void writeLabelImage( LabeledImageType::Pointer image, const std::string &fname) {
try {
ColorMapFilterType::Pointer colormapper = ColorMapFilterType::New();
colormapper->SetInput( image );
colormapper->Update();
RGBImageType::ConstPointer colorImage = colormapper->GetOutput();
colormapper = NULL;
typedef itk::Image< RGBPixelType, 2 > OutputImage2DType;
typedef itk::ImageSeriesWriter< RGBImageType, OutputImage2DType > WriterType;
WriterType::Pointer writer = WriterType::New();
typedef itk::NumericSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetSeriesFormat( fname.c_str() );
nameGenerator->SetStartIndex( 1 );
nameGenerator->SetEndIndex( colorImage->GetBufferedRegion().GetSize()[2] );
writer->SetFileNames( nameGenerator->GetFileNames() );
writer->SetInput( colorImage );
writer->Update();
} catch( itk::ExceptionObject & exp ) {
std::cerr << "Exception caught !" << std::endl;
std::cerr << exp << std::endl;
}
}
/**
* draws the tree from the TreeDrawer into a volumetric 3D
* image as a series of 2D png slices
*/
void drawImage(TreeDrawer * td, const char* rootName){
typedef unsigned char PixelType;
const unsigned int Dimension = 3;
typedef itk::Image< PixelType, Dimension > ImageType;
ImageType::Pointer image = ImageType::New();
ImageType::SizeType size;
size[0] = td->dim[0]; // size along X
size[1] = td->dim[1]; // size along Y
size[2] = td->dim[2]; // size along Z
ImageType::IndexType start;
start[0] = 0; // first index on X
start[1] = 0; // first index on Y
start[2] = 0; // first index on Z
ImageType::RegionType region;
region.SetSize( size );
region.SetIndex( start );
image->SetRegions( region );
image->Allocate();
ImageType::IndexType pixelIndex;
pixelIndex[0] = 0; // x position
pixelIndex[1] = 0; // y position
pixelIndex[2] = 0; // z position
for(int i = 0; i < td->dim[0]; i++){
for(int j = 0; j < td->dim[1]; j++){
for(int k = 0 ; k < td->dim[2]; k++){
pixelIndex[0] = i;
pixelIndex[1] = j;
pixelIndex[2] = k;
image->SetPixel(pixelIndex, td->imageAt(i, j, k));
}
}
}
typedef itk::Image< unsigned char, 2 > Image2DType;
typedef itk::ImageSeriesWriter< ImageType, Image2DType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput( image);
typedef itk::NumericSeriesFileNames NameGeneratorType;
NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
std::string format = rootName;
format += "%03d";
format += ".jpg";
nameGenerator->SetSeriesFormat( format.c_str() );
const unsigned int firstSlice = start[2];
const unsigned int lastSlice = start[2] + size[2] - 1;
nameGenerator->SetStartIndex( firstSlice );
nameGenerator->SetEndIndex( lastSlice );
nameGenerator->SetIncrementIndex( 1 );
writer->SetFileNames( nameGenerator->GetFileNames() );
try{
writer->Update();
}catch( itk::ExceptionObject & excp ){
throw "Exception thrown while reading the image";
}
return;
}