segmentation/clitkExtractBonesFilter.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 CLITKEXTRACTBONESSFILTER_H
  20 #define CLITKEXTRACTBONESSFILTER_H
  21
  22 // clitk
  23 #include "clitkFilterBase.h"
  24 #include "clitkDecomposeAndReconstructImageFilter.h"
  25 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
  26 #include "clitkSegmentationUtils.h"
  27 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
  28
  29 // itk
  30 #include "itkStatisticsImageFilter.h"
  31
  32 namespace clitk {
  33
  34   //--------------------------------------------------------------------
  35   /*
  36     Extract bony anatomy through thresholding and connected component
  37     labelling.
  38   */
  39   //--------------------------------------------------------------------
  40
  41   template <class TInputImageType>
  42   class ITK_EXPORT ExtractBonesFilter:
  43     public virtual clitk::FilterBase,
  44     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  45     public itk::ImageToImageFilter<TInputImageType,
  46                                    itk::Image<uchar, TInputImageType::ImageDimension> >
  47   {
  48
  49   public:
  50     /** Standard class typedefs. */
  51     typedef itk::Image<uchar, TInputImageType::ImageDimension>      MaskImageType;
  52     typedef ExtractBonesFilter                                      Self;
  53     typedef itk::ImageToImageFilter<TInputImageType, MaskImageType> Superclass;
  54     typedef itk::SmartPointer<Self>                                 Pointer;
  55     typedef itk::SmartPointer<const Self>                           ConstPointer;
  56
  57     /** Method for creation through the object factory. */
  58     itkNewMacro(Self);
  59
  60     /** Run-time type information (and related methods). */
  61     itkTypeMacro(ExtractBonesFilter, ImageToImageFilter);
  62     FILTERBASE_INIT;
  63
  64     /** Some convenient typedefs */
  65     typedef TInputImageType                       InputImageType;
  66     typedef typename InputImageType::ConstPointer InputImageConstPointer;
  67     typedef typename InputImageType::Pointer      InputImagePointer;
  68     typedef typename InputImageType::RegionType   InputImageRegionType;
  69     typedef typename InputImageType::PixelType    InputImagePixelType;
  70     typedef typename InputImageType::SizeType     InputImageSizeType;
  71     typedef typename InputImageType::IndexType    InputImageIndexType;
  72
  73     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
  74     typedef typename MaskImageType::Pointer      MaskImagePointer;
  75     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  76     typedef typename MaskImageType::PixelType    MaskImagePixelType;
  77     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  78     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  79
  80     itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
  81     typedef int InternalPixelType;
  82     typedef itk::Image<InternalPixelType, InputImageType::ImageDimension> InternalImageType;
  83     typedef typename InternalImageType::Pointer                           InternalImagePointer;
  84     typedef typename InternalImageType::IndexType                         InternalIndexType;
  85     typedef LabelizeParameters<InternalPixelType>                         LabelParamType;
  86
  87     /** Connect inputs */
  88     void SetInput(const InputImageType * image);
  89
  90     // Background / Foreground
  91     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  92     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  93
  94     itkSetMacro(MinimalComponentSize, int);
  95     itkGetConstMacro(MinimalComponentSize, int);
  96
  97     // Output filename  (for AFBD)
  98     itkSetMacro(OutputBonesFilename, std::string);
  99     itkGetMacro(OutputBonesFilename, std::string);
 100
 101     // Step 0
 102     itkBooleanMacro(InitialSmoothing);
 103     itkSetMacro(InitialSmoothing, bool);
 104     itkGetMacro(InitialSmoothing, bool);
 105
 106     itkSetMacro(SmoothingConductanceParameter, double);
 107     itkGetConstMacro(SmoothingConductanceParameter, double);
 108
 109     itkSetMacro(SmoothingNumberOfIterations, int);
 110     itkGetConstMacro(SmoothingNumberOfIterations, int);
 111
 112     itkSetMacro(SmoothingTimeStep, double);
 113     itkGetConstMacro(SmoothingTimeStep, double);
 114
 115     itkSetMacro(SmoothingUseImageSpacing, bool);
 116     itkGetConstMacro(SmoothingUseImageSpacing, bool);
 117     itkBooleanMacro(SmoothingUseImageSpacing);
 118
 119     // Step 1
 120     itkSetMacro(UpperThreshold1, InputImagePixelType);
 121     itkGetMacro(UpperThreshold1, InputImagePixelType);
 122
 123     itkSetMacro(LowerThreshold1, InputImagePixelType);
 124     itkGetMacro(LowerThreshold1, InputImagePixelType);
 125
 126     itkSetMacro(FullConnectivity, bool);
 127     itkGetConstMacro(FullConnectivity, bool);
 128     itkBooleanMacro(FullConnectivity);
 129
 130     // Step 2
 131     itkSetMacro(UpperThreshold2, InputImagePixelType);
 132     itkGetMacro(UpperThreshold2, InputImagePixelType);
 133
 134     itkSetMacro(LowerThreshold2, InputImagePixelType);
 135     itkGetMacro(LowerThreshold2, InputImagePixelType);
 136
 137     itkSetMacro(Radius2, InputImageSizeType);
 138     itkGetConstMacro(Radius2, InputImageSizeType);
 139
 140     itkSetMacro(SampleRate2, int);
 141     itkGetConstMacro(SampleRate2, int);
 142
 143     // Step fill holes
 144     itkSetMacro(FillHoles, bool);
 145     itkGetConstMacro(FillHoles, bool);
 146     itkBooleanMacro(FillHoles);
 147
 148     // Step Auto Crop
 149     itkSetMacro(AutoCrop, bool);
 150     itkGetConstMacro(AutoCrop, bool);
 151     itkBooleanMacro(AutoCrop);
 152
 153   protected:
 154     ExtractBonesFilter();
 155     virtual ~ExtractBonesFilter() {}
 156
 157     // Global options
 158     itkSetMacro(BackgroundValue, MaskImagePixelType);
 159     itkSetMacro(ForegroundValue, MaskImagePixelType);
 160     MaskImagePixelType m_BackgroundValue;
 161     MaskImagePixelType m_ForegroundValue;
 162     bool m_AutoCrop;
 163
 164     // Step 0 : Initial Filtering
 165     bool m_InitialSmoothing;
 166     double m_SmoothingConductanceParameter;
 167     int m_SmoothingNumberOfIterations;
 168     double m_SmoothingTimeStep;
 169     bool m_SmoothingUseImageSpacing;
 170
 171     // Step 1
 172     InputImagePixelType m_UpperThreshold1;
 173     InputImagePixelType m_LowerThreshold1;
 174     int m_MinimalComponentSize;
 175     bool m_FullConnectivity;
 176
 177     // Step 2
 178     InputImagePixelType m_UpperThreshold2;
 179     InputImagePixelType m_LowerThreshold2;
 180     InputImageSizeType m_Radius2;
 181     int m_SampleRate2;
 182
 183     // Step
 184     bool m_FillHoles;
 185     InputImageSizeType m_FillHolesDirections;
 186
 187     virtual void GenerateOutputInformation();
 188     virtual void GenerateData();
 189
 190     // Steps
 191     void RemoveAir();
 192     void FindTrachea();
 193     void ExtractBones();
 194     void RemoveTrachea();
 195     void BonesSeparation();
 196     std::string m_OutputBonesFilename;
 197     InputImageConstPointer input;
 198     InputImagePointer filtered_input;
 199     MaskImageConstPointer patient;
 200     InputImagePointer working_input;
 201     typename InternalImageType::Pointer working_image;
 202     typename InternalImageType::Pointer trachea;
 203     typename InternalImageType::Pointer output;
 204
 205   private:
 206     ExtractBonesFilter(const Self&); //purposely not implemented
 207     void operator=(const Self&); //purposely not implemented
 208
 209   }; // end class
 210   //--------------------------------------------------------------------
 211
 212 } // end namespace clitk
 213 //--------------------------------------------------------------------
 214
 215 #ifndef ITK_MANUAL_INSTANTIATION
 216 #include "clitkExtractBonesFilter.txx"
 217 #endif
 218
 219 #endif