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diff --git a/appli/TempAirwaysAppli/TempAirwaysAppli.cxx b/appli/TempAirwaysAppli/TempAirwaysAppli.cxx
index 3dfbcc3fc818ca291b033c0537ea12f314ae9d49..d5cc42f602600ac9fab927a262f3d404bcea5170 100644 (file)
--- a/appli/TempAirwaysAppli/TempAirwaysAppli.cxx
+++ b/appli/TempAirwaysAppli/TempAirwaysAppli.cxx
@@ -23,10 +23,38 @@ namespace
 
 typedef std::vector< AirwaysTree > AirwaysVector;
 
+#include <itkCastImageFilter.h>
+
 // Auxiliar struct to save info for execution.
 typedef void* TImagePointer;
 struct TreeInfo{
-  TImagePointer image;
+
+  TreeInfo( )
+    {
+      this->myWorkspace = new cpPlugins::Workspace( );
+    }
+  ~TreeInfo( )
+    {
+      /*
+        if( this->IsMyWorkspace )
+        delete this->myWorkspace;
+      */
+    }
+
+  void CastImage( )
+    {
+      auto image = this->myWorkspace->GetFilter( "reader" )->GetOutputData( "Output" )->GetITK< itk::Image< unsigned char, 3 > >( );
+      typedef itk::CastImageFilter< itk::Image< unsigned char, 3 >, TInputImage > _TCast;
+      _TCast::Pointer cast = _TCast::New( );
+      cast->SetInput( image );
+      cast->Update( );
+      this->Image = cast->GetOutput( );
+      this->Image->DisconnectPipeline( );
+    }
+
+  TInputImage::Pointer Image;
+  cpPlugins::Workspace* myWorkspace;
+  bool IsMyWorkspace;
   Vec3 seed;
   std::string folderpath_pigResults;
   std::string pig_name;
@@ -42,13 +70,12 @@ unsigned char purple[3]= { 255, 0, 255 };
 unsigned char cyan[3]= { 0, 255, 255 };
 
 cpPlugins::Interface myPlugins;
-cpPlugins::Workspace myWorkspace;
 
 // -------------------------------------------------------------------------
-void Load_cpPlugins( const std::string& plugins, const std::string& ws );
+void Load_cpPlugins( const std::string& plugins );
 void CreateResultDirectory(AirwaysTree tree);
 void DrawVTKLinesFromTree(AirwaysTree& tree, const std::string filename, bool common);
-AirwaysTree& CreateAirwaysTreeFromSegmentation(Vec3 seed, TImagePointer input_image);
+AirwaysTree& CreateAirwaysTreeFromSegmentation(Vec3 seed, TInputImage* input_image, cpPlugins::Workspace& ws );
 vector<TreeInfo> ReadInputFile(const char* filename);
 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);
 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);
@@ -57,6 +84,8 @@ void createLinesAndPointsForVTK(const Node* node, vtkSmartPointer<vtkPoints>& pt
 // -------------------------------------------------------------------------
 int main( int argc, char* argv[] )
 {
+  Load_cpPlugins( "./plugins.cfg" );
+
   try
   {
     // Define and parse the program options
@@ -92,7 +121,15 @@ int main( int argc, char* argv[] )
       {
         for(unsigned int i = 0; i < treeInfoVector.size(); ++ i){
           TreeInfo info = treeInfoVector[i];
-          AirwaysTree tree = CreateAirwaysTreeFromSegmentation(info.seed, info.image);
+          std::string err = info.myWorkspace->Execute( "eb" );
+          if( err != "" )
+          {
+            std::cerr << "Error: " << err << std::endl;
+            std::exit( 1 );
+
+          } // fi
+          info.CastImage( );
+          AirwaysTree tree = CreateAirwaysTreeFromSegmentation( info.seed, info.Image, *(info.myWorkspace ));
           tree.SetResultPath(info.folderpath_pigResults);
           tree.SetImageName(info.image_name);
           aVector.push_back(tree);
@@ -326,17 +363,9 @@ int main( int argc, char* argv[] )
 }
 
 // -------------------------------------------------------------------------
-void Load_cpPlugins( const std::string& plugins, const std::string& ws )
+void Load_cpPlugins( const std::string& plugins )
 {
   myPlugins.LoadConfiguration( plugins );
-  myWorkspace.SetInterface( &myPlugins );
-  std::string err = myWorkspace.LoadWorkspace( ws );
-  if( err != "" )
-  {
-    std::cerr << "Error: " << err << std::endl;
-    std::exit( 1 );
-
-  } // fi
 }
 
 // -------------------------------------------------------------------------
@@ -446,7 +475,7 @@ Node* FAVertexToNode( TVertex vertex, TImage* image )
   return new Node(alfPoint);
 }
 
-AirwaysTree& ConvertFilterToAirwaysTree( )
+AirwaysTree& ConvertFilterToAirwaysTree( TInputImage* input_image, cpPlugins::Workspace& ws )
 {
   /*
     typedef FilterType TFilter;
@@ -474,12 +503,12 @@ AirwaysTree& ConvertFilterToAirwaysTree( )
   std::time(&start);
   std::cout << "Starting conversion " << std::endl;
 
-  auto w_filter = myWorkspace.GetFilter( "eb" );
+  auto w_filter = ws.GetFilter( "eb" );
   auto branches = w_filter->GetOutputData( "Skeleton" )->GetITK< TFASkeleton >( );
   auto& endpoints = w_filter->GetOutputData( "EndPoints" )->GetITK< TVerticesFA >( )->Get( );
   auto& bifurcations = w_filter->GetOutputData( "Bifurcations" )->GetITK< TVerticesFA >( )->Get( );
-  auto image = myWorkspace.GetFilter( "reader" )->GetOutputData( "Output" )->GetITK< itk::ImageBase< 3 > >( );
-  auto distance_map = myWorkspace.GetFilter( "dmap" )->GetOutputData( "Output" )->GetITK< itk::Image< float, 3 > >( );
+  auto image = ws.GetFilter( "reader" )->GetOutputData( "Output" )->GetITK< itk::ImageBase< 3 > >( );
+  auto distance_map = ws.GetFilter( "dmap" )->GetOutputData( "Output" )->GetITK< itk::Image< float, 3 > >( );
 
   /*
     TBranchesFA* branches = filter->GetBranches( );
@@ -488,7 +517,7 @@ AirwaysTree& ConvertFilterToAirwaysTree( )
   int leoTreeWeigth = endpoints.size()+bifurcations.size()+1;
   std::cout<< "Creates FA Tree with : "<<leoTreeWeigth << " nodes "<<std::endl;
 
-  auto seed0 = myWorkspace.GetFilter( "seed" )->GetOutputData( "Output" )->GetITK< TVerticesFA >( )->Get( )[ 0 ];
+  auto seed0 = ws.GetFilter( "seed" )->GetOutputData( "Output" )->GetITK< TVerticesFA >( )->Get( )[ 0 ];
   //Fill vertex map. Gotta do it with bifurcations, endpoints and the root.
   //Do the root
   vertexMap[ seed0 ] = FAVertexToNode( seed0, image );
@@ -496,7 +525,7 @@ AirwaysTree& ConvertFilterToAirwaysTree( )
   auto eIt = endpoints.begin();
   for( ; eIt != endpoints.end(); ++eIt )
   {
-    vertexMap[*eIt]=FAVertexToNode( *eIt,image );
+    vertexMap[*eIt]=FAVertexToNode( *eIt, image );
   }
 
   auto biIt = bifurcations.begin();
@@ -529,15 +558,13 @@ AirwaysTree& ConvertFilterToAirwaysTree( )
       destination->SetFather(source);
       source->AddChild(destination);
       TEdgeAirways* edge = new Edge();
-      edge->SetSource(source);
-      edge->SetTarget(destination);
       //Update path info for the edge. This is why we don't need to call UpdateEdges on the constructor of the tree.
 
       auto edgePath = brIt->second->GetVertexList( );
       for( unsigned int pIt = 0; pIt < edgePath->Size( ); ++pIt )
       {
-        auto cidx = edgePath->GetElement(pIt);
         itk::ImageBase< 3 >::PointType pnt;
+        auto cidx = edgePath->GetElement( pIt );
         image->TransformContinuousIndexToPhysicalPoint(cidx,pnt);
         TVertexFA idx;
         image->TransformPhysicalPointToIndex(pnt,idx);
@@ -545,26 +572,19 @@ AirwaysTree& ConvertFilterToAirwaysTree( )
         pair_posVox_rad skPair(coords,distance_map->GetPixel(idx));
         edge->AddSkeletonPairInfo(skPair);
       }
-      destination->SetEdge(edge);
     }
   }
-  AirwaysTree* tree = new AirwaysTree(dynamic_cast< TInputImage* >( image ), NULL, vertexMap[seed0], false);
+  AirwaysTree* tree = new AirwaysTree( input_image, NULL, vertexMap[seed0], false);
   std::time(&end);
+  std::cout << input_image << std::endl;
   std::cout << "Finished conversion. New AlfTree has weight: "<<tree->GetWeight()<<". Takes "<<(end-start)<<" s." << std::endl;
   return *tree;
 }
 
 // -------------------------------------------------------------------------
-AirwaysTree& CreateAirwaysTreeFromSegmentation(Vec3 seed, TImagePointer input_image)
+AirwaysTree& CreateAirwaysTreeFromSegmentation(Vec3 seed, TInputImage* input_image, cpPlugins::Workspace& ws )
 {
-  std::string err = myWorkspace.Execute( "eb" );
-  if( err != "" )
-  {
-    std::cerr << "Error: " << err << std::endl;
-    std::exit( 1 );
-
-  } // fi
-  return( ConvertFilterToAirwaysTree( ) );
+  return( ConvertFilterToAirwaysTree( input_image, ws ) );
 }
 
 // -------------------------------------------------------------------------
@@ -621,16 +641,23 @@ vector<TreeInfo> ReadInputFile(const char* filename)
       /*
         treeInfo.image = ReadImage<TInputImage>(filepath_airwayImage);
       */
-      Load_cpPlugins( "./plugins.cfg", "./workspace_airwaysappli.wxml" );
-
       // Execute first pipeline's part
       std::stringstream seed_stream;
       seed_stream
         << point_trachea[0] << " "
         << point_trachea[1] << " "
         << point_trachea[2];
-      myWorkspace.SetParameter( "FileNames@reader", filepath_airwayImage );
-      myWorkspace.SetParameter( "Text@seed", seed_stream.str( ) );
+
+      treeInfo.myWorkspace->SetInterface( &myPlugins );
+      std::string err = treeInfo.myWorkspace->LoadWorkspace( "./workspace_airwaysappli.wxml" );
+      if( err != "" )
+      {
+        std::cerr << "Error: " << err << std::endl;
+        std::exit( 1 );
+
+      } // fi
+      treeInfo.myWorkspace->SetParameter( "FileNames@reader", filepath_airwayImage );
+      treeInfo.myWorkspace->SetParameter( "Text@seed", seed_stream.str( ) );
       vectorInfo.push_back(treeInfo);
 
     } //else

diff --git a/lib/fpa/Image/MinimumSpanningTree.hxx b/lib/fpa/Image/MinimumSpanningTree.hxx
index a4dc47ec98a0565fa7ad487ea9dbbdb6709c1961..616365ef18689afb8065b958130fd9f9da0cc943 100644 (file)
--- a/lib/fpa/Image/MinimumSpanningTree.hxx
+++ b/lib/fpa/Image/MinimumSpanningTree.hxx
@@ -142,6 +142,7 @@ _Path( TVertices& path, const TVertex& a ) const
       it += this->GetPixel( it ).Parent;
 
     } while( this->GetPixel( it ).Parent != zero );
+    path.push_back( it );
 
   } // fi
 }