+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+
+#include <chrono>
+#include <map>
+#include <itkImage.h>
+#include <itkImageFileReader.h>
+#include <itkImageFileWriter.h>
+#include <itkMinimumMaximumImageCalculator.h>
+#include <itkInvertIntensityImageFilter.h>
+#include <itkHessianRecursiveGaussianImageFilter.h>
+#include <itkHessian3DToVesselnessMeasureImageFilter.h>
+
+// -------------------------------------------------------------------------
+const unsigned int Dim = 3;
+typedef short TPixel;
+typedef itk::NumericTraits< TPixel >::RealType TScalar;
+typedef itk::Image< TPixel, Dim > TImage;
+typedef itk::Image< TScalar, Dim > TScalarImage;
+
+// -------------------------------------------------------------------------
+double MeasureTime( itk::ProcessObject* f )
+{
+ std::chrono::time_point< std::chrono::high_resolution_clock > s, e;
+ std::chrono::duration< double > t;
+ s = std::chrono::high_resolution_clock::now( );
+ f->Update( );
+ e = std::chrono::high_resolution_clock::now( );
+ t = e - s;
+ return( t.count( ) );
+}
+
+// -------------------------------------------------------------------------
+template< class _TImagePtr >
+void ReadImage( _TImagePtr& image, const std::string& fname )
+{
+ typedef typename _TImagePtr::ObjectType _TImage;
+ typedef itk::ImageFileReader< _TImage > _TReader;
+ typename _TReader::Pointer reader = _TReader::New( );
+ reader->SetFileName( fname );
+ double t = MeasureTime( reader );
+ std::cout << "Read " << fname << " in " << t << " s" << std::endl;
+ image = reader->GetOutput( );
+ image->DisconnectPipeline( );
+}
+
+// -------------------------------------------------------------------------
+template< class _TImage >
+void WriteImage( const _TImage* image, const std::string& fname )
+{
+ typedef itk::ImageFileWriter< _TImage > _TWriter;
+ typename _TWriter::Pointer writer = _TWriter::New( );
+ writer->SetFileName( fname );
+ writer->SetInput( image );
+ double t = MeasureTime( writer );
+ std::cout << "Wrote " << fname << " in " << t << " s" << std::endl;
+}
+
+// -------------------------------------------------------------------------
+bool ParseArgs(
+ std::map< std::string, std::string >& args, int argc, char* argv[]
+ )
+{
+ std::set< std::string > mandatory;
+ mandatory.insert( "in" );
+ mandatory.insert( "out" );
+
+ args[ "sigma" ] = "0.5";
+ args[ "alpha1" ] = "0.5";
+ args[ "alpha2" ] = "2";
+
+ int i = 1;
+ while( i < argc )
+ {
+ std::string cmd = argv[ i ] + 1;
+ args[ cmd ] = argv[ i + 1 ];
+ i += 2;
+
+ } // elihw
+
+ bool complete = true;
+ for( std::string t: mandatory )
+ complete &= ( args.find( t ) != args.end( ) );
+
+ if( !complete )
+ {
+ std::cerr
+ << "Usage: " << argv[ 0 ] << std::endl
+ << "\t-in filename" << std::endl
+ << "\t-out filename" << std::endl
+ << "\t[-sigma val]" << std::endl
+ << "\t[-alpha1 val]" << std::endl
+ << "\t[-alpha2 val]" << std::endl;
+ return( false );
+
+ } // fi
+ return( true );
+}
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+ std::map< std::string, std::string > args;
+ try
+ {
+ if( ParseArgs( args, argc, argv ) )
+ {
+ // Read input image
+ TImage::Pointer input_image;
+ ReadImage( input_image, args[ "in" ] );
+
+ // Vesselness
+ typedef itk::MinimumMaximumImageCalculator< TImage > TMinMax;
+ typedef itk::InvertIntensityImageFilter< TImage > TInverter;
+ typedef itk::HessianRecursiveGaussianImageFilter< TImage > THessian;
+ typedef itk::Hessian3DToVesselnessMeasureImageFilter< TScalar > TVesselness;
+
+ TMinMax::Pointer minMax = TMinMax::New( );
+ minMax->SetImage( input_image );
+ minMax->Compute( );
+
+ TInverter::Pointer inverter = TInverter::New( );
+ inverter->SetInput( input_image );
+ inverter->SetMaximum( minMax->GetMaximum( ) );
+ double t = MeasureTime( inverter );
+ std::cout << "Inversion executed in " << t << " s" << std::endl;
+
+ THessian::Pointer hessian = THessian::New( );
+ hessian->SetInput( inverter->GetOutput( ) );
+ hessian->SetSigma(
+ std::atof( args[ "sigma" ].c_str( ) )
+ );
+ t = MeasureTime( hessian );
+ std::cout << "Hessian executed in " << t << " s" << std::endl;
+
+ TVesselness::Pointer vesselness = TVesselness::New( );
+ vesselness->SetInput( hessian->GetOutput( ) );
+ vesselness->SetAlpha1(
+ std::atof( args[ "alpha1" ].c_str( ) )
+ );
+ vesselness->SetAlpha2(
+ std::atof( args[ "alpha2" ].c_str( ) )
+ );
+ t = MeasureTime( vesselness );
+ std::cout << "Vesselness executed in " << t << " s" << std::endl;
+
+ WriteImage( vesselness->GetOutput( ), args[ "out" ] );
+ }
+ else
+ return( 1 );
+ }
+ catch( std::exception& err )
+ {
+ std::cerr
+ << "===============================" << std::endl
+ << "Error caught: " << std::endl
+ << err.what( )
+ << "===============================" << std::endl
+ << std::endl;
+ return( 1 );
+
+ } // yrt
+ return( 0 );
+}
+
+// eof - $RCSfile$