ENH: Added support for oriented grid Transform

* Added a new class, vtkOrientedGridTransform, which is based on vtkGridTransform but orientation of the grid can be specified as well. * Added test for vtkOrientedGridTransform to verify its derivative and inverse computation and equivalence with ITK displacement field transform. * Simplified vtkMRMLGridTransform node: transform parameters are read/written into ITK transform file, no duplicate saving is done in the scene. * Removed unused vtkITK files: itkDisplacementFieldTransform, itkEncodedTransformFileReader/Writer, as they were not used (and some of them even had the same name as existing ITK files). * Support reading/writing of grid transform from/to nrrd, nhdr, mha, mhd, nii, nii.gz files Resolves: http://www.na-mic.org/Bug/view.php?id=3597 http://www.na-mic.org/Bug/view.php?id=3444 http://na-mic.org/Bug/view.php?id=2273 Partially resolves: http://www.na-mic.org/Bug/view.php?id=3598 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23185 3bd1e089-480b-0410-8dfb-8563597acbee
naucoin · May 16, 2014 · 979d08b · 979d08b
1 parent 7d06959
commit 979d08b
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Showing 19 changed files with 1,268 additions and 2,043 deletions.
diff --git a/Libs/MRML/Core/CMakeLists.txt b/Libs/MRML/Core/CMakeLists.txt
@@ -182,6 +182,7 @@ set(MRMLCore_SRCS
   vtkMRMLDoubleArrayStorageNode.cxx
   # Classes for transforms computation
   vtkOrientedBSplineTransform.cxx
+  vtkOrientedGridTransform.cxx
   # Note: when you add new node types, add
   # register code to the vtkMRMLScene constructor
   )

diff --git a/Libs/MRML/Core/Testing/CMakeLists.txt b/Libs/MRML/Core/Testing/CMakeLists.txt
@@ -96,6 +96,7 @@ create_test_sourcelist(Tests ${KIT}CxxTests.cxx
   vtkMRMLdGEMRICProceduralColorNodeTest1.cxx
   vtkObserverManagerTest1.cxx
   vtkOrientedBSplineTransformTest1.cxx
+  vtkOrientedGridTransformTest1.cxx
   EXTRA_INCLUDE vtkMRMLDebugLeaksMacro.h
   )
 

diff --git a/Libs/MRML/Core/Testing/vtkMRMLNonlinearTransformNodeTest1.cxx b/Libs/MRML/Core/Testing/vtkMRMLNonlinearTransformNodeTest1.cxx
@@ -15,7 +15,7 @@
 #include <itkFactoryRegistration.h>
 
 #include "vtkOrientedBSplineTransform.h"
-#include "vtkGridTransform.h"
+#include "vtkOrientedGridTransform.h"
 #include "vtkMRMLTransformNode.h"
 #include "vtkMRMLBSplineTransformNode.h"
 #include "vtkMRMLGridTransformNode.h"
@@ -148,8 +148,8 @@ bool TestGridTransform(const char *filename)
     return false;
     }
 
-  vtkAbstractTransform *xfp = gridTransformNode->GetTransformFromParentAs("vtkGridTransform");
-  vtkAbstractTransform *xtp = gridTransformNode->GetTransformToParentAs("vtkGridTransform");
+  vtkAbstractTransform *xfp = gridTransformNode->GetTransformFromParentAs("vtkOrientedGridTransform");
+  vtkAbstractTransform *xtp = gridTransformNode->GetTransformToParentAs("vtkOrientedGridTransform");
 
   if (xfp == 0 || xtp == 0)
     {

diff --git a/Libs/MRML/Core/Testing/vtkOrientedBSplineTransformTest1.cxx b/Libs/MRML/Core/Testing/vtkOrientedBSplineTransformTest1.cxx
@@ -24,6 +24,8 @@
 
 typedef itk::BSplineDeformableTransform<double,3,3> itkBSplineType;
 
+double DisplacementScale=0.63;
+
 //----------------------------------------------------------------------------
 void CreateBSplineVtk(vtkOrientedBSplineTransform* bsplineTransform,
   double origin[3], double spacing[3], double direction[3][3], double dims[3],
@@ -78,6 +80,7 @@ void CreateBSplineVtk(vtkOrientedBSplineTransform* bsplineTransform,
   bsplineTransform->SetBulkTransformMatrix(bulkTransform.GetPointer());
 
   bsplineTransform->SetBorderModeToZero();
+  bsplineTransform->SetDisplacementScale(DisplacementScale);
 }
 
 //----------------------------------------------------------------------------
@@ -166,9 +169,9 @@ void SetBSplineNodeItk(itkBSplineType::Pointer bspline,int nodeIndex[3], double
   itkBSplineType::ParametersType parameters = bspline->GetParameters();
 
   const unsigned int numberOfNodes = dims[0] * dims[1] * dims[2];
-  parameters.SetElement( numberOfNodes*0 + nodeIndex[0] + nodeIndex[1]*dims[0] + nodeIndex[2]*dims[0]*dims[1], nodeValue[0] );
-  parameters.SetElement( numberOfNodes*1 + nodeIndex[0] + nodeIndex[1]*dims[0] + nodeIndex[2]*dims[0]*dims[1], nodeValue[1] );
-  parameters.SetElement( numberOfNodes*2 + nodeIndex[0] + nodeIndex[1]*dims[0] + nodeIndex[2]*dims[0]*dims[1], nodeValue[2] );
+  parameters.SetElement( numberOfNodes*0 + nodeIndex[0] + nodeIndex[1]*dims[0] + nodeIndex[2]*dims[0]*dims[1], DisplacementScale*nodeValue[0] );
+  parameters.SetElement( numberOfNodes*1 + nodeIndex[0] + nodeIndex[1]*dims[0] + nodeIndex[2]*dims[0]*dims[1], DisplacementScale*nodeValue[1] );
+  parameters.SetElement( numberOfNodes*2 + nodeIndex[0] + nodeIndex[1]*dims[0] + nodeIndex[2]*dims[0]*dims[1], DisplacementScale*nodeValue[2] );
 
   bspline->SetParameters( parameters );
 }