[Insight-developers] Bugs with respect to ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
Tom Vercauteren
tom.vercauteren at m4x.org
Wed Nov 12 06:31:51 EST 2008
Thanks Gaëtan,
I actually didn't try the configuration that you send me:
ITK_USE_ORIENTED_IMAGE_DIRECTION:BOOL=ON
ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE:BOOL=OFF
As far as I understand it, it makes sense that my tests fail with such
a configuration since I am trying to register images that have a
non-identity orientation. But then again, I am confused with how these
two flags interact...
A simple solution would be to use non-identity orientation in the
tests only if both ITK_USE_ORIENTED_IMAGE_DIRECTION and
ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE are ON. Does that make sense?
Tom
On Wed, Nov 12, 2008 at 12:08 PM, Gaëtan Lehmann
<gaetan.lehmann at jouy.inra.fr> wrote:
>
> Le 12 nov. 08 à 11:24, Tom Vercauteren a écrit :
>
>> Hi all,
>>
>> Some tests are failing on the dashboard but I cannot reproduce them on
>> my machine. E.g.:
>>
>> http://www.cdash.org/CDash/testSummary.php?project=2&name=itkDiffeomorphicDemonsRegistrationFilterTest01&date=2008-11-12
>
>
> One is mine (marvin). It has consolidated morphology and use optimized
> registration on, and is built in Debug mode.
> I'm sending you the CMakeCache.txt in case you need more configuration
> informations.
>
>
>>
>>
>> The problem is that I cannot find out which flags are enabled on these
>> machines. Problems might indeed arise only on certain configurations.
>>
>> Can someone help?
>>
>> Tom
>>
>> On Mon, Nov 10, 2008 at 2:17 PM, Hans Johnson <hans-johnson at uiowa.edu>
>> wrote:
>>>
>>> Oops,
>>>
>>> Sorry about this. I just realized that this code was correctly placed in
>>> the test driver, and not in the filter itself!
>>>
>>> Thank you very much for addressing this issue quickly, I've been fighting
>>> with it all weekend. I have a few more changes to submit with regards to
>>> making all of ITK work consistently with OrientedImages, but I am running
>>> some more extensive testing to ensure that they all work OK before
>>> submitting them.
>>>
>>> Hans
>>>
>>>
>>>
>>>
>>> On 11/10/08 7:12 AM, "Hans Johnson" <hans-johnson at uiowa.edu> wrote:
>>>
>>>> Tom,
>>>>
>>>> This code looks very suspicious to me:
>>>>
>>>> 149 DirectionType direction;
>>>> 150 direction.SetIdentity();
>>>> 151 #ifdef ITK_USE_ORIENTED_IMAGE_DIRECTION
>>>> 152 direction(1,1)=-1;
>>>> 153 #endif
>>>>
>>>> 162 moving->SetDirection(direction);
>>>> 163
>>>>
>>>>
>>>> It looks like the directions are being hard coded rather than taken from
>>>> the
>>>> input images.
>>>>
>>>> On 11/10/08 6:45 AM, "Tom Vercauteren" <tom.vercauteren at m4x.org> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> The orientation issue in the ESMDemonsFunction code should now be
>>>>> fixed. It would however be great if someone could review the change
>>>>> that I committed. Especially what I did with
>>>>> #ifdef ITK_USE_ORIENTED_IMAGE_DIRECTION
>>>>>
>>>
>>> http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkESMDemonsRegistrationFu>>
>>> n
>>>>>
>>>>> ction.txx?root=Insight&r1=1.9&r2=1.10&sortby=date
>>>>>
>>>
>>> http://www.itk.org/cgi-bin/viewcvs.cgi/Testing/Code/Review/itkDiffeomorphicDe>>
>>> m
>>>>>
>>>>> onsRegistrationFilterTest.cxx?root=Insight&r1=1.8&r2=1.9&sortby=date
>>>>>
>>>>> I am not yet confident with how orientation should be managed within
>>>>> ITK depending on what flag is turned on or off...
>>>>>
>>>>> Thanks,
>>>>> Tom
>>>>>
>>>>> On Sun, Nov 9, 2008 at 7:07 PM, Bill Lorensen <bill.lorensen at gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> Hans,
>>>>>>
>>>>>> FYI, #warning is GNU specific. Look at my changes to the ESM code. I
>>>>>> also modified the code to only throw an exception if the Direction is
>>>>>> non-identity.
>>>>>>
>>>>>> Bill
>>>>>>
>>>>>> On Fri, Nov 7, 2008 at 11:38 AM, Stephen Aylward
>>>>>> <Stephen.Aylward at kitware.com> wrote:
>>>>>>>
>>>>>>> Not certain if registration with directions will work otherwise.
>>>>>>>
>>>>>>> In particular, I think the BSplineInterpolateImageFunction would not
>>>>>>> work...Heck, I think you also need to make sure you turn on
>>>>>>> "ITK_USE_ORIENTED_IMAGE_DIRECTIONS" - see line 278 (and others) in
>>>>>>> ITK/Code/Review/itkOptBSplineInterpoleImageFunction.txx
>>>>>>>
>>>>>>> Note that there is no corresponding use of image directions in the
>>>>>>> ITK/Code/Common/itkBSplineInterpolateImageFunction.txx - as a result,
>>>>>>> the
>>>>>>> BSpline grid may not actually overlap the image :)
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Nov 7, 2008 at 11:18 AM, Hans Johnson
>>>>>>> <hans-johnson at uiowa.edu>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Stephen,
>>>>>>>>
>>>>>>>> USE_OPTIMIZED_REGISTRATION_METHODS is not turned on because it
>>>>>>>> causes our
>>>>>>>> local Mutual Information application to fail on some platforms (a
>>>>>>>> separate
>>>>>>>> issue that we are working through).
>>>>>>>>
>>>>>>>> It is my understanding that USE_OPTIMIZED_REGISTRATION_METHODS
>>>>>>>> provide
>>>>>>>> new optimized versions of some algorithms that are a drop in
>>>>>>>> replacement
>>>>>>>> (i.e. Provide the same results as) the non optimized versions.
>>>>>>>>
>>>>>>>> Hans
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Hans J. Johnson, Ph.D.
>>>>>>>> Hans-johnson at uiowa.edu
>>>>>>>>
>>>>>>>> 278 GH
>>>>>>>> The University of Iowa
>>>>>>>> Iowa City, IA 52241
>>>>>>>> (319) 353 8587
>>>>>>>>
>>>>>>>>
>>>>>>>> ________________________________
>>>>>>>> From: Stephen Aylward <Stephen.Aylward at kitware.com>
>>>>>>>> Date: Fri, 7 Nov 2008 11:13:36 -0500
>>>>>>>> To: Johnson Hans <hans-johnson at uiowa.edu>
>>>>>>>> Cc: Luis Ibanez <luis.ibanez at kitware.com>, ITK
>>>>>>>> <insight-developers at itk.org>
>>>>>>>> Subject: Re: [Insight-developers] Bugs with respect to
>>>>>>>> ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
>>>>>>>>
>>>>>>>> Do you also have USE_REVIEW and USE_OPTIMIZED_REGISTRATION_METHODS
>>>>>>>> turned
>>>>>>>> on? Those are needed to enable the registration methods that
>>>>>>>> SHOULD
>>>>>>>> (may?)
>>>>>>>> correctly handle directions.
>>>>>>>>
>>>>>>>> Stephen
>>>>>>>>
>>>>>>>> On Fri, Nov 7, 2008 at 11:07 AM, Hans Johnson
>>>>>>>> <hans-johnson at uiowa.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Luis,
>>>>>>>>
>>>>>>>> I'm sorry to spring this on you just hours after the release, but I
>>>>>>>> discovered several bugs when ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE is
>>>>>>>> turned
>>>>>>>> on, and images with different directions are used.
>>>>>>>>
>>>>>>>> I'm working on a patch right now, but it does touch many many files.
>>>>>>>> So
>>>>>>>> far my tests have shown that regression tests pass both with or
>>>>>>>> without
>>>>>>>> setting the output directions. The problem showed up when
>>>>>>>> attempting to
>>>>>>>> register images that have different orientations, spacing's, size,
>>>>>>>> and
>>>>>>>> origins. I think that our test data is too uniformly defined to
>>>>>>>> catch
>>>>>>>> these
>>>>>>>> problems.
>>>>>>>>
>>>>>>>> =======================================================
>>>>>>>> grep -A 2 -B 2 "Set.*Spacing.*Get.*Spacing" Insight/Code/*/* >
>>>>>>>> ReviewList
>>>>>>>>
>>>>>>>> From this I look for patterns like the following:
>>>>>>>>
>>>>>>>> Code/Algorithms/itkBayesianClassifierImageFilter.txx-
>>>>>>>> this->GetOutput()->SetRegions( membershipImage->GetBufferedRegion()
>>>>>>>> );
>>>>>>>> Code/Algorithms/itkBayesianClassifierImageFilter.txx:
>>>>>>>> this->GetOutput()->SetSpacing( membershipImage->GetSpacing() );
>>>>>>>> Code/Algorithms/itkBayesianClassifierImageFilter.txx-
>>>>>>>> this->GetOutput()->SetOrigin( membershipImage->GetOrigin() );
>>>>>>>> Code/Algorithms/itkBayesianClassifierImageFilter.txx-
>>>>>>>> this->GetOutput()->Allocate();
>>>>>>>>
>>>>>>>> NOTICE: The output of this filter does not set the Direction!!!!
>>>>>>>> this->GetOutput()->SetDirection( membershipImage->GetDirection() );
>>>>>>>> =======================================================
>>>>>>>>
>>>>>>>> Unfortunately this seems like a very common problem throughout ITK.
>>>>>>>> It
>>>>>>>> is my assumption that most filters that: a) take input image, b) do
>>>>>>>> something to the intensity values, c) generate and output image;
>>>>>>>> will
>>>>>>>> behave
>>>>>>>> in such a way that the output image has the same origin, spacing,
>>>>>>>> size,
>>>>>>>> AND
>>>>>>>> direction as the input image. Filters that: a)take an input image,
>>>>>>>> b)
>>>>>>>> take
>>>>>>>> parameters for desired output physical space defintion, c) generate
>>>>>>>> the
>>>>>>>> new
>>>>>>>> output image; must have options for setting Spacing, Origin, AND
>>>>>>>> Direction.
>>>>>>>>
>>>>>>>> Experimental build:
>>>>>>>> http://www.cdash.org/CDash/buildSummary.php?buildid=210257
>>>>>>>>
>>>>>>>> I hope to have the code committed and bugs reported in about 1 hour.
>>>>>>>>
>>>>>>>> Hans
>>>>>>>> --
>>>>>>>> Hans J. Johnson, Ph.D.
>>>>>>>> Hans-johnson at uiowa.edu <http://Hans-johnson@uiowa.edu>
>>>>>>>>
>>>>>>>> 278 GH
>>>>>>>> The University of Iowa
>>>>>>>> Iowa City, IA 52241
>>>>>>>> (319) 353 8587
>>>>>>>>
>>>>>>>> Notice: This UI Health Care e-mail (including attachments) is
>>>>>>>> covered by
>>>>>>>> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>>>>>>> confidential and may be legally privileged. If you are not the
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>>>>>>>> recipient, you are hereby notified that any retention,
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>>>>>>>> distribution, or copying of this communication is strictly
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>>>>>>>> Please reply to the sender that you have received the message in
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>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Insight-developers mailing list
>>>>>>>> Insight-developers at itk.org
>>>>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Stephen R. Aylward, Ph.D.
>>>>>>>> Chief Medical Scientist
>>>>>>>> Kitware, Inc. - North Carolina Office
>>>>>>>> http://www.kitware.com
>>>>>>>> (518) 371-3971 x300
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Stephen R. Aylward, Ph.D.
>>>>>>> Chief Medical Scientist
>>>>>>> Kitware, Inc. - North Carolina Office
>>>>>>> http://www.kitware.com
>>>>>>> (518) 371-3971 x300
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Insight-developers mailing list
>>>>>>> Insight-developers at itk.org
>>>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>
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>
> --
> 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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