[ITK-users] Patch for ApproximateSignedDistanceMapImageFilter

Thu Apr 6 09:27:58 EDT 2017

Thanks Christina for taking care of this problem! The patch you submitted
looks good to me. It would be perfect if you could create a test using the
images your generate to ensure that the problem does not appear again in
the future.

Francois

On Mon, Apr 3, 2017 at 3:18 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Christina,
>
> > 2nd attempt using approach 1)  (see below). What about typos in comments
> I
> > removed during bug fixing? Include into this patch as well or keep them
> > separate?
>
> Thanks! This patch has been uploaded:
>
>   http://review.source.kitware.com/#/c/22149/3
>
>
> The typos could go in a different patch (ideally), but it is OK, if
> they are included.
>
> Thanks,
> Matt
>
>
>
> > Additionally you find a small application creating an image with a bright
> > square on dark background which displays the image together with the
> result
> > of ApproximateSignedDistanceMapImageFilter. The pixel value of the
> square is
> > 1 by default but can be changed via command line.
> >
> > Regards,
> > Christina
> >
> >
> > On 29.03.2017 15:12, Francois Budin wrote:
> >
> > Hello Christina,
> >
> > I see different paths to try to solve this issue and I am not sure which
> one
> > is the best one:
> > 1) You could modify the itkIsoContourDistanceImageFilter class so that
> > m_LevelSetValue is of some real type. When looking in the implementation
> of
> > this filter,  you can see that sometimes, m_LevelSetValue is casted to a
> > real type [1], so maybe it makes sense to do that.
> > 2) Casting is one solution, but you have to be careful if you want to
> cast
> > to float or double. If you cast to float, and the input is of type
> double,
> > you will loose precision. If you always cast to double, you might use a
> lot
> > of memory. Sadly, in the itkNumericTraits, there is no way of asking for
> > "the smallest floating type that contains my current type". You can call
> > "RealType" which will be "double", or "FloatType" which will be float.
> One
> > strength of casting, is that if you perform it in place, it can actually
> not
> > do anything if it doesn't need to [2].
> > 3) To avoid casting when you don't need to (your type is float or
> double),
> > you could use the SFINAE concept like it is used here [3]. This is more
> > complex and may not be worth it.
> >
> > Beware that images may contain pixels that are not only scalar values,
> but
> > also RGB, RGBA, vectors. I am not sure if the ApproximateDistance filter
> > supports these types, but it is good to be careful, when modifying the
> code,
> > to not restrict the usage of a filter to scalar if not required. To avoid
> > that kind of issues, and to answer your original question, you can use
> the
> > Rebind structure [4].
> >
> > I hope this helps.
> > I will be out of town for a week, and most likely will have limited to no
> > access to the internet, so don't be surprised if I do not answer your
> next
> > message within the next week.
> >
> > Thanks for helping!
> > Francois
> >
> > [1]
> > https://github.com/InsightSoftwareConsortium/ITK/
> blob/master/Modules/Filtering/DistanceMap/include/
> itkIsoContourDistanceImageFilter.hxx#L314
> > [2]
> > https://github.com/InsightSoftwareConsortium/ITK/
> blob/master/Modules/Filtering/ImageFilterBase/include/
> itkCastImageFilter.hxx#L42
> > [3]
> > https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/
> ImageBase/include/itkConvertPixelBuffer.h#L153-L161
> > [4]
> > https://github.com/InsightSoftwareConsortium/ITK/
> blob/master/Modules/Filtering/Smoothing/include/
> itkSmoothingRecursiveGaussianImageFilter.h#L84-L85
> >
> > On Wed, Mar 29, 2017 at 7:10 AM, Chr. Rossmanith
> > <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>
> >> Hi Francois,
> >>
> >> I'm getting back to this issue. I'll introduce an intermediate image in
> >> the mini pipeline used in ApproximateSignedDistanceMapImageFilter
> which has
> >> a floating type for pixel values. Given
> >>
> >>   /** Type for input image. */
> >>   typedef TInputImage InputImageType;
> >>
> >> how can I define a corresponding image type FloatImageType replacing the
> >> unknown pixel type by float? I can't write itk::Image< float, xxx >
> because
> >> I don't know xxx.
> >>
> >> Is there a way to query the pixel type to avoid applying the
> >> CastImageFilter in case we already get floating valued pixels?
> >>
> >> Christina
> >>
> >>
> >>
> >> On 03.03.2017 14:58, Francois Budin wrote:
> >>
> >> Hi Christina,
> >>
> >> Maybe your idea was good but needs more work (e.g. cast the input image
> to
> >> the output type? at least if input is not a float, or maybe something
> else).
> >> I am glad you found a solution that works for you. If you need your
> software
> >> to be faster, you can also replace the SignedDanielssonDistanceMap with
> the
> >> SignedMauerDistanceMap [1].
> >>
> >> Hope this helps, and thanks for your contribution. Do not hesitate to
> >> submit a new patch to solve your original problem if you find a
> solution.
> >>
> >> Francois
> >> [1]
> >> https://itk.org/Doxygen/html/classitk_1_1SignedMaurerDistanceMapImageF
> ilter.html
> >>
> >> On Fri, Mar 3, 2017 at 8:23 AM, Chr. Rossmanith
> >> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>
> >>> Hi Francois,
> >>>
> >>> really strange, on Wednesday changing the data type made my application
> >>> work as expected (but obviously there must have been an additional
> change
> >>> which really made the application work...). When trying to build a
> small
> >>> example for you, I failed. I still think that feeding a 0/1 image into
> >>> ApproximateSignedDistanceMapImageFilter makes sense.
> >>>
> >>> Originally I'm interested in ContourExtractor2D, which operates on a
> >>> distance map using 0 as contour level. Unlike in the
> ContourExtractor2D
> >>> example I've decided to use SignedDanielssonDistanceMap which works
> fine
> >>> without any patches.
> >>>
> >>> So send the patch to /dev/null for the moment...
> >>>
> >>> Christina
> >>>
> >>>
> >>>  On 02.03.2017 16:17, Francois Budin wrote:
> >>>
> >>> Hello Christina,
> >>>
> >>> I just reviewed you patch. You are changing the type of the variable
> >>> levelSetValue to OutputPixelType which is suppose to be a floating
> point
> >>> value.
> >>> However, the computation is done with InputPixelType variables
> >>> (m_InsideValue and m_OutsideValue) and divided by an integer.
> Additionally,
> >>> the resulting value is used in:
> >>>   m_IsoContourFilter->SetLevelSetValue(levelSetValue);
> >>>
> >>> which accepts values of InputPixelType [1] since IsoContourType is
> >>> defined as:
> >>>   typedef IsoContourDistanceImageFilter< InputImageType,
> OutputImageType
> >>> >   IsoContourType;
> >>>
> >>> I am not sure if your patch solves the problem that you mentioned. Do
> you
> >>> have a test that would verify that the new behavior corresponds to your
> >>> expectations? Based on the code review I have done, I would not expect
> the
> >>> behavior of the filter to change.
> >>>
> >>> Let me know if I missed a detail. Thank you for your contribution!
> >>> Francois
> >>>
> >>> [1]
> >>> https://itk.org/Doxygen/html/classitk_1_1IsoContourDistanceImageFilter
> .html
> >>>
> >>> On Wed, Mar 1, 2017 at 8:12 AM, Chr. Rossmanith
> >>> <cr at neuro.ma.uni-heidelberg.de> wrote:
> >>>>
> >>>> For binary images with 0 for background and 1 for objects with an
> >>>> integer input pixel type there is a problem representing the average
> of 0
> >>>> and 1 = 0.5 with the input pixel type. The output pixel type is
> required to
> >>>> be a floating pixel type (filter documentation), so it should be safe
> to
> >>>> change the type of levelSetValue to OutputPixelType.
> >>>>
> >>>> Regards,
> >>>> Christina
> >>>>
> >>>>
> >>>> _____________________________________
> >>>> Powered by www.kitware.com
> >>>>
> >>>> Visit other Kitware open-source projects at
> >>>> http://www.kitware.com/opensource/opensource.html
> >>>>
> >>>> Kitware offers ITK Training Courses, for more information visit:
> >>>> http://www.kitware.com/products/protraining.php
> >>>>
> >>>> 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://public.kitware.com/mailman/listinfo/insight-users
> >>>>
> >>>
> >>>
> >>
> >>
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > 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://public.kitware.com/mailman/listinfo/insight-users
> >
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> 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://public.kitware.com/mailman/listinfo/insight-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20170406/df12e40f/attachment.html>