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WIP: PERF: Use NeighborhoodRange for metric image computation #98

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WIP: PERF: Use NeighborhoodRange for metric image computation #98

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62 changes: 52 additions & 10 deletions include/itkBlockMatchingNormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,14 @@
#include "itkConstantBoundaryCondition.h"
#include "itkConstNeighborhoodIterator.h"
#include "itkImageKernelOperator.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionIterator.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkNeighborhoodInnerProduct.h"
#include "itkConstantBoundaryImageNeighborhoodPixelAccessPolicy.h"
#include "itkShapedImageNeighborhoodRange.h"
#include "itkImageNeighborhoodOffsets.h"
#include <numeric>

namespace itk
{
Expand Down Expand Up @@ -88,7 +92,8 @@ NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter< TFixedImage, TM
typedef ImageRegionIterator< MetricImageType > MetricIteratorType;
MetricImageRegionType metricRegion;
typename MovingImageType::IndexType fitIndex;
typedef ImageRegionConstIterator< MetricImageType > MetricConstIteratorType;
//typedef ImageRegionConstIterator< MetricImageType > MetricConstIteratorType;
typedef ImageRegionConstIteratorWithIndex< MetricImageType > MetricConstIteratorType;
typedef ConstantBoundaryCondition< MetricImageType > BoundaryConditionType;
BoundaryConditionType boundaryCondition;
boundaryCondition.SetConstant( NumericTraits< MetricImagePixelType >::Zero );
Expand Down Expand Up @@ -116,9 +121,10 @@ NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter< TFixedImage, TM
typename FaceCalculatorType::FaceListType faceList = faceCalculator(
movingPtr, this->m_MovingImageRegion, radius );
typename FaceCalculatorType::FaceListType::iterator fit;
const MetricImagePixelType negativeOne = -1 * NumericTraits< MetricImagePixelType >::One;
const MetricImagePixelType positiveOne = NumericTraits< MetricImagePixelType >::One;
MetricImagePixelType normXcorr;
constexpr MetricImagePixelType negativeOne = -1 * NumericTraits< MetricImagePixelType >::One;
constexpr MetricImagePixelType positiveOne = NumericTraits< MetricImagePixelType >::One;
const std::vector<Offset<ImageDimension>> offsets =
Experimental::GenerateRectangularImageNeighborhoodOffsets(radius);
for( fit = faceList.begin(); fit != faceList.end(); ++fit )
{
(*fit).Crop( outputRegion );
Expand All @@ -136,24 +142,60 @@ NormalizedCrossCorrelationNeighborhoodIteratorMetricImageFilter< TFixedImage, TM
MetricIteratorType metricIt( metricPtr, metricRegion );

MetricConstIteratorType denomIt( denom, *fit );
NeighborhoodIteratorType movingNeighborIt( radius, movingMinusMean, *fit );
movingNeighborIt.OverrideBoundaryCondition( &boundaryCondition );


// for every pixel in the output
for( metricIt.GoToBegin(), denomIt.GoToBegin(), movingNeighborIt.GoToBegin();
//NeighborhoodIteratorType movingNeighborIt( radius, movingMinusMean, *fit );
//movingNeighborIt.OverrideBoundaryCondition( &boundaryCondition );
//for( metricIt.GoToBegin(), denomIt.GoToBegin(), movingNeighborIt.GoToBegin();
//!metricIt.IsAtEnd();
//++metricIt, ++denomIt, ++movingNeighborIt )
//{
//if( !(denomIt.Get() == NumericTraits< MetricImagePixelType >::Zero) )
//{
//const MetricImagePixelType normXcorr = innerProduct( movingNeighborIt, fixedKernelOperator ) / denomIt.Get();

//// Why does this happen? Bug? Funky floating point behavior?
//if( normXcorr < negativeOne )
//{
//metricIt.Set( negativeOne );
//}
//else if ( normXcorr > positiveOne )
//{
//metricIt.Set( positiveOne );
//}
//else
//{
//metricIt.Set( normXcorr );
//}
//}
//}
for( metricIt.GoToBegin(), denomIt.GoToBegin();
!metricIt.IsAtEnd();
++metricIt, ++denomIt, ++movingNeighborIt )
++metricIt, ++denomIt)
{
if( !(denomIt.Get() == NumericTraits< MetricImagePixelType >::Zero) )
{
normXcorr = innerProduct( movingNeighborIt, fixedKernelOperator ) / denomIt.Get();
using RangeType = Experimental::ShapedImageNeighborhoodRange<const MetricImageType,
Experimental::ConstantBoundaryImageNeighborhoodPixelAccessPolicy<const MetricImageType> >;
const RangeType movingRange{ *movingMinusMean, denomIt.GetIndex(), offsets };
const RangeType kernelRange{ *fixedMinusMean, denomIt.GetIndex(), offsets };
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@N-Dekker N-Dekker Oct 18, 2018

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Is it really intended that the kernel is set on a new location (denomIt.GetIndex()) with every iteration?


const MetricImagePixelType normXcorr = std::inner_product( movingRange.begin(), movingRange.end(), kernelRange.begin(), 0.0 ) / denomIt.Get();
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@N-Dekker N-Dekker Oct 18, 2018

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I have to admit I could not get optimal performance when using std::inner_product at https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/ImageFunction/include/itkGaussianDerivativeImageFunction.hxx#L219, so instead I just manually wrote the inner product calculation in a few lines of code. In this case, it might look as follows:

auto normXcorr = NumericTraits<MetricImagePixelType>::Zero;
auto movingRangeIterator = movingRange.cbegin();

for (const auto& kernelValue : kernelRange)
{
  normXcorr += kernelValue * (*movingRangeIterator);
  ++movingRangeIterator;
}
normXcorr /= denomIt.Get();


// Why does this happen? Bug? Funky floating point behavior?
if( normXcorr < negativeOne )
{
metricIt.Set( negativeOne );
}
else if ( normXcorr > positiveOne )
{
metricIt.Set( positiveOne );
}
else
{
metricIt.Set( normXcorr );
}
}
}
}
Expand Down