When an image is opened it is now added to the recently opened files menu

[clitk.git] / itk / clitkSegmentationUtils.txx

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 00f3392f17a91477f3c4bc5790da0c97f05f95a0..16c184c0d1e36ff0e3ace5cec61df5c94de295a4 100644 (file)
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -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
@@ -420,7 +420,7 @@ namespace clitk {
   //--------------------------------------------------------------------
   template<class ImageType>
   typename ImageType::Pointer
-  CropImageAbove(const ImageType * image, 
+  CropImageRemoveGreaterThan(const ImageType * image, 
                  int dim, double min, bool autoCrop,
                  typename ImageType::PixelType BG) 
   {
@@ -435,7 +435,7 @@ namespace clitk {
   //--------------------------------------------------------------------
   template<class ImageType>
   typename ImageType::Pointer
-  CropImageBelow(const ImageType * image, 
+  CropImageRemoveLowerThan(const ImageType * image, 
                  int dim, double max, bool autoCrop,
                  typename ImageType::PixelType BG) 
   {
@@ -506,12 +506,56 @@ namespace clitk {
     statFilter->Update();
     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 
+    centroids.clear();
+    typename ImageType::PointType dummy;
+    centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG 
+    //DS FIXME (not useful ! to change ..)
+    DD(labelMap->GetNumberOfLabelObjects());
+    for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
+      int label = labelMap->GetLabels()[i];
+      centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
+    } 
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  ComputeCentroids2(const ImageType * image, 
+                   typename ImageType::PixelType BG, 
+                   std::vector<typename ImageType::PointType> & centroids) 
+  {
+    typedef long LabelType;
+    static const unsigned int Dim = ImageType::ImageDimension;
+    typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
+    typedef itk::LabelMap< LabelObjectType > LabelMapType;
+    typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
+    typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New(); 
+    typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType; 
+    typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
+    imageToLabelFilter->SetBackgroundValue(BG);
+    imageToLabelFilter->SetInput(image);
+    statFilter->SetInput(imageToLabelFilter->GetOutput());
+    statFilter->Update();
+    typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
+
     centroids.clear();
     typename ImageType::PointType dummy;
     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
       centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
     } 
+    
+    for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
+      DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
+      DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
+      DD(labelMap->GetLabelObject(i)->GetRoundness ());      
+
+      // search for the point on the boundary alog PA
+
+    }
+
   }
   //--------------------------------------------------------------------
 
@@ -558,7 +602,7 @@ namespace clitk {
   //--------------------------------------------------------------------
   template<class ImageType>
   void 
-  PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map, 
+  PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map, 
                                             const ImageType * image, 
                                             VectorPoint3DType & list)
   {
@@ -572,6 +616,24 @@ namespace clitk {
   }
   //--------------------------------------------------------------------
 
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D, 
+                                                int slice,
+                                                const ImageType * image, 
+                                                VectorPoint3DType & list) 
+  {
+    for(uint i=0; i<p2D.size(); i++) {
+      PointType3D p;
+      Convert2DTo3D(p2D[i], image, slice, p);
+      list.push_back(p);
+    }
+  }
+  //--------------------------------------------------------------------
+
+
   //--------------------------------------------------------------------
   template<class ImageType>
   void 
@@ -820,6 +882,7 @@ namespace clitk {
     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
     typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
     binarizeFilter->SetInput(input);
+    binarizeFilter->InPlaceOff();
     binarizeFilter->SetLowerThreshold(lower);
     binarizeFilter->SetUpperThreshold(upper);
     binarizeFilter->SetInsideValue(FG);
@@ -940,7 +1003,7 @@ namespace clitk {
     }
     
     // Convert 2D points in slice into 3D points
-    clitk::PointsUtils<ImageType>::Convert2DTo3DList(position2D, input, A);
+    clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
     
     // Create additional point just right to the previous ones, on the
     // given lineDirection, in order to create a horizontal/vertical line.