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itkSTAPLEImageFilter.txx
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itkSTAPLEImageFilter.txx
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkSTAPLEImageFilter.txx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) 2002 Insight 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 _itkSTAPLEImageFilter_txx
#define _itkSTAPLEImageFilter_txx
#include "itkSTAPLEImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkImageRegionConstIterator.h"
namespace itk
{
template <typename TInputImage, typename TOutputImage>
void
STAPLEImageFilter<TInputImage, TOutputImage>
::PrintSelf(std::ostream& os, Indent indent) const
{
Superclass::PrintSelf(os,indent);
os << indent << "m_MaximumIterations = " << m_MaximumIterations << std::endl;
os << indent << "m_ForegroundValue = " << m_ForegroundValue << std::endl;
os << indent << "m_ConfidenceWeight = " << m_ConfidenceWeight << std::endl;
os << indent << "m_ElapsedIterations = " << m_ElapsedIterations << std::endl;
}
template< typename TInputImage, typename TOutputImage >
void
STAPLEImageFilter< TInputImage, TOutputImage >
::GenerateData()
{
const double epsilon = 1.0e-10;
typedef ImageRegionConstIterator< TInputImage > IteratorType;
typedef ImageRegionIterator< TOutputImage> FuzzyIteratorType;
const double min_rms_error = 1.0e-14; // 7 digits of precision
unsigned int i, iter, number_of_input_files;
// Allocate the output "fuzzy" image.
this->GetOutput()->SetBufferedRegion(this->GetOutput()->GetRequestedRegion());
this->GetOutput()->Allocate();
typename TOutputImage::Pointer W = this->GetOutput();
// Initialize the output to all 0's
FuzzyIteratorType out = FuzzyIteratorType(W, W->GetRequestedRegion());
for (out.GoToBegin(); !out.IsAtEnd(); ++out)
{
out.Set(0.0);
}
// Record the number of input files.
number_of_input_files = this->GetNumberOfInputs();
IteratorType *D_it = new IteratorType[number_of_input_files];
double *p = new double[number_of_input_files]; // sensitivity
double *q = new double[number_of_input_files]; // specificity
double *last_q = new double[number_of_input_files];
double *last_p = new double[number_of_input_files];
for (i=0; i < number_of_input_files; ++i)
{
last_p[i] = -10.0;
last_q[i] = -10.0;
}
// Come up with an initial Wi which is simply the average of
// all the segmentations.
IteratorType in;
for (i = 0; i < number_of_input_files; ++i)
{
if ( this->GetInput(i)->GetRequestedRegion() != W->GetRequestedRegion() )
{
itkExceptionMacro(<<"One or more input images do not contain matching RequestedRegions");
}
in = IteratorType( this->GetInput(i), W->GetRequestedRegion() );
out = FuzzyIteratorType( W, W->GetRequestedRegion() );
for (in.GoToBegin(), out.GoToBegin(); !in.IsAtEnd(); ++in, ++out)
{
if (in.Get() > m_ForegroundValue - epsilon && in.Get()
< m_ForegroundValue + epsilon)
{
out.Set(out.Get() + 1.0);
}
}
} // end for
// Divide sum by num of files, calculate the estimate of g_t
double N = 0.0;
double g_t = 0.0;
for (out.GoToBegin(); !out.IsAtEnd(); ++out)
{
out.Set( out.Get() / static_cast<double>(number_of_input_files) );
g_t += out.Get();
N = N +1.0;
}
g_t = (g_t / N) * m_ConfidenceWeight;
double p_num, p_denom, q_num, q_denom;
for (iter = 0; iter < m_MaximumIterations; ++iter)
{
// Now iterate on estimating specificity and sensitivity
for (i=0; i < number_of_input_files; ++i)
{
in = IteratorType(this->GetInput(i), W->GetRequestedRegion());
out = FuzzyIteratorType(W, W->GetRequestedRegion());
p_num = p_denom = q_num = q_denom = 0.0;
// Sensitivity and specificity of this user
for (in.GoToBegin(), out.GoToBegin(); !in.IsAtEnd(); ++in, ++out)
{
if (in.Get() > m_ForegroundValue - epsilon
&& in.Get() < m_ForegroundValue + epsilon) // Dij == 1
{
p_num += out.Get(); // out.Get() := Wi
}
else // if (in.Get() != m_ForegroundValue) // Dij == 0
{
q_num += (1.0 - out.Get()); // out.Get() := Wi
}
p_denom += out.Get();
q_denom += (1.0 - out.Get());
}
p[i] = p_num / p_denom;
q[i] = q_num / q_denom;
}
// Now recreate W using the new p's and q's
// Need an iterator on each D
// const double g_t = 0.1; // prior likelihood that a pixel is incl.in segmentation
double alpha1, beta1;
for (i = 0; i < number_of_input_files; ++i)
{
D_it[i] = IteratorType(this->GetInput(i), W->GetRequestedRegion());
}
out = FuzzyIteratorType(W, W->GetRequestedRegion());
for (out.GoToBegin(); !out.IsAtEnd(); ++out)
{
alpha1 = beta1 = 1.0;
for (i =0; i < number_of_input_files; ++i)
{
if (D_it[i].Get() > m_ForegroundValue - epsilon && D_it[i].Get() < m_ForegroundValue + epsilon) // Dij == 1
{
alpha1 = alpha1 * p[i];
beta1 = beta1 * (1.0 - q[i]);
}
else //Dij == 0
{
alpha1 = alpha1 * (1.0 -p[i]);
beta1 = beta1 * q[i];
}
++D_it[i];
}
out.Set(g_t * alpha1 /
( g_t * alpha1 + (1.0 - g_t) * beta1) );
}
this->InvokeEvent( IterationEvent() );
// Check for convergence
bool flag = false;
if (iter !=0 ) // not on the first iteration
{
flag = true;
for (i=0; i < number_of_input_files; ++i)
{
if ( ( (p[i] - last_p[i]) * (p[i] - last_p[i]) ) > min_rms_error )
{
flag = false;
break;
}
if ( ( (q[i] - last_q[i]) * (q[i] - last_q[i]) ) > min_rms_error )
{
flag = false;
break;
}
}
}
for (i = 0; i < number_of_input_files; ++i)
{
last_p[i] = p[i];
last_q[i] = q[i];
}
if( this->GetAbortGenerateData() )
{
this->ResetPipeline();
flag = true;
}
if (flag == true)
{
break;
}
}
// Copy p's, q's, etc. to member variables
m_Sensitivity.clear();
m_Specificity.clear();
for (i = 0; i< number_of_input_files; i++)
{
m_Sensitivity.push_back( p[i] );
m_Specificity.push_back( q[i] );
}
m_ElapsedIterations = iter;
delete[] q;
delete[] p;
delete[] last_q;
delete[] last_p;
delete[] D_it;
}
} // end namespace itk
#endif