ITK/Examples/Statistics/ExpectationMaximizationMixtureModelEstimator 2D: Difference between revisions

From KitwarePublic
< ITK‎ | Examples
Jump to navigationJump to search
mNo edit summary
No edit summary
Line 114: Line 114:
</source>
</source>


==CMakeLists.txt==
{{ITKCMakeLists|ExpectationMaximizationMixtureModelEstimator_2D}}
<source lang="cmake">
cmake_minimum_required(VERSION 2.6)
 
PROJECT(ExpectationMaximizationMixtureModelEstimator)
 
FIND_PACKAGE(ITK REQUIRED)
INCLUDE(${ITK_USE_FILE})
 
ADD_EXECUTABLE(ExpectationMaximizationMixtureModelEstimator ExpectationMaximizationMixtureModelEstimator.cxx)
TARGET_LINK_LIBRARIES(ExpectationMaximizationMixtureModelEstimator
ITKBasicFilters ITKCommon ITKIO ITKStatistics)
 
</source>

Revision as of 03:05, 2 March 2011

Calculate a mixture model on a collection of measurements using EM.

ExpectationMaximizationMixtureModelEstimator_2D.cxx

<source lang="cpp">

  1. include "itkVector.h"
  2. include "itkListSample.h"
  3. include "itkGaussianMixtureModelComponent.h"
  4. include "itkExpectationMaximizationMixtureModelEstimator.h"
  5. include "itkNormalVariateGenerator.h"

int main(int, char *[]) {

 unsigned int numberOfClasses = 2;
 typedef itk::Vector< double, 2 > MeasurementVectorType;
 typedef itk::Statistics::ListSample< MeasurementVectorType > SampleType;
 SampleType::Pointer sample = SampleType::New();
 
 typedef itk::Statistics::NormalVariateGenerator NormalGeneratorType;
 NormalGeneratorType::Pointer normalGenerator = NormalGeneratorType::New();
 // Create the first set of 2D Gaussian samples
 normalGenerator->Initialize( 101 );
 MeasurementVectorType mv;
 double mean = 100;
 double standardDeviation = 30;
 for ( unsigned int i = 0 ; i < 100 ; ++i )
   {
   mv[0] = ( normalGenerator->GetVariate() * standardDeviation ) + mean;
   mv[1] = ( normalGenerator->GetVariate() * standardDeviation ) + mean;
   sample->PushBack( mv );
   }
 // Create the second set of 2D Gaussian samples
 normalGenerator->Initialize( 3024 );
 mean = 200;
 standardDeviation = 30;
 for ( unsigned int i = 0 ; i < 100 ; ++i )
   {
   mv[0] = ( normalGenerator->GetVariate() * standardDeviation ) + mean;
   mv[1] = ( normalGenerator->GetVariate() * standardDeviation ) + mean;
   sample->PushBack( mv );
   }
 typedef itk::Array< double > ParametersType;
 ParametersType params( 6 );
 // Create the first set of initial parameters
 std::vector< ParametersType > initialParameters( numberOfClasses );
 params[0] = 110.0; // mean of dimension 1
 params[1] = 115.0; // mean of dimension 2
 params[2] = 800.0; // covariance(0,0)
 params[3] = 0; // covariance(0,1)
 params[4] = 0; // covariance(1,0)
 params[5] = 805.0; // covariance(1,1)
 initialParameters[0] = params;
 // Create the second set of initial parameters
 params[0] = 210.0; // mean of dimension 1
 params[1] = 215.0; // mean of dimension 2
 params[2] = 850.0; // covariance(0,0)
 params[3] = 0; // covariance(0,1)
 params[4] = 0; // covariance(1,0)
 params[5] = 855.0; // covariance(1,1)
 initialParameters[1] = params;
 typedef itk::Statistics::GaussianMixtureModelComponent< SampleType >
   ComponentType;
 // Create the components
 std::vector< ComponentType::Pointer > components;
 for ( unsigned int i = 0 ; i < numberOfClasses ; i++ )
   {
   components.push_back( ComponentType::New() );
   (components[i])->SetSample( sample );
   (components[i])->SetParameters( initialParameters[i] );
   }
 typedef itk::Statistics::ExpectationMaximizationMixtureModelEstimator<
   SampleType > EstimatorType;
 EstimatorType::Pointer estimator = EstimatorType::New();
 estimator->SetSample( sample );
 estimator->SetMaximumIteration( 200 );
 itk::Array< double > initialProportions(numberOfClasses);
 initialProportions[0] = 0.5;
 initialProportions[1] = 0.5;
 estimator->SetInitialProportions( initialProportions );
 for ( unsigned int i = 0 ; i < numberOfClasses ; i++)
   {
   estimator->AddComponent( (ComponentType::Superclass*)
                            (components[i]).GetPointer() );
   }
 estimator->Update();
 // Output the results
 for ( unsigned int i = 0 ; i < numberOfClasses ; i++ )
   {
   std::cout << "Cluster[" << i << "]" << std::endl;
   std::cout << "    Parameters:" << std::endl;
   std::cout << "         " << (components[i])->GetFullParameters()
             << std::endl;
   std::cout << "    Proportion: ";
   std::cout << "         " << estimator->GetProportions()[i] << std::endl;
   }
   
 return EXIT_SUCCESS;

} </source>

CMakeLists.txt

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

project(ExpectationMaximizationMixtureModelEstimator_2D)

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

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

endif()

add_executable(ExpectationMaximizationMixtureModelEstimator_2D MACOSX_BUNDLE ExpectationMaximizationMixtureModelEstimator_2D.cxx)

if( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(ExpectationMaximizationMixtureModelEstimator_2D ITKReview ${ITK_LIBRARIES})

else( "${ITK_VERSION_MAJOR}" LESS 4 )

 target_link_libraries(ExpectationMaximizationMixtureModelEstimator_2D ${ITK_LIBRARIES})

endif( "${ITK_VERSION_MAJOR}" LESS 4 )

</syntaxhighlight>

Download and Build ExpectationMaximizationMixtureModelEstimator_2D

Click here to download ExpectationMaximizationMixtureModelEstimator_2D and its CMakeLists.txt file. Once the tarball ExpectationMaximizationMixtureModelEstimator_2D.tar has been downloaded and extracted,

cd ExpectationMaximizationMixtureModelEstimator_2D/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:

./ExpectationMaximizationMixtureModelEstimator_2D

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.