X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.h;h=50d553ae41ce9c130d9ba7acfde941354f3d1fd6;hb=573d80d0f7a17607d2ee883c21c940c0ba020282;hp=6ec698d3a204bc98dddd17190dafa44ba8e83209;hpb=44ebb81a500e42cf19964d209e14a59812a0dd4d;p=clitk.git

diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h
index 6ec698d..50d553a 100644
--- a/segmentation/clitkExtractLungFilter.h
+++ b/segmentation/clitkExtractLungFilter.h
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 #ifndef CLITKEXTRACTLUNGSFILTER_H
 #define CLITKEXTRACTLUNGSFILTER_H
@@ -24,6 +24,7 @@
 #include "clitkDecomposeAndReconstructImageFilter.h"
 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
 #include "clitkSegmentationUtils.h"
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
 
 // itk
 #include "itkStatisticsImageFilter.h"
@@ -55,15 +56,17 @@ namespace clitk {
   //--------------------------------------------------------------------
   
   //--------------------------------------------------------------------
-  template <class TImageType, class TMaskImageType>
+  template <class TImageType>
   class ITK_EXPORT ExtractLungFilter: 
     public virtual clitk::FilterBase, 
-    public itk::ImageToImageFilter<TImageType, TMaskImageType> 
+    public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
+    public itk::ImageToImageFilter<TImageType, itk::Image<uchar, TImageType::ImageDimension> > 
   {
     
   public:
     /** Standard class typedefs. */
-    typedef itk::ImageToImageFilter<TImageType, TMaskImageType> Superclass;
+    typedef itk::Image<uchar, TImageType::ImageDimension> MaskImageType;
+    typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
     typedef ExtractLungFilter              Self;
     typedef itk::SmartPointer<Self>        Pointer;
     typedef itk::SmartPointer<const Self>  ConstPointer;
@@ -85,7 +88,6 @@ namespace clitk {
     typedef typename ImageType::IndexType    InputImageIndexType; 
     typedef typename ImageType::PointType    InputImagePointType; 
         
-    typedef TMaskImageType                       MaskImageType;
     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
     typedef typename MaskImageType::Pointer      MaskImagePointer;
     typedef typename MaskImageType::RegionType   MaskImageRegionType; 
@@ -95,7 +97,8 @@ namespace clitk {
     typedef typename MaskImageType::PointType    MaskImagePointType; 
 
     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
-    typedef int InternalPixelType;
+    //    typedef int InternalPixelType;
+    typedef uchar InternalPixelType;
     typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
     typedef typename InternalImageType::Pointer                      InternalImagePointer;
     typedef typename InternalImageType::IndexType                    InternalIndexType;
@@ -103,14 +106,15 @@ namespace clitk {
     
     /** Connect inputs */
     void SetInput(const ImageType * image);
-    void SetInputPatientMask(MaskImageType * mask, MaskImagePixelType BG);
     itkSetMacro(PatientMaskBackgroundValue, MaskImagePixelType);
     itkGetConstMacro(PatientMaskBackgroundValue, MaskImagePixelType);
-    GGO_DefineOption(patientBG, SetPatientMaskBackgroundValue, MaskImagePixelType);
 
-    // Set all options at a time
-    template<class ArgsInfoType>
-      void SetArgsInfo(ArgsInfoType arg);
+    // Output filename  (for AFBD)
+    itkSetMacro(OutputLungFilename, std::string);
+    itkGetMacro(OutputLungFilename, std::string);
+
+    itkSetMacro(OutputTracheaFilename, std::string);
+    itkGetMacro(OutputTracheaFilename, std::string);
 
     // Get output (only availabe after update !)
     typename MaskImageType::Pointer GetTracheaImage() { return trachea; }
@@ -122,72 +126,70 @@ namespace clitk {
     // For common segmentation processes
     itkSetMacro(MinimalComponentSize, int);
     itkGetConstMacro(MinimalComponentSize, int);
-    GGO_DefineOption(minSize, SetMinimalComponentSize, int);
 
     // Step 1 options RemoveAir
     itkSetMacro(UpperThreshold, InputImagePixelType);
     itkGetConstMacro(UpperThreshold, InputImagePixelType);
-    GGO_DefineOption(upper, SetUpperThreshold, InputImagePixelType);
 
     itkSetMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
     itkGetConstMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
-    GGO_DefineOption(skipslices, SetNumberOfSlicesToSkipBeforeSearchingSeed, int);
     
     itkSetMacro(LowerThreshold, InputImagePixelType);
     itkGetConstMacro(LowerThreshold, InputImagePixelType);
     itkSetMacro(UseLowerThreshold, bool);
     itkGetConstMacro(UseLowerThreshold, bool);
     itkBooleanMacro(UseLowerThreshold);
-    GGO_DefineOption_WithTest(lower, SetLowerThreshold, InputImagePixelType, UseLowerThreshold);
 
     void SetLabelizeParameters1(LabelParamType * a) { m_LabelizeParameters1 = a; }
     itkGetConstMacro(LabelizeParameters1, LabelParamType*);
-    GGO_DefineOption_LabelParam(1, SetLabelizeParameters1, LabelParamType);
 
     // Step 2 options FindTrachea
     itkSetMacro(UpperThresholdForTrachea, InputImagePixelType);
     itkGetConstMacro(UpperThresholdForTrachea, InputImagePixelType);
-    GGO_DefineOption(upperThresholdForTrachea, SetUpperThresholdForTrachea, InputImagePixelType);
 
     itkSetMacro(MultiplierForTrachea, double);
     itkGetConstMacro(MultiplierForTrachea, double);
-    GGO_DefineOption(multiplierForTrachea, SetMultiplierForTrachea, double);
 
     itkSetMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
     itkGetConstMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
-    GGO_DefineOption(thresholdStepSizeForTrachea, SetThresholdStepSizeForTrachea, InputImagePixelType);
 
     void AddSeed(InternalIndexType s);
     std::vector<InternalIndexType> & GetSeeds() { return  m_Seeds; }
-    GGO_DefineOption_Vector(seed, AddSeed, InternalIndexType, ImageType::ImageDimension, true);
+
+    itkSetMacro(TracheaVolumeMustBeCheckedFlag, bool);
+    itkGetConstMacro(TracheaVolumeMustBeCheckedFlag, bool);
+    itkBooleanMacro(TracheaVolumeMustBeCheckedFlag);    
+
+    itkSetMacro(VerboseRegionGrowingFlag, bool);
+    itkGetConstMacro(VerboseRegionGrowingFlag, bool);
+    itkBooleanMacro(VerboseRegionGrowingFlag);    
 
     // Step 3 options ExtractLung
     itkSetMacro(NumberOfHistogramBins, int);
     itkGetConstMacro(NumberOfHistogramBins, int);
-    GGO_DefineOption(bins, SetNumberOfHistogramBins, int);
 
     void SetLabelizeParameters2(LabelParamType* a) { m_LabelizeParameters2 = a; }
     itkGetConstMacro(LabelizeParameters2, LabelParamType*);
-    GGO_DefineOption_LabelParam(2, SetLabelizeParameters2, LabelParamType);
 
     // Step 4 options RemoveTrachea
     itkSetMacro(RadiusForTrachea, int);
     itkGetConstMacro(RadiusForTrachea, int);
-    GGO_DefineOption(radius, SetRadiusForTrachea, int);
     
     void SetLabelizeParameters3(LabelParamType * a) { m_LabelizeParameters3 = a; }
     itkGetConstMacro(LabelizeParameters3, LabelParamType*);
-    GGO_DefineOption_LabelParam(3, SetLabelizeParameters3, LabelParamType);
 
     // Step 5 final openclose
-    itkSetMacro(FinalOpenClose, bool);
-    itkGetConstMacro(FinalOpenClose, bool);
-    itkBooleanMacro(FinalOpenClose);
-    GGO_DefineOption_Flag(openclose, SetFinalOpenClose);
+    itkSetMacro(OpenCloseFlag, bool);
+    itkGetConstMacro(OpenCloseFlag, bool);
+    itkBooleanMacro(OpenCloseFlag);
 
-    itkSetMacro(FinalOpenCloseRadius, int);
-    itkGetConstMacro(FinalOpenCloseRadius, int);
-    GGO_DefineOption(opencloseRadius, SetFinalOpenCloseRadius, int);
+    itkSetMacro(OpenCloseRadius, int);
+    itkGetConstMacro(OpenCloseRadius, int);
+    
+    // Step 6 fill holes
+    itkSetMacro(FillHolesFlag, bool);
+    itkGetConstMacro(FillHolesFlag, bool);
+    itkBooleanMacro(FillHolesFlag);
 
   protected:
     ExtractLungFilter();
@@ -195,12 +197,12 @@ namespace clitk {
 
     // Main members
     InputImageConstPointer input;
-    MaskImageConstPointer patient;
+    MaskImagePointer patient;
     InputImagePointer working_input;
-    typename InternalImageType::Pointer working_image;  
-    typename InternalImageType::Pointer trachea_tmp;
+    std::string m_OutputLungFilename;
+    std::string m_OutputTracheaFilename;
+    MaskImagePointer working_mask;  
     MaskImagePointer trachea;
-    MaskImagePointer output;
     unsigned int m_MaxSeedNumber;
 
     // Global options
@@ -223,6 +225,8 @@ namespace clitk {
     double m_MultiplierForTrachea;
     std::vector<InternalIndexType> m_Seeds;
     int m_NumberOfSlicesToSkipBeforeSearchingSeed;
+    bool m_TracheaVolumeMustBeCheckedFlag;
+    bool m_VerboseRegionGrowingFlag;
 
     // Step 3
     int m_NumberOfHistogramBins;
@@ -233,11 +237,16 @@ namespace clitk {
     LabelParamType* m_LabelizeParameters3;
 
     // Step 5
-    bool m_FinalOpenClose;    
-    int m_FinalOpenCloseRadius;
+    bool m_OpenCloseFlag;    
+    int m_OpenCloseRadius;
+
+    // Step 6
+    bool m_FillHolesFlag;    
+    InputImageSizeType m_FillHolesDirections;
 
     // Main functions
     virtual void GenerateOutputInformation();
+    virtual void GenerateInputRequestedRegion();
     virtual void GenerateData();
     
     // Functions for trachea extraction