// @email florez-l@javeriana.edu.co
// =========================================================================
-#include <sstream>
#include <string>
#include <tclap/CmdLine.h>
#include <itkImage.h>
_TStringArg vesselness( "v", "vesselness", "Input vesselness", true, "", "file" );
_TStringArg out( "o", "output", "Output image", true, "", "file" );
_TRealArg vThr( "a", "vesselness_thr", "Vesselness threshold", false, 0.05, "value (0.05)" );
- _TPixelArg uThr( "u", "upper_thr", "Upper threshold", false, -650, "value (-650)" );
+ _TPixelArg uThr( "u", "upper_thr", "Upper threshold", false, -400, "value (-400)" );
try
{
TCLAP::CmdLine cmd( "Labelling", ' ', "1.0.0" );
return( 0 );
}
-/* 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 );
- }
-*/
-
// eof - $RCSfile$
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff