X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.h;h=77270d1a542b4d2c1bb7bc3346bcb91967b49f2c;hb=3c1886a2789de650bebcbcbc60e454b248f83e38;hp=6959883a98b38e946ffff01928ace77fa29c2652;hpb=68674d29b9dd06b4a786d8ce7a14acd1d97f907e;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.h b/itk/clitkSegmentationUtils.h
index 6959883..77270d1 100644
--- a/itk/clitkSegmentationUtils.h
+++ b/itk/clitkSegmentationUtils.h
@@ -19,9 +19,12 @@
 #ifndef CLITKSEGMENTATIONUTILS_H
 #define CLITKSEGMENTATIONUTILS_H
 
+// clitk
 #include "clitkCommon.h"
 #include "clitkAutoCropFilter.h"
 #include "clitkLabelizeParameters.h"
+
+// itk
 #include <itkBoundingBox.h>
 
 namespace clitk {
@@ -31,7 +34,7 @@ namespace clitk {
   void ComputeBBFromImageRegion(typename ImageType::Pointer image, 
                                 typename ImageType::RegionType region,
                                 typename itk::BoundingBox<unsigned long, 
-                                ImageType::ImageDimension>::Pointer bb);
+                                                          ImageType::ImageDimension>::Pointer bb);
   
   //--------------------------------------------------------------------
   template<int Dimension>
@@ -51,7 +54,8 @@ namespace clitk {
   SetBackground(const TInternalImageType * input,
                 const TMaskInternalImageType * mask, 
                 typename TMaskInternalImageType::PixelType maskBG, 
-                typename TInternalImageType::PixelType outValue);
+                typename TInternalImageType::PixelType outValue, 
+                bool inPlace);
   //--------------------------------------------------------------------
 
 
@@ -66,7 +70,7 @@ namespace clitk {
   //-------------------------------------------------------------------- 
   template<class TImageType>
   typename TImageType::Pointer
-  Labelize(typename TImageType::Pointer input, 
+  Labelize(const TImageType * input, 
            typename TImageType::PixelType BG, 
            bool isFullyConnected, 
            int minimalComponentSize);
@@ -84,23 +88,23 @@ namespace clitk {
 
   //--------------------------------------------------------------------
   template<class ImageType>
-    typename ImageType::Pointer
-    AutoCrop(typename ImageType::Pointer input, 
-	     typename ImageType::PixelType BG) {
-      typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
-      typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
-      autoCropFilter->SetInput(input);
-      autoCropFilter->Update();   
-      return autoCropFilter->GetOutput();
+  typename ImageType::Pointer
+  AutoCrop(typename ImageType::Pointer input, 
+           typename ImageType::PixelType BG) {
+    typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
+    typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
+    autoCropFilter->SetInput(input);
+    autoCropFilter->SetBackgroundValue(BG);
+    autoCropFilter->Update();   
+    return autoCropFilter->GetOutput();
   }
-
   //--------------------------------------------------------------------
 
 
   //--------------------------------------------------------------------
   template<class TImageType>
   typename TImageType::Pointer
-  KeepLabels(typename TImageType::Pointer input,
+  KeepLabels(const TImageType * input,
              typename TImageType::PixelType BG, 
              typename TImageType::PixelType FG,  
              typename TImageType::PixelType firstKeep, 
@@ -122,9 +126,164 @@ namespace clitk {
   //--------------------------------------------------------------------
   template<class ImageType>
   typename ImageType::Pointer
-  EnlargeImageLike(typename ImageType::Pointer input,
-                   typename ImageType::Pointer like, 
-                   typename ImageType::PixelType BG);
+  ResizeImageLike(typename ImageType::Pointer input,
+                  typename ImageType::Pointer like, 
+                  typename ImageType::PixelType BG);
+
+
+  //--------------------------------------------------------------------
+  template<class MaskImageType>
+  typename MaskImageType::Pointer
+  SliceBySliceRelativePosition(const MaskImageType * input,
+			       const MaskImageType * object,
+			       int direction, 
+			       double threshold, 
+			       std::string orientation, 
+                               bool uniqueConnectedComponent=false, 
+                               double spacing=-1, 
+			       bool notflag=false);
+
+  //--------------------------------------------------------------------
+  // In a binary image, search for the point belonging to the FG that
+  // is the most exterma in the direction 'direction' (or in the
+  // opposite if notFlag is given). 
+  template<class ImageType>
+  bool
+  FindExtremaPointInAGivenDirection(const ImageType * input, 
+                                    typename ImageType::PixelType bg, 
+                                    int direction, bool opposite, 
+                                    typename ImageType::PointType & p);
+
+  //--------------------------------------------------------------------
+
+  //--------------------------------------------------------------------
+  // Same as above but check that the found point is not more than
+  // 'distanceMax' away from 'refPoint'
+  template<class ImageType>
+  bool
+  FindExtremaPointInAGivenDirection(const ImageType * input, 
+                                    typename ImageType::PixelType bg, 
+                                    int direction, bool opposite, 
+                                    typename ImageType::PointType refPoint,
+                                    double distanceMax, 
+                                    typename ImageType::PointType & p);
+
+  //--------------------------------------------------------------------
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  CropImageAlongOneAxis(typename ImageType::Pointer image, 
+                        int dim, double min, double max, 
+                        bool autoCrop = false,
+                        typename ImageType::PixelType BG=0);
+  template<class ImageType>
+  typename ImageType::Pointer
+  CropImageAbove(typename ImageType::Pointer image, 
+                 int dim, double min, 
+                 bool autoCrop = false,
+                 typename ImageType::PixelType BG=0);
+  template<class ImageType>
+  typename ImageType::Pointer
+  CropImageBelow(typename ImageType::Pointer image, 
+                 int dim, double max,
+                 bool autoCrop = false,
+                 typename ImageType::PixelType BG=0);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  ComputeCentroids(typename ImageType::Pointer image, 
+                   typename ImageType::PixelType BG, 
+                   std::vector<typename ImageType::PointType> & centroids);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  ExtractSlices(typename ImageType::Pointer image, 
+		int dim, 
+		std::vector< typename itk::Image<typename ImageType::PixelType, 
+		ImageType::ImageDimension-1>::Pointer > & slices);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType, 
+	     ImageType::ImageDimension-1>::Pointer > & slices, 
+	     typename ImageType::Pointer input, 
+	     int dim);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  // Set of tools to manage 3D points and 2D points in slices  
+  template<class ImageType>
+  class PointsUtils
+  {
+    typedef typename ImageType::PointType PointType3D;
+    typedef typename ImageType::PixelType PixelType;
+    typedef typename ImageType::Pointer ImagePointer;
+    typedef typename ImageType::ConstPointer ImageConstPointer;
+    typedef itk::Image<PixelType, 2> SliceType;
+    typedef typename SliceType::PointType PointType2D;
+    
+    typedef std::map<int, PointType2D> MapPoint2DType;
+    typedef std::vector<PointType3D> VectorPoint3DType;
+  public:
+    static void Convert2DTo3D(const PointType2D & p2D, 
+                              ImagePointer image, 
+                              const int slice, 
+                              PointType3D & p3D);
+    static void Convert2DTo3DList(const MapPoint2DType & map, 
+                                  ImagePointer image, 
+                                  VectorPoint3DType & list);
+  };
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  WriteListOfLandmarks(std::vector<typename ImageType::PointType> points, 
+                       std::string filename);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  Dilate(typename ImageType::Pointer image, 
+              double radiusInMM,               
+              typename ImageType::PixelType BG, 
+              typename ImageType::PixelType FG, 
+              bool extendSupport);
+  template<class ImageType>
+  typename ImageType::Pointer
+  Dilate(typename ImageType::Pointer image, 
+              typename ImageType::SizeType radius, 
+              typename ImageType::PixelType BG, 
+              typename ImageType::PixelType FG, 
+              bool extendSupport);
+  template<class ImageType>
+  typename ImageType::Pointer  
+  Dilate(typename ImageType::Pointer image, 
+              typename ImageType::PointType radiusInMM, 
+              typename ImageType::PixelType BG, 
+              typename ImageType::PixelType FG, 
+              bool extendSupport);
+  //--------------------------------------------------------------------
+
+  //--------------------------------------------------------------------
+  template<class ValueType, class VectorType>
+  void ConvertOption(std::string optionName, uint given, 
+                     ValueType * values, VectorType & p, 
+                     uint dim, bool required);
+#define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED)         \
+  ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
 
 }