+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+
#include <chrono>
+#include <map>
+
#include <itkImage.h>
#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
-#include <CTBronchi/MoriLabelling.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>
// -------------------------------------------------------------------------
const unsigned int Dim = 3;
-typedef short TPixel;
-typedef unsigned short TLabel;
+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;
+ }
-typedef itk::Image< TPixel, Dim > TInputImage;
-typedef itk::Image< TLabel, Dim > TLabelImage;
+ 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;
-typedef CTBronchi::MoriLabelling< TInputImage, TLabelImage > TFilter;
+ 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;
+};
// -------------------------------------------------------------------------
-int main( int argc, char* argv[] )
+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
+ )
{
- // Get arguments
- if( argc < 8 )
+ 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" );
+
+ args[ "upper_threshold" ] = "-600";
+
+ 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
- << " input_image label_image output_image" << std::endl
- << " upper_threshold(-400)" << std::endl
- << " inside_value(255)" << std::endl
- << " inside_label(1) outside_label(2)"
- << std::endl;
- return( 1 );
+ << "\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 );
} // fi
- std::string input_image_filename = argv[ 1 ];
- std::string label_image_filename = argv[ 2 ];
- std::string output_image_filename = argv[ 3 ];
- TLabel upper_threshold = std::atoi( argv[ 4 ] );
- TLabel inside_value = std::atoi( argv[ 5 ] );
- TLabel inside_label = std::atoi( argv[ 6 ] );
- TLabel outside_label = std::atoi( argv[ 7 ] );
-
- // Read images
- itk::ImageFileReader< TInputImage >::Pointer input_image_reader =
- itk::ImageFileReader< TInputImage >::New( );
- input_image_reader->SetFileName( input_image_filename );
-
- itk::ImageFileReader< TLabelImage >::Pointer label_image_reader =
- itk::ImageFileReader< TLabelImage >::New( );
- label_image_reader->SetFileName( label_image_filename );
-
- // Prepare filter
- TFilter::Pointer filter = TFilter::New( );
- filter->SetInputLabelImage( label_image_reader->GetOutput( ) );
- filter->SetInputRawImage( input_image_reader->GetOutput( ) );
- filter->SetUpperThreshold( upper_threshold );
- filter->SetInsideValue( inside_value );
- filter->SetInsideLabel( inside_label );
- filter->SetOutsideLabel( outside_label );
-
- // Show some information
- std::cout << "----------------------------------------------" << std::endl;
- std::cout << "Image: " << input_image_filename << std::endl;
-
- // Execute pipeline
- std::chrono::time_point< std::chrono::high_resolution_clock > ts, te;
- std::chrono::duration< double > tr;
+ return( true );
+}
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+ std::map< std::string, std::string > args;
try
{
- ts = std::chrono::high_resolution_clock::now( );
- input_image_reader->Update( );
- te = std::chrono::high_resolution_clock::now( );
- tr = te - ts;
- std::cout << "Raw read time: " << tr.count( ) << " s" << std::endl;
-
- ts = std::chrono::high_resolution_clock::now( );
- label_image_reader->Update( );
- te = std::chrono::high_resolution_clock::now( );
- tr = te - ts;
- std::cout << "Label read time: " << tr.count( ) << " s" << std::endl;
-
- ts = std::chrono::high_resolution_clock::now( );
- filter->Update( );
- te = std::chrono::high_resolution_clock::now( );
- tr = te - ts;
- std::cout
- << "Labelling time: " << tr.count( ) << " s" << std::endl;
- }
- catch( std::exception& err )
- {
- std::cerr << "Error caught: " << err.what( ) << std::endl;
- return( 1 );
+ if( ParseArgs( args, argc, argv ) )
+ {
+ // Read input image
+ TImage::Pointer input_image;
+ ReadImage( input_image, args[ "in" ] );
- } // yrt
+ // Read labels image
+ TLabels::Pointer input_labels;
+ ReadImage( input_labels, args[ "labels" ] );
- // Save output image
- itk::ImageFileWriter< TLabelImage >::Pointer output_image_writer =
- itk::ImageFileWriter< TLabelImage >::New( );
- output_image_writer->SetInput( filter->GetOutput( ) );
- output_image_writer->SetFileName( output_image_filename );
- try
- {
- ts = std::chrono::high_resolution_clock::now( );
- output_image_writer->Update( );
- te = std::chrono::high_resolution_clock::now( );
- tr = te - ts;
- std::cout << "Write time: " << tr.count( ) << " s" << std::endl;
+ // 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 );
}
catch( std::exception& err )
{
- std::cerr << "Error caught: " << err.what( ) << std::endl;
+ std::cerr
+ << "===============================" << std::endl
+ << "Error caught: " << std::endl
+ << err.what( )
+ << "===============================" << std::endl
+ << std::endl;
return( 1 );
} // yrt
- std::cout << "----------------------------------------------" << std::endl;
-
return( 0 );
}
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / blobdiff