appli/TempAirwaysAppli/TempAirwaysAppli.cxx

   1 #include <iostream>
   2 #include <cstdlib>
   3 #include <sstream>
   4
   5 #include <boost/filesystem.hpp>
   6 #include <boost/program_options.hpp>
   7
   8 #include "vec3.h"
   9 #include "airwaysTree.h"
  10
  11 #include <cpPlugins/Interface.h>
  12 #include <cpPlugins/Workspace.h>
  13
  14 using namespace airways;
  15 namespace po = boost::program_options;
  16
  17 namespace
  18 {
  19   const size_t ERROR_IN_COMMAND_LINE = 1;
  20   const size_t SUCCESS = 0;
  21   const size_t ERROR_UNHANDLED_EXCEPTION = 2;
  22 } // namespace
  23
  24 typedef std::vector< AirwaysTree > AirwaysVector;
  25
  26 #include <itkCastImageFilter.h>
  27
  28 // Auxiliar struct to save info for execution.
  29 typedef void* TImagePointer;
  30 struct TreeInfo{
  31
  32   TreeInfo( )
  33     {
  34       this->myWorkspace = new cpPlugins::Workspace( );
  35     }
  36   ~TreeInfo( )
  37     {
  38       /*
  39         if( this->IsMyWorkspace )
  40         delete this->myWorkspace;
  41       */
  42     }
  43
  44   void CastImage( )
  45     {
  46       auto image = this->myWorkspace->GetFilter( "reader" )->GetOutputData( "Output" )->GetITK< itk::Image< unsigned char, 3 > >( );
  47       typedef itk::CastImageFilter< itk::Image< unsigned char, 3 >, TInputImage > _TCast;
  48       _TCast::Pointer cast = _TCast::New( );
  49       cast->SetInput( image );
  50       cast->Update( );
  51       this->Image = cast->GetOutput( );
  52       this->Image->DisconnectPipeline( );
  53     }
  54
  55   TInputImage::Pointer Image;
  56   cpPlugins::Workspace* myWorkspace;
  57   bool IsMyWorkspace;
  58   Vec3 seed;
  59   std::string folderpath_pigResults;
  60   std::string pig_name;
  61   std::string image_name;
  62
  63 };
  64 // Constants
  65 unsigned char red[3]   = { 255, 0, 0 };
  66 unsigned char green[3] = { 0, 255, 0 };
  67 unsigned char blue[3]  = { 0, 0, 255 };
  68 unsigned char yellow[3]= { 255, 255, 0 };
  69 unsigned char purple[3]= { 255, 0, 255 };
  70 unsigned char cyan[3]= { 0, 255, 255 };
  71
  72 cpPlugins::Interface myPlugins;
  73
  74 // -------------------------------------------------------------------------
  75 void Load_cpPlugins( const std::string& plugins );
  76 void CreateResultDirectory(AirwaysTree tree);
  77 void DrawVTKLinesFromTree(AirwaysTree& tree, const std::string filename, bool common);
  78 AirwaysTree& CreateAirwaysTreeFromSegmentation(Vec3 seed, TInputImage* input_image, cpPlugins::Workspace& ws );
  79 vector<TreeInfo> ReadInputFile(const char* filename);
  80 void printCommonTreeBetweenTwoTrees(AirwaysTree tree_A, AirwaysTree tree_B, std::vector< std::pair< std::pair<Node*, Node*>, std::pair<Node*, Node*> > > vector_pair_edges_A_to_B, unsigned int Q, unsigned int F);
  81 void printMatchingResultToFile(AirwaysTree tree_A, AirwaysTree tree_B, std::map< unsigned int, std::vector<Node*> > map_A_to_B, std::map< unsigned int, std::vector<Node*> > map_B_to_A, unsigned int Q, unsigned int F);
  82 void createLinesAndPointsForVTK(const Node* node, vtkSmartPointer<vtkPoints>& pts,vtkSmartPointer<vtkCellArray>& lines, vtkSmartPointer<vtkUnsignedCharArray>& colors, bool common, bool isRoot);
  83
  84 // -------------------------------------------------------------------------
  85 int main( int argc, char* argv[] )
  86 {
  87   Load_cpPlugins( "./plugins.cfg" );
  88
  89   try
  90   {
  91     // Define and parse the program options
  92     po::options_description desc("Options");
  93     desc.add_options()("use_file", po::value<std::string>(), "Adds the filepath containing the file to be used in creaAirwaysTree -- Mandatory")
  94       ("build_trees","Creates trees from a given filepath (arg) and stores it in a .vtk file")
  95       ("subtree_levels", po::value<int>(),"Get a subtree(s) by levels - result: a vtk and reconstructed img .mhd")
  96       ("subtree_length", po::value<float>(),"Get a subtree(s) by length - result: a vtk and reconstructed img .mhd")
  97       ("subtree_diameter", po::value<float>(),"Get a subtree(s) by diameter - result: a vtk and reconstructed img .mhd")
  98       ("compare_trees", "Compare the trees given in the input file or the subtrees using an option - result: a vtk and reconstructed img .mhd");
  99     //TODO: Fix image segmentation. ("segment_images",  "Creates a binary image corresponding to the segmentation of of a given original image (arg) and seed (arg), saves it to a .mhd file and uses it for subsequent operations")
 100     po::variables_map vm;
 101     try
 102     {
 103       std::string fileName;
 104       vector<TreeInfo> treeInfoVector;
 105       AirwaysVector aVector;
 106       TImagePointer segmentationImage;
 107       Vec3 seed;
 108       po::store(po::parse_command_line(argc, argv, desc), vm); // can throw
 109       if (vm.count("use_file"))
 110       {
 111         fileName = vm["use_file"].as<std::string>();
 112         treeInfoVector = ReadInputFile(fileName.c_str());
 113       }
 114
 115       if(vm.count("segment_images"))
 116       {
 117       }
 118
 119       // Build trees option
 120       if (vm.count("build_trees"))
 121       {
 122         for(unsigned int i = 0; i < treeInfoVector.size(); ++ i){
 123           TreeInfo info = treeInfoVector[i];
 124           try
 125           {
 126             info.myWorkspace->Execute( "eb" );
 127           }
 128           catch( itk::ExceptionObject& err )
 129           {
 130             std::cerr << "Error: " << err << std::endl;
 131             std::exit( 1 );
 132
 133           } // fi
 134           info.CastImage( );
 135           AirwaysTree tree = CreateAirwaysTreeFromSegmentation( info.seed, info.Image, *(info.myWorkspace ));
 136           tree.SetResultPath(info.folderpath_pigResults);
 137           tree.SetImageName(info.image_name);
 138           aVector.push_back(tree);
 139         }
 140         for (unsigned int i = 0; i < aVector.size(); ++i)
 141         {
 142           CreateResultDirectory(aVector[i]);
 143           std::string fullPath = aVector[i].GetResultPath() + "/" + aVector[i].GetImageName() + ".vtk";
 144           DrawVTKLinesFromTree(aVector[i], fullPath, false);
 145
 146         } //for
 147       } //if
 148
 149       // Subtree levels option
 150       if (vm.count("subtree_levels"))
 151       {
 152       } //if
 153       else if (vm.count("subtree_length"))
 154       {
 155       } //if
 156       else if (vm.count("subtree_diameter"))
 157       {
 158       } //if
 159
 160       if (vm.count("compare_trees"))
 161       {
 162         std::cout << "Option: Compare trees" << std::endl;
 163         /**
 164          * this piece of code only test in the case of two trees, so it can be replaced
 165          * to a code which does a cascade
 166          */
 167
 168         //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 169         //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 170         //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 171         //CODIGO DE COMPARACIÓN DE ARBOLES
 172         //std::cout << "Comparing trees ..." << std::endl;
 173         //aVector[0].CompareTrees(aVector[1]);
 174         //std::cout << "Comparing trees ... OK" << std::endl;
 175
 176         std::cout << "Tree A ... " << std::endl;
 177         //aVector[0].printNodeAndChildrenIds();
 178         std::cout << "Tree A ... OK" << std::endl;
 179
 180         std::cout << "Tree B ... " << std::endl;
 181         //aVector[1].printNodeAndChildrenIds();
 182         std::cout << "Tree B ... OK" << std::endl;
 183
 184         std::cout << "Comparing trees Orkisz-Morales..." << std::endl;
 185         // Vectors to save the common and uncommon nodes
 186         vec_nodes commonA;
 187         vec_nodes commonB;
 188         vec_nodes nonCommonA;
 189         vec_nodes nonCommonB;
 190         std::map< unsigned int, std::vector<Node*> > map_A_to_B;
 191         std::map< unsigned int, std::vector<Node*> > map_B_to_A;
 192         std::vector< std::pair< std::pair<Node*, Node*>, std::pair<Node*, Node*> > > vector_pair_edges_A_to_B;
 193
 194         // Input parameter for comparison
 195         unsigned int Q = 1; // Corresponds to the depth to select "fathers" nodes
 196         unsigned int F = 1; // Correspond to the depth to select "family" nodes
 197         std::cout << "Q = " << Q << std::endl;
 198         std::cout << "F = " << F << std::endl;
 199
 200         clock_t before_compare = clock();
 201         aVector[0].CompareTreesOrkiszMorales(aVector[1], Q, F, commonA, commonB, nonCommonA, nonCommonB, map_A_to_B, map_B_to_A, vector_pair_edges_A_to_B);
 202         clock_t after_compare = clock();
 203         double compare_time = double(after_compare - before_compare) / CLOCKS_PER_SEC;
 204         std::cout << "Matching time: " << compare_time << std::endl;
 205
 206         // Print the common tree with common edges
 207         printCommonTreeBetweenTwoTrees(aVector[0], aVector[1], vector_pair_edges_A_to_B, Q, F);
 208         printMatchingResultToFile(aVector[0], aVector[1], map_A_to_B, map_B_to_A, Q, F);
 209         //printSeparatedCommonTrees(aVector[0], aVector[1], vector_pair_edges_A_to_B, Q, F);
 210         //reconstructAndSaveCommonTrees(aVector[0], aVector[1], vector_pair_edges_A_to_B, Q, F);
 211
 212         // Print all the maps that have more that two connections
 213         std::cout << "Printing multiple relation A to B. Total relations: " << map_A_to_B.size() << std::endl;
 214         for(std::map< unsigned int, std::vector<Node*> >::iterator it_map_A_to_B = map_A_to_B.begin(); it_map_A_to_B != map_A_to_B.end(); ++it_map_A_to_B)
 215         {
 216           if((*it_map_A_to_B).second.size() > 1)
 217           {
 218             std::cout << "Multiple relation A to B with size:" << (*it_map_A_to_B).second.size() << ", from Id:" << (*it_map_A_to_B).first << std::endl;
 219             for(std::vector<Node*>::iterator it_node = (*it_map_A_to_B).second.begin(); it_node != (*it_map_A_to_B).second.end(); ++it_node)
 220             {
 221               std::cout << "Id: " << (*it_node)->GetId() << std::endl;
 222             }
 223           }
 224         }
 225         std::cout << "Printing multiple relation A to B ... OK" << std::endl;
 226
 227         std::cout << "Printing multiple relation B to A. Total relations: " << map_B_to_A.size() << std::endl;
 228         for(std::map< unsigned int, std::vector<Node*> >::iterator it_map_B_to_A = map_B_to_A.begin(); it_map_B_to_A != map_B_to_A.end(); ++it_map_B_to_A)
 229         {
 230           if((*it_map_B_to_A).second.size() > 1)
 231           {
 232             std::cout << "Multiple relation B to A with size:" << (*it_map_B_to_A).second.size() << ", from Id:" << (*it_map_B_to_A).first << std::endl;
 233             for(std::vector<Node*>::iterator it_node = (*it_map_B_to_A).second.begin(); it_node != (*it_map_B_to_A).second.end(); ++it_node)
 234             {
 235               std::cout << "Id: " << (*it_node)->GetId() << std::endl;
 236             }
 237           }
 238         }
 239         std::cout << "Printing multiple relation B to A  ... OK" << std::endl;
 240
 241         // Mark only the common nodes
 242         aVector[0].UnMarkAll();
 243         aVector[1].UnMarkAll();
 244
 245         // --------------------------------------
 246         // ------ Get common paths marked -------
 247         // --------------------------------------
 248
 249         /*
 250           std::string path_folder = "/run/media/alfredo/Data/Pulmones/results/airwaysGraphs/comparisonResutls/probes/";
 251           std::string suffix_vtk = ".vtk";
 252           std::string name_tree = "TreeA_dP2P";
 253           int iteration = 1;
 254           for(vec_nodes::iterator it_A = commonA.begin(); it_A != commonA.end(); ++it_A)
 255           {
 256           aVector[0].MarkPathFromNodeToNode(aVector[0].GetRoot(), (*it_A));
 257
 258           std::stringstream filepath_actualIteration;
 259           filepath_actualIteration << path_folder << name_tree << "__" << iteration << "_idA_" << (*it_A)->GetId() << suffix_vtk;
 260
 261           DrawVTKLinesFromTree(aVector[0], filepath_actualIteration.str(), true);
 262           ++iteration;
 263           }
 264
 265           iteration = 1;
 266           name_tree = "TreeB_dP2P";
 267           for(vec_nodes::iterator it_B = commonB.begin(); it_B != commonB.end(); ++it_B)
 268           {
 269           aVector[1].MarkPathFromNodeToNode(aVector[1].GetRoot(), (*it_B));
 270
 271           std::stringstream filepath_actualIteration;
 272           filepath_actualIteration << path_folder << name_tree << "__" << iteration << "_idB_" << (*it_B)->GetId() << suffix_vtk;
 273
 274           DrawVTKLinesFromTree(aVector[1], filepath_actualIteration.str(), true);
 275           ++iteration;
 276           }
 277         */
 278
 279         // --------------------------------------
 280         // --------------------------------------
 281
 282         /*
 283         //XXXXXXXXXXXXXXXXXXXXXXXXXXXX
 284         //1. PRINT EACH NODE OF EACH TREE AND SAVE IT USING AS NAME ITS ID
 285
 286         // Tree A
 287         for(int i = 2; i < aVector[0].GetWeight(); ++i)
 288         {
 289         //std::cout << "Writing idA: " << i << std::endl;
 290         AirwaysTree* tree_id = aVector[0].GetSingleDetachedTreeNodeById(i);
 291         //std::cout << "Got id: " << i << ", numberOfNodes: " << tree_id->GetWeight() <<  std::endl;
 292         if(tree_id)
 293         {
 294         std::stringstream filepath_actualIteration;
 295         filepath_actualIteration << aVector[0].GetResultPath() << "/" << aVector[0].GetImageName() << "_id_" << i << suffix_vtk;
 296         DrawVTKLinesFromTree(*tree_id, filepath_actualIteration.str(), false);
 297         delete(tree_id);
 298         }
 299         else
 300         std::cout << "Tree NULL" << std::endl;
 301         }
 302
 303         // Tree B
 304         for(int i = 2; i < aVector[1].GetWeight(); ++i)
 305         {
 306         //std::cout << "Writing idA: " << i << std::endl;
 307         AirwaysTree* tree_id = aVector[1].GetSingleDetachedTreeNodeById(i);
 308         //std::cout << "Got id: " << i << ", numberOfNodes: " << tree_id->GetWeight() <<  std::endl;
 309         if(tree_id)
 310         {
 311         std::stringstream filepath_actualIteration;
 312         filepath_actualIteration << aVector[1].GetResultPath() << "/" << aVector[1].GetImageName() << "_id_" << i << suffix_vtk;
 313         DrawVTKLinesFromTree(*tree_id, filepath_actualIteration.str(), false);
 314         delete(tree_id);
 315         }
 316         else
 317         std::cout << "Tree NULL" << std::endl;
 318         }
 319
 320         std::cout << "Comparing trees Orkisz-Morales... OK" << std::endl;
 321
 322         */
 323
 324         //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 325         //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 326         //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 327
 328         /*// AMP
 329           aVector[0].SubIsomorphism(aVector[1]);
 330
 331           std::cout << "Flag after SubIsomorphism" << std::endl;
 332           std::string fullPathA = aVector[0].GetResultPath() + "/" + aVector[0].GetImageName() + "_CMP.vtk";
 333           std::string fullPathB = aVector[1].GetResultPath() + "/" + aVector[1].GetImageName() + "_CMP.vtk";
 334           DrawVTKLinesFromTree(aVector[0], fullPathA, true);
 335           DrawVTKLinesFromTree(aVector[1], fullPathB, true);
 336
 337           std::cout << "Flag after write vtk" << std::endl;
 338           TInputImage::Pointer imgA, imgB;
 339           aVector[0].ImageReconstruction(imgA);
 340           std::cout << "Flag after Reconstruction A" << std::endl;
 341
 342           aVector[1].ImageReconstruction(imgB);
 343           std::cout << "Flag after Reconstruction B" << std::endl;
 344
 345           std::string fullPathA_mhd = aVector[0].GetResultPath() + "/" + aVector[0].GetImageName() + "_CMP.vtk";
 346           std::string fullPathB_mhd = aVector[1].GetResultPath() + "/" + aVector[1].GetImageName() + "_CMP.vtk";
 347           WriteImage(imgA, fullPathA_mhd);
 348           WriteImage(imgB, fullPathB_mhd);
 349
 350           //AMP*/
 351       }
 352       po::notify(vm); // throws on error, so do after help in case
 353     }
 354     catch (std::exception& e)
 355     {
 356       std::cerr << "Unhandled Exception reached the top of main: " << e.what() << ", application will now exit" << std::endl;
 357       return ERROR_UNHANDLED_EXCEPTION;
 358     } // yrt
 359   }
 360   catch (std::exception& e)
 361   {
 362     std::cerr << "Unhandled Exception reached the top of main: " << e.what() << ", application will now exit" << std::endl;
 363     return ERROR_UNHANDLED_EXCEPTION;
 364   } // yrt
 365   return( 0 );
 366 }
 367
 368 // -------------------------------------------------------------------------
 369 void Load_cpPlugins( const std::string& plugins )
 370 {
 371   myPlugins.LoadConfiguration( plugins );
 372 }
 373
 374 // -------------------------------------------------------------------------
 375 void CreateResultDirectory(AirwaysTree tree)
 376 {
 377   boost::filesystem::path dir(tree.GetResultPath());
 378   if (boost::filesystem::create_directories(dir))
 379   {
 380     std::cout << "FolderName = " << tree.GetResultPath() << " has been created" << std::endl;
 381   } //if
 382   else
 383     std::cout << "FolderName = " << tree.GetResultPath() << " already exists" << std::endl;
 384 }
 385
 386 // -------------------------------------------------------------------------
 387 void DrawVTKLinesFromTree(AirwaysTree& tree, const std::string filepath, bool common)
 388 {
 389   // Create the array of points, lines, and colors
 390   vtkSmartPointer<vtkPoints> pts = vtkSmartPointer<vtkPoints>::New();
 391   vtkSmartPointer<vtkCellArray> lines = vtkSmartPointer<vtkCellArray>::New();
 392   vtkSmartPointer<vtkUnsignedCharArray> colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
 393   colors->SetNumberOfComponents(3);
 394   colors->SetName("Colors");
 395
 396   //vtk sphere for sources
 397   //vtkSmartPointer<vtkSphereSource> sphereSource = vtkSmartPointer<vtkSphereSource>::New();
 398   //Vec3 root = tree.GetRoot()->GetCoords();
 399   //sphereSource->SetCenter(root[0], root[1], root[2]);
 400   //sphereSource->SetRadius(1);
 401   //UndirectedGraph
 402
 403   srand(time(NULL));
 404   unsigned int id = 1;
 405
 406   // Create and fill the points, lines, and color vectors
 407   //CalculateVTKLinesFromEdges(tree.GetRoot(), 0, id, pts, lines, colors, common);
 408   pts->SetNumberOfPoints(tree.GetWeight()+1);
 409   createLinesAndPointsForVTK(tree.GetRoot(), pts, lines, colors, common, true);
 410
 411   // Create the polydata
 412   vtkSmartPointer<vtkPolyData> linesPolyData = vtkSmartPointer<vtkPolyData>::New();
 413
 414   // Set the points, lines, and colors
 415   linesPolyData->SetPoints(pts);
 416   linesPolyData->SetLines(lines);
 417   linesPolyData->GetCellData()->SetScalars(colors);
 418
 419   // Write the file
 420   vtkSmartPointer<vtkPolyDataWriter> writer = vtkSmartPointer<vtkPolyDataWriter>::New();
 421   writer->SetFileName(filepath.c_str());
 422
 423 #if VTK_MAJOR_VERSION <= 5
 424   writer->SetInput(linesPolyData);
 425 #else
 426   writer->SetInputData(linesPolyData);
 427 #endif
 428   writer->Write();
 429
 430   //The following code is to test the vtk polydata and visualize it
 431   /*    // Visualize
 432         vtkSmartPointer<vtkPolyDataMapper> mapper =
 433         vtkSmartPointer<vtkPolyDataMapper>::New();
 434         #if VTK_MAJOR_VERSION <= 5
 435         mapper->SetInput(linesPolyData);
 436         #else
 437         mapper->SetInputData(linesPolyData);
 438         #endif
 439         vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
 440         actor->SetMapper(mapper);
 441
 442         //sphere
 443         vtkSmartPointer<vtkPolyDataMapper> mapperSphere = vtkSmartPointer<
 444         vtkPolyDataMapper>::New();
 445         mapperSphere->SetInputConnection(sphereSource->GetOutputPort());
 446
 447         vtkSmartPointer<vtkActor> actorSphere = vtkSmartPointer<vtkActor>::New();
 448         actorSphere->SetMapper(mapperSphere);
 449         //end sphere
 450
 451         vtkSmartPointer<vtkRenderer> renderer = vtkSmartPointer<vtkRenderer>::New();
 452         vtkSmartPointer<vtkRenderWindow> renderWindow = vtkSmartPointer<
 453         vtkRenderWindow>::New();
 454         renderWindow->AddRenderer(renderer);
 455         vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
 456         vtkSmartPointer<vtkRenderWindowInteractor>::New();
 457         renderWindowInteractor->SetRenderWindow(renderWindow);
 458         renderer->AddActor(actorSphere);
 459         renderer->AddActor(actor);
 460
 461         renderWindow->Render();
 462         renderWindowInteractor->Start();*/
 463 }
 464
 465 // -------------------------------------------------------------------------
 466 #include <fpa/Base/ImageSkeleton.h>
 467 #include <fpa/Image/MinimumSpanningTree.h>
 468 #include <cpExtensions/DataStructures/ImageIndexesContainer.h>
 469 #include <itkImage.h>
 470 #include <queue>
 471
 472 template< class TImage, class TVertex >
 473 Node* FAVertexToNode( TVertex vertex, TImage* image )
 474 {
 475   //The FrontAlgorithms Vertex is an TImageType::IndexType
 476   typename TImage::PointType point;
 477   image->TransformIndexToPhysicalPoint( vertex, point );
 478   Vec3 alfPoint(point[0],point[1],point[2]);
 479   return new Node(alfPoint);
 480 }
 481
 482 AirwaysTree& ConvertFilterToAirwaysTree( TInputImage* input_image, cpPlugins::Workspace& ws )
 483 {
 484   typedef
 485     fpa::Base::ImageSkeleton< fpa::Image::MinimumSpanningTree< 3 > >
 486     TFASkeleton;
 487   typedef TFASkeleton::TVertex    TVertexFA;
 488   typedef TFASkeleton::TVertexCmp TVertexCompareFA;
 489   typedef cpExtensions::DataStructures::ImageIndexesContainer< 3 > TVerticesFA;
 490
 491   typedef Node TVertexAirways;
 492   typedef Edge TEdgeAirways;
 493   typedef pair_posVox_rad TSkelePoint;
 494   typedef vec_pair_posVox_rad TSkelePoints;
 495   typedef std::map< TVertexFA, TVertexAirways*, TVertexCompareFA > VertexMap;
 496   VertexMap vertexMap;
 497   std::time_t start,end;
 498   std::time(&start);
 499   std::cout << "Starting conversion " << std::endl;
 500
 501   auto w_filter = ws.GetFilter( "eb" );
 502   auto distance_map =
 503     ws.GetFilter( "dmap" )->GetOutputData( "Output" )->
 504     GetITK< itk::Image< float, 3 > >( );
 505   auto sk =
 506     w_filter->GetOutputData( "Skeleton" )->GetITK< TFASkeleton >( );
 507   const auto& branches = sk->Get( );
 508   auto seed0 =
 509     ws.GetFilter( "seed" )->GetOutputData( "Output" )->
 510     GetITK< TVerticesFA >( )->Get( )[ 0 ];
 511
 512   std::queue< TVertexFA > q;
 513   // TODO: std::set< TVertexFA, TVertexCompareFA > marks;
 514   q.push( seed0 );
 515   while( !q.empty( ) )
 516   {
 517     auto sVertex = q.front( );
 518     q.pop( );
 519     auto sIt = branches.find( sVertex );
 520     /* TODO
 521        if( marks.find( sVertex ) != marks.end( ) )
 522        {
 523        std::cout << "MARK!!!!! : " << sVertex << std::endl;
 524        }
 525        marks.insert( sVertex );
 526     */
 527
 528     // End node... do nothing
 529     if( sIt == branches.end( ) )
 530       continue;
 531
 532     // Create source node
 533     auto srcIt = vertexMap.find( sVertex );
 534     if( srcIt == vertexMap.end( ) )
 535       srcIt = vertexMap.insert(
 536         VertexMap::value_type(
 537           sVertex, FAVertexToNode( sVertex, input_image )
 538           )
 539         ).first;
 540
 541     // TODO: std::cout << sVertex << " " << " " << sLevel << " " << seed0 << std::endl;
 542     // Create destination nodes
 543     for( auto eIt = sIt->second.begin( ); eIt != sIt->second.end( ); ++eIt )
 544     {
 545       auto dstIt = vertexMap.find( eIt->first );
 546       if( dstIt == vertexMap.end( ) )
 547         dstIt = vertexMap.insert(
 548           VertexMap::value_type(
 549             eIt->first, FAVertexToNode( eIt->first, input_image )
 550             )
 551           ).first;
 552
 553       // Connect in the acyclic graph
 554       dstIt->second->SetFather( srcIt->second );
 555       srcIt->second->AddChild( dstIt->second );
 556
 557       // Create detailed edge
 558       TEdgeAirways* edge = new Edge( );
 559       edge->SetSource( srcIt->second );
 560       edge->SetTarget( dstIt->second );
 561       auto path = eIt->second->GetVertexList( );
 562       for( unsigned int pIt = 0; pIt < path->Size( ); ++pIt )
 563       {
 564         itk::ImageBase< 3 >::PointType pnt;
 565         auto cidx = path->GetElement( pIt );
 566         input_image->TransformContinuousIndexToPhysicalPoint( cidx, pnt );
 567         TVertexFA idx;
 568         input_image->TransformPhysicalPointToIndex( pnt, idx );
 569         Vec3 coords = FAVertexToNode( idx, input_image )->GetCoords( );
 570         pair_posVox_rad skPair( coords, distance_map->GetPixel( idx ) );
 571         edge->AddSkeletonPairInfo( skPair );
 572
 573       } // rof
 574
 575       // Finish association
 576       dstIt->second->SetEdge( edge );
 577
 578       // Put it as next candidate
 579       q.push( eIt->first );
 580
 581     } // rof
 582
 583   } // elihw
 584
 585   AirwaysTree* tree =
 586     new AirwaysTree( input_image, NULL, vertexMap[ seed0 ], false );
 587   std::time(&end);
 588   std::cout << "Finished conversion. New AlfTree has weight: "<<tree->GetWeight()<<". Takes "<<(end-start)<<" s." << std::endl;
 589   return *tree;
 590 }
 591
 592 // -------------------------------------------------------------------------
 593 AirwaysTree& CreateAirwaysTreeFromSegmentation(Vec3 seed, TInputImage* input_image, cpPlugins::Workspace& ws )
 594 {
 595   return( ConvertFilterToAirwaysTree( input_image, ws ) );
 596 }
 597
 598 // -------------------------------------------------------------------------
 599 vector<TreeInfo> ReadInputFile(const char* filename)
 600 {
 601   // Variables
 602   std::ifstream infile(filename);
 603   std::string line;
 604   std::string folderpath_allResults;
 605   vector<TreeInfo> vectorInfo;
 606   // Parse the file
 607   bool firstLine = false;
 608
 609   while (std::getline(infile, line))
 610   {
 611     // First line contains the output folder
 612     std::istringstream iss(line);
 613     if (!firstLine)
 614     {
 615       if (!(iss >> folderpath_allResults))
 616       {
 617         std::cout << "no file" << std::endl;
 618         return vectorInfo;
 619       } //if
 620       firstLine = true;
 621     } //if
 622     // Other lines, not the first one, contain the information for the airways to be created
 623     else
 624     {
 625       TreeInfo treeInfo;
 626       float point_trachea[3];
 627       std::string filepath_airwayImage, name_pig, name_image;
 628       if (!(iss >> point_trachea[0] >> point_trachea[1] >> point_trachea[2] >> filepath_airwayImage >> name_pig >> name_image))
 629       {
 630         std::cout << "There is no tree information in the file." << std::endl;
 631         break;
 632       } //if
 633       else
 634       {
 635         // Print information
 636         std::cout << "Point trachea:[" << point_trachea[0] << "," << point_trachea[1] << "," << point_trachea[2] << "]" << std::endl;
 637       }
 638
 639       //Save info.
 640
 641       //Save seed info.
 642       Vec3 seed(point_trachea[0], point_trachea[1], point_trachea[2]); //real coords seed
 643       treeInfo.seed = seed;
 644       // Create the outputs
 645       treeInfo.folderpath_pigResults = folderpath_allResults + "/" + name_pig + "/";
 646       treeInfo.pig_name = name_pig;
 647       treeInfo.image_name = name_image;
 648       // Read the image
 649       /*
 650         treeInfo.image = ReadImage<TInputImage>(filepath_airwayImage);
 651       */
 652       // Execute first pipeline's part
 653       std::stringstream seed_stream;
 654       seed_stream
 655         << point_trachea[0] << " "
 656         << point_trachea[1] << " "
 657         << point_trachea[2];
 658
 659       treeInfo.myWorkspace->SetInterface( &myPlugins );
 660       std::string err = treeInfo.myWorkspace->LoadWorkspace( "./workspace_airwaysappli.wxml" );
 661       if( err != "" )
 662       {
 663         std::cerr << "Error: " << err << std::endl;
 664         std::exit( 1 );
 665
 666       } // fi
 667       treeInfo.myWorkspace->SetParameter( "FileNames@reader", filepath_airwayImage );
 668       treeInfo.myWorkspace->SetParameter( "Text@seed", seed_stream.str( ) );
 669       vectorInfo.push_back(treeInfo);
 670
 671     } //else
 672   } //while
 673   return vectorInfo;
 674 }
 675
 676 // -------------------------------------------------------------------------
 677 void printCommonTreeBetweenTwoTrees(AirwaysTree tree_A, AirwaysTree tree_B, std::vector< std::pair< std::pair<Node*, Node*>, std::pair<Node*, Node*> > > vector_pair_edges_A_to_B, unsigned int Q, unsigned int F)
 678 {
 679   std::cout << "printCommonTreeBetweenTwoTrees, edges:" << vector_pair_edges_A_to_B.size() << std::endl;
 680
 681   // Vtk points, cell array, and colors
 682   vtkSmartPointer<vtkPoints> points_common = vtkSmartPointer<vtkPoints>::New();
 683   vtkSmartPointer<vtkCellArray> lines_common = vtkSmartPointer<vtkCellArray>::New();
 684   vtkSmartPointer<vtkUnsignedCharArray> colors_common = vtkSmartPointer<vtkUnsignedCharArray>::New();
 685   colors_common->SetNumberOfComponents(3);
 686   colors_common->SetName("Colors");
 687
 688   // Add all the points
 689   // 0 - 1000 points for tree A and from 1001 for tree B
 690   points_common->SetNumberOfPoints(1000 + tree_B.GetWeight() + 100);
 691
 692   // Add points for tree A
 693   vec_nodes vector_nodesA = tree_A.GetNodes();
 694   for(vec_nodes::iterator it_nodesA = vector_nodesA.begin(); it_nodesA != vector_nodesA.end(); ++it_nodesA)
 695   {
 696     points_common->SetPoint((*it_nodesA)->GetId(),(*it_nodesA)->GetCoords().GetVec3());
 697   }
 698
 699   // Add points for tree B
 700   vec_nodes vector_nodesB = tree_B.GetNodes();
 701   for(vec_nodes::iterator it_nodesB = vector_nodesB.begin(); it_nodesB != vector_nodesB.end(); ++it_nodesB)
 702   {
 703     points_common->SetPoint((*it_nodesB)->GetId()+1000,(*it_nodesB)->GetCoords().GetVec3());
 704   }
 705
 706   // Add the edges for both trees
 707   std::vector< std::pair< std::pair<Node*, Node*>, std::pair<Node*, Node*> > >::iterator it_edges = vector_pair_edges_A_to_B.begin();
 708   int number_pairs = 0;
 709   for(; it_edges != vector_pair_edges_A_to_B.end(); ++it_edges)
 710   {
 711     std::cout << "Pair:" << number_pairs << std::endl;
 712     std::pair<Node*, Node*> edge_A = (*it_edges).first;
 713     std::pair<Node*, Node*> edge_B = (*it_edges).second;
 714
 715     vec_nodes path_A;
 716     edge_A.first->GetPathToNode(edge_A.second, path_A);
 717
 718     vec_nodes path_B;
 719     edge_B.first->GetPathToNode(edge_B.second, path_B);
 720
 721     // Set color to be used
 722     int numColor = number_pairs % 6;
 723     unsigned char color[3];
 724     color[0] = green[0];
 725     color[1] = green[1];
 726     color[2] = green[2];
 727     if(numColor == 1)
 728     {
 729       color[0] = red[0];
 730       color[1] = red[1];
 731       color[2] = red[2];
 732     }
 733     else if(numColor == 2)
 734     {
 735       color[0] = blue[0];
 736       color[1] = blue[1];
 737       color[2] = blue[2];
 738     }
 739     else if(numColor == 3)
 740     {
 741       color[0] = yellow[0];
 742       color[1] = yellow[1];
 743       color[2] = yellow[2];
 744     }
 745     else if(numColor == 4)
 746     {
 747       color[0] = purple[0];
 748       color[1] = purple[1];
 749       color[2] = purple[2];
 750     }
 751     else if(numColor == 5)
 752     {
 753       color[0] = cyan[0];
 754       color[1] = cyan[1];
 755       color[2] = cyan[2];
 756     }
 757
 758     number_pairs++;
 759
 760     // Trace line A
 761     //if(path_A.size() > 0 && number_pairs < 50)
 762     if( path_A.size() )
 763     {
 764       vtkSmartPointer<vtkLine> line = vtkSmartPointer<vtkLine>::New();
 765       lines_common->InsertNextCell(path_A.size());
 766       int id_point = 0;
 767       for(vec_nodes::iterator it_pathA = path_A.begin(); it_pathA != path_A.end(); ++it_pathA)
 768       {
 769         lines_common->InsertCellPoint((*it_pathA)->GetId());
 770         //line->GetPointIds()->SetId( id_point, (*it_pathA)->GetId() );
 771         //id_point++;
 772       }
 773       //lines_common->InsertNextCell(line);
 774       colors_common->InsertNextTupleValue(color);
 775     }
 776     else
 777     {
 778       std::cout << "No path A" << std::endl;
 779     }
 780
 781
 782     // Trace line B
 783     //if(path_B.size() > 0 && number_pairs < 50)
 784     if( path_B.size() )
 785     {
 786       vtkSmartPointer<vtkLine> line = vtkSmartPointer<vtkLine>::New();
 787       lines_common->InsertNextCell(path_B.size());
 788       int id_point = 0;
 789       for(vec_nodes::iterator it_pathB = path_B.begin(); it_pathB != path_B.end(); ++it_pathB)
 790       {
 791         lines_common->InsertCellPoint((*it_pathB)->GetId()+1000);
 792         //line->GetPointIds()->SetId( id_point, (*it_pathB)->GetId()+1000 );
 793         id_point++;
 794       }
 795       //lines_common->InsertNextCell(line);
 796       colors_common->InsertNextTupleValue(color);
 797     }
 798     else
 799     {
 800       std::cout << "No path B" << std::endl;
 801     }
 802   }
 803
 804   // Save the polydata
 805   // Create the polydata
 806   vtkSmartPointer<vtkPolyData> linesPolyData = vtkSmartPointer<vtkPolyData>::New();
 807
 808   // Set the points, lines, and colors
 809   linesPolyData->SetPoints(points_common);
 810   linesPolyData->SetLines(lines_common);
 811   linesPolyData->GetCellData()->SetScalars(colors_common);
 812
 813   // ------------------------------------------------
 814   // Write the vtk file
 815
 816   // Create the pathfile to save
 817   std::stringstream filepath_actualIteration;
 818   filepath_actualIteration << tree_A.GetResultPath() << "/" << tree_A.GetImageName() << "_" << tree_B.GetImageName() << "_Q_" << Q << "_F_" << F << ".vtk";
 819   std::cout << "File to save:" << filepath_actualIteration.str() << std::endl;
 820
 821   // Create the writer
 822   vtkSmartPointer<vtkPolyDataWriter> writer = vtkSmartPointer<vtkPolyDataWriter>::New();
 823   writer->SetFileName(filepath_actualIteration.str().c_str());
 824
 825   // Set input and write
 826 #if VTK_MAJOR_VERSION <= 5
 827   writer->SetInput(linesPolyData);
 828 #else
 829   writer->SetInputData(linesPolyData);
 830 #endif
 831   writer->Write();
 832
 833
 834
 835   // ***************************************
 836   // Save the links in a file
 837   // *******
 838
 839   // Create the outputfile
 840   std::stringstream filepath_evaluation;
 841   filepath_evaluation << tree_A.GetResultPath() << "/" << tree_A.GetImageName() << "_" << tree_B.GetImageName() << "_Q_" << Q << "_F_" << F << ".csv";
 842
 843   std::ofstream file(filepath_evaluation.str().c_str());
 844   if(file.is_open())
 845   {
 846     // Save the header
 847     //file << "Node_" << tree_A.GetImageName() << " " << "Node_" << tree_B.GetImageName()<< "\n";
 848     file << "TreeName "
 849       "idLocalN1 idLocalN2 "
 850       "Node1x Node1y Node1z "
 851       "Node2x Node2y Node2z "
 852       "idGlobalN1 "
 853       "idMatch" << std::endl;
 854
 855
 856     std::vector< std::pair< std::pair<Node*, Node*>, std::pair<Node*, Node*> > >::iterator it_edges = vector_pair_edges_A_to_B.begin();
 857     for(; it_edges != vector_pair_edges_A_to_B.end(); ++it_edges)
 858     {
 859
 860       std::pair<Node*, Node*> edge_A = (*it_edges).first;
 861       std::pair<Node*, Node*> edge_B = (*it_edges).second;
 862
 863       //file << edge_A.second->GetId() << " " << edge_B.second->GetId()+1000 << "\n";
 864       Vec3 coord_EndNodeA = edge_A.second->GetCoords();
 865       Vec3 coord_EndNodeB = edge_B.second->GetCoords();
 866       file << tree_A.GetImageName() << " " <<
 867         edge_A.second->GetId() << " " << edge_B.second->GetId()+1000 << " " <<
 868         coord_EndNodeA[0] << " " << coord_EndNodeA[1] << " " << coord_EndNodeA[2] << " " <<
 869         coord_EndNodeB[0] << " " << coord_EndNodeB[1] << " " << coord_EndNodeB[2] << " " <<
 870         tree_A.GetImageName() << coord_EndNodeA[0] << coord_EndNodeA[1] << coord_EndNodeA[2] << " " <<
 871         tree_B.GetImageName() << coord_EndNodeB[0] << coord_EndNodeB[1] << coord_EndNodeB[2] <<"\n";
 872
 873       file << tree_B.GetImageName() << " " <<
 874         edge_B.second->GetId()+1000 << " " << edge_A.second->GetId() << " " <<
 875         coord_EndNodeB[0] << " " << coord_EndNodeB[1] << " " << coord_EndNodeB[2] << " " <<
 876         coord_EndNodeA[0] << " " << coord_EndNodeA[1] << " " << coord_EndNodeA[2] << " " <<
 877         tree_B.GetImageName() << coord_EndNodeB[0] << coord_EndNodeB[1] << coord_EndNodeB[2] << " " <<
 878         tree_A.GetImageName() << coord_EndNodeA[0] << coord_EndNodeA[1] << coord_EndNodeA[2] << "\n";
 879     }
 880   }
 881
 882   file.close();
 883   // *******
 884   // ***************************************
 885
 886
 887
 888
 889   std::cout << "printCommonTreeBetweenTwoTrees ... OK" << std::endl;
 890 }
 891
 892 // -------------------------------------------------------------------------
 893 void printMatchingResultToFile(AirwaysTree tree_A, AirwaysTree tree_B, std::map< unsigned int, std::vector<Node*> > map_A_to_B, std::map< unsigned int, std::vector<Node*> > map_B_to_A, unsigned int Q, unsigned int F)
 894 {
 895   std::cout << "Printing matching result ... " << std::endl;
 896
 897   // Variables and types
 898   typedef std::map< unsigned int, vec_nodes > map_id_node;
 899
 900   // Create the outputfile
 901   std::stringstream filepath_evaluation;
 902   filepath_evaluation << tree_A.GetResultPath() << "/" << tree_A.GetImageName() << "_" << tree_B.GetImageName() << "_Q_" << Q << "_F_" << F << "_matching.csv";
 903
 904   std::ofstream file(filepath_evaluation.str().c_str());
 905   if(file.is_open())
 906   {
 907     // Save the header
 908     file << "TreeName idLocalN1 idLocalN2 "
 909       "Node1x Node1y Node1z "
 910       "Node2x Node2y Node2z "
 911       "idGlobalN1 "
 912       "idMatch "
 913       "typeMatch_match_1_nonmatch_0 "
 914       "depth "
 915       "leaf"<< std::endl;
 916
 917     // ---------------
 918     // From A to B
 919
 920     // Save the match or non-match for each node from A to B
 921     for(int id_a=1; id_a <= tree_A.GetWeight( ); ++id_a)
 922     {
 923       // Get the actual node in tree A
 924       Node* node_a = tree_A.GetNodeById( id_a );
 925       Vec3 coords_a = node_a->GetCoords();
 926       unsigned int depth_a = tree_A.GetDepthById(id_a);
 927       bool leaf_a = node_a->IsLeaf();
 928
 929       // Check if the node was matched
 930       map_id_node::iterator it_a2b = map_A_to_B.find( id_a );
 931       if( it_a2b != map_A_to_B.end( ) )
 932       {
 933         // Get the correspoding matching nodes and print them
 934         vec_nodes nodes_B = (*it_a2b).second;
 935
 936         vec_nodes::iterator it_nodes_b = nodes_B.begin( );
 937         for( ; it_nodes_b != nodes_B.end( ); ++it_nodes_b)
 938         {
 939           Vec3 coords_b = (*it_nodes_b)->GetCoords();
 940
 941           file << tree_A.GetImageName() << " " << id_a << " " << (*it_nodes_b)->GetId()+1000 << " "
 942                << coords_a[0] << " " << coords_a[1] << " " << coords_a[2] << " "
 943                << coords_b[0] << " " << coords_b[1] << " " << coords_b[2] << " "
 944                << tree_A.GetImageName() << coords_a[0] << coords_a[1] << coords_a[2] << " "
 945                << tree_A.GetImageName() << coords_a[0] << coords_a[1] << coords_a[2] << coords_b[0] << coords_b[1] << coords_b[2] << " "
 946                << "1" << " "
 947                << depth_a << " "
 948                << leaf_a << "\n";
 949         }
 950       }
 951       else
 952       {
 953         file << tree_A.GetImageName() << " " << id_a << " " << "0" << " "
 954              << coords_a[0] << " " << coords_a[1] << " " << coords_a[2] << " "
 955              << "0" << " " << "0" << " " << "0" << " "
 956              << tree_A.GetImageName() << coords_a[0] << coords_a[1] << coords_a[2] << " "
 957              << tree_A.GetImageName() << coords_a[0] << coords_a[1] << coords_a[2] << "0" << "0" << "0" << " "
 958              << "0" << " "
 959              << depth_a << " "
 960              << leaf_a  << "\n";
 961       }
 962     }
 963
 964     // ---------------
 965     // From B to A
 966
 967     // Save the match or non-match for each node from A to B
 968     for(int id_b=1; id_b <= tree_B.GetWeight( ); ++id_b)
 969     {
 970       // Get the actual node in tree B
 971       Node* node_b = tree_B.GetNodeById( id_b );
 972       Vec3 coords_b = node_b->GetCoords();
 973       unsigned int depth_b = tree_B.GetDepthById(id_b);
 974       bool leaf_b = node_b->IsLeaf();
 975
 976       // Check if the node was matched
 977       map_id_node::iterator it_b2a = map_B_to_A.find( id_b );
 978       if( it_b2a != map_B_to_A.end( ) )
 979       {
 980         // Get the correspoding matching nodes and print them
 981         vec_nodes nodes_A = (*it_b2a).second;
 982
 983         vec_nodes::iterator it_nodes_a = nodes_A.begin( );
 984         for( ; it_nodes_a != nodes_A.end( ); ++it_nodes_a)
 985         {
 986           Vec3 coords_a = (*it_nodes_a)->GetCoords();
 987
 988           file << tree_B.GetImageName() << " " << id_b+1000 << " " << (*it_nodes_a)->GetId() << " "
 989                << coords_b[0] << " " << coords_b[1] << " " << coords_b[2] << " "
 990                << coords_a[0] << " " << coords_a[1] << " " << coords_a[2] << " "
 991                << tree_B.GetImageName() << coords_b[0] << coords_b[1] << coords_b[2] << " "
 992                << tree_B.GetImageName() << coords_b[0] << coords_b[1] << coords_b[2] << coords_a[0] << coords_a[1] << coords_a[2] << " "
 993                << "1" << " "
 994                << depth_b << " "
 995                << leaf_b  << "\n";
 996         }
 997       }
 998       else
 999       {
1000         file << tree_B.GetImageName() << " " << id_b+1000 << " " << "0" << " "
1001              << coords_b[0] << " " << coords_b[1] << " " << coords_b[2] << " "
1002              << "0" << " " << "0" << " " << "0" << " "
1003              << tree_B.GetImageName() << coords_b[0] << coords_b[1] << coords_b[2] << " "
1004              << tree_B.GetImageName() << coords_b[0] << coords_b[1] << coords_b[2] << "0" << "0" << "0" << " "
1005              << "0" << " "
1006              << depth_b << " "
1007              << leaf_b  << "\n";
1008       }//esle
1009     }//rof
1010   }//fi
1011
1012   file.close(); // Close the file
1013
1014   std::cout << "Printing matching result DONE" << std::endl;
1015 }
1016
1017 // -------------------------------------------------------------------------
1018 void createLinesAndPointsForVTK(const Node* node, vtkSmartPointer<vtkPoints>& pts,vtkSmartPointer<vtkCellArray>& lines, vtkSmartPointer<vtkUnsignedCharArray>& colors, bool common, bool isRoot)
1019 {
1020   // Insert the actual point/node
1021   //vtkIdType id_father = idNonRoot;
1022   //if(isRoot)
1023   //id_father = pts->InsertNextPoint(node->GetCoords().GetVec3());
1024   vtkIdType id_father = node->GetId();
1025   if(isRoot)
1026     pts->SetPoint(id_father,node->GetCoords().GetVec3());
1027
1028   // Iterate over the children
1029   const vec_nodes children = node->GetChildren();
1030   for (vec_nodes::const_iterator it_child = children.begin(); it_child != children.end(); ++it_child)
1031   {
1032     if (!(*it_child)->IsMarked() && common)
1033       continue;
1034
1035     //vtkIdType id_son = pts->InsertNextPoint((*it_child)->GetCoords().GetVec3());
1036     vtkIdType id_son = (*it_child)->GetId();
1037     pts->SetPoint(id_son,(*it_child)->GetCoords().GetVec3());
1038
1039     // Set color to be used
1040     int numColor = (*it_child)->GetLevel() % 4;
1041     if(numColor == 0)
1042       colors->InsertNextTupleValue(green);
1043     else if(numColor == 1)
1044       colors->InsertNextTupleValue(red);
1045     else if(numColor == 2)
1046       colors->InsertNextTupleValue(red);
1047     else
1048       colors->InsertNextTupleValue(red);
1049
1050     // Add the line
1051     vtkSmartPointer<vtkLine> line = vtkSmartPointer<vtkLine>::New();
1052     line->GetPointIds()->SetId(0, id_father);
1053     line->GetPointIds()->SetId(1, id_son);
1054     lines->InsertNextCell(line);
1055
1056     createLinesAndPointsForVTK(*it_child, pts, lines, colors, common, false);
1057   } //for
1058 }
1059
1060 // eof - $RCSfile$