examples/BronchiiInitialSegmentationWithBinaryThresholdRegionGrow.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/RegionGrow.h>
  12 #include <fpa/Image/Functors/RegionGrow/BinaryThreshold.h>
  13
  14 // -------------------------------------------------------------------------
  15 static const unsigned int Dim = 3;
  16 typedef short TPixel;
  17 typedef itk::Image< TPixel, Dim > TImage;
  18
  19 // -------------------------------------------------------------------------
  20 std::string GetFullPath( const std::string& filename )
  21 {
  22   /* On windows:
  23      #include <windows.h>
  24      TCHAR full_path[MAX_PATH];
  25      GetFullPathName(_T("foo.dat"), MAX_PATH, full_path, NULL);
  26   */
  27
  28   char* buffer = realpath( filename.c_str( ), NULL );
  29   std::string path = buffer;
  30   std::free( buffer );
  31   return( path );
  32 }
  33
  34 // -------------------------------------------------------------------------
  35 std::string GetFullPathToDirectory( const std::string& filename )
  36 {
  37   std::string path = GetFullPath( filename );
  38   std::size_t found = path.find_last_of( "/\\" );
  39   return( path.substr( 0, found + 1 ) );
  40 }
  41
  42 // -------------------------------------------------------------------------
  43 int main( int argc, char* argv[] )
  44 {
  45   // Command configuration
  46   if( argc < 5 )
  47   {
  48     std::cerr
  49       << "Usage: " << argv[ 0 ] << " input_image output_image lower upper"
  50       << std::endl;
  51     return( 1 );
  52
  53   } // fi
  54   std::string input_image_filename = GetFullPath( argv[ 1 ] );
  55   std::string output_image_filename = argv[ 2 ];
  56   std::string output_auxiliary_image_filename = output_image_filename + "_aux.mhd";
  57   TPixel lower = std::atoi( argv[ 3 ] );
  58   TPixel upper = std::atoi( argv[ 4 ] );
  59
  60   // Try to guess initial seed
  61   std::string seed_filename = GetFullPathToDirectory( argv[ 1 ] ) + "seed.txt";
  62   std::ifstream seed_str( seed_filename.c_str( ) );
  63   if( !seed_str )
  64   {
  65     std::cerr
  66       << "No \"seed.txt\" file in the same input image directory."
  67       << std::endl;
  68     return( 1 );
  69
  70   } // fi
  71   TImage::IndexType seed;
  72   seed_str >> seed[ 0 ] >> seed[ 1 ] >> seed[ 2 ];
  73   seed_str.close( );
  74
  75   // Read image
  76   typedef itk::ImageFileReader< TImage > TReader;
  77   TReader::Pointer reader = TReader::New( );
  78   reader->SetFileName( input_image_filename );
  79
  80   // Growing predicate
  81   typedef fpa::Image::Functors::RegionGrow::BinaryThreshold< TImage, TImage::PixelType > TPredicate;
  82   TPredicate::Pointer predicate = TPredicate::New( );
  83   predicate->SetLower( lower );
  84   predicate->SetUpper( upper );
  85
  86   // RegionGrow algorithm
  87   typedef fpa::Image::RegionGrow< TImage, TImage > TFilter;
  88   TFilter::Pointer filter = TFilter::New( );
  89   filter->SetInput( reader->GetOutput( ) );
  90   filter->AddSeed( seed, 1 );
  91   filter->SetInsideValue( 1 );
  92   filter->SetOutsideValue( 0 );
  93   filter->SetGrowFunction( predicate );
  94
  95   // Write results
  96   typedef itk::ImageFileWriter< TImage > TWriter;
  97   TWriter::Pointer writer = TWriter::New( );
  98   writer->SetInput( filter->GetOutput( ) );
  99   writer->SetFileName( output_image_filename );
 100
 101   // Execute pipeline
 102   try
 103   {
 104     writer->Update( );
 105   }
 106   catch( std::exception& err )
 107   {
 108     std::cerr << "Error caught: " << err.what( ) << std::endl;
 109     return( 1 );
 110
 111   } // yrt
 112
 113   return( 0 );
 114 }
 115
 116 // eof - $RCSfile$