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://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 CLITKEXTRACTMEDIASTINUMFILTER_H
  20 #define CLITKEXTRACTMEDIASTINUMFILTER_H
  21
  22 #include "clitkFilterBase.h"
  23 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
  24
  25 namespace clitk {
  26
  27   //--------------------------------------------------------------------
  28   /*
  29     Try to extract the mediastinum part of a thorax CT.
  30     Inputs :
  31     - Patient label image
  32     - Lungs label image
  33     - Bones label image
  34     - Trachea label image
  35   */
  36   //--------------------------------------------------------------------
  37
  38   template <class TImageType>
  39   class ITK_EXPORT ExtractMediastinumFilter:
  40     public virtual clitk::FilterBase,
  41     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  42     public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
  43   {
  44
  45   public:
  46     /** Some convenient typedefs. */
  47     typedef TImageType                       ImageType;
  48     typedef typename ImageType::ConstPointer ImageConstPointer;
  49     typedef typename ImageType::Pointer      ImagePointer;
  50     typedef typename ImageType::RegionType   ImageRegionType;
  51     typedef typename ImageType::PixelType    ImagePixelType;
  52     typedef typename ImageType::SizeType     ImageSizeType;
  53     typedef typename ImageType::IndexType    ImageIndexType;
  54     typedef typename ImageType::PointType    ImagePointType;
  55
  56     /** Some convenient typedefs. */
  57     typedef uchar MaskImagePixelType;
  58     typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
  59     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
  60     typedef typename MaskImageType::Pointer      MaskImagePointer;
  61     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  62     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  63     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  64     typedef typename MaskImageType::PointType    MaskImagePointType;
  65
  66     /** Standard class typedefs. */
  67     typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
  68     typedef ExtractMediastinumFilter            Self;
  69     typedef itk::SmartPointer<Self>             Pointer;
  70     typedef itk::SmartPointer<const Self>       ConstPointer;
  71
  72     /** Method for creation through the object factory. */
  73     itkNewMacro(Self);
  74
  75     /** Run-time type information (and related methods). */
  76     itkTypeMacro(ExtractMediastinumFilter, InPlaceImageFilter);
  77     FILTERBASE_INIT;
  78
  79     /** Connect inputs */
  80     void SetInput(const ImageType * image);
  81     void SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  82     void SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg=0,
  83                                 MaskImagePixelType fgLeftLung=1, MaskImagePixelType fgRightLung=2);
  84     void SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  85     void SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  86
  87    // Output filename  (for AFBD)
  88     itkSetMacro(OutputMediastinumFilename, std::string);
  89     itkGetConstMacro(OutputMediastinumFilename, std::string);
  90
  91     /** ImageDimension constants */
  92     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  93
  94     // Background / Foreground
  95     itkSetMacro(BackgroundValuePatient, MaskImagePixelType);
  96     itkGetConstMacro(BackgroundValuePatient, MaskImagePixelType);
  97
  98     itkSetMacro(BackgroundValueLung, MaskImagePixelType);
  99     itkGetConstMacro(BackgroundValueLung, MaskImagePixelType);
 100
 101     itkSetMacro(BackgroundValueBones, MaskImagePixelType);
 102     itkGetConstMacro(BackgroundValueBones, MaskImagePixelType);
 103
 104     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
 105     itkGetConstMacro(ForegroundValue, 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     itkSetMacro(FuzzyThreshold1, double);
 120     itkGetConstMacro(FuzzyThreshold1, double);
 121
 122     itkSetMacro(FuzzyThreshold2, double);
 123     itkGetConstMacro(FuzzyThreshold2, double);
 124
 125     itkSetMacro(FuzzyThreshold3, double);
 126     itkGetConstMacro(FuzzyThreshold3, double);
 127
 128     itkBooleanMacro(UseBones);
 129     itkSetMacro(UseBones, bool);
 130     itkGetConstMacro(UseBones, bool);
 131
 132     itkSetMacro(UpperThreshold, double);
 133     itkGetConstMacro(UpperThreshold, double);
 134
 135     itkSetMacro(LowerThreshold, double);
 136     itkGetConstMacro(LowerThreshold, double);
 137
 138   protected:
 139     ExtractMediastinumFilter();
 140     virtual ~ExtractMediastinumFilter() {}
 141
 142     virtual void GenerateOutputInformation();
 143     virtual void GenerateInputRequestedRegion();
 144     virtual void GenerateData();
 145
 146     itkSetMacro(BackgroundValue, MaskImagePixelType);
 147     itkSetMacro(ForegroundValue, MaskImagePixelType);
 148
 149     MaskImagePixelType m_BackgroundValuePatient;
 150     MaskImagePixelType m_BackgroundValueLung;
 151     MaskImagePixelType m_BackgroundValueBones;
 152     MaskImagePixelType m_BackgroundValueTrachea;
 153     MaskImagePixelType m_ForegroundValueLeftLung;
 154     MaskImagePixelType m_ForegroundValueRightLung;
 155
 156     MaskImagePixelType m_BackgroundValue;
 157     MaskImagePixelType m_ForegroundValue;
 158
 159     typename MaskImageType::Pointer output;
 160
 161     double m_IntermediateSpacing;
 162     double m_FuzzyThreshold1;
 163     double m_FuzzyThreshold2;
 164     double m_FuzzyThreshold3;
 165     bool   m_UseBones;
 166     double m_UpperThreshold;
 167     double m_LowerThreshold;
 168
 169     std::string m_OutputMediastinumFilename;
 170
 171   private:
 172     ExtractMediastinumFilter(const Self&); //purposely not implemented
 173     void operator=(const Self&); //purposely not implemented
 174
 175   }; // end class
 176   //--------------------------------------------------------------------
 177
 178 } // end namespace clitk
 179 //--------------------------------------------------------------------
 180
 181 #ifndef ITK_MANUAL_INSTANTIATION
 182 #include "clitkExtractMediastinumFilter.txx"
 183 #endif
 184
 185 #endif