[Insight-developers] Bugs with respect to ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
Tom Vercauteren
tom.vercauteren at m4x.org
Mon Nov 10 07:45:02 EST 2008
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/itkESMDemonsRegistrationFunction.txx?root=Insight&r1=1.9&r2=1.10&sortby=date
http://www.itk.org/cgi-bin/viewcvs.cgi/Testing/Code/Review/itkDiffeomorphicDemonsRegistrationFilterTest.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
>>>
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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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