segmentation/clitkExtractMediastinumFilter.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://www.centreleonberard.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 CLITKEXTRACTMEDIASTINUMFILTER_H
  20 #define CLITKEXTRACTMEDIASTINUMFILTER_H
  21
  22 #include "clitkStructuresExtractionFilter.h"
  23
  24 namespace clitk {
  25
  26   //--------------------------------------------------------------------
  27   /*
  28     Try to extract the mediastinum part of a thorax CT.
  29     Input masks needed :
  30     - Patient
  31     - Lungs
  32     - Bones [Optional]
  33     - Trachea
  34     - VertebralBody
  35   */
  36   //--------------------------------------------------------------------
  37
  38   template <class TImageType>
  39   class ITK_EXPORT ExtractMediastinumFilter:
  40     public clitk::StructuresExtractionFilter<TImageType>
  41   {
  42
  43   public:
  44     /** Some convenient typedefs. */
  45     typedef TImageType                       ImageType;
  46     typedef typename ImageType::ConstPointer ImageConstPointer;
  47     typedef typename ImageType::Pointer      ImagePointer;
  48     typedef typename ImageType::RegionType   ImageRegionType;
  49     typedef typename ImageType::PixelType    ImagePixelType;
  50     typedef typename ImageType::SizeType     ImageSizeType;
  51     typedef typename ImageType::IndexType    ImageIndexType;
  52     typedef typename ImageType::PointType    ImagePointType;
  53
  54     /** Some convenient typedefs. */
  55     typedef uchar MaskImagePixelType;
  56     typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
  57     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
  58     typedef typename MaskImageType::Pointer      MaskImagePointer;
  59     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  60     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  61     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  62     typedef typename MaskImageType::PointType    MaskImagePointType;
  63
  64     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
  65     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
  66     typedef typename MaskSliceType::PointType    MaskSlicePointType;
  67
  68     /** Standard class typedefs. */
  69     //    typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
  70     typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
  71     typedef ExtractMediastinumFilter            Self;
  72     typedef itk::SmartPointer<Self>             Pointer;
  73     typedef itk::SmartPointer<const Self>       ConstPointer;
  74
  75     /** Method for creation through the object factory. */
  76     itkNewMacro(Self);
  77
  78     /** Run-time type information (and related methods). */
  79     itkTypeMacro(ExtractMediastinumFilter, InPlaceImageFilter);
  80     FILTERBASE_INIT;
  81
  82     /** Connect inputs */
  83     void SetInput(const ImageType * image);
  84     void SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  85     void SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg=0,
  86                                 MaskImagePixelType fgLeftLung=1, MaskImagePixelType fgRightLung=2);
  87     void SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  88     void SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  89
  90     // Output filename  (for AFBD)
  91     itkSetMacro(OutputMediastinumFilename, std::string);
  92     itkGetConstMacro(OutputMediastinumFilename, std::string);
  93
  94     /** ImageDimension constants */
  95     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  96
  97     // Background / Foreground
  98     itkSetMacro(BackgroundValuePatient, MaskImagePixelType);
  99     itkGetConstMacro(BackgroundValuePatient, MaskImagePixelType);
 100
 101     itkSetMacro(BackgroundValueLung, MaskImagePixelType);
 102     itkGetConstMacro(BackgroundValueLung, MaskImagePixelType);
 103
 104     itkSetMacro(BackgroundValueBones, MaskImagePixelType);
 105     itkGetConstMacro(BackgroundValueBones, MaskImagePixelType);
 106
 107     itkSetMacro(ForegroundValueLeftLung, MaskImagePixelType);
 108     itkGetConstMacro(ForegroundValueLeftLung, MaskImagePixelType);
 109
 110     itkSetMacro(ForegroundValueRightLung, MaskImagePixelType);
 111     itkGetConstMacro(ForegroundValueRightLung, MaskImagePixelType);
 112
 113     itkSetMacro(BackgroundValueTrachea, MaskImagePixelType);
 114     itkGetConstMacro(BackgroundValueTrachea, MaskImagePixelType);
 115
 116     itkSetMacro(IntermediateSpacing, double);
 117     itkGetConstMacro(IntermediateSpacing, double);
 118
 119     itkBooleanMacro(UseBones);
 120     itkSetMacro(UseBones, bool);
 121     itkGetConstMacro(UseBones, bool);
 122
 123     itkSetMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
 124     itkGetConstMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
 125
 126     void SetFuzzyThreshold(std::string tag, double value);
 127     double GetFuzzyThreshold(std::string tag);
 128
 129   protected:
 130     ExtractMediastinumFilter();
 131     virtual ~ExtractMediastinumFilter() {}
 132
 133     virtual void GenerateOutputInformation();
 134     virtual void GenerateInputRequestedRegion();
 135     virtual void GenerateData();
 136
 137     MaskImagePixelType m_BackgroundValuePatient;
 138     MaskImagePixelType m_BackgroundValueLung;
 139     MaskImagePixelType m_BackgroundValueBones;
 140     MaskImagePixelType m_BackgroundValueTrachea;
 141     MaskImagePixelType m_ForegroundValueLeftLung;
 142     MaskImagePixelType m_ForegroundValueRightLung;
 143
 144     MaskImagePointer output;
 145     MaskImagePointer patient;
 146     MaskImagePointer lung;
 147     MaskImagePointer bones;
 148     MaskImagePointer trachea;
 149
 150     std::map<std::string, double> m_FuzzyThreshold;
 151     double m_IntermediateSpacing;
 152     bool   m_UseBones;
 153     double m_DistanceMaxToAnteriorPartOfTheVertebralBody;
 154
 155     void RemovePostPartOfVertebralBody();
 156
 157     std::string m_OutputMediastinumFilename;
 158
 159   private:
 160     ExtractMediastinumFilter(const Self&); //purposely not implemented
 161     void operator=(const Self&); //purposely not implemented
 162
 163   }; // end class
 164   //--------------------------------------------------------------------
 165
 166 } // end namespace clitk
 167 //--------------------------------------------------------------------
 168
 169 #ifndef ITK_MANUAL_INSTANTIATION
 170 #include "clitkExtractMediastinumFilter.txx"
 171 #endif
 172
 173 #endif