[Insight-users] PCAnalisys successful !

[Lucas Lorenzo]

Jim and Lydia,

thanks a lot. Now it works perfectly !

Lucas

On Thursday, January 8, 2004, at 09:17 AM, Miller, James V (Research)  
wrote:

> Lucas,
>
> Since you are reusing a reader, I think you want to change
> the lines of code that are like this
>
>    reader->SetFileName( argv[2] );
>    reader->Update();
>    applyPCAShapeEstimator->SetInput(1,reader->GetOutput());
>
> to look like this
>
>    InputImageType::Pointer img;
>
>    reader->SetFileName( argv[2] );
>    reader->Update();
>    img = reader->GetOutput();  // grab a handle to the output of the  
> reader
>    img->DisconnectPipeline();  // disassociate the reader output from  
> the
> reader
>    applyPCAShapeEstimator->SetInput(1,img);
>
> If you do not disconnect the image from the reader, then all the inputs
> to the PCA estimator will be same.
>
> The other option is to use multiple readers.
>
> Jim
>
>
> -----Original Message-----
> From: lucas [mailto:lucas at xserve.cvrti.utah.edu]
> Sent: Thursday, January 08, 2004 3:04 AM
> To: Luis Ibanez
> Cc: Insight-users at itk.org
> Subject: [Insight-users] PCAnalisys
>
>
> Hi Luis,
>
> I'm trying to perform a PCA on a set of training signed
> distance functions but although they are different from
> each other all the eigenvalues are zero.
> I think I might be making a mistake when loading the
> training datasets but I'm not sure.
> The following one is the code I'm using:
>
>
> #include "itkImage.h"
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "vnl/vnl_matrix_fixed.h"
> #include "vnl/vnl_math.h"
> #include "itkTextOutput.h"
> #include "itkVector.h"
> #include "itkImagePCAShapeModelEstimator.h"
>
>
> int main( int argc, char * argv[] )
> {
>    if( argc < 4 )
>      {
>      std::cerr << "Usage: " << argv[0];
>      std::cerr << std::endl;
>      return 1;
>      }
>
>    typedef short InputPixelType;
>    typedef double   OutputPixelType;
>
>    typedef itk::Image<InputPixelType,2> InputImageType;
>    typedef itk::Image<OutputPixelType,2> OutputImageType;
>
>    typedef itk::ImageFileReader< InputImageType  >
>  ReaderType;
>    typedef itk::ImageFileWriter< OutputImageType >
>  WriterType;
>
>    ReaderType::Pointer reader = ReaderType::New();
>    WriterType::Pointer writer = WriterType::New();
>
>     
> / 
> /----------------------------------------------------------------------
>     
> / 
> /----------------------------------------------------------------------
>    //Set the image model estimator
>     
> / 
> /----------------------------------------------------------------------
>    typedef
> itk::ImagePCAShapeModelEstimator<InputImageType,
> OutputImageType>
>      ImagePCAShapeModelEstimatorType;
>
>    ImagePCAShapeModelEstimatorType::Pointer
>      applyPCAShapeEstimator =
> ImagePCAShapeModelEstimatorType::New();
>
>     
> / 
> /----------------------------------------------------------------------
>    //Set the parameters of the clusterer
>     
> / 
> /----------------------------------------------------------------------
>    applyPCAShapeEstimator->SetNumberOfTrainingImages(4);
>    applyPCAShapeEstimator->SetNumberOfPrincipalComponentsRequired(2);
>
>    reader->SetFileName( argv[1] );
>    reader->Update();
>    applyPCAShapeEstimator->SetInput(0,reader->GetOutput()
> );
>
>    reader->SetFileName( argv[2] );
>    reader->Update();
>    applyPCAShapeEstimator->SetInput(1,reader->GetOutput());
>
>    reader->SetFileName( argv[3] );
>    reader->Update();
>    applyPCAShapeEstimator->SetInput(2,
> reader->GetOutput());
>
>    reader->SetFileName( argv[4] );
>    reader->Update();
>    applyPCAShapeEstimator->SetInput(3,
> reader->GetOutput());
>
>    applyPCAShapeEstimator->Update();
>
>     
> / 
> /----------------------------------------------------------------------
>    // Write the mean image
>     
> / 
> /----------------------------------------------------------------------
>    writer->SetFileName("mean.vtk");
>    writer->SetInput(applyPCAShapeEstimator->GetOutput( 0 )
> );
>    try
>      {
>        writer->Update();
>      }
>    catch( itk::ExceptionObject exp )
>      {
>      std::cerr << "Exception caught ! mean writer" <<
> std::endl;
>      std::cerr <<     exp    << std::endl;
>      }
>
>      
> / 
> /----------------------------------------------------------------------
>    // Write first mode image
>     
> / 
> /----------------------------------------------------------------------
>    writer->SetFileName("1mode.vtk");
>    writer->SetInput(applyPCAShapeEstimator->GetOutput( 1 )
> );
>    try
>      {
>        writer->Update();
>      }
>    catch( itk::ExceptionObject exp )
>      {
>      std::cerr << "Exception caught ! 1st mode writer" <<
> std::endl;
>      std::cerr <<     exp    << std::endl;
>      }
>
>      
> / 
> /----------------------------------------------------------------------
>    // Write second mode image
>     
> / 
> /----------------------------------------------------------------------
>    writer->SetFileName("2mode.vtk");
>    writer->SetInput(applyPCAShapeEstimator->GetOutput( 2 )
> );
>    try
>      {
>        writer->Update();
>      }
>    catch( itk::ExceptionObject exp )
>      {
>      std::cerr << "Exception caught ! 2nd mode writer" <<
> std::endl;
>      std::cerr <<     exp    << std::endl;
>      }
>
>    vnl_vector<double> eigenValues =
>      applyPCAShapeEstimator->GetEigenValues();
>
>    for(unsigned int i= 0; i< 4 ; i++ )
>      {
>      std::cout << eigenValues[ i ] << std::endl;
>      }
>
>    return 0;
> }
>
> If you have any clue of what am I doing wrong please let
> me know.
> Thanks,
>
> Lucas Lorenzo
>
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>
Lucas Lorenzo

University of Utah
Nora Eccles Harrison CardioVascular Research and Training Institute
Fellows Room
95 South 2000 East
Salt Lake City, UT 84112-5000

e-mail:  lucas at cvrti.utah.edu
telephone: 801-587-9536