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CannySegmentationLevelSetImageFilter.cxx
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CannySegmentationLevelSetImageFilter.cxx
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/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// INPUTS: {ThresholdSegmentationLevelSetImageFilterVentricle.png}
// OUTPUTS: {CannySegmentationLevelSetImageFilterVentricle1.png}
// ARGUMENTS: 7.0 0.1 10.0 127.5 15
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
// \index{itk::Canny\-Segmentation\-LevelSet\-Image\-Filter}
//
// The \doxygen{CannySegmentationLevelSetImageFilter} defines a speed term
// that minimizes distance to the Canny edges in an image. The initial
// level set model moves through a gradient advection field until it locks
// onto those edges. This filter is more suitable for refining existing
// segmentations than as a region-growing algorithm.
//
// The two terms defined for the CannySegmentationLevelSetImageFilter
// are the advection term and the propagation term from
// Equation~\ref{eqn:LevelSetEquation}. The advection term is constructed by
// minimizing the squared distance transform from the Canny edges.
//
// \begin{equation}
// \label{eqn:CannySegmentationLevelSetImageFilterAdvection}
// \mbox{min} \int D^2 \Rightarrow D \nabla D
// \end{equation}
//
// where the distance transform $D$ is calculated using a
// \doxygen{DanielssonDistanceMapImageFilter} applied to the output of the
// \doxygen{CannyEdgeDetectionImageFilter}.
//
// For cases in which some surface expansion is to be allowed, a non-zero
// value may be set for the propagation term. The propagation term is simply
// $D$. As with all ITK level set segmentation filters, the curvature term
// controls the smoothness of the surface.
//
// CannySegmentationLevelSetImageFilter expects two inputs. The first is an
// initial level set in the form of an \doxygen{Image}. The second input is
// the feature image $g$ from which propagation and advection terms are
// calculated. It is generally a good idea to do some preprocessing of the
// feature image to remove noise.
//
// Figure~\ref{fig:CannySegmentationLevelSetImageFilterDiagram} shows how the
// image processing pipeline is constructed. We read two images: the image to
// segment and the image that contains the initial implicit surface. The goal
// is to refine the initial model from the second input and not to grow a new
// segmentation from seed points. The \code{feature} image is preprocessed
// with a few iterations of an anisotropic diffusion filter.
//
// \begin{figure} \center
// \includegraphics[width=0.9\textwidth]{CannySegmentationLevelSetImageFilterCollaborationDiagram1}
// \itkcaption[CannySegmentationLevelSetImageFilter collaboration
// diagram]{Collaboration diagram for the CannySegmentationLevelSetImageFilter
// applied to a segmentation task.}
// \label{fig:CannySegmentationLevelSetImageFilterDiagram}
// \end{figure}
//
// Let's start by including the appropriate header file.
//
// Software Guide : EndLatex
#include "itkImage.h"
// Software Guide : BeginCodeSnippet
#include "itkCannySegmentationLevelSetImageFilter.h"
#include "itkGradientAnisotropicDiffusionImageFilter.h"
// Software Guide : EndCodeSnippet
#include "itkFastMarchingImageFilter.h"
#include "itkBinaryThresholdImageFilter.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkZeroCrossingImageFilter.h"
int main( int argc, char *argv[] )
{
if( argc < 9 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " InputImage InitialModel OutputImage";
std::cerr << " CannyThreshold ";
std::cerr << " CannyVariance ";
std::cerr << " AdvectionWeight";
std::cerr << " InitialModelIsovalue";
std::cerr << " MaximumIterations";
std::cerr << " [OutputSpeedImage]" << std::endl;
return 1;
}
// Software Guide : BeginLatex
//
// We define the image type using a particular pixel type and
// dimension. In this case we will use 2D \code{float} images.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef float InternalPixelType;
const unsigned int Dimension = 2;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
// Software Guide : EndCodeSnippet
typedef unsigned char OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::BinaryThresholdImageFilter<
InternalImageType,
OutputImageType > ThresholdingFilterType;
ThresholdingFilterType::Pointer thresholder = ThresholdingFilterType::New();
thresholder->SetUpperThreshold( 10.0 );
thresholder->SetLowerThreshold( 0.0 );
thresholder->SetOutsideValue( 0 );
thresholder->SetInsideValue( 255 );
typedef itk::ImageFileReader< InternalImageType > ReaderType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
ReaderType::Pointer reader1 = ReaderType::New();
ReaderType::Pointer reader2 = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader1->SetFileName( argv[1] );
reader2->SetFileName( argv[2] );
writer->SetFileName( argv[3] );
// Software Guide : BeginLatex
//
// The input image will be processed with a few iterations of
// feature-preserving diffusion. We create a filter and set the
// appropriate parameters.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::GradientAnisotropicDiffusionImageFilter< InternalImageType,
InternalImageType> DiffusionFilterType;
DiffusionFilterType::Pointer diffusion = DiffusionFilterType::New();
diffusion->SetNumberOfIterations(5);
diffusion->SetTimeStep(0.125);
diffusion->SetConductanceParameter(1.0);
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The following lines define and instantiate a
// CannySegmentationLevelSetImageFilter.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef itk::CannySegmentationLevelSetImageFilter< InternalImageType,
InternalImageType > CannySegmentationLevelSetImageFilterType;
CannySegmentationLevelSetImageFilterType::Pointer cannySegmentation =
CannySegmentationLevelSetImageFilterType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// As with the other ITK level set segmentation filters, the terms of the
// CannySegmentationLevelSetImageFilter level set equation can be
// weighted by scalars. For this application we will modify the relative
// weight of the advection term. The propagation and curvature term weights
// are set to their defaults of $0$ and $1$, respectively.
//
// \index{itk::Canny\-Segmentation\-LevelSet\-Image\-Filter!SetAdvectionScaling()}
// \index{itk::Segmentation\-LevelSet\-ImageFilter!SetAdvectionScaling()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
cannySegmentation->SetAdvectionScaling( ::atof(argv[6]) );
cannySegmentation->SetCurvatureScaling( 1.0 );
cannySegmentation->SetPropagationScaling( 0.0 );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The maximum number of iterations is specified from the command line.
// It may not be desirable in some applications to run the filter to
// convergence. Only a few iterations may be required.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
cannySegmentation->SetMaximumRMSError( 0.01 );
cannySegmentation->SetNumberOfIterations( ::atoi(argv[8]) );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// There are two important parameters in the
// CannySegmentationLevelSetImageFilter to control the behavior of the
// Canny edge detection. The \emph{variance} parameter controls the
// amount of Gaussian smoothing on the input image. The \emph{threshold}
// parameter indicates the lowest allowed value in the output image.
// Thresholding is used to suppress Canny edges whose gradient magnitudes
// fall below a certain value.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
cannySegmentation->SetThreshold( ::atof(argv[4]) );
cannySegmentation->SetVariance( ::atof(argv[5]) );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Finally, it is very important to specify the isovalue of the surface in
// the initial model input image. In a binary image, for example, the
// isosurface is found midway between the foreground and background values.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
cannySegmentation->SetIsoSurfaceValue( ::atof(argv[7]) );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filters are now connected in a pipeline indicated in
// Figure~\ref{fig:CannySegmentationLevelSetImageFilterDiagram}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
diffusion->SetInput( reader1->GetOutput() );
cannySegmentation->SetInput( reader2->GetOutput() );
cannySegmentation->SetFeatureImage( diffusion->GetOutput() );
thresholder->SetInput( cannySegmentation->GetOutput() );
writer->SetInput( thresholder->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Invoking the \code{Update()} method on the writer triggers the
// execution of the pipeline. As usual, the call is placed in a
// \code{try/catch} block to handle any exceptions that may be thrown.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
writer->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
// Software Guide : EndCodeSnippet
// Print out some useful information
std::cout << std::endl;
std::cout << "Max. no. iterations: " << cannySegmentation->GetNumberOfIterations() << std::endl;
std::cout << "Max. RMS error: " << cannySegmentation->GetMaximumRMSError() << std::endl;
std::cout << std::endl;
std::cout << "No. elpased iterations: " << cannySegmentation->GetElapsedIterations() << std::endl;
std::cout << "RMS change: " << cannySegmentation->GetRMSChange() << std::endl;
// Software Guide : BeginLatex
//
// We can use this filter to make some subtle refinements to the ventricle
// segmentation from the previous example that used the
// \doxygen{ThresholdSegmentationLevelSetImageFilter}. The application
// was run using \code{Examples/Data/BrainProtonDensitySlice.png} and
// \code{Examples/Data/VentricleModel.png} as inputs, a \code{threshold}
// of $7.0$, \code{variance} of $0.1$, \code{advection weight} of $10.0$,
// and an initial isosurface value of $127.5$. One case was run for $15$
// iterations and the second was run to convergence. Compare the results
// in the two rightmost images of
// Figure~\ref{fig:CannySegmentationLevelSetImageFilter} with the
// ventricle segmentation from
// Figure~\ref{fig:ThresholdSegmentationLevelSetImageFilter} shown in the
// middle. Jagged edges are straightened and the small spur at the upper
// right-hand side of the mask has been removed.
//
// \begin{figure}
// \includegraphics[width=0.24\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.24\textwidth]{ThresholdSegmentationLevelSetImageFilterVentricle}
// \includegraphics[width=0.24\textwidth]{CannySegmentationLevelSetImageFilterVentricle1}
// \includegraphics[width=0.24\textwidth]{CannySegmentationLevelSetImageFilterVentricle2}
// \itkcaption[Segmentation results of CannyLevelSetImageFilter]{Results of
// applying the CannySegmentationLevelSetImageFilter to a prior ventricle
// segmentation. Shown from left to right are the original image, the
// prior segmentation of the ventricle from
// Figure~\ref{fig:ThresholdSegmentationLevelSetImageFilter}, $15$ iterations of
// the CannySegmentationLevelSetImageFilter, and the
// CannySegmentationLevelSetImageFilter run to convergence.}
// \label{fig:CannySegmentationLevelSetImageFilter}
// \end{figure}
//
// The free parameters of this filter can be adjusted to achieve a wide
// range of shape variations from the original model. Finding the right
// parameters for your particular application is usually a process of
// trial and error. As with most ITK level set segmentation filters,
// examining the propagation (speed) and advection images can help the
// process of tuning parameters. These images are available using
// \code{Set/Get} methods from the filter after it has been updated.
//
// Software Guide : EndLatex
if( argc > 9 )
{
const char * speedImageFileName = argv[9];
// Software Guide : BeginLatex
//
// In some cases it is interesting to take a direct look at the speed image
// used internally by this filter. This may help for setting the correct
// parameters for driving the segmentation. In order to obtain such speed
// image, the method \code{GenerateSpeedImage()} should be invoked first.
// Then we can recover the speed image with the \code{GetSpeedImage()} method
// as illustrated in the following lines.
//
// \index{itk::Canny\-Segmentation\-LevelSet\-Image\-Filter!GenerateSpeedImage()}
// \index{itk::Segmentation\-LevelSet\-ImageFilter!GenerateSpeedImage()}
// \index{itk::Canny\-Segmentation\-LevelSet\-Image\-Filter!GetSpeedImage()}
// \index{itk::Segmentation\-LevelSet\-ImageFilter!GetSpeedImage()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
cannySegmentation->GenerateSpeedImage();
typedef CannySegmentationLevelSetImageFilterType::SpeedImageType
SpeedImageType;
typedef itk::ImageFileWriter<SpeedImageType> SpeedWriterType;
SpeedWriterType::Pointer speedWriter = SpeedWriterType::New();
speedWriter->SetInput( cannySegmentation->GetSpeedImage() );
// Software Guide : EndCodeSnippet
speedWriter->SetFileName( speedImageFileName );
try
{
speedWriter->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Exception caught ! while writing the speed image" << std::endl;
std::cerr << "Filename : " << speedImageFileName << std::endl;
std::cerr << excep << std::endl;
}
}
return 0;
}