+/* TODO
+ #include <chrono>
+ #include <map>
+
+ #include <itkImage.h>
+ #include <itkImageFileReader.h>
+ #include <itkImageFileWriter.h>
+ #include <itkRegionOfInterestImageFilter.h>
+ #include <itkMinimumMaximumImageCalculator.h>
+
+ #include <fpa/Filters/BaseMarksInterface.h>
+ #include <fpa/Filters/Image/SeedsFromLabelsInterface.h>
+ #include <fpa/Filters/Image/DefaultTraits.h>
+ #include <fpa/Filters/Image/RegionGrow.h>
+ #include <fpa/Functors/RegionGrow/BinaryThreshold.h>
+
+ // -------------------------------------------------------------------------
+ const unsigned int Dim = 3;
+ typedef short TPixel;
+ typedef unsigned char TLabel;
+ typedef itk::NumericTraits< TPixel >::RealType TScalar;
+ typedef itk::Image< TPixel, Dim > TImage;
+ typedef itk::Image< TLabel, Dim > TLabels;
+ typedef itk::Image< TScalar, Dim > TScalarImage;
+
+ class MoriLabellingTraits
+ : public fpa::Filters::Image::DefaultTraits< TImage, TLabels, TLabel >
+ {
+ public:
+ typedef fpa::Filters::Image::DefaultTraits< TImage, TLabels, TLabel > Superclass;
+ typedef typename Superclass::TInternalTraits TInternalTraits;
+ typedef typename Superclass::TMarksImage TMarksImage;
+ typedef typename Superclass::TFilterInterface TFilterInterface;
+
+ typedef fpa::Filters::BaseMarksInterface< TInternalTraits > TMarksInterface;
+ typedef fpa::Filters::Image::SeedsFromLabelsInterface< TInternalTraits > TSeedsInterface;
+ };
+
+ class MoriLabelling
+ : public fpa::Filters::Image::RegionGrow< TImage, TLabels, TLabel, MoriLabellingTraits >
+ {
+ public:
+ typedef MoriLabellingTraits TTraits;
+ fpaTraitsMacro( TTraits );
+
+ typedef fpa::Filters::Image::RegionGrow< TImage, TLabels, TMark, TTraits > Superclass;
+ typedef MoriLabelling Self;
+ typedef itk::SmartPointer< Self > Pointer;
+ typedef itk::SmartPointer< const Self > ConstPointer;
+ typedef fpa::Functors::RegionGrow::BinaryThreshold< TInputValue > TFunctor;
+
+ public:
+ itkNewMacro( Self );
+ itkTypeMacro( MoriLabelling, fpa::Filters::Image::RegionGrow );
+
+ itkGetConstMacro( LastThreshold, TInputValue );
+ itkSetMacro( LastThreshold, TInputValue );
+
+ itkGetConstMacro( MinVertex, TVertex );
+ itkGetConstMacro( MaxVertex, TVertex );
+
+ ivqITKInputMacro( InputLabels, TLabels );
+ ivqITKInputMacro( InputVesselness, TScalarImage );
+
+ public:
+ TInputValue GetUpperThreshold( ) const
+ {
+ return( this->m_Functor->GetUpperThreshold( ) );
+ }
+ void SetUpperThreshold( TInputValue t )
+ {
+ this->m_Functor->SetUpperThreshold( t );
+ }
+
+ protected:
+ MoriLabelling( )
+ : Superclass( ),
+ m_LastThreshold( TInputValue( 0 ) ),
+ m_VesselnessThr( TScalar( 0.05 ) )
+ {
+ ivqITKInputConfigureMacro( InputLabels, TLabels );
+ ivqITKInputConfigureMacro( InputVesselness, TScalarImage );
+ this->m_Functor = TFunctor::New( );
+ this->SetPredicate( this->m_Functor );
+ }
+
+ virtual ~MoriLabelling( )
+ {
+ }
+
+ virtual const itk::DataObject* _GetReferenceInput( ) const override
+ {
+ return( this->GetInputLabels( ) );
+ }
+ virtual void _BeforeGenerateData( ) override
+ {
+ this->Superclass::_BeforeGenerateData( );
+ this->m_FirstVertex = true;
+
+ typedef itk::MinimumMaximumImageCalculator< TScalarImage > _TMinMax;
+ _TMinMax::Pointer minMax = _TMinMax::New( );
+ minMax->SetImage( this->GetInputVesselness( ) );
+ minMax->Compute( );
+ this->m_MaxVesselness = ( 1.0 - this->m_VesselnessThr ) * minMax->GetMaximum( );
+ }
+
+ virtual void _PostComputeOutputValue( TNode& n ) override
+ {
+ this->Superclass::_PostComputeOutputValue( n );
+ if( n.Value == this->GetInsideValue( ) )
+ {
+ const TImage* input = this->GetInput( );
+ const TLabels* labels = this->GetInputLabels( );
+ const TScalarImage* vesselness = this->GetInputVesselness( );
+ double x = input->GetPixel( n.Vertex );
+ if( labels->GetPixel( n.Vertex ) == 0 )
+ {
+ if( vesselness->GetPixel( n.Vertex ) > this->m_MaxVesselness )
+ n.Value = this->GetInsideValue( );
+ else
+ n.Value = 0;
+
+ } // fi
+
+ if( !( this->m_FirstVertex ) )
+ {
+ for( unsigned int d = 0; d < TImage::ImageDimension; ++d )
+ {
+ if( n.Vertex[ d ] < this->m_MinVertex[ d ] )
+ this->m_MinVertex[ d ] = n.Vertex[ d ];
+ if( this->m_MaxVertex[ d ] < n.Vertex[ d ] )
+ this->m_MaxVertex[ d ] = n.Vertex[ d ];
+
+ } // rof
+ }
+ else
+ {
+ this->m_MinVertex = n.Vertex;
+ this->m_MaxVertex = n.Vertex;
+ this->m_FirstVertex = false;
+
+ } // fi
+
+ } // fi
+ }
+
+ private:
+ // Purposely not implemented.
+ MoriLabelling( const Self& other );
+ Self& operator=( const Self& other );
+
+ protected:
+ TFunctor::Pointer m_Functor;
+ TInputValue m_LastThreshold;
+ bool m_FirstVertex;
+ TVertex m_MinVertex;
+ TVertex m_MaxVertex;
+
+ TScalar m_MaxVesselness;
+ TScalar m_VesselnessThr;
+ };
+
+ // -------------------------------------------------------------------------
+ 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;
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TImagePtr, class _TRegion >
+ void ROI(
+ _TImagePtr& output,
+ const typename _TImagePtr::ObjectType* input,
+ const _TRegion& roi
+ )
+ {
+ typedef typename _TImagePtr::ObjectType _TImage;
+ typedef itk::RegionOfInterestImageFilter< _TImage, _TImage > _TFilter;
+
+ typename _TFilter::Pointer filter = _TFilter::New( );
+ filter->SetInput( input );
+ filter->SetRegionOfInterest( roi );
+ double t = MeasureTime( filter );
+ std::cout << "ROI computed in " << t << " s" << std::endl;
+ output = filter->GetOutput( );
+ output->DisconnectPipeline( );
+ }
+
+ // -------------------------------------------------------------------------
+ bool ParseArgs(
+ std::map< std::string, std::string >& args, int argc, char* argv[]
+ )
+ {
+ std::set< std::string > mandatory;
+ mandatory.insert( "in" );
+ mandatory.insert( "out" );
+ mandatory.insert( "labels" );
+ mandatory.insert( "vesselness" );
+
+ args[ "upper_threshold" ] = "-650";
+
+ 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-labels filename" << std::endl
+ << "\t-vesselness filename" << std::endl
+ << "\t[-roi] filename" << std::endl
+ << "\t[-upper_threshold value]" << 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" ] );
+
+ // Read labels image
+ TLabels::Pointer input_labels;
+ ReadImage( input_labels, args[ "labels" ] );
+
+ // Read vesselness image
+ TScalarImage::Pointer input_vesselness;
+ ReadImage( input_vesselness, args[ "vesselness" ] );
+
+ // Mori labelling
+ MoriLabelling::Pointer labelling = MoriLabelling::New( );
+ labelling->SetInput( input_image );
+ labelling->SetInputLabels( input_labels );
+ labelling->SetInputVesselness( input_vesselness );
+ labelling->SetOutsideValue( 2 );
+ labelling->SetFillValue( 2 );
+ labelling->SetInsideValue( 1 );
+ labelling->SetUpperThreshold(
+ TPixel( std::atof( args[ "upper_threshold" ].c_str( ) ) )
+ );
+ double t = MeasureTime( labelling );
+ std::cout << "Labelling executed in " << t << " s" << std::endl;
+
+ std::map< std::string, std::string >::const_iterator i =
+ args.find( "roi" );
+ if( i != args.end( ) )
+ {
+ TImage::IndexType minV = labelling->GetMinVertex( );
+ TImage::IndexType maxV = labelling->GetMaxVertex( );
+ TImage::SizeType roiS;
+ for( unsigned d = 0; d < TImage::ImageDimension; ++d )
+ roiS[ d ] = maxV[ d ] - minV[ d ] + 1;
+ TImage::RegionType roi;
+ roi.SetIndex( minV );
+ roi.SetSize( roiS );
+
+ // ROI input image
+ TImage::Pointer input_image_roi;
+ ROI( input_image_roi, input_image.GetPointer( ), roi );
+ WriteImage( input_image_roi.GetPointer( ), i->second );
+
+ // ROI output image
+ TLabels::Pointer output_roi;
+ ROI( output_roi, labelling->GetOutput( ), roi );
+ WriteImage( output_roi.GetPointer( ), args[ "out" ] );
+ }
+ else
+ WriteImage( labelling->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 );
+ }
+*/
+