COMP: Upgrade ITK from v5.2.0 to v5.3rc03

Upgraded to ITK version 5.3 (RC03), which was tagged on 16 January 2022: https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.3rc03 Including upgrade to C++14, and various performance improvements: InsightSoftwareConsortium/ITK@6a8569e Use the faster `TransformPhysicalPointToContinuousIndex` overload InsightSoftwareConsortium/ITK@eb6ac88 Use the faster `TransformPhysicalPointToIndex` overload in filter InsightSoftwareConsortium/ITK@0539a2c Remove protected `itk::Transform` data member `m_DirectionChange` InsightSoftwareConsortium/ITK@eec9fe6 Remove unnecessary `IdentityTransform::m_ZeroJacobian` InsightSoftwareConsortium/ITK@9961ccd Use FastEvaluate in MattesMutualInformationImageToImageMetric + v4 InsightSoftwareConsortium/ITK@9745409 Use FixedArray for table within BSplineInterpolationWeightFunction InsightSoftwareConsortium/ITK@c23944b Remove BSplineInterpolationWeightFunction Kernel, use FastEvaluate InsightSoftwareConsortium/ITK@bc7c5df Use FixedArray for BSplineBaseTransform ParameterIndexArrayType InsightSoftwareConsortium/ITK@9bf745b Use FixedArray for BSplineInterpolationWeightFunction OutputType InsightSoftwareConsortium/ITK@c64a58d Make `ResampleImageFilter::LinearThreadedGenerateData` faster Follow-up to pull request #475 commit 6803b26 "COMP: Upgrade ITK from v5.1.1 to v5.2.0" (merged on 31 May 2021). Note: The last elastix git revision on the develop branch that still supported ITK 5.2 was tagged: "last-itk5.2-support"
SuperElastix · Feb 18, 2022 · 58e5f1a · 58e5f1a
1 parent d3d1fe8
commit 58e5f1a
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diff --git a/.github/workflows/ElastixGitHubActions.yml b/.github/workflows/ElastixGitHubActions.yml
@@ -18,21 +18,21 @@ jobs:
           - os: ubuntu-18.04
             c-compiler: "gcc"
             cxx-compiler: "g++"
-            itk-git-tag: "v5.2.0"
+            itk-git-tag: "v5.3rc03"
             cmake-build-type: "Release"
             ANNLib: "libANNlib-5.0.so"
             ANNLib2: "libANNlib-5.0.so.1"
           - os: windows-2019
             c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
-            itk-git-tag: "v5.2.0"
+            itk-git-tag: "v5.3rc03"
             cmake-build-type: "Release"
             ANNLib: "ANNlib-5.0.dll"
             vcvars64: "C:/Program Files (x86)/Microsoft Visual Studio/2019/Enterprise/VC/Auxiliary/Build/vcvars64.bat"
           - os: macos-10.15
             c-compiler: "clang"  
             cxx-compiler: "clang++"
-            itk-git-tag: "v5.2.0"
+            itk-git-tag: "v5.3rc03"
             cmake-build-type: "Release"
             ANNLib: "libANNlib-5.0.1.dylib"
             ANNLib2: "libANNlib-5.0.dylib"

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -29,7 +29,7 @@ if(ELASTIX_USE_OPENCL)
 endif()
 
 # Find ITK.
-find_package( ITK 5.2.0 REQUIRED COMPONENTS
+find_package( ITK 5.3 REQUIRED COMPONENTS
     ITKCommon
     ITKDisplacementField
     ITKDistanceMap

diff --git a/Common/Transforms/itkAdvancedBSplineDeformableTransform.hxx b/Common/Transforms/itkAdvancedBSplineDeformableTransform.hxx
@@ -193,9 +193,8 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::Tran
 {
   /** Allocate memory on the stack: */
   const unsigned long                         numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType             weightsArray[numberOfWeights];
   typename ParameterIndexArrayType::ValueType indicesArray[numberOfWeights];
-  WeightsType                                 weights(weightsArray, numberOfWeights, false);
+  WeightsType                                 weights;
   ParameterIndexArrayType                     indices(indicesArray, numberOfWeights, false);
 
   OutputPointType outputPoint;
@@ -352,9 +351,8 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Compute the number of affected B-spline parameters.
    * Allocate memory on the stack.
    */
-  const unsigned long             numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray[numberOfWeights];
-  WeightsType                     weights(weightsArray, numberOfWeights, false);
+  const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
+  WeightsType         weights;
 
   /** Compute the weights. */
   IndexType supportIndex;
@@ -418,9 +416,8 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::Eval
   /** Compute the number of affected B-spline parameters.
    * Allocate memory on the stack.
    */
-  const unsigned long             numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray[numberOfWeights];
-  WeightsType                     weights(weightsArray, numberOfWeights, false);
+  const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
+  WeightsType         weights;
 
   /** Compute the B-spline derivative weights. */
   IndexType supportIndex;
@@ -475,9 +472,8 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetS
 
   /** Compute the number of affected B-spline parameters. */
   /** Allocate memory on the stack: */
-  const unsigned long             numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray[numberOfWeights];
-  WeightsType                     weights(weightsArray, numberOfWeights, false);
+  const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
+  WeightsType         weights;
 
   /** Array for CoefficientImage values */
   std::array<typename WeightsType::ValueType, numberOfWeights * SpaceDimension> coeffs;
@@ -579,8 +575,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetS
   /** Helper variables. */
   /** Allocate memory on the stack: */
   const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  WeightsValueType    weightsArray[numberOfWeights];
-  WeightsType         weights(weightsArray, numberOfWeights, false);
+  WeightsType         weights;
 
   /** Array for CoefficientImage values */
   std::array<WeightsValueType, numberOfWeights * SpaceDimension> coeffs;
@@ -702,9 +697,8 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Helper variables. */
 
   /** Allocate memory on the stack: */
-  const unsigned long             numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray[numberOfWeights];
-  WeightsType                     weights(weightsArray, numberOfWeights, false);
+  const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
+  WeightsType         weights;
 
   IndexType supportIndex;
   this->m_DerivativeWeightsFunctions[0]->ComputeStartIndex(cindex, supportIndex);
@@ -806,8 +800,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Allocate weight on the stack. */
   using WeightsValueType = typename WeightsType::ValueType;
   const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  WeightsValueType    weightsArray[numberOfWeights];
-  WeightsType         weights(weightsArray, numberOfWeights, false);
+  WeightsType         weights;
 
   /** Allocate coefficients on the stack. */
   std::array<WeightsValueType, numberOfWeights * SpaceDimension> coeffs;
@@ -957,9 +950,8 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Compute the number of affected B-spline parameters. */
 
   /** Allocate memory on the stack: */
-  const unsigned long             numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray[numberOfWeights];
-  WeightsType                     weights(weightsArray, numberOfWeights, false);
+  const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
+  WeightsType         weights;
 
   IndexType supportIndex;
   this->m_SODerivativeWeightsFunctions[0][0]->ComputeStartIndex(cindex, supportIndex);
@@ -1082,8 +1074,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Allocate weight on the stack. */
   using WeightsValueType = typename WeightsType::ValueType;
   const unsigned long numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  WeightsValueType    weightsArray[numberOfWeights];
-  WeightsType         weights(weightsArray, numberOfWeights, false);
+  WeightsType         weights;
 
   /** Allocate coefficients on the stack. */
   std::array<WeightsValueType, numberOfWeights * SpaceDimension> coeffs;

diff --git a/Common/Transforms/itkBSplineInterpolationWeightFunctionBase.h b/Common/Transforms/itkBSplineInterpolationWeightFunctionBase.h
@@ -48,12 +48,14 @@ namespace itk
  */
 template <class TCoordRep = float, unsigned int VSpaceDimension = 2, unsigned int VSplineOrder = 3>
 class ITK_TEMPLATE_EXPORT BSplineInterpolationWeightFunctionBase
-  : public FunctionBase<ContinuousIndex<TCoordRep, VSpaceDimension>, Array<double>>
+  : public FunctionBase<ContinuousIndex<TCoordRep, VSpaceDimension>,
+                        FixedArray<double, Math::UnsignedPower(VSplineOrder + 1, VSpaceDimension)>>
 {
 public:
   /** Standard class typedefs. */
   using Self = BSplineInterpolationWeightFunctionBase;
-  using Superclass = FunctionBase<ContinuousIndex<TCoordRep, VSpaceDimension>, Array<double>>;
+  using Superclass = FunctionBase<ContinuousIndex<TCoordRep, VSpaceDimension>,
+                                  FixedArray<double, Math::UnsignedPower(VSplineOrder + 1, VSpaceDimension)>>;
   using Pointer = SmartPointer<Self>;
   using ConstPointer = SmartPointer<const Self>;
 
@@ -70,7 +72,7 @@ class ITK_TEMPLATE_EXPORT BSplineInterpolationWeightFunctionBase
   static constexpr unsigned long NumberOfWeights = Math::UnsignedPower(VSplineOrder + 1, VSpaceDimension);
 
   /** OutputType typedef support. */
-  using WeightsType = Array<double>;
+  using WeightsType = FixedArray<double, NumberOfWeights>;
 
   /** Index and size typedef support. */
   using IndexType = Index<VSpaceDimension>;

diff --git a/Common/Transforms/itkCyclicBSplineDeformableTransform.hxx b/Common/Transforms/itkCyclicBSplineDeformableTransform.hxx
@@ -141,9 +141,8 @@ CyclicBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::Transf
 {
   /** Allocate memory on the stack: */
   const unsigned long                         numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType             weightsArray[numberOfWeights];
   typename ParameterIndexArrayType::ValueType indicesArray[numberOfWeights];
-  WeightsType                                 weights(weightsArray, numberOfWeights, false);
+  WeightsType                                 weights;
   ParameterIndexArrayType                     indices(indicesArray, numberOfWeights, false);
 
   OutputPointType outputPoint;
@@ -319,9 +318,7 @@ CyclicBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetSpa
 
   /** Compute the number of affected B-spline parameters. */
   /** Allocate memory on the stack: */
-  const SizeValueType             numberOfWeights = WeightsFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray[numberOfWeights];
-  WeightsType                     weights(weightsArray, numberOfWeights, false);
+  WeightsType weights;
 
   IndexType supportIndex;
   this->m_DerivativeWeightsFunctions[0]->ComputeStartIndex(cindex, supportIndex);

diff --git a/Common/Transforms/itkRecursiveBSplineTransform.hxx b/Common/Transforms/itkRecursiveBSplineTransform.hxx
@@ -47,15 +47,11 @@ auto
 RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::TransformPoint(const InputPointType & point) const
   -> OutputPointType
 {
-  /** Define some constants. */
-  const unsigned int numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-
   /** Initialize output point. */
   OutputPointType outputPoint;
 
   /** Allocate weights on the stack: */
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
+  WeightsType weights1D;
 
   /** Check if the coefficient image has been set. */
   if (!this->m_CoefficientImages[0])
@@ -151,10 +147,8 @@ RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::GetJacobian(
    * In contrast to the normal B-spline weights function, the recursive version
    * returns the individual weights instead of the multiplied ones.
    */
-  const unsigned int              numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
-  IndexType                       supportIndex;
+  WeightsType weights1D;
+  IndexType   supportIndex;
   this->m_RecursiveBSplineWeightFunction->Evaluate(cindex, weights1D, supportIndex);
 
   /** Recursively compute the first numberOfIndices entries of the Jacobian.
@@ -209,10 +203,8 @@ RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::EvaluateJacobianW
    * In contrast to the normal B-spline weights function, the recursive version
    * returns the individual weights instead of the multiplied ones.
    */
-  const unsigned int              numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
-  IndexType                       supportIndex;
+  WeightsType weights1D;
+  IndexType   supportIndex;
   this->m_RecursiveBSplineWeightFunction->Evaluate(cindex, weights1D, supportIndex);
 
   /** Recursively compute the inner product of the Jacobian and the moving image gradient.
@@ -262,11 +254,8 @@ RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::GetSpatialJacobia
   }
 
   /** Create storage for the B-spline interpolation weights. */
-  const unsigned int              numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
-  typename WeightsType::ValueType derivativeWeightsArray1D[numberOfWeights];
-  WeightsType                     derivativeWeights1D(derivativeWeightsArray1D, numberOfWeights, false);
+  WeightsType weights1D;
+  WeightsType derivativeWeights1D;
 
   double * weightsPointer = &(weights1D[0]);
   double * derivativeWeightsPointer = &(derivativeWeights1D[0]);
@@ -349,13 +338,9 @@ RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::GetSpatialHessian
   }
 
   /** Create storage for the B-spline interpolation weights. */
-  const unsigned int              numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
-  typename WeightsType::ValueType derivativeWeightsArray1D[numberOfWeights];
-  WeightsType                     derivativeWeights1D(derivativeWeightsArray1D, numberOfWeights, false);
-  typename WeightsType::ValueType hessianWeightsArray1D[numberOfWeights];
-  WeightsType                     hessianWeights1D(hessianWeightsArray1D, numberOfWeights, false);
+  WeightsType weights1D;
+  WeightsType derivativeWeights1D;
+  WeightsType hessianWeights1D;
 
   double * weightsPointer = &(weights1D[0]);
   double * derivativeWeightsPointer = &(derivativeWeights1D[0]);
@@ -468,11 +453,8 @@ RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::GetJacobianOfSpat
   }
 
   /** Create storage for the B-spline interpolation weights. */
-  const unsigned int              numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
-  typename WeightsType::ValueType derivativeWeightsArray1D[numberOfWeights];
-  WeightsType                     derivativeWeights1D(derivativeWeightsArray1D, numberOfWeights, false);
+  WeightsType weights1D;
+  WeightsType derivativeWeights1D;
 
   double * weightsPointer = &(weights1D[0]);
   double * derivativeWeightsPointer = &(derivativeWeights1D[0]);
@@ -567,13 +549,9 @@ RecursiveBSplineTransform<TScalar, NDimensions, VSplineOrder>::GetJacobianOfSpat
   }
 
   /** Create storage for the B-spline interpolation weights. */
-  const unsigned int              numberOfWeights = RecursiveBSplineWeightFunctionType::NumberOfWeights;
-  typename WeightsType::ValueType weightsArray1D[numberOfWeights];
-  WeightsType                     weights1D(weightsArray1D, numberOfWeights, false);
-  typename WeightsType::ValueType derivativeWeightsArray1D[numberOfWeights];
-  WeightsType                     derivativeWeights1D(derivativeWeightsArray1D, numberOfWeights, false);
-  typename WeightsType::ValueType hessianWeightsArray1D[numberOfWeights];
-  WeightsType                     hessianWeights1D(hessianWeightsArray1D, numberOfWeights, false);
+  WeightsType weights1D;
+  WeightsType derivativeWeights1D;
+  WeightsType hessianWeights1D;
 
   double * weightsPointer = &(weights1D[0]);
   double * derivativeWeightsPointer = &(derivativeWeights1D[0]);

diff --git a/Testing/CI/Azure/ci.yml b/Testing/CI/Azure/ci.yml
@@ -1,5 +1,5 @@
 variables:
-  ITKv5_VERSION: v5.2.0
+  ITKv5_VERSION: v5.3rc03
   ITK_GIT_URL: https://github.com/InsightSoftwareConsortium/ITK
   ITK_SOURCE_DIR: $(Agent.BuildDirectory)/ITK-source
   ITK_BINARY_DIR: $(Agent.BuildDirectory)/ITK-build

diff --git a/Testing/itkBSplineTransformPointPerformanceTest.cxx b/Testing/itkBSplineTransformPointPerformanceTest.cxx
@@ -61,9 +61,8 @@ class BSplineTransform_TEST : public AdvancedBSplineDeformableTransform<TScalarT
   TransformPoint_OLD(const InputPointType & point) const
   {
     const unsigned long                         numberOfWeights = WeightsFunctionType::NumberOfWeights;
-    typename WeightsType::ValueType             weightsArray[numberOfWeights];
     typename ParameterIndexArrayType::ValueType indicesArray[numberOfWeights];
-    WeightsType                                 weights(weightsArray, numberOfWeights, false);
+    WeightsType                                 weights;
     ParameterIndexArrayType                     indices(indicesArray, numberOfWeights, false);
 
     OutputPointType outputPoint;