appli/examples/example_ImageAlgorithmDijkstra_03.cxx

   1 #include <cmath>
   2 #include <ctime>
   3 #include <deque>
   4 #include <fstream>
   5 #include <iostream>
   6 #include <iomanip>
   7 #include <limits>
   8 #include <map>
   9 #include <string>
  10
  11 #include <itkConstNeighborhoodIterator.h>
  12 #include <itkNeighborhoodIterator.h>
  13 #include <itkDanielssonDistanceMapImageFilter.h>
  14 #include <itkImage.h>
  15 #include <itkImageFileReader.h>
  16 #include <itkImageFileWriter.h>
  17 #include <itkImageToVTKImageFilter.h>
  18
  19 #include <itkMinimumMaximumImageCalculator.h>
  20 #include <itkInvertIntensityImageFilter.h>
  21
  22 #include <vtkPoints.h>
  23 #include <vtkCellArray.h>
  24 #include <vtkFloatArray.h>
  25 #include <vtkPolyData.h>
  26 #include <vtkPolyDataWriter.h>
  27 #include <vtkSmartPointer.h>
  28 #include <vtkImageMarchingCubes.h>
  29 #include <vtkLookupTable.h>
  30
  31 #include <fpa/Image/DijkstraWithSphereBacktracking.h>
  32 #include <fpa/VTK/ImageMPR.h>
  33 #include <fpa/VTK/Image3DObserver.h>
  34
  35 // -------------------------------------------------------------------------
  36 const unsigned int Dim = 3;
  37 typedef float                                TPixel;
  38 typedef float                                TScalar;
  39 typedef itk::Image< TPixel, Dim >            TImage;
  40 typedef itk::ImageToVTKImageFilter< TImage > TVTKImage;
  41
  42 typedef itk::ImageFileReader< TImage >          TImageReader;
  43 typedef itk::ImageFileWriter< TImage >    TImageWriter;
  44 typedef fpa::Image::DijkstraWithSphereBacktracking< TImage, TScalar > TDijkstra;
  45
  46 typedef fpa::VTK::ImageMPR TMPR;
  47 typedef fpa::VTK::Image3DObserver< TDijkstra, vtkRenderWindow > TDijkstraObs;
  48
  49 struct TBranch
  50 {
  51   double Length;
  52   TImage::PointType::VectorType V1;
  53   TImage::PointType::VectorType V2;
  54
  55   bool operator<( const TBranch& other ) const
  56     {
  57       return( other.Length < this->Length );
  58     }
  59 };
  60 typedef std::multiset< TBranch > TBranches;
  61
  62 // -------------------------------------------------------------------------
  63 int main( int argc, char* argv[] )
  64 {
  65   if( argc < 8 )
  66   {
  67     std::cerr
  68       << "Usage: " << argv[ 0 ]
  69       << " input_image x y z output_image output_imagej output_vtk"
  70       << " visual_debug"
  71       << std::endl;
  72     return( 1 );
  73
  74   } // fi
  75   std::string input_image_fn = argv[ 1 ];
  76   TImage::PointType seed_pnt;
  77   seed_pnt[ 0 ] = std::atof( argv[ 2 ] );
  78   seed_pnt[ 1 ] = std::atof( argv[ 3 ] );
  79   seed_pnt[ 2 ] = std::atof( argv[ 4 ] );
  80   std::string output_image_fn = argv[ 5 ];
  81   std::string output_imagej_fn = argv[ 6 ];
  82   std::string output_vtk_fn = argv[ 7 ];
  83   bool visual_debug = false;
  84   if( argc > 8 )
  85     visual_debug = ( std::atoi( argv[ 8 ] ) == 1 );
  86
  87   // Read image
  88   TImageReader::Pointer input_image_reader = TImageReader::New( );
  89   input_image_reader->SetFileName( input_image_fn );
  90   try
  91   {
  92     input_image_reader->Update( );
  93   }
  94   catch( itk::ExceptionObject& err )
  95   {
  96     std::cerr << "Error caught: " << err << std::endl;
  97     return( 1 );
  98
  99   } // yrt
 100   TImage::ConstPointer input_image = input_image_reader->GetOutput( );
 101
 102   // Show image
 103   TVTKImage::Pointer vtk_image = TVTKImage::New( );
 104   vtk_image->SetInput( input_image );
 105   vtk_image->Update( );
 106
 107   TMPR view;
 108   view.SetBackground( 0.3, 0.2, 0.8 );
 109   view.SetSize( 800, 800 );
 110   view.SetImage( vtk_image->GetOutput( ) );
 111
 112   /* TODO
 113      vtkSmartPointer< vtkImageMarchingCubes > mc =
 114      vtkSmartPointer< vtkImageMarchingCubes >::New( );
 115      mc->SetInputData( vtk_image->GetOutput( ) );
 116      mc->SetValue( 0, 1e-2 );
 117      mc->Update( );
 118      view.AddPolyData( mc->GetOutput( ), 1, 1, 1, 0.4 );
 119   */
 120
 121   // Allow some interaction
 122   view.Render( );
 123   if( visual_debug )
 124     view.Start( );
 125
 126   TImage::IndexType seed_idx;
 127   input_image->TransformPhysicalPointToIndex( seed_pnt, seed_idx );
 128   /* TODO
 129      std::cout << seed_idx << " " << seed_pnt << std::endl;
 130      seed_idx[ 0 ] = 256;
 131      seed_idx[ 1 ] = 313;
 132      seed_idx[ 2 ] = 381;
 133   */
 134
 135   // Extract paths
 136   TDijkstra::Pointer paths = TDijkstra::New( );
 137   paths->AddSeed( seed_idx, TScalar( 0 ) );
 138   paths->SetInput( input_image );
 139   paths->SetNeighborhoodOrder( 2 );
 140
 141   if( visual_debug )
 142   {
 143     // Configure observer
 144     TDijkstraObs::Pointer obs = TDijkstraObs::New( );
 145     obs->SetRenderWindow( view.GetWindow( ) );
 146     paths->AddObserver( itk::AnyEvent( ), obs );
 147     paths->ThrowEventsOn( );
 148   }
 149   else
 150     paths->ThrowEventsOff( );
 151   std::clock_t start = std::clock( );
 152   paths->Update( );
 153   std::clock_t end = std::clock( );
 154   double seconds = double( end - start ) / double( CLOCKS_PER_SEC );
 155   std::cout << "Paths extraction time = " << seconds << std::endl;
 156
 157   // Create polydata
 158   vtkSmartPointer< vtkPoints > points =
 159     vtkSmartPointer< vtkPoints >::New( );
 160   vtkSmartPointer< vtkCellArray > cells =
 161     vtkSmartPointer< vtkCellArray >::New( );
 162   vtkSmartPointer< vtkFloatArray > scalars =
 163     vtkSmartPointer< vtkFloatArray >::New( );
 164
 165   TDijkstra::TMarkImage::Pointer new_marks = TDijkstra::TMarkImage::New( );
 166   new_marks->SetLargestPossibleRegion( input_image->GetLargestPossibleRegion( ) );
 167   new_marks->SetRequestedRegion( input_image->GetRequestedRegion( ) );
 168   new_marks->SetBufferedRegion( input_image->GetBufferedRegion( ) );
 169   new_marks->SetOrigin( input_image->GetOrigin( ) );
 170   new_marks->SetSpacing( input_image->GetSpacing( ) );
 171   new_marks->SetDirection( input_image->GetDirection( ) );
 172   new_marks->Allocate( );
 173   new_marks->FillBuffer( 0 );
 174
 175   const TDijkstra::TMarkImage* marks = paths->GetOutputMarkImage( );
 176   TDijkstra::TMark max_mark = paths->GetNumberOfBranches( );
 177   const TDijkstra::TVertices& endpoints = paths->GetEndPoints( );
 178   const TDijkstra::TVertices& bifurcations = paths->GetBifurcationPoints( );
 179   const TDijkstra::TTree& tree = paths->GetFullTree( );
 180   const TDijkstra::TTree& reduced_tree = paths->GetReducedTree( );
 181   TDijkstra::TVertices::const_iterator epIt = endpoints.begin( );
 182
 183   TBranches branches;
 184   TImage::PointType ori = input_image->GetOrigin( );
 185
 186   TDijkstra::TTree::const_iterator rIt = reduced_tree.begin( );
 187   for( ; rIt != reduced_tree.end( ); ++rIt )
 188   {
 189     TDijkstra::TTree::const_iterator tIt = tree.find( rIt->first );
 190
 191     // Prepare branch "a la ImageJ"
 192     TBranch branch;
 193     TImage::PointType p1, p2;
 194     input_image->TransformIndexToPhysicalPoint( rIt->second.first, p1 );
 195     input_image->TransformIndexToPhysicalPoint( rIt->first, p2 );
 196     branch.V1 = p1 - ori;
 197     branch.V2 = p2 - ori;
 198     branch.Length = double( 0 );
 199
 200     double pd =
 201       ( double( tIt->second.second ) - double( 1 ) ) /
 202       ( double( max_mark ) - double( 1 ) );
 203     bool start = true;
 204     TImage::PointType prev;
 205     do
 206     {
 207       TDijkstra::TVertex idx = tIt->first;
 208       new_marks->SetPixel( idx, 255 );
 209       TImage::PointType pnt;
 210       input_image->TransformIndexToPhysicalPoint( idx, pnt );
 211       points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
 212       scalars->InsertNextTuple1( pd );
 213       if( !start )
 214       {
 215         cells->InsertNextCell( 2 );
 216         cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
 217         cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
 218         branch.Length += prev.EuclideanDistanceTo( pnt );
 219
 220       } // fi
 221       start = false;
 222       prev = pnt;
 223       tIt = tree.find( tIt->second.first );
 224
 225     } while( tIt->first != rIt->second.first );
 226
 227     // Last point
 228     TDijkstra::TVertex idx = tIt->first;
 229     new_marks->SetPixel( idx, 255 );
 230     TImage::PointType pnt;
 231     input_image->TransformIndexToPhysicalPoint( idx, pnt );
 232     points->InsertNextPoint( pnt[ 0 ], pnt[ 1 ], pnt[ 2 ] );
 233     scalars->InsertNextTuple1( pd );
 234     if( !start )
 235     {
 236       cells->InsertNextCell( 2 );
 237       cells->InsertCellPoint( points->GetNumberOfPoints( ) - 2 );
 238       cells->InsertCellPoint( points->GetNumberOfPoints( ) - 1 );
 239       branch.Length += prev.EuclideanDistanceTo( pnt );
 240
 241     } // fi
 242     branches.insert( branch );
 243
 244   } // rof
 245
 246   std::ofstream bout( output_imagej_fn.c_str( ) );
 247   if( !bout )
 248   {
 249     std::cerr << "Error: could not open " << output_imagej_fn << std::endl;
 250     return( 1 );
 251
 252   } // fi
 253   int i = 1;
 254   for( TBranches::const_iterator bIt = branches.begin( ); bIt != branches.end( ); ++bIt, ++i )
 255   {
 256     bout
 257       << std::setiosflags( std::ios::fixed) << std::setprecision( 3 )
 258       << i << "\t1.000\t"
 259       << bIt->Length << "\t"
 260       << bIt->V1[ 0 ] << "\t"
 261       << bIt->V1[ 1 ] << "\t"
 262       << bIt->V1[ 2 ] << "\t"
 263       << bIt->V2[ 0 ] << "\t"
 264       << bIt->V2[ 1 ] << "\t"
 265       << bIt->V2[ 2 ] << "\t"
 266       << ( bIt->V2 - bIt->V1 ).GetNorm( )
 267       << std::endl;
 268
 269   } // rof
 270   bout.close( );
 271
 272   vtkSmartPointer< vtkPolyData > vtk_tree =
 273     vtkSmartPointer< vtkPolyData >::New( );
 274   vtk_tree->SetPoints( points );
 275   vtk_tree->SetLines( cells );
 276   vtk_tree->GetPointData( )->SetScalars( scalars );
 277
 278   view.AddPolyData( vtk_tree );
 279   view.Render( );
 280   if( visual_debug )
 281     view.Start( );
 282
 283   vtkSmartPointer< vtkPolyDataWriter > writer =
 284     vtkSmartPointer< vtkPolyDataWriter >::New( );
 285   writer->SetInputData( vtk_tree );
 286   writer->SetFileName( output_vtk_fn.c_str( ) );
 287   writer->Update( );
 288
 289   itk::ImageFileWriter< TDijkstra::TMarkImage >::Pointer marks_writer =
 290     itk::ImageFileWriter< TDijkstra::TMarkImage >::New( );
 291   marks_writer->SetInput( new_marks );
 292   marks_writer->SetFileName( output_image_fn );
 293   marks_writer->Update( );
 294
 295   TImageWriter::Pointer dijkstra_writer =
 296     TImageWriter::New( );
 297   dijkstra_writer->SetInput( paths->GetOutput( ) );
 298   dijkstra_writer->SetFileName( "dijkstra.mhd" );
 299   dijkstra_writer->Update( );
 300
 301   return( 0 );
 302 }
 303
 304 // eof - $RCSfile$