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itkScalarImageToRunLengthMatrixFilter.hxx
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itkScalarImageToRunLengthMatrixFilter.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
*
* http://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 itkScalarImageToRunLengthMatrixFilter_hxx
#define itkScalarImageToRunLengthMatrixFilter_hxx
#include "itkScalarImageToRunLengthMatrixFilter.h"
#include "itkConstNeighborhoodIterator.h"
#include "itkNeighborhood.h"
#include "itkMath.h"
#include "itkMacro.h"
#include "itkMath.h"
namespace itk
{
namespace Statistics
{
template <typename TImageType, typename THistogramFrequencyContainer>
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::ScalarImageToRunLengthMatrixFilter()
: m_NumberOfBinsPerAxis(Self::DefaultBinsPerAxis)
, m_Min(NumericTraits<PixelType>::NonpositiveMin())
, m_Max(NumericTraits<PixelType>::max())
, m_MinDistance(NumericTraits<RealType>::ZeroValue())
, m_MaxDistance(NumericTraits<RealType>::max())
, m_InsidePixelValue(NumericTraits<PixelType>::OneValue())
{
this->SetNumberOfRequiredInputs(1);
this->SetNumberOfRequiredOutputs(1);
constexpr unsigned int measurementVectorSize = 2;
this->ProcessObject::SetNthOutput(0, this->MakeOutput(0));
auto * output = const_cast<HistogramType *>(this->GetOutput());
output->SetMeasurementVectorSize(measurementVectorSize);
this->m_LowerBound.SetSize(measurementVectorSize);
this->m_UpperBound.SetSize(measurementVectorSize);
this->m_LowerBound[0] = this->m_Min;
this->m_LowerBound[1] = this->m_MinDistance;
this->m_UpperBound[0] = this->m_Max;
this->m_UpperBound[1] = this->m_MaxDistance;
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::SetOffset(const OffsetType offset)
{
OffsetVectorPointer offsetVector = OffsetVector::New();
offsetVector->push_back(offset);
this->SetOffsets(offsetVector);
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::SetInput(const ImageType * image)
{
// Process object is not const-correct so the const_cast is required here
this->ProcessObject::SetNthInput(0, const_cast<ImageType *>(image));
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::SetMaskImage(const ImageType * image)
{
// Process object is not const-correct so the const_cast is required here
this->ProcessObject::SetNthInput(1, const_cast<ImageType *>(image));
}
template <typename TImageType, typename THistogramFrequencyContainer>
const TImageType *
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::GetInput() const
{
if (this->GetNumberOfInputs() < 1)
{
return nullptr;
}
return static_cast<const ImageType *>(this->ProcessObject::GetInput(0));
}
template <typename TImageType, typename THistogramFrequencyContainer>
const TImageType *
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::GetMaskImage() const
{
if (this->GetNumberOfInputs() < 2)
{
return nullptr;
}
return static_cast<const ImageType *>(this->ProcessObject::GetInput(1));
}
template <typename TImageType, typename THistogramFrequencyContainer>
const typename ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::HistogramType *
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::GetOutput() const
{
const auto * output = static_cast<const HistogramType *>(this->ProcessObject::GetOutput(0));
return output;
}
template <typename TImageType, typename THistogramFrequencyContainer>
typename ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::DataObjectPointer
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::MakeOutput(
DataObjectPointerArraySizeType itkNotUsed(idx))
{
return HistogramType::New().GetPointer();
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::GenerateData()
{
auto * output = static_cast<HistogramType *>(this->ProcessObject::GetOutput(0));
const ImageType * inputImage = this->GetInput();
// First, create an appropriate histogram with the right number of bins
// and mins and maxes correct for the image type.
typename HistogramType::SizeType size(output->GetMeasurementVectorSize());
size.Fill(this->m_NumberOfBinsPerAxis);
this->m_LowerBound[0] = this->m_Min;
this->m_LowerBound[1] = this->m_MinDistance;
this->m_UpperBound[0] = this->m_Max;
this->m_UpperBound[1] = this->m_MaxDistance;
output->Initialize(size, this->m_LowerBound, this->m_UpperBound);
MeasurementVectorType run(output->GetMeasurementVectorSize());
typename HistogramType::IndexType hIndex;
// Iterate over all of those pixels and offsets, adding each
// distance/intensity pair to the histogram
using NeighborhoodIteratorType = ConstNeighborhoodIterator<ImageType>;
typename NeighborhoodIteratorType::RadiusType radius;
radius.Fill(1);
NeighborhoodIteratorType neighborIt(radius, inputImage, inputImage->GetRequestedRegion());
// this temp image has the same dimension for each offset
// moving the allocation out of loop of offsets
// while keeping FillBuffer with boolean false in each loop
using BoolImageType = Image<bool, ImageDimension>;
typename BoolImageType::Pointer alreadyVisitedImage = BoolImageType::New();
alreadyVisitedImage->CopyInformation(inputImage);
alreadyVisitedImage->SetRegions(inputImage->GetRequestedRegion());
alreadyVisitedImage->Allocate();
typename OffsetVector::ConstIterator offsets;
for (offsets = this->GetOffsets()->Begin(); offsets != this->GetOffsets()->End(); ++offsets)
{
alreadyVisitedImage->FillBuffer(false);
neighborIt.GoToBegin();
OffsetType offset = offsets.Value();
this->NormalizeOffsetDirection(offset);
for (neighborIt.GoToBegin(); !neighborIt.IsAtEnd(); ++neighborIt)
{
const PixelType centerPixelIntensity = neighborIt.GetCenterPixel();
IndexType centerIndex = neighborIt.GetIndex();
if (centerPixelIntensity < this->m_Min || centerPixelIntensity > this->m_Max ||
alreadyVisitedImage->GetPixel(centerIndex) ||
(this->GetMaskImage() && this->GetMaskImage()->GetPixel(centerIndex) != this->m_InsidePixelValue))
{
continue; // don't put a pixel in the histogram if the value
// is out-of-bounds or is outside the mask.
}
itkDebugMacro("===> offset = " << offset << std::endl);
MeasurementType centerBinMin = this->GetOutput()->GetBinMinFromValue(0, centerPixelIntensity);
MeasurementType centerBinMax = this->GetOutput()->GetBinMaxFromValue(0, centerPixelIntensity);
MeasurementType lastBinMax = this->GetOutput()->GetDimensionMaxs(0)[this->GetOutput()->GetSize(0) - 1];
PixelType pixelIntensity(NumericTraits<PixelType>::ZeroValue());
IndexType index;
index = centerIndex + offset;
IndexType lastGoodIndex = centerIndex;
bool runLengthSegmentAlreadyVisited = false;
// Scan from the current pixel at index, following
// the direction of offset. Run length is computed as the
// length of continuous pixels whose pixel values are
// in the same bin.
while (inputImage->GetRequestedRegion().IsInside(index))
{
// For the same offset, each run length segment can
// only be visited once
if (alreadyVisitedImage->GetPixel(index))
{
runLengthSegmentAlreadyVisited = true;
break;
}
pixelIntensity = inputImage->GetPixel(index);
// Special attention paid to boundaries of bins.
// For the last bin,
// it is left close and right close (following the previous
// gerrit patch).
// For all
// other bins,
// the bin is left close and right open.
if (pixelIntensity >= centerBinMin &&
(pixelIntensity < centerBinMax ||
(Math::ExactlyEquals(pixelIntensity, centerBinMax) && Math::ExactlyEquals(centerBinMax, lastBinMax))))
{
alreadyVisitedImage->SetPixel(index, true);
lastGoodIndex = index;
index += offset;
}
else
{
break;
}
}
if (runLengthSegmentAlreadyVisited)
{
continue;
}
PointType centerPoint;
inputImage->TransformIndexToPhysicalPoint(centerIndex, centerPoint);
PointType point;
inputImage->TransformIndexToPhysicalPoint(lastGoodIndex, point);
run[0] = centerPixelIntensity;
run[1] = centerPoint.EuclideanDistanceTo(point);
if (run[1] >= this->m_MinDistance && run[1] <= this->m_MaxDistance)
{
output->GetIndex(run, hIndex);
output->IncreaseFrequencyOfIndex(hIndex, 1);
itkDebugStatement(typename HistogramType::IndexType tempMeasurementIndex);
itkDebugStatement(output->GetIndex(run, tempMeasurementIndex));
itkDebugMacro("centerIndex<->index: " << static_cast<int>(centerPixelIntensity) << "@" << centerIndex << "<->"
<< static_cast<int>(pixelIntensity) << "@" << index << ", Bin# "
<< tempMeasurementIndex << ", Measurement: (" << run[0] << ", " << run[1]
<< ")"
<< ", Center bin [" << this->GetOutput()->GetBinMinFromValue(0, run[0])
<< "," << this->GetOutput()->GetBinMaxFromValue(0, run[0]) << "]"
<< "~[" << this->GetOutput()->GetBinMinFromValue(1, run[1]) << ","
<< this->GetOutput()->GetBinMaxFromValue(1, run[1]) << "]" << std::endl);
}
}
}
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::SetPixelValueMinMax(PixelType min,
PixelType max)
{
if (this->m_Min != min || this->m_Max != max)
{
itkDebugMacro("setting Min to " << min << "and Max to " << max);
this->m_Min = min;
this->m_Max = max;
this->Modified();
}
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::SetDistanceValueMinMax(RealType min,
RealType max)
{
if (Math::NotExactlyEquals(this->m_MinDistance, min) || Math::NotExactlyEquals(this->m_MaxDistance, max))
{
itkDebugMacro("setting MinDistance to " << min << "and MaxDistance to " << max);
this->m_MinDistance = min;
this->m_MaxDistance = max;
this->Modified();
}
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::PrintSelf(std::ostream & os,
Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "Offsets: " << this->GetOffsets() << std::endl;
os << indent << "Min: " << this->m_Min << std::endl;
os << indent << "Max: " << this->m_Max << std::endl;
os << indent << "Min distance: " << this->m_MinDistance << std::endl;
os << indent << "Max distance: " << this->m_MaxDistance << std::endl;
os << indent << "NumberOfBinsPerAxis: " << this->m_NumberOfBinsPerAxis << std::endl;
os << indent << "InsidePixelValue: " << this->m_InsidePixelValue << std::endl;
}
template <typename TImageType, typename THistogramFrequencyContainer>
void
ScalarImageToRunLengthMatrixFilter<TImageType, THistogramFrequencyContainer>::NormalizeOffsetDirection(
OffsetType & offset)
{
itkDebugMacro("old offset = " << offset << std::endl);
int sign = 1;
bool metLastNonZero = false;
for (int i = offset.GetOffsetDimension() - 1; i >= 0; i--)
{
if (metLastNonZero)
{
offset[i] *= sign;
}
else if (offset[i] != 0)
{
sign = (offset[i] > 0) ? 1 : -1;
metLastNonZero = true;
offset[i] *= sign;
}
}
itkDebugMacro("new offset = " << offset << std::endl);
}
} // end of namespace Statistics
} // end of namespace itk
#endif