[ITK] Bspline registration with Mutual Information v4 : memory concern

[Timothee Evain]

Hi Dženan,

Sure!
You could find here an archive https://www.dropbox.com/s/9scgn9if39i4a1x/V4RegistrationMemoryLeak.tar?dl=0
It contains:
-Fixed and moving images in mhd format
-The binary (for windows)
-The source code with its CMakeLists if you want to compile for another OS

Thanks,

Tim


----- Mail original -----
De: "Dženan Zukić" <dzenanz at gmail.com>
À: "Timothee Evain" <tevain at telecom-paristech.fr>
Cc: community at itk.org
Envoyé: Lundi 5 Septembre 2016 20:54:29
Objet: Re: [ITK] Bspline registration with Mutual Information v4 : memory concern

Hi Tim,

can you turn this snippet into a runnable example which reproduces the
memory leak?

Regards,
Dženan

On Mon, Sep 5, 2016 at 12:27 PM, Timothee Evain <tevain at telecom-paristech.fr
> wrote:

> Hello everyone,
>
> I'm trying a Bspline registration based on the Mutual Information metric
> (v4) and I'm facing a memory problem.
> When running the registration, the memory usage skyrockets in a second
> until freezing the PC by lack of memory.
> I don't know why : this doesn't happen when I'm switching to another
> metric (e.g. Correlation), the images aren't that big (~400k voxels) and a
> previous rigid registration phase behaved correctly.
> Here is my code snippet, what am I doing wrong ? (Image overlap had been
> ensured)
>
>    typedef itk::Image<float,3> ImageTypef;
>
>    itk::ImageRegistrationMethodv4<ImageTypef,ImageTypef>::Pointer
> WarpHelper=
>       itk::ImageRegistrationMethodv4<ImageTypef,ImageTypef>::New();
>    itk::MattesMutualInformationImageToImageMetricv4<ImageTypef,ImageTypef>::Pointer
> MIMetrics=
>       itk::MattesMutualInformationImageToImageMetricv4<ImageTypef,
> ImageTypef>::New();
>    itk::BSplineTransform<double,3,3>::Pointer BSplineTransform=
>       itk::BSplineTransform<double,3,3>::New();
>    itk::LBFGSOptimizerv4::Pointer Optimizer=
>       itk::LBFGSOptimizerv4::New();
>
>    MIMetrics->SetNumberOfHistogramBins(50);
>    MIMetrics->SetUseMovingImageGradientFilter(false);
>    MIMetrics->SetUseFixedImageGradientFilter(false);
>    MIMetrics->SetUseFixedSampledPointSet(false);
>    MIMetrics->SetVirtualDomainFromImage(TestIm);
>
>
>    WarpHelper->SetFixedImage(TestIm);
>    WarpHelper->SetMetricSamplingPercentage(0.002);
>    WarpHelper->SetMovingImage(MovIm);
>    WarpHelper->SetMetric(MIMetrics);
>    //WarpHelper->SetMetricSamplingStrategy(WarpHelper->RANDOM);
>    WarpHelper->InPlaceOn();
>    WarpHelper->SetInitialTransform(BSplineTransform);
>    WarpHelper->SetOptimizer(Optimizer);
>
>    itk::Array<double> ShrinkFactorPerLevel(1);
>    ShrinkFactorPerLevel[0]=1;
>    itk::Array<double> SmoothSigmaPerLevel(1);
>    SmoothSigmaPerLevel[0]=0;
>    WarpHelper->SetNumberOfLevels(1);
>    WarpHelper->SetSmoothingSigmasPerLevel(SmoothSigmaPerLevel);
>    WarpHelper->SetShrinkFactorsPerLevel(ShrinkFactorPerLevel);
>
>    /* ----- Initialize the Bspline Transform ----- */
>    BSplineTransform->SetTransformDomainOrigin(TestIm->GetOrigin());
>    BSplineTransform->SetTransformDomainDirection(TestIm->GetDirection());
>
>    itk::Vector<double,3> PhysicalDim;
>    for (int dim = 0; dim < 3; dim++)
>    {
>       PhysicalDim=(TestIm->GetSpacing()[dim])*float((TestIm->
> GetLargestPossibleRegion().GetSize()[dim])-1);
>    }
>    BSplineTransform->SetTransformDomainPhysicalDimensions(PhysicalDim);
>
>    itk::Size<3> meshSize;
>    meshSize.Fill(10-3);// NbGridNodesEachDim-SplineOrder
>    BSplineTransform->SetTransformDomainMeshSize(meshSize);
>
>    BSplineTransform->SetIdentity();
>
>    /* ----- Optimizer setup ----- */
>    itk::Array<double> ScaleBspline(BSplineTransform-
> >GetNumberOfParameters());
>    ScaleBspline.fill(1);
>
>    Optimizer->SetLineSearchAccuracy(0.9);
>    Optimizer->SetDefaultStepLength(1.5);
>    Optimizer->TraceOn();
>    Optimizer->SetGradientConvergenceTolerance(1e-3);
>    Optimizer->SetMaximumNumberOfFunctionEvaluations(20);
>    Optimizer->SetDoEstimateScales(false);
>    Optimizer->SetScales(ScaleBspline);
>
>
>    try
>    {
>       WarpHelper->Update();
>    }
>    catch (itk::ExceptionObject &err)
>    {
>       std::cerr<<err;
>       return 0;
>    }
>
> Thanks,
>
> Tim
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