Thanks for the quick replies. I'm afraid I'm not that well versed in detailed Java development.<div><br></div><div>I'm a clinician using Matlab for imaging research and I'm interfacing to the Java wrapper of SimpleITK to use the segmentation tools.</div>
<div><br></div><div>Nonetheless, for my own interest and learning I will look into the wrapping of the getBufferAs* and see if I can make any progress.</div><div><br></div><div>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!</div>
<div><br></div><div>Thanks again, and for all the hard work on SimpleITK as a whole.</div><div><br></div><div>M<br><br><div class="gmail_quote">On 13 March 2013 19:53, Dan Mueller <span dir="ltr"><<a href="mailto:dan.muel@gmail.com" target="_blank">dan.muel@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Mathew,<br>
<br>
I proposed the sitk::Image::GetBufferAs methods specifically for the<br>
problem you have encountered — an efficient way of transferring an<br>
sitk::Image to a numeric array. (The sitk::ImportImageFilter allows<br>
for conversion the other way from a numeric array to an sitk::Image).<br>
<br>
However, my expertise is mainly in C# and so these methods are<br>
currently only wrapped for the C# language. Python has a customized<br>
conversion method using Numpy, which uses the GetBufferAs methods<br>
under-the-hood.<br>
<br>
So AFAIK the only reason the GetBufferAs methods are not available in<br>
Java as yet is that the SimpleITK development team has not had the<br>
know-how to wrap the methods specifically for Java. Do you know how<br>
Java might interact with say GetBufferAsFloat which returns float* ?<br>
Any input you have in order to improve SimpleITK is greatly<br>
appreciated!<br>
<br>
Cheers, Dan<br>
<div class="HOEnZb"><div class="h5"><br>
On 14 March 2013 05:32, Mathew Guilfoyle <<a href="mailto:mrguilfoyle@gmail.com">mrguilfoyle@gmail.com</a>> wrote:<br>
> Hi, I am trying to use the Java SimpleITK wrapper for medical image<br>
> processing.<br>
><br>
> I need to do some manipulation of the image as a plain numerical array<br>
> before and after leveraging the ITK segmentation filters. However, I can't<br>
> find an efficient way of either transferring a numerical array to an SITK<br>
> Image object or reverting an Image object back to a numerical array. Using<br>
> nested loops to do a per-pixel setPixelAs* or getPixelAs* operation takes an<br>
> inordinate amount of time.<br>
><br>
> I understand the getPixelContainer method is now deprecated (?) and was<br>
> supposed to be replaced by the getBufferAs* methods, which I can see in the<br>
> Doxygen Image class listing but seem to be suppressed in the Java wrapper<br>
> (v0.6.1). Is there a way round this?<br>
><br>
> Many thanks for any help/advice<br>
><br>
> Mathew<br>
><br>
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