[Insight-developers] how to provide A2D2 denoising code?

[Kris Zygmunt]

Hi Bill and Xiaoxiao,
    Thanks for your responses.  My main concern was polluting other  
modules with all of these dependencies, so it sounds like it is best  
to create a fresh one.  There is definitely room for expansion via  
subclassing later, but for now it will be a small module.  I'll pose  
the question again in gerrit  as it may be possible to reduce the  
dependencies by changing the API.  ( A long discussion, I'll wait for  
gerrit to explain).  For now I'll create the new module and add the  
topic.

For the Statistics module, I don't have any specific suggestions yet  
for reorganizing it.  I just wanted to know whether there were any  
short-term plans to do so, so that I could organize my files  
accordingly.

As far as VNL goes, I guess my question is really related to defining  
the module dependencies for the new Filtering/Denoising module.  Do I  
say that I'm dependent on ITKVNL or ITKVNLInstantiation or both or  
something else?  The library linking seems to have worked via the  
magic of ITK_LIBRARIES.

Thanks!
Kris

On Sep 22, 2011, at 3:51 PM, Bill Lorensen wrote:

> For the time being, I suggest placing it in Filtering/Denoising. It
> has a lot of dependencies for such a small module. As Xiaoxiao
> mentioned, you will get more feedback once it is in gerrit.
>
> On Thu, Sep 22, 2011 at 5:44 PM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com 
> > wrote:
>> Hi Kris,
>> Please see my comments below.
>> Once you put your patch on gerrit, I am sure you will  receive more  
>> detailed
>> and  insightful suggestions from everyone.
>> Thanks.
>>
>> On Thu, Sep 22, 2011 at 5:14 PM, Kris Zygmunt <krismz at sci.utah.edu>  
>> wrote:
>>>
>>> Hello!
>>>    I am (finally!) ready to provide the A2D2 denoising code and just
>>> wanted to discuss the best way to do so.  I will create a gerrit  
>>> topic
>>> called a2d2-denoising and put my changes there.  I think it makes  
>>> the most
>>> sense to create a new Denoising module in Filtering, but please  
>>> let me know
>>> if I should put the code elsewhere.  I have the following files:
>>>
>>> denoising filter hierarchy that will be dependent on
>>> ITKStatistics, ITKCommon, vnl, ITKImageStatistics, ITKImageGrid,
>>> ITKTransform, ITKImageFunction, ITKImageAdaptors
>>> This hierarchy should be in Filtering somewhere, but does it go  
>>> into a new
>>> module (called Denoising?) or an existing one?
>>> itkPatchBasedDenoisingBaseImageFilter.{h,hxx}
>>> itkPatchBasedDenoisingImageFilter.{h,hxx}
>>> <associated test code will go in the associated test directory>
>>>
>> How many new classes you are going to introduce into ITK? Are there
>> potential growth or further development if we make it
>> as a module called ITKDenoising?
>>
>>>
>>> Image to sample adaptor to be put in the Modules/Numerics/ 
>>> Statistics area
>>> itkImageToNeighborhoodSampleAdaptor.{h,hxx}
>>>
>>>
>>> Generic subsampler hierarchy that I think fits in the
>>> Modules/Numerics/Statistics area
>>> itkSubsamplerBase.{h,hxx}
>>> itkRegionConstrainedSubsampler.{h,hxx}
>>> itkSpatialNeighborSubsampler.{h,hxx}
>>> itkUniformRandomSpatialNeighborSubsampler.{h,hxx}
>>> itkGaussianRandomSpatialNeighborSubsampler.{h,hxx}
>>>
>>> It seems like Modules/Numerics/Statistics is rather large, are  
>>> there any
>>> plans to split this into smaller modules?  What is the recommended  
>>> way to
>>> include vnl in CMake for ITKv4?
>>>
>>>>  There are 64 classes right now in ITKStatistics. A couple of more
>>>> classes won't hurt.
>> If you have suggestions about how we should divide it up to  
>> meaningful
>> smaller modules, please advice.
>> We have a ITKVNL module distributed inside ITK as a third party  
>> library
>> (have you tried to use this module yet?).
>> Uses could choose to use their own system installed version of  VXL  
>> by
>> turning on ITK_USE_SYSTEM_VXL.
>>
>>>
>>> Thanks!
>>> Kris
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>>
>>
>> --
>>
>>
>> ---------------------------------------------
>> Xiaoxiao Liu, Ph.D.
>> R & D Engineer
>> Kitware Inc.
>> Clifton Park, NY
>> Phone: (518) 881-4924  or  (518) 371-3971 x124
>>
>>
>> _______________________________________________
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>>
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