[Insight-users] Why are getBufferAs* methods not available in Java?

[Mathew Guilfoyle]

Thanks for the quick replies.  I'm afraid I'm not that well versed in
detailed Java development.

I'm a clinician using Matlab for imaging research and I'm interfacing to
the Java wrapper of SimpleITK to use the segmentation tools.

Nonetheless, for my own interest and learning I will look into the wrapping
of the getBufferAs* and see if I can make any progress.

For now I've come up with a more than satisfactory workaround by writing a
couple of m-files that write out arrays to a .nii file and in turn import
the file into ITK, then doing the reverse to get the post-processed image
back into the Matlab workspace.  Not elegant perhaps but far better than
the 30+min it was taking with nested for loops of set/getPixel operations!

Thanks again, and for all the hard work on SimpleITK as a whole.

M

On 13 March 2013 19:53, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Mathew,
>
> I proposed the sitk::Image::GetBufferAs methods specifically for the
> problem you have encountered — an efficient way of transferring an
> sitk::Image to a numeric array. (The sitk::ImportImageFilter allows
> for conversion the other way from a numeric array to an sitk::Image).
>
> However, my expertise is mainly in C# and so these methods are
> currently only wrapped for the C# language. Python has a customized
> conversion method using Numpy, which uses the GetBufferAs methods
> under-the-hood.
>
> So AFAIK the only reason the GetBufferAs methods are not available in
> Java as yet is that the SimpleITK development team has not had the
> know-how to wrap the methods specifically for Java. Do you know how
> Java might interact with say GetBufferAsFloat which returns float* ?
> Any input you have in order to improve SimpleITK is greatly
> appreciated!
>
> Cheers, Dan
>
> On 14 March 2013 05:32, Mathew Guilfoyle <mrguilfoyle at gmail.com> wrote:
> > Hi, I am trying to use the Java SimpleITK wrapper for medical image
> > processing.
> >
> > I need to do some manipulation of the image as a plain numerical array
> > before and after leveraging the ITK segmentation filters.  However, I
> can't
> > find an efficient way of either transferring a numerical array to an SITK
> > Image object or reverting an Image object back to a numerical array.
>  Using
> > nested loops to do a per-pixel setPixelAs* or getPixelAs* operation
> takes an
> > inordinate amount of time.
> >
> > I understand the getPixelContainer method is now deprecated (?) and was
> > supposed to be replaced by the getBufferAs* methods, which I can see in
> the
> > Doxygen Image class listing but seem to be suppressed in the Java wrapper
> > (v0.6.1).  Is there a way round this?
> >
> > Many thanks for any help/advice
> >
> > Mathew
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.itk.org/mailman/listinfo/insight-users
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20130314/6e633397/attachment.htm>