[Insight-users] Connected component statistics

Tue Jul 19 09:18:11 EDT 2005

Richard, 

A one pass algorithm is what I would want ITK to have to compute these
statististics for all components.  Glad to hear you were already thinking
along those lines.

As for a representation, I would start with an approach like the RelabelComponentImageFilter
and LabelStatisticsImageFilter.  After these filters run, you can query the filter for 
the statistics of interest for a given component.

If this information needs to flow through the pipeline, then a separate data structure, 
say a std::map<itk::ComponentStatistics> could be used and wrapped with a DataObjectDecorator
to add a DataObject API to the std::map.  We would still have to create an itk::ComponentStatistics
class (or some other named class) to store the statistics for a given component.

Jim

-----Original Message-----
From: Richard Beare [mailto:richard.beare at gmail.com]
Sent: Monday, July 18, 2005 7:37 PM
To: Miller, James V (Research)
Cc: Gaetan Lehmann; Karthik Krishnan; insight-users at itk.org
Subject: Re: [Insight-users] Connected component statistics

Hi everyone,

It seems that there are a few starting points around already. The
measures we computed in my previous job could all be done in a single
pass and consolidated at the end. I think that most of them have
already been covered in the discussion.

The only thing I'm not sure about now is an ITK specific question -
how should the statistics be represented. The previous function of
this type that I used produced a table of statistics as output, with
one row for each connected component. This table was easily
represented as an image. I suspect that this approach wouldn't be
appropriate in ITK, but I'm not sure what the right mechanism is,
since I'm still learning my way around.

On 7/18/05, Miller, James V (Research) <millerjv at crd.ge.com> wrote:
> Gaeton,
> 
> Center of gravity and bounding box could be added to the RelabelStatisticsImageFilter
> since they are simple calculations.  However, it is a bit of a side-effect.  The
> volume is calculated in the RelabelStatisticsImageFilter because it is used by the
> filter to order the labels.  Since it was already calculated, it made sense to allow
> the user to access it.
> 
> The best place for these measures and the more complicated measures would be a class
> similar to the LabelStatisticsImageFilter. The filter should be called something like
> LabelMomentsImageFilter (and calculate ImageMoments as well as geometric moments. Or maybe
> something like LabelShapeImageFilter.
> 
> I do not see any reason to use the ImageSpatialMaskObject for this task.  Usually, you
> would want to calculate these features for EVERY component.  So it best to run through a
> filter that does it.
> 
> Jim
> 
> -----Original Message-----
> From: Gaetan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr]
> Sent: Monday, July 18, 2005 4:57 AM
> To: Miller, James V (Research); Karthik Krishnan; Richard.Beare at ieee.org
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] Connected component statistics
> 
> 
> 
> Hi,
> 
> I'm also interested in basic measures such as volume, center of gravity
> and bounding box.
> I think to work on it this week, so it should be great to define where to
> implement methods to get those informations.
> 
> RelabelComponentImageFilter is already able to give volume, so it should
> be a good place to add other very simple informations like center of
> gravity and bounding box.
> It don't seem to be the good place for more complex info such as
> perimeter/surface... perhap's ImageMaskSpatialObject is a better place ?
> 
> WDYT ?
> 
> Gaetan
> 
> On Fri, 15 Jul 2005 20:39:46 +0200, Miller, James V (Research)
> <millerjv at crd.ge.com> wrote:
> 
> > The LabelStatisticsImageFilter will calculate statistics for each
> > component.
> > Currently, the LabelStatisticsImageFilter calculate mean, variance, sum,
> > count,
> > and histograms.
> >
> > We plan to add another filter that calculated the moments (either image
> > moments or
> > geometric moments) of each component. I have been waiting for it to be
> > completed and
> > may have to just write it myself.
> >
> > Also, the RelabelComponentImageFilter allows you to query the volume of
> > a component.
> >
> > Jim
> >
> > -----Original Message-----
> > From: insight-users-bounces+millerjv=crd.ge.com at itk.org
> > [mailto:insight-users-bounces+millerjv=crd.ge.com at itk.org]On Behalf Of
> > Karthik Krishnan
> > Sent: Friday, July 15, 2005 10:10 AM
> > To: Richard.Beare at ieee.org
> > Cc: insight-users at itk.org
> > Subject: Re: [Insight-users] Connected component statistics
> >
> >
> >
> >
> > Richard Beare wrote:
> >
> >> Hi,
> >>
> >> I've found ConnectedComponentImageFilter and
> >> RelabelConnectedImageFilter, but I haven't been able to find anything
> >> that returns measures of the connected components -- e.g. area/volume,
> >> perimeter/surface area, centre of gravity, ellipse moments and minimum
> >> enclosing rectangles.
> >>
> >>
> > You could threshold the labelled image to get each connected component
> > and...
> >
> > If you are using CVS ITK, I had put a method recently :
> > ImageMaskSpatialObject::GetAxisAlignedBoundingBoxRegion()
> > that computes the minimum axis aligned bounding box of a 3D binary image.
> >
> > ImageMomentsCalculator can help you with moments, CG etc.
> >
> > An appropriate class to add methods to compute volume, perimeter,
> > surface area etc may be theImageMaskSpatialObject class . You could
> > write them and put them back into ITK :)
> >
> > I don't think ITK has many CAD measurement methods.
> >
> >> Also, what is the recommended approach for making greyscale measures
> >> of regions defined by a connected component image?
> >>
> >> Thanks
> >>
> >> Richard
> >> _______________________________________________
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> >> Insight-users at itk.org
> >> http://www.itk.org/mailman/listinfo/insight-users
> >>
> >>
> >>
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> 
> 
> --
> Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr>
> Tel: +33 1 34 65 29 66
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> Web: http://voxel.jouy.inra.fr
>