...

diff --git a/data/binary_test_2D_00.png b/data/binary_test_2D_00.png
new file mode 100644 (file)
index 0000000..fbe9d39
Binary files /dev/null and b/data/binary_test_2D_00.png differ

diff --git a/data/ones_image.png b/data/ones_image.png
new file mode 100644 (file)
index 0000000..f7afaab
Binary files /dev/null and b/data/ones_image.png differ

diff --git a/data/workspaces/workspace_airwaysappli.wxml b/data/workspaces/workspace_airwaysappli.wxml
new file mode 100644 (file)
index 0000000..9b80164
--- /dev/null
+++ b/data/workspaces/workspace_airwaysappli.wxml
@@ -0,0 +1,73 @@
+<cpPlugins_Workspace>
+    <filter category="ImageFilters" class="CastImageFilter" name="cast" ViewX="-1098" ViewY="-242">
+        <parameter name="CastType" value="char#short#int#long#uchar#ushort#uint#ulong#float#double@double" type="Choices"/>
+    </filter>
+    <filter category="fpaImageAlgorithmFunctors" class="InvertCostFunction" name="cost" ViewX="-951" ViewY="-428">
+        <parameter name="Alpha" value="1" type="Real"/>
+        <parameter name="Beta" value="1" type="Real"/>
+        <parameter name="ScalarType" value="float#double@float" type="Choices"/>
+    </filter>
+    <filter category="fpaImageAlgorithm" class="ImageDijkstra" name="dijkstra" ViewX="-735" ViewY="-176">
+        <parameter name="FillNodeQueue" value="1" type="Bool"/>
+        <parameter name="NeighborhoodOrder" value="1#2@1" type="Choices"/>
+        <parameter name="StopAtOneFront" value="0" type="Bool"/>
+        <parameter name="VisualDebug" value="1" type="Bool"/>
+    </filter>
+    <filter category="ImageFilters" class="SignedMaurerDistanceMapImageFilter" name="dmap" ViewX="-1093" ViewY="-379">
+        <parameter name="BackgroundValue" value="0" type="Real"/>
+        <parameter name="InsideIsPositive" value="1" type="Bool"/>
+        <parameter name="OutputResolution" value="float#double@float" type="Choices"/>
+        <parameter name="SquaredDistance" value="0" type="Bool"/>
+        <parameter name="UseImageSpacing" value="1" type="Bool"/>
+    </filter>
+    <filter category="fpaImageAlgorithm" class="ExtractEndPointsAndBifurcationsFromMinimumSpanningTree" name="eb" ViewX="-491" ViewY="-267">
+        <parameter name="SquaredDistanceMap" value="0" type="Bool"/>
+    </filter>
+    <filter category="IO" class="ImageReader" name="reader" ViewX="-1366" ViewY="-264">
+        <parameter name="FileNames" value="" type="OpenFileNameList"/>
+    </filter>
+    <filter category="Widgets" class="NoInteractiveSeedWidget" name="seed" ViewX="-1116" ViewY="-124">
+        <parameter name="Text" value="" type="String"/>
+    </filter>
+    <connection>
+        <origin filter="cost" name="Output"/>
+        <destination filter="dijkstra" name="CostFunctor"/>
+    </connection>
+    <connection>
+        <origin filter="dijkstra" name="Output"/>
+        <destination filter="eb" name="CostsImage"/>
+    </connection>
+    <connection>
+        <origin filter="dijkstra" name="MST"/>
+        <destination filter="eb" name="MST"/>
+    </connection>
+    <connection>
+        <origin filter="dmap" name="Output"/>
+        <destination filter="dijkstra" name="Input"/>
+    </connection>
+    <connection>
+        <origin filter="dmap" name="Output"/>
+        <destination filter="eb" name="DistanceMap"/>
+    </connection>
+    <connection>
+        <origin filter="reader" name="Output"/>
+        <destination filter="cast" name="Input"/>
+    </connection>
+    <connection>
+        <origin filter="reader" name="Output"/>
+        <destination filter="dmap" name="Input"/>
+    </connection>
+    <connection>
+        <origin filter="reader" name="Output"/>
+        <destination filter="seed" name="ReferenceImage"/>
+    </connection>
+    <connection>
+        <origin filter="seed" name="Output"/>
+        <destination filter="dijkstra" name="Seeds"/>
+    </connection>
+    <exposed_output_port port_name="bifurcations" filter="eb" filter_port_name="Bifurcations"/>
+    <exposed_output_port port_name="endpoints" filter="eb" filter_port_name="EndPoints"/>
+    <exposed_output_port port_name="input_image_casted" filter="CastImageFilter" filter_port_name="Output"/>
+    <exposed_output_port port_name="input_image_dmap" filter="dmap" filter_port_name="Output"/>
+    <exposed_output_port port_name="skeleton" filter="eb" filter_port_name="Skeleton"/>
+</cpPlugins_Workspace>

diff --git a/lib/fpa/Image/SkeletonFilter.hxx b/lib/fpa/Image/SkeletonFilter.hxx
index fa78819576064ad47164d0668b62e8a146809f4a..010c6945391c518eedd08a3fade1dca64723cd14 100644 (file)
--- a/lib/fpa/Image/SkeletonFilter.hxx
+++ b/lib/fpa/Image/SkeletonFilter.hxx
@@ -3,6 +3,7 @@
 
 #include <queue>
 #include <itkImageRegionConstIteratorWithIndex.h>
+#include <itkImageRegionIteratorWithIndex.h>
 
 // -------------------------------------------------------------------------
 #define fpa_Image_SkeletonFilter_InputMacro( i_n, i_t, i_i )            \
@@ -107,6 +108,7 @@ GenerateData( )
 
   // 2. Detect end-points
   this->_EndPoints( dmap, cmap, mst, ep->Get( ) );
+  std::cout << "endpoints" << std::endl;
 
   // 3. Build skeleton and keep track of bifurcations
   this->_Skeleton( dmap, cmap, mst, ep->Get( ), bi->Get( ), sk );
@@ -126,10 +128,11 @@ _EndPoints(
   typedef itk::ImageRegionConstIteratorWithIndex< _TCostMap > _TCostMapIt;
   typedef std::multimap< double, TIndex, std::greater< double > > _TQueue;
   typedef typename _TQueue::value_type _TQueueValue;
-  typedef itk::Image< unsigned char, _TCostMap::ImageDimension > _TMarks;
+  typedef itk::ImageRegionIteratorWithIndex< TMarks > _TMarksIt;
+
+  static const double _eps = std::sqrt( double( TMarks::ImageDimension + 1 ) );
 
   // Some values
-  // typename _TMarks::Pointer marks = _TMarks::New( );
   auto marks = this->GetMarks( );
   marks->SetLargestPossibleRegion( dmap->GetLargestPossibleRegion( ) );
   marks->SetRequestedRegion( dmap->GetRequestedRegion( ) );
@@ -149,7 +152,7 @@ _EndPoints(
   for( ; !dIt.IsAtEnd( ) && !cIt.IsAtEnd( ); ++dIt, ++cIt )
   {
     double d = double( dIt.Get( ) );
-    if( d > 0 )
+    if( d > double( 0 ) )
     {
       double v = double( cIt.Get( ) ) / ( d * d );
       queue.insert( _TQueueValue( v, dIt.GetIndex( ) ) );
@@ -169,16 +172,18 @@ _EndPoints(
     queue.erase( nIt );
 
     unsigned char m = marks->GetPixel( n.second );
-    // if( ( m & 0x01 ) == 0x01 )
-    if( m != 0 || ( n.first / init_v ) < double( 1e-1 ) )
+    if( m != 0 )
       continue;
 
+    std::cout << queue.size( ) << std::endl;
+
     // Mark it and update end-points
     m |= 0x01;
     marks->SetPixel( n.second, m );
     end_points.insert( n.second );
 
-    // Get path
+    // Mark path
+    auto spac = marks->GetSpacing( );
     typename TMST::TPath::Pointer path;
     mst->GetPath( path, n.second );
     for( unsigned long i = 0; i < path->GetSize( ); ++i )
@@ -186,41 +191,43 @@ _EndPoints(
       TIndex idx = path->GetVertex( i );
       typename _TCostMap::PointType cnt;
       cmap->TransformIndexToPhysicalPoint( idx, cnt );
-      double d = double( 2 ) * double( dmap->GetPixel( idx ) );
+      double r = double( dmap->GetPixel( idx ) ) * _eps;
+
+      TIndex i0, i1;
+      for( unsigned int d = 0; d < TMarks::ImageDimension; ++d )
+      {
+        long off = long( std::ceil( r / double( spac[ d ] ) ) );
+        if( off == 0 )
+          off = 1;
+        i0[ d ] = idx[ d ] - off;
+        i1[ d ] = idx[ d ] + off;
+
+        if( i0[ d ] < region.GetIndex( )[ d ] )
+          i0[ d ] = region.GetIndex( )[ d ];
 
-      // Mark sphere
-      std::queue< TIndex > q;
-      q.push( idx );
-      while( q.size( ) > 0 )
+        if( i1[ d ] >= region.GetIndex( )[ d ] + region.GetSize( )[ d ] )
+          i1[ d ] = region.GetIndex( )[ d ] + region.GetSize( )[ d ] - 1;
+
+      } // rof
+
+      typename TMarks::SizeType size;
+      for( unsigned int d = 0; d < TMarks::ImageDimension; ++d )
+        size[ d ] = i1[ d ] - i0[ d ] + 1;
+
+      typename TMarks::RegionType neighRegion;
+      neighRegion.SetIndex( i0 );
+      neighRegion.SetSize( size );
+
+      _TMarksIt mIt( marks, neighRegion );
+      for( mIt.GoToBegin( ); !mIt.IsAtEnd( ); ++mIt )
       {
-        TIndex v = q.front( );
-        q.pop( );
-        unsigned char m = marks->GetPixel( v );
-        if( ( m & 0x02 ) == 0x02 )
-          continue;
-        m |= 0x02;
-        marks->SetPixel( v, m );
-
-        for( unsigned int x = 0; x < _TCostMap::ImageDimension; ++x )
-        {
-          for( int y = -1; y <= 1; y += 2 )
-          {
-            TIndex w = v;
-            w[ x ] += y;
-            if( region.IsInside( w ) )
-            {
-              typename _TCostMap::PointType p;
-              cmap->TransformIndexToPhysicalPoint( w, p );
-              if( cnt.EuclideanDistanceTo( p ) <= d )
-                q.push( w );
-
-            } // fi
-
-          } // rof
-
-        } // rof
-
-      } // elihw
+        TIndex w = mIt.GetIndex( );
+        typename _TCostMap::PointType p;
+        marks->TransformIndexToPhysicalPoint( w, p );
+        if( cnt.EuclideanDistanceTo( p ) <= r )
+          mIt.Set( mIt.Get( ) | 0x02 );
+
+      } // rof
 
     } // rof
 

diff --git a/plugins/CMakeLists.txt b/plugins/CMakeLists.txt
index bbc5d327684a34f5fec1845d57fea08a58444452..36271c8b100633f945cdba331b40ac5246fb6059 100644 (file)
--- a/plugins/CMakeLists.txt
+++ b/plugins/CMakeLists.txt
@@ -2,26 +2,18 @@
 ## == Build plugin library ==
 ## ==========================
 
-INCLUDE_DIRECTORIES(
-  ${PROJECT_SOURCE_DIR}/lib
-  ${PROJECT_BINARY_DIR}/lib
-  )
-CreatePlugin(fpaPlugins Plugins ${cpPlugins_CONFIG_NUMBER_OF_FILES})
-TARGET_LINK_LIBRARIES(
-  fpaPlugins
-  cpPlugins cpExtensions
-  ${cpPlugins_Instances}
-  ${fpa_Instances}
-  )
-
-#IF(USE_cpPlugins)
-#  Wrap_cpPlugins(
-#    _plugin
-#    ${CMAKE_CURRENT_SOURCE_DIR}/Plugins
-#    ${prj_VERSION} ${prj_SHORT_VERSION}
-#    fpa
-#    )
-#  TARGET_LINK_LIBRARIES(${_plugin} ${VTK_LIBRARIES} ${cpPlugins_LIB} ${cpPlugins_ImageIterators_LIB} ${fpa_Instances})
-#ENDIF(USE_cpPlugins)
+IF(USE_cpPlugins)
+  INCLUDE_DIRECTORIES(
+    ${PROJECT_SOURCE_DIR}/lib
+    ${PROJECT_BINARY_DIR}/lib
+    )
+  CreatePlugin(fpaPlugins Plugins ${cpPlugins_CONFIG_NUMBER_OF_FILES})
+  TARGET_LINK_LIBRARIES(
+    fpaPlugins
+    cpPlugins cpExtensions
+    ${cpPlugins_Instances}
+    ${fpa_Instances}
+    )
+ENDIF(USE_cpPlugins)
 
 ## eof - $RCSfile$
\ No newline at end of file