void PatchTracking::extractPatch(int i, bool newPatch) {
typedef itk::ExtractImageFilter<RealImage, RealImage> ExtractFilter;
ExtractFilter::Pointer filter = ExtractFilter::New();
filter->SetInput(_images[i]);
filter->SetExtractionRegion(_patchRegion[i]);
try {
filter->Update();
} catch (itk::ExceptionObject& ex) {
ex.Print(cout);
}
_patches[i] = filter->GetOutput();
_patches[i]->DisconnectPipeline();
}
int main( int argc, char *argv[] )
{
string input_name;
string output_dir;
if (argc == 3) {
input_name = argv[1];
output_dir = argv[2];
}
const unsigned int Dimension = 3;
const unsigned int OutDimension = 2;
typedef short InputPixelType;
typedef int FilterPixelType;
typedef itk::Image< InputPixelType, Dimension > InputImageType;
typedef itk::Image< FilterPixelType, Dimension > FilterImageType;
typedef itk::Image< FilterPixelType, OutDimension > OutFilterImageType;
InputImageType::Pointer image;
itk::MetaDataDictionary dict;
if (input_name.size() && output_dir.size())
{
if (boost::filesystem::is_regular_file( input_name )) {
typedef itk::ImageFileReader< InputImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( input_name );
try
{
reader->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
image = reader->GetOutput();
dict = reader->GetMetaDataDictionary();
} else if (boost::filesystem::is_directory( input_name )) {
itkBasic::SeriesReader sreader( input_name );
sreader.readSeriesData( 2 );
try
{
itkBasic::ReaderType::Pointer imageReader = itkBasic::ReaderType::New();
itkBasic::FileNamesContainer fc;
sreader.getSeriesFileNames(0, fc);
image = itkBasic::getDicomSerie( fc, imageReader, 1 );
dict = *((*imageReader->GetMetaDataDictionaryArray())[0]);
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ERROR: ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
}
}
if (!image) {
std::cerr << argv[0] << ": input output" << std::endl;
exit(1);
}
typedef itk::SigmoidImageFilter< InputImageType, FilterImageType > SigmoidCasterType;
SigmoidCasterType::Pointer sigmoidcaster = SigmoidCasterType::New();
sigmoidcaster->SetInput( image );
sigmoidcaster->SetOutputMaximum( 4000 );
sigmoidcaster->SetOutputMinimum( 1000 );
typedef itk::AccumulateImageFilter< FilterImageType, FilterImageType > AccumulateFilter;
AccumulateFilter::Pointer accumulator = AccumulateFilter::New();
accumulator->SetAccumulateDimension(1);
accumulator->SetInput( sigmoidcaster->GetOutput() );
typedef itk::ExtractImageFilter< FilterImageType, OutFilterImageType > ExtractFilter;
ExtractFilter::Pointer extractor = ExtractFilter::New();
extractor->SetInput( accumulator->GetOutput() );
FilterImageType::Pointer accuOut = accumulator->GetOutput();
accuOut->UpdateOutputInformation();
FilterImageType::RegionType extractRegion = accuOut->GetLargestPossibleRegion();
extractRegion.SetSize(1,0);
extractor->SetExtractionRegion( extractRegion );
typedef itk::ResampleImageFilter<OutFilterImageType, OutFilterImageType > ResampleFilter;
ResampleFilter::Pointer resampler = ResampleFilter::New();
resampler->SetInput( extractor->GetOutput() );
typedef itk::BSplineInterpolateImageFunction< OutFilterImageType > InterpolatorType;
InterpolatorType::Pointer interpolator = InterpolatorType::New();
interpolator->SetSplineOrder(3);
resampler->SetInterpolator( interpolator );
OutFilterImageType::Pointer exOut = extractor->GetOutput();
exOut->UpdateOutputInformation();
typedef itk::CenteredRigid2DTransform< double > TransformType;
TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
OutFilterImageType::PointType exOutCenter = exOut->GetOrigin();
exOutCenter[0] += (exOut->GetLargestPossibleRegion().GetSize()[0]-1) * exOut->GetSpacing()[0] *.5;
exOutCenter[1] += (exOut->GetLargestPossibleRegion().GetSize()[1]-1) * exOut->GetSpacing()[1] *.5;
transform->SetCenter( exOutCenter );
transform->SetAngleInDegrees( 180 );
resampler->SetTransform( transform );
resampler->SetOutputParametersFromImage( exOut );
OutFilterImageType::SpacingType resampleSpacing = exOut->GetSpacing();
resampleSpacing.Fill( std::min( resampleSpacing[0], resampleSpacing[1] ) );
OutFilterImageType::SizeType resampleSize;
resampleSize[0] = exOut->GetLargestPossibleRegion().GetSize()[0] * exOut->GetSpacing()[0] / resampleSpacing[0];
resampleSize[1] = exOut->GetLargestPossibleRegion().GetSize()[1] * exOut->GetSpacing()[1] / resampleSpacing[1];
resampler->SetSize( resampleSize );
resampler->SetOutputSpacing( resampleSpacing );
OutFilterImageType::Pointer result = resampler->GetOutput();
sigmoidcaster->SetBeta( -500 );
sigmoidcaster->SetAlpha( 5 );
result->Update();
int outDicomIndex = 0;
itk::EncapsulateMetaData( dict, "0008|0008", string("DERIVED\\SECONDARY\\AXIAL"));
boost::filesystem::path outpath = output_dir;
outpath = outpath / "IM%06d";
std::vector< itk::MetaDataDictionary* > dictArray;
dictArray.push_back(&dict);
itkBasic::writeDicomSeries( itkBasic::ImageRescale(itkBasic::ImageSharp(result, 0.5), -1000, 4000), outpath.string(), &dictArray, outDicomIndex);
// itkBasic::ImageSave( itkBasic::ImageSharp(result, 0.5), boost::str( boost::format("%s.%s.png") % output_name % "lung" ), 1, 0); // Auto Level
sigmoidcaster->SetBeta( 1000 );
sigmoidcaster->SetAlpha( 300 );
result->Update();
itkBasic::writeDicomSeries( itkBasic::ImageRescale(itkBasic::ImageSharp(result, 0.5), -1000, 4000), outpath.string(), &dictArray, outDicomIndex);
// itkBasic::ImageSave( itkBasic::ImageSharp(result, 0.5), boost::str( boost::format("%s.%s.png") % output_name % "bone" ), 1, 0); // Auto Level
sigmoidcaster->SetBeta( 0 );
sigmoidcaster->SetAlpha( 2000 );
result->Update();
itkBasic::writeDicomSeries( itkBasic::ImageRescale(itkBasic::ImageSharp(result, 0.5), -1000, 4000), outpath.string(), &dictArray, outDicomIndex);
// itkBasic::ImageSave( itkBasic::ImageSharp(result, 0.5), boost::str( boost::format("%s.%s.png") % output_name % "normal" ), 1, 0); // Auto Level
}