: this class contains a lot of functional code, which actually does not belong here.

Class elastix::AdaptiveStochasticGradientDescent< TElastix >

: this class contains a lot of functional code, which actually does not belong here.

Class elastix::AdaptiveStochasticLBFGS< TElastix >

: this class contains a lot of functional code, which actually does not belong here.

Class elastix::AdaptiveStochasticVarianceReducedGradient< TElastix >

: this class contains a lot of functional code, which actually does not belong here.

Class elastix::AdvancedBSplineTransform< TElastix >

It is unsure what happens when one of the image dimensions has length 1.

Class elastix::BSplineStackTransform< TElastix >

It is unsure what happens when one of the image dimensions has length 1.

Class elastix::BSplineTransformWithDiffusion< TElastix >

: this Transform has not been tested for images with Direction cosines matrix other than the identity matrix.

Global elastix::ELASTIX::RegisterImages (ImagePointer fixedImage, ImagePointer movingImage, const ParameterMapType &parameterMap, const std::string &outputPath, bool performLogging, bool performCout, ImagePointer fixedMask=nullptr, ImagePointer movingMask=nullptr)

generate file elastix_errors.h containing error codedefines (e.g. #define ELASTIX_NO_ERROR 0)

Global elastix::ElastixTemplate< TFixedImage, TMovingImage >::InputImageType

How useful is this? It is not consequently supported, since the the input image is stored in the MovingImageContainer anyway.

Class elastix::EulerStackTransform< TElastix >

It is unsure what happens when one of the image dimensions has length 1.

The center of rotation point is not transformed with the initial transform yet.

Global elastix::FullSearch< TElastix >::itkGetModifiableObjectMacro (OptimizationSurface, NDImageType)

BeforeAll, checking parameters.

Global elastix::MetricBase< TElastix >::m_ShowExactMetricValue

the method GetExactDerivative could as well be added here.

Class elastix::MultiBSplineTransformWithNormal< TElastix >

It is unsure what happens when one of the image dimensions has length 1.

Class elastix::PreconditionedStochasticGradientDescent< TElastix >

: this class contains a lot of functional code, which actually does not belong here.

Class elastix::RandomSamplerSparseMask< TElastix >

Write something similar for the RandomCoordinate sampler.

Class elastix::RecursiveBSplineTransform< TElastix >

It is unsure what happens when one of the image dimensions has length 1.

Global elastix::RegistrationBase< TElastix >::ReadMaskParameters (UseMaskErosionArrayType &useMaskErosionArray, const unsigned int nrOfMasks, const std::string &whichMask, const unsigned int level) const

: move to RegistrationBase Input:

Class itk::AdvancedImageMomentsCalculator< TImage >

It's not yet clear how multi-echo images should be handled here.

Class itk::AdvancedVersorTransform< TScalarType >

Need to make sure that the translation parameters in the baseclass cannot be set to non-zero values.

Class itk::FullSearchOptimizer

This optimizer has similar functionality as the recently added itkExhaustiveOptimizer. See if we can replace it by that optimizer, or inherit from it.

Global itk::ImageSamplerBase< TInputImage >::SetUseMultiThread (bool _arg)

: Temporary, should think about interface.

Global itk::KNNGraphAlphaMutualInformationImageToImageMetric< TFixedImage, TMovingImage >::EvaluateMovingFeatureImageDerivatives (const MovingImagePointType &mappedPoint, SpatialDerivativeType &featureGradients) const

move this to base class.

Class itk::NDImageBase< TPixel >

not all! An internal writer and reader are included for convenience.

Global itk::NDImageBase< TPixel >::CopyInformation (const DataObject *data)=0

Transform IndexToPoint methods.

Global itk::NDImageBase< TPixel >::SetRegions (SizeType size)=0

: extend to direction cosines; but not needed for now in elastix

an NDRegionType should first be declared, in the same way as NDImage use SetRegions(size) for now. then knowlegde of the RegionType is not necessary. alternative: forget about the regiontype and add the functions SetLargestPossibleRegion, SetRegions etc with arguments (index,size) or maybe: ImageIORegion

Global itk::NDImageTemplate< TPixel, VDimension >::CopyInformation (const DataObject *data) override

Transform IndexToPoint methods.

Global itk::ParzenWindowHistogramImageToImageMetric< TFixedImage, TMovingImage >::UpdateJointPDFAndIncrementalPDFs (RealType fixedImageValue, RealType movingImageValue, RealType movingMaskValue, const DerivativeType &movingImageValuesRight, const DerivativeType &movingImageValuesLeft, const DerivativeType &movingMaskValuesRight, const DerivativeType &movingMaskValuesLeft, const NonZeroJacobianIndicesType &nzji) const

The IsInsideMovingMask return bools are converted to doubles (1 or 0) to simplify the computation. But this may not be necessary.

Class itk::Statistics::ListSampleCArray< TMeasurementVector, TInternalValue >

: the second template argument should be removed, since the GetMeasurementVector method is incorrect when TMeasurementVector::ValueType != TInternalValue.

Global itk::WeightedCombinationTransform< TScalarType, NInputDimensions, NOutputDimensions >::TransformPointer

: shouldn't these be ConstPointers?

Class TranslationStackTransform

It is unsure what happens when one of the image dimensions has length 1.