/usr/include/gofigure2/itkCellPreprocess.txx is in libgofigure-dev 0.9.0-3+b1.
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 | /*=========================================================================
Author: $Author$ // Author of last commit
Version: $Rev$ // Revision of last commit
Date: $Date$ // Date of last commit
=========================================================================*/
/*=========================================================================
Authors: The GoFigure Dev. Team.
at Megason Lab, Systems biology, Harvard Medical school, 2009
Copyright (c) 2009, President and Fellows of Harvard College.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
Neither the name of the President and Fellows of Harvard College
nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=========================================================================*/
#ifndef __itkCellPreprocess_txx
#define __itkCellPreprocess_txx
#include "itkCellPreprocess.h"
namespace itk
{
template< class TInputImage, class TOutputImage >
CellPreprocess< TInputImage, TOutputImage >
::CellPreprocess():m_LargestCellRadius (4.0)
{
m_MembraneData = false;
this->Superclass::SetNumberOfRequiredInputs (1);
this->Superclass::SetNumberOfRequiredOutputs (1);
this->Superclass::SetNthOutput ( 0, TOutputImage::New() );
}
template< class TInputImage, class TOutputImage >
void
CellPreprocess< TInputImage, TOutputImage >::GenerateData()
{
InputCastPointer m_CastInput = InputCastType::New();
m_CastInput->SetInput ( this->GetInput() );
m_CastInput->Update();
ImageSpacingType spacing = this->GetInput()->GetSpacing();
ImageSizeType radius;
for ( unsigned int j = 0; j < ImageDimension; j++ )
{
radius[j] = static_cast< ImageSizeValueType >(
0.3 * m_LargestCellRadius / spacing[j]);
}
ImagePointer cellImg;
{
MedianFilterPointer m_Median = MedianFilterType::New();
m_Median = MedianFilterType::New();
m_Median->SetRadius (radius);
m_Median->SetInput ( m_CastInput->GetOutput() );
m_Median->Update();
SmoothingFilterPointer m_smooth = SmoothingFilterType::New();
m_smooth->SetInput ( m_Median->GetOutput() );
m_smooth->SetNumberOfIterations(5);
m_smooth->SetTimeStep(0.0125);
m_smooth->SetConductanceParameter(3);
m_smooth->UseImageSpacingOn();
m_smooth->Update();
if ( m_MembraneData )
{
cellImg = m_smooth->GetOutput();
cellImg->DisconnectPipeline();
}
else
{
GrayscaleFillholePointer m_fillHole = GrayscaleFillholeFilterType::New();
m_fillHole->SetInput ( m_smooth->GetOutput() );
m_fillHole->SetFullyConnected (0);
m_fillHole->Update();
cellImg = m_fillHole->GetOutput();
cellImg->DisconnectPipeline();
}
}
OutputCastPointer m_CastOutput = OutputCastType::New();
m_CastOutput->SetInput (cellImg);
m_CastOutput->GraftOutput ( this->GetOutput() );
m_CastOutput->Update();
this->GraftOutput ( m_CastOutput->GetOutput() );
}
template< class TInputImage, class TOutputImage >
void
CellPreprocess< TInputImage, TOutputImage >::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf (os, indent);
os << indent << "Class Name: " << GetNameOfClass() << std::endl;
os << indent << "Largest cell radius: " << GetLargestCellRadius()
<< std::endl;
}
} /* end namespace itk */
#endif
|