[Insight-users] Memory management

[Arunachalam Kana]

Hi ITK Users,

I need some advice on memory management and speed.

My system details: 64 bit windowsXP system and 4Gb RAM.

My goal: To obtain eigen vectors for 100Mb unsigned short image. Eigen vectors not for the whole image but for certain regions (approx occupies 40% of image).



I have to do some preprocessing too.

The pipeline is :

Original image -> discretegaussian -> gradientmagnitude -> HessianRecursiveGaussianImageFilter->symmetric eigenvalue analysis -> finally 3 vector image

For the above pipeline for a 100Mb image, i am running out of RAM.

After reading itkmails, i decided to use streamfilter to stream part of the image so that the RAM usage is low. I only tested half way and the RAM was overloaded.



I am using streamimagefilter to reduce the memory usage. After calculation of gradientmagnitude i have used 1.08Gb RAM. After this i need 1.2Gb RAM

For hessianimageoutput, so by using streamfilter i thought i would be reaching 2.5Gm RAM but i reach approx 6Gb(virtual memory is used).

1.       Am i doing something wrong with the stream filter ? (code given below)

2.       I tried another option: As i do not need hessian for the whole image, I used discretehessianfunction for hessian calculation but it is 30 times slower that the recursivehessian. Is discretegaussianimagefunction multithreaded?

3.       Is there any other way to achieve speed vs RAM compromised solution?

4.       The 100Mb data set is test data. The real data is 10Gb for which i will use 64 bit linux system (opensuse 11.2) . will the pipeline be executed in linux too?

Below is my code and after application of filter show the RAM usage:



  char *infilename = "StreamTest.mhd";

  typedef itk::CovariantVector<float,3> VectorPixelType;

  typedef itk::Vector< VectorPixelType, 3 > EV_PixelType;



  //Image type

  typedef itk::Image<unsigned short, 3>              InputImageType;

  typedef itk::Image<float, 3>                       FloatImageType;

  typedef itk::Image<EV_PixelType,3>                                                 EVImageType;

**** RAM usage = 674Mb****

  //reader initialisation and reading file

  typedef itk::ImageFileReader<InputImageType>                     ReaderType;

  ReaderType::Pointer reader = ReaderType::New();

  reader->SetFileName( infilename );

  reader->Update();

  InputImageType::Pointer inImage = reader->GetOutput();



**** RAM usage = 783Mb****

  typedef itk::DiscreteGaussianImageFilter<InputImageType, FloatImageType> RGIFType;

  RGIFType::Pointer gaussfilter = RGIFType::New();

  gaussfilter->SetInput(inImage);

  gaussfilter->SetVariance(4.0);

  gaussfilter->SetMaximumError(0.01);



  typedef itk::CastImageFilter<FloatImageType,InputImageType> CIFType;

  CIFType::Pointer castfilter = CIFType::New();

  castfilter->SetInput(gaussfilter->GetOutput());



  typedef itk::GradientMagnitudeImageFilter<InputImageType,FloatImageType> GMIFType;

  GMIFType::Pointer gmfilter = GMIFType::New();

  gmfilter->SetInput(castfilter->GetOutput());

  gmfilter->Update();



  FloatImageType::Pointer gmImage = gmfilter->GetOutput();

**** RAM usage = 1290Mb****



  gaussfilter->UnRegister();

  castfilter->UnRegister();

  **** RAM usage = 1080Mb****



  typedef itk::HessianRecursiveGaussianImageFilter<FloatImageType> HessianRecursiveGaussianFilterType;

  typedef HessianRecursiveGaussianFilterType::OutputImageType HessianImageType;

  HessianRecursiveGaussianFilterType::Pointer hessianfilter = HessianRecursiveGaussianFilterType::New();

  hessianfilter->SetInput(gmImage);

  hessianfilter->SetSigma(1);



  typedef itk::StreamingImageFilter<HessianImageType,HessianImageType> StreamerType;

  StreamerType::Pointer streamer = StreamerType::New();

  streamer->SetInput( hessianfilter->GetOutput() );

  streamer->SetNumberOfStreamDivisions( 20 );

  streamer->Update();

**** RAM usage = 3600Mb**** after few seconds it came to **** RAM usage = 6120Mb****


Thank you in advance.

Regards,
Kana Arunachalam Kannappan
Research Associate
FH OÖ Forschungs & Entwicklungs GmbH
Stelzhamer Strasse 23,
4600 Wels,
Austria.
Phone: +43 (0)7242 72811 -4420
kana.arunachalam at fh-wels.at
www.fh-ooe.at; www.3dct.at

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