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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: itkMaskConnectedComponentImageFilterTest.cxx,v $
Language: C++
Date: $Date: 2007-08-10 14:34:02 $
Version: $Revision: 1.6 $
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.
=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif
#include "itkConnectedComponentImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkImageFileReader.h"
#include "itkVTKImageIO.h"
#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"
#include "itkFilterWatcher.h"
#include "itkImageRegionIterator.h"
#include "itkMersenneTwisterRandomVariateGenerator.h"
int itkMaskConnectedComponentImageFilterTest(int argc, char* argv[] )
{
if( argc < 5 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImage outputImage threshold_low threshold_hi [fully_connected] [minimum_object_size]" << std::endl;
return EXIT_FAILURE;
}
typedef unsigned short InternalPixelType;
typedef bool MaskPixelType;
const unsigned int Dimension = 2;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::Image< MaskPixelType, Dimension > MaskImageType;
typedef itk::Image<unsigned short,Dimension> OutputImageType;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<RGBPixelType, Dimension> RGBImageType;
typedef itk::ImageFileReader< InternalImageType > ReaderType;
typedef itk::ImageFileWriter< RGBImageType > WriterType;
typedef itk::BinaryThresholdImageFilter< InternalImageType, InternalImageType > ThresholdFilterType;
typedef itk::ConnectedComponentImageFilter< InternalImageType, OutputImageType, MaskImageType > FilterType;
typedef itk::RelabelComponentImageFilter< OutputImageType, OutputImageType > RelabelType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
ThresholdFilterType::Pointer threshold = ThresholdFilterType::New();
FilterType::Pointer filter = FilterType::New();
RelabelType::Pointer relabel = RelabelType::New();
FilterWatcher watcher(filter);
watcher.QuietOn();
reader->SetFileName( argv[1] );
InternalPixelType threshold_low, threshold_hi;
threshold_low = atoi( argv[3]);
threshold_hi = atoi( argv[4]);
threshold->SetInput (reader->GetOutput());
threshold->SetInsideValue(itk::NumericTraits<InternalPixelType>::One);
threshold->SetOutsideValue(itk::NumericTraits<InternalPixelType>::Zero);
threshold->SetLowerThreshold(threshold_low);
threshold->SetUpperThreshold(threshold_hi);
threshold->Update();
// create a mask containing the upper left hand corner and
// a chunk out of the middle
MaskImageType::Pointer mask = MaskImageType::New();
mask->SetRegions(threshold->GetOutput()->GetLargestPossibleRegion());
mask->CopyInformation(threshold->GetOutput());
mask->Allocate();
mask->FillBuffer(itk::NumericTraits<MaskPixelType>::Zero);
MaskImageType::RegionType maskRegion = mask->GetLargestPossibleRegion();
MaskImageType::SizeType maskSize = maskRegion.GetSize();
MaskImageType::RegionType region;
MaskImageType::SizeType size;
MaskImageType::IndexType index;
// use upper left corner
index.Fill(0);
for (unsigned int i=0; i<MaskImageType::ImageDimension; i++)
{
size[i] = static_cast<unsigned long> (0.375 * maskSize[i]);
}
region.SetIndex (index);
region.SetSize (size);
itk::ImageRegionIterator<MaskImageType> mit(mask,region);
while (!mit.IsAtEnd())
{
mit.Set(itk::NumericTraits<MaskPixelType>::max());
++mit;
}
// use middle section
for (unsigned int i=0; i<MaskImageType::ImageDimension; i++)
{
index[i] = static_cast<long> (0.375 * maskSize[i]);
size[i] = static_cast<unsigned long> (0.25 * maskSize[i]);
}
region.SetIndex (index);
region.SetSize (size);
itk::ImageRegionIterator<MaskImageType> mit2(mask,region);
while (!mit2.IsAtEnd())
{
mit2.Set(itk::NumericTraits<MaskPixelType>::max());
++mit2;
}
filter->SetInput (threshold->GetOutput());
filter->SetMaskImage (mask);
if (argc > 5)
{
int fullyConnected = atoi( argv[5] );
filter->SetFullyConnected( fullyConnected );
}
relabel->SetInput( filter->GetOutput() );
if (argc > 6)
{
int minSize = atoi( argv[6] );
relabel->SetMinimumObjectSize( minSize );
std::cerr << "minSize: " << minSize << std::endl;
}
try
{
relabel->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Relabel: exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
// Remap the labels to viewable colors
RGBImageType::Pointer colored = RGBImageType::New();
colored->SetRegions( filter->GetOutput()->GetBufferedRegion() );
colored->Allocate();
unsigned short numObjects = relabel->GetNumberOfObjects();
std::vector<RGBPixelType> colormap;
RGBPixelType px;
colormap.resize( numObjects+1 );
itk::Statistics::MersenneTwisterRandomVariateGenerator::GetInstance()->SetSeed(1031571);
itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer rvgen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
for (unsigned short i=0; i < colormap.size(); ++i)
{
px.SetRed(
static_cast<unsigned char>(255*rvgen->GetUniformVariate( 0.3333, 1.0 ) ));
px.SetGreen(
static_cast<unsigned char>(255*rvgen->GetUniformVariate( 0.3333, 1.0 ) ));
px.SetBlue(
static_cast<unsigned char>(255*rvgen->GetUniformVariate( 0.3333, 1.0 ) ));
colormap[i] = px;
}
itk::ImageRegionIterator<OutputImageType>
it(relabel->GetOutput(), relabel->GetOutput()->GetBufferedRegion());
itk::ImageRegionIterator<RGBImageType> cit(colored,
colored->GetBufferedRegion());
while( !it.IsAtEnd() )
{
if (it.Get() == 0)
{
cit.Set(RGBPixelType(static_cast<unsigned char>(0)));
}
else
{
cit.Set( colormap[it.Get()] );
}
++it;
++cit;
}
try
{
writer->SetInput (colored);
writer->SetFileName( argv[2] );
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
return EXIT_SUCCESS;
}
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