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