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/*=========================================================================
Program: Advanced Normalization Tools
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt
for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __antsBoxPlotQuantileListSampleFilter_hxx
#define __antsBoxPlotQuantileListSampleFilter_hxx
#include "itkDenseFrequencyContainer2.h"
#include "itkHistogram.h"
#include "itkSampleToHistogramFilter.h"
namespace itk
{
namespace ants
{
namespace Statistics
{
template <typename TScalarListSample>
BoxPlotQuantileListSampleFilter<TScalarListSample>::BoxPlotQuantileListSampleFilter()
{
this->AllocateOutput();
this->GetOutput()->SetMeasurementVectorSize(1);
this->m_OutlierHandling = Winsorize;
this->m_WhiskerScalingFactor = 1.5;
this->m_LowerPercentile = 0.25;
this->m_UpperPercentile = 0.75;
}
template <typename TScalarListSample>
BoxPlotQuantileListSampleFilter<TScalarListSample>::~BoxPlotQuantileListSampleFilter() = default;
template <typename TScalarListSample>
void
BoxPlotQuantileListSampleFilter<TScalarListSample>::GenerateData()
{
if (this->GetInput()->GetMeasurementVectorSize() != 1)
{
itkExceptionMacro("The input sample must be univariate.");
}
if (this->m_LowerPercentile >= this->m_UpperPercentile)
{
itkExceptionMacro("Lower percentile must be less than upper percentile.");
}
const unsigned int scalarMeasurementVectorSize = this->GetInput()->GetMeasurementVectorSize();
this->GetOutput()->SetMeasurementVectorSize(scalarMeasurementVectorSize);
/**
* Initialize the histogram in preparation
*/
typedef itk::Statistics::Histogram<RealType, itk::Statistics::DenseFrequencyContainer2> HistogramType;
typedef itk::Statistics::SampleToHistogramFilter<ScalarListSampleType, HistogramType> SampleFilterType;
typename SampleFilterType::HistogramSizeType histogramSize(1);
histogramSize.Fill(200);
typename SampleFilterType::Pointer sampleFilter = SampleFilterType::New();
sampleFilter->SetInput(this->GetInput());
sampleFilter->SetHistogramSize(histogramSize);
sampleFilter->Update();
RealType lowerQuantile = sampleFilter->GetOutput()->Quantile(0, this->m_LowerPercentile);
RealType upperQuantile = sampleFilter->GetOutput()->Quantile(0, this->m_UpperPercentile);
RealType upperBound = upperQuantile + this->m_WhiskerScalingFactor * (upperQuantile - lowerQuantile);
RealType lowerBound = lowerQuantile - this->m_WhiskerScalingFactor * (upperQuantile - lowerQuantile);
typename ScalarListSampleType::ConstIterator It = this->GetInput()->Begin();
It = this->GetInput()->Begin();
while (It != this->GetInput()->End())
{
MeasurementVectorType inputMeasurement = It.GetMeasurementVector();
typename ScalarListSampleType::MeasurementVectorType outputMeasurement;
outputMeasurement.SetSize(scalarMeasurementVectorSize);
if (static_cast<RealType>(inputMeasurement[0]) < lowerBound ||
static_cast<RealType>(inputMeasurement[0]) > upperBound)
{
this->m_OutlierInstanceIdentifiers.push_back(It.GetInstanceIdentifier());
if (this->m_OutlierHandling == None)
{
outputMeasurement[0] = inputMeasurement[0];
this->GetOutput()->PushBack(outputMeasurement);
}
// else trim from the output
}
else
{
outputMeasurement[0] = inputMeasurement[0];
this->GetOutput()->PushBack(outputMeasurement);
}
++It;
}
if (this->m_OutlierHandling == Winsorize)
{
/** Retabulate the histogram with the outliers removed */
typename SampleFilterType::Pointer sampleFilter2 = SampleFilterType::New();
sampleFilter2->SetInput(this->GetOutput());
sampleFilter2->SetHistogramSize(histogramSize);
sampleFilter2->Update();
RealType lowerQuantile2 = sampleFilter2->GetOutput()->Quantile(0, this->m_LowerPercentile);
RealType upperQuantile2 = sampleFilter2->GetOutput()->Quantile(0, this->m_UpperPercentile);
RealType upperBound2 = upperQuantile2 + this->m_WhiskerScalingFactor * (upperQuantile2 - lowerQuantile2);
RealType lowerBound2 = lowerQuantile2 - this->m_WhiskerScalingFactor * (upperQuantile2 - lowerQuantile2);
this->GetOutput()->Clear();
It = this->GetInput()->Begin();
while (It != this->GetInput()->End())
{
MeasurementVectorType inputMeasurement = It.GetMeasurementVector();
typename ScalarListSampleType::MeasurementVectorType outputMeasurement;
outputMeasurement.SetSize(scalarMeasurementVectorSize);
outputMeasurement[0] = inputMeasurement[0];
if (static_cast<RealType>(inputMeasurement[0]) < lowerBound)
{
outputMeasurement[0] = lowerBound2;
}
else if (static_cast<RealType>(inputMeasurement[0]) > upperBound)
{
outputMeasurement[0] = upperBound2;
}
this->GetOutput()->PushBack(outputMeasurement);
++It;
}
}
}
template <typename TScalarListSample>
void
BoxPlotQuantileListSampleFilter<TScalarListSample>::PrintSelf(std::ostream & os, Indent indent) const
{
os << indent << "Percentile Bounds: [" << this->m_LowerPercentile << ", " << this->m_UpperPercentile << "]"
<< std::endl;
os << indent << "Whisker scaling factor: " << this->m_WhiskerScalingFactor << std::endl;
os << indent << "Outlier handling: ";
if (this->m_OutlierHandling == None)
{
os << "None" << std::endl;
}
if (this->m_OutlierHandling == Trim)
{
os << "Trim" << std::endl;
}
if (this->m_OutlierHandling == Winsorize)
{
os << "Winsorize" << std::endl;
}
}
} // end of namespace Statistics
} // end of namespace ants
} // end of namespace itk
#endif
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