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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 itkFFTConvolutionImageFilter_hxx
#define itkFFTConvolutionImageFilter_hxx
#include "itkCastImageFilter.h"
#include "itkChangeInformationImageFilter.h"
#include "itkConstantPadImageFilter.h"
#include "itkCyclicShiftImageFilter.h"
#include "itkExtractImageFilter.h"
#include "itkFFTPadImageFilter.h"
#include "itkImageBase.h"
#include "itkMultiplyImageFilter.h"
#include "itkNormalizeToConstantImageFilter.h"
#include "itkMath.h"
#include "itkRegionOfInterestImageFilter.h"
namespace itk
{
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::FFTConvolutionImageFilter()
{
m_SizeGreatestPrimeFactor = FFTFilterType::New()->GetSizeGreatestPrimeFactor();
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::GenerateInputRequestedRegion()
{
// Pad the input image with the radius of the kernel.
if (this->GetInput())
{
InputRegionType inputRegion = this->GetOutput()->GetRequestedRegion();
// Pad the output request region by the kernel radius.
// Note that FFT padding will always be generated by a boundary condition
// as an implementation detail, while pixels for kernel radius padding may be taken
// from the original image if they lies inside the image bounds.
inputRegion.PadByRadius(this->GetKernelRadius());
// Crop the output requested region to fit within the largest
// possible region.
InputImageType * inputPtr = itkDynamicCastInDebugMode<InputImageType *>(this->GetPrimaryInput());
bool wasPartiallyInside = inputRegion.Crop(inputPtr->GetLargestPossibleRegion());
if (!wasPartiallyInside)
{
itkExceptionMacro("Requested region is outside the largest possible region.");
}
// Input is an image, cast away the constness so we can set
// the requested region.
inputPtr->SetRequestedRegion(inputRegion);
}
if (this->GetKernelImage())
{
// Input kernel is an image, cast away the constness so we can set
// the requested region.
typename KernelImageType::Pointer kernelPtr = const_cast<KernelImageType *>(this->GetKernelImage());
kernelPtr->SetRequestedRegionToLargestPossibleRegion();
}
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::GenerateData()
{
// Create a process accumulator for tracking the progress of this minipipeline
auto progress = ProgressAccumulator::New();
progress->SetMiniPipelineFilter(this);
auto localInput = InputImageType::New();
localInput->Graft(this->GetInput());
const KernelImageType * kernelImage = this->GetKernelImage();
InternalComplexImagePointerType input = nullptr;
InternalComplexImagePointerType kernel = nullptr;
this->PrepareInputs(localInput, kernelImage, input, kernel, progress, 0.7f);
// Convolve
using MultiplyFilterType =
MultiplyImageFilter<InternalComplexImageType, InternalComplexImageType, InternalComplexImageType>;
auto multiplyFilter = MultiplyFilterType::New();
multiplyFilter->SetInput1(input);
multiplyFilter->SetInput2(kernel);
multiplyFilter->ReleaseDataFlagOn();
progress->RegisterInternalFilter(multiplyFilter, 0.1);
multiplyFilter->Update();
// Free up the memory for the prepared inputs
input = nullptr;
kernel = nullptr;
this->ProduceOutput(multiplyFilter->GetOutput(), progress, 0.2);
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::PrepareInputs(
const InputImageType * input,
const KernelImageType * kernel,
InternalComplexImagePointerType & preparedInput,
InternalComplexImagePointerType & preparedKernel,
ProgressAccumulator * progress,
float progressWeight)
{
this->PrepareInput(input, preparedInput, progress, 0.5f * progressWeight);
this->PrepareKernel(kernel, preparedKernel, progress, 0.5f * progressWeight);
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::PrepareInput(
const InputImageType * input,
InternalComplexImagePointerType & preparedInput,
ProgressAccumulator * progress,
float progressWeight)
{
InternalImagePointerType paddedInput;
this->PadInput(input, paddedInput, progress, 0.3f * progressWeight);
this->TransformPaddedInput(paddedInput, preparedInput, progress, 0.7f * progressWeight);
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::PadInput(
const InputImageType * input,
InternalImagePointerType & paddedInput,
ProgressAccumulator * progress,
float progressWeight)
{
float remainingProgress = 1.0f;
InputRegionType inputLargestRegion = input->GetLargestPossibleRegion();
InputSizeType inputLargestSize = inputLargestRegion.GetSize();
InputIndexType inputLargestIndex = inputLargestRegion.GetIndex();
InputRegionType inputRequestedRegion = input->GetRequestedRegion();
InputSizeType inputRequestedSize = inputRequestedRegion.GetSize();
InputIndexType inputRequestedIndex = inputRequestedRegion.GetIndex();
OutputRegionType outputRequestedRegion = this->GetOutput()->GetRequestedRegion();
OutputSizeType outputRequestedSize = outputRequestedRegion.GetSize();
OutputIndexType outputRequestedIndex = outputRequestedRegion.GetIndex();
// Pad the input image such that the requested region, expanded by
// twice the kernel radius, lies entirely within the buffered region.
// If the requested region is at least the kernel radius away from
// all boundaries of the buffered input region then padding is skipped.
using InputPadFilterType = PadImageFilter<InputImageType, InputImageType>;
using PadSizeType = typename InputPadFilterType::SizeType;
PadSizeType lowerPad, upperPad;
bool needsKernelPadding = false;
KernelSizeType kernelRadius = this->GetKernelRadius();
for (unsigned int dim = 0; dim < ImageDimension; ++dim)
{
// Use signed int for arithmetic
int largestUpperCorner = inputLargestIndex[dim] + inputLargestSize[dim];
int requestedUpperCorner = inputRequestedIndex[dim] + inputRequestedSize[dim];
int largestLowerCorner = inputLargestIndex[dim];
int requestedLowerCorner = inputRequestedIndex[dim];
// Pad for difference between lower corner of largest vs requested region
int lower = static_cast<int>(kernelRadius[dim]) - (requestedLowerCorner - largestLowerCorner);
// Pad for difference between upper corner of largest vs requested region
int upper = static_cast<int>(kernelRadius[dim]) - (largestUpperCorner - requestedUpperCorner);
lowerPad[dim] = (lower > 0 ? lower : 0);
upperPad[dim] = (upper > 0 ? upper : 0);
needsKernelPadding = needsKernelPadding || lower > 0 || upper > 0;
}
const InputImageType * kernelPaddedInput;
if (needsKernelPadding)
{
auto inputPadder = InputPadFilterType::New();
inputPadder->SetBoundaryCondition(this->GetBoundaryCondition());
inputPadder->SetPadLowerBound(lowerPad);
inputPadder->SetPadUpperBound(upperPad);
inputPadder->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
inputPadder->SetInput(input);
inputPadder->ReleaseDataFlagOn();
progress->RegisterInternalFilter(inputPadder, 0.2f * progressWeight);
remainingProgress -= 0.2f;
inputPadder->Update();
kernelPaddedInput = inputPadder->GetOutput();
}
else
{
kernelPaddedInput = input;
}
// Crop to region of interest to minimize FFT requested region size.
// This blocks forward FFT from requesting the entire input image
// when only a subregion (output requested region + kernel radius padding)
// is required for convolution to succeed.
// TODO: Improve readability by keeping the output index as-is rather than resetting to 0, if the filter allows it
const InputImageType * regionOfInterestImage;
InputRegionType regionOfInterest;
InputSizeType regionOfInterestSize;
InputIndexType regionOfInterestIndex;
for (unsigned int dim = 0; dim < ImageDimension; ++dim)
{
regionOfInterestSize[dim] = outputRequestedSize[dim] + 2 * kernelRadius[dim];
regionOfInterestIndex[dim] = outputRequestedIndex[dim] - kernelRadius[dim];
}
regionOfInterest = InputRegionType(regionOfInterestIndex, regionOfInterestSize);
if (outputRequestedRegion != inputLargestRegion)
{
using CropFilterType = RegionOfInterestImageFilter<InputImageType, InputImageType>;
auto cropFilter = CropFilterType::New();
cropFilter->SetInput(kernelPaddedInput);
cropFilter->SetRegionOfInterest(regionOfInterest);
cropFilter->ReleaseDataFlagOn();
progress->RegisterInternalFilter(cropFilter, 0.1f * progressWeight);
remainingProgress -= 0.1f;
// Shift region of interest back to original index
// so that filter output is physically correct
using InfoFilterType = ChangeInformationImageFilter<InputImageType>;
using InfoOffsetValueType = typename InfoFilterType::OutputImageOffsetValueType;
auto inputInfoFilter = InfoFilterType::New();
inputInfoFilter->SetInput(cropFilter->GetOutput());
inputInfoFilter->ChangeRegionOn();
InfoOffsetValueType offset[ImageDimension];
for (unsigned int dim = 0; dim < ImageDimension; ++dim)
{
offset[dim] = regionOfInterestIndex[dim];
}
inputInfoFilter->SetOutputOffset(offset);
inputInfoFilter->ReleaseDataFlagOn();
inputInfoFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
progress->RegisterInternalFilter(inputInfoFilter, 0.001f * progressWeight);
remainingProgress -= 0.001f;
inputInfoFilter->Update();
regionOfInterestImage = inputInfoFilter->GetOutput();
}
else
{
regionOfInterestImage = kernelPaddedInput;
}
// Pad for FFT so that each image side is factorable by at most
// the specified greatest prime factor.
// Note that FFT padding is always taken from the boundary condition
// to avoid introducing extra information to FFT convolution vs spatial convolution
using FFTPadFilterType = itk::FFTPadImageFilter<InputImageType, InputImageType>;
auto fftPadder = FFTPadFilterType::New();
fftPadder->SetInput(regionOfInterestImage);
fftPadder->SetSizeGreatestPrimeFactor(m_SizeGreatestPrimeFactor);
fftPadder->SetBoundaryCondition(this->GetBoundaryCondition());
fftPadder->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
fftPadder->ReleaseDataFlagOn();
progress->RegisterInternalFilter(fftPadder, 0.199f * progressWeight);
remainingProgress -= 0.199f;
fftPadder->Update();
// Save FFT padding size to assist in output cropping
InputSizeType fftPaddedSize = fftPadder->GetOutput()->GetLargestPossibleRegion().GetSize();
for (unsigned int dim = 0; dim < ImageDimension; ++dim)
{
m_FFTPadSize[dim] = fftPaddedSize[dim] - regionOfInterestSize[dim];
}
// We could avoid a separate cast here by setting the output type of
// the padder to the InternalImageType, but doing so complicates the
// definition of the boundary condition passed into this class and
// requires the InternalImageType to be exposed publicly.
// TODO: Casting has been observed to take the bulk of image prep time, up to 75%.
// Optimize to avoid unnecessary casting and copying of memory.
using InputCastFilterType = CastImageFilter<InputImageType, InternalImageType>;
auto inputCaster = InputCastFilterType::New();
inputCaster->InPlaceOn();
inputCaster->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
inputCaster->SetInput(fftPadder->GetOutput());
inputCaster->ReleaseDataFlagOn();
progress->RegisterInternalFilter(inputCaster, remainingProgress * progressWeight);
inputCaster->Update();
// Cache padded input size to use in kernel preparation and output cropping
m_PaddedInputRegion = inputCaster->GetOutput()->GetLargestPossibleRegion();
paddedInput = inputCaster->GetOutput();
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::TransformPaddedInput(
const InternalImageType * paddedInput,
InternalComplexImagePointerType & transformedInput,
ProgressAccumulator * progress,
float progressWeight)
{
// Take the Fourier transform of the padded image.
auto imageFFTFilter = FFTFilterType::New();
imageFFTFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
imageFFTFilter->SetInput(paddedInput);
imageFFTFilter->ReleaseDataFlagOn();
progress->RegisterInternalFilter(imageFFTFilter, progressWeight);
imageFFTFilter->Update();
transformedInput = imageFFTFilter->GetOutput();
transformedInput->DisconnectPipeline();
imageFFTFilter->SetInput(nullptr);
imageFFTFilter = nullptr;
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::PrepareKernel(
const KernelImageType * kernel,
InternalComplexImagePointerType & preparedKernel,
ProgressAccumulator * progress,
float progressWeight)
{
KernelRegionType kernelRegion = kernel->GetLargestPossibleRegion();
KernelSizeType kernelSize = kernelRegion.GetSize();
InputSizeType inputPadSize = m_PaddedInputRegion.GetSize();
typename KernelImageType::SizeType kernelUpperBound;
for (unsigned int i = 0; i < ImageDimension; ++i)
{
kernelUpperBound[i] = inputPadSize[i] - kernelSize[i];
}
InternalImagePointerType paddedKernelImage = nullptr;
float paddingWeight = 0.2f;
if (this->GetNormalize())
{
using NormalizeFilterType = NormalizeToConstantImageFilter<KernelImageType, InternalImageType>;
auto normalizeFilter = NormalizeFilterType::New();
normalizeFilter->SetConstant(NumericTraits<TInternalPrecision>::OneValue());
normalizeFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
normalizeFilter->SetInput(kernel);
normalizeFilter->ReleaseDataFlagOn();
progress->RegisterInternalFilter(normalizeFilter, 0.2f * paddingWeight * progressWeight);
// Pad the kernel image with zeros.
using KernelPadType = ConstantPadImageFilter<InternalImageType, InternalImageType>;
using KernelPadPointer = typename KernelPadType::Pointer;
KernelPadPointer kernelPadder = KernelPadType::New();
kernelPadder->SetConstant(TInternalPrecision{});
kernelPadder->SetPadUpperBound(kernelUpperBound);
kernelPadder->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
kernelPadder->SetInput(normalizeFilter->GetOutput());
kernelPadder->ReleaseDataFlagOn();
progress->RegisterInternalFilter(kernelPadder, 0.8f * paddingWeight * progressWeight);
kernelPadder->Update();
paddedKernelImage = kernelPadder->GetOutput();
}
else
{
// Pad the kernel image with zeros.
using KernelPadType = ConstantPadImageFilter<KernelImageType, InternalImageType>;
using KernelPadPointer = typename KernelPadType::Pointer;
KernelPadPointer kernelPadder = KernelPadType::New();
kernelPadder->SetConstant(TInternalPrecision{});
kernelPadder->SetPadUpperBound(kernelUpperBound);
kernelPadder->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
kernelPadder->SetInput(kernel);
kernelPadder->ReleaseDataFlagOn();
progress->RegisterInternalFilter(kernelPadder, paddingWeight * progressWeight);
paddedKernelImage = kernelPadder->GetOutput();
}
// Shift the padded kernel image.
using KernelShiftFilterType = CyclicShiftImageFilter<InternalImageType, InternalImageType>;
auto kernelShifter = KernelShiftFilterType::New();
typename KernelShiftFilterType::OffsetType kernelShift;
for (unsigned int i = 0; i < ImageDimension; ++i)
{
kernelShift[i] = -(static_cast<typename KernelShiftFilterType::OffsetType::OffsetValueType>(kernelSize[i] / 2));
}
kernelShifter->SetShift(kernelShift);
kernelShifter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
kernelShifter->SetInput(paddedKernelImage);
kernelShifter->ReleaseDataFlagOn();
progress->RegisterInternalFilter(kernelShifter, 0.1f * progressWeight);
// Compute the kernel complex image
auto kernelFFTFilter = FFTFilterType::New();
kernelFFTFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
kernelFFTFilter->SetInput(kernelShifter->GetOutput());
progress->RegisterInternalFilter(kernelFFTFilter, 0.699f * progressWeight);
kernelFFTFilter->Update();
// Shift the kernel complex image in space so that it coincides with the
// input complex image
using InfoFilterType = ChangeInformationImageFilter<InternalComplexImageType>;
auto kernelInfoFilter = InfoFilterType::New();
kernelInfoFilter->ChangeRegionOn();
using InfoOffsetValueType = typename InfoFilterType::OutputImageOffsetValueType;
const InputIndexType & inputIndex = m_PaddedInputRegion.GetIndex();
const KernelIndexType & kernelIndex = kernel->GetLargestPossibleRegion().GetIndex();
InfoOffsetValueType kernelOffset[ImageDimension];
for (unsigned int i = 0; i < ImageDimension; ++i)
{
kernelOffset[i] = static_cast<InfoOffsetValueType>(inputIndex[i] - kernelIndex[i]);
}
kernelInfoFilter->SetOutputOffset(kernelOffset);
kernelInfoFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
kernelInfoFilter->SetInput(kernelFFTFilter->GetOutput());
progress->RegisterInternalFilter(kernelInfoFilter, 0.001f * progressWeight);
kernelInfoFilter->Update();
preparedKernel = kernelInfoFilter->GetOutput();
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::ProduceOutput(
InternalComplexImageType * paddedOutput,
ProgressAccumulator * progress,
float progressWeight)
{
// Transform the convolution result back into physical space
auto ifftFilter = IFFTFilterType::New();
ifftFilter->SetActualXDimensionIsOdd(this->GetXDimensionIsOdd());
ifftFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
ifftFilter->SetInput(paddedOutput);
ifftFilter->ReleaseDataFlagOn();
progress->RegisterInternalFilter(ifftFilter, 0.6f * progressWeight);
ifftFilter->Update();
this->CropOutput(ifftFilter->GetOutput(), progress, 0.4f * progressWeight);
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::CropOutput(
InternalImageType * paddedOutput,
ProgressAccumulator * progress,
float progressWeight)
{
InternalIndexType paddedOutputIndex = paddedOutput->GetLargestPossibleRegion().GetIndex();
// Allocate the output
this->AllocateOutputs();
// Now crop the output to the desired size.
using ExtractFilterType = ExtractImageFilter<InternalImageType, OutputImageType>;
auto extractFilter = ExtractFilterType::New();
extractFilter->InPlaceOn();
extractFilter->GraftOutput(this->GetOutput());
// Set up the crop sizes.
InternalIndexType extractionIndex;
for (unsigned int dim = 0; dim < ImageDimension; ++dim)
{
extractionIndex[dim] = paddedOutputIndex[dim] + m_FFTPadSize[dim] / 2 + GetKernelRadius()[dim];
}
auto requestedRegionSize = this->GetOutput()->GetRequestedRegion().GetSize();
InternalRegionType extractionRegion(extractionIndex, requestedRegionSize);
extractFilter->SetExtractionRegion(extractionRegion);
// Graft the minipipeline output to this filter.
extractFilter->SetNumberOfWorkUnits(this->GetNumberOfWorkUnits());
extractFilter->SetInput(paddedOutput);
extractFilter->GetOutput()->SetRequestedRegion(this->GetOutput()->GetRequestedRegion());
progress->RegisterInternalFilter(extractFilter, progressWeight);
extractFilter->Update();
OutputImageType * extractedImage = extractFilter->GetOutput();
OutputImageType * output = this->GetOutput();
// Only manually copy the buffer via the pixel container.
// The output meta-data of the extract filter is not correct and
// different that the GenerateOutputInformation method. So just copy
// the buffer.
output->SetBufferedRegion(extractedImage->GetBufferedRegion());
output->SetPixelContainer(extractedImage->GetPixelContainer());
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
auto
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::GetKernelRadius() const
-> KernelSizeType
{
KernelSizeType kernelSize = this->GetKernelImage()->GetLargestPossibleRegion().GetSize();
KernelSizeType kernelRadius;
for (unsigned int i = 0; i < ImageDimension; ++i)
{
kernelRadius[i] = kernelSize[i] / 2;
}
return kernelRadius;
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
bool
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::GetXDimensionIsOdd() const
{
return (m_PaddedInputRegion.GetSize()[0] % 2 != 0);
}
template <typename TInputImage, typename TKernelImage, typename TOutputImage, typename TInternalPrecision>
void
FFTConvolutionImageFilter<TInputImage, TKernelImage, TOutputImage, TInternalPrecision>::PrintSelf(std::ostream & os,
Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "SizeGreatestPrimeFactor: " << m_SizeGreatestPrimeFactor << std::endl;
}
} // namespace itk
#endif // itkFFTConvolutionImageFilter_hxx
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