[Insight-developers] ITKv4: Features vs Clean up
Nicholas Tustison
ntustison at gmail.com
Thu Jun 30 09:31:35 EDT 2011
Hi Rupert,
Much of the work is in the RegistrationRefactoring branch on github
as mentioned. However, more-or-less self-encapsulated units are
currently on gerrit and you're certainly welcome to review them. For
example, some fundamental fixes to the B-spline deformable transform
and initializer are proposed here
http://review.source.kitware.com/#change,1856
Additionally, a good chunk of the point set metric refactoring/enhancements
are proposed here
http://review.source.kitware.com/#change,1976
I don't know if they fall within your interest but we're always looking for
feedback.
Nick
On Jun 30, 2011, at 9:19 AM, Rupert Brooks wrote:
> Procrastinate for two weeks. Absolutely ;-)
>
> The latter part of the email seems to suggest though that it might
> help if i follow along during the process of putting the refactored
> code into ITK4. I assume this would best be done via the Gerrit
> review process. If i understand correctly, whats in
> RegistrationRefactoring will soon be pushed to the ITKV4 master. Is
> this the right way to proceed?
>
> Rupert
>
>
> --------------------------------------------------------------
> Rupert Brooks
> rupert.brooks at gmail.com
>
>
>
>
> On Thu, Jun 30, 2011 at 08:27, Johnson, Hans J <hans-johnson at uiowa.edu> wrote:
>> Rupert and Brian,
>>
>> I have a proposal:
>>
>> Rupert: Would you be able to wait two weeks to do your review? We just
>> finished our ITKv4 developers meeting, and there will be a lot of action
>> in the next two weeks to bring this directly into ITKv4.
>>
>> Brian: Could we help get the current alpha pieces pushed into ITKv4
>> proper?
>>
>> ==========================
>> I am concerned about getting distracted from the primary goal of getting
>> the registration into ITKv4 directly.
>>
>> Hans: I was planning to do extensive registration testing, and external
>> tool code refactoring to match the ITKv4 registration framework during the
>> second 1/2 of July. If Rupert and Hans could assist Brian's team in
>> getting the source code moved and integrated with ITKv4 between now and
>> July 15, then we will be more efficient in identifying use case problems
>> related to algorithmic and api problems.
>>
>> Does this timeline work for the two of you?
>>
>> Hans
>>
>>
>>
>> On 6/30/11 7:12 AM, "Rupert Brooks" <rupert.brooks at gmail.com> wrote:
>>
>>> Hi Brian,
>>>
>>> This looks very interesting. I hope you dont mind a few questions.
>>> If theres a written document to refer me to, feel free.
>>>
>>> I've been reading this:
>>> http://www.itk.org/Wiki/ITK_Release_4/Enhancing_Image_Registration_Framewo
>>> rk
>>> but i have trouble mapping it to what i see in the GIT.
>>>
>>> I'm having some trouble identifying all the diffs between the
>>> Registration branch and current ITK master, but it seems to me that
>>> most is in Modules/Registration/Refactoring. Would that be the case?
>>> Is this ImageToObjectRegistration framework intended to replace one or
>>> more of the current Parametric / PDE / FEM registration frameworks, or
>>> to be in parallel with them. Or, to ask my question another way - I
>>> currently have some feedback / commentary regarding
>>> itkOptimizer.h and its children...
>>> itkCompositeTransform.txx
>>> itkImageToImageMetric.txx
>>> itkNormalizedCorrelationImageToImageMetric.txx
>>> which are in Modules/Registration/Common
>>>
>>> Currently in RegistrationRefactoringNew these seem to be the same as
>>> in master. Will the new refactored framework replace these classes,
>>> so i shouldnt spend any time fiddling with them, or is it more or less
>>> independent.
>>>
>>> I've only had about half an hour to look at it, and i havent had time
>>> to compile it yet, so i may be about to embarrass myself with a stupid
>>> question. I'll ask anyway. A core fundamental refactoring - looking
>>> at the example you pointed me to - is that the update to the
>>> parameters seems to have been pushed down all the way to the
>>> transform, via the metric in the middle. This is a very interesting
>>> choice - for transforms such as the versor transform, which must
>>> remain on a manifold that doesnt embed well in Euclidean space, this
>>> removes the constraint issue from the optimizer. However - it did make
>>> me wonder - what if i want to do anything other than gradient descent?
>>> Also, it seems to force the computation to complete an entire
>>> computation of the gradient, and hold it in memory, even though for a
>>> local transform, it may be possible to perform the same update without
>>> ever actually creating the whole gradient object in memory at once?
>>>
>>> I saw tantalizing pieces of GPU registration code commented out. Is
>>> that in process somewhere?
>>>
>>> In any case, i will spend more time on it which should hopefully lead
>>> to more intelligent commentary, over the weekend.
>>>
>>> Cheers,
>>> Rupert
>>> --------------------------------------------------------------
>>> Rupert Brooks
>>> rupert.brooks at gmail.com
>>>
>>>
>>>
>>>
>>> On Wed, Jun 29, 2011 at 21:13, brian avants <stnava at gmail.com> wrote:
>>>> rupert
>>>>
>>>> help is very welcome.
>>>>
>>>> refactored registration framework is here:
>>>>
>>>> https://github.com/picslITK/ITK4_topics/tree/RegistrationRefactoringNew
>>>>
>>>> take a look at :
>>>>
>>>>
>>>> ITK4_topics/Modules/Registration/Refactoring/test/itkDemonsImageToImageOb
>>>> jectRegistrationTest.cxx
>>>>
>>>> which gives an example of a demons registration run in the standard
>>>> framework. the framework is changing, though, so realize what's there
>>>> now is a mid-stream snapshot.
>>>>
>>>> brian
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, Jun 29, 2011 at 8:59 PM, Rupert Brooks
>>>> <rupert.brooks at gmail.com> wrote:
>>>>> Hi Luis and everyone,
>>>>>
>>>>> As a pretty heavy user of ITK, I'm interested in helping out as well.
>>>>> At the moment im working on some registration problems and im trying
>>>>> to explore the refactored registration framework in ITK 4.
>>>>> As im going through the current master, im noticing various things
>>>>> ranging from typos to classes that seem to have gotten left behind to
>>>>> questionable math. I'd be happy to give this information as feedback
>>>>> or fixes if its helpful.
>>>>>
>>>>> So question 1 - is the registration refactoring well represented in
>>>>> ITK master, or is there more work elsewhere? Is this the right time
>>>>> to review it from a user perspective or is it premature?
>>>>>
>>>>> Question 2 - whats the best way to proceed? Do i need to configure
>>>>> Gerrit access, etc as a developer to contribute to the textual notes
>>>>> you mentioned?
>>>>>
>>>>> Cheers,
>>>>> Rupert
>>>>> --------------------------------------------------------------
>>>>> Rupert Brooks
>>>>> rupert.brooks at gmail.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Jun 3, 2011 at 09:46, Luis Ibanez <luis.ibanez at kitware.com>
>>>>> wrote:
>>>>>> Hi Tom,
>>>>>>
>>>>>> Thanks for volunteering.
>>>>>>
>>>>>>
>>>>>> The plans for the global clean up are here:
>>>>>> http://www.itk.org/Wiki/ITK_Release_4/Global_Code_Review
>>>>>>
>>>>>> The procedure is described here
>>>>>>
>>>>>> http://www.itk.org/Wiki/ITK_Release_4/Modularization/Code_Reviews/Proce
>>>>>> ss#Git-Based
>>>>>>
>>>>>> Essentially:
>>>>>>
>>>>>> We have a duplicate Git repository
>>>>>> https://github.com/InsightSoftwareConsortium/itk-retroactive-review
>>>>>>
>>>>>> that contains a .txt file for every source code file in ITK.
>>>>>>
>>>>>> Instead of making bug entries in MANTIS,
>>>>>> just edit those .txt files, and commit them.
>>>>>>
>>>>>> Of course, if some issues are actual bugs,
>>>>>> please feel free to report them in MANTIS.
>>>>>>
>>>>>>
>>>>>> More comments below...
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 3, 2011 at 5:11 AM, Tom Vercauteren
>>>>>> <tom.vercauteren at m4x.org> wrote:
>>>>>>> Hi Luis,
>>>>>>>
>>>>>>> I would like to help in the cleanup process (especially for the code
>>>>>>> I
>>>>>>> worked on in the past) but have unfortunately very little time for
>>>>>>> it.
>>>>>>> The least I could do is pinpoint some places that I believe require
>>>>>>> cleanup. The problem is I don't really know if such a task is wanted
>>>>>>> and if so, how it should be done. Should I file bug reports for each
>>>>>>> cleanup task and mark them as feature requests? But then, who would
>>>>>>> be
>>>>>>> in charge of triaging these feature requests? Are other more
>>>>>>> effective
>>>>>>> options available?
>>>>>>>
>>>>>>
>>>>>>
>>>>>> http://www.itk.org/Wiki/ITK_Release_4/Modularization/Code_Reviews/Proce
>>>>>> ss#Git-Based
>>>>>> https://github.com/InsightSoftwareConsortium/itk-retroactive-review
>>>>>>
>>>>>>> For the time being, there are a least a few places on the top of my
>>>>>>> head that require cleanup (some of which might be considered as
>>>>>>> features depending on how you look at it). Sorted by order of
>>>>>>> importance:
>>>>>>>
>>>>>>> 1) Bad design in ImportImageContainer.
>>>>>>>
>>>>>>> https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/include
>>>>>>> /itkImportImageContainer.h
>>>>>>> The memory allocation and deallocation functions have an inconsistent
>>>>>>> signature. One uses a member and the others returns a pointer:
>>>>>>> virtual TElement * AllocateElements(ElementIdentifier size) const;
>>>>>>> virtual void DeallocateManagedMemory();
>>>>>>>
>>>>>>> This makes it really difficult to override the class in a correct
>>>>>>> manner. I have actually stumped into a bug in
>>>>>>> TestImportImageContainer
>>>>>>> coming from this design issue ( that I haven't filed yet :( )
>>>>>>>
>>>>>>> https://github.com/Kitware/ITK/blob/master/Modules/Core/Common/test/it
>>>>>>> kFactoryTestLib.cxx
>>>>>>> With this TestImportImageContainer class, reallocating an image will
>>>>>>> fail. This is bad since it will most certainly be the first thing
>>>>>>> people will look at when trying to override the default memory
>>>>>>> handling of ITK.
>>>>>>>
>>>>>>
>>>>>> Fair enough...
>>>>>>
>>>>>>>
>>>>>>> 2) The unicode filename problem on windows.
>>>>>>> Most of the low-level code necessary to deal with unicode filenames
>>>>>>> through utf-8 encoding is already in the repository but it isn't used
>>>>>>> yet. What still need to be done is use this low-level code for all IO
>>>>>>> operations. More detail in:
>>>>>>> http://www.itk.org/Bug/view.php?id=9623
>>>>>>>
>>>>>>>
>>>>>>> 3) There are a lot of useless vector-specific classes that were
>>>>>>> introduced probably for MSVC 6. It might be the right time to merge
>>>>>>> them back into the corresponding "scalar" classes.
>>>>>>> http://itk.org/Bug/view.php?id=2712
>>>>>>> http://www.itk.org/Wiki/ITK_Release_4/Wish_List#Image_Registration
>>>>>>>
>>>>>>
>>>>>> Yes,
>>>>>> Cory, Arnaud, Gaetan and Brad L. have been improving
>>>>>> the support for multiple components...
>>>>>> We need raise the priority of this one,
>>>>>> since it is so fundamental for
>>>>>> Microscopy and for Remote Sensing.
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> 4) Some default options are not the most meaningful ones:
>>>>>>>
>>>>>>> http://www.itk.org/Wiki/ITK_Release_4/Wish_List#Backward_compatibility
>>>>>>> _and_cleanup
>>>>>>> For example Gaussian smoothing uses either a sigma defined in terms
>>>>>>> of
>>>>>>> physical space or pixel space depending on its implementation
>>>>>>> (discrete versus recursive).
>>>>>>>
>>>>>>
>>>>>> Yeap, the API is inconsistent.
>>>>>> Plus some take Sigma, while others take Variance...
>>>>>>
>>>>>>>
>>>>>>> 5) Others inconsistencies
>>>>>>> http://www.itk.org/Bug/view.php?id=7351
>>>>>>> http://www.itk.org/Bug/view.php?id=8944
>>>>>>>
>>>>>>> http://www.itk.org/Wiki/ITK_Release_4/Wish_List#Make_the_boundary_cond
>>>>>>> itions_usage_consistent_across_the_toolkit
>>>>>>> For example the behavior of the interpolators outside the image
>>>>>>> domain
>>>>>>> is not practical. This is one of the reason why I implemented
>>>>>>> VectorLinearInterpolateNearestNeighborExtrapolateImageFunction
>>>>>>>
>>>>>>> https://github.com/Kitware/ITK/blob/master/Modules/Nonunit/Review/incl
>>>>>>> ude/itkVectorLinearInterpolateNearestNeighborExtrapolateImageFunction.
>>>>>>> h
>>>>>>> Ideally, the functionnality of this class should be handled by
>>>>>>> LinearInterpolateImageFunction.
>>>>>>>
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>
>>>>>>
>>>>>> It certainly does.
>>>>>>
>>>>>>
>>>>>> Many Thanks
>>>>>>
>>>>>>
>>>>>> Luis
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----------------------------
>>>>>>> Tom
>>>>>>>
>>>>>>> On Thu, Jun 2, 2011 at 15:06, Luis Ibanez <luis.ibanez at kitware.com>
>>>>>>> wrote:
>>>>>>>> I want to second Brad L. comment regarding
>>>>>>>> our current misplaced focus on ITKv4.
>>>>>>>>
>>>>>>>> There is a disproportionate number of changes
>>>>>>>> that are introducing new features in the toolkit,
>>>>>>>> when we are supposed to be focused on cleaning
>>>>>>>> up and restructuring for the next 10 years.
>>>>>>>>
>>>>>>>> I suggest that we prioritize every patch in Gerrit
>>>>>>>> based on whether it is:
>>>>>>>>
>>>>>>>>
>>>>>>>> 1) Bug fix
>>>>>>>> 2) Clean up resulting from code reviews
>>>>>>>> 3) Needed for refactoring (FEM, Regist, LevelSets)
>>>>>>>> ....
>>>>>>>> 99) New features
>>>>>>>>
>>>>>>>>
>>>>>>>> We have limited time and resources to do all
>>>>>>>> the refactoring and revision of ITKv4 and we
>>>>>>>> are being side-tracked dealing with changes
>>>>>>>> that are not part of the ITKv4 charter.
>>>>>>>>
>>>>>>>>
>>>>>>>> Luis
>>>>>>>> _______________________________________________
>>>>>>>> Powered by www.kitware.com
>>>>>>>>
>>>>>>>> Visit other Kitware open-source projects at
>>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>>
>>>>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>>>>> http://kitware.com/products/protraining.html
>>>>>>>>
>>>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>>>>
>>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>>> http://kitware.com/products/protraining.html
>>>>>>
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>>
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>>>
>>>>> _______________________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://kitware.com/products/protraining.html
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
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>>>>>
>>>>
>>> _______________________________________________
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>>>
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>>>
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>>
>>
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