRightBronchi();
 185     void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
 186     MaskImagePointer FindAntPostVesselsOLD();
 187     MaskImagePointer FindAntPostVessels2();
 188
 189     // Global parameters
 190     typedef std::map<std::string, double> FuzzyThresholdByStructureType;
 191     std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
 192     typedef std::map<std::string, double> ThresholdByStructureType;
 193     std::map<std::string, ThresholdByStructureType> m_Threshold;
 194
 195     // Station's supports
 196     void ExtractStationSupports();
 197     void Support_LeftRight_S1R_S1L();
 198     void Support_LeftRight_S2R_S2L();
 199     void Support_LeftRight_S4R_S4L();
 200     void Support_Post_S1S2S4();
 201
 202     MaskImagePointer LimitsWithTrachea(MaskImageType * input,
 203                                        int extremaDirection, int lineDirection,
 204                                        double offset, double maxSupPosition);
 205     MaskImagePointer LimitsWithTrachea(MaskImageType * input,
 206                                        int extremaDirection, int lineDirection,
 207                                        double offset);
 208     // Station 8
 209     double m_DiaphragmInferiorLimit;
 210     double m_OriginOfRightMiddleLobeBronchusZ;
 211     double m_InjectedThresholdForS8;
 212     MaskImagePointer m_Esophagus;
 213     MaskImagePointType m_EsophagusDiltationForAnt;
 214     MaskImagePointType m_EsophagusDiltationForRight;
 215
 216     void ExtractStation_8();
 217     void ExtractStation_8_SetDefaultValues();
 218     void ExtractStation_8_SI_Limits();
 219     void ExtractStation_8_Ant_Limits();
 220     void ExtractStation_8_Left_Sup_Limits();
 221     void ExtractStation_8_Left_Inf_Limits();
 222     void ExtractStation_8_Single_CCL_Limits();
 223     void ExtractStation_8_Remove_Structures();
 224
 225     // Station 3P
 226     void ExtractStation_3P();
 227     void ExtractStation_3P_SetDefaultValues();
 228     void ExtractStation_3P_LR_inf_Limits();
 229     void ExtractStation_3P_LR_sup_Limits_2();
 230     void ExtractStation_3P_Remove_Structures();
 231     void ExtractStation_3P_LR_sup_Limits();
 232
 233     // Station 3A
 234     void ExtractStation_3A();
 235     void ExtractStation_3A_SetDefaultValues();
 236     void ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support();
 237     void ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support();
 238     void ExtractStation_3A_AntPost_Superiorly();
 239     void ExtractStation_3A_Remove_Structures();
 240
 241     // Station 2RL
 242     void ExtractStation_2RL();
 243     void ExtractStation_2RL_SetDefaultValues();
 244     void ExtractStation_2RL_Ant_Limits(std::string s);
 245     void ExtractStation_2RL_Remove_Structures(std::string s);
 246     void ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split();
 247     vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
 248
 249     // Station 1RL
 250     void ExtractStation_1RL();
 251     void ExtractStation_1RL_SetDefaultValues();
 252     void ExtractStation_1RL_Ant_Limits();
 253     void ExtractStation_1RL_Post_Limits();
 254
 255     // Station 4RL
 256     void ExtractStation_4RL_SetDefaultValues();
 257     void ExtractStation_4L();
 258     void ExtractStation_4R();
 259     void ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint);
 260
 261     // Station 5
 262     void ExtractStation_5_SetDefaultValues();
 263     void ExtractStation_5();
 264     void ExtractStation_5_Limits_AscendingAorta_Ant();
 265
 266     // Station 6
 267     void ExtractStation_6_SetDefaultValues();
 268     void ExtractStation_6();
 269
 270
 271     // Station 7
 272     void ExtractStation_7();
 273     void ExtractStation_7_SetDefaultValues();
 274     void ExtractStation_7_SI_Limits();
 275     void ExtractStation_7_RL_Interior_Limits();
 276
 277     void ExtractStation_7_RL_Limits_OLD();
 278     void ExtractStation_7_Posterior_Limits();
 279     void ExtractStation_7_Remove_Structures();
 280     bool m_S7_UseMostInferiorPartOnlyFlag;
 281     bool m_ForceSupportsFlag;
 282     bool m_CheckSupportFlag;
 283     MaskImagePointer m_Working_Trachea;
 284     MaskImagePointer m_LeftBronchus;
 285     MaskImagePointer m_RightBronchus;
 286     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
 287     ListOfPointsType  m_RightMostInLeftBronchus;
 288     ListOfPointsType  m_AntMostInLeftBronchus;
 289     ListOfPointsType  m_PostMostInLeftBronchus;
 290     ListOfPointsType  m_LeftMostInRightBronchus;
 291     ListOfPointsType  m_AntMostInRightBronchus;
 292     ListOfPointsType  m_PostMostInRightBronchus;
 293
 294     void FindExtremaPointsInBronchus(MaskImagePointer input,
 295                                      int direction,
 296                                      double distance_max_from_center_point,
 297                                      ListOfPointsType & LR,
 298                                      ListOfPointsType & Ant,
 299                                      ListOfPointsType & Post);
 300   private:
 301     ExtractLymphStationsFilter(const Self&); //purposely not implemented
 302     void operator=(const Self&); //purposely not implemented
 303
 304   }; // end class
 305   //--------------------------------------------------------------------
 306
 307 } // end namespace clitk
 308 //--------------------------------------------------------------------
 309
 310 #ifndef ITK_MANUAL_INSTANTIATION
 311 #include "clitkExtractLymphStationsFilter.txx"
 312 #include "clitkExtractLymphStation_Supports.txx"
 313 #include "clitkExtractLymphStation_3P.txx"
 314 #include "clitkExtractLymphStation_2RL.txx"
 315 #include "clitkExtractLymphStation_3A.txx"
 316 #include "clitkExtractLymphStation_4RL.txx"
 317 #include "clitkExtractLymphStation_1RL.txx"
 318 #include "clitkExtractLymphStation_5.txx"
 319 #include "clitkExtractLymphStation_6.txx"
 320
 321 #include "clitkExtractLymphStation_8.txx"
 322 #include "clitkExtractLymphStation_7.txx"
 323 #endif
 324
 325 #endif