Be sure Number of Frame of Rotation exists in dicom tags

[clitk.git] / common / clitkDicomRTStruct2ImageFilter.cxx

diff --git a/common/clitkDicomRTStruct2ImageFilter.cxx b/common/clitkDicomRTStruct2ImageFilter.cxx
index e52fc0f17be8a3e16acee8517409b5b224205615..bf4d4c432d8649ba2c4c5566b356070cd708c535 100644 (file)
--- a/common/clitkDicomRTStruct2ImageFilter.cxx
+++ b/common/clitkDicomRTStruct2ImageFilter.cxx
@@ -25,6 +25,7 @@
 #include "clitkImageCommon.h"
 
 // vtk
+#include <vtkVersion.h>
 #include <vtkPolyDataToImageStencil.h>
 #include <vtkSmartPointer.h>
 #include <vtkImageStencil.h>
@@ -101,10 +102,15 @@ void clitk::DicomRTStruct2ImageFilter::SetImage(vvImage::Pointer image)
   mSpacing.resize(3);
   mOrigin.resize(3);
   mSize.resize(3);
+  mDirection.resize(3);
+  mTransformMatrix = image->GetTransform()[0]->GetMatrix();
   for(unsigned int i=0; i<3; i++) {
     mSpacing[i] = image->GetSpacing()[i];
     mOrigin[i] = image->GetOrigin()[i];
     mSize[i] = image->GetSize()[i];
+    mDirection[i].resize(3);
+    for(unsigned int j=0; j<3; j++)
+      mDirection[i][j] = image->GetDirection()[i][j];
   }
 }
 //--------------------------------------------------------------------
@@ -124,10 +130,14 @@ void clitk::DicomRTStruct2ImageFilter::SetImageFilename(std::string f)
   mSpacing.resize(3);
   mOrigin.resize(3);
   mSize.resize(3);
+  mDirection.resize(3);
   for(unsigned int i=0; i<3; i++) {
     mSpacing[i] = header->GetSpacing(i);
     mOrigin[i] = header->GetOrigin(i);
     mSize[i] = header->GetDimensions(i);
+    mDirection[i].resize(3);
+    for(unsigned int j=0; j<3; j++)
+      mDirection[i][j] = header->GetDirection(i)[j];
   }
 }
 //--------------------------------------------------------------------
@@ -160,7 +170,6 @@ void clitk::DicomRTStruct2ImageFilter::SetOutputSize(const unsigned long* size)
 //--------------------------------------------------------------------
 void clitk::DicomRTStruct2ImageFilter::Update()
 {
-  DD("DicomRTStruct2ImageFilter::Update");
   if (!mROI) {
     std::cerr << "Error. No ROI set, please use SetROI." << std::endl;
     exit(0);
@@ -171,13 +180,42 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   }
 
   // Get Mesh
-  vtkPolyData * mesh = mROI->GetMesh();  
+  vtkPolyData * mesh = mROI->GetMesh();
 
   // Get bounds
   double *bounds=mesh->GetBounds();
-  // for(int i=0; i<6; i++){
-//     DD(bounds[i]);
-//   }
+
+  //Change mOrigin, mSize and mSpacing with respect to the directions
+  // Spacing is influenced by input direction
+  std::vector<double> tempSpacing;
+  tempSpacing.resize(3);
+  for(int i=0; i<3; i++) {
+    tempSpacing[i] = 0.0;
+    for(int j=0; j<3; j++) {
+      tempSpacing[i] += mDirection[i][j] * mSpacing[j];
+    }
+  }
+  for(int i=0; i<3; i++)
+    mSpacing[i] = tempSpacing[i];
+
+  // Size is influenced by affine transform matrix and input direction
+  // Size is converted to double, transformed and converted back to size type.
+  std::vector<double> tempSize;
+  tempSize.resize(3);
+  for(int i=0; i<3; i++) {
+    tempSize[i] = 0.0;
+    for(int j=0; j<3; j++) {
+      tempSize[i] += mDirection[i][j] * mSize[j];
+    }
+  }
+  for(int i=0; i<3; i++) {
+    if (tempSize[i] < 0.0) {
+      tempSize[i] *= -1;
+      mOrigin[i] += mSpacing[i]*(tempSize[i] -1);
+      mSpacing[i] *= -1;
+    }
+    mSize[i] = lrint(tempSize[i]);
+  }
 
   // Compute origin
   std::vector<double> origin;
@@ -192,7 +230,6 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
   extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
   extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
-
   // If no crop, set initial image size/origin
   if (!mCropMask) {
     for(int i=0; i<3; i++) {
@@ -201,27 +238,34 @@ void clitk::DicomRTStruct2ImageFilter::Update()
     }
   }
 
+std::cout << "origin " << origin[0] << " " << origin[1] << " " << origin[2] << std::endl;
+std::cout << "extend " << extend[0] << " " << extend[1] << " " << extend[2] << std::endl;
   // Create new output image
   mBinaryImage = vtkSmartPointer<vtkImageData>::New();
+#if VTK_MAJOR_VERSION <= 5
   mBinaryImage->SetScalarTypeToUnsignedChar();
+#endif
   mBinaryImage->SetOrigin(&origin[0]);
   mBinaryImage->SetSpacing(&mSpacing[0]);
   mBinaryImage->SetExtent(0, extend[0],
                           0, extend[1],
                           0, extend[2]);
+#if VTK_MAJOR_VERSION <= 5
   mBinaryImage->AllocateScalars();
+#else
+  mBinaryImage->AllocateScalars(VTK_UNSIGNED_CHAR, 1);
+#endif
 
-  // for(int i=0; i<3; i++){
-  //     DD(origin[i]);
-  //     DD(extend[i]);
-  //     DD(mBinaryImage->GetDimensions()[i]);
-  //   }
   memset(mBinaryImage->GetScalarPointer(), 0,
          mBinaryImage->GetDimensions()[0]*mBinaryImage->GetDimensions()[1]*mBinaryImage->GetDimensions()[2]*sizeof(unsigned char));
 
   // Extrude
   vtkSmartPointer<vtkLinearExtrusionFilter> extrude=vtkSmartPointer<vtkLinearExtrusionFilter>::New();
+#if VTK_MAJOR_VERSION <= 5
   extrude->SetInput(mesh);
+#else
+  extrude->SetInputData(mesh);
+#endif
   ///We extrude in the -slice_spacing direction to respect the FOCAL convention (NEEDED !)
   extrude->SetVector(0, 0, -mSpacing[2]);
 
@@ -231,12 +275,24 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   //http://www.nabble.com/Bug-in-vtkPolyDataToImageStencil--td23368312.html#a23370933
   sts->SetTolerance(0);
   sts->SetInformationInput(mBinaryImage);
+#if VTK_MAJOR_VERSION <= 5
   sts->SetInput(extrude->GetOutput());
+#else
+  sts->SetInputConnection(extrude->GetOutputPort(0));
+#endif
   //sts->SetInput(mesh);
 
   vtkSmartPointer<vtkImageStencil> stencil=vtkSmartPointer<vtkImageStencil>::New();
+#if VTK_MAJOR_VERSION <= 5
   stencil->SetStencil(sts->GetOutput());
+#else
+  stencil->SetStencilConnection(sts->GetOutputPort(0));
+#endif
+#if VTK_MAJOR_VERSION <= 5
   stencil->SetInput(mBinaryImage);
+#else
+  stencil->SetInputData(mBinaryImage);
+#endif
   stencil->ReverseStencilOn();
   stencil->Update();