Add pixel coordinate instead of mm coordinates into Xml2DicomRTStruct

[clitk.git] / itk / clitkSegmentationUtils.h

diff --git a/itk/clitkSegmentationUtils.h b/itk/clitkSegmentationUtils.h
index 70388fe6cdb7380511bbda45373abd7f71a1200a..5ac8c4c51e86c2d7b5345fcefda25ea8ba8b3ec0 100644 (file)
--- a/itk/clitkSegmentationUtils.h
+++ b/itk/clitkSegmentationUtils.h
@@ -28,6 +28,7 @@
 // itk
 #include <itkBoundingBox.h>
 #include <itkJoinSeriesImageFilter.h>
+#include <itkChangeInformationImageFilter.h>
 
 /*
   According to 
@@ -38,25 +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,
@@ -103,11 +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();
   }
@@ -136,13 +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>
@@ -156,6 +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
@@ -350,7 +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);
   //--------------------------------------------------------------------
 
 
@@ -500,7 +498,12 @@ namespace clitk {
                       typename ImageType::PixelType & BG);
   //--------------------------------------------------------------------
   
-
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  RemoveNegativeIndexFromRegion(ImageType * input);
+  //--------------------------------------------------------------------
+  
 
 } // end clitk namespace