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 #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 labelling.
  37   */
  38   //--------------------------------------------------------------------
  39
  40   template <class TInputImageType>
  41   class ITK_EXPORT ExtractBonesFilter:
  42     public virtual clitk::FilterBase,
  43     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
  44     public itk::ImageToImageFilter<TInputImageType,
  45                                    itk::Image<uchar, TInputImageType::ImageDimension> >
  46   {
  47
  48   public:
  49     /** Standard class typedefs. */
  50     typedef itk::Image<uchar, TInputImageType::ImageDimension>      MaskImageType;
  51     typedef ExtractBonesFilter                                      Self;
  52     typedef itk::ImageToImageFilter<TInputImageType, MaskImageType> Superclass;
  53     typedef itk::SmartPointer<Self>                                 Pointer;
  54     typedef itk::SmartPointer<const Self>                           ConstPointer;
  55
  56     /** Method for creation through the object factory. */
  57     itkNewMacro(Self);
  58
  59     /** Run-time type information (and related methods). */
  60     itkTypeMacro(ExtractBonesFilter, ImageToImageFilter);
  61     FILTERBASE_INIT;
  62
  63     /** Some convenient typedefs */
  64     typedef TInputImageType                       InputImageType;
  65     typedef typename InputImageType::ConstPointer InputImageConstPointer;
  66     typedef typename InputImageType::Pointer      InputImagePointer;
  67     typedef typename InputImageType::RegionType   InputImageRegionType;
  68     typedef typename InputImageType::PixelType    InputImagePixelType;
  69     typedef typename InputImageType::SizeType     InputImageSizeType;
  70     typedef typename InputImageType::IndexType    InputImageIndexType;
  71
  72     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
  73     typedef typename MaskImageType::Pointer      MaskImagePointer;
  74     typedef typename MaskImageType::RegionType   MaskImageRegionType;
  75     typedef typename MaskImageType::PixelType    MaskImagePixelType;
  76     typedef typename MaskImageType::SizeType     MaskImageSizeType;
  77     typedef typename MaskImageType::IndexType    MaskImageIndexType;
  78
  79     itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
  80     typedef int InternalPixelType;
  81     typedef itk::Image<InternalPixelType, InputImageType::ImageDimension> InternalImageType;
  82     typedef typename InternalImageType::Pointer                           InternalImagePointer;
  83     typedef typename InternalImageType::IndexType                         InternalIndexType;
  84     typedef LabelizeParameters<InternalPixelType>                         LabelParamType;
  85
  86     /** Connect inputs */
  87     void SetInput(const InputImageType * image);
  88
  89     // Set all options at a time
  90     template<class ArgsInfoType>
  91       void SetArgsInfo(ArgsInfoType arg);
  92
  93     // Background / Foreground
  94     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
  95     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
  96
  97     itkSetMacro(MinimalComponentSize, int);
  98     itkGetConstMacro(MinimalComponentSize, int);
  99     GGO_DefineOption(minSize, SetMinimalComponentSize, int);
 100
 101     // Output filename  (for AFBD)
 102     itkSetMacro(OutputBonesFilename, std::string);
 103     itkGetMacro(OutputBonesFilename, std::string);
 104     GGO_DefineOption(output, SetOutputBonesFilename, std::string);
 105
 106     // Step 0
 107     itkBooleanMacro(InitialSmoothing);
 108     itkSetMacro(InitialSmoothing, bool);
 109     itkGetMacro(InitialSmoothing, bool);
 110     GGO_DefineOption_Flag(smooth, SetInitialSmoothing);
 111
 112     itkSetMacro(SmoothingConductanceParameter, double);
 113     itkGetConstMacro(SmoothingConductanceParameter, double);
 114     GGO_DefineOption(cond, SetSmoothingConductanceParameter, double);
 115
 116     itkSetMacro(SmoothingNumberOfIterations, int);
 117     itkGetConstMacro(SmoothingNumberOfIterations, int);
 118     GGO_DefineOption(iter, SetSmoothingNumberOfIterations, int);
 119
 120     itkSetMacro(SmoothingTimeStep, double);
 121     itkGetConstMacro(SmoothingTimeStep, double);
 122     GGO_DefineOption(time, SetSmoothingTimeStep, double);
 123
 124     itkSetMacro(SmoothingUseImageSpacing, bool);
 125     itkGetConstMacro(SmoothingUseImageSpacing, bool);
 126     itkBooleanMacro(SmoothingUseImageSpacing);
 127     GGO_DefineOption_Flag(spacing, SetSmoothingUseImageSpacing);
 128
 129     // Step 1
 130     itkSetMacro(UpperThreshold1, InputImagePixelType);
 131     itkGetMacro(UpperThreshold1, InputImagePixelType);
 132     GGO_DefineOption(upper1, SetUpperThreshold1, InputImagePixelType);
 133
 134     itkSetMacro(LowerThreshold1, InputImagePixelType);
 135     itkGetMacro(LowerThreshold1, InputImagePixelType);
 136     GGO_DefineOption(lower1, SetLowerThreshold1, InputImagePixelType);
 137
 138     itkSetMacro(FullConnectivity, bool);
 139     itkGetConstMacro(FullConnectivity, bool);
 140     itkBooleanMacro(FullConnectivity);
 141     GGO_DefineOption_Flag(full, SetFullConnectivity);
 142
 143     // Step 2
 144     itkSetMacro(UpperThreshold2, InputImagePixelType);
 145     itkGetMacro(UpperThreshold2, InputImagePixelType);
 146     GGO_DefineOption(upper2, SetUpperThreshold2, InputImagePixelType);
 147
 148     itkSetMacro(LowerThreshold2, InputImagePixelType);
 149     itkGetMacro(LowerThreshold2, InputImagePixelType);
 150     GGO_DefineOption(lower2, SetLowerThreshold2, InputImagePixelType);
 151
 152     itkSetMacro(Radius2, InputImageSizeType);
 153     itkGetConstMacro(Radius2, InputImageSizeType);
 154     GGO_DefineOption_Vector(radius2, SetRadius2, InputImageSizeType, ImageDimension, true);
 155
 156     itkSetMacro(SampleRate2, int);
 157     itkGetConstMacro(SampleRate2, int);
 158     GGO_DefineOption(sampleRate2, SetSampleRate2, int);
 159
 160     // Step fill holes
 161     itkSetMacro(FillHoles, bool);
 162     itkGetConstMacro(FillHoles, bool);
 163     itkBooleanMacro(FillHoles);
 164     GGO_DefineOption_Flag(doNotFillHoles, SetFillHoles);
 165
 166     // Step Auto Crop
 167     itkSetMacro(AutoCrop, bool);
 168     itkGetConstMacro(AutoCrop, bool);
 169     itkBooleanMacro(AutoCrop);
 170     GGO_DefineOption_Flag(noAutoCrop, SetAutoCrop);
 171
 172   protected:
 173     ExtractBonesFilter();
 174     virtual ~ExtractBonesFilter() {}
 175
 176     // Global options
 177     itkSetMacro(BackgroundValue, MaskImagePixelType);
 178     itkSetMacro(ForegroundValue, MaskImagePixelType);
 179     MaskImagePixelType m_BackgroundValue;
 180     MaskImagePixelType m_ForegroundValue;
 181     bool m_AutoCrop;
 182
 183     // Step 0 : Initial Filtering
 184     bool m_InitialSmoothing;
 185     double m_SmoothingConductanceParameter;
 186     int m_SmoothingNumberOfIterations;
 187     double m_SmoothingTimeStep;
 188     bool m_SmoothingUseImageSpacing;
 189
 190     // Step 1
 191     InputImagePixelType m_UpperThreshold1;
 192     InputImagePixelType m_LowerThreshold1;
 193     int m_MinimalComponentSize;
 194     bool m_FullConnectivity;
 195
 196     // Step 2
 197     InputImagePixelType m_UpperThreshold2;
 198     InputImagePixelType m_LowerThreshold2;
 199     InputImageSizeType m_Radius2;
 200     int m_SampleRate2;
 201
 202     // Step
 203     bool m_FillHoles;
 204     InputImageSizeType m_FillHolesDirections;
 205
 206     virtual void GenerateOutputInformation();
 207     virtual void GenerateData();
 208
 209     // Steps
 210     void RemoveAir();
 211     void FindTrachea();
 212     void ExtractBones();
 213     void RemoveTrachea();
 214     void BonesSeparation();
 215     std::string m_OutputBonesFilename;
 216     InputImageConstPointer input;
 217     InputImagePointer filtered_input;
 218     MaskImageConstPointer patient;
 219     InputImagePointer working_input;
 220     typename InternalImageType::Pointer working_image;
 221     typename InternalImageType::Pointer trachea;
 222     typename InternalImageType::Pointer output;
 223
 224   private:
 225     ExtractBonesFilter(const Self&); //purposely not implemented
 226     void operator=(const Self&); //purposely not implemented
 227
 228   }; // end class
 229   //--------------------------------------------------------------------
 230
 231 } // end namespace clitk
 232 //--------------------------------------------------------------------
 233
 234 #ifndef ITK_MANUAL_INSTANTIATION
 235 #include "clitkExtractBonesFilter.txx"
 236 #endif
 237
 238 #endif