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BUG: Need to fill buffer for R and Python interfaces. #1699

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Mar 18, 2024
Merged

BUG: Need to fill buffer for R and Python interfaces. #1699

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34 changes: 23 additions & 11 deletions Utilities/itkDiReCTImageFilter.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -259,19 +259,23 @@ DiReCTImageFilter<TInputImage, TOutputImage>::GenerateData()
{
CumulativeVelocityFieldPointer forwardCumulativeVelocityField = this->GetForwardCumulativeVelocityField();
forwardCumulativeVelocityField->Allocate();
forwardCumulativeVelocityField->FillBuffer(zeroVector);
CumulativeVelocityFieldPointer inverseCumulativeVelocityField = this->GetInverseCumulativeVelocityField();
inverseCumulativeVelocityField->Allocate();
inverseCumulativeVelocityField->FillBuffer(zeroVector);
}

DisplacementFieldPointer forwardIncrementalField = DisplacementFieldType::New();
forwardIncrementalField->CopyInformation(segmentationImage);
forwardIncrementalField->SetRegions(segmentationImage->GetRequestedRegion());
forwardIncrementalField->Allocate();
forwardIncrementalField->FillBuffer(zeroVector);

RealImagePointer hitImage = RealImageType::New();
hitImage->CopyInformation(segmentationImage);
hitImage->SetRegions(segmentationImage->GetRequestedRegion());
hitImage->Allocate();
hitImage->FillBuffer(0.0);

DisplacementFieldPointer integratedField = DisplacementFieldType::New();
integratedField->CopyInformation(segmentationImage);
Expand All @@ -283,26 +287,31 @@ DiReCTImageFilter<TInputImage, TOutputImage>::GenerateData()
inverseField->CopyInformation(segmentationImage);
inverseField->SetRegions(segmentationImage->GetRequestedRegion());
inverseField->Allocate();
inverseField->FillBuffer(zeroVector);

DisplacementFieldPointer inverseIncrementalField = DisplacementFieldType::New();
inverseIncrementalField->CopyInformation(segmentationImage);
inverseIncrementalField->SetRegions(segmentationImage->GetRequestedRegion());
inverseIncrementalField->Allocate();
inverseIncrementalField->FillBuffer(zeroVector);

RealImagePointer speedImage = RealImageType::New();
speedImage->CopyInformation(segmentationImage);
speedImage->SetRegions(segmentationImage->GetRequestedRegion());
speedImage->Allocate();
speedImage->FillBuffer(0.0);

RealImagePointer thicknessImage = RealImageType::New();
thicknessImage->CopyInformation(segmentationImage);
thicknessImage->SetRegions(segmentationImage->GetRequestedRegion());
thicknessImage->Allocate();
thicknessImage->FillBuffer(0.0);

RealImagePointer totalImage = RealImageType::New();
totalImage->CopyInformation(segmentationImage);
totalImage->SetRegions(segmentationImage->GetRequestedRegion());
totalImage->Allocate();
totalImage->FillBuffer(0.0);

DisplacementFieldPointer velocityField = DisplacementFieldType::New();
velocityField->CopyInformation(segmentationImage);
Expand Down Expand Up @@ -398,7 +407,7 @@ DiReCTImageFilter<TInputImage, TOutputImage>::GenerateData()

// Generate speed image

speedImage->FillBuffer(0.0);
speedImage->FillBuffer(NumericTraits<RealType>::Zero);

ItGradientImage.GoToBegin();
ItGrayMatterProbabilityMap.GoToBegin();
Expand All @@ -424,19 +433,18 @@ DiReCTImageFilter<TInputImage, TOutputImage>::GenerateData()
ItGradientImage.Set(zeroVector);
}
RealType delta = (ItWarpedWhiteMatterProbabilityMap.Get() - ItGrayMatterProbabilityMap.Get());
currentEnergy += itk::Math::abs(delta);
currentEnergy += Math::abs(delta);
numberOfGrayMatterVoxels++;
RealType speedValue =
static_cast<RealType>(-1.0) * delta * ItGrayMatterProbabilityMap.Get() * this->m_CurrentGradientStep;
RealType speedValue = -delta * ItGrayMatterProbabilityMap.Get() * this->m_CurrentGradientStep;
if (std::isnan(speedValue) || std::isinf(speedValue))
{
speedValue = 0.0;
speedValue = NumericTraits<RealType>::Zero;
}
ItSpeedImage.Set(speedValue);
}
else
{
ItSpeedImage.Set(0.0);
ItSpeedImage.Set(NumericTraits<RealType>::Zero);
}

++ItGradientImage;
Expand Down Expand Up @@ -698,7 +706,7 @@ DiReCTImageFilter<TInputImage, TOutputImage>::GenerateData()
}
else if (this->m_UseMaskedSmoothing)
{
using MaskedSmootherType = MaskedSmoothingImageFilter<DisplacementFieldType, InputImageType>;
using MaskedSmootherType = MaskedSmoothingImageFilter<DisplacementFieldType, InputImageType, DisplacementFieldType>;
typename MaskedSmootherType::Pointer maskedSmoother = MaskedSmootherType::New();
maskedSmoother->SetInput(velocityField);
maskedSmoother->SetMaskImage(thresholdedRegion);
Expand Down Expand Up @@ -871,14 +879,18 @@ typename DiReCTImageFilter<TInputImage, TOutputImage>::RealImagePointer
DiReCTImageFilter<TInputImage, TOutputImage>::WarpImage(const RealImageType * inputImage,
const DisplacementFieldType * displacementField)
{
using InterpolatorType = itk::LinearInterpolateImageFunction<RealImageType, double>;
auto interpolator = InterpolatorType::New();

using WarperType = WarpImageFilter<RealImageType, RealImageType, DisplacementFieldType>;
typename WarperType::Pointer warper = WarperType::New();
warper->SetInput(inputImage);
warper->SetDisplacementField(displacementField);
warper->SetInterpolator(interpolator);
warper->SetEdgePaddingValue(0);
warper->SetOutputSpacing(inputImage->GetSpacing());
warper->SetOutputOrigin(inputImage->GetOrigin());
warper->SetOutputDirection(inputImage->GetDirection());
warper->SetOutputSpacing(displacementField->GetSpacing());
warper->SetOutputOrigin(displacementField->GetOrigin());
warper->SetOutputDirection(displacementField->GetDirection());
warper->SetDisplacementField(displacementField);

RealImagePointer warpedImage = warper->GetOutput();
warpedImage->Update();
Expand Down