[ITK] [ITK-dev] image and deformation field physical space check

brian avants stnava at gmail.com
Tue Nov 4 09:28:48 EST 2014 

so - just to be clear ... same thing needs to be done here:

ITKv4/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.h

and how does Get/SetGlobalDefault  differ from  Set/GetCoordinateTolerance
Set/GetDirectionTolerance

which already exists in the image to image filter (but not displacement
field)?


brian



On Tue, Nov 4, 2014 at 9:26 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> I agree that would be good.
>
> The other thing which can be done concurrently is add the
> ImageToImageFilter::Get/SetGlobalDefault methods. Any one want to volunteer
> for that one?
>
> Brad
>
> On Nov 4, 2014, at 9:21 AM, brian avants <stnava at gmail.com> wrote:
>
> i guess the next step is to dig up a couple of examples of this behavior
> and post them somewhere.
>
>
> brian
>
>
>
> On Tue, Nov 4, 2014 at 9:14 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> That is a question: why is an exact copy not happening? Is is due to
>> runtime errors or accumulation of errors during IO?
>>
>> Brad
>>
>>
>> On Nov 4, 2014, at 3:51 AM, <M.Staring at lumc.nl> <M.Staring at lumc.nl>
>> wrote:
>>
>> > Hi all,
>> >
>> > Would it be possible to fix this issue by passing the physical space by
>> reference, or by performing an exact copy?
>> >
>> > Regards, Marius
>> >
>> >> -----Original Message-----
>> >> From: Insight-developers [mailto:insight-developers-bounces at itk.org]
>> On
>> >> Behalf Of Matt McCormick
>> >> Sent: maandag 3 november 2014 18:39
>> >> To: brian avants
>> >> Cc: Insight-developers at itk.org
>> >> Subject: Re: [ITK-dev] image and deformation field physical space check
>> >>
>> >> Hi Brian,
>> >>
>> >> Thanks for discussing this.
>> >>
>> >> I think a combination of fixing the underlying issue that is being
>> brought up by
>> >> the exception, relaxing the tolerance, and improving the documentation
>> is a
>> >> good approach.
>> >>
>> >> 2 cents,
>> >> Matt
>> >>
>> >> On Mon, Nov 3, 2014 at 11:40 AM, brian avants <stnava at gmail.com>
>> wrote:
>> >>> This email is motivated by this issue:
>> >>>
>> >>> https://github.com/stnava/ANTs/issues/74
>> >>>
>> >>> but it is not isolated to ants.   Worth a read for additional context.
>> >>>
>> >>> ITK currently enforces a relatively strict check that image and
>> >>> displacement fields "occupy the same physical space."  However, for
>> >>> some unclear (to me) reasons, the direction matrices or origins of
>> >>> images can lose precision when passing through ITK pipelines (
>> >>> especially through resampling or resolution-changing filters ).  This
>> >>> results in filters aborting and this can occur at various different
>> >>> places in a complex series of ITK-based operations.
>> >>>
>> >>> My concern with this is that it can lead to a very severe loss of
>> >>> productivity when this somewhat unpredictable error occurs.   For
>> instance,
>> >>> a user downloads a toolkit based on ITK ( itk-snap, ants, elastic,
>> >>> brainsfit, joint label fusion, etc).   The user expects registration
>> or
>> >>> segmentation filters to "work well" especially when the data is of a
>> >>> standard sort.   Then, after some oft-substantial execution time, this
>> >>> mysterious error appears:
>> >>>
>> >>> itk::ERROR: ImageToImageFilter(0x7fb3b2307ac0): Inputs do not occupy
>> >>> the same physical space!
>> >>>
>> >>>
>> >>> While I am all for correctness, when the impact on productivity
>> exceeds a
>> >>> certain threshold, I think it is useful to bend the rules a bit.
>>  Perhaps
>> >>> one of these would improve the situation:
>> >>>
>> >>> 1)    change:
>> >>>
>> >>> ITKv4/Modules/Filtering/DisplacementField/include/itkDisplacementField
>> >>> Transform.hxx
>> >>>
>> >>> and
>> >>>
>> >>> ITKv4/Modules/Core/Common/include/itkImageToImageFilter.hxx
>> >>>
>> >>> changing direction tolerance and coordinate tolerance to 1.e-4
>> >>>
>> >>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/F
>> >>> iltering/DisplacementField/include/itkDisplacementFieldTransform.hxx#L
>> >>> 454-L457
>> >>>
>> >>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/C
>> >>> ore/Common/include/itkImageToImageFilter.hxx#L40-L41
>> >>>
>> >>> and change the documentation too:
>> >>>
>> >>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/C
>> >>> ore/Common/include/itkImageToImageFilter.h#L76-L87
>> >>>
>> >>> 2)  Change the exception to a warning.  This would at least allow
>> >>> complex pipelines to execute while notifying the user of a possible
>> issue.
>> >>>
>> >>> 3)  Document all of the places that the user/developer should call:
>> >>>
>> >>> Set/GetCoordinateTolerance  Set/GetDirectionTolerance  .
>> >>>
>> >>> This last solution would require adding Set/GetCoordinate and
>> >>> Direction tolerance to:
>> >>>
>> >>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/F
>> >>> iltering/DisplacementField/include/itkDisplacementFieldTransform.h
>> >>>
>> >>> as well, for consistency.
>> >>>
>> >>> Anyway, I raise this issue b/c of the many man and computer hours lost
>> >>> by this check.
>> >>>
>> >>> Not once has this check actually helped us, in any measurable way,
>> >>> avoid errors.
>> >>>
>> >>>
>> >>>
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