--- /dev/null
+// =========================================================================
+// @author Leonardo Florez Valencia
+// @email florez-l@javeriana.edu.co
+// =========================================================================
+
+#include <string>
+#include <tclap/CmdLine.h>
+#include <itkImage.h>
+#include <fpa/Common/SliceBySliceRandomWalker.h>
+#include "Functions.h"
+
+// -------------------------------------------------------------------------
+const unsigned int Dim = 3;
+typedef short TPixel;
+typedef unsigned char TLabel;
+typedef itk::NumericTraits< TPixel >::RealType TScalar;
+typedef itk::Image< TPixel, Dim > TImage;
+typedef itk::Image< TLabel, Dim > TLabels;
+typedef itk::Image< TScalar, Dim > TScalarImage;
+
+// -------------------------------------------------------------------------
+int main( int argc, char* argv[] )
+{
+ typedef TCLAP::ValueArg< std::string > _TStringArg;
+ typedef TCLAP::ValueArg< TScalar > _TRealArg;
+
+ // Parse input line
+ _TStringArg in( "i", "input", "Input image", true, "", "file" );
+ _TStringArg labels( "l", "labels", "Input labels", true, "", "file" );
+ _TStringArg vesselness( "v", "vesselness", "Input vesselness", true, "", "file" );
+ _TStringArg out( "o", "output", "Output image", true, "", "file" );
+ _TRealArg beta( "b", "beta", "Beta", false, 2.5, "value (2.5)" );
+ _TRealArg eps( "e", "epsilon", "Epsilon", false, 1e-5, "value (1e-5)" );
+ try
+ {
+ TCLAP::CmdLine cmd( "FastRandomWalker", ' ', "1.0.0" );
+ cmd.add( eps );
+ cmd.add( beta );
+ cmd.add( out );
+ cmd.add( vesselness );
+ cmd.add( labels );
+ 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
+ << std::endl;
+ return( 1 );
+
+ } // yrt
+
+ try
+ {
+ // Read input image
+ TImage::Pointer input_image;
+ CTBronchi::ReadImage( input_image, in.getValue( ) );
+
+ // Read input labels
+ TLabels::Pointer input_labels;
+ CTBronchi::ReadImage( input_labels, labels.getValue( ) );
+
+ // Read input vesselness
+ TScalarImage::Pointer input_vesselness;
+ CTBronchi::ReadImage( input_vesselness, vesselness.getValue( ) );
+
+ // Random walk
+ typedef fpa::Common::SliceBySliceRandomWalker< TImage, TLabels, TScalarImage > TFilter;
+ TFilter::Pointer filter = TFilter::New( );
+ filter->SetInput( input_image );
+ filter->SetInputLabels( input_labels );
+ filter->SetInputVesselness( input_vesselness );
+
+ // Prepare weight functor
+ /* TODO
+ typedef fpa::Functors::Dijkstra::Image::Gaussian< TImage, TScalar > TWeight;
+ TWeight::Pointer weight = TWeight::New( );
+ weight->SetBeta( beta.getValue( ) );
+ weight->SetEpsilon( eps.getValue( ) );
+
+ // Random walk
+ typedef fpa::Filters::Image::RandomWalker< TImage, TLabels, TScalar > TFilter;
+ TFilter::Pointer filter = TFilter::New( );
+ filter->SetInputImage( input_image );
+ filter->SetInputLabels( input_labels );
+ filter->SetWeightFunction( weight );
+ double t = CTBronchi::MeasureTime( filter );
+ std::cout << "FastRandomWalk executed in " << t << " s" << std::endl;
+
+ // Write result
+ CTBronchi::WriteImage( filter->GetOutputLabels( ), out.getValue( ) );
+ */
+ }
+ catch( std::exception& err )
+ {
+ std::cerr
+ << "===============================" << std::endl
+ << "Error caught: " << std::endl
+ << err.what( ) << std::endl
+ << "===============================" << std::endl
+ << std::endl;
+ return( 1 );
+
+ } // yrt
+ return( 0 );
+}
+
+// eof - $RCSfile$
this->m_VesselnessThreshold * this->m_VesselnessMax / TScalar( 100 );
// Composite image
- typename TScalarImage::Pointer composite = TScalarImage::New( );
- composite->CopyInformation( vesselness );
- composite->SetBufferedRegion( vesselness->GetBufferedRegion( ) );
- composite->Allocate( );
+ typename TScalarImage::Pointer composite;
this->_Composite( composite, labels, vesselness );
// Extract slices
} // rof
// Random walker slice-by-slice
- this->_GoDown( binaryTree, data3D, fusion, numSlices );
- this->_GoUp( binaryTree, data3D, fusion, numSlices );
+ this->_RandomWalker( binaryTree, data3D, fusion, true );
+ this->_RandomWalker( binaryTree, data3D, fusion, false );
// Join results
typedef itk::JoinSeriesImageFilter< _TSliceImage, TImage > _TJoin;
typename TScalarImage::RegionType region = labels->GetRequestedRegion( );
// Composite image
- typename TScalarImage::Pointer composite = TScalarImage::New( );
+ composite = TScalarImage::New( );
composite->CopyInformation( vesselness );
composite->SetBufferedRegion( vesselness->GetBufferedRegion( ) );
composite->Allocate( );
template< class _TBinaryTree, class _TData3D, class _TFusion >
void
fpa::Common::SliceBySliceRandomWalker< _TImage, _TLabels, _TScalarImage >::
-_GoDown(
+_RandomWalker(
_TBinaryTree& binaryTree,
const _TData3D& data3D,
const _TFusion& fusion,
- int numSlices
+ bool down
)
{
typedef typename _TBinaryTree::value_type _TSliceBinaryPtr;
typedef typename _TSliceFusionPtr::ObjectType _TSliceFusion;
typedef typename _TSliceFusion::PixelType _TSliceScalar;
- int z = -1;
- while( z < numSlices - 2 )
+ int numSlices = binaryTree.size( );
+ int z = ( down )? -1: numSlices;
+ int o = ( down )? 1: -1;
+ while( ( down && z < numSlices - 2 ) || ( !down && z > 1 ) )
{
- z++;
+ z += o;
_TSliceBinaryPtr tmp = binaryTree[ z ];
- _TSliceBinaryPtr next = binaryTree[ z + 1 ];
- _TSliceData3DPtr data = data3D[ z + 1 ];
- _TSliceFusionPtr vess = fusion[ z + 1 ];
+ _TSliceBinaryPtr next = binaryTree[ z + o ];
+ _TSliceData3DPtr data = data3D[ z + o ];
+ _TSliceFusionPtr vess = fusion[ z + o ];
typename _TSliceBinary::RegionType region = tmp->GetRequestedRegion( );
// Create seeds and background
rw->SetEdgeFunction( edge );
// Keep maximum
- /* TODO
- typedef itk::MaximumImageFilter<SliceType> MaxFilterType;
- MaxFilterType::Pointer maxFilter = MaxFilterType::New();
- maxFilter->SetInput(0, img2);
- maxFilter->SetInput(1, next);
- maxFilter->Update();
-
- SliceType::Pointer sth = maxFilter->GetOutput();
- ImageAlgorithm::Copy(sth.GetPointer(), binaryTree[z + 1].GetPointer(), sth->GetRequestedRegion(), binaryTree[z + 1]->GetRequestedRegion());
- delete[] probs;
- */
- }
-}
-
-// -------------------------------------------------------------------------
-template< class _TImage, class _TLabels, class _TScalarImage >
-template< class _TBinaryTree, class _TData3D, class _TFusion >
-void
-_GoUp(
- _TBinaryTree& binaryTree,
- const _TData3D& data3D,
- const _TFusion& fusion,
- int numSlices
- )
-{
+ typedef itk::MaximumImageFilter< _TSliceBinary > _TMax;
+ _TMax::Pointer max = _TMax::New();
+ max->SetInput( 0, rw->GetOutput( ) );
+ max->SetInput( 1, next );
+ max->Update( );
+ binaryTree[ z + o ] = max->GetOutput( );
+ binaryTree[ z + o ]->DisconnectPipeline( );
+
+ } // elihw
}
#endif // __fpa__Common__SliceBySliceRandomWalker__hxx__
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / commitdiff