ITK/Examples/Math/AmoebaOptimization

ITK optimizers are generic classes, which can be used independently of registration. This example demonstrates use of the itk::AmoebaOptimizer class in optimizing a simple paraboloid function.

Contributed by: Davis Vigneault

AmoebaOptimization.cxx

<source lang="cpp"> // Include the Amoeba optimizer and a custom cost function

1. include "itkAmoebaOptimizer.h"
2. include "ExampleCostFunction.h"

// Typedef the optimizer and cost function, for convenience typedef itk::AmoebaOptimizer OptimizerType; typedef itk::ExampleCostFunction2 CostType;

int main(int argc, char ** argv) {

 // Instantiate the optimizer
 OptimizerType::Pointer optimizer = OptimizerType::New();
 
 // Set properties pertinent to convergence
 optimizer->SetMaximumNumberOfIterations( 100 );
 optimizer->SetParametersConvergenceTolerance( 0.01 );
 optimizer->SetFunctionConvergenceTolerance( 0.01 );

 // Instantiate the cost function
 // The cost function is a 2D paraboloid in the x-y plane
 // with the equation f(x,y) = (x+5)^2+(y-7)^2 + 5
 // and a global minimum at (x,y) = (-5, 7)
 CostType::Pointer cost = CostType::New();

 // Assign the cost function to the optimizer
 optimizer->SetCostFunction( cost.GetPointer() );
 
 // Set the initial parameters of the cost function
 OptimizerType::ParametersType initial(2);
 initial[0] = 123;
 initial[1] = -97.4;
 optimizer->SetInitialPosition( initial );
 
 // Begin the optimization!
 optimizer->StartOptimization();

 // Print out some information about the optimization
 std::cout << "Position: " << optimizer->GetCurrentPosition() << std::endl;
 std::cout << "Value: " << optimizer->GetValue() << std::endl;
 
 // As expected, the position is near to (-5, 7) and the value to 5
 // Position: [-5.003825599641884, 6.998563761340231]
 // Value: 5.00002
 return EXIT_SUCCESS;

} </source>

ExampleCostFunction.h

<source lang="cpp">

1. ifndef itkExampleCostFunction_h
2. define itkExampleCostFunction_h

1. include "itkSingleValuedCostFunction.h"

namespace itk { class ExampleCostFunction : public SingleValuedCostFunction { public:

 /** Standard class typedefs. */
 typedef ExampleCostFunction      Self;
 typedef SingleValuedCostFunction Superclass;
 typedef SmartPointer<Self>       Pointer;
 typedef SmartPointer<const Self> ConstPointer;

 /** Method for creation through the object factory. */
 itkNewMacro(Self);

 /** Run-time type information (and related methods). */
 itkTypeMacro(ExampleCostFunction, SingleValuedCostfunction);

 unsigned int GetNumberOfParameters(void) const { return 2; } // itk::CostFunction

 MeasureType GetValue(const ParametersType & parameters) const {
   return pow(parameters[0]+5, 2)+pow(parameters[1]-7, 2)+5;
 }

 void GetDerivative(const ParametersType & parameters,
                    DerivativeType & derivative ) const {
   throw itk::ExceptionObject( __FILE__, __LINE__, "No derivative is available for this cost function.");
 }

protected:

 ExampleCostFunction(){};
 ~ExampleCostFunction(){};

private:

 ExampleCostFunction(const Self &); //purposely not implemented
 void operator = (const Self &); //purposely not implemented

};

} // end namespace itk

1. endif

</source>

CMakeLists.txt

<syntaxhighlight lang="cmake"> cmake_minimum_required(VERSION 3.9.5)

project(AmoebaOptimization)

find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED)

 find_package(VTK REQUIRED)
 include(${VTK_USE_FILE})

endif()

add_executable(AmoebaOptimization MACOSX_BUNDLE AmoebaOptimization.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(AmoebaOptimization ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(AmoebaOptimization ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build AmoebaOptimization

Click here to download AmoebaOptimization and its CMakeLists.txt file. Once the tarball AmoebaOptimization.tar has been downloaded and extracted,

cd AmoebaOptimization/build

• If ITK is installed:

cmake ..

• If ITK is not installed but compiled on your system, you will need to specify the path to your ITK build:

cmake -DITK_DIR:PATH=/home/me/itk_build ..

Build the project:

make

and run it:

./AmoebaOptimization

WINDOWS USERS PLEASE NOTE: Be sure to add the ITK bin directory to your path. This will resolve the ITK dll's at run time.

Building All of the Examples

Many of the examples in the ITK Wiki Examples Collection require VTK. You can build all of the the examples by following these instructions. If you are a new VTK user, you may want to try the Superbuild which will build a proper ITK and VTK.

ItkVtkGlue

ITK >= 4

For examples that use QuickView (which depends on VTK), you must have built ITK with Module_ITKVtkGlue=ON.

ITK < 4

Some of the ITK Examples require VTK to display the images. If you download the entire ITK Wiki Examples Collection, the ItkVtkGlue directory will be included and configured. If you wish to just build a few examples, then you will need to download ItkVtkGlue and build it. When you run cmake it will ask you to specify the location of the ItkVtkGlue binary directory.