[Insight-users] Connected component statistics
Gaetan Lehmann
gaetan.lehmann at jouy.inra.fr
Fri Jul 22 07:18:58 EDT 2005
Hi everyone,
Here is the first work I have done on this filter. It's mainly a
modification of LabelStatisticsImageFilter.
Comment would be highly appreciated, especially for :
+ Name of method/class
+ Choice of class or type to represent data
+ GetLabels method (not present in LabelStatisticsImageFilter)
+ computation of center of gravity in pysical units
I will work on computation of perimeter/area next week
Regards,
Gaetan
On Wed, 20 Jul 2005 13:47:18 +0200, Miller, James V (Research)
<millerjv at crd.ge.com> wrote:
> A map should be used for the internal implementation. Like you
> suggested,
> however, it is important to provide access methods (or queries) into the
> map.
> One reason this is particularly important is in MSVC++ you cannot pass a
> reference
> or iterators to map across DLL boundaries.
>
> Jim
>
> -----Original Message-----
> From: Gaetan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr]
> Sent: Wednesday, July 20, 2005 3:01 AM
> To: Richard.Beare at ieee.org; Sayan Pathak
> Cc: insight-users at itk.org; Miller, James V (Research);
> Karthik.Krishnan at kitware.com
> Subject: Re: [Insight-users] Connected component statistics
>
>
>
> Hi,
>
> even if a map is a good thing for c++ developers, I'm not sure it's
> really
> usable for python (and java, and tcl) ones.
> Or the filter must provide methods to access content of the map without
> using the map directly. Something like methods in
> LabelStatisticsImageFilter :
> RealType GetMinimum (LabelPixelType label) const
> RealType GetMaximum (LabelPixelType label) const
> RealType GetMean (LabelPixelType label) const
> RealType GetMedian (LabelPixelType label) const
> RealType GetSigma (LabelPixelType label) const
> RealType GetVariance (LabelPixelType label) const
> RealType GetSum (LabelPixelType label) const
> unsigned long GetCount (LabelPixelType label) const
>
> it would be great also to choose consistent name : in other filters, we
> have the word "component" and the word "object" for the same thing.
> Component seems better to me.
>
> Richard, are you working on this filter ?
> I don't think we need to do the work twice :-)
>
> Gaetan
>
> On Wed, 20 Jul 2005 01:14:40 +0200, Richard Beare
> <richard.beare at gmail.com> wrote:
>
>> Hi,
>> I guess that the ordering can be made somewhat arbitary.
>>
>> Here's a summary of how the equivalent functions I used in my previous
>> job:
>>
>> step 1 was labelling. This produced an integer image with each
>> connected component having a separate label. Labels were consecutive
>> and assigned in raster order.
>>
>> step 2 was computing binary statistics, given this label image. This
>> was a single pass process that produced a table of results. Each row
>> in the table corresponded to a connected component and included the
>> label. The label was somewhat redundant until you started to
>> manipulate the table.
>>
>> Subsequent steps were somewhat arbitary - they may include filtering
>> objects based on combinations of these attributes to produce another
>> label image, or colouring the regions according to some parameter
>> (like area) or any number of other things.
>>
>> If the aim is to minimize the number of passes through the image then
>> relabelling according to ordering of connected component pixels should
>> be left as an option to applications that need it - perhaps some sort
>> of substitution filter could be developed for that purpose.
>>
>> Starting on this might be a good introduction to filter writing for me.
>>
>> On 7/20/05, Sayan Pathak <SayanP at alleninstitute.org> wrote:
>>>
>>>
>>> Hi Jim/Richard,
>>> I like the idea of using
>>> std::map<itk::CommponentStatistics> type storage. The first
>>> entry of the map (the Key) could be the component label index. It
>>> would
>>> probably be desirable to assign label for each of the connected
>>> components
>>> in descending order of their size (as it is done in the current
>>> filter).
>>>
>>> Sayan
>>>
>>> > Date: Tue, 19 Jul 2005 09:18:11 -0400
>>> > From: "Miller, James V (Research)" <millerjv at crd.ge.com>
>>> > Subject: RE: [Insight-users] Connected component statistics
>>> > To: <Richard.Beare at ieee.org>
>>> > Cc: insight-users at itk.org, Karthik Krishnan
>>> > <Karthik.Krishnan at kitware.com>
>>> > Message-ID:
>>> >
>>> <FA26BEF1EA775E4584FB34B91E14A1C403F34F82 at SCHMLVEM01.e2k.ad.ge.com>
>>> > Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> >
>>> > 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
>>> > >> _______________________________________________
>>> > >> 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
>>> > > _______________________________________________
>>> > > Insight-users mailing list
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>>> > > http://www.itk.org/mailman/listinfo/insight-users
>>> >
>>> >
>>> >
>>> > --
>>> > 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
>>> >
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
--
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
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