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 "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     Input masks needed :
  31     - Patient
  32     - Lungs
  33     - Bones [Optional]
  34     - Trachea
  35     - VertebralBody
  36   */
  37   //--------------------------------------------------------------------
  38
  39   template <class TImageType>
  40   class ITK_EXPORT ExtractMediastinumFilter:
  41     public virtual clitk::FilterBase,
  42     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  43     public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
  44   {
  45
  46   public:
  47     /** Some convenient typedefs. */
  48     typedef TImageType                       ImageType;
  49     typedef typename ImageType::ConstPointer ImageConstPointer;
  50     typedef typename ImageType::Pointer      ImagePointer;
  51     typedef typename ImageType::RegionType   ImageRegionType;
  52     typedef typename ImageType::PixelType    ImagePixelType;
  53     typedef typename ImageType::SizeType     ImageSizeType;
  54     typedef typename ImageType::IndexType    ImageIndexType;
  55     typedef typename ImageType::PointType    ImagePointType;
  56
  57     /** Some convenient typedefs. */
  58     typedef uchar MaskImagePixelType;
  59     typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
  60     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
  61     typedef typename MaskImageType::Pointer      MaskImagePointer;
  62     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  63     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  64     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  65     typedef typename MaskImageType::PointType    MaskImagePointType;
  66
  67     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
  68     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
  69     typedef typename MaskSliceType::PointType    MaskSlicePointType;
  70
  71     /** Standard class typedefs. */
  72     typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
  73     typedef ExtractMediastinumFilter            Self;
  74     typedef itk::SmartPointer<Self>             Pointer;
  75     typedef itk::SmartPointer<const Self>       ConstPointer;
  76
  77     /** Method for creation through the object factory. */
  78     itkNewMacro(Self);
  79
  80     /** Run-time type information (and related methods). */
  81     itkTypeMacro(ExtractMediastinumFilter, InPlaceImageFilter);
  82     FILTERBASE_INIT;
  83
  84     /** Connect inputs */
  85     void SetInput(const ImageType * image);
  86     void SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  87     void SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg=0,
  88                                 MaskImagePixelType fgLeftLung=1, MaskImagePixelType fgRightLung=2);
  89     void SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  90     void SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
  91
  92    // Output filename  (for AFBD)
  93     itkSetMacro(OutputMediastinumFilename, std::string);
  94     itkGetConstMacro(OutputMediastinumFilename, std::string);
  95
  96     /** ImageDimension constants */
  97     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
  98
  99     // Background / Foreground
 100     itkSetMacro(BackgroundValuePatient, MaskImagePixelType);
 101     itkGetConstMacro(BackgroundValuePatient, MaskImagePixelType);
 102
 103     itkSetMacro(BackgroundValueLung, MaskImagePixelType);
 104     itkGetConstMacro(BackgroundValueLung, MaskImagePixelType);
 105
 106     itkSetMacro(BackgroundValueBones, MaskImagePixelType);
 107     itkGetConstMacro(BackgroundValueBones, MaskImagePixelType);
 108
 109     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
 110     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
 111
 112     itkSetMacro(ForegroundValueLeftLung, MaskImagePixelType);
 113     itkGetConstMacro(ForegroundValueLeftLung, MaskImagePixelType);
 114
 115     itkSetMacro(ForegroundValueRightLung, MaskImagePixelType);
 116     itkGetConstMacro(ForegroundValueRightLung, MaskImagePixelType);
 117
 118     itkSetMacro(BackgroundValueTrachea, MaskImagePixelType);
 119     itkGetConstMacro(BackgroundValueTrachea, MaskImagePixelType);
 120
 121     itkSetMacro(IntermediateSpacing, double);
 122     itkGetConstMacro(IntermediateSpacing, double);
 123
 124     itkBooleanMacro(UseBones);
 125     itkSetMacro(UseBones, bool);
 126     itkGetConstMacro(UseBones, bool);
 127
 128     itkSetMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
 129     itkGetConstMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
 130
 131     void SetFuzzyThreshold(std::string tag, double value);
 132     double GetFuzzyThreshold(std::string tag);
 133
 134   protected:
 135     ExtractMediastinumFilter();
 136     virtual ~ExtractMediastinumFilter() {}
 137
 138     virtual void GenerateOutputInformation();
 139     virtual void GenerateInputRequestedRegion();
 140     virtual void GenerateData();
 141
 142     itkSetMacro(BackgroundValue, MaskImagePixelType);
 143     itkSetMacro(ForegroundValue, MaskImagePixelType);
 144
 145     MaskImagePixelType m_BackgroundValuePatient;
 146     MaskImagePixelType m_BackgroundValueLung;
 147     MaskImagePixelType m_BackgroundValueBones;
 148     MaskImagePixelType m_BackgroundValueTrachea;
 149     MaskImagePixelType m_ForegroundValueLeftLung;
 150     MaskImagePixelType m_ForegroundValueRightLung;
 151
 152     MaskImagePixelType m_BackgroundValue;
 153     MaskImagePixelType m_ForegroundValue;
 154
 155     MaskImagePointer output;
 156     MaskImagePointer patient;
 157     MaskImagePointer lung;
 158     MaskImagePointer bones;
 159     MaskImagePointer trachea;
 160
 161     std::map<std::string, double> m_FuzzyThreshold;
 162     double m_IntermediateSpacing;
 163     bool   m_UseBones;
 164     double m_DistanceMaxToAnteriorPartOfTheVertebralBody;
 165
 166     void RemovePostPartOfVertebralBody();
 167
 168     std::string m_OutputMediastinumFilename;
 169
 170   private:
 171     ExtractMediastinumFilter(const Self&); //purposely not implemented
 172     void operator=(const Self&); //purposely not implemented
 173
 174   }; // end class
 175   //--------------------------------------------------------------------
 176
 177 } // end namespace clitk
 178 //--------------------------------------------------------------------
 179
 180 #ifndef ITK_MANUAL_INSTANTIATION
 181 #include "clitkExtractMediastinumFilter.txx"
 182 #endif
 183
 184 #endif