void Mask::KeepLargestHole()
{
throw std::runtime_error("Mask::KeepLargestHole() needs to be tested!");
typedef itk::Image<unsigned int> LabelImageType;
// Only keep the largest segment
typedef itk::ConnectedComponentImageFilter<Mask, LabelImageType>
ConnectedComponentImageFilterType;
ConnectedComponentImageFilterType::Pointer connectedComponentFilter =
ConnectedComponentImageFilterType::New();
connectedComponentFilter->SetInput(this);
connectedComponentFilter->Update();
WriteImage(connectedComponentFilter->GetOutput(), "ConnectedComponents.mha");
typedef itk::LabelShapeKeepNObjectsImageFilter<LabelImageType>
LabelShapeKeepNObjectsImageFilterType;
LabelShapeKeepNObjectsImageFilterType::Pointer labelShapeKeepNObjectsImageFilter =
LabelShapeKeepNObjectsImageFilterType::New();
labelShapeKeepNObjectsImageFilter->SetInput(connectedComponentFilter->GetOutput());
labelShapeKeepNObjectsImageFilter->SetBackgroundValue(0); // TODO: why zero?
labelShapeKeepNObjectsImageFilter->SetNumberOfObjects(1);
labelShapeKeepNObjectsImageFilter
->SetAttribute(LabelShapeKeepNObjectsImageFilterType::LabelObjectType::NUMBER_OF_PIXELS);
labelShapeKeepNObjectsImageFilter->Update();
WriteImage(labelShapeKeepNObjectsImageFilter->GetOutput(),
"LargestComponent.mha");
// TODO: replace whatever value is the foreground (by looking at the output above)
// with HOLE
// DeepCopy(rescaleFilter->GetOutput(), this);
}
Matrix<int> getCCLabeling(Matrix<int> p, bool recip){
Matrix<int> m = Matrix<int>(p.getXdim(), p.getYdim(), 1);
if(recip){
for(int i=0; i<p.getXdim(); i++)
for(int j=0; j<p.getYdim(); j++)
if(p(i,j) == 1)
m(i,j) = 0;
}else{
for(int i=0; i<p.getXdim(); i++)
for(int j=0; j<p.getYdim(); j++)
m(i,j) = p(i,j);
}
const unsigned int Dimension = 2;
typedef unsigned char PixelType;
typedef itk::RGBPixel<unsigned char> RGBPixelType;
typedef itk::Image<PixelType, 2> ImageType;
typedef itk::Image<RGBPixelType, 2> RGBImageType;
//fill ITK image type
ImageType::Pointer image = ImageType::New();
typename ImageType::IndexType start;// = {{0,0}};//TImage::IndexType start = {{0,0}};
start[0] = 0;
start[1] = 0;
typename ImageType::SizeType size;
unsigned int NumRows = m.getXdim();
unsigned int NumCols = m.getYdim();
size[0] = NumRows;
size[1] = NumCols;
ImageType::RegionType region;// region(start, size);
region.SetSize(size);
region.SetIndex(start);
//region.SetSize(size);
image->SetRegions(region);
image->Allocate();
//cout << "here" << endl;
for(typename ImageType::IndexValueType r = 0; r < m.getXdim(); r++)
{
for(typename ImageType::IndexValueType c = 0; c < m.getYdim(); c++)
{
typename ImageType::IndexType pixelIndex = {{r,c}};
if(m(r,c) == 1)
image->SetPixel(pixelIndex, 255);
else
image->SetPixel(pixelIndex, 0);
//image->SetPixel(pixelIndex, 255);
}
}
//cout << "got here" << endl;
typedef itk::Image< unsigned short, Dimension > OutputImageType;
typedef itk::ConnectedComponentImageFilter <ImageType, OutputImageType >
ConnectedComponentImageFilterType;
ConnectedComponentImageFilterType::Pointer connected =
ConnectedComponentImageFilterType::New ();
connected->SetInput(image);
connected->Update();
//cout << "got CC" << endl;
//std::cout << "Number of objects: " << connected->GetObjectCount() << std::endl;
Matrix<int> out = Matrix<int>(m.getXdim(), m.getYdim(), 0);
//connected->SetMaskImage(image);
//connected->GetOutput();
for(typename ImageType::IndexValueType r = 0; r < m.getXdim(); r++)
{
for(typename ImageType::IndexValueType c = 0; c < m.getYdim(); c++)
{
typename ImageType::IndexType pixelIndex = {{r,c}};
out(r,c) = connected->GetOutput()->GetPixel(pixelIndex);
//out(r,c) = image->GetPixel(pixelIndex);
}
}
return out;
}
