appli/CTBronchi/RandomWalker.cxx

   1 #include <chrono>
   2 #include <itkImage.h>
   3 #include <itkImageFileReader.h>
   4 #include <itkImageFileWriter.h>
   5
   6 #include <fpa/Image/RandomWalker.h>
   7 #include <fpa/Image/Functors/Dijkstra/Gaussian.h>
   8 #include <ivq/ITK/ExtractLabelFunction.h>
   9 #include <ivq/ITK/ImageUnaryFunctionFilter.h>
  10
  11 // -------------------------------------------------------------------------
  12 const unsigned int Dim = 3;
  13 typedef short          TPixel;
  14 typedef unsigned short TLabel;
  15 typedef unsigned char  TBinary;
  16 typedef double         TScalar;
  17
  18 typedef itk::Image< TPixel, Dim > TInputImage;
  19 typedef itk::Image< TLabel, Dim > TLabelImage;
  20 typedef itk::Image< TBinary, Dim > TBinaryImage;
  21
  22 typedef fpa::Image::RandomWalker< TInputImage, TLabelImage, TScalar > TFilter;
  23 typedef fpa::Image::Functors::Dijkstra::Gaussian< TInputImage, TScalar > TWeight;
  24
  25 typedef ivq::ITK::ExtractLabelFunction< TLabel, TBinary > TLabelFunction;
  26 typedef ivq::ITK::ImageUnaryFunctionFilter< TLabelImage, TBinaryImage > TLabelExtractor;
  27
  28 // -------------------------------------------------------------------------
  29 int main( int argc, char* argv[] )
  30 {
  31   // Get arguments
  32   if( argc < 6 )
  33   {
  34     std::cerr
  35       << "Usage: " << argv[ 0 ] << std::endl
  36       << "   input_image label_image output_image" << std::endl
  37       << "   label beta(100)"
  38       << std::endl;
  39     return( 1 );
  40
  41   } // fi
  42   std::string input_image_filename = argv[ 1 ];
  43   std::string label_image_filename = argv[ 2 ];
  44   std::string output_image_filename = argv[ 3 ];
  45   TLabel label = TLabel( std::atoi( argv[ 4 ] ) );
  46   double beta = std::atof( argv[ 5 ] );
  47
  48   // Read images
  49   itk::ImageFileReader< TInputImage >::Pointer input_image_reader =
  50     itk::ImageFileReader< TInputImage >::New( );
  51   input_image_reader->SetFileName( input_image_filename );
  52
  53   itk::ImageFileReader< TLabelImage >::Pointer label_image_reader =
  54     itk::ImageFileReader< TLabelImage >::New( );
  55   label_image_reader->SetFileName( label_image_filename );
  56
  57   // Prepare weight
  58   TWeight::Pointer weight = TWeight::New( );
  59   weight->SetBeta( beta );
  60
  61   // Prepare filter
  62   TFilter::Pointer filter = TFilter::New( );
  63   filter->SetInput( input_image_reader->GetOutput( ) );
  64   filter->SetLabels( label_image_reader->GetOutput( ) );
  65   filter->SetWeightFunction( weight );
  66
  67   // Label extraction
  68   TLabelFunction::Pointer label_function = TLabelFunction::New( );
  69   label_function->SetLabel( label );
  70   label_function->SetInsideValue( 255 );
  71   label_function->SetOutsideValue( 0 );
  72
  73   TLabelExtractor::Pointer label_extractor = TLabelExtractor::New( );
  74   label_extractor->SetInput( filter->GetMarks( ) );
  75   label_extractor->SetFunction( label_function );
  76
  77
  78   // Show some information
  79   std::cout << "----------------------------------------------" << std::endl;
  80   std::cout << "Image: " << input_image_filename << std::endl;
  81
  82   // Execute pipeline
  83   std::chrono::time_point< std::chrono::high_resolution_clock > ts, te;
  84   std::chrono::duration< double > tr;
  85   try
  86   {
  87     ts = std::chrono::high_resolution_clock::now( );
  88     input_image_reader->Update( );
  89     te = std::chrono::high_resolution_clock::now( );
  90     tr = te - ts;
  91     std::cout << "Raw read time: " << tr.count( ) << " s" << std::endl;
  92
  93     ts = std::chrono::high_resolution_clock::now( );
  94     label_image_reader->Update( );
  95     te = std::chrono::high_resolution_clock::now( );
  96     tr = te - ts;
  97     std::cout << "Label read time: " << tr.count( ) << " s" << std::endl;
  98
  99     ts = std::chrono::high_resolution_clock::now( );
 100     filter->Update( );
 101     te = std::chrono::high_resolution_clock::now( );
 102     tr = te - ts;
 103     std::cout
 104       << "Labelling time: " << tr.count( ) << " s" << std::endl;
 105
 106     ts = std::chrono::high_resolution_clock::now( );
 107     label_extractor->Update( );
 108     te = std::chrono::high_resolution_clock::now( );
 109     tr = te - ts;
 110     std::cout
 111       << "Extract label time: " << tr.count( ) << " s" << std::endl;
 112   }
 113   catch( std::exception& err )
 114   {
 115     std::cerr << "Error caught: " << err.what( ) << std::endl;
 116     return( 1 );
 117
 118   } // yrt
 119
 120   // Save output image
 121   itk::ImageFileWriter< TBinaryImage >::Pointer output_image_writer =
 122     itk::ImageFileWriter< TBinaryImage >::New( );
 123   output_image_writer->SetInput( label_extractor->GetOutput( ) );
 124   output_image_writer->SetFileName( output_image_filename );
 125   try
 126   {
 127     ts = std::chrono::high_resolution_clock::now( );
 128     output_image_writer->Update( );
 129     te = std::chrono::high_resolution_clock::now( );
 130     tr = te - ts;
 131     std::cout << "Write time: " << tr.count( ) << " s" << std::endl;
 132   }
 133   catch( std::exception& err )
 134   {
 135     std::cerr << "Error caught: " << err.what( ) << std::endl;
 136     return( 1 );
 137
 138   } // yrt
 139   std::cout << "----------------------------------------------" << std::endl;
 140
 141   return( 0 );
 142 }
 143
 144 // eof - $RCSfile$