examples/BronchiiInitialSegmentationWithMori.cxx

   1 #include <climits>
   2 #include <cstdlib>
   3 #include <fstream>
   4 #include <iostream>
   5 #include <string>
   6
   7 #include <itkImage.h>
   8 #include <itkImageFileReader.h>
   9 #include <itkImageFileWriter.h>
  10
  11 #include <fpa/Image/MoriFilter.h>
  12
  13 // -------------------------------------------------------------------------
  14 static const unsigned int Dim = 3;
  15 typedef short TPixel;
  16 typedef itk::Image< TPixel, Dim > TImage;
  17
  18 // -------------------------------------------------------------------------
  19 std::string GetFullPath( const std::string& filename )
  20 {
  21   /* On windows:
  22      #include <windows.h>
  23      TCHAR full_path[MAX_PATH];
  24      GetFullPathName(_T("foo.dat"), MAX_PATH, full_path, NULL);
  25   */
  26
  27   char* buffer = realpath( filename.c_str( ), NULL );
  28   std::string path = buffer;
  29   std::free( buffer );
  30   return( path );
  31 }
  32
  33 // -------------------------------------------------------------------------
  34 std::string GetFullPathToDirectory( const std::string& filename )
  35 {
  36   std::string path = GetFullPath( filename );
  37   std::size_t found = path.find_last_of( "/\\" );
  38   return( path.substr( 0, found + 1 ) );
  39 }
  40
  41 // -------------------------------------------------------------------------
  42 int main( int argc, char* argv[] )
  43 {
  44   // Command configuration
  45   if( argc < 3 )
  46   {
  47     std::cerr
  48       << "Usage: " << argv[ 0 ] << " input_image output_image"
  49       << std::endl;
  50     return( 1 );
  51
  52   } // fi
  53   std::string input_image_filename = GetFullPath( argv[ 1 ] );
  54   std::string output_image_filename = argv[ 2 ];
  55
  56   // Try to guess initial seed
  57   std::string seed_filename = GetFullPathToDirectory( argv[ 1 ] ) + "seed.txt";
  58   std::ifstream seed_str( seed_filename.c_str( ) );
  59   if( !seed_str )
  60   {
  61     std::cerr
  62       << "No \"seed.txt\" file in the same input image directory."
  63       << std::endl;
  64     return( 1 );
  65
  66   } // fi
  67   TImage::IndexType seed;
  68   seed_str >> seed[ 0 ] >> seed[ 1 ] >> seed[ 2 ];
  69
  70   // Read image
  71   typedef itk::ImageFileReader< TImage > TReader;
  72   TReader::Pointer reader = TReader::New( );
  73   reader->SetFileName( input_image_filename );
  74
  75   // Mori's algorithms
  76   typedef fpa::Image::MoriFilter< TImage, TImage > TFilter;
  77   TFilter::Pointer filter = TFilter::New( );
  78   filter->SetInput( reader->GetOutput( ) );
  79   filter->SetSeed( seed );
  80   filter->SetThresholdRange( -1024, 0 );
  81   filter->SetInsideValue( 1 );
  82   filter->SetOutsideValue( 0 );
  83
  84   // Write results
  85   typedef itk::ImageFileWriter< TImage > TWriter;
  86   TWriter::Pointer writer = TWriter::New( );
  87   writer->SetInput( filter->GetOutput( ) );
  88   writer->SetFileName( output_image_filename );
  89
  90   // Execute pipeline
  91   try
  92   {
  93     writer->Update( );
  94   }
  95   catch( std::exception& err )
  96   {
  97     std::cerr << "Error caught: " << err.what( ) << std::endl;
  98     return( 1 );
  99
 100   } // yrt
 101   return( 0 );
 102 }
 103
 104 // eof - $RCSfile$