[Insight-users] Curvature in ShapeDetectionLevelSetImageFilter
Nils Hanssen
hanssen at caesar . de
Fri, 11 Jul 2003 11:57:53 +0200
Hi Luis.
thank you so much for your suggestions; the support is really great!
I'm currently compiling the latest CVS to be up-to-date. Then I will try
your parameters to see what happens for my case.
I'll report about the progress next week.
Have a nice weekend,
Nils
> 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/Ci
> rcle.png?cvsroot=Insight
> http://www . itk . org/cgi-bin/cvsweb . cgi/Insight/Examples/Data/Ci
> rcleSpikes.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/Segment
> ation/ShapeDetectionLevelSetFilter.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
> >>>>
> >>>
> >>>_______________________________________________
> >>>Insight-users mailing list
> >>>Insight-users at itk . org
> >>>http://www . itk . org/mailman/listinfo/insight-users
> >>>
> >>
> >>
> >>
> >>
> >
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