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itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter.hxx
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itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter.hxx
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/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#ifndef itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter_hxx
#define itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter_hxx
#include "itkConstNeighborhoodIterator.h"
#include "itkImageKernelOperator.h"
#include "itkNeighborhoodAlgorithm.h"
#include "itkNeighborhoodInnerProduct.h"
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionIterator.h"
namespace itk
{
namespace BlockMatching
{
template <typename TFixedImage, typename TMovingImage, typename TMetricImage>
NormalizedCrossCorrelationMetricImageFilter<TFixedImage, TMovingImage, TMetricImage>::
NormalizedCrossCorrelationMetricImageFilter()
{
// Only #1 is needed by the user in the output. The others are for subclasses
// or to simply use the pipeline memory allocation system.
// 1. Metric image.
// 2. Denominator of the normalized cross correlation coefficient.
// 3. Fixed Kernel - Fixed Mean
// 4. Moving Search Region - Moving Kernel Mean
// 5. Moving image of ones.
// 6. FixedPseudoSigmaImage.
// 7. FixedMinusMeanSquared.
this->SetNumberOfIndexedOutputs(7);
// ImageSource only does this for the first output.
for (unsigned int i = 1; i < 7; i++)
this->SetNthOutput(i, this->MakeOutput(i));
m_BoxMeanFilter = BoxMeanFilterType::New();
m_BoxPseudoSigmaFilter = BoxPseudoSigmaFilterType::New();
m_BoundaryCondition.SetConstant(NumericTraits<MetricImagePixelType>::Zero);
}
template <typename TFixedImage, typename TMovingImage, typename TMetricImage>
void
NormalizedCrossCorrelationMetricImageFilter<TFixedImage, TMovingImage, TMetricImage>::GenerateOutputInformation()
{
// We generate the information for the first output ( the metric image );
Superclass::GenerateOutputInformation();
FixedImageConstPointerType fixedPtr = this->GetInput(0);
if (!fixedPtr)
{
return;
}
MovingImageConstPointerType movingPtr = this->GetInput(1);
if (!movingPtr)
{
return;
}
// Then we copy the information to all the other outputs.
MetricImagePointerType metricPtr = this->GetOutput();
if (!metricPtr)
{
return;
}
if (!this->m_MovingImageRegionDefined)
{
itkExceptionMacro(<< "Moving image Region has not been set.");
}
// Denominator of normalized cross correlation coefficient.
MetricImagePointerType outputPtr;
outputPtr = this->GetOutput(1);
outputPtr->CopyInformation(movingPtr);
outputPtr->SetRegions(this->m_MovingImageRegion);
// Fixed kernel - fixed mean.
outputPtr = this->GetOutput(2);
outputPtr->CopyInformation(fixedPtr);
outputPtr->SetRegions(this->m_FixedImageRegion);
// Moving search region - moving kernel mean.
outputPtr = this->GetOutput(3);
outputPtr->CopyInformation(movingPtr);
MovingImageRegionType movingRegion = this->m_MovingImageRegion;
movingRegion.PadByRadius(this->m_MovingRadius);
// Make sure the requested region is within the largest possible.
if (movingRegion.Crop(movingPtr->GetLargestPossibleRegion()))
{
outputPtr->SetRegions(movingRegion);
}
else
{
outputPtr->SetRegions(movingRegion);
itkExceptionMacro(<< "Moving image requested region is at least partially outside the LargestPossibleRegion.");
}
if (!this->m_FixedImageRegionDefined)
{
itkExceptionMacro(<< "Fixed image Region has not been set.");
}
// Moving image of ones.
outputPtr = this->GetOutput(4);
outputPtr->CopyInformation(movingPtr);
// FixedPseudoSigmaImage.
outputPtr = this->GetOutput(5);
outputPtr->CopyInformation(movingPtr);
outputPtr->SetRegions(this->m_MovingImageRegion);
// FixedMinusMeanSquared.
outputPtr = this->GetOutput(6);
outputPtr->CopyInformation(movingPtr);
outputPtr->SetRegions(this->m_FixedImageRegion);
}
template <typename TFixedImage, typename TMovingImage, typename TMetricImage>
void
NormalizedCrossCorrelationMetricImageFilter<TFixedImage, TMovingImage, TMetricImage>::EnlargeOutputRequestedRegion(
DataObject * itkNotUsed(data))
{
MetricImagePointerType outputPtr = this->GetOutput(0);
outputPtr->SetRequestedRegionToLargestPossibleRegion();
}
template <typename TFixedImage, typename TMovingImage, typename TMetricImage>
void
NormalizedCrossCorrelationMetricImageFilter<TFixedImage, TMovingImage, TMetricImage>::GenerateHelperImages()
{
FixedImageConstPointerType fixedPtr = this->GetInput(0);
MovingImageConstPointerType movingPtr = this->GetInput(1);
if (!fixedPtr || !movingPtr)
return;
// It will screw up all the requested region assumptions.
if (fixedPtr.GetPointer() == movingPtr.GetPointer())
{
itkExceptionMacro(<< "The fixed image and the moving image must be different.");
}
if (!(fixedPtr->GetSpacing() == movingPtr->GetSpacing()))
{
itkExceptionMacro(<< "This metric image filter assumes the moving and fixed image have the same spacing.");
}
// This is the m_MovingImageRegion dilated by the radius and cropped by the
// LargestPossibleRegion.
MovingImageRegionType movingRequestedRegion = movingPtr->GetRequestedRegion();
bool movingImageRegionIsSmall = false;
for (unsigned int i = 0; i < ImageDimension; ++i)
{
if (2 * this->m_MovingRadius[i] + 1 >= this->m_MovingImageRegion.GetSize()[i])
{
movingImageRegionIsSmall = true;
}
}
if (movingImageRegionIsSmall)
{
MetricImagePixelType movingMean = NumericTraits<MetricImagePixelType>::Zero;
using movingImageIteratorType = ImageRegionConstIterator<MovingImageType>;
movingImageIteratorType movingIt(movingPtr, movingRequestedRegion);
for (movingIt.GoToBegin(); !movingIt.IsAtEnd(); ++movingIt)
{
movingMean += static_cast<MetricImagePixelType>(movingIt.Get());
}
movingMean /= static_cast<MetricImagePixelType>(movingRequestedRegion.GetNumberOfPixels());
MetricImagePointerType movingMeanImg = m_BoxMeanFilter->GetOutput();
movingMeanImg->SetBufferedRegion(movingRequestedRegion);
movingMeanImg->Allocate();
movingMeanImg->FillBuffer(movingMean);
}
else
{
// Calculate the means.
m_BoxMeanFilter->SetRadius(this->m_MovingRadius);
m_BoxMeanFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
m_BoxMeanFilter->SetInput(movingPtr);
m_BoxMeanFilter->GetOutput()->SetRequestedRegion(movingRequestedRegion);
m_BoxMeanFilter->Update();
}
MetricImagePixelType fixedMean = NumericTraits<MetricImagePixelType>::Zero;
using FixedImageIteratorType = ImageRegionConstIterator<FixedImageType>;
FixedImageIteratorType fixedIt(fixedPtr, this->m_FixedImageRegion);
for (fixedIt.GoToBegin(); !fixedIt.IsAtEnd(); ++fixedIt)
{
fixedMean += static_cast<MetricImagePixelType>(fixedIt.Get());
}
fixedMean /= static_cast<MetricImagePixelType>(this->m_FixedImageRegion.GetNumberOfPixels());
// Calculate the fixed image less the fixed image mean.
MetricImagePointerType fixedMinusMean = this->GetOutput(2);
ImageRegionIterator<MetricImageType> fixedMinusMeanIt(fixedMinusMean, this->m_FixedImageRegion);
for (fixedIt.GoToBegin(), fixedMinusMeanIt.GoToBegin(); !fixedIt.IsAtEnd(); ++fixedIt, ++fixedMinusMeanIt)
{
fixedMinusMeanIt.Set(static_cast<MetricImagePixelType>(fixedIt.Get()) - fixedMean);
}
// Calculate the psuedo standard deviations.
// We have to be careful about the border.
// Fill an image with ones to signify we are within the image.
MetricImagePointerType fixedOnes = this->GetOutput(4);
fixedOnes->FillBuffer(NumericTraits<MetricImagePixelType>::One);
// The value of the fixed pseudo sigma when we are away from the image
// boundary.
ImageRegionConstIterator<MetricImageType> fixedMinusMeanConstIt(fixedMinusMean, this->m_FixedImageRegion);
MetricImagePixelType fixedPseudoSigma = NumericTraits<MetricImagePixelType>::Zero;
MetricImagePixelType temp;
for (fixedMinusMeanConstIt.GoToBegin(); !fixedMinusMeanConstIt.IsAtEnd(); ++fixedMinusMeanConstIt)
{
temp = static_cast<MetricImagePixelType>(fixedMinusMeanConstIt.Get());
fixedPseudoSigma += temp * temp;
}
fixedPseudoSigma = std::sqrt(fixedPseudoSigma);
// Has the same value everywhere but the border.
MetricImagePointerType fixedPseudoSigmaImage = this->GetOutput(5);
// Set the value in the interior.
fixedPseudoSigmaImage->FillBuffer(fixedPseudoSigma);
// Modify the value at the borders.
MetricImagePointerType fixedMinusMeanSquared = this->GetOutput(6);
ImageRegionIterator<MetricImageType> fixedMinusMeanSquaredIt(fixedMinusMeanSquared, this->m_FixedImageRegion);
for (fixedMinusMeanConstIt.GoToBegin(), fixedMinusMeanSquaredIt.GoToBegin(); !fixedMinusMeanConstIt.IsAtEnd();
++fixedMinusMeanConstIt, ++fixedMinusMeanSquaredIt)
{
fixedMinusMeanSquaredIt.Set(fixedMinusMeanConstIt.Get() * fixedMinusMeanConstIt.Get());
}
ImageKernelOperator<typename MetricImageType::PixelType, ImageDimension> fixedKernelOperator;
fixedKernelOperator.SetImageKernel(fixedMinusMeanSquared);
fixedKernelOperator.CreateToRadius(this->m_FixedRadius);
NeighborhoodInnerProduct<MetricImageType> innerProduct;
using NeighborhoodIteratorType = ConstNeighborhoodIterator<MetricImageType>;
using FaceCalculatorType = typename NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<MovingImageType>;
FaceCalculatorType faceCalculator;
typename FaceCalculatorType::FaceListType faceList =
faceCalculator(movingPtr, this->m_MovingImageRegion, this->m_MovingRadius);
typename FaceCalculatorType::FaceListType::iterator fit;
for (fit = faceList.begin(), ++fit; fit != faceList.end(); ++fit)
{
if ((*fit).IsInside(this->m_MovingImageRegion))
{
ImageRegionIterator<MetricImageType> fixedPseudoSigmaFaceIt(fixedPseudoSigmaImage, *fit);
NeighborhoodIteratorType nIt(this->m_FixedRadius, fixedOnes, *fit);
nIt.OverrideBoundaryCondition(&m_BoundaryCondition);
for (fixedPseudoSigmaFaceIt.GoToBegin(), nIt.GoToBegin(); !fixedPseudoSigmaFaceIt.IsAtEnd();
++fixedPseudoSigmaFaceIt, ++nIt)
{
fixedPseudoSigmaFaceIt.Set(std::sqrt(innerProduct(nIt, fixedKernelOperator)));
}
}
}
// Calculate the moving search region less the moving kernel means.
MetricImagePointerType movingMinusMean = this->GetOutput(3);
ImageRegionIterator<MetricImageType> movingMinusMeanIt(movingMinusMean, movingRequestedRegion);
ImageRegionConstIterator<MetricImageType> meanIt(m_BoxMeanFilter->GetOutput(), movingRequestedRegion);
ImageRegionConstIterator<MovingImageType> movingIt(movingPtr, movingRequestedRegion);
for (movingMinusMeanIt.GoToBegin(), meanIt.GoToBegin(), movingIt.GoToBegin(); !movingMinusMeanIt.IsAtEnd();
++movingMinusMeanIt, ++meanIt, ++movingIt)
{
movingMinusMeanIt.Set(movingIt.Get() - meanIt.Get());
}
if (movingImageRegionIsSmall)
{
// The cropped region is too small.
MetricImagePixelType movingPseudoSigmaVal = NumericTraits<MetricImagePixelType>::Zero;
MetricImagePointerType movingPseudoSigma = m_BoxPseudoSigmaFilter->GetOutput();
for (movingMinusMeanIt.GoToBegin(); !movingMinusMeanIt.IsAtEnd(); ++movingMinusMeanIt)
{
movingPseudoSigmaVal += movingMinusMeanIt.Get() * movingMinusMeanIt.Get();
}
movingPseudoSigmaVal = std::sqrt(movingPseudoSigmaVal);
movingPseudoSigma->SetBufferedRegion(this->m_MovingImageRegion);
movingPseudoSigma->Allocate();
movingPseudoSigma->FillBuffer(movingPseudoSigmaVal);
}
else
{
// Calculate the pseudo sigma in the moving image.
m_BoxPseudoSigmaFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
m_BoxPseudoSigmaFilter->SetRadius(this->m_MovingRadius);
m_BoxPseudoSigmaFilter->SetInput(movingPtr);
m_BoxPseudoSigmaFilter->GetOutput()->SetRequestedRegion(this->m_MovingImageRegion);
m_BoxPseudoSigmaFilter->Update();
}
MetricImagePointerType denom = this->GetOutput(1);
ImageRegionConstIterator<MetricImageType> fixedPseudoSigmaConstIt(fixedPseudoSigmaImage, this->m_MovingImageRegion);
ImageRegionConstIterator<MetricImageType> movingPseudoSigmaConstIt(m_BoxPseudoSigmaFilter->GetOutput(),
this->m_MovingImageRegion);
ImageRegionIterator<MetricImageType> denomIt(denom, this->m_MovingImageRegion);
for (fixedPseudoSigmaConstIt.GoToBegin(), denomIt.GoToBegin(), movingPseudoSigmaConstIt.GoToBegin();
!fixedPseudoSigmaConstIt.IsAtEnd();
++fixedPseudoSigmaConstIt, ++denomIt, ++movingPseudoSigmaConstIt)
{
denomIt.Set(movingPseudoSigmaConstIt.Get() * fixedPseudoSigmaConstIt.Get());
}
}
} // end namespace BlockMatching
} // end namespace itk
#endif