Moved from repository clitk to clitk.private/tests_dav

[clitk.git] / segmentation / clitkExtractMediastinumFilter.h

diff --git a/segmentation/clitkExtractMediastinumFilter.h b/segmentation/clitkExtractMediastinumFilter.h
index ea7f86aace0697dcf793cf246d3aec0d97e52b53..3144c95be73a468f37d27e453342a6e406f73240 100644 (file)
--- a/segmentation/clitkExtractMediastinumFilter.h
+++ b/segmentation/clitkExtractMediastinumFilter.h
@@ -19,27 +19,25 @@
 #ifndef CLITKEXTRACTMEDIASTINUMFILTER_H
 #define CLITKEXTRACTMEDIASTINUMFILTER_H
 
-#include "clitkFilterBase.h"
-#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+#include "clitkStructuresExtractionFilter.h"
 
 namespace clitk {
   
   //--------------------------------------------------------------------
   /*
     Try to extract the mediastinum part of a thorax CT.
-    Inputs : 
-    - Patient label image
-    - Lungs label image
-    - Bones label image
-    - Trachea label image
+    Input masks needed : 
+    - Patient
+    - Lungs 
+    - Bones [Optional]
+    - Trachea
+    - VertebralBody 
   */
   //--------------------------------------------------------------------
   
   template <class TImageType>
   class ITK_EXPORT ExtractMediastinumFilter: 
-    public virtual clitk::FilterBase, 
-    public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
-    public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > 
+    public clitk::StructuresExtractionFilter<TImageType>
   {
 
   public:
@@ -63,8 +61,13 @@ namespace clitk {
     typedef typename MaskImageType::IndexType    MaskImageIndexType; 
     typedef typename MaskImageType::PointType    MaskImagePointType; 
         
+    typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
+    typedef typename MaskSliceType::Pointer      MaskSlicePointer;
+    typedef typename MaskSliceType::PointType    MaskSlicePointType;
+
     /** Standard class typedefs. */
-    typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
+    //    typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
+    typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
     typedef ExtractMediastinumFilter            Self;
     typedef itk::SmartPointer<Self>             Pointer;
     typedef itk::SmartPointer<const Self>       ConstPointer;
@@ -83,8 +86,8 @@ namespace clitk {
                                 MaskImagePixelType fgLeftLung=1, MaskImagePixelType fgRightLung=2);
     void SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
     void SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
-   
-   // Output filename  (for AFBD)
+
+    // Output filename  (for AFBD)
     itkSetMacro(OutputMediastinumFilename, std::string);
     itkGetConstMacro(OutputMediastinumFilename, std::string);
 
@@ -101,9 +104,6 @@ namespace clitk {
     itkSetMacro(BackgroundValueBones, MaskImagePixelType);
     itkGetConstMacro(BackgroundValueBones, MaskImagePixelType);
     
-    itkGetConstMacro(BackgroundValue, MaskImagePixelType);
-    itkGetConstMacro(ForegroundValue, MaskImagePixelType);
-
     itkSetMacro(ForegroundValueLeftLung, MaskImagePixelType);
     itkGetConstMacro(ForegroundValueLeftLung, MaskImagePixelType);
     
@@ -116,24 +116,15 @@ namespace clitk {
     itkSetMacro(IntermediateSpacing, double);
     itkGetConstMacro(IntermediateSpacing, double);
 
-    itkSetMacro(FuzzyThreshold1, double);
-    itkGetConstMacro(FuzzyThreshold1, double);
-
-    itkSetMacro(FuzzyThreshold2, double);
-    itkGetConstMacro(FuzzyThreshold2, double);
-
-    itkSetMacro(FuzzyThreshold3, double);
-    itkGetConstMacro(FuzzyThreshold3, double);
-
     itkBooleanMacro(UseBones);
     itkSetMacro(UseBones, bool);
     itkGetConstMacro(UseBones, bool);
 
-    itkSetMacro(UpperThreshold, double);
-    itkGetConstMacro(UpperThreshold, double);
+    itkSetMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
+    itkGetConstMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
 
-    itkSetMacro(LowerThreshold, double);
-    itkGetConstMacro(LowerThreshold, double);
+    void SetFuzzyThreshold(std::string tag, double value);
+    double GetFuzzyThreshold(std::string tag);
 
   protected:
     ExtractMediastinumFilter();
@@ -142,10 +133,7 @@ namespace clitk {
     virtual void GenerateOutputInformation();
     virtual void GenerateInputRequestedRegion();
     virtual void GenerateData();
-       
-    itkSetMacro(BackgroundValue, MaskImagePixelType);
-    itkSetMacro(ForegroundValue, MaskImagePixelType);
-    
+         
     MaskImagePixelType m_BackgroundValuePatient;
     MaskImagePixelType m_BackgroundValueLung;
     MaskImagePixelType m_BackgroundValueBones;
@@ -153,18 +141,18 @@ namespace clitk {
     MaskImagePixelType m_ForegroundValueLeftLung;
     MaskImagePixelType m_ForegroundValueRightLung;
 
-    MaskImagePixelType m_BackgroundValue;
-    MaskImagePixelType m_ForegroundValue;
-
-    typename MaskImageType::Pointer output;
+    MaskImagePointer output;
+    MaskImagePointer patient;
+    MaskImagePointer lung;
+    MaskImagePointer bones;
+    MaskImagePointer trachea;
 
+    std::map<std::string, double> m_FuzzyThreshold;
     double m_IntermediateSpacing;
-    double m_FuzzyThreshold1;
-    double m_FuzzyThreshold2;
-    double m_FuzzyThreshold3;
     bool   m_UseBones;
-    double m_UpperThreshold;
-    double m_LowerThreshold;
+    double m_DistanceMaxToAnteriorPartOfTheVertebralBody;
+
+    void RemovePostPartOfVertebralBody();
     
     std::string m_OutputMediastinumFilename;