Correct color FA for orientation as we assume gradients are in image …

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git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/ttk/trunk@213 0a38917d-65eb-41a1-bb20-5b51c338416a

Algorithms/itkTensorToColorFAFunction.h

@@ -18,6 +18,7 @@
 #define _itk_TensorToColorFAFunction_h_
 
 #include "itkTensorToScalarFunction.h"
+#include <itkImageBase.h>
 
 namespace itk
 {
@@ -41,6 +42,12 @@ namespace itk
     typedef TOutputPixelType  OutputPixelType;    
 
     OutputPixelType ComputeScalar (const InputPixelType&) const;
+
+      void SetTransformColorWithDirection (bool value) {m_TransformColorWithDirection = value;}
+
+      typedef itk::ImageBase <3>::DirectionType MatrixType;
+      //! Transform used if TransformColorWithDirection is on, has to be the image direction matrix
+      void SetDirection(const MatrixType &matrix) {m_Direction = matrix;}
 
   protected:
     TensorToColorFAFunction(){};
@@ -55,6 +62,10 @@ namespace itk
      TensorToColorFAFunction (const Self&);
      void operator=(const Self&);
 
+      bool m_TransformColorWithDirection;
+      MatrixType m_Direction;
+
+
   };
 
 

Algorithms/itkTensorToColorFAFunction.txx

@@ -46,6 +46,20 @@ namespace itk
     typedef typename InputPixelType::VectorType VectorType;
     VectorType vec = T.GetEigenvector (2);
 
+    if (m_TransformColorWithDirection)
+    {
+        VectorType rotatedVec = vec;
+
+        for (unsigned int i = 0;i < 3;++i)
+        {
+            rotatedVec[i] = 0;
+            for (unsigned int j = 0;j < 3;++j)
+                rotatedVec[i] += m_Direction(i,j) * vec[j];
+        }
+
+        vec = rotatedVec;
+    }
+
     typedef typename OutputPixelType::ComponentType ComponentType;
 
     double r = fabs (vec[0])*255.0;

Commands/itkTensorToScalarCommand.cxx

@@ -52,6 +52,7 @@ namespace itk
     m_LongDescription = "Usage:\n";
     m_LongDescription += "-i [fileIn]\n";
     m_LongDescription += "-f [Function: FA / LFA / CFA / ADC / VOL / CL / CP / CS / RA / VR / L1 / L2 / L3]\n";
+    m_LongDescription += "-c [correct for tensor image orientation]\n\n";
     m_LongDescription += "-o [fileOut]\n\n";
     m_LongDescription += m_ShortDescription;
   }
@@ -93,6 +94,7 @@ namespace itk
     const char* file_in = cl.follow("NoFile", 2, "-i","-I");
     const char* file_out = cl.follow("NoFile", 2, "-o","-O");
     const char* function = cl.follow ("NoFunction", 2, "-f", "-F");
+      const bool correction  = cl.search (2, "-c","-C");
 
     if(strcmp(file_in,"NoFile")==0 || strcmp(file_out,"NoFile")==0)
     {
@@ -252,7 +254,14 @@ namespace itk
       myFilter->SetTensorToScalarFunction (myFunction);
       myFilter->SetInput (io->GetOutput());
 
-
+      if( strcmp (function, "cfa")==0 || strcmp (function, "CFA")==0 )
+      {
+          itk::TensorToColorFAFunction<TensorImageType::PixelType, ColorImageType::PixelType> *tmpFunction = dynamic_cast <itk::TensorToColorFAFunction<TensorImageType::PixelType, ColorImageType::PixelType> *> (myColorFunction.GetPointer());
+
+          tmpFunction->SetTransformColorWithDirection(correction);
+          tmpFunction->SetDirection(io->GetOutput()->GetDirection());
+      }
+
       try
       {
 	myFilter->Update();