[Insight-developers] ITK 3.10 : Turning ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE = ON by default

Fri Oct 17 10:30:19 EDT 2008

Hi Tom,

Thanks for clarifying your question.

         Fortunately, the answer again is: Yes !

You will find these tests under:

   Insight/Examples/Registration

               ImageRegistration1od1Test
               ImageRegistration1od1Test

The use as input the following images:

Insight/Examples/Data/BrainProtonDensitySliceBorder20DirectionPlus30.mhd
Insight/Examples/Data/BrainProtonDensitySliceShifted13x17yDirectionPlus30.mhd

These MetaImage headers have a non-identity direction matrix
(e.g. "TransformMatrix")

These tests were added on October 9th 2007,
http://www.itk.org/cgi-bin/viewcvs.cgi/Examples/Registration/CMakeLists.txt?root=Insight&r1=1.121&r2=1.122
so they have been working for over a year now.

Of course,
It will be a good idea to add more tests with non-identiy matrix values.

    Regards,

       Luis

----------------------
Tom Vercauteren wrote:
> Hi Luis,
> 
> I need to clarify my first question :)
> 
> I am wondering whether the current registration unit tests actully use
> images that have a non-identity orientation. If I remember correctly,
> so far the registration tests were only using images that had an
> identity orientation. In that case, using (or not using) the
> orientation information should of course not change the result.
> 
> To rephrase it: Are there any tests that now fail only if the flag is
> set to OFF? I would indeed expect that since orientation is not used
> within registration when the flag is OFF (old behavior), registering
> two images with non-identity orientation should fail. The same tests
> should however pass with the flag set to ON (new behavior).
> 
> Am I missing something?
> 
> Best,
> Tom
> 
> On Fri, Oct 17, 2008 at 3:05 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
> 
>>Hi Tom,
>>
>>
>>Excellent question.
>>
>>
>>              Fortunately the answer is:  Yes !
>>
>>
>>We have been testing the toolkit with this flag ON for several weeks
>>now in specific machines. (Redwall, Zion, Camelot), and they have been
>>producing green builds.
>>
>>
>>As further confirmation, we turned the flag ON, yesterday, so today's
>>Nightly builds are all (unless they explicitly turned the flag OFF)
>>reporting results by having the itk::Image behave just like the
>>itk::OrientedImage.
>>
>>
>>Unfortunately, I broke the build while fixing coding style violations
>>in Code/Common, so we will have to wait for tomorrow's Dashboard to
>>have a clear picture of the effect of turning the flag ON in all the
>>Nightly submissions.
>>
>>
>>Point taken about the Software Guide, and update of the book is overdue.
>>
>>
>> Regards,
>>
>>
>>     Luis
>>
>>
>>----------------------
>>Tom Vercauteren wrote:
>>
>>>Hi Luis,
>>>
>>>It's great to see ITK becoming more consistent with respect to image
>>>orientation!
>>>
>>>Out of curiosity, I am wondering whether the correct behavior of the
>>>registration (parametric or not) with oriented images is already being
>>>tested by the unit tests?
>>>
>>>Also I think that once the orientation framework becomes stable, it
>>>would be worth updating the ITK user guide to explain how orientation
>>>information is used (or should be) in ITK.
>>>
>>>Just my two cents.
>>>
>>>Regards,
>>>Tom
>>>
>>>On Thu, Oct 16, 2008 at 7:42 PM, Luis Ibanez <luis.ibanez at kitware.com>
>>>wrote:
>>>
>>>
>>>>Hi Leila,
>>>>
>>>>Thanks for the feedback.
>>>>
>>>>BTW,
>>>>to make the fix complete we will also turn ON by default the
>>>>CMake variable
>>>>
>>>>         ITK_USE_ORIENTED_IMAGE_DIRECTION
>>>>
>>>>
>>>>This flag is used by gradient computation classes, to make the
>>>>gradient orientations consistent with the image orientation.
>>>>
>>>>This fixes an long standing bug in the registration framework.
>>>>
>>>>
>>>>Regards,
>>>>
>>>>
>>>> Luis
>>>>
>>>>
>>>>------------------------
>>>>Leila Baghdadi wrote:
>>>>
>>>>
>>>>>Hi Luis,
>>>>>
>>>>>It sounds like a great plan. If the direction cosines are taken into
>>>>>account the image is read ( this is the behavior of all the software
>>>>>that we have in our center), then there is nothing to worry about.
>>>>>
>>>>>I also like the idea that the cmake flag gets rid of alot of confusion
>>>>>for the developers.
>>>>>
>>>>>Leila
>>>>>
>>>>>On Thu, 2008-10-16 at 09:03 -0400, Luis Ibanez wrote:
>>>>>
>>>>>
>>>>>
>>>>>>In preparation for the release of ITK 3.10,
>>>>>>
>>>>>>
>>>>>>We are proposing to turn ON by default the CMake flag:
>>>>>>
>>>>>>
>>>>>>        ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
>>>>>>
>>>>>>
>>>>>>When this flag is ON, the itk::Image provides a behavior identical
>>>>>>to the itk::OrientedImage. Essentially taking the image direction
>>>>>>into account when converting Indices to Physical Points and back.
>>>>>>
>>>>>>
>>>>>>The itk::OrientedImage should be retained for backward compatibility,
>>>>>>despite of becoming redundant at this point.
>>>>>>
>>>>>>
>>>>>>The rational for turning this flag ON by default is that this is
>>>>>>the correct behavior to expect from a medical image, while ignoring
>>>>>>the direction when converting indices to points is actually a bug.
>>>>>>
>>>>>>
>>>>>>The buggy behavior will still be available as an option, to those
>>>>>>who require a backward compatible frame (e.g. applications that
>>>>>>have already worked around the previous bug). In those cases you
>>>>>>should simply turn the flag OFF, in order to get the old behavior.
>>>>>>
>>>>>>
>>>>>>Please let us know if you have any questions or concerns.
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>   Luis
>>>>>>
>>>>>>
>>>>>>
>>>>>>-------------------------
>>>>>>Karthik Krishnan wrote:
>>>>>>Perhaps that
>>>>>>
>>>>>>
>>>>>>
>>>>>>>could be on the list of things ToDo whenever the next lengthy
>>>>>>>discussion on Orientation comes up in ITK. I think we have one
>>>>>>>every month. :)
>>>>>>>
>>>>>>>Thanks
>>>>>>>
>>>>>>
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>>>>>>Insight-developers at itk.org
>>>>>>http://www.itk.org/mailman/listinfo/insight-developers
>>>>>
>>>>>
>>>>>
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>>>>
>>>
>>>
> 