## == Build different parts ==
## ===========================
-subdirs(lib tests)
+subdirs(appli lib tests)
## ===============================
## == Global installation rules ==
set(_pfx fpa_CTBronchi_)
set(
_examples
- MoriSegmentation
- MoriLabelling
- RandomWalker
+ Process
)
foreach(_e ${_examples})
add_executable(${_pfx}${_e} ${_e}.cxx)
- target_link_libraries(${_pfx}${_e} ivq::ivq fpa)
+ target_link_libraries(${_pfx}${_e} fpa)
endforeach(_e)
endif(fpa_BUILD_CTBronchi)
#ifndef __CTBronchi__MoriLabelling__h__
#define __CTBronchi__MoriLabelling__h__
-#include <fpa/Base/RegionGrow.h>
-#include <fpa/Base/MarksInterface.h>
-#include <fpa/Base/Functors/RegionGrow/BinaryThreshold.h>
-#include <fpa/Image/Algorithm.h>
-#include <fpa/Image/DefaultTraits.h>
-#include <fpa/Image/LabelledSeedsInterface.h>
+/* TODO
+ #include <fpa/Base/RegionGrow.h>
+ #include <fpa/Base/MarksInterface.h>
+ #include <fpa/Base/Functors/RegionGrow/BinaryThreshold.h>
+ #include <fpa/Image/Algorithm.h>
+ #include <fpa/Image/DefaultTraits.h>
+ #include <fpa/Image/LabelledSeedsInterface.h>
+*/
namespace CTBronchi
{
/**
*/
- template< class _TInputImage, class _TLabelImage, class _TTraits = fpa::Image::DefaultTraits< _TInputImage, _TLabelImage, typename _TLabelImage::PixelType > >
- class MoriLabelling
- : public fpa::Base::RegionGrow< fpa::Image::Algorithm< _TTraits, fpa::Base::MarksInterface< _TTraits >, fpa::Image::LabelledSeedsInterface< _TTraits > > >
- {
- public:
- typedef _TInputImage TInputImage;
- typedef _TLabelImage TLabelImage;
- typedef _TTraits TTraits;
- fpa_Base_TraitTypes( typename TTraits );
-
- typedef fpa::Base::MarksInterface< TTraits > TMarksInterface;
- typedef fpa::Image::LabelledSeedsInterface< TTraits > TSeedsInterface;
- typedef fpa::Image::Algorithm< TTraits, TMarksInterface, TSeedsInterface > TAlgorithm;
-
- typedef MoriLabelling Self;
- typedef fpa::Base::RegionGrow< TAlgorithm > Superclass;
- typedef itk::SmartPointer< Self > Pointer;
- typedef itk::SmartPointer< const Self > ConstPointer;
-
- typedef fpa::Base::Functors::RegionGrow::BinaryThreshold< TInputValue > TThresholdFunction;
-
- public:
- itkNewMacro( Self );
- itkTypeMacro( MoriLabelling, fpa::Base::RegionGrow );
-
- itkGetConstMacro( InsideLabel, TOutputValue );
- itkSetMacro( InsideLabel, TOutputValue );
-
- public:
- const TLabelImage* GetInputLabelImage( ) const;
- void SetInputLabelImage( TLabelImage* image );
-
- const TInputImage* GetInputRawImage( ) const;
- void SetInputRawImage( TInputImage* image );
-
- TInputValue GetUpperThreshold( ) const;
- void SetUpperThreshold( TInputValue t );
-
- TOutputValue GetOutsideValue( ) const;
- void SetOutsideLabel( TOutputValue o );
-
- protected:
- MoriLabelling( );
- virtual ~MoriLabelling( );
-
- virtual TNodes _UnifySeeds( ) override;
- virtual void _UpdateOutputValue( TNode& n ) override;
-
- private:
- // Purposely not implemented.
- MoriLabelling( const Self& other );
- Self& operator=( const Self& other );
-
- protected:
- TOutputValue m_InsideLabel;
- };
+ /* TODO
+ template< class _TInputImage, class _TLabelImage, class _TTraits = fpa::Image::DefaultTraits< _TInputImage, _TLabelImage, typename _TLabelImage::PixelType > >
+ class MoriLabelling
+ : public fpa::Base::RegionGrow< fpa::Image::Algorithm< _TTraits, fpa::Base::MarksInterface< _TTraits >, fpa::Image::LabelledSeedsInterface< _TTraits > > >
+ {
+ public:
+ typedef _TInputImage TInputImage;
+ typedef _TLabelImage TLabelImage;
+ typedef _TTraits TTraits;
+ fpa_Base_TraitTypes( typename TTraits );
+
+ typedef fpa::Base::MarksInterface< TTraits > TMarksInterface;
+ typedef fpa::Image::LabelledSeedsInterface< TTraits > TSeedsInterface;
+ typedef fpa::Image::Algorithm< TTraits, TMarksInterface, TSeedsInterface > TAlgorithm;
+
+ typedef MoriLabelling Self;
+ typedef fpa::Base::RegionGrow< TAlgorithm > Superclass;
+ typedef itk::SmartPointer< Self > Pointer;
+ typedef itk::SmartPointer< const Self > ConstPointer;
+
+ typedef fpa::Base::Functors::RegionGrow::BinaryThreshold< TInputValue > TThresholdFunction;
+
+ public:
+ itkNewMacro( Self );
+ itkTypeMacro( MoriLabelling, fpa::Base::RegionGrow );
+
+ itkGetConstMacro( InsideLabel, TOutputValue );
+ itkSetMacro( InsideLabel, TOutputValue );
+
+ public:
+ const TLabelImage* GetInputLabelImage( ) const;
+ void SetInputLabelImage( TLabelImage* image );
+
+ const TInputImage* GetInputRawImage( ) const;
+ void SetInputRawImage( TInputImage* image );
+
+ TInputValue GetUpperThreshold( ) const;
+ void SetUpperThreshold( TInputValue t );
+
+ TOutputValue GetOutsideValue( ) const;
+ void SetOutsideLabel( TOutputValue o );
+
+ protected:
+ MoriLabelling( );
+ virtual ~MoriLabelling( );
+
+ virtual TNodes _UnifySeeds( ) override;
+ virtual void _UpdateOutputValue( TNode& n ) override;
+
+ private:
+ // Purposely not implemented.
+ MoriLabelling( const Self& other );
+ Self& operator=( const Self& other );
+
+ protected:
+ TOutputValue m_InsideLabel;
+ };
+ */
} // ecapseman
#ifndef __CTBronchi__MoriLabelling__hxx__
#define __CTBronchi__MoriLabelling__hxx__
-#include <itkImageRegionConstIteratorWithIndex.h>
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-const typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-TLabelImage* CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-GetInputLabelImage( ) const
-{
- return( this->GetLabels( ) );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-SetInputLabelImage( TLabelImage* image )
-{
- this->SetLabels( image );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-const typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-TInputImage* CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-GetInputRawImage( ) const
-{
- return( this->GetInput( ) );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-SetInputRawImage( TInputImage* image )
-{
- this->SetInput( image );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-TInputValue CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-GetUpperThreshold( ) const
-{
- const TThresholdFunction* func =
- dynamic_cast< const TThresholdFunction* >( this->GetValuePredicate( ) );
- if( func != NULL )
- return( func->GetUpper( ) );
- else
- return( TInputValue( 0 ) );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-SetUpperThreshold( TInputValue t )
-{
- TThresholdFunction* func =
- dynamic_cast< TThresholdFunction* >( this->GetValuePredicate( ) );
- if( func != NULL )
- func->SetUpper( t );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-TOutputValue CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-GetOutsideValue( ) const
-{
- return( this->GetInitValue( ) );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-SetOutsideLabel( TOutputValue o )
-{
- this->SetInitValue( o );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-MoriLabelling( )
- : Superclass( ),
- m_InsideLabel( TOutputValue( 0 ) )
-{
- typename TThresholdFunction::Pointer func = TThresholdFunction::New( );
- this->SetPredicate( func );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-~MoriLabelling( )
-{
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-TNodes CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-_UnifySeeds( )
-{
- this->m_Seeds.clear( );
- const TLabelImage* lbl = this->GetLabels( );
- if( lbl == NULL )
- {
- std::ostringstream msg;
- msg << "itk::ERROR: CTBronchi::MoriLabelling (" << this
- << "): Labelled image not defined.";
- ::itk::ExceptionObject e(
- __FILE__, __LINE__, msg.str( ).c_str( ), ITK_LOCATION
- );
- throw e;
-
- } // fi
-
- // Iterate over labels
- typename TLabelImage::RegionType reg = lbl->GetRequestedRegion( );
- itk::ImageRegionConstIteratorWithIndex< TLabelImage > lIt( lbl, reg );
- for( lIt.GoToBegin( ); !lIt.IsAtEnd( ); ++lIt )
- {
- if( lIt.Get( ) > 0 )
- {
- bool is_seed = false;
- for( unsigned int d = 0; d < TLabelImage::ImageDimension; ++d )
- {
- for( int s = -1; s <= 1; s += 2 )
- {
- TVertex neigh = lIt.GetIndex( );
- neigh[ d ] += s;
- if( reg.IsInside( neigh ) )
- is_seed |= ( lbl->GetPixel( neigh ) == 0 );
-
- } // rof
-
- } // rof
-
- if( !is_seed )
- {
- typename TSeedsInterface::TNode node;
- node.Vertex = lIt.GetIndex( );
- node.Parent = lIt.GetIndex( );
- node.FrontId = lIt.Get( );
- node.Value = this->m_InsideLabel;
- this->_Mark( node.Vertex, node.FrontId );
- this->_UpdateOutputValue( node );
- }
- else
- {
- typename TSeedsInterface::TSeed seed;
- seed.Vertex = lIt.GetIndex( );
- seed.IsPoint = false;
- seed.FrontId = lIt.Get( );
- this->m_Seeds.push_back( seed );
-
- } // fi
-
- } // fi
-
- } // rof
-
- // Ok, finish initialization
- return( this->Superclass::_UnifySeeds( ) );
-}
-
-// -------------------------------------------------------------------------
-template< class _TInputImage, class _TLabelImage, class _TTraits >
-void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
-_UpdateOutputValue( TNode& n )
-{
- const TLabelImage* input_labels = this->GetInputLabelImage( );
-
- this->Superclass::_UpdateOutputValue( n );
- if( n.FrontId != 0 )
- {
- if( input_labels->GetPixel( n.Vertex ) == this->GetInsideValue( ) )
- n.Value = this->GetInsideLabel( );
- else
- n.Value = TOutputValue( 0 );
- this->TAlgorithm::_UpdateOutputValue( n );
-
- } // fi
-}
+/* TODO
+ #include <itkImageRegionConstIteratorWithIndex.h>
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ const typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ TLabelImage* CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ GetInputLabelImage( ) const
+ {
+ return( this->GetLabels( ) );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ SetInputLabelImage( TLabelImage* image )
+ {
+ this->SetLabels( image );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ const typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ TInputImage* CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ GetInputRawImage( ) const
+ {
+ return( this->GetInput( ) );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ SetInputRawImage( TInputImage* image )
+ {
+ this->SetInput( image );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ TInputValue CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ GetUpperThreshold( ) const
+ {
+ const TThresholdFunction* func =
+ dynamic_cast< const TThresholdFunction* >( this->GetValuePredicate( ) );
+ if( func != NULL )
+ return( func->GetUpper( ) );
+ else
+ return( TInputValue( 0 ) );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ SetUpperThreshold( TInputValue t )
+ {
+ TThresholdFunction* func =
+ dynamic_cast< TThresholdFunction* >( this->GetValuePredicate( ) );
+ if( func != NULL )
+ func->SetUpper( t );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ TOutputValue CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ GetOutsideValue( ) const
+ {
+ return( this->GetInitValue( ) );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ SetOutsideLabel( TOutputValue o )
+ {
+ this->SetInitValue( o );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ MoriLabelling( )
+ : Superclass( ),
+ m_InsideLabel( TOutputValue( 0 ) )
+ {
+ typename TThresholdFunction::Pointer func = TThresholdFunction::New( );
+ this->SetPredicate( func );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ ~MoriLabelling( )
+ {
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ typename CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ TNodes CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ _UnifySeeds( )
+ {
+ this->m_Seeds.clear( );
+ const TLabelImage* lbl = this->GetLabels( );
+ if( lbl == NULL )
+ {
+ std::ostringstream msg;
+ msg << "itk::ERROR: CTBronchi::MoriLabelling (" << this
+ << "): Labelled image not defined.";
+ ::itk::ExceptionObject e(
+ __FILE__, __LINE__, msg.str( ).c_str( ), ITK_LOCATION
+ );
+ throw e;
+
+ } // fi
+
+ // Iterate over labels
+ typename TLabelImage::RegionType reg = lbl->GetRequestedRegion( );
+ itk::ImageRegionConstIteratorWithIndex< TLabelImage > lIt( lbl, reg );
+ for( lIt.GoToBegin( ); !lIt.IsAtEnd( ); ++lIt )
+ {
+ if( lIt.Get( ) > 0 )
+ {
+ bool is_seed = false;
+ for( unsigned int d = 0; d < TLabelImage::ImageDimension; ++d )
+ {
+ for( int s = -1; s <= 1; s += 2 )
+ {
+ TVertex neigh = lIt.GetIndex( );
+ neigh[ d ] += s;
+ if( reg.IsInside( neigh ) )
+ is_seed |= ( lbl->GetPixel( neigh ) == 0 );
+
+ } // rof
+
+ } // rof
+
+ if( !is_seed )
+ {
+ typename TSeedsInterface::TNode node;
+ node.Vertex = lIt.GetIndex( );
+ node.Parent = lIt.GetIndex( );
+ node.FrontId = lIt.Get( );
+ node.Value = this->m_InsideLabel;
+ this->_Mark( node.Vertex, node.FrontId );
+ this->_UpdateOutputValue( node );
+ }
+ else
+ {
+ typename TSeedsInterface::TSeed seed;
+ seed.Vertex = lIt.GetIndex( );
+ seed.IsPoint = false;
+ seed.FrontId = lIt.Get( );
+ this->m_Seeds.push_back( seed );
+
+ } // fi
+
+ } // fi
+
+ } // rof
+
+ // Ok, finish initialization
+ return( this->Superclass::_UnifySeeds( ) );
+ }
+
+ // -------------------------------------------------------------------------
+ template< class _TInputImage, class _TLabelImage, class _TTraits >
+ void CTBronchi::MoriLabelling< _TInputImage, _TLabelImage, _TTraits >::
+ _UpdateOutputValue( TNode& n )
+ {
+ const TLabelImage* input_labels = this->GetInputLabelImage( );
+
+ this->Superclass::_UpdateOutputValue( n );
+ if( n.FrontId != 0 )
+ {
+ if( input_labels->GetPixel( n.Vertex ) == this->GetInsideValue( ) )
+ n.Value = this->GetInsideLabel( );
+ else
+ n.Value = TOutputValue( 0 );
+ this->TAlgorithm::_UpdateOutputValue( n );
+
+ } // fi
+ }
+*/
#endif // __CTBronchi__MoriLabelling__hxx__
+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+
+#include <chrono>
+#include <fstream>
+#include <limits>
+#include <map>
+#include <set>
+#include <sstream>
+#include <string>
+#include <itkImage.h>
+#include <itkImageFileReader.h>
+#include <itkImageFileWriter.h>
+#include <fpa/Filters/Image/Mori.h>
+#include <CTBronchi/MoriLabelling.h>
+
+// -------------------------------------------------------------------------
+const unsigned int Dim = 3;
+typedef short TInputPixel;
+typedef unsigned char TLabelPixel;
+typedef itk::Image< TInputPixel, Dim > TInputImage;
+typedef itk::Image< TLabelPixel, Dim > TLabelImage;
+typedef std::map< std::string, std::string > TMap;
+
+// -------------------------------------------------------------------------
+TMap Args;
+TInputImage::PointType global_seed;
+TLabelPixel inside_value = std::numeric_limits< TLabelPixel >::max( );
+TLabelPixel outside_value = TLabelPixel( 0 );
+
+// -------------------------------------------------------------------------
+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 _TImagePtr >
+void WriteImage( const _TImagePtr& image, const std::string& fname )
+{
+ typedef typename _TImagePtr::ObjectType _TImage;
+ 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 _TInputPtr, class _TOutputPtr >
+void Mori( _TOutputPtr& output, const _TInputPtr& input )
+{
+ typedef typename _TInputPtr::ObjectType _TInput;
+ typedef typename _TOutputPtr::ObjectType _TOutput;
+ typedef fpa::Filters::Image::Mori< _TInput, _TOutput > _TMori;
+
+ typename _TMori::Pointer mori = _TMori::New( );
+ mori->SetInput( input );
+ mori->SetSeed( global_seed );
+ mori->SetInsideValue( inside_value );
+ mori->SetOutsideValue( outside_value );
+ mori->SetMinimumThreshold(
+ TInputPixel( std::atof( Args[ "mori_minimum_threshold" ].c_str( ) ) )
+ );
+ mori->SetSignalKernelSize(
+ std::atoi( Args[ "mori_signal_kernel_size" ].c_str( ) )
+ );
+ mori->SetSignalThreshold(
+ std::atof( Args[ "mori_signal_threshold" ].c_str( ) )
+ );
+ mori->SetSignalInfluence(
+ std::atof( Args[ "mori_signal_influence" ].c_str( ) )
+ );
+ mori->SetThresholds(
+ TInputPixel( std::atof( Args[ "mori_lower_threshold" ].c_str( ) ) ),
+ TInputPixel( std::atof( Args[ "mori_upper_threshold" ].c_str( ) ) ),
+ TInputPixel( std::atof( Args[ "mori_delta_threshold" ].c_str( ) ) )
+ );
+ double t = MeasureTime( mori );
+ std::cout << "Mori executed in " << t << " s" << std::endl;
+ output = mori->GetOutput( );
+
+ TMap::const_iterator i = Args.find( "out_mori" );
+ if( i != Args.end( ) )
+ WriteImage( output, i->second );
+
+ 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
+ output->DisconnectPipeline( );
+}
+
+// -------------------------------------------------------------------------
+template< class _TInputPtr, class _TOutputPtr >
+void Label( _TOutputPtr& output, const _TInputPtr& input )
+{
+}
+
+// -------------------------------------------------------------------------
+bool ParseArgs( int argc, char* argv[] )
+{
+ std::set< std::string > mandatory;
+ mandatory.insert( "in" );
+ mandatory.insert( "out_segmentation" );
+ mandatory.insert( "seed_x" );
+ mandatory.insert( "seed_y" );
+ mandatory.insert( "seed_z" );
+
+ Args[ "mori_minimum_threshold" ] = "-850";
+ Args[ "mori_signal_kernel_size" ] = "20";
+ Args[ "mori_signal_threshold" ] = "100";
+ Args[ "mori_signal_influence" ] = "0.5";
+ Args[ "mori_lower_threshold" ] = "-1024";
+ Args[ "mori_upper_threshold" ] = "0";
+ Args[ "mori_delta_threshold" ] = "1";
+ for( int i = 1; i < argc; i += 2 )
+ Args[ argv[ i ] + 1 ] = argv[ i + 1 ];
+
+ 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_segmentation filename" << std::endl
+ << "\t-seed_x value -seed_y value -seed_z value" << std::endl
+ << "\t[-out_mori filename]" << std::endl
+ << "\t[-out_signal filename]" << std::endl
+ << "\t[-out_labels filename]" << std::endl
+ << "\t[-mori_minimum_threshold value]" << std::endl
+ << "\t[-mori_signal_kernel_size value]" << std::endl
+ << "\t[-mori_signal_threshold value]" << std::endl
+ << "\t[-mori_signal_influence value]" << std::endl
+ << "\t[-mori_lower_threshold value]" << std::endl
+ << "\t[-mori_upper_threshold value]" << std::endl
+ << "\t[-mori_delta_threshold value]" << std::endl;
+ return( false );
+
+ } // fi
+ return( true );
+}
+
+// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
{
+ try
+ {
+ if( ParseArgs( argc, argv ) )
+ {
+ // Parse seed
+ global_seed[ 0 ] = std::atof( Args[ "seed_x" ].c_str( ) );
+ global_seed[ 1 ] = std::atof( Args[ "seed_y" ].c_str( ) );
+ global_seed[ 2 ] = std::atof( Args[ "seed_z" ].c_str( ) );
+
+ // Read input image
+ TInputImage::Pointer input_image;
+ ReadImage( input_image, Args[ "in" ] );
+
+ // Mori segmentation
+ TLabelImage::Pointer mori;
+ Mori( mori, input_image );
+
+ // Create labels
+ TLabelImage::Pointer labels;
+ Label( labels, mori );
+
+ return( 0 );
+
+ } // fi
+ return( 1 );
+ }
+ catch( std::exception& err )
+ {
+ std::cerr
+ << "===============================" << std::endl
+ << "Error caught: " << std::endl
+ << err.what( )
+ << "===============================" << std::endl
+ << std::endl;
+ return( 1 );
+
+ } // yrt
/* TODO
- -input input_raw_image
- -seed x y z
- [-mori mori_image_dfilename]
- [-labels labels_image_filename]
- [-output output_image_filename]
+ if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
+ if [ -z "$label_inside" ]; then label_inside="1"; fi
+ if [ -z "$label_outside" ]; then label_outside="2"; fi
+ if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
*/
-
- /* TODO
- if [ -z "$mori_init_threshold" ]; then mori_init_threshold="-1024"; fi
- if [ -z "$mori_end_threshold" ]; then mori_end_threshold="0"; fi
- if [ -z "$mori_delta" ]; then mori_delta="1"; fi
- if [ -z "$mori_minimum_threshold" ]; then mori_minimum_threshold="-850"; fi
- if [ -z "$mori_inside_value" ]; then mori_inside_value="255"; fi
- if [ -z "$mori_outside_value" ]; then mori_outside_value="0"; fi
- if [ -z "$mori_signal_kernel_size" ]; then mori_signal_kernel_size="20"; fi
- if [ -z "$mori_signal_threshold" ]; then mori_signal_threshold="500"; fi
- if [ -z "$mori_signal_influence" ]; then mori_signal_influence="0.5"; fi
- if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
- if [ -z "$label_inside" ]; then label_inside="1"; fi
- if [ -z "$label_outside" ]; then label_outside="2"; fi
- if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
- */
-
- return( 0 );
}
+
+// eof - $RCSfile$
);
protected:
- Mori( )
- : Superclass( )
- {
- }
- virtual ~Mori( )
- {
- }
+ Mori( );
+ virtual ~Mori( );
+
+ virtual void _AfterGenerateData( ) override;
private:
// Purposely not implemented.
} // ecapseman
+#ifndef ITK_MANUAL_INSTANTIATION
+# include <fpa/Filters/Image/Mori.hxx>
+#endif // ITK_MANUAL_INSTANTIATION
#endif // __fpa__Filters__Image__Mori__h__
// eof - $RCSfile$
--- /dev/null
+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+#ifndef __fpa__Filters__Image__Mori__hxx__
+#define __fpa__Filters__Image__Mori__hxx__
+
+#include <itkBinaryThresholdImageFilter.h>
+
+// -------------------------------------------------------------------------
+template< class _TInputImage, class _TOutputImage, class _TTraits >
+fpa::Filters::Image::Mori< _TInputImage, _TOutputImage, _TTraits >::
+Mori( )
+ : Superclass( )
+{
+}
+
+// -------------------------------------------------------------------------
+template< class _TInputImage, class _TOutputImage, class _TTraits >
+fpa::Filters::Image::Mori< _TInputImage, _TOutputImage, _TTraits >::
+~Mori( )
+{
+}
+
+// -------------------------------------------------------------------------
+template< class _TInputImage, class _TOutputImage, class _TTraits >
+void fpa::Filters::Image::Mori< _TInputImage, _TOutputImage, _TTraits >::
+_AfterGenerateData( )
+{
+ this->Superclass::_AfterGenerateData( );
+
+ // Extract correct mark
+ typedef typename Superclass::TMarksImage _TMarks;
+ typedef itk::BinaryThresholdImageFilter< _TMarks, TOutputImage > _TFilter;
+ typename _TFilter::Pointer filter = _TFilter::New( );
+ filter->SetInput( this->GetMarks( ) );
+ filter->SetLowerThreshold( 1 );
+ filter->SetUpperThreshold( this->m_PeakDetector.GetNumberOfSamples( ) - 2 );
+ filter->SetInsideValue( this->GetInsideValue( ) );
+ filter->SetOutsideValue( this->GetOutsideValue( ) );
+ filter->Update( );
+ this->GraftOutput( filter->GetOutput( ) );
+}
+
+#endif // __fpa__Filters__Image__Mori__hxx__
+// eof - $RCSfile$
#ifndef ITK_MANUAL_INSTANTIATION
# include <fpa/Filters/Mori.hxx>
#endif // ITK_MANUAL_INSTANTIATION
-
#endif // __fpa__Filters__Mori__h__
// eof - $RCSfile$
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / commitdiff