[Insight-users] Registration Example in java?

[Michael Bell]

Here is some java code to do an affine registration on windows. It is
modelled after Examples/ImageRegistration9.cxx. The cvs version of
WrapITK was necessary for some of the classes. The parameters are
tuned for the specific images I am using, so you might have to set
them differently for your application. It's not a full application,
but it should get you started.

            System.loadLibrary("ITKCommon");
            itkMeanSquaresImageToImageMetricIF2IF2_Pointer metric =
          itkMeanSquaresImageToImageMetricIF2IF2.itkMeanSquaresImageToImageMetricIF2IF2_New();
            itkCenteredTransformInitializerA2DTDIF2IF2_Pointer
initializer =
itkCenteredTransformInitializerA2DTDIF2IF2.itkCenteredTransformInitializerA2DTDIF2IF2_New();
            itkAffineTransformD2_Pointer transform =
itkAffineTransformD2.itkAffineTransformD2_New();
            itkRegularStepGradientDescentOptimizer_Pointer optimizer =
               itkRegularStepGradientDescentOptimizer.itkRegularStepGradientDescentOptimizer_New();
            itkLinearInterpolateImageFunctionIF2D_Pointer interpolator
=
itkLinearInterpolateImageFunctionIF2D.itkLinearInterpolateImageFunctionIF2D_New();
            itkImageRegistrationMethodIF2IF2_Pointer registration =

itkImageRegistrationMethodIF2IF2.itkImageRegistrationMethodIF2IF2_New();

            itkImageFileReaderIF2_Pointer fixedReader =
itkImageFileReaderIF2.itkImageFileReaderIF2_New();
            fixedReader.SetFileName( fixedName);
            fixedReader.Update();
            itkImageFileReaderIF2_Pointer moveReader =
itkImageFileReaderIF2.itkImageFileReaderIF2_New();
            moveReader.SetFileName( movingName);
            moveReader.Update();

            registration.SetMetric(metric.GetPointer());
            registration.SetOptimizer(optimizer.GetPointer());
            registration.SetTransform(transform.GetPointer());
            registration.SetInterpolator(interpolator.GetPointer());
            registration.SetFixedImageRegion(fixedReader.GetOutput().GetBufferedRegion());

            initializer.SetTransform(transform.GetPointer());
            initializer.SetFixedImage(fixedReader.GetOutput());
            initializer.SetMovingImage(moveReader.GetOutput());
            initializer.MomentsOn();
            initializer.InitializeTransform();

            registration.SetFixedImage(fixedReader.GetOutput());
            registration.SetMovingImage(moveReader.GetOutput());
            registration.SetFixedImageRegion(fixedReader.GetOutput().GetBufferedRegion());

            registration.SetInitialTransformParameters(transform.GetParameters());

            itkArrayD scales = new itkArrayD(6);
            scales.Fill(1.0);
            scales.SetElement(4,0.001);
            scales.SetElement(5,0.001);
            optimizer.SetScales(scales);

            optimizer.SetMaximumStepLength( 0.7 );
            optimizer.SetMinimumStepLength( 0.1 );
            optimizer.SetNumberOfIterations( 300 );
            optimizer.MinimizeOn();

            registration.StartRegistration();

            itkArrayD finalParameters =
registration.GetLastTransformParameters();
            System.out.println("Result = ");
            System.out.println(" Center X      = " +
transform.GetCenter().GetElement(0));
            System.out.println(" Center Y      = " +
transform.GetCenter().GetElement(1));
            System.out.println(" Translation X = " +
finalParameters.GetElement(4));
            System.out.println(" Translation Y = " +
finalParameters.GetElement(5));
            System.out.println(" Iterations    = " +
optimizer.GetCurrentIteration());
            System.out.println(" Metric value  = " + optimizer.GetValue());

            System.out.println(finalParameters.GetElement(0) + " " +
finalParameters.GetElement(1));

            itkResampleImageFilterIF2IF2_Pointer resampler =
itkResampleImageFilterIF2IF2.itkResampleImageFilterIF2IF2_New();
            resampler.SetInput(moveReader.GetOutput());
            resampler.SetTransform(registration.GetTransform());
            resampler.SetSize(moveReader.GetOutput().GetLargestPossibleRegion().GetSize());
            resampler.SetOutputOrigin(moveReader.GetOutput().GetOrigin());
            resampler.SetOutputSpacing(moveReader.GetOutput().GetSpacing());
            resampler.SetDefaultPixelValue(100);
            resampler.Update();


On 9/6/06, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> Hi 歐陽儒
>
> Unfortunately we don't have any Java examples for registration.
>
> However, you can easily convert the Python examples in to Java.
>
> Please look at the Java examples in the Examples/Filtering
> directory, and compare them with the equivalent Python examples
> in the same directory.
>
> That comparison will give you an idea on how to convert from
> Python to Java.
>
>
>   Regards,
>
>
>     Luis
>
>
> -------------
> 歐陽儒 wrote:
> > Hello
> >
> >       Is there any Java example in "Registration" application of ITK?
> >
> >       I am a Student in Taiwan Tzu Chi University and I'm working on content-based
> > retrival in medical images.
> >
> >       Please reply this mail as soon as possible. :P
> >
> >
> >
> > P.S. I have a problem casting unsigned long 2 image  to unsighed short
> > image in java before, and I solve it. :D
> >
> >
> > Best Regard.
>
>
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>


-- 
michael.bell at acm.org