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://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 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
  28 // itk
  29 #include "itkStatisticsImageFilter.h"
  30
  31 namespace clitk {
  32
  33   //--------------------------------------------------------------------
  34   /*
  35     Extract bony anatomy through thresholding and connected component labelling.
  36   */
  37   //--------------------------------------------------------------------
  38
  39   template <class TInputImageType, class TOutputImageType>
  40   class ITK_EXPORT ExtractBonesFilter:
  41     public clitk::FilterBase,
  42     public itk::ImageToImageFilter<TInputImageType, TOutputImageType>
  43   {
  44
  45   public:
  46     /** Standard class typedefs. */
  47     typedef ExtractBonesFilter              Self;
  48     typedef itk::ImageToImageFilter<TInputImageType, TOutputImageType> Superclass;
  49     typedef itk::SmartPointer<Self>         Pointer;
  50     typedef itk::SmartPointer<const Self>   ConstPointer;
  51
  52     /** Method for creation through the object factory. */
  53     itkNewMacro(Self);
  54
  55     /** Run-time type information (and related methods). */
  56     itkTypeMacro(ExtractBonesFilter, ImageToImageFilter);
  57     FILTERBASE_INIT;
  58
  59     /** Some convenient typedefs */
  60     typedef TInputImageType                       InputImageType;
  61     typedef typename InputImageType::ConstPointer InputImageConstPointer;
  62     typedef typename InputImageType::Pointer      InputImagePointer;
  63     typedef typename InputImageType::RegionType   InputImageRegionType;
  64     typedef typename InputImageType::PixelType    InputImagePixelType;
  65     typedef typename InputImageType::SizeType     InputImageSizeType;
  66     typedef typename InputImageType::IndexType    InputImageIndexType;
  67
  68     typedef TOutputImageType                       OutputImageType;
  69     typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
  70     typedef typename OutputImageType::Pointer      OutputImagePointer;
  71     typedef typename OutputImageType::RegionType   OutputImageRegionType;
  72     typedef typename OutputImageType::PixelType    OutputImagePixelType;
  73     typedef typename OutputImageType::SizeType     OutputImageSizeType;
  74     typedef typename OutputImageType::IndexType    OutputImageIndexType;
  75
  76     itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
  77     typedef int InternalPixelType;
  78     typedef itk::Image<InternalPixelType, InputImageType::ImageDimension> InternalImageType;
  79     typedef typename InternalImageType::Pointer                           InternalImagePointer;
  80     typedef typename InternalImageType::IndexType                         InternalIndexType;
  81     typedef LabelizeParameters<InternalPixelType>                         LabelParamType;
  82
  83     /** Connect inputs */
  84     void SetInput(const InputImageType * image);
  85
  86     // Set all options at a time
  87     template<class ArgsInfoType>
  88       void SetArgsInfo(ArgsInfoType arg);
  89
  90     // Background / Foreground
  91     itkGetConstMacro(BackgroundValue, OutputImagePixelType);
  92     itkGetConstMacro(ForegroundValue, OutputImagePixelType);
  93
  94     itkSetMacro(MinimalComponentSize, int);
  95     itkGetConstMacro(MinimalComponentSize, int);
  96     GGO_DefineOption(minSize, SetMinimalComponentSize, int);
  97
  98     // Step 0
  99     itkBooleanMacro(InitialSmoothing);
 100     itkSetMacro(InitialSmoothing, bool);
 101     itkGetMacro(InitialSmoothing, bool);
 102     GGO_DefineOption_Flag(smooth, SetInitialSmoothing);
 103
 104     itkSetMacro(SmoothingConductanceParameter, double);
 105     itkGetConstMacro(SmoothingConductanceParameter, double);
 106     GGO_DefineOption(cond, SetSmoothingConductanceParameter, double);
 107
 108     itkSetMacro(SmoothingNumberOfIterations, int);
 109     itkGetConstMacro(SmoothingNumberOfIterations, int);
 110     GGO_DefineOption(iter, SetSmoothingNumberOfIterations, int);
 111
 112     itkSetMacro(SmoothingTimeStep, double);
 113     itkGetConstMacro(SmoothingTimeStep, double);
 114     GGO_DefineOption(time, SetSmoothingTimeStep, double);
 115
 116     itkSetMacro(SmoothingUseImageSpacing, bool);
 117     itkGetConstMacro(SmoothingUseImageSpacing, bool);
 118     itkBooleanMacro(SmoothingUseImageSpacing);
 119     GGO_DefineOption_Flag(spacing, SetSmoothingUseImageSpacing);
 120
 121     // Step 1
 122     itkSetMacro(UpperThreshold1, InputImagePixelType);
 123     itkGetMacro(UpperThreshold1, InputImagePixelType);
 124     GGO_DefineOption(upper1, SetUpperThreshold1, InputImagePixelType);
 125
 126     itkSetMacro(LowerThreshold1, InputImagePixelType);
 127     itkGetMacro(LowerThreshold1, InputImagePixelType);
 128     GGO_DefineOption(lower1, SetLowerThreshold1, InputImagePixelType);
 129
 130     itkSetMacro(FullConnectivity, bool);
 131     itkGetConstMacro(FullConnectivity, bool);
 132     itkBooleanMacro(FullConnectivity);
 133     GGO_DefineOption_Flag(full, SetFullConnectivity);
 134
 135     // Step 2
 136     itkSetMacro(UpperThreshold2, InputImagePixelType);
 137     itkGetMacro(UpperThreshold2, InputImagePixelType);
 138     GGO_DefineOption(upper2, SetUpperThreshold2, InputImagePixelType);
 139
 140     itkSetMacro(LowerThreshold2, InputImagePixelType);
 141     itkGetMacro(LowerThreshold2, InputImagePixelType);
 142     GGO_DefineOption(lower2, SetLowerThreshold2, InputImagePixelType);
 143
 144     itkSetMacro(Radius2, InputImageSizeType);
 145     itkGetConstMacro(Radius2, InputImageSizeType);
 146     GGO_DefineOption_Vector(radius2, SetRadius2, InputImageSizeType, ImageDimension, true);
 147
 148     itkSetMacro(SampleRate2, int);
 149     itkGetConstMacro(SampleRate2, int);
 150     GGO_DefineOption(sampleRate2, SetSampleRate2, int);
 151
 152     // Final Step
 153     itkSetMacro(AutoCrop, bool);
 154     itkGetConstMacro(AutoCrop, bool);
 155     itkBooleanMacro(AutoCrop);
 156     GGO_DefineOption_Flag(autoCrop, SetAutoCrop);
 157
 158   protected:
 159     ExtractBonesFilter();
 160     virtual ~ExtractBonesFilter() {}
 161
 162     // Global options
 163     itkSetMacro(BackgroundValue, OutputImagePixelType);
 164     itkSetMacro(ForegroundValue, OutputImagePixelType);
 165     OutputImagePixelType m_BackgroundValue;
 166     OutputImagePixelType m_ForegroundValue;
 167     bool m_AutoCrop;
 168
 169     // Step 0 : Initial Filtering
 170     bool m_InitialSmoothing;
 171     double m_SmoothingConductanceParameter;
 172     int m_SmoothingNumberOfIterations;
 173     double m_SmoothingTimeStep;
 174     bool m_SmoothingUseImageSpacing;
 175
 176     // Step 1
 177     InputImagePixelType m_UpperThreshold1;
 178     InputImagePixelType m_LowerThreshold1;
 179     int m_MinimalComponentSize;
 180     bool m_FullConnectivity;
 181
 182     // Step 2
 183     InputImagePixelType m_UpperThreshold2;
 184     InputImagePixelType m_LowerThreshold2;
 185     InputImageSizeType m_Radius2;
 186     int m_SampleRate2;
 187
 188     virtual void GenerateOutputInformation();
 189     virtual void GenerateData();
 190
 191     // Steps
 192     void RemoveAir();
 193     void FindTrachea();
 194     void ExtractBones();
 195     void RemoveTrachea();
 196     void BonesSeparation();
 197     InputImageConstPointer input;
 198     InputImagePointer filtered_input;
 199     OutputImageConstPointer 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