WIP: COMP: Upgrade ITK from v5.2.0 to v5.3rc02

Upgraded to ITK version 5.3 (RC02), which was released on 11 November 2021.

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

Release Notes: https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.3rc02

Follow-up to pull request #475 commit 6803b26 "COMP: Upgrade ITK from v5.1.1 to v5.2.0" (merged on 31 May 2021).

.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: "v5.3rc02"
             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: "v5.3rc02"
             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: "v5.3rc02"
             cmake-build-type: "Release"
             ANNLib: "libANNlib-5.0.1.dylib"
             ANNLib2: "libANNlib-5.0.dylib"

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

Common/Transforms/itkAdvancedBSplineDeformableTransform.hxx

@@ -292,9 +292,8 @@ 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;
@@ -380,9 +379,8 @@ 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;
@@ -447,9 +445,7 @@ 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);
+  WeightsType weights;
 
   /** Compute the B-spline derivative weights. */
   IndexType supportIndex;
@@ -505,9 +501,8 @@ 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;
@@ -610,8 +605,7 @@ 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;
@@ -734,9 +728,8 @@ 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);
@@ -839,8 +832,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Allocate weight on the stack. */
   typedef typename WeightsType::ValueType WeightsValueType;
   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;
@@ -991,9 +983,8 @@ 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);
@@ -1117,8 +1108,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
   /** Allocate weight on the stack. */
   typedef typename WeightsType::ValueType WeightsValueType;
   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;

Common/Transforms/itkBSplineInterpolationWeightFunctionBase.h

@@ -48,14 +48,17 @@ 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. */
-  typedef BSplineInterpolationWeightFunctionBase                                   Self;
-  typedef FunctionBase<ContinuousIndex<TCoordRep, VSpaceDimension>, Array<double>> Superclass;
-  typedef SmartPointer<Self>                                                       Pointer;
-  typedef SmartPointer<const Self>                                                 ConstPointer;
+  typedef BSplineInterpolationWeightFunctionBase Self;
+  typedef FunctionBase<ContinuousIndex<TCoordRep, VSpaceDimension>,
+                       FixedArray<double, Math::UnsignedPower(VSplineOrder + 1, VSpaceDimension)>>
+                                   Superclass;
+  typedef SmartPointer<Self>       Pointer;
+  typedef SmartPointer<const Self> ConstPointer;
 
   /** Run-time type information (and related methods). */
   itkTypeMacro(BSplineInterpolationWeightFunctionBase, FunctionBase);
@@ -70,7 +73,7 @@ class ITK_TEMPLATE_EXPORT BSplineInterpolationWeightFunctionBase
   static constexpr unsigned long NumberOfWeights = Math::UnsignedPower(VSplineOrder + 1, VSpaceDimension);
 
   /** OutputType typedef support. */
-  typedef Array<double> WeightsType;
+  typedef FixedArray<double, NumberOfWeights> WeightsType;
 
   /** Index and size typedef support. */
   typedef Index<VSpaceDimension> IndexType;

Common/Transforms/itkCyclicBSplineDeformableTransform.hxx

@@ -317,9 +317,7 @@ 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);

Common/Transforms/itkRecursiveBSplineTransform.hxx

@@ -50,15 +50,11 @@ 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])
@@ -156,10 +152,8 @@ 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.
@@ -215,10 +209,8 @@ 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.
@@ -269,11 +261,8 @@ 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]);
@@ -357,13 +346,9 @@ 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]);
@@ -477,11 +462,8 @@ 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]);
@@ -577,13 +559,9 @@ 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]);

Testing/CI/Azure/ci.yml

@@ -1,5 +1,5 @@
 variables:
-  ITKv5_VERSION: v5.2.0
+  ITKv5_VERSION: v5.3rc02
   ITK_GIT_URL: https://github.com/InsightSoftwareConsortium/ITK
   ITK_SOURCE_DIR: $(Agent.BuildDirectory)/ITK-source
   ITK_BINARY_DIR: $(Agent.BuildDirectory)/ITK-build

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;