// @email florez-l@javeriana.edu.co
// =========================================================================
-#include <chrono>
-#include <map>
-
+#include <string>
+#include <tclap/CmdLine.h>
#include <itkImage.h>
-#include <itkImageFileReader.h>
-#include <itkImageFileWriter.h>
-#include <itkRegionOfInterestImageFilter.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>
+#include "MoriLabelling.h"
+#include "Functions.h"
// -------------------------------------------------------------------------
const unsigned int Dim = 3;
-typedef short TPixel;
-typedef unsigned char TLabel;
-typedef itk::Image< TPixel, Dim > TImage;
-typedef itk::Image< TLabel, Dim > TLabels;
-
-/**
- */
-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 );
-
- fpaFilterInputMacro( InputLabels, TLabels );
-
-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 ) )
- {
- fpaFilterInputConfigureMacro( InputLabels, TLabels );
- 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;
- }
-
- 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( );
- double x = input->GetPixel( n.Vertex );
- /* TODO
- double a = std::fabs( x - double( this->m_Functor->GetUpperThreshold( ) ) );
- double b = std::fabs( x - double( this->m_LastThreshold ) );
- */
- if( labels->GetPixel( n.Vertex ) == 0 /* && b < a*/ )
- n.Value = 0;
-
- 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;
-};
-
-// -------------------------------------------------------------------------
-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( );
-}
+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;
// -------------------------------------------------------------------------
-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[]
- )
+int main( int argc, char* argv[] )
{
- std::set< std::string > mandatory;
- mandatory.insert( "in" );
- mandatory.insert( "out" );
- mandatory.insert( "labels" );
-
- args[ "upper_threshold" ] = "-600";
-
- int i = 1;
- while( i < argc )
+ typedef TCLAP::ValueArg< std::string > _TStringArg;
+ typedef TCLAP::ValueArg< double > _TRealArg;
+ typedef TCLAP::ValueArg< TPixel > _TPixelArg;
+
+ // Parse input line
+ _TStringArg in( "i", "input", "Input image", true, "", "file" );
+ _TStringArg labels( "l", "labels", "Input labels", true, "", "file" );
+ _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, -400, "value (-400)" );
+ try
{
- 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 )
+ TCLAP::CmdLine cmd( "Labelling", ' ', "1.0.0" );
+ cmd.add( uThr );
+ cmd.add( vThr );
+ cmd.add( out );
+ cmd.add( vesselness );
+ cmd.add( labels );
+ cmd.add( in );
+ cmd.parse( argc, argv );
+ }
+ catch( TCLAP::ArgException& err )
{
std::cerr
- << "Usage: " << argv[ 0 ] << std::endl
- << "\t-in filename" << std::endl
- << "\t-out filename" << std::endl
- << "\t-labels filename" << std::endl
- << "\t[-roi] filename" << std::endl
- << "\t[-upper_threshold value]" << std::endl;
- return( false );
+ << "===============================" << std::endl
+ << "Error caught: " << std::endl
+ << err.error( ) << " " << err.argId( ) << std::endl
+ << "===============================" << std::endl
+ << std::endl;
+ return( 1 );
- } // fi
- return( true );
-}
+ } // yrt
-// -------------------------------------------------------------------------
-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" ] );
-
- // Mori labelling
- MoriLabelling::Pointer labelling = MoriLabelling::New( );
- labelling->SetInput( input_image );
- labelling->SetInputLabels( input_labels );
- labelling->SetOutsideValue( 2 );
- labelling->SetInsideValue( 1 );
- labelling->SetUpperThreshold(
- TPixel( std::atof( args[ "upper_threshold" ].c_str( ) ) )
- );
- /* TODO
- labelling->SetLastThreshold( last_thr );
- */
- 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 );
+ // Read input image
+ TImage::Pointer input_image;
+ CTBronchi::ReadImage( input_image, in.getValue( ) );
+
+ // Read input labels
+ TLabels::Pointer input_labels;
+ CTBronchi::ReadImage( input_labels, labels.getValue( ) );
+
+ // Read input vesselness
+ TScalarImage::Pointer input_vesselness;
+ CTBronchi::ReadImage( input_vesselness, vesselness.getValue( ) );
+
+ // Create labels
+ typedef CTBronchi::MoriLabelling< TImage, TLabels, TScalarImage > _TLabelling;
+ _TLabelling::Pointer labelling = _TLabelling::New( );
+ labelling->SetInput( input_image );
+ labelling->SetInputLabels( input_labels );
+ labelling->SetInputVesselness( input_vesselness );
+ labelling->SetVesselnessThreshold( vThr.getValue( ) );
+ labelling->SetUpperThreshold( uThr.getValue( ) );
+ labelling->SetInsideValue( 1 );
+ labelling->SetOutsideValue( 2 );
+ labelling->SetFillValue( 2 );
+ double t = CTBronchi::MeasureTime( labelling );
+ std::cout << "Labelling executed in " << t << " s" << std::endl;
+
+ // Write result
+ CTBronchi::WriteImage( labelling->GetOutput( ), out.getValue( ) );
}
catch( std::exception& err )
{
std::cerr
<< "===============================" << std::endl
<< "Error caught: " << std::endl
- << err.what( )
+ << err.what( ) << std::endl
<< "===============================" << std::endl
<< std::endl;
return( 1 );