[Insight-users] Odd java wrappers behavior

[Brian Eastwood]

Hi Luis,

Here's a little background: I'm using registration to align a video 
sequence.  I have a class that generates a list of transforms, one for 
each frame.  I first ran across this problem when I tried to use this 
list of transforms to generate a modified sequence (using 
itkResampleImageFilter)--I first saw the problem when I was trying to 
compose the transforms.

Now I simply save the transform data to a file--this works better for me 
anyway, since I may want to use the same transforms on a different file 
sequence that may not be otherwise registered (different image data, 
same capturing method).  One line of my output file looks like:

InsightToolkit.itkCenteredRigid2DTransform 5: -0.0054248555345777095, 
111.99813266896304, 114.49967542970687, 0.14514270891024816, 
-0.6813850112138921

So, we have the class name, the number of parameters, and then the 
actual transform parameters.  Here's the method I use to read this file:

    public static List loadTransforms(String fileName)
    {
        List transforms = new ArrayList();
        try
        {
            BufferedReader reader = new BufferedReader(new 
FileReader(fileName));
            String line;
            String delims = " " + OBJECT_DELIM + ATTRIB_DELIM; // space, 
colon, comma
            while ((line = reader.readLine()) != null)
            {
                StringTokenizer tokenizer = new StringTokenizer(line, 
delims);
                String xformClass = tokenizer.nextToken(); // ignored
                int paramCount = Integer.parseInt(tokenizer.nextToken());
               
                // @todo Maybe handle other types of transforms?
                itkCenteredRigid2DTransform_Pointer transform = 
itkCenteredRigid2DTransform.itkCenteredRigid2DTransform_New();
                transform.SetIdentity();
                itkArrayD params = new itkArrayD(paramCount);
               
                for (int i = 0; i < paramCount; i++)
                {
                    params.SetElement(i, 
Double.parseDouble(tokenizer.nextToken()));
                }
               
                transform.SetParameters(params);
                transforms.add(transform.GetPointer());
            }
           
            reader.close();
        }
        catch (IOException ioe)
        {
            System.err.println("RegistrationOutput: IO exception 
occurred:");
            ioe.printStackTrace();           
        }
       
        System.out.println(transforms.size() + " transforms read from 
file " + fileName + ".");
        return transforms;
    }

With this list of transforms I run across the same problems as with the 
list I obtain directly from registration--I can do certain things, but 
at some point I might get that odd error.  Here's an extended example of 
the code block I gave yesterday:

        System.out.println("\n--- Before ---");
        TransformIO.printTranforms(transforms);
       
        reader = itkImageFileReaderUS2.itkImageFileReaderUS2_New(); // 
this one is instantiated
        caster = null; // 
itkCastImageFilterUS2F2.itkCastImageFilterUS2F2_New();
        rescaler = null; // 
itkRescaleIntensityImageFilterF2US2.itkRescaleIntensityImageFilterF2US2_New();
        writer = null; // itkImageFileWriterUS2.itkImageFileWriterUS2_New();
       
        System.out.println("\n--- After ---");
        TransformIO.printTranforms(transforms);
        if (true) return;

When I run this, all of the transforms print out from the "before" 
group; six print out from the "after" group before it crashes.  If I 
instantiate the caster instead, only one transform prints out from the 
"after" group.  If I don't instantiate any objects, all transforms print 
out.  That's why I'm scratching my head so much on this one.

Thanks, again, for your help.
Cheers,
Brian