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WIP: COMP: Upgrade ITK from v5.2.0 to v5.3rc02
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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).
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@N-Dekker
N-Dekker committed Jan 2, 2022
1 parent c9a0db8 commit e2071d8
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Showing 8 changed files with 57 additions and 92 deletions.
6 changes: 3 additions & 3 deletions .github/workflows/ElastixGitHubActions.yml
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Expand Up @@ -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
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65 changes: 26 additions & 39 deletions Common/Transforms/itkAdvancedBSplineDeformableTransform.hxx
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Expand Up @@ -41,6 +41,7 @@
#include "itkImageScanlineConstIterator.h"
#include "itkIdentityTransform.h"
#include <vnl/vnl_math.h>
#include <array>
#include <vector>
#include <algorithm> // For std::copy_n.

Expand Down Expand Up @@ -291,9 +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;
Expand Down Expand Up @@ -379,9 +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;
Expand Down Expand Up @@ -446,9 +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;
Expand Down Expand Up @@ -504,20 +501,18 @@ 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 */
typename WeightsType::ValueType coeffArray[numberOfWeights * SpaceDimension];
WeightsType coeffs(coeffArray, numberOfWeights * SpaceDimension, false);
std::array<typename WeightsType::ValueType, numberOfWeights * SpaceDimension> coeffs;

IndexType supportIndex;
this->m_DerivativeWeightsFunctions[0]->ComputeStartIndex(cindex, supportIndex);
const RegionType supportRegion(supportIndex, Superclass::m_SupportSize);

/** Copy values from coefficient image to linear coeffs array. */
typename WeightsType::iterator itCoeffsLinear = coeffs.begin();
auto itCoeffsLinear = coeffs.begin();
for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
{
ImageScanlineConstIterator<ImageType> itCoef(this->m_CoefficientImages[dim], supportRegion);
Expand All @@ -544,7 +539,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetS
this->m_DerivativeWeightsFunctions[i]->Evaluate(cindex, supportIndex, weights);

/** Create an iterator over the coeffs vector. */
typename WeightsType::const_iterator itCoeffs = coeffs.begin();
auto itCoeffs = coeffs.cbegin();

/** Compute the spatial Jacobian sj:
* dT_{dim} / dx_i = \sum coefs_{dim} * weights.
Expand Down Expand Up @@ -610,19 +605,17 @@ 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 */
WeightsValueType coeffArray[numberOfWeights * SpaceDimension];
WeightsType coeffs(coeffArray, numberOfWeights * SpaceDimension, false);
std::array<WeightsValueType, numberOfWeights * SpaceDimension> coeffs;

IndexType supportIndex;
this->m_SODerivativeWeightsFunctions[0][0]->ComputeStartIndex(cindex, supportIndex);
const RegionType supportRegion(supportIndex, Superclass::m_SupportSize);

/** Copy values from coefficient image to linear coeffs array. */
typename WeightsType::iterator itCoeffsLinear = coeffs.begin();
auto itCoeffsLinear = coeffs.begin();
for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
{
ImageScanlineConstIterator<ImageType> itCoef(this->m_CoefficientImages[dim], supportRegion);
Expand Down Expand Up @@ -653,7 +646,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetS
this->m_SODerivativeWeightsFunctions[i][j]->Evaluate(cindex, supportIndex, weights);

/** Create an iterator over the coeffs vector. */
typename WeightsType::const_iterator itCoeffs = coeffs.begin();
auto itCoeffs = coeffs.cbegin();

/** Compute d^2T_{dim} / dx_i dx_j = \sum coefs_{dim} * weights. */
for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
Expand Down Expand Up @@ -735,9 +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);
Expand Down Expand Up @@ -840,16 +832,14 @@ 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. */
WeightsValueType coeffArray[numberOfWeights * SpaceDimension];
WeightsType coeffs(coeffArray, numberOfWeights * SpaceDimension, false);
std::array<WeightsValueType, numberOfWeights * SpaceDimension> coeffs;

/** Copy values from coefficient image to linear coeffs array. */
// takes considerable amount of time : 27% of this function. // with old region iterator, check with new
typename WeightsType::iterator itCoeffsLinear = coeffs.begin();
auto itCoeffsLinear = coeffs.begin();
for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
{
ImageScanlineConstIterator<ImageType> itCoef(this->m_CoefficientImages[dim], supportRegion);
Expand Down Expand Up @@ -887,7 +877,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
std::copy_n(weights.begin(), numberOfWeights, weightVector + i * numberOfWeights);

/** Reset coeffs iterator */
typename WeightsType::const_iterator itCoeffs = coeffs.begin();
auto itCoeffs = coeffs.cbegin();

/** Compute the spatial Jacobian sj:
* dT_{dim} / dx_i = delta_{dim,i} + \sum coefs_{dim} * weights.
Expand Down Expand Up @@ -993,9 +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);
Expand Down Expand Up @@ -1119,16 +1108,14 @@ 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. */
WeightsValueType coeffArray[numberOfWeights * SpaceDimension];
WeightsType coeffs(coeffArray, numberOfWeights * SpaceDimension, false);
std::array<WeightsValueType, numberOfWeights * SpaceDimension> coeffs;

/** Copy values from coefficient image to linear coeffs array. */
// takes considerable amount of time : 27% of this function. // with old region iterator, check with new
typename WeightsType::iterator itCoeffsLinear = coeffs.begin();
auto itCoeffsLinear = coeffs.begin();
for (unsigned int dim = 0; dim < SpaceDimension; ++dim)
{
ImageScanlineConstIterator<ImageType> itCoef(this->m_CoefficientImages[dim], supportRegion);
Expand Down Expand Up @@ -1168,7 +1155,7 @@ AdvancedBSplineDeformableTransform<TScalarType, NDimensions, VSplineOrder>::GetJ
count++;

/** Reset coeffs iterator */
typename WeightsType::const_iterator itCoeffs = coeffs.begin();
auto itCoeffs = coeffs.cbegin();

/** Compute the spatial Hessian sh:
* d^2T_{dim} / dx_i dx_j = \sum coefs_{dim} * weights.
Expand Down
15 changes: 9 additions & 6 deletions Common/Transforms/itkBSplineInterpolationWeightFunctionBase.h
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Expand Up @@ -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);
Expand All @@ -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;
Expand Down
4 changes: 1 addition & 3 deletions Common/Transforms/itkCyclicBSplineDeformableTransform.hxx
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Expand Up @@ -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);
Expand Down
52 changes: 15 additions & 37 deletions Common/Transforms/itkRecursiveBSplineTransform.hxx
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Expand Up @@ -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])
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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]);
Expand Down Expand Up @@ -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]);
Expand Down Expand Up @@ -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]);
Expand Down Expand Up @@ -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]);
Expand Down
2 changes: 1 addition & 1 deletion Testing/CI/Azure/ci.yml
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@@ -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
Expand Down
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