[Insight-users] Import/Export Java images

[sumit shah]

Hi,

I've pasted some Java code that I use.  It may not compile as is, but  
should give you a head start.


Here is an example of how to get an itkImageF3 from a stack of  
BufferedImages:


public itkImageF3 getITK(Stack<BufferedImage> is, double voxsize[]) {

itkImportImageFilterF3_Pointer importer =  
itkImportImageFilterF3.itkImportImageFilterF3_New();

     itkIndex3 start = new itkIndex3();
     itkSize3 size = new itkSize3();
     itkImageRegion3 region = new itkImageRegion3();
     itkPointD3 origin = new itkPointD3();

     BufferedImage secondToLast = is.elementAt(is.size() - 2), last =  
is.lastElement();

     int x = last.getWidth();
     int y = last.getHeight();
     int z = is.size();

     size.SetElement(0, x);
     size.SetElement(1, y);
     size.SetElement(2, z);

     start.SetElement(0, 0);
     start.SetElement(1, 0);
     start.SetElement(2, 0);

     region.SetSize(size);
     region.SetIndex(start);

double[] pix = new double[2];
     itkVectorD3 spacing = new itkVectorD3();
     spacing.SetElement(0, voxSize[0]);
     spacing.SetElement(1, voxSize[1]);
     spacing.SetElement(2, voxSize[2]);
     importer.SetSpacing(spacing);

     origin.SetElement(0, 0);
     origin.SetElement(1, 0);
     origin.SetElement(2, 0);
     importer.SetOrigin(origin);
     importer.SetRegion(region);

     buf = SwigExtras.new_FArray(x * y * z);

     float f[] = new float[x*y];
     int i = 0;
     itkProg = 0;

     for(BufferedImage  b:is) {
       Raster r = b.getData();
       f = r.getSamples(0, 0, x, y, 0, f);
       for(int j = 0; j < f.length; j++) {
         SwigExtras.FArray_setitem(buf, i, f[i]);
         i++;
       }
     }
     importer.SetImportPointer(buf, x * y * x, false);

     itkProg = 0;
     importer.Update();

     return importer.GetOutput();

// don't forget to call SwigExtras.delete_FArray(buf); when you are  
done using it!!!
}


Here is an example to do an affine transform on an image (tarITK  
variable which is an object of type itkImageF3):

final itkResampleImageFilterF3F3_Pointer resample =  
itkResampleImageFilterF3F3.itkResampleImageFilterF3F3_New();
final itkLinearInterpolateImageFunctionF3D_Pointer interpolator =  
itkLinearInterpolateImageFunctionF3D.itkLinearInterpolateImageFunctionF3 
D_New();
final itkAffineTransform3_Pointer transform =  
itkAffineTransform3.itkAffineTransform3_New();
             final itkArrayD parameters =  new itkArrayD(12);
             for(int i = 0; i < fp.length; i++) parameters.SetElement 
(i,  fp[i]);
             transform.SetParameters(parameters);
             resample.SetTransform(transform.GetPointer());
             resample.SetInterpolator(interpolator.GetPointer());
             resample.SetInput(tarITK);
             resample.SetSize(tarITK.GetLargestPossibleRegion 
().GetSize());
             resample.SetOutputOrigin(tarITK.GetOrigin());
             resample.SetOutputSpacing(tarITK.GetSpacing());
             resample.SetDefaultPixelValue(-32768);

             SwingUtilities.invokeLater(new Runnable() {
                 public void run() {
                   tp.setMaximum(100);
                   tp.setValue(0);
                 }
               }
             );

             class CommandIterationUpdate extends itkJavaCommand {
               public void Execute() {
                 updateTask.val = (int)(100*resample.GetProgress());
                 SwingUtilities.invokeLater(updateTask);
               }
             }
             CommandIterationUpdate p = new CommandIterationUpdate();
             resample.AddObserver(new itkProgressEvent(), p);
             resample.Update();



On May 17, 2005, at 2:09 AM, Stefan Lindenau wrote:

> Hi,
>
> currently I am trying to use the ITK with the Java Wrapping. For my  
> applications I need to import/export itk images into Java Images.
>
> Although I have found out that there should be a mechanism to  
> import/export itk images to Java images (http://public.kitware.com/ 
> pipermail/insight-users/2004-June/008887.html). I did not find out  
> how to use these mechanisms.
>
> Do you have any documentation for the Java Wrapping or a starting  
> point?
>
> Thank you,
> Stefan
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