Merge pull request #3 from OpenCMT/andrea-dev

fix mismatch Origin - Position

src/Math/Transform.h

@@ -110,6 +110,17 @@ public:
 
     inline void Rotate(const Matrix3f &m) { this->m_T.rotate(m); }
 
+    inline void Rotate(const float angle, Vector3f axis)
+    {
+        axis.normalize(); // prehaps not necessary ( see eigens )
+        Eigen::AngleAxisf ax(angle,axis);
+        this->m_T.rotate(Eigen::Quaternion<float>(ax));
+    }
+
+    inline void Rotate(const Vector3f euler_axis) {
+        float angle = euler_axis.norm();
+        Rotate(angle,euler_axis);
+    }
 
     inline void PreRotate(const Matrix3f &m) { this->m_T.prerotate(m); }
 

src/Math/VoxImage.cpp

@@ -99,7 +99,7 @@ void Abstract::VoxImage::ExportToVti (const char *file, bool density_type, bool
     vtkSmartPointer<vtkImageData> image = vtkSmartPointer<vtkImageData>::New();
     image->SetDimensions(voxels->GetDims()(0), voxels->GetDims()(1), voxels->GetDims()(2));
     image->SetSpacing(voxels->GetSpacing()(0), voxels->GetSpacing()(1), voxels->GetSpacing()(2));
-    image->SetOrigin(voxels->GetOrigin()(0), voxels->GetOrigin()(1), voxels->GetOrigin()(2));
+    image->SetOrigin(voxels->GetPosition()(0), voxels->GetPosition()(1), voxels->GetPosition()(2));
     image->AllocateScalars(VTK_FLOAT, 1);
 
     float norm;
@@ -114,8 +114,11 @@ void Abstract::VoxImage::ExportToVti (const char *file, bool density_type, bool
     size_t npoints = nx*ny*nz;
     float *scalar = static_cast<float*>(image->GetScalarPointer());
 
+    StructuredData unwrap(*voxels);
+    unwrap.SetDataOrder(StructuredData::XYZ); // move to XYZ order (VTK)
     for (size_t i = 0; i < npoints; i++) {
-        scalar[i] = static_cast<float>(voxels->GetValue(i) * norm);
+        Vector3i idx = unwrap.UnMap(i);
+        scalar[i] = static_cast<float>(voxels->GetValue(idx) * norm);
     }
 
     // Create a custom string key
@@ -161,7 +164,7 @@ int Abstract::VoxImage::ImportFromVti(const char *file, bool density_type) {
     
     voxels->SetDims(Vector3i(nx,ny,nz));
     voxels->SetSpacing(Vector3f(image->GetSpacing()[0],image->GetSpacing()[1],image->GetSpacing()[2]));
-    voxels->SetOrigin(Vector3f(image->GetOrigin()[0],image->GetOrigin()[1],image->GetOrigin()[2]));
+    voxels->SetPosition(Vector3f(image->GetOrigin()[0],image->GetOrigin()[1],image->GetOrigin()[2]));
 
     float norm;
     if (density_type) {
@@ -170,8 +173,12 @@ int Abstract::VoxImage::ImportFromVti(const char *file, bool density_type) {
 
     size_t npoints = nx*ny*nz;
     float *scalar = static_cast<float*>(image->GetScalarPointer());
+
+    StructuredData wrap(*voxels);
+    wrap.SetDataOrder(StructuredData::XYZ);
     for (size_t i = 0; i < npoints; i++) {
-        voxels->SetValue(i, scalar[i] / norm);
+        Vector3i idx = wrap.UnMap(i);
+        voxels->SetValue(idx, scalar[i] / norm);
     }
 
     return true;