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

[Bill Lorensen]

Kris,

I don't think you need to mention vnl in the dependencies.

BTW, will you be in Bethesda next week? There will be working sessions
on Tuesday for A2D2's and it could be an opportunity to push your
patch through gerrit.

Knowledge and Thoroughness,

Bill

On Thu, Sep 22, 2011 at 5:59 PM, Kris Zygmunt <krismz at sci.utah.edu> wrote:
> 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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