#!/bin/bash
-## Command line arguments
-while [[ "$#" -gt 1 ]]; do
- key="$1"
- case $key in
- -input)
- input="$2"
- shift
- ;;
- -seed)
- sx="$2"
- sy="$3"
- sz="$4"
- shift
- ;;
- -mori)
- mori="$2"
- shift
- ;;
- -labels)
- labels="$2"
- shift
- ;;
- -output)
- output="$2"
- shift
- ;;
- *)
- # Do nothing
- ;;
- esac
- shift
-done
-if [ -z "$input" ] || [ -z "$sx" ] || [ -z "$sy" ] || [ -z "$sz" ]; then
- (>&2 echo "Usage: $0 -input input_raw_image -seed x y z [-mori mori_image_dfilename] [-labels labels_image_filename] [-output output_image_filename] [-mori_init_threshold value] [-mori_end_threshold value] [-mori_delta value] [-mori_minimum_threshold value] [-mori_inside_value value] [-mori_outside_value value] [-mori_signal_kernel_size value] [-mori_signal_threshold value] [-mori_signal_influence value] [-label_upper_threshold value] [-label_inside value] [-label_outside value] [-random_walker_beta value]")
- exit 1
-fi
-if [ -z "$mori_init_threshold" ]; then mori_init_threshold="-1024"; fi
-if [ -z "$mori_end_threshold" ]; then mori_end_threshold="0"; fi
-if [ -z "$mori_delta" ]; then mori_delta="1"; fi
-if [ -z "$mori_minimum_threshold" ]; then mori_minimum_threshold="-850"; fi
-if [ -z "$mori_inside_value" ]; then mori_inside_value="255"; fi
-if [ -z "$mori_outside_value" ]; then mori_outside_value="0"; fi
-if [ -z "$mori_signal_kernel_size" ]; then mori_signal_kernel_size="20"; fi
-if [ -z "$mori_signal_threshold" ]; then mori_signal_threshold="500"; fi
-if [ -z "$mori_signal_influence" ]; then mori_signal_influence="0.5"; fi
-if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
-if [ -z "$label_inside" ]; then label_inside="1"; fi
-if [ -z "$label_outside" ]; then label_outside="2"; fi
-if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
+input=$1
+dir=`dirname $input`
+base=`basename $1 .mhd`_florez-l
+output="$dir/$base"_segmentation.mhd
+mori="$dir/$base"_mori.mhd
+signal="$dir/$base"_mori_signal.txt
+labels="$dir/$base"_labels.mhd
+diff="$dir/$base"_diff.mhd
+seed="$dir"/seed_florez-l.txt
-base_name=`dirname $input`/`basename $input .mhd`
-if [ -z "$mori" ]; then
- mori="$base_name"_mori.mhd
-fi
-signal="$mori"_signal.txt
-if [ -z "$labels" ]; then
- labels="$base_name"_labels.mhd
-fi
-if [ -z "$output" ]; then
- output="$base_name"_rw.mhd
-fi
-
-exec_dir=`dirname $0`
-mori_seg=`dirname $0`/fpa_CTBronchi_MoriSegmentation
-mori_lab=`dirname $0`/fpa_CTBronchi_MoriLabelling
-random_walker=`dirname $0`/fpa_CTBronchi_RandomWalker
-
-$mori_seg \
- $input $mori $signal \
- $mori_init_threshold \
- $mori_end_threshold \
- $mori_delta \
- $mori_minimum_threshold \
- $mori_inside_value \
- $mori_outside_value \
- $mori_signal_kernel_size \
- $mori_signal_threshold \
- $mori_signal_influence \
- $sx $sy $sz
-
-$mori_lab \
- $input $mori $labels \
- $label_upper_threshold \
- $mori_inside_value \
- $label_inside \
- $label_outside
-
-$random_walker \
- $input $labels $output \
- $label_inside \
- $random_walker_beta
+(>&2 echo -n "Processing $input... ")
+echo "************************************************"
+./fpa_CTBronchi_Process \
+ -in $input \
+ -out $output \
+ -seed `cat $seed` \
+ -out_mori $mori \
+ -out_signal $signal \
+ -out_labels $labels \
+ -out_diff $diff
+echo "************************************************"
+(>&2 echo "done.")
## eof - $RCSfile$
// =========================================================================
#include <itkImage.h>
+#include <itkAbsoluteValueDifferenceImageFilter.h>
+#include <itkBinaryThresholdImageFilter.h>
#include <CTBronchi/Functions.h>
#include <CTBronchi/Mori.h>
#include <CTBronchi/MoriLabelling.h>
const unsigned int Dim = 3;
typedef short TInputPixel;
typedef unsigned char TLabelPixel;
-typedef float TScalar;
typedef itk::Image< TInputPixel, Dim > TImage;
typedef itk::Image< TLabelPixel, Dim > TLabelImage;
-typedef itk::Image< TScalar, Dim > TScalarImage;
-
-// -------------------------------------------------------------------------
-/* TODO
- TMap Args;
- TInputImage::PointType global_seed;
- TLabelPixel inside_value = TLabelPixel( 1 );
- TLabelPixel outside_value = TLabelPixel( 0 );
- TLabelPixel inside_label = TLabelPixel( 1 );
- TLabelPixel outside_label = TLabelPixel( 2 );
-*/
-
-// -------------------------------------------------------------------------
-/* TODO
- template< class _TInputPtr, class _TOutputPtr >
- void Label( _TOutputPtr& output, const _TInputPtr& input, const _TOutputPtr& labels )
- {
- typedef typename _TInputPtr::ObjectType _TInput;
- typedef typename _TOutputPtr::ObjectType _TOutput;
- typedef CTBronchi::MoriLabelling< _TInput, _TOutput > _TLabelling;
-
- typename _TLabelling::Pointer labelling = _TLabelling::New( );
- labelling->SetInput( input );
- labelling->SetInputLabels( labels );
- labelling->SetOutsideValue( outside_label );
- labelling->SetInsideValue( inside_label );
- labelling->SetInputInsideValue( inside_value );
- labelling->SetUpperThreshold(
- TInputPixel( std::atof( Args[ "labelling_upper_threshold" ].c_str( ) ) )
- );
- double t = MeasureTime( labelling );
- std::cout << "Labelling executed in " << t << " s" << std::endl;
- output = labelling->GetOutput( );
- TMap::const_iterator i = Args.find( "out_labels" );
- if( i != Args.end( ) )
- WriteImage( output, i->second );
- output->DisconnectPipeline( );
- }
-
- // -------------------------------------------------------------------------
- template< class _TRawPtr, class _TLabelPtr >
- void RandomWalker( _TLabelPtr& output, const _TRawPtr& raw, const _TLabelPtr& labels )
- {
- typedef typename _TRawPtr::ObjectType _TRaw;
- typedef typename _TLabelPtr::ObjectType _TLabel;
- }
-
- // -------------------------------------------------------------------------
- bool ParseArgs( int argc, char* argv[] )
- {
- std::set< std::string > mandatory;
- mandatory.insert( "in" );
- mandatory.insert( "out_segmentation" );
- mandatory.insert( "seed_x" );
- mandatory.insert( "seed_y" );
- mandatory.insert( "seed_z" );
-
- Args[ "mori_minimum_threshold" ] = "-850";
- Args[ "mori_signal_kernel_size" ] = "20";
- Args[ "mori_signal_threshold" ] = "100";
- Args[ "mori_signal_influence" ] = "0.5";
- Args[ "mori_lower_threshold" ] = "-1024";
- Args[ "mori_upper_threshold" ] = "0";
- Args[ "mori_delta_threshold" ] = "1";
- Args[ "labelling_upper_threshold" ] = "-400";
-
- for( int i = 1; i < argc; i += 2 )
- Args[ argv[ i ] + 1 ] = argv[ i + 1 ];
-
- bool complete = true;
- for( std::string t: mandatory )
- complete &= ( Args.find( t ) != Args.end( ) );
-
- if( !complete )
- {
- std::cerr
- << "Usage: " << argv[ 0 ] << std::endl
- << "\t-in filename" << std::endl
- << "\t-out_segmentation filename" << std::endl
- << "\t-seed_x value -seed_y value -seed_z value" << std::endl
- << "\t[-out_mori filename]" << std::endl
- << "\t[-out_signal filename]" << std::endl
- << "\t[-out_labels filename]" << std::endl
- << "\t[-mori_minimum_threshold value]" << std::endl
- << "\t[-mori_signal_kernel_size value]" << std::endl
- << "\t[-mori_signal_threshold value]" << std::endl
- << "\t[-mori_signal_influence value]" << std::endl
- << "\t[-mori_lower_threshold value]" << std::endl
- << "\t[-mori_upper_threshold value]" << std::endl
- << "\t[-mori_delta_threshold value]" << std::endl
- << "\t[-labelling_upper_threshold value]" << std::endl;
- return( false );
-
- } // fi
- return( true );
- }
-*/
// -------------------------------------------------------------------------
int main( int argc, char* argv[] )
TLabelImage::Pointer labels;
CTBronchi::Label( labels, input_image, mori, opt_thr, args );
- // Final segmentation
- TScalarImage::Pointer segmentation;
- CTBronchi::RandomWalker( segmentation, input_image, labels, args );
+ // Final labels
+ TLabelImage::Pointer final_labels;
+ CTBronchi::RandomWalker( final_labels, input_image, labels, args );
+
+ // Extract label 1
+ typedef itk::BinaryThresholdImageFilter< TLabelImage, TLabelImage > TBinThr;
+ TBinThr::Pointer bin_thr = TBinThr::New( );
+ bin_thr->SetInput( final_labels );
+ bin_thr->SetLowerThreshold( 1 );
+ bin_thr->SetUpperThreshold( 1 );
+ bin_thr->SetInsideValue( 1 );
+ bin_thr->SetOutsideValue( 0 );
+ double t = CTBronchi::MeasureTime( bin_thr );
+ std::cout << "Label extracted in " << t << " s" << std::endl;
+ TLabelImage::Pointer segmentation = bin_thr->GetOutput( );
// Save
CTBronchi::WriteImage( segmentation, args[ "out" ] );
+
+ // Save difference
+ std::map< std::string, std::string >::const_iterator i =
+ args.find( "out_diff" );
+ if( i != args.end( ) )
+ {
+ typedef itk::AbsoluteValueDifferenceImageFilter< TLabelImage, TLabelImage, TLabelImage > TDiff;
+ TDiff::Pointer diff = TDiff::New( );
+ diff->SetInput1( mori );
+ diff->SetInput2( segmentation );
+ t = CTBronchi::MeasureTime( diff );
+ std::cout << "Difference computed in " << t << " s" << std::endl;
+ TLabelImage::Pointer difference = diff->GetOutput( );
+ CTBronchi::WriteImage( difference, i->second );
+
+ } // fi
}
else
return( 1 );
} // yrt
return( 0 );
-
- /* TODO
- try
- {
- if( ParseArgs( argc, argv ) )
- {
- // Parse seed
- global_seed[ 0 ] = std::atof( Args[ "seed_x" ].c_str( ) );
- global_seed[ 1 ] = std::atof( Args[ "seed_y" ].c_str( ) );
- global_seed[ 2 ] = std::atof( Args[ "seed_z" ].c_str( ) );
-
- // Read input image
- TInputImage::Pointer input_image;
- ReadImage( input_image, Args[ "in" ] );
-
- // Mori segmentation
- TLabelImage::Pointer mori;
- Mori( mori, input_image );
-
- // Create labels
- TLabelImage::Pointer labels;
- Label( labels, input_image, mori );
-
- return( 0 );
-
- } // fi
- return( 1 );
- }
- */
- /* TODO
- if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
- if [ -z "$label_inside" ]; then label_inside="1"; fi
- if [ -z "$label_outside" ]; then label_outside="2"; fi
- if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
- */
}
// eof - $RCSfile$
namespace CTBronchi
{
// -----------------------------------------------------------------------
- template< class _TInputPtr, class _TOutputPtr, class _TLabelPtr >
+ template< class _TInputPtr, class _TLabelPtr >
void RandomWalker(
- _TOutputPtr& output,
+ _TLabelPtr& output,
const _TInputPtr& input, const _TLabelPtr& labels,
std::map< std::string, std::string >& args
)
{
typedef typename _TInputPtr::ObjectType _TInput;
- typedef typename _TOutputPtr::ObjectType _TOutput;
typedef typename _TLabelPtr::ObjectType _TLabel;
- typedef typename _TOutput::PixelType _TOutputPixel;
- typedef fpa::Filters::Image::RandomWalker< _TInput, _TLabel, _TOutputPixel > _TRandomWalker;
- typedef fpa::Functors::Dijkstra::Image::Gaussian< _TInput, _TOutputPixel > _TWeight;
+ typedef float _TScalar;
+ typedef fpa::Filters::Image::RandomWalker< _TInput, _TLabel, _TScalar > _TRandomWalker;
+ typedef fpa::Functors::Dijkstra::Image::Gaussian< _TInput, _TScalar > _TWeight;
typename _TWeight::Pointer weight = _TWeight::New( );
weight->SetAlpha( std::atof( args[ "random_walker_alpha" ].c_str( ) ) );
rw->SetWeightFunction( weight );
double t = CTBronchi::MeasureTime( rw );
std::cout << "RandomWalker executed in " << t << " s" << std::endl;
- output = rw->GetOutput( );
+ output = rw->GetOutputLabels( );
output->DisconnectPipeline( );
}
git://git.creatis.insa-lyon.fr / FrontAlgorithms.git / commitdiff