X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=appli%2FCTBronchi%2FMoriLabelling.cxx;h=b2c901baf8fd06f980b2eec9142cad55bc16290c;hb=0251081f09de5bd702c01565c9401c1eb1983ae5;hp=0ad694d9027a1249f56f76c6b760c447fa499841;hpb=d2f5533aef455b7d862dbfbe72c42c5497eaf98b;p=FrontAlgorithms.git diff --git a/appli/CTBronchi/MoriLabelling.cxx b/appli/CTBronchi/MoriLabelling.cxx index 0ad694d..b2c901b 100644 --- a/appli/CTBronchi/MoriLabelling.cxx +++ b/appli/CTBronchi/MoriLabelling.cxx @@ -3,174 +3,95 @@ // @email florez-l@javeriana.edu.co // ========================================================================= -#include -#include +#include +#include #include -#include -#include -#include +#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; +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; // ------------------------------------------------------------------------- -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[] - ) +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[-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 segmentation - /* TODO - typedef fpa::Filters::Image::Mori< TImage, TLabels > TMori; - TMori::Pointer mori = TMori::New( ); - mori->SetInput( input_image ); - mori->SetSeed( seed ); - mori->SetInsideValue( 1 ); - mori->SetOutsideValue( 0 ); - mori->SetMinimumThreshold( - TPixel( std::atof( args[ "minimum_threshold" ].c_str( ) ) ) - ); - mori->SetSignalKernelSize( - std::atoi( args[ "signal_kernel_size" ].c_str( ) ) - ); - mori->SetSignalThreshold( - std::atof( args[ "signal_threshold" ].c_str( ) ) - ); - mori->SetSignalInfluence( - std::atof( args[ "signal_influence" ].c_str( ) ) - ); - mori->SetThresholds( - TPixel( std::atof( args[ "lower_threshold" ].c_str( ) ) ), - TPixel( std::atof( args[ "upper_threshold" ].c_str( ) ) ), - TPixel( std::atof( args[ "delta_threshold" ].c_str( ) ) ) - ); - double t = MeasureTime( mori ); - std::cout << "Mori executed in " << t << " s" << std::endl; - WriteImage( mori->GetOutput( ), args[ "out" ] ); - - std::map< std::string, std::string >::const_iterator i = - args.find( "out_signal" ); - if( i != args.end( ) ) - { - std::stringstream signal; - unsigned long nthr = mori->GetNumberOfEvaluatedThresholds( ); - signal << "# nThr = " << nthr << std::endl; - signal << "# Opt = " << mori->GetOptimumThreshold( ) << std::endl; - for( unsigned long j = 0; j < nthr; ++j ) - { - typename TMori::TPeak p; - double x, y; - mori->GetSignalValues( j, x, y, p ); - signal << x << " " << y << std::endl; - - } // rof - std::ofstream signals_str( i->second.c_str( ) ); - signals_str << signal.str( ); - signals_str.close( ); - - } // fi - */ - } - 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 );