[Insight-users] [Insight-developers] fixing a few remaining failing tests relating to pixel-centered coordinates

Michel Audette michel.audette at kitware.com
Thu May 21 11:12:03 EDT 2009 

Hi gents,

I can certainly write a test that implements what Bill was proposing. For
the time being, my attention is still focused on the failing tests on the
Dashboard, but assuming that Luis is okay with this, we can tackle this test
shortly.

Best wishes,

Michel

On Thu, May 21, 2009 at 9:05 AM, Wes Turner <wes.turner at kitware.com> wrote:

> I think a warning makes sense until we have better validation.
> Michel/Luis is this something that fits in with what you are doing?
> - Wes
>
>
> On Thu, May 21, 2009 at 8:37 AM, Bill Lorensen <bill.lorensen at gmail.com>wrote:
>
>> Simon,
>>
>> My point is that we have not validated the new code as far as I can tell.
>>
>> Bill
>>
>> On Thu, May 21, 2009 at 7:57 AM, Simon Warfield
>> <simon.warfield at childrens.harvard.edu> wrote:
>> > Bill Lorensen wrote:
>> >>
>> >> Yes, I think that will be OK. We should add an Attention: warning to
>> >> the CMakeLists.txt file. Something like:
>> >>
>> >>  SET(msg "Attention: You have chosen to enable the use of
>> >> cell-centered coordinates.")
>> >>
>> >
>> > The tool kit currently uses a mixture of both, so the above is a bit
>> > misleading. How about instead:
>> > SET(msg "Attention: You have chosen to enable the consistent use of
>> centered
>> > pixel coordinates.")
>> >
>> > We should explain the pros and cons of the choice e.g.:
>> >>
>> >>  SET(msg "${msg} This new functionality has not been fully validated.
>> >> USE AT YOUR OWN RISK.")
>> >>
>> >
>> > SET(msg "${msg} The old functionality creates an inconsistent physical
>> > coordinate system.")
>> >>
>> >>  SET(msg "${msg} With this ON, you can expect to see differences in
>> >> registration and interpolation results.")
>> >>
>> >
>> > differences -> improvements
>> >>
>> >> # display the message during the setup
>> >> MESSAGE("${msg}")
>> >>
>> >
>> > --
>> > Simon
>> >>
>> >> On Wed, May 20, 2009 at 11:23 PM, Wes Turner <wes.turner at kitware.com>
>> >> wrote:
>> >>
>> >>>
>> >>> Bill,
>> >>> I think the idea is to disable the cell-centered functionality until
>> >>> after
>> >>> the release.  I.e. the code will be in, but not enabled in the CMake
>> >>> options.  Is this an acceptable alternative?
>> >>> - Wes
>> >>> On Wed, May 20, 2009 at 7:20 PM, Bill Lorensen <
>> bill.lorensen at gmail.com>
>> >>> wrote:
>> >>>
>> >>>>
>> >>>> I understand the current situation. I do believe however that we
>> >>>> should validate the new techniques. Regression testing is meant to
>> >>>> track changes in the code but they do not validate the code. Before
>> we
>> >>>> release ITK with these new capabilities I think we should make sure
>> >>>> the code is correct. Even if this means we have to delay the release.
>> >>>>
>> >>>> Bill
>> >>>>
>> >>>> On Wed, May 20, 2009 at 1:57 PM, Michel Audette
>> >>>> <michel.audette at kitware.com> wrote:
>> >>>>
>> >>>>>
>> >>>>> Hi Bill,
>> >>>>>
>> >>>>> so far we are only modifying existing tests that were failing. The
>> >>>>> following
>> >>>>> tests include new code,
>> >>>>>
>> >>>>> Code/BasicFilters/itkExpandImageFilterTest.cxx:
>> >>>>> Code/BasicFilters/itkVectorExpandImageFilterTest.cxx:
>> >>>>> Code/Common/itkBSplineDeformableTransformTest2.cxx
>> >>>>>
>> >>>>> which assume pixel-centeredness. Moreover, many other tests have new
>> >>>>> regression data committed, and ctest selects the appropriate data
>> set
>> >>>>> depending on the value of these flags.
>> >>>>>
>> >>>>> Best wishes,
>> >>>>>
>> >>>>> Michel
>> >>>>>
>> >>>>> On Wed, May 20, 2009 at 1:48 PM, Bill Lorensen
>> >>>>> <bill.lorensen at gmail.com>
>> >>>>> wrote:
>> >>>>>
>> >>>>>>
>> >>>>>> Do we have a test that validates the centered pixel and portable
>> round
>> >>>>>> options? For example, a 1D example that can be manual verified.
>> >>>>>>
>> >>>>>> Bill
>> >>>>>>
>> >>>>>>
>> >>>>>> On Wed, May 20, 2009 at 1:12 PM, Michel Audette
>> >>>>>> <michel.audette at kitware.com> wrote:
>> >>>>>>
>> >>>>>>>
>> >>>>>>> Dear members of the Insight Community,
>> >>>>>>>
>> >>>>>>> in response to bug 6558, Luis and I have implemented some changes
>> >>>>>>> that
>> >>>>>>> produce pixel-centered coordinates, as well as a few other needed
>> >>>>>>> refinements, which are enabled by the flags
>> >>>>>>> ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY,
>> >>>>>>> ITK_USE_REGION_VALIDATION_IN_ITERATORS and
>> >>>>>>> ITK_USE_PORTABLE_ROUND
>> >>>>>>>
>> >>>>>>> With the flags turned off, the code behaves as before, with no
>> >>>>>>> failing
>> >>>>>>> tests. With the flags turned on there are still a number of
>> failing
>> >>>>>>> tests,
>> >>>>>>> that are related to these new coordinates, and which have been
>> >>>>>>> whittled
>> >>>>>>> down
>> >>>>>>> from more than 25 to 14 currently.
>> >>>>>>>
>> >>>>>>> Nonetheless, we would like to get rid of as many of these as we
>> can
>> >>>>>>> by
>> >>>>>>> next
>> >>>>>>> Monday, for the upcoming release of ITK, and consequently, we
>> would
>> >>>>>>> respectfully ask interested members of the community to lend a
>> hand
>> >>>>>>> with
>> >>>>>>> the
>> >>>>>>> remaining tests.
>> >>>>>>>
>> >>>>>>> I will be submitting an Experimental ctest on a regular basis,
>> with
>> >>>>>>> the
>> >>>>>>> signature metropolis-pixelcentered.kitware
>> >>>>>>> Currently the failing tests are the following.
>> >>>>>>>    169 - itkSampleSelectiveMeanShiftBlurringFilterTest (Failed)
>> >>>>>>>    340 - itkMedialNodeCorrespondencesTest (Failed)
>> >>>>>>>    543 - itkImportImageTest (Failed)
>> >>>>>>>    572 - itkNonThreadedShrinkImageTest (Failed)
>> >>>>>>>    594 - itkShrinkImageTest (Failed)
>> >>>>>>>    615 - itkStreamingImageFilterTest2 (Failed)
>> >>>>>>>    630 - itkWarpImageFilterTest (Failed)
>> >>>>>>>    632 - itkWarpVectorImageFilterTest (Failed)
>> >>>>>>>    800 - itkMattesMutualInformationImageToImageMetricTest (Failed)
>> >>>>>>>    801 - itkMattesMutualInformationImageToImageMetricTest2
>> (Failed)
>> >>>>>>>    802 - itkMattesMutualInformationImageToImageMetricTest3
>> (Failed)
>> >>>>>>>    803 - itkMattesMutualInformationImageToImageMetricTest4
>> (Failed)
>> >>>>>>>    816 - itkMultiResolutionPDEDeformableRegistrationTest (Failed)
>> >>>>>>>    1470 - ResampleImageFilter9Test (Failed)
>> >>>>>>>
>> >>>>>>> I plan to work on failing tests relating to the
>> itkShrinkImageFilter
>> >>>>>>> class.
>> >>>>>>>
>> >>>>>>> Thank you for your kind consideration.
>> >>>>>>>
>> >>>>>>> Best wishes,
>> >>>>>>>
>> >>>>>>> Michel
>> >>>>>>> --
>> >>>>>>> Michel Audette, Ph.D.
>> >>>>>>> R & D Engineer,
>> >>>>>>> Kitware Inc.,
>> >>>>>>> Chapel Hill, N.C.
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> _______________________________________________
>> >>>>>>> Powered by www.kitware.com
>> >>>>>>>
>> >>>>>>> Visit other Kitware open-source projects at
>> >>>>>>> http://www.kitware.com/opensource/opensource.html
>> >>>>>>>
>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>>>>
>> >>>>>>> Follow this link to subscribe/unsubscribe:
>> >>>>>>> http://www.itk.org/mailman/listinfo/insight-developers
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Michel Audette, Ph.D.
>> >>>>> R & D Engineer,
>> >>>>> Kitware Inc.,
>> >>>>> Chapel Hill, N.C.
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>
>> >>>> _______________________________________________
>> >>>> Powered by www.kitware.com
>> >>>>
>> >>>> Visit other Kitware open-source projects at
>> >>>> http://www.kitware.com/opensource/opensource.html
>> >>>>
>> >>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>
>> >>>> Follow this link to subscribe/unsubscribe:
>> >>>> http://www.itk.org/mailman/listinfo/insight-developers
>> >>>>
>> >>>
>> >>> --
>> >>> Wesley D. Turner, Ph.D.
>> >>> Kitware, Inc.
>> >>> R&D Engineer
>> >>> 28 Corporate Drive
>> >>> Clifton Park, NY 12065-8662
>> >>> Phone: 518-371-3971 x120
>> >>>
>> >>>
>> >>
>> >>
>> >>
>> >
>> >
>> >
>> >
>> >
>>
>
>
>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> R&D Engineer
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-371-3971 x120
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.
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