+// =========================================================================
+// @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 );
+}
+
+// -------------------------------------------------------------------------