[Insight-users] Simple ITK Iterators & Registration

[Bradley Lowekamp]

Hello,

There is WrapITK, which is closer to a direct mapping of much of ITK to python and maybe Java [1]. With ITK v4 it is now part of the ITK source tree and can be compiled as part with ITK by turn on the cmake variable ITK_WRAP_PYTHON.

While SimpleITK is not designed to implement pixel wise algorithms, as that is likely best done and the C++ level of ITK, the Image class does contain the __iter__, next, __len__, __getitem__, and __setitem__ methods to allow convenient ( not fast ) access to the image as a python container. The iterator interface may be optimized further in the future. 

It is also correct that SimpleITK does not have an interface to the ITK registration framework yet. If you are looking for a simple interface to ITK registration that are the application orient project such as University of Iowa BRAINS, or the University of Pennsylvania ANTS.

Brad


[1] http://www.insight-journal.org/browse/publication/85/

On Jul 12, 2012, at 12:12 PM, Ahmed Halaweish, Ph.D. wrote:

> Willi,
>    Thanks for the prompt reply … I guess I'll have to go back to the roots again :D.
>     Is there any other way to utilize the full functionality of ITK with Python?
> 
> Cheers
> 
> Ahmed F. Halaweish Ph.D.
> Postdoctoral Research Fellow
> Duke Image Analysis Laboratory (DIAL)
> Center for Advanced MR Development (CAMRD)
> Department of Radiology
> Duke University School of Medicine
> 
> 
> From: Willi Huber <w.huber at ymail.com>
> Reply-To: Willi Huber <w.huber at ymail.com>
> Date: Thursday, July 12, 2012 10:31 AM
> To: Ahmed Halaweish <ahmed.halaweish at dm.duke.edu>, "insight-users at itk.org" <insight-users at itk.org>
> Subject: Re: [Insight-users] Simple ITK Iterators & Registration
> 
> Hello Ahmed,
> 
> no it is so far not implemented in SimpleITK.
> 
> SimpleITK is a very young project and has a different philosophy. Its goal is to allow an easier access to the ITK therefore it will take some time until everybody agreed the implementation of a new way for example to use registration.
> 
> For registration you have to use the ITK itself and maybe build it by yourself. http://www.itk.org/Wiki/ITK should be a good starting point
> 
> Cheers,
> Willi
> 
> Von: "Ahmed Halaweish, Ph.D." <ahmed.halaweish at duke.edu>
> An: "insight-users at itk.org" <insight-users at itk.org> 
> Gesendet: 15:21 Donnerstag, 12.Juli 2012
> Betreff: [Insight-users] Simple ITK Iterators & Registration
> 
>  I have looked at the doxygen site and I can't seem to find any iterator and/or registration classes in the list of implemented classes. Have these been implemented yet? If not, when will they be? I keep getting a "module object has no attribute" error when trying to implement an iterator in my python scripts.
> 
> I am running Python 2.7 & SimpleITK 0.4.0 on Mac OSX 10.6.8.
> 
> Cheers
> 
> Ahmed F. Halaweish Ph.D.
> Postdoctoral Research Fellow
> Duke Image Analysis Laboratory (DIAL)
> Center for Advanced MR Development (CAMRD)
> Department of Radiology
> Duke University School of Medicine
> 
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========================================================
Bradley Lowekamp  
Medical Science and Computing for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov



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