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[FrontAlgorithms.git] / appli / CTBronchi / Skeleton.cxx

diff --git a/appli/CTBronchi/Skeleton.cxx b/appli/CTBronchi/Skeleton.cxx
new file mode 100644 (file)
index 0000000..4110825
--- /dev/null
+++ b/appli/CTBronchi/Skeleton.cxx
@@ -0,0 +1,119 @@
+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+
+#include <sstream>
+#include <string>
+#include <tclap/CmdLine.h>
+#include <itkImage.h>
+#include <ivq/ITK/ImageSkeletonWriter.h>
+#include <fpa/Filters/Image/ExtractSkeleton.h>
+#include "Functions.h"
+
+// -------------------------------------------------------------------------
+const unsigned int Dim = 3;
+typedef unsigned char             TPixel;
+typedef itk::Image< TPixel, Dim > TImage;
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+  typedef TCLAP::ValueArg< std::string >   _TStringArg;
+  typedef TCLAP::ValueArg< double >        _TRealArg;
+  typedef TCLAP::ValueArg< unsigned long > _TUIntArg;
+  typedef TCLAP::ValueArg< TPixel >        _TPixelArg;
+
+  // Parse input line
+  _TStringArg in( "i", "input", "Input image", true, "", "file" );
+  _TStringArg out( "o", "output", "Output skeleton", true, "", "file" );
+  _TStringArg oute( "e", "end_points", "Output end points", false, "", "file" );
+  _TStringArg aSeed( "p", "seed", "Input seed", true, "", "\"x y z\"" );
+  try
+  {
+    TCLAP::CmdLine cmd( "Skeleton", ' ', "1.0.0" );
+    cmd.add( aSeed );
+    cmd.add( oute );
+    cmd.add( out );
+    cmd.add( in );
+    cmd.parse( argc, argv );
+  }
+  catch( TCLAP::ArgException& err )
+  {
+    std::cerr
+      << "===============================" << std::endl
+      << "Error caught: " << std::endl
+      << err.error( ) << " " << err.argId( )
+      << "===============================" << std::endl
+      << std::endl;
+    return( 1 );
+
+  } // yrt
+
+  // Get seed
+  std::istringstream sSeed( aSeed.getValue( ) );
+  TImage::PointType pnt;
+  sSeed >> pnt[ 0 ] >> pnt[ 1 ] >> pnt[ 2 ];
+
+  try
+  {
+    // Read image
+    TImage::Pointer input_image;
+    CTBronchi::ReadImage( input_image, in.getValue( ) );
+
+    TImage::IndexType seed;
+    input_image->TransformPhysicalPointToIndex( pnt, seed );
+
+    // Skeleton extraction
+    typedef fpa::Filters::Image::ExtractSkeleton< TImage > TFilter;
+    TFilter::Pointer filter = TFilter::New( );
+    filter->SetInput( input_image );
+    filter->SeedFromMaximumDistanceOff( );
+    filter->SetSeed( seed );
+    filter->GetDistanceMap( )->InsideIsPositiveOn( );
+    filter->GetDistanceMap( )->SquaredDistanceOff( );
+    filter->GetDistanceMap( )->UseImageSpacingOn( );
+    double t = CTBronchi::MeasureTime( filter );
+    std::cout << "Skeleton executed in " << t << " s" << std::endl;
+
+    // Save results
+    typedef ivq::ITK::ImageSkeletonWriter< TFilter::TSkeleton > TWriter;
+    TWriter::Pointer skeleton_writer = TWriter::New( );
+    skeleton_writer->SetInput( filter->GetOutput( ) );
+    skeleton_writer->SetFileName( out.getValue( ) );
+    skeleton_writer->Update( );
+
+    // Write end points
+    if( oute.getValue( ) != "" )
+    {
+      std::stringstream eStr;
+      auto pnts = filter->GetEndPoints( );
+      for( unsigned int i = 0; i < 10; ++i )
+      {
+        eStr
+          << pnts[ i ][ 0 ] << " "
+          << pnts[ i ][ 1 ] << " "
+          << pnts[ i ][ 2 ] << " " << i % 3 << std::endl;
+
+      } // rof
+      std::ofstream oStrE( oute.getValue( ).c_str( ) );
+      oStrE << eStr.str( );
+      oStrE.close( );
+
+    } // fi
+  }
+  catch( std::exception& err )
+  {
+    std::cerr
+      << "===============================" << std::endl
+      << "Error caught: " << std::endl
+      << err.what( )
+      << "===============================" << std::endl
+      << std::endl;
+    return( 1 );
+
+  } // yrt
+  return( 0 );
+}
+
+// eof - $RCSfile$