X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.h;h=5ac8c4c51e86c2d7b5345fcefda25ea8ba8b3ec0;hb=ae51e9bb80bdcd9468718a9473c1e9316cef2fd5;hp=fcc7f2840ac88d2fd8d29742b94c63e29807e65e;hpb=765020625fbc092d283e221e36c83e60a1844cb7;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.h b/itk/clitkSegmentationUtils.h
index fcc7f28..5ac8c4c 100644
--- a/itk/clitkSegmentationUtils.h
+++ b/itk/clitkSegmentationUtils.h
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://www.centreleonberard.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
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ===========================================================================**/
+  ======================================================================-====*/
 
 #ifndef CLITKSEGMENTATIONUTILS_H
 #define CLITKSEGMENTATIONUTILS_H
@@ -23,10 +23,12 @@
 #include "clitkCommon.h"
 #include "clitkAutoCropFilter.h"
 #include "clitkLabelizeParameters.h"
+#include "clitkExtractSliceFilter.h"
 
 // itk
 #include <itkBoundingBox.h>
 #include <itkJoinSeriesImageFilter.h>
+#include <itkChangeInformationImageFilter.h>
 
 /*
   According to 
@@ -37,25 +39,6 @@
 namespace clitk {
 
   //--------------------------------------------------------------------
-  template<class ImageType>
-  void ComputeBBFromImageRegion(const ImageType * image, 
-                                typename ImageType::RegionType region,
-                                typename itk::BoundingBox<unsigned long, 
-                                                          ImageType::ImageDimension>::Pointer bb);
-  
-  //--------------------------------------------------------------------
-  template<int Dimension>
-  void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo, 
-                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1, 
-                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);
-
-  //--------------------------------------------------------------------
-  template<class ImageType>
-  void ComputeRegionFromBB(const ImageType * image, 
-                           const typename itk::BoundingBox<unsigned long, 
-                                                           ImageType::ImageDimension>::Pointer bb, 
-                           typename ImageType::RegionType & region);
-  //--------------------------------------------------------------------
   template<class TInternalImageType, class TMaskInternalImageType>
   typename TInternalImageType::Pointer
   SetBackground(const TInternalImageType * input,
@@ -102,11 +85,13 @@ namespace clitk {
   template<class ImageType>
   typename ImageType::Pointer
   AutoCrop(const ImageType * input, 
-           typename ImageType::PixelType BG) {
+           typename ImageType::PixelType BG, 
+           const bool useBorderFlag=false) {
     typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
     typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
     autoCropFilter->SetInput(input);
     autoCropFilter->SetBackgroundValue(BG);
+    autoCropFilter->SetUseBorder(useBorderFlag);
     autoCropFilter->Update();   
     return autoCropFilter->GetOutput();
   }
@@ -135,13 +120,6 @@ namespace clitk {
                           int minimalComponentSize,
                           LabelizeParameters<typename TImageType::PixelType> * param);
 
-  //--------------------------------------------------------------------
-  template<class ImageType>
-  typename ImageType::Pointer
-  ResizeImageLike(const ImageType * input,
-                  const itk::ImageBase<ImageType::ImageDimension> * like, 
-                  typename ImageType::PixelType BG);
-
 
   //--------------------------------------------------------------------
   template<class MaskImageType>
@@ -155,6 +133,18 @@ namespace clitk {
                                double spacing=-1, 
                                bool autocropflag=true, 
                                bool singleObjectCCL=true);
+  template<class MaskImageType>
+  typename MaskImageType::Pointer
+  SliceBySliceRelativePosition(const MaskImageType * input,
+			       const MaskImageType * object,
+			       int direction, 
+			       double threshold, 
+			       double angle, 
+                               bool inverseflag,
+                               bool uniqueConnectedComponent=false, 
+                               double spacing=-1, 
+                               bool autocropflag=true, 
+                               bool singleObjectCCL=true);
 
   //--------------------------------------------------------------------
   // In a binary image, search for the point belonging to the FG that
@@ -192,32 +182,52 @@ namespace clitk {
                         typename ImageType::PixelType BG=0);
   template<class ImageType>
   typename ImageType::Pointer
-  CropImageAbove(const ImageType * image, 
-                 int dim, double min, bool autoCrop = false,
-                 typename ImageType::PixelType BG=0);
+  CropImageRemoveGreaterThan(const ImageType * image, 
+                             int dim, double min, bool autoCrop = false,
+                             typename ImageType::PixelType BG=0);
   template<class ImageType>
   typename ImageType::Pointer
-  CropImageBelow(const ImageType * image, 
-                 int dim, double max,bool autoCrop = false,
-                 typename ImageType::PixelType BG=0);
+  CropImageRemoveLowerThan(const ImageType * image, 
+                           int dim, double max,bool autoCrop = false,
+                           typename ImageType::PixelType BG=0);
   //--------------------------------------------------------------------
 
 
   //--------------------------------------------------------------------
+  template<class ImageType, class LabelType>
+  typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
+  ComputeLabelMap(const ImageType * image, 
+                  typename ImageType::PixelType BG,                   
+                  bool computePerimeterFlag=false);
   template<class ImageType>
   void
   ComputeCentroids(const ImageType * image, 
                    typename ImageType::PixelType BG, 
                    std::vector<typename ImageType::PointType> & centroids);
+  template<class ImageType>
+  void
+  ComputeCentroids2(const ImageType * image, 
+                   typename ImageType::PixelType BG, 
+                   std::vector<typename ImageType::PointType> & centroids);
   //--------------------------------------------------------------------
 
 
   //--------------------------------------------------------------------
   template<class ImageType>
   void
-  ExtractSlices(const ImageType * image, int dim, 
-		std::vector< typename itk::Image<typename ImageType::PixelType, 
-                                                 ImageType::ImageDimension-1>::Pointer > & slices);
+  ExtractSlices(const ImageType * image, int direction,
+                std::vector<typename itk::Image<typename ImageType::PixelType,
+                                                ImageType::ImageDimension-1>::Pointer > & slices)
+  {
+    typedef ExtractSliceFilter<ImageType> ExtractSliceFilterType;
+    typedef typename ExtractSliceFilterType::SliceType SliceType;
+    typename ExtractSliceFilterType::Pointer
+      extractSliceFilter = ExtractSliceFilterType::New();
+    extractSliceFilter->SetInput(image);
+    extractSliceFilter->SetDirection(direction);
+    extractSliceFilter->Update();
+    extractSliceFilter->GetOutputSlices(slices);
+  }
   //--------------------------------------------------------------------
 
 
@@ -226,7 +236,7 @@ namespace clitk {
   typename ImageType::Pointer
   JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType, 
                                              ImageType::ImageDimension-1>::Pointer > & slices, 
-             const ImageType * input, 
+             const itk::ImageBase<ImageType::ImageDimension> * input, //const ImageType * input, 
              int direction) {
     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
     typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
@@ -258,14 +268,20 @@ namespace clitk {
     
     typedef std::map<int, PointType2D> MapPoint2DType;
     typedef std::vector<PointType3D> VectorPoint3DType;
+    typedef std::vector<PointType2D> VectorPoint2DType;
+
   public:
     static void Convert2DTo3D(const PointType2D & p2D, 
                               const ImageType * image, 
                               const int slice, 
                               PointType3D & p3D);
-    static void Convert2DTo3DList(const MapPoint2DType & map, 
+    static void Convert2DMapTo3DList(const MapPoint2DType & map, 
                                   const ImageType * image, 
                                   VectorPoint3DType & list);
+    static void Convert2DListTo3DList(const VectorPoint2DType & p, 
+                                      int slice,
+                                      const ImageType * image, 
+                                      VectorPoint3DType & list);
   };
 
   //--------------------------------------------------------------------
@@ -297,6 +313,15 @@ namespace clitk {
          bool extendSupport);
   //--------------------------------------------------------------------
 
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer 
+  Opening(const ImageType * image, typename ImageType::SizeType radius,
+          typename ImageType::PixelType BG, typename ImageType::PixelType FG);
+  //--------------------------------------------------------------------
+
+
   //--------------------------------------------------------------------
   template<class ValueType, class VectorType>
   void ConvertOption(std::string optionName, uint given, 
@@ -314,7 +339,16 @@ namespace clitk {
                                               std::vector<typename ImageType::PointType> & lB, 
                                               typename ImageType::PixelType BG, 
                                               int mainDirection, 
-                                              double offsetToKeep);
+                                              double offsetToKeep, 
+                                              bool keepIfEqual=false);
+  template<class ImageType>
+  void 
+  SliceBySliceSetBackgroundFromLineSeparation_pt(ImageType * input, 
+                                              std::vector<typename ImageType::PointType> & lA, 
+                                              std::vector<typename ImageType::PointType> & lB, 
+                                              typename ImageType::PixelType BG, 
+                                              typename ImageType::PointType offsetToKeep, 
+                                              bool keepIfEqual=false);
   //--------------------------------------------------------------------
 
 
@@ -323,6 +357,14 @@ namespace clitk {
   void AndNot(ImageType * input, 
               const ImageType * object, 
               typename ImageType::PixelType BG=0);
+  template<class ImageType>
+  void And(ImageType * input, 
+           const ImageType * object, 
+           typename ImageType::PixelType BG=0);
+  template<class ImageType>
+  void Or(ImageType * input, 
+          const ImageType * object, 
+          typename ImageType::PixelType BG=0);
   //--------------------------------------------------------------------
  
 
@@ -375,10 +417,95 @@ namespace clitk {
                                                          double margin,
                                                          std::vector<typename ImageType::PointType> & A, 
                                                          std::vector<typename ImageType::PointType> & B);  
+  template<class ImageType>
+  void 
+  SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1, 
+                                                                          const ImageType * S2, 
+                                                                          typename ImageType::PixelType BG, 
+                                                                          int sliceDimension, 
+                                                                          std::vector<typename ImageType::PointType> & A, 
+                                                                          std::vector<typename ImageType::PointType> & B);  
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceKeepMainCCL(const ImageType * input, 
+                          typename ImageType::PixelType BG,
+                          typename ImageType::PixelType FG);
+  //--------------------------------------------------------------------
+  
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  Clone(const ImageType * input);
+  //--------------------------------------------------------------------
+  
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceSetBackgroundFromSingleLine(const ImageType * input, 
+                                          typename ImageType::PixelType BG, 
+                                          typename ImageType::PointType & A, 
+                                          typename ImageType::PointType & B, 
+                                          int dim1, int dim2, bool removeLowerPartFlag);
+  //--------------------------------------------------------------------
+  
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceSetBackgroundFromPoints(const ImageType * input, 
+                                      typename ImageType::PixelType BG, 
+                                      int sliceDim,
+                                      std::vector<typename ImageType::PointType> & A, 
+                                      bool removeGreaterThanXFlag,
+                                      bool removeGreaterThanYFlag);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, 
+                      typename ImageType::RegionType & region);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min, 
+                    typename ImageType::PointType & max);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename itk::Image<float, ImageType::ImageDimension>::Pointer//void
+  DistanceMap(const ImageType * input, typename ImageType::PixelType BG);//, 
   //--------------------------------------------------------------------
 
 
-}
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::PointType
+  ComputeClosestPoint(const ImageType * input, 
+                      const itk::Image<float, ImageType::ImageDimension> * dmap, 
+                      typename ImageType::PixelType & BG);
+  //--------------------------------------------------------------------
+  
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  RemoveNegativeIndexFromRegion(ImageType * input);
+  //--------------------------------------------------------------------
+  
+
+} // end clitk namespace
 
 #include "clitkSegmentationUtils.txx"