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Hmmm.... I get it. Distance Map is just Euclidean Dist. Similar to
bwdist of matlab. <br>
<br>
I just observed there is SignedDistanceMap as well... I think that
should do the trick.<br>
<pre class="moz-signature" cols="72">thanks
Vimal Singh
Graduate Student
ECE Dept.
Univ of Texas, Austin</pre>
<br>
On 2/1/2011 3:22 PM, Kishore Mosaliganti wrote:
<blockquote
cite="mid:AANLkTinrrJ94-t73y9riY4SjfDyKbmWFiJUbydeQN-R-@mail.gmail.com"
type="cite">
<pre wrap="">Hi Vimal,
The levelset function is supposed to be initialized in such a way that
there is a negative and positive part in the range of the function.
The fast marching filter allows one to specify negative seeds and
therefore it generates a 0 levelset which is a circle.
The output of the Danielsson Distance map is a fully positive function.
To make it work, subtract some value from its output before setting it
as input to the levelset filter.
Kishore
On Tue, Feb 1, 2011 at 4:15 PM, Vimal Singh <a class="moz-txt-link-rfc2396E" href="mailto:vimal@mail.utexas.edu"><vimal@mail.utexas.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi all,
I'm a new User to ITK and have been learning it for past few days. I
managed to run the example codes and observe the same results available in
software guide document.
Currently I'm trying to develop my GeodesicActiveContourImageFilter, which
is similar to the one provided in the examples/segmentation folder but does
not use FastMarchingImageFilter for generation of initial Level Set. Instead
relies on user input for this initial level-set.
I've modified the example code accordingly and observed that the DistanceMap
obtained using DanielssonDistanceMapImageFilter matches exactly the
distance-map of initial level set generated by Example code. However my
final segmentation result is not the same, despite the parameters for all
other filters in two codes have been kept the same. My complete code is
below.
Can anyone give me hints as to what I might be missing. I've removed the
FastMarchingImageFilter all together. Any kind off help would be highly
appreciated !!! Or cite me an easier way to debug things ?
#include "itkImage.h"
#include "itkGeodesicActiveContourLevelSetImageFilter.h"
#include "itkCurvatureAnisotropicDiffusionImageFilter.h"
#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
#include "itkSigmoidImageFilter.h"
//#include "itkFastMarchingImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkDanielssonDistanceMapImageFilter.h" //Include for distance map
int main( int argc, char *argv[] )
{
if( argc < 10 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImage initialLevelSet outputImage";
std::cerr << " Sigma SigmoidAlpha SigmoidBeta";
std::cerr << " CurvatureScaling AdvectionTerm PropagationScaling" <<
std::endl;
return 1;
}
std::cout << "Debug Point 1" << std::endl;
typedef float InternalPixelType;
const unsigned int Dimension = 2;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::BinaryThresholdImageFilter<
InternalImageType,
OutputImageType > ThresholdingFilterType;
ThresholdingFilterType::Pointer thresholder =
ThresholdingFilterType::New();
thresholder->SetLowerThreshold( -1000.0 );
thresholder->SetUpperThreshold( 0.0 );
thresholder->SetOutsideValue( 0 );
thresholder->SetInsideValue( 255 );
typedef itk::DanielssonDistanceMapImageFilter<
InternalImageType, InternalImageType >
DistanceMapFilterType;
DistanceMapFilterType::Pointer distanceMap =
DistanceMapFilterType::New(); //Instantiating the DistanceMap filter
std::cout << "Debug Point 3" << std::endl;
typedef itk::ImageFileReader< InternalImageType > ReaderType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New(); //reads image
ReaderType::Pointer reader2 = ReaderType::New(); //reads thresholded
initial level-set //reading the inital binary level-set image
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( argv[1] );
reader2->SetFileName( argv[2] );
writer->SetFileName( argv[3] );
typedef itk::RescaleIntensityImageFilter<
InternalImageType,
OutputImageType > CastFilterType;
typedef itk::CurvatureAnisotropicDiffusionImageFilter<
InternalImageType,
InternalImageType > SmoothingFilterType;
SmoothingFilterType::Pointer smoothing = SmoothingFilterType::New();
typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<
InternalImageType,
InternalImageType > GradientFilterType;
typedef itk::SigmoidImageFilter<
InternalImageType,
InternalImageType > SigmoidFilterType;
GradientFilterType::Pointer gradientMagnitude =
GradientFilterType::New();
SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();
sigmoid->SetOutputMinimum( 0.0 );
sigmoid->SetOutputMaximum( 1.0 );
typedef itk::GeodesicActiveContourLevelSetImageFilter< InternalImageType,
InternalImageType > GeodesicActiveContourFilterType;
GeodesicActiveContourFilterType::Pointer geodesicActiveContour =
GeodesicActiveContourFilterType::New();
const double propagationScaling = atof( argv[9] );
const double curvatureScaling = atof( argv[7] );
const double advectionScaling = atof( argv[8] );
geodesicActiveContour->SetPropagationScaling( propagationScaling );
geodesicActiveContour->SetCurvatureScaling( curvatureScaling );
geodesicActiveContour->SetAdvectionScaling( advectionScaling );
std::cout << "Debug Point 7" << std::endl;
geodesicActiveContour->SetMaximumRMSError( 0.02 );
geodesicActiveContour->SetNumberOfIterations(800);
smoothing->SetInput( reader->GetOutput() );
gradientMagnitude->SetInput( smoothing->GetOutput() );
sigmoid->SetInput( gradientMagnitude->GetOutput() );
distanceMap->SetInput( reader2->GetOutput() );
geodesicActiveContour->SetInput( distanceMap->GetOutput() ); //our
distance Mapped initial level-set
geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );
thresholder->SetInput( geodesicActiveContour->GetOutput() );
writer->SetInput( thresholder->GetOutput() );
smoothing->SetTimeStep( 0.125 );
smoothing->SetNumberOfIterations( 5 );
smoothing->SetConductanceParameter( 9.0 );
std::cout << "Debug Point 9" << std::endl;
const double sigma = atof( argv[4] );
gradientMagnitude->SetSigma( sigma );
const double alpha = atof( argv[5] );
const double beta = atof( argv[6] );
sigmoid->SetAlpha( alpha );
sigmoid->SetBeta( beta );
std::cout << "Debug Point 9.1" << std::endl;
CastFilterType::Pointer caster1 = CastFilterType::New();
CastFilterType::Pointer caster2 = CastFilterType::New();
CastFilterType::Pointer caster3 = CastFilterType::New();
CastFilterType::Pointer caster4 = CastFilterType::New();
WriterType::Pointer writer1 = WriterType::New();
WriterType::Pointer writer2 = WriterType::New();
WriterType::Pointer writer3 = WriterType::New();
WriterType::Pointer writer4 = WriterType::New();
std::cout << "Debug Point 9.15" << std::endl;
caster1->SetInput( smoothing->GetOutput() );
writer1->SetInput( caster1->GetOutput() );
writer1->SetFileName("myGeodesicActiveContourImageFilterOutput1.png");
caster1->SetOutputMinimum( 0 );
caster1->SetOutputMaximum( 255 );
writer1->Update();
std::cout << "Debug Point 9.2" << std::endl;
caster2->SetInput( gradientMagnitude->GetOutput() );
writer2->SetInput( caster2->GetOutput() );
writer2->SetFileName("myGeodesicActiveContourImageFilterOutput2.png");
caster2->SetOutputMinimum( 0 );
caster2->SetOutputMaximum( 255 );
writer2->Update();
std::cout << "Debug Point 9.3" << std::endl;
caster3->SetInput( sigmoid->GetOutput() );
writer3->SetInput( caster3->GetOutput() );
writer3->SetFileName("myGeodesicActiveContourImageFilterOutput3.png");
caster3->SetOutputMinimum( 0 );
caster3->SetOutputMaximum( 255 );
writer3->Update();
//caster4->SetInput( distanceMap->GetOutput() );
caster4->SetInput( geodesicActiveContour->GetInput());
writer4->SetInput( caster4->GetOutput() );
writer4->SetFileName("myGeodesicActiveContourImageFilterOutput4.png");
caster4->SetOutputMinimum( 0 );
caster4->SetOutputMaximum( 255 );
//writer4->Update();
std::cout << "Debug Point 10" << std::endl;
try
{
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
// Print out some useful information
std::cout << std::endl;
std::cout << "Max. no. iterations: " <<
geodesicActiveContour->GetNumberOfIterations() << std::endl;
std::cout << "Max. RMS error: " <<
geodesicActiveContour->GetMaximumRMSError() << std::endl;
std::cout << std::endl;
std::cout << "No. elpased iterations: " <<
geodesicActiveContour->GetElapsedIterations() << std::endl;
std::cout << "RMS change: " << geodesicActiveContour->GetRMSChange() <<
std::endl;
writer4->Update();
return 0;
}
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</pre>
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