[Insight-users] Curvature in ShapeDetectionLevelSetImageFilter
Joshua Cates
cates at sci . utah . edu
Thu, 10 Jul 2003 16:28:24 -0600 (MDT)
Hi Lydia,
Can you send Ross and I an example of data/parameters which cause problems
in (ideally) one of the Example applications? We'll hack on this next
week.
thanks,
Josh.
______________________________
Josh Cates
School of Computer Science
University of Utah
Email: cates at sci . utah . edu
Phone: (801) 587-7697
URL: http://www . sci . utah . edu/~cates
On Thu, 10 Jul 2003, Lydia Ng wrote:
> Hi Nils and Luis,
>
> There is issue in the current implementation of the level set framework
> in that the curvature term is not taken into account when computing the
> time step. Ideally, the time step should computed to maintain numerical
> stability.
>
> Thus, setting the curvature weight is high relative to the propagation
> term will cause problem most likely due to the time step being too
> large.
>
> This is a known problem - computing the time step to meet the CFL
> criterion is not widely reported in the literature - a few of us is
> still trying to figure out what is the mathematically sound thing to do
> here.
>
> BTW - I have also fixed the problem of when the propagation weight is
> zero - it shouldn't crash now - but you will still get the numerical
> instability issue as above.
>
> - Lydia
>
> > -----Original Message-----
> > From: Luis Ibanez [mailto:luis . ibanez at kitware . com]
> > Sent: Thursday, July 10, 2003 6:58 AM
> > To: Nils Hanssen
> > Cc: Insight-users at public . kitware . com
> > Subject: Re: [Insight-users] Curvature in
> > ShapeDetectionLevelSetImageFilter
> >
> >
> > Hi Nils,
> >
> > I just performed a couple of tests, and the
> > ShapeDetectionLSIF is behaving as expected.
> > (Note that I did this with the current CVS
> > version, not ITK 1.2).
> >
> > A couple of sample images that help to test
> > your case were checked in under:
> >
> > - Insight/Examples/Data/Circle.png
> > - Insight/Examples/Data/CircleSpikes.png
> >
> > http://www . itk . org/cgi-
> > bin/cvsweb.cgi/Insight/Examples/Data/Circle.png?cvsroot=Insight
> > http://www . itk . org/cgi-
> > bin/cvsweb.cgi/Insight/Examples/Data/CircleSpikes.png?cvsroot=Insight
> >
> > CircleSpikes.png simulates the conditions of your
> > tube but in 2D.
> >
> > The example ShapeDetectionLevelSetImageFilter
> > was also slightly modified in order to take the
> > scaling parameter from the command line arguments.
> >
> > http://www . itk . org/cgi-
> >
> bin/cvsweb.cgi/Insight/Examples/Segmentation/ShapeDetectionLevelSetFilte
> r.
> > cxx?cvsroot=Insight&sortby=date
> >
> > Running this example with the parameters below
> > succeded to segment the internal circle without
> > taking the spikes (bridges). Note that although
> > the segmentation doesn't goes into the spikes, they
> > excert some influence on the shape of the final
> > contour.
> >
> > Here are the parameters:
> >
> > ShapeDetectionLevelSetFilter
> >
> > input image: CirclesSpikes.png
> > output image: SegmentedCircle.png
> > seed point: 50 50
> > distance: 20
> > sigma: 1.0
> > sigmoid alpha: -40
> > sigmoid beta: 128
> > curvatureScaling: 3.1
> > propagationScaling: 0.97
> >
> > The overlay of the segmented circle, on top
> > of the CircleSpikes.png image is shown in
> > the attachement.
> >
> > ---
> >
> > The balance between the curvatureScaling and the
> > propagationScaling parameters is quite delicate.
> >
> > For example:
> >
> > keeping curvature scaling = 3.1
> > propagation scaling = 0.98 will overflow the whole image
> > while prop. scaling = 0.96 will grow just to half the circle
> >
> > OR
> >
> > keeping propagation scaling = 0.97
> > curvature scaling = 3.0 will overflow the image
> > curvature scaling = 3.2 will fall short on reaching the edges
> >
> >
> >
> > My guess is that it may be possible to find a
> > continuous function F():
> >
> > curvatureScaling = F( propagationScaling )
> >
> > for which the segmentation grabs on the circle edges,
> > but at some threshold of "PropagationScaling" the
> > computation will start presenting numerical
> > instabilities.
> >
> >
> >
> >
> > Regards,
> >
> >
> >
> > Luis
> >
> >
> >
> > ---------------------
> > Nils Hanssen wrote:
> > > Hi Luis,
> > >
> > > thank you for the detailed answer.
> > >
> > >
> > > My initial level set conforms to the "negative inside" convention.
> > > Now, I am using a curvature weighting of 1000 (just to see what
> happens
> > in
> > > the extreme case) and a propagation weighting of 0.001. When running
> the
> > > ShapeDetectionLSIF, the contour is not collapsing at all. Maybe
> that's
> > > because of the feature image that dictates the curvature speed (==
> > > propagation speed in the ShapeDetectionLSIF)?
> > >
> > > Since the curvature speed in the ShapeDetectionLSF equals the
> > propagation
> > > speed, I derived my own classes called "TubularLevelSetFunction" and
> > > "TubularLevelSetImageFilter". These are basically clones of the
> > > ShapeDetection* classes, but with the difference that I set the
> > curvature
> > > speed to (constant) one in the Level-set function.
> > > Now, the contour is collapsing according to the mean curvature but
> all
> > this
> > > happens _very_ slowly (the curvature weighting is 1000!).
> > >
> > > In itk::LevelSetFunction::ComputeUpdate(...) I see the following:
> > > ---
> > > curvature_term = curve;
> > > curvature_term *= m_CurvatureWeight * this->CurvatureSpeed(it,
> > offset);
> > > ---
> > > so it should make no difference when I set the curvature weight to 1
> and
> > the
> > > curvature speed to (constant) 1000 (and not vice versa), right? But
> when
> > I
> > > do this, I get numerical instabilities during the evolution. What is
> > wrong
> > > with my assumption?
> > >
> > > Luis, what was the curvature weighting and curvature speed when you
> > tested
> > > the collapsing contour with the syntethic sphere image? Was the
> > curvature
> > > speed constant or dependent on the image?
> > >
> > > For now, I do all calculations in 2D. Could that be a problem? I
> have
> > > installed a observer that shows me the progress of the contour after
> > each
> > > update event.
> > >
> > >
> > > Regards,
> > > Nils
> > >
> > >
> > >
> > >>-----Original Message-----
> > >>From: Luis Ibanez [mailto:luis . ibanez at kitware . com]
> > >>Sent: Wednesday, July 09, 2003 6:14 PM
> > >>To: Nils Hanssen
> > >>Cc: Insight-users at public . kitware . com
> > >>Subject: Re: [Insight-users] Crash in
> > >>ShapeDetectionLevelSetImageFilter
> > >>
> > >>
> > >>
> > >>Hi Nils,
> > >>
> > >>You are right in your interpretation of the
> > >>behavior for the ShapeDetectionLevelSetFilter.
> > >>
> > >>Increasing the curvature scaling while decreasing
> > >>the propagation scaling should make the contour
> > >>collapse (contract).
> > >>
> > >>I just verified this behavior using a syntethic
> > >>image of a sphere.
> > >>
> > >>Note that in version 1.2 this filter is expecting
> > >>the input level set to conform to the convention
> > >>of "negative inside" which means that the level
> > >>set has negative values 'inside' the contour and
> > >>positive values outside the contour.
> > >>
> > >>You may have to push the curvature scaling to
> > >>a value higher than 1.0. (e.g. 5.0 or so).
> > >>
> > >>I would avoid to use 0.0 for the propagation
> > >>scaling ( in part just for superstition against
> > >>zeros values as parameters). You may want to
> > >>try something like 0.1 for the propagation
> > >>scaling.
> > >>
> > >>Please verify the convention used by your initial
> > >>level set. That may be the cause for the contour
> > >>not behaving as expected.
> > >>
> > >>
> > >>Regards,
> > >>
> > >>
> > >> Luis
> > >>
> > >>
> > >>
> > >>---------------------
> > >>Nils Hanssen wrote:
> > >>
> > >>>Hi Luis,
> > >>>
> > >>>I am using the 1.2.0 web release.
> > >>>
> > >>>Regards,
> > >>>Nils
> > >>>
> > >>>
> > >>>
> > >>>>-----Original Message-----
> > >>>>From: insight-users-admin at itk . org
> > >>>>[mailto:insight-users-admin at itk . org]On
> > >>>>Behalf Of Luis Ibanez
> > >>>>Sent: Tuesday, July 08, 2003 3:55 PM
> > >>>>To: Nils Hanssen
> > >>>>Cc: Insight-users at public . kitware . com
> > >>>>Subject: Re: [Insight-users] Crash in
> > >>>>ShapeDetectionLevelSetImageFilter
> > >>>>
> > >>>>
> > >>>>
> > >>>>Hi Nils,
> > >>>>
> > >>>>Are you using a very recent checkout of ITK ?
> > >>>>
> > >>>>The level set filters have been reworked in
> > >>>>recent days, so it will help us to know if you
> > >>>>are experiencing this behavior with the current
> > >>>>version or with the version as it was two weeks
> > >>>>ago (or before that).
> > >>>>
> > >>>>Please let us know,
> > >>>>
> > >>>> Thanks
> > >>>>
> > >>>>
> > >>>> Luis
> > >>>>
> > >>>>
> > >>>>------------------------
> > >>>>Nils Hanssen wrote:
> > >>>>
> > >>>>
> > >>>>>Hi,
> > >>>>>
> > >>>>>I am trying to understand the behaviour of the
> ShapeDetectionLSIF.
> > >>>>>Therefore, I set the propagation-weighting to zero. By setting
> the
> > >>>>>curvature-weighting to a value of one I would expect that
> > >>>>
> > >>>>the inital
> > >>>>
> > >>>>
> > >>>>>surface is shrinking to a point (I set the MaxRMSError to
> > >>>>
> > >>>>zero) and the
> > >>>>
> > >>>>
> > >>>>>number of iterations very high.
> > >>>>>
> > >>>>>The filter is crashing in
> > >>>>>SegmentationLevelSetFunction<TImageType, TFeatureImageType>
> > >>>>>::PropagationSpeed(const NeighborhoodType &neighborhood, const
> > >>>>>FloatOffsetType &offset) const
> > >>>>>[...]
> > >>>>>--> else return (
> > >>>>
> > >>>>static_cast<ScalarValueType>(m_SpeedImage->GetPixel(idx)) );
> > >>>>// crashing here
> > >>>>
> > >>>>
> > >>>>>[...]
> > >>>>>
> > >>>>>When I set the propagation-weighting to - for instance -
> > >>>>
> > >>0.0001 the
> > >>
> > >>>>>filter is not crashing, but the contour is not shrinking
> > >>>>
> > >>>>according to
> > >>>>
> > >>>>
> > >>>>>the mean curvature.
> > >>>>>
> > >>>>>Is that the correct behaviour of the filter?
> > >>>>>
> > >>>>>I would appreciate any suggestions. Thanks!
> > >>>>>
> > >>>>>
> > >>>>>Regards,
> > >>>>>Nils
> > >>>>>
> > >>>>>
> > >>>>>-------------------------
> > >>>>>Nils Hanssen
> > >>>>>Surgical Systems Laboratory
> > >>>>>research center c ae sa r
> > >>>>>Ludwig-Erhard-Allee 2
> > >>>>>53175 Bonn
> > >>>>>fon: +49-228-9656-197
> > >>>>>fax: +49-228-9656-117
> > >>>>>___http://www . caesar . de/ssl_
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>_______________________________________________
> > >>>>Insight-users mailing list
> > >>>>Insight-users at itk . org
> > >>>>http://www . itk . org/mailman/listinfo/insight-users
> > >>>>
> > >>>
> > >>>_______________________________________________
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> > >>>http://www . itk . org/mailman/listinfo/insight-users
> > >>>
> > >>
> > >>
> > >>
> > >>
> > >
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> > >
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>
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