/usr/include/InsightToolkit/Review/itkKappaSigmaThresholdImageCalculator.txx is in libinsighttoolkit3-dev 3.20.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 | /*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkKappaSigmaThresholdImageCalculator.txx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 __itkKappaSigmaThresholdImageCalculator_txx
#define __itkKappaSigmaThresholdImageCalculator_txx
#include "itkKappaSigmaThresholdImageCalculator.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionConstIterator.h"
namespace itk
{
template < class TInputImage, class TMaskImage >
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>
::KappaSigmaThresholdImageCalculator(void)
{
this->m_Valid = false;
this->m_Image = NULL;
this->m_Mask = NULL;
this->m_MaskValue = NumericTraits< MaskPixelType >::max();
this->m_Output = NumericTraits< InputPixelType >::Zero;
this->m_SigmaFactor = 2;
this->m_NumberOfIterations = 2;
}
template < class TInputImage, class TMaskImage >
void
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>
::PrintSelf( std::ostream& os, Indent indent ) const
{
Superclass::PrintSelf(os,indent);
os << indent << "Input: " << this->m_Image.GetPointer() << std::endl;
os << indent << "Mask: " << this->m_Mask.GetPointer() << std::endl;
os << indent << "Valid: " << this->m_Valid << std::endl;
os << indent << "MaskValue: " << this->m_MaskValue << std::endl;
os << indent << "SigmaFactor: " << this->m_SigmaFactor << std::endl;
os << indent << "NumberOfIterations: " << this->m_NumberOfIterations << std::endl;
os << indent << "Output: " << this->m_Output << std::endl;
}
template < class TInputImage, class TMaskImage >
void
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>
::Compute()
{
typedef typename InputImageType::IndexType IndexType;
if( !this->m_Image )
{
return;
}
// init the values
InputPixelType threshold = NumericTraits< InputPixelType >::max(); // use all the pixels to begin
for( unsigned int iteration = 0; iteration < this->m_NumberOfIterations; iteration++ )
{
ImageRegionConstIteratorWithIndex< InputImageType > iIt( this->m_Image,
this->m_Image->GetRequestedRegion() );
// compute the mean
iIt.GoToBegin();
unsigned long count = 0;
double mean = 0;
while( !iIt.IsAtEnd() )
{
if( !this->m_Mask || this->m_Mask->GetPixel( iIt.GetIndex() ) == this->m_MaskValue )
{
const InputPixelType & v = iIt.Get();
if( v <= threshold )
{
mean += v;
count++;
}
}
++iIt;
}
mean = mean / count;
// compute sigma
iIt.GoToBegin();
double sigma = 0;
while( !iIt.IsAtEnd() )
{
if( !this->m_Mask || this->m_Mask->GetPixel( iIt.GetIndex() ) == this->m_MaskValue )
{
const InputPixelType & v = iIt.Get();
if( v <= threshold )
{
sigma += vnl_math_sqr( v - mean );
}
}
++iIt;
}
sigma = vcl_sqrt( sigma / ( count - 1) );
// compute the threshold for the next iteration
InputPixelType newThreshold = static_cast< InputPixelType >( mean + this->m_SigmaFactor * sigma );
if( newThreshold == threshold )
{
// no need to continue - the threshold is the same and will produce the same result
break;
}
threshold = newThreshold;
}
this->m_Output = threshold;
this->m_Valid = true;
}
template < class TInputImage, class TMaskImage >
const typename KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>::InputPixelType &
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>
::GetOutput() const
{
if (!this->m_Valid)
{
itkExceptionMacro( << "GetOutput() invoked, but the output have not been computed. Call Compute() first.");
}
return this->m_Output;
}
} // end namespace itk
#endif
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