ITK  4.13.0
Insight Segmentation and Registration Toolkit
Examples/Filtering/SecondDerivativeRecursiveGaussianImageFilter.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 : BeginLatex
//
// This example illustrates how to compute second derivatives of
// a 3D image using the \doxygen{RecursiveGaussianImageFilter}.
//
// It's good to be able to compute the raw derivative without any smoothing,
// but this can be problematic in a medical imaging scenario, when images will
// often have a certain amount of noise. It's almost always more desirable to
// include a smoothing step first, where an image is convolved with a Gaussian
// kernel in whichever directions the user desires a derivative. The nature of
// the Gaussian kernel makes it easy to combine these two steps into one,
// using an infinite impulse response (IIR) filter. In this example, all the
// second derivatives are computed independently in the same way, as if they
// were intended to be used for building the Hessian matrix of the image (a
// square matrix of second-order derivatives of an image, which is useful in
// many image processing techniques).
//
// Software Guide : EndLatex
// Software Guide : BeginLatex
//
// First, we will include the relevant header files: the
// itkRecursiveGaussianImageFilter, the image reader, writer, and duplicator.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
#include <string>
// Software Guide : EndCodeSnippet
int main(int argc, char * argv [] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " inputImage outputPrefix [sigma] " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Next, we declare our pixel type and output pixel type to be floats, and
// our image dimension to be $3$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef float PixelType;
typedef float OutputPixelType;
const unsigned int Dimension = 3;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Using these definitions, define the image types, reader and writer types,
// and duplicator types, which are templated over the pixel types and
// dimension. Then, instantiate the reader, writer, and duplicator with
// the \code{New()} method.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ImageType,
ImageType > FilterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
DuplicatorType::Pointer duplicator = DuplicatorType::New();
// Software Guide : EndCodeSnippet
reader->SetFileName( argv[1] );
std::string outputPrefix = argv[2];
std::string outputFileName;
try
{
reader->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Problem reading the input file" << std::endl;
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// Here we create three new filters. For each derivative we take, we will
// want to smooth in that direction first. So after the filters are created,
// each is given a dimension, and set to (in this example) the same sigma.
// Note that here, $\sigma$ represents the standard deviation, whereas the
// \doxygen{DiscreteGaussianImageFilter} exposes the \code{SetVariance}
// method.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
FilterType::Pointer ga = FilterType::New();
FilterType::Pointer gb = FilterType::New();
FilterType::Pointer gc = FilterType::New();
ga->SetDirection( 0 );
gb->SetDirection( 1 );
gc->SetDirection( 2 );
if( argc > 3 )
{
const float sigma = atof( argv[3] );
ga->SetSigma( sigma );
gb->SetSigma( sigma );
gc->SetSigma( sigma );
}
// Software Guide: EndCodeSnippet
// Software Guide : BeginLatex
//
// First we will compute the second derivative of the $z$-direction.
// In order to do this, we smooth in the $x$- and $y$- directions, and
// finally smooth and compute the derivative in the $z$-direction. Taking
// the zero-order derivative is equivalent to simply smoothing in that
// direction. This result is commonly notated $I_{zz}$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ga->SetZeroOrder();
gb->SetZeroOrder();
gc->SetSecondOrder();
ImageType::Pointer inputImage = reader->GetOutput();
ga->SetInput( inputImage );
gb->SetInput( ga->GetOutput() );
gc->SetInput( gb->GetOutput() );
duplicator->SetInputImage( gc->GetOutput() );
gc->Update();
duplicator->Update();
ImageType::Pointer Izz = duplicator->GetModifiableOutput();
// Software Guide: EndCodeSnippet
writer->SetInput( Izz );
outputFileName = outputPrefix + "-Izz.mhd";
writer->SetFileName( outputFileName.c_str() );
writer->Update();
// Software Guide : BeginLatex
//
// Recall that \code{gc} is the filter responsible for taking the second
// derivative. We can now take advantage of the pipeline architecture and,
// without much hassle, switch the direction of \code{gc} and \code{gb},
// so that \code{gc} now takes the derivatives in the $y$-direction. Now we
// only need to call \code{Update()} on \code{gc} to re-run the entire pipeline
// from \code{ga} to \code{gc}, obtaining the second-order derivative in the
// $y$-direction, which is commonly notated $I_{yy}$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
gc->SetDirection( 1 ); // gc now works along Y
gb->SetDirection( 2 ); // gb now works along Z
gc->Update();
duplicator->Update();
ImageType::Pointer Iyy = duplicator->GetModifiableOutput();
// Software Guide : EndCodeSnippet
writer->SetInput( Iyy );
outputFileName = outputPrefix + "-Iyy.mhd";
writer->SetFileName( outputFileName.c_str() );
writer->Update();
// Software Guide : BeginLatex
//
// Now we switch the directions of \code{gc} with that of \code{ga} in order
// to take the derivatives in the $x$-direction. This will give us $I_{xx}$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
gc->SetDirection( 0 ); // gc now works along X
ga->SetDirection( 1 ); // ga now works along Y
gc->Update();
duplicator->Update();
ImageType::Pointer Ixx = duplicator->GetModifiableOutput();
// Software Guide : EndCodeSnippet
writer->SetInput( Ixx );
outputFileName = outputPrefix + "-Ixx.mhd";
writer->SetFileName( outputFileName.c_str() );
writer->Update();
// Software Guide : BeginLatex
//
// Now we can reset the directions to their original values, and compute
// first derivatives in different directions. Since we set both \code{gb}
// and \code{gc} to compute first derivatives, and \code{ga} to zero-order
// (which is only smoothing) we will obtain $I_{yz}$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ga->SetDirection( 0 );
gb->SetDirection( 1 );
gc->SetDirection( 2 );
ga->SetZeroOrder();
gb->SetFirstOrder();
gc->SetFirstOrder();
gc->Update();
duplicator->Update();
ImageType::Pointer Iyz = duplicator->GetModifiableOutput();
// Software Guide : EndCodeSnippet
writer->SetInput( Iyz );
outputFileName = outputPrefix + "-Iyz.mhd";
writer->SetFileName( outputFileName.c_str() );
writer->Update();
// Software Guide : BeginLatex
//
// Here is how you may easily obtain $I_{xz}$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ga->SetDirection( 1 );
gb->SetDirection( 0 );
gc->SetDirection( 2 );
ga->SetZeroOrder();
gb->SetFirstOrder();
gc->SetFirstOrder();
gc->Update();
duplicator->Update();
ImageType::Pointer Ixz = duplicator->GetModifiableOutput();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// For the sake of completeness, here is how you may compute
// $I_{xz}$ and $I_{xy}$.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
writer->SetInput( Ixz );
outputFileName = outputPrefix + "-Ixz.mhd";
writer->SetFileName( outputFileName.c_str() );
writer->Update();
ga->SetDirection( 2 );
gb->SetDirection( 0 );
gc->SetDirection( 1 );
ga->SetZeroOrder();
gb->SetFirstOrder();
gc->SetFirstOrder();
gc->Update();
duplicator->Update();
ImageType::Pointer Ixy = duplicator->GetModifiableOutput();
writer->SetInput( Ixy );
outputFileName = outputPrefix + "-Ixy.mhd";
writer->SetFileName( outputFileName.c_str() );
writer->Update();
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}