void mitk::RegionGrowingTool::StartRegionGrowing(itk::Image<TPixel, imageDimension>* inputImage, itk::Index<imageDimension> seedIndex, std::array<ScalarType, 2> thresholds, mitk::Image::Pointer& outputImage)
{
MITK_DEBUG << "Starting region growing at index " << seedIndex << " with lower threshold " << thresholds[0] << " and upper threshold " << thresholds[1];
typedef itk::Image<TPixel, imageDimension> InputImageType;
typedef itk::Image<DefaultSegmentationDataType, imageDimension> OutputImageType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> RegionGrowingFilterType;
typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// perform region growing in desired segmented region
regionGrower->SetInput(inputImage);
regionGrower->AddSeed(seedIndex);
regionGrower->SetLower(thresholds[0]);
regionGrower->SetUpper(thresholds[1]);
try
{
regionGrower->Update();
}
catch(...)
{
return; // Should we do something?
}
typename OutputImageType::Pointer resultImage = regionGrower->GetOutput();
// Smooth result: Every pixel is replaced by the majority of the neighborhood
typedef itk::NeighborhoodIterator<OutputImageType> NeighborhoodIteratorType;
typedef itk::ImageRegionIterator<OutputImageType> ImageIteratorType;
typename NeighborhoodIteratorType::RadiusType radius;
radius.Fill(2); // for now, maybe make this something the user can adjust in the preferences?
NeighborhoodIteratorType neighborhoodIterator(radius, resultImage, resultImage->GetRequestedRegion());
ImageIteratorType imageIterator(resultImage, resultImage->GetRequestedRegion());
for (neighborhoodIterator.GoToBegin(), imageIterator.GoToBegin(); !neighborhoodIterator.IsAtEnd(); ++neighborhoodIterator, ++imageIterator)
{
DefaultSegmentationDataType voteYes(0);
DefaultSegmentationDataType voteNo(0);
for (unsigned int i = 0; i < neighborhoodIterator.Size(); ++i)
{
if (neighborhoodIterator.GetPixel(i) > 0)
{
voteYes += 1;
}
else
{
voteNo += 1;
}
}
if (voteYes > voteNo)
{
imageIterator.Set(1);
}
else
{
imageIterator.Set(0);
}
}
if (resultImage.IsNull())
{
MITK_DEBUG << "Region growing result is empty.";
}
// Can potentially have multiple regions, use connected component image filter to label disjunct regions
typedef itk::ConnectedComponentImageFilter<OutputImageType, OutputImageType> ConnectedComponentImageFilterType;
typename ConnectedComponentImageFilterType::Pointer connectedComponentFilter = ConnectedComponentImageFilterType::New();
connectedComponentFilter->SetInput(resultImage);
connectedComponentFilter->Update();
typename OutputImageType::Pointer resultImageCC = connectedComponentFilter->GetOutput();
m_ConnectedComponentValue = resultImageCC->GetPixel(seedIndex);
outputImage = mitk::GrabItkImageMemory(resultImageCC);
}
