[Insight-developers] Dashboard woes
Johnson, Hans J
hans-johnson at uiowa.edu
Thu Jun 2 14:16:56 EDT 2011
I am supportive of option (B) for the purpose of restoring the dashboard,
but not as an outright rejection of this as POSSIBLE approach to
addressing the underlying needs.
I agree that adding a module dependency needs much more consideration than
was original considered.
Hans
--
Hans J. Johnson, Ph.D.
hans-johnson at uiowa.edu
Assistant Professor of Psychiatry
University of Iowa Carver College of Medicine
W278 GH, 200 Hawkins Drive
Iowa City, Iowa 52242
Phone: 319-353-8587
-----Original Message-----
From: Luis Ibanez <luis.ibanez at kitware.com>
Date: Thu, 2 Jun 2011 13:34:24 -0400
To: Hans Johnson <hans-johnson at uiowa.edu>, Bill Lorensen
<bill.lorensen at gmail.com>
Cc: Bradley Lowekamp <blowekamp at mail.nih.gov>, Kent Williams
<norman-k-williams at uiowa.edu>, ITK <insight-developers at itk.org>
Subject: Re: [Insight-developers] Dashboard woes
We still need to fix the Dashboard:
The current option are:
A) Add a module dependency:
http://review.source.kitware.com/#change,1774
or
B) Remove recently added code:
http://review.source.kitware.com/#change,1777
Unless we reach a different consensus
I'll apply (B) by 3pm EDT.
Luis
-----------------------------------------------
On Thu, Jun 2, 2011 at 12:41 PM, Johnson, Hans J <hans-johnson at uiowa.edu>
wrote:
> It seems like there is at least consensus on adding the verification
>steps
> that Brad mentions. Let's put this small step on the agenda for
>tomorrow.
> I'd rather not spend another week working on a solution that is going to
> get shot down.
>
> Hans
>
> --
> Hans J. Johnson, Ph.D.
> hans-johnson at uiowa.edu
> Assistant Professor of Psychiatry
> University of Iowa Carver College of Medicine
> W278 GH, 200 Hawkins Drive
>
> Iowa City, Iowa 52242
> Phone: 319-353-8587
>
>
>
>
>
>
>
> -----Original Message-----
> From: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Thu, 2 Jun 2011 12:23:01 -0400
> To: Luis Ibanez <luis.ibanez at kitware.com>
> Cc: Kent Williams <norman-k-williams at uiowa.edu>, Hans Johnson
> <hans-johnson at uiowa.edu>, ITK <insight-developers at itk.org>
> Subject: Re: [Insight-developers] Dashboard woes
>
> Hans,
>
> It make since to me to require that images line up in physical space
> before performing index base operations. In fact I would be in favor of
> moving this check way up in the pipeline for all filters, and when this
> behavior is not desired having to overload a method. I have suggested
> adding a new method in the pipeline, called something like,
> VerifyAllInputs(), which is called before the UpdateOutputInformation()
> methods are called. This method could verify that the required inputs are
> set and that they match is size, and physical location. Currently, many
> filters don't check that any of this information matches.
>
> Luis,
>
> On Jun 2, 2011, at 12:05 PM, Luis Ibanez wrote:
>
>> On Thu, Jun 2, 2011 at 12:00 PM, Bradley Lowekamp
>> <blowekamp at mail.nih.gov> wrote:
>>> Hello,
>>>
>>> For some reason my e-mail sometimes seem to be very slow to get to the
>>>developers list.
>>>
>>> I have suggested writing an ImageAdaptor which does the interpolating
>>>as opposed to a new filter hierarchy. This should be more flexible, fix
>>>more filters for the physical space alignment, and be more maintainable
>>>in the long run, along with likely being less code and new classes too.
>>>
>>
>> Brad,
>>
>> Are you referring to ImageAdaptors as we already have them
>> implemented ? or are you using that term loosely ?
>
> I would think that only minor changes to the ImageAdaptor is needed to
> enable it to perform linear interpolation at each sample.
>
>>
>> ImageAdaptors, as currently implemented in ITK are only
>> suitable for Pixel-wise operations, and are unaware of
>> many of the transactions that filters have to deal with.
>
> The ImageAdaptor is a data object not a process object, so I am not sure
> about what you are referring to.
>
> I was thinking of being able to define a filter as:
>
> itk::AddIImageFilter< InputImageType,
> ColocatedImageAdaptor<InputImageType>, OutputImageType>.
>
> Where the adaptor object would need some information from the first input
> object, to ensure they are on the same grid.
>
> Brad
>
>
>>
>>
>> Luis
>>
>>
>>>
>>> Brad
>>>
>>> On Jun 2, 2011, at 11:43 AM, Williams, Norman K wrote:
>>>
>>>> How about this -- once Luis's patch backing out my changes are in
>>>>place, I
>>>> will do a patch that creates a module for physical space
>>>>binary/ternary
>>>> functor classes.
>>>>
>>>>
>>>> Since the changes to the existing class are minimal and
>>>>straightforward, I
>>>> can derive the new classes from the existing functor classes. There
>>>>would
>>>> be no 'UsePhysicalSpace' attribute.
>>>>
>>>> I would implement Multiplication/Division/Addition/Subtraction for 2
>>>> images and add for 3 images.
>>>>
>>>> I would use Interpolators rather than ResampleImageFilter unless
>>>>someone
>>>> can explain why using a ResampleImageFilter would actually be better.
>>>>
>>>> Actually there's one advantage of ResampleImageFilter -- when the
>>>>first
>>>> image parameter has a larger size than the second (and-or third) the
>>>> interpolator reports that the physical point of edge pixels on the
>>>>first
>>>> image are outside the image volume of the second. This wouldn't
>>>>happen
>>>> with ResampleImagefilter, and I'm not sure how to make the
>>>>Interpolators
>>>> behave the same way.
>>>>
>>>>
>>>> On 6/2/11 10:27 AM, "Luis Ibanez" <luis.ibanez at kitware.com> wrote:
>>>>
>>>>> On Thu, Jun 2, 2011 at 10:55 AM, Johnson, Hans J
>>>>><hans-johnson at uiowa.edu>
>>>>> wrote:
>>>>>> OK.
>>>>>>
>>>>>> --I'll take responsibility for the mistakes make in this approach.
>>>>>>
>>>>>> There are two separate issues here, let's not let the first unduly
>>>>>> influence our decisions on the second:
>>>>>>
>>>>>
>>>>> Agree,
>>>>> there are two separate issues here.
>>>>>
>>>>>
>>>>>> 1) The redness of the dashboard. This is somewhat tangential to the
>>>>>>the
>>>>>> algorithmic concerns. It illustrates that more experience and rigor
>>>>>>is
>>>>>> needed to avoid introducing inter-module dependancies. It was my
>>>>>> over-eagerness to get this in place that is the cause of these
>>>>>>problems.
>>>>>>
>>>>>
>>>>>
>>>>> It turns out that our software process has a window
>>>>> of opportunity for compilation errors to go unnoticed.
>>>>>
>>>>> a) We currently review every Gerrit patch independently
>>>>>
>>>>> b) In this case, we are seeing the effect of two
>>>>> combined patches leading to a red dashboard.
>>>>>
>>>>> c) The second patch exposes an incomplete
>>>>> aspect of the first patch.
>>>>>
>>>>> d) One of the culprits here is the absence
>>>>> of unit testing in:
>>>>>
>>>>> ITK/Modules/Filtering/ImageFilterBase/test
>>>>>
>>>>> for the itkBinaryFunctorImageFilter class,
>>>>> there is no unit test.
>>>>>
>>>>> Should we have had a unit test here, the
>>>>> dependency problem will have been spotted
>>>>> in Kent's patch.
>>>>>
>>>>> I'm now adding a unit test for this class.
>>>>>
>>>>>
>>>>> This reinforces the original point about:
>>>>>
>>>>> What is it that we should be doing now in ITKv4 ?
>>>>>
>>>>> - Increasing code coverage
>>>>> - Performing code reviews of the 2,300 files in the toolkit
>>>>> - Cleaning up the Review directory
>>>>> - Doing refactoring
>>>>> - Fixing bugs
>>>>>
>>>>>
>>>>>> 2) What the meaning of a "BinaryFunctorImageFilter" is for. Perhaps
>>>>>>it
>>>>>> should be "BinaryFunctorIndexSpaceImageFilter" and a new
>>>>>> "BinaryFunctorPhysicalSpaceImageFilter" needs to be created. I
>>>>>>thought
>>>>>> (and still think) that it is possible for these to co-exists in one
>>>>>> filter, in a backwards compatible way, thus providing performance
>>>>>> advantages in the common case where index & physical spaces coincide
>>>>>>for
>>>>>> all images.
>>>>>>
>>>>>
>>>>> I agree that a new specialized class
>>>>> is what is required here.
>>>>>
>>>>> The overall design of the toolkit is that
>>>>> classes should do one thing and they
>>>>> should do it right.
>>>>>
>>>>> Now that we have SimpleITK, the simplified
>>>>> watered down presentations of ITK features
>>>>> should be implemented at the level of that layer.
>>>>>
>>>>> While ITK itself remains a layer where:
>>>>>
>>>>> "one filter does one-thing"
>>>>>
>>>>>
>>>>>> I know we've had this conversation (I think it was at the ITKv4
>>>>>>kickoff
>>>>>> meeting) regarding the add/subtract/multiply/divide image filters
>>>>>>and
>>>>>> what
>>>>>> the "correct" behavior should be. There was clearly a need to
>>>>>>support
>>>>>> both the index space and the physical space computation methods.
>>>>>>Let's
>>>>>> focus on how to supply both feature sets rather than if we should
>>>>>> provide
>>>>>> both. Should we have two separate class hierarchies? I am
>>>>>>perfectly
>>>>>> happy if the answer is yes. We'll back out the changes and
>>>>>>implement a
>>>>>> parallel hierarchal tree that supports physical space.
>>>>>>
>>>>>
>>>>> This sounds reasonable to me.
>>>>>
>>>>> In this way, only the applications that need such
>>>>> functionality will have to pay for the code overhead
>>>>> of the feature.
>>>>>
>>>>>
>>>>>> Ultimately, all I want is a way to add/subtract/multiply/divide
>>>>>>images
>>>>>> in
>>>>>> physical space in a way that is consistent and compatible with these
>>>>>> same
>>>>>> operations in index space. The current approach seemed like a
>>>>>>logical
>>>>>> way
>>>>>> forward that minimized highly redundant and code duplication, and
>>>>>>also
>>>>>> would highlight other places in the code where one should consider
>>>>>> carefully what the correct physical space behavior should be.
>>>>>>
>>>>>> I can always go back to using my private physical space filters that
>>>>>> we've
>>>>>> used for years, but that seems selfish and wrong.
>>>>>>
>>>>>
>>>>> Agree,
>>>>> That's not the spirit of open source communities.
>>>>>
>>>>>
>>>>> Luis
>>>>>
>>>>>
>>>>> -------------------------
>>>>>> Hans
>>>>>> --
>>>>>> Hans J. Johnson, Ph.D.
>>>>>> hans-johnson at uiowa.edu
>>>>>> Assistant Professor of Psychiatry
>>>>>> University of Iowa Carver College of Medicine
>>>>>> W278 GH, 200 Hawkins Drive
>>>>>>
>>>>>> Iowa City, Iowa 52242
>>>>>> Phone: 319-353-8587
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Luis Ibanez <luis.ibanez at kitware.com>
>>>>>> Date: Thu, 2 Jun 2011 10:17:15 -0400
>>>>>> To: Hans Johnson <hans-johnson at uiowa.edu>
>>>>>> Cc: Bill Lorensen <bill.lorensen at gmail.com>, ITK
>>>>>> <insight-developers at itk.org>
>>>>>> Subject: Re: [Insight-developers] Dashboard woes
>>>>>>
>>>>>> Hi Hans,
>>>>>>
>>>>>> The proper fix for this issue could have been to check for
>>>>>>consistency
>>>>>> on the grid parameters of the two input images in the BinaryFunctor
>>>>>> filter, and to throw exceptions when the grids are not consistent.
>>>>>>
>>>>>> The check should include:
>>>>>>
>>>>>> 1) Origin
>>>>>> 2) Spacing
>>>>>> 3) Orientation
>>>>>> 4) Number of pixels along every dimension
>>>>>>
>>>>>> and given that most of these are "float" values, a tolerance
>>>>>> must be involved in the comparison.
>>>>>>
>>>>>> The current introduction of the resampling functionalities in
>>>>>> the BinaryFunctorImageFilter is overloading what this filter
>>>>>> is supposed to do, and yet not fully solving the problem.
>>>>>>
>>>>>> All other filters in ITK that take multiple input are not being
>>>>>> fixed to match this new behavior: LevelSets, MorphoMath ?
>>>>>> ...even the TernaryFunctorImageFilter...
>>>>>>
>>>>>> The responsibility of the filter should go just up to checking
>>>>>> for consistency. Introducing the option of performing the
>>>>>> resampling into the filter itself converts this filter into a
>>>>>> small application.
>>>>>>
>>>>>> The change also has many arbitrary decisions.
>>>>>>
>>>>>> For example, it uses a LinerInterpolator
>>>>>> which is not the right option for any of the image filters
>>>>>> derived from BinaryImageFunctor that deal with binary
>>>>>> images or images of labels.
>>>>>>
>>>>>> The changes were implemented with the narrow scenario
>>>>>> of Addition and multiplication in mind, and disregard the
>>>>>> fact that the BinaryFunctorImageFilter is the parent of
>>>>>> many other filters in the toolkit.
>>>>>>
>>>>>> This is not just a "Math" filter.
>>>>>>
>>>>>>
>>>>>> Luis
>>>>>>
>>>>>>
>>>>>> ---------------------------------
>>>>>> On Thu, Jun 2, 2011 at 9:56 AM, Johnson, Hans J
>>>>>><hans-johnson at uiowa.edu>
>>>>>> wrote:
>>>>>>> I dis-agree on the feature creep. This is a longstanding
>>>>>>>deficiency in
>>>>>>> ITK that arose from an initial avoidance of oriented physical image
>>>>>>> space.
>>>>>>> Now is our chance to fix it!
>>>>>>>
>>>>>>> One of my favorite ITK powerpoint training slides is Bart Simpson
>>>>>>> writing
>>>>>>> "I will not register images in index space" over and over and over
>>>>>>>on a
>>>>>>> chalk board as punishment. It is my opinion, (and hopefully the
>>>>>>> opinion
>>>>>>> of every student that I've ever taught) that image operations on
>>>>>>> medical
>>>>>>> images only make sense in physical space. For those processing
>>>>>>>steps
>>>>>>> that
>>>>>>> work only on the voxel lattice, there is still an implied physical
>>>>>>> space
>>>>>>> that must be considered. There are times when the developer can
>>>>>>>VERIFY
>>>>>>> THAT ALL THE PHYSICAL SPACES AND INDEX SPACES ARE CONSISTENT for
>>>>>>>both
>>>>>>> operand images, and then optimize the computation by using only the
>>>>>>> voxel
>>>>>>> lattice, thus skipping the implied sameness of the physical space.
>>>>>>>
>>>>>>> After all the effort put into making most of the ITK toolkit work
>>>>>>> properly
>>>>>>> in physical space, one still could not add two images together
>>>>>>>unless
>>>>>>> their voxel lattice was the same. Even more disturbing, one could
>>>>>>>add
>>>>>>> two
>>>>>>> images together that had the same voxel lattice, but have
>>>>>>>completely
>>>>>>> different physical space representations, and no warning/error was
>>>>>>> thrown
>>>>>>> (I know this because it has bitten me several times, I've begun to
>>>>>>> trust
>>>>>>> ITK to compute properly in physical space, or at least fail with
>>>>>>> rigor).
>>>>>>>
>>>>>>> It was naive to think that folding it into the current "Math"
>>>>>>>filters
>>>>>>> was
>>>>>>> the correct place to put this. In my programs (and Slicers, and
>>>>>>> hopefully
>>>>>>> other medical imaging applications) there is a need to compute in
>>>>>>> physical
>>>>>>> space.
>>>>>>>
>>>>>>> ***
>>>>>>> * At a minimum, the filters that only work on voxel lattices should
>>>>>>>at
>>>>>>> least check that the physical space representations are compatible,
>>>>>>>and
>>>>>>> provide a warning if they are not. There are too many 256^3 voxel
>>>>>>> medical
>>>>>>> images that do not have the same physical space representations.
>>>>>>> * A parallel set of operators is needed that can work on images in
>>>>>>> physical space, and if they have consistent physical space
>>>>>>> representations, it should fall trough to the highly optimized
>>>>>>>index
>>>>>>> only
>>>>>>> based computation.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Hans
>>>>>>> --
>>>>>>> Hans J. Johnson, Ph.D.
>>>>>>> hans-johnson at uiowa.edu
>>>>>>> Assistant Professor of Psychiatry
>>>>>>> University of Iowa Carver College of Medicine
>>>>>>> W278 GH, 200 Hawkins Drive
>>>>>>>
>>>>>>> Iowa City, Iowa 52242
>>>>>>> Phone: 319-353-8587
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Luis Ibanez <luis.ibanez at kitware.com>
>>>>>>> Date: Thu, 2 Jun 2011 08:57:29 -0400
>>>>>>> To: Bill Lorensen <bill.lorensen at gmail.com>
>>>>>>> Cc: ITK <insight-developers at itk.org>
>>>>>>> Subject: Re: [Insight-developers] Dashboard woes
>>>>>>>
>>>>>>> Bill,
>>>>>>>
>>>>>>> This is the consequence of an incomplete analysis
>>>>>>> of dependencies when making changes.
>>>>>>>
>>>>>>> 1) The Changes in BinaryFunctorImageFilter
>>>>>>> introduced the use of the LinearInterpolator
>>>>>>> in a filter that up to now was quite self-sufficient.
>>>>>>>
>>>>>>> 2) BinaryFunctorImageFilter in in Core/Common
>>>>>>>
>>>>>>> 3) ITK-Common DEPENDS ITK-VNLInstantiation ITK-KWSys
>>>>>>> (only)
>>>>>>>
>>>>>>> 4) With the changes in BinaryFunctor, now Common
>>>>>>> depends (in practice) on the ITK-ImageFunctions module.
>>>>>>> because that's where the Interpolators are. But, the
>>>>>>> module dependency was not made explicit because...
>>>>>>>
>>>>>>> 5) ITK-ImageFunction already depends on ITK-Common
>>>>>>>
>>>>>>> 6) Ergo sum: Circular dependency
>>>>>>>
>>>>>>> 7) Why did this go unnoticed before ?
>>>>>>>
>>>>>>> Because the test of the BinaryFunctor was made to
>>>>>>> depend on the ITK-ImageFunction module, giving
>>>>>>> the false impression that the problem was fixed.
>>>>>>>
>>>>>>> 8) The recent relocation of the ImageCompose - related
>>>>>>> filters exposed the missing dependency between
>>>>>>> the BinaryFunctorImageFitler and the Interpolators.
>>>>>>>
>>>>>>> ---
>>>>>>>
>>>>>>> I would have to agree with Brad L. on that this change
>>>>>>> in BinaryFunctorImageFilter is feature creep, and that
>>>>>>> we should reconsider the usefulness of that change.
>>>>>>>
>>>>>>>
>>>>>>> Luis
>>>>>>>
>>>>>>>
>>>>>>> --------------------
>>>>>>> On Wed, Jun 1, 2011 at 11:55 PM, Bill Lorensen
>>>>>>> <bill.lorensen at gmail.com>
>>>>>>> wrote:
>>>>>>>> Folks,
>>>>>>>>
>>>>>>>> I suggest we hold off on any new merges except for those that will
>>>>>>>> bring the Dashboard back to normalcy. There is no sense in
>>>>>>>>checking in
>>>>>>>> code when there are so many compile errors on so many platforms.
>>>>>>>>
>>>>>>>> Bill
>>>>>>>> _______________________________________________
>>>>>>>> Powered by www.kitware.com
>>>>>>>>
>>>>>>>> Visit other Kitware open-source projects at
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>>>>>>>>
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>>>>>>>>
>>>>>>>> Please keep messages on-topic and check the ITK FAQ at:
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>>>>>>>
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