[Insight-developers] [Insight-users] INSIGHT JOURNAL: managedITK (ITK 3.8 ?) & Release Schedule.

Luis Ibanez luis.ibanez at kitware.com
Wed Jul 9 09:33:33 EDT 2008 

Hi Dan,

That sounds very reasonable.  This is an effort worth pursuing,
but is definitely something that can be done just in a couple
of weeks.


Integrating the code in the Google Code page sounds fine.
Gaeatan probably can advice if this should be done in the current
WrapITK project or if a new Google Code repository is needed.


What I would suggest is to configure the code in such a way that
we can still build it in some experimental machines Nightly and
submit the results to the ITK Dashboard.


---

In one of your first emails you pointed out that a number of
patches and additions were worth to include in ITK 3.8.

It seems that we already took care of the RGBA NumericTraits,
and yesterday we added the CombineRBGImageFilter.

If you have a chance, could you remind us of what other (small)
changes will be worth to undertake in the following day, before
we freeze the CVS repository on Tuesday ?


    Thanks


       Luis


------------------
Dan Mueller wrote:
> Hi Luis,
> 
> As you said, there are many options.
> 
> Seeing ManagedITK will not make it into ITK 3.8, perhaps the best
> option is to take the leap and directly integrate ManagedITK with the
> refactored WrapITK (rather than the original suggestion of ITK, then
> WrapITK). This can be done at either the Google Code page currently
> hosting the refactored WrapITK or via the NAMIC Sandbox. ITK 4.0 is
> due in November 2008 so we have plenty of time.
> 
> Apologies for changing my mind, but after further consideration this
> makes the most sense (at least in my mind).
> 
> Regards, Dan
> 
> 2008/7/9 Luis Ibanez <luis.ibanez at kitware.com>:
> 
>>Hi Dan,
>>
>>The concern about creating temporary directories is
>>mostly related to keeping things neat in the repository.
>>
>>One alternative is to use the NAMIC Sandbox (public a
>>Subversion repository) for performing the integration of
>>ManagedITK and WrapITK, until it is stable. Then move
>>the resulting version into ITK.
>>
>>There are probably many other options...
>>
>>
>>  Luis
>>
>>
>>--------------------
>>Dan Mueller wrote:
>>
>>>Hi Luis,
>>>
>>>1. Release schedule.
>>>Unfortunately I feel the 15th July deadline for ITK 3.8 is too tight.
>>>I have two (2) concerns:
>>>   A. The bureaucratic wheels at my university move very slow. I have
>>>initiated the copyright transfer procedure, but I doubt the issue will
>>>be fully resolved by this date.
>>>   B. I am moving house this weekend and will not have access to the
>>>internet for 1-2 weeks thereafter. As such my communication with ITK
>>>developers during this critical time may be hindered.
>>>
>>>Unfortunately, I think it best we aim for ITK 4.0 (unless the release
>>>date has some more give in it).
>>>
>>>2. CVS 'temporary' directory
>>>I feel that the new WrapITK -- which will subsume ManagedITK -- will
>>>look very different to the existing ManagedITK (different directory
>>>structure, shared cmake scripts, etc.). If we stick to the option of
>>>including ManagedITK "as is" before the refactoring, I don't think
>>>there is much we can do to prevent the 'temporary' non-deletable
>>>directory. What is the actual concern regarding this temporary
>>>directory? Just keeping things neat? Disk space?
>>>
>>>Regards, Dan
>>>
>>>
>>>2008/7/8 Luis Ibanez <luis.ibanez at kitware.com>:
>>>
>>>
>>>>Dan, Gaetan,
>>>>
>>>>It is great that you two have found common ground
>>>>on how to integrate ManagedITK with WrapITK.
>>>>
>>>>Following your discussion, it seems that the current
>>>>consensus is:
>>>>
>>>>1) Introduce ManagedITK in Insight/Wrapping
>>>>
>>>>2) Once the code is there, rework ManagedITK
>>>> and WrapITK in order to factorize the common
>>>> infrastructure
>>>>
>>>>
>>>>If I got this right, then the immediate question at
>>>>this point is:
>>>>
>>>>
>>>>  Do we do (1) before releasing ITK 3.8 ?
>>>>
>>>>
>>>>and to put this in context, the release schedule
>>>>http://www.itk.org/Wiki/ITK_Release_Schedule#Release_3.8_Schedule
>>>>
>>>>had a feature freeze expected at July 1st (which we already passed...).
>>>>
>>>>Since we are running behind and we are still moving contributions from
>>>>the Insight Journal into the Code/Review directory, the suggested freeze
>>>>time would be *July 15th*, and we will still keep the date of July 30th
>>>>for releasing ITK 3.8.
>>>>
>>>>
>>>>This translates into:
>>>>
>>>>
>>>> Do we want to introduce ManagedITK in
>>>> Insight/Wrapping before Monday July 14th ?
>>>>
>>>>
>>>>Note that ManagedITK is too large for making it pass
>>>>first through the Review directory, so we will have
>>>>to put it directly in Insight/Wrapping and expose it
>>>>conditionally under CMake variables.
>>>>
>>>>One concern with this move is whether you anticipate
>>>>that the subdirectory structure of ManageITK will
>>>>change when we move into factorizing common pieces
>>>>with WrapITK.
>>>>
>>>>As you know, the limitation of CVS is that we can
>>>>never fully get rid of subdirectories. Therefore,
>>>>if we introduce ManagedITK with a 'temporary'
>>>>sub-directory structure, that tree, will somehow
>>>>become permanent.
>>>>
>>>>
>>>>Please let us know what will be your preference
>>>>between:
>>>>
>>>>
>>>> a) ManagedITK by ITK 3.8 ?
>>>> b) ManagedITK by ITK 4.0 ?
>>>>
>>>>
>>>>
>>>>Thanks
>>>>
>>>>
>>>>   Luis
>>>>
>>>>
>>>>
>>>>-----------------------
>>>>Gaëtan Lehmann wrote:
>>>>
>>>>
>>>>>Le 8 juil. 08 à 08:07, Dan Mueller a écrit :
>>>>>
>>>>>
>>>>>
>>>>>>Hi Gaetan,
>>>>>>
>>>>>>(FYI: I have moved this discussion to the developers list).
>>>>>>
>>>>>>Firstly, thanks for your work on WrapITK. As you have surmised, at
>>>>>>some point last year I took WrapITK and mangled it for my own
>>>>>>purposes. There *are* a lot of similarities between the two projects,
>>>>>>however there are also a number of differences (the biggest being the
>>>>>>code generation as you have pointed out). I have a number of concerns
>>>>>>regarding the integration of ManagedITK with the new WrapITK:
>>>>>>
>>>>>>1. Code generation.
>>>>>>To make my feelings clear, I do not want to use SWIG for the code
>>>>>>generation of ManagedITK. SWIG C# code generation uses what is called
>>>>>>P/Invoke, which is a lot less flexible than the "It Just Works"
>>>>>>mechanism currently employed by ManagedITK. That said, if the new
>>>>>>WrapITK will support other code generation mechanisms, then I do not
>>>>>>foresee any issues moving the code generation make files to
>>>>>>Languages/ManagedITK.
>>>>>
>>>>>
>>>>>Yes, no swig on manageditk side is fine.
>>>>>
>>>>>
>>>>>
>>>>>>2. Refactoring.
>>>>>>I have taken a brief look at the new WrapITK. Although you said it was
>>>>>>designed to be reusable for something else than CableSWIG or SWIG, it
>>>>>>seems there is still (significant?) refactoring work for this to
>>>>>>become a reality. For example, it still assumes CableSWIG is required.
>>>>>>As with many ITK developers, I do ITK stuff during my personal time,
>>>>>>and therefore I have limited resources to spend on this particular
>>>>>>project. How much help would you (and other ITK Developers) be
>>>>>>providing to make the new WrapITK truly independent from SWIG? Or have
>>>>>>I misinterpreted things?
>>>>>
>>>>>
>>>>>There are only a few things to do to not require cableswig and swig
>>>>>anymore.
>>>>>It hasn't been done yet, because both python and java requires it, but
>>>>>all the internal code is well separated. I can complete that part
>>>>> alone,
>>>>>as soon as I found a little time to work on wrapitk.
>>>>>
>>>>>
>>>>>
>>>>>>3. Wrapped types.
>>>>>>As you pointed out, there are some types wrapped by one project and
>>>>>>not the other. The main reason for this is that type conversion in
>>>>>>ManagedITK (ie. native ImageRegion to "managed" ImageRegion) is
>>>>>>performed manually (see Source/Common/itkManagedTypes.cxx). To support
>>>>>>"complex" (real and imaginary) types for example, a manual mapping
>>>>>>must be made between the native complex object and a managed object.
>>>>>>Therefore, if these two projects come together, I feel there must be a
>>>>>>mechanism to exclude some wrap_*.cmake files for ManagedITK. The same
>>>>>>may be needed for WrapITK, which for example does not (currently)
>>>>>>support mesh filters, and may not be able to in the same way as
>>>>>>ManagedITK does.
>>>>>
>>>>>
>>>>>Meshes are not supported because I know nearly nothing about them, and
>>>>> so
>>>>>I was not able to choose the relevant types to wrap.
>>>>>Meshes support would definitely be a positive impact of manageditk on
>>>>>wrapitk.
>>>>>
>>>>>Excluding some stuff in one language or the other is already
>>>>> implemented
>>>>>at the module level. It can be refined to fit all of our  needs.
>>>>>
>>>>>
>>>>>
>>>>>>4. Module names.
>>>>>>The module names *are* important for ManagedITK -- in the sense that
>>>>>>each module is compiled as a separate *.dll. The Microsoft compiler
>>>>>>can not handle putting all the files into a single dll. As such the
>>>>>>dll names need to be meaningful so that users can intuitively find
>>>>>>their filters. I do not think the WrapITK module names are intuitive.
>>>>>>For example: how do you differentiate which filters are in
>>>>>>"SimpleFilters" versus "Filtering"?
>>>>>
>>>>>
>>>>>I don't differentiate them. I've never been pleased by the current
>>>>> module
>>>>>names.
>>>>>There is for sure a big place for discussions on this side.
>>>>>
>>>>>
>>>>>
>>>>>>5. Underscore before template definition.
>>>>>>This is not a problem. The underscore can be removed in ManagedITK to
>>>>>>make it the same as WrapITK.
>>>>>
>>>>>
>>>>>Or they can be used in wrapitk — it would make no difference in  python,
>>>>>and can make things much clear in java and tcl.
>>>>>
>>>>>
>>>>>
>>>>>>6. Backwards compatibility.
>>>>>>Does WrapITK fall under the same backwards compatibility policy as the
>>>>>>rest of ITK? If so, I'm not sure I would be willing to concede on all
>>>>>>the above points in order for ManagedITK to be integrated with
>>>>>>WrapITK. However, if a middle ground could be found, then I think it
>>>>>>may be possible to move forward.
>>>>>
>>>>>
>>>>>WrapITK is marked as experimental, so I don't think it fall under the
>>>>>ITK's backward policy.
>>>>>That being said, I tried to make things as backward compatible as
>>>>>possible in python, with deprecation warnings when required (and
>>>>>possible).
>>>>>
>>>>>Currently, external projects may need some small changes to build with
>>>>>wrapitk unstable. Python code made for wrapitk stable runs without
>>>>> changes
>>>>>on wrapitk unstable, but produce some deprecation warnings.
>>>>>
>>>>>
>>>>>
>>>>>>In summary:
>>>>>>1. It should be possible to move the code generation to the  Languages
>>>>>>folder.
>>>>>>2. The new WrapITK needs to support wrapper generation without SWIG or
>>>>>>CableSWIG.
>>>>>>3. There needs to be a mechanism to turn some wrapped types off and
>>>>>>on, depending on whether WrapITK or ManagedITK, or other.
>>>>>>4. Module names are a point of contention for me. More discussion is
>>>>>>needed.
>>>>>>5. Underscores -- no problem.
>>>>>>6. Backwards compatibility must be a consideration as we plan the  next
>>>>>>steps.
>>>>>
>>>>>
>>>>>No major problem so — nice :-)
>>>>>
>>>>>Gaëtan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>Cheers, Dan
>>>>>>
>>>>>>2008/7/8 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>:
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Le 7 juil. 08 à 22:15, Gaëtan Lehmann a écrit :
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>>>Is there material that can be merged/shared with the other
>>>>>>>>>wrappings ?
>>>>>>>>
>>>>>>>>
>>>>>>>>Dan,
>>>>>>>>
>>>>>>>>I wanted to ask you the same question — Luis did it first :-)
>>>>>>>>
>>>>>>>>Despite you said that WrapITK is a "totally separate project",
>>>>>>>>ManagedITK
>>>>>>>>has reused lot of code from WrapITK. Actually, they still share a
>>>>>>>> lot
>>>>>>>>of
>>>>>>>>code — a quick look at  managed_itkCastImageFilter.cmake, from
>>>>>>>>ManagedITK,
>>>>>>>>and wrap_itkCastImageFilter.cmake would be quite convincing: they
>>>>>>>> even
>>>>>>>>share
>>>>>>>>the comments :-)
>>>>>>>>They are not all as similar of course, so the question is:
>>>>>>>>
>>>>>>>>Would it be possible to avoid the current code duplication?
>>>>>>>>
>>>>>>>>The reason why I wanted to ask that question now, is because  WrapITK
>>>>>>>>has
>>>>>>>>made great progress in the last weeks. Some times ago, I began to
>>>>>>>> work
>>>>>>>>on a
>>>>>>>>pure swig implementation of WrapITK. The work was left unchanged  for
>>>>>>>>a
>>>>>>>>quite
>>>>>>>>long time, but recently, Ali decided to work on the java part. His
>>>>>>>>work
>>>>>>>>convinced me to work again on python part. At this time, wrapitk
>>>>>>>>unstable is
>>>>>>>>nearly completed in python — I already began to use it for real
>>>>>>>> image
>>>>>>>>analysis task, to benefit of the numerous improvements — and Ali  is
>>>>>>>>using
>>>>>>>>java part on his side. The code is available at:
>>>>>>>>
>>>>>>>>http://code.google.com/p/wrapitk/source
>>>>>>>>
>>>>>>>>In WrapITK unstable, I took care to completely separe the type
>>>>>>>>declarations — in the wrap_*.cmake — and the language specific  code.
>>>>>>>>The
>>>>>>>>goal is to make all that hard job of defining template parameters
>>>>>>>> for
>>>>>>>>type
>>>>>>>>instantiation fully reusable for something else than wrapping with
>>>>>>>>cableswig
>>>>>>>>or swig. The examples I had in mind were:
>>>>>>>>* wrapping python with PyBoost
>>>>>>>>* ExplicitITK
>>>>>>>>* ManagedITK
>>>>>>>>
>>>>>>>>If you agree, I would be pleased to try to see with you a way to
>>>>>>>> merge
>>>>>>>>ManagedITK and WrapITK.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>After a bit of reading of ManagedITK code, I'm quite convinced that
>>>>>>>there is
>>>>>>>some factorizing to do, and that it would benefit to both projects.
>>>>>>>The big differences I see are:
>>>>>>>* the code generator, of course very specific of ManagedITK
>>>>>>>* the Common directory, which is specific of ManagedITK
>>>>>>>* the wrapped types — some types available in WrapITK are not in
>>>>>>>ManagedITK
>>>>>>>(complex types for example) and some in ManagedITK are not in  WrapITK
>>>>>>>(RGBA
>>>>>>>for example). It would be nice for both to have them :-)
>>>>>>>* the modules names
>>>>>>>* the managed property definitions
>>>>>>>* the underscore before the template parameters in the instantiated
>>>>>>>name
>>>>>>>* the external projects implementation
>>>>>>>
>>>>>>>Specific code is quite well separated, and some of the code  specific
>>>>>>>of
>>>>>>>one
>>>>>>>project would benefit to the other.
>>>>>>>The only specific code mixed with generic code at this time is the
>>>>>>>managed
>>>>>>>property definitions. I do think they can be quite nicely moved
>>>>>>> outside
>>>>>>>the
>>>>>>>generic files, in the /Languages/Managed/Properties/ for example  (to
>>>>>>>reuse
>>>>>>>the wrapitk directory layout). Then, when END_WRAP_CLASS() is  called
>>>>>>>in
>>>>>>>the
>>>>>>>/Modules/*/wrap_*.cmake files, the content of corresponding
>>>>>>>managed_*.cmake
>>>>>>>file can be read (if it exists), to define the properties for the
>>>>>>>current
>>>>>>>classes.
>>>>>>>That way, all generic code can be common to both projects, and
>>>>>>> specific
>>>>>>>code
>>>>>>>is localized in a single subdirectory of the /Languages directory.
>>>>>>>
>>>>>>>The module names may be a problem depending on their importance in
>>>>>>>ManagedITK.
>>>>>>>
>>>>>>>The rest looks much like details — underscore in name can be used  in
>>>>>>>wrapitk
>>>>>>>or can be manageditk specific without problem, and external project
>>>>>>>shouldn't be that difficult to implement in one way or the other.
>>>>>>>
>>>>>>>Do you think this kind of organization for managed properties would
>>>>>>> fit
>>>>>>>your
>>>>>>>needs?
>>>>>>>There are surely many other problems — I hope they are not too
>>>>>>>difficult :-)
>>>>>>>
>>>>>>>Regards,
>>>>>>>
>>>>>>>Gaëtan
>>>>>>>
>>>>>>>
>>>>>>>--
>>>>>>>Gaëtan Lehmann
>>>>>>>Biologie du Développement et de la Reproduction
>>>>>>>INRA de Jouy-en-Josas (France)
>>>>>>>tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
>>>>>>>http://voxel.jouy.inra.fr  http://www.mandriva.org
>>>>>>>http://www.itk.org  http://www.clavier-dvorak.org
>>>>>
>>>>>
>

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