[Insight-developers] The Insight Journal-New Submission

[Stephen R. Aylward]

A new version of the paper on ITK registration framework refactoring 
(threading) has been posted to the Insight Journal:
http://insight-journal.org/dspace/handle/1926/566

It is a complete paper (13 pages) but there is room for improvement.  We 
look forward to your feedback.

Best regards,
Stephen

Marius Staring wrote:
> Hi all,
> 
> The refactoring of the registration framework is a very nice initiative.
> 
> We have a few remarks/suggestions:
> 
> 1. From the powerpoint presentation in the Insight journal we noticed 
> that the new OptImageToImageMetric now includes the functionality to 
> sample the fixed image, like the MattesMutualInformation used to do 
> already. We have implemented something similar. You may be interested to 
> inspect our implementation. We have tried to seperate the sampling 
> functionality from the ImageToImageMetric, by designing a set of filters 
> that accept an image as input and return a vector containing the samples 
> as output (in a so-called itk::VectorDataContainer). For this purpose we 
> wrote a base class, the itk::ImageSamplerBase, from which different 
> image samplers can inherit. We have implemented several of them: the 
> itk::ImageFullSampler (takes all voxels within mask), the 
> itk::ImageRandomSampler (which does the same as the 
> MattesMutualInformation class does), and some others. The ImageSampler 
> is just another component to be set in the metric, just like the 
> Interpolator, Transform, etc.
> 
> The code (metricwithsampler.zip) can be found at 
> www.isi.uu.nl/People/Stefan. The AdvancedImageToImageMetric inherits 
> from the ImageToImageMetric and supports setting an ImageSampler. Don't 
> mind the somewhat ambitious name, by the way :)
> The relevant methods are:
> - SetImageSampler() and GetImageSampler()
> - SetUseImageSampler() and GetUseImageSampler()
> - InitializeImageSampler()
> The provided code won't compile as is, since it contains some references 
> to other code that we use, see www.isi.uu.nl/Elastix.
> 
> 2. The same class includes also some functions that benefit from 
> transforms that have sparse Jacobians (compact suppport), such as the 
> B-spline transform. The code does essentially the same as the code in 
> the MattesMutualInformation, but can be re-used by all inheriting 
> metrics. The relevant functions for this are:
> - CheckForBSplineTransform()
> - TransformPoint()
> - EvaluateTransformJacobian()
> 
> If you are interested, feel free to adopt (parts of) the code. If you 
> have any questions, don't hesitate to contact us.
> 
> Stefan and Marius
> 
> 
> Insight Journal wrote:
>> Hello,
>> A new submission has been added to the Insight Journal.
>>
>> Title: Optimizing ITK’s Registration Methods for Multi-processor, 
>> Shared-Memory Systems
>> Author(s): Aylward, Stephen; Jomier, Julien; Barre, Sebastien; Davis, 
>> Brad; Ibanez, Luis
>> Abstract: This document describes work-in-progress for refactoring 
>> ITK’s registration methods to exploit the parallel, computation 
>> power of multi-processor, shared-memory systems.  Refactoring includes 
>> making the methods multi-threaded as well as optimizing the 
>> algorithms.  API backward compatibility is being maintained.  Helper 
>> classes that solve common registration tasks are also being developed.
>>
>>
>> The refactoring has reduced computation times by factors of 2 to 200 
>> for metrics, interpolators, and transforms computed on multi-processor 
>> systems.  Extensive sets of tests are being developed to further test 
>> operation and backward compatibility.
>>
>> Download the paper at: http://hdl.handle.net/1926/566
>> Review the paper at: http://insight-journal.org
>>
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>>
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>>   
> 

-- 
=============================================================
Stephen R. Aylward, Ph.D.
Chief Medical Scientist
Kitware, Inc. - Chapel Hill Office
http://www.kitware.com
Phone: (518)371-3971 x300