+#include <chrono>
+#include <itkImage.h>
+#include <itkImageFileReader.h>
+#include <itkImageFileWriter.h>
+#include <fpa/Image/Mori.h>
+
+// -------------------------------------------------------------------------
+const unsigned int Dim = 3;
+typedef short TPixel;
+typedef unsigned short TLabel;
+
+typedef itk::Image< TPixel, Dim > TInputImage;
+typedef itk::Image< TLabel, Dim > TLabelImage;
+typedef fpa::Image::Mori< TInputImage, TLabelImage > TFilter;
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+ // Get arguments
+ if( argc < 17 )
+ {
+ std::cerr
+ << "Usage: " << argv[ 0 ] << std::endl
+ << " input_image output_image output_signal" << std::endl
+ << " init_threshold(-1024) end_threshold(0) delta(1)" << std::endl
+ << " minimum_threshold(-850)" << std::endl
+ << " inside_value(255) outside_value(0)" << std::endl
+ << " signal_kernel_size(20) signal_threshold(500) signal_influence(0.5)"
+ << std::endl
+ << " [index/point] seed_x seed_y seed_z"
+ << std::endl;
+ return( 1 );
+
+ } // fi
+ std::string input_image_filename = argv[ 1 ];
+ std::string output_image_filename = argv[ 2 ];
+ std::string output_signal_filename = argv[ 3 ];
+ TPixel init_threshold = std::atoi( argv[ 4 ] );
+ TPixel end_threshold = std::atoi( argv[ 5 ] );
+ TPixel delta = std::atoi( argv[ 6 ] );
+ TPixel minimum_threshold = std::atoi( argv[ 7 ] );
+ TLabel inside_value = std::atoi( argv[ 8 ] );
+ TLabel outside_value = std::atoi( argv[ 9 ] );
+ unsigned long signal_kernel_size = std::atoi( argv[ 10 ] );
+ double signal_threshold = std::atof( argv[ 11 ] );
+ double signal_influence = std::atof( argv[ 12 ] );
+ std::string seed_type = argv[ 13 ];
+ TInputImage::IndexType iseed;
+ TInputImage::PointType pseed;
+ for( unsigned int i = 0; i < Dim; ++i )
+ {
+ if( seed_type == "index" )
+ iseed[ i ] = std::atoi( argv[ 14 + i ] );
+ else
+ pseed[ i ] = std::atof( argv[ 14 + i ] );
+
+ } // rof
+
+ // Read image
+ itk::ImageFileReader< TInputImage >::Pointer input_image_reader =
+ itk::ImageFileReader< TInputImage >::New( );
+ input_image_reader->SetFileName( input_image_filename );
+
+ // Prepare filter
+ TFilter::Pointer filter = TFilter::New( );
+ filter->SetInput( input_image_reader->GetOutput( ) );
+ if( seed_type == "index" )
+ filter->SetSeed( iseed );
+ else
+ filter->SetSeed( pseed );
+ filter->SetThresholds( init_threshold, end_threshold, delta );
+ filter->SetMinimumThreshold( minimum_threshold );
+ filter->SetInsideValue( inside_value );
+ filter->SetOutsideValue( outside_value );
+ filter->SetSignalKernelSize( signal_kernel_size );
+ filter->SetSignalThreshold( signal_threshold );
+ filter->SetSignalInfluence( signal_influence );
+
+ // 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;
+ try
+ {
+ ts = std::chrono::high_resolution_clock::now( );
+ input_image_reader->Update( );
+ te = std::chrono::high_resolution_clock::now( );
+ tr = te - ts;
+ std::cout << "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
+ << "Mori time: " << tr.count( ) << " s" << std::endl
+ << "Optimum threshold: " << filter->GetOptimumThreshold( ) << std::endl
+ << "Number of thresholds: "
+ << filter->GetNumberOfEvaluatedThresholds( ) << std::endl;
+ }
+ catch( std::exception& err )
+ {
+ std::cerr << "Error caught: " << err.what( ) << std::endl;
+ return( 1 );
+
+ } // yrt
+
+ // Save output image
+ itk::ImageFileWriter< TLabelImage >::Pointer output_image_writer =
+ itk::ImageFileWriter< TLabelImage >::New( );
+ output_image_writer->SetInput( filter->GetThresholdedOutput( ) );
+ 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;
+ }
+ catch( std::exception& err )
+ {
+ std::cerr << "Error caught: " << err.what( ) << std::endl;
+ return( 1 );
+
+ } // yrt
+
+ // Save output signal
+ std::ofstream osignal( output_signal_filename.c_str( ) );
+ for(
+ unsigned long i = 0; i < filter->GetNumberOfEvaluatedThresholds( ); ++i
+ )
+ {
+ double x, y;
+ TFilter::TPeak p;
+ filter->GetSignalValues( i, x, y, p );
+ osignal << x << " " << y << std::endl;
+
+ } // rof
+ osignal.close( );
+ std::cout << "----------------------------------------------" << std::endl;
+
+ return( 0 );
+}
+
+// eof - $RCSfile$