some segmentation tools (most from jef)

[clitk.git] / segmentation / clitkExtractMediastinumFilter.h

diff --git a/segmentation/clitkExtractMediastinumFilter.h b/segmentation/clitkExtractMediastinumFilter.h
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+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+  ======================================================================-====*/
+
+#ifndef CLITKEXTRACTMEDIASTINUMFILTER_H
+#define CLITKEXTRACTMEDIASTINUMFILTER_H
+
+#include "clitkFilterBase.h"
+
+namespace clitk {
+  
+  //--------------------------------------------------------------------
+  /*
+    Try to extract the mediastinum part of a thorax CT.
+    Inputs : 
+    - Patient label image
+    - Lungs label image
+    - Bones label image
+  */
+  //--------------------------------------------------------------------
+  
+  template <class TImageType>
+  class ITK_EXPORT ExtractMediastinumFilter: 
+    public clitk::FilterBase, 
+    public itk::ImageToImageFilter<TImageType, TImageType> 
+  {
+
+  public:
+    /** Standard class typedefs. */
+    typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
+    typedef ExtractMediastinumFilter            Self;
+    typedef itk::SmartPointer<Self>             Pointer;
+    typedef itk::SmartPointer<const Self>       ConstPointer;
+    
+    /** Method for creation through the object factory. */
+    itkNewMacro(Self);
+    
+    /** Run-time type information (and related methods). */
+    itkTypeMacro(ExtractMediastinumFilter, InPlaceImageFilter);
+    FILTERBASE_INIT;
+
+    /** Some convenient typedefs. */
+    typedef TImageType                       ImageType;
+    typedef typename ImageType::ConstPointer ImageConstPointer;
+    typedef typename ImageType::Pointer      ImagePointer;
+    typedef typename ImageType::RegionType   ImageRegionType; 
+    typedef typename ImageType::PixelType    ImagePixelType; 
+    typedef typename ImageType::SizeType     ImageSizeType; 
+    typedef typename ImageType::IndexType    ImageIndexType; 
+        
+    /** Connect inputs */
+    void SetInputPatientLabelImage(const TImageType * image, ImagePixelType bg=0);
+    void SetInputLungLabelImage(const TImageType * image, ImagePixelType bg=0, 
+                                 ImagePixelType fgLeftLung=1, ImagePixelType fgRightLung=2);
+    void SetInputBonesLabelImage(const TImageType * image, ImagePixelType bg=0);
+   
+    /** ImageDimension constants */
+    itkStaticConstMacro(ImageDimension, unsigned int, TImageType::ImageDimension);
+
+    // Set all options at a time
+    template<class ArgsInfoType>
+      void SetArgsInfo(ArgsInfoType arg);
+   
+    // Background / Foreground
+    itkSetMacro(BackgroundValuePatient, ImagePixelType);
+    itkGetConstMacro(BackgroundValuePatient, ImagePixelType);
+    GGO_DefineOption(patientBG, SetBackgroundValuePatient, ImagePixelType);
+    
+    itkSetMacro(BackgroundValueLung, ImagePixelType);
+    itkGetConstMacro(BackgroundValueLung, ImagePixelType);
+    GGO_DefineOption(lungBG, SetBackgroundValueLung, ImagePixelType);
+    
+    itkSetMacro(BackgroundValueBones, ImagePixelType);
+    itkGetConstMacro(BackgroundValueBones, ImagePixelType);
+    GGO_DefineOption(bonesBG, SetBackgroundValueBones, ImagePixelType);
+    
+    itkGetConstMacro(BackgroundValue, ImagePixelType);
+    itkGetConstMacro(ForegroundValue, ImagePixelType);
+
+    itkSetMacro(ForegroundValueLeftLung, ImagePixelType);
+    itkGetConstMacro(ForegroundValueLeftLung, ImagePixelType);
+    GGO_DefineOption(lungLeft, SetForegroundValueLeftLung, ImagePixelType);
+    
+    itkSetMacro(ForegroundValueRightLung, ImagePixelType);
+    itkGetConstMacro(ForegroundValueRightLung, ImagePixelType);
+    GGO_DefineOption(lungRight, SetForegroundValueRightLung, ImagePixelType);
+    
+    itkSetMacro(IntermediateSpacing, double);
+    itkGetConstMacro(IntermediateSpacing, double);
+    GGO_DefineOption(spacing, SetIntermediateSpacing, double);
+
+    itkSetMacro(FuzzyThreshold1, double);
+    itkGetConstMacro(FuzzyThreshold1, double);
+    GGO_DefineOption(fuzzy1, SetFuzzyThreshold1, double);
+
+    itkSetMacro(FuzzyThreshold2, double);
+    itkGetConstMacro(FuzzyThreshold2, double);
+    GGO_DefineOption(fuzzy2, SetFuzzyThreshold2, double);
+
+  protected:
+    ExtractMediastinumFilter();
+    virtual ~ExtractMediastinumFilter() {}
+    
+    virtual void GenerateOutputInformation();
+    virtual void GenerateInputRequestedRegion();
+    virtual void GenerateData();
+       
+    itkSetMacro(BackgroundValue, ImagePixelType);
+    itkSetMacro(ForegroundValue, ImagePixelType);
+    
+    ImagePixelType m_BackgroundValuePatient;
+    ImagePixelType m_BackgroundValueLung;
+    ImagePixelType m_BackgroundValueBones;
+    ImagePixelType m_ForegroundValueLeftLung;
+    ImagePixelType m_ForegroundValueRightLung;
+
+    ImagePixelType m_BackgroundValue;
+    ImagePixelType m_ForegroundValue;
+    
+    double m_IntermediateSpacing;
+    double m_FuzzyThreshold1;
+    double m_FuzzyThreshold2;
+    
+  private:
+    ExtractMediastinumFilter(const Self&); //purposely not implemented
+    void operator=(const Self&); //purposely not implemented
+    
+  }; // end class
+  //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkExtractMediastinumFilter.txx"
+#endif
+
+#endif