[Insight-developers] LabelObject attributes
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Wed Sep 29 06:28:06 EDT 2010
Le 28 sept. 10 à 10:46, David Pastor a écrit :
> Hello,
Hi David,
>
> - About the Size / PhysicalSize I think current names are ok, a bit
> vague, but as you say which suits for 2D does not suit for 3D (or
> even 4D).
Not much people seems to like Volume as a name for that attribute!
Do you think there would be a consistency problem if we have
NumberOfPixels and PhysicalSize ?
>
> - For me, it would be helpful to have the centroid coordinates in
> pixels as output (just a friendly programming issue). Said that, I
> don't know if it is too redundant to have all measures in Pixel vs
> Phyisical returned values being Physical the adjective to specifiy
> they are physical and not pixel-based.
I'd say this is too much redundant, given that the continuous index
can very easily be computed with dedicated methods in itk::ImageBase.
> I have not used StatisticsLabelObject, but I am a bit confussed now
> as I thought that when you work with label objects you lose the
> intensity information.
StatisticsLabelObject can store some values about the intensity in the
region covered by the label object. There is no way to recreate the
image of the intensities in that region from this values.
> Anyway I find very interesting the CenterOfGravitiy and I imagine
> that "sum" stands for the intensity accumuled in the object region?
that's it
>
> A more general suggestion is to be able to specify the structuring
> element used to find the connectivity of the label objects
I fully agree, but that may be quite difficult to implement in an
efficient way.
LabelMap and LabelObject are not defining the connectivity though -
LabelObject are not even necessarily connected, so if someone wants to
develop a new filter for this task, that would make a very nice
contribution for the insight journal :-)
> or being able to perform a wider range of attribute openings/
> closings (generalization of area opening contribution and object
> tree contribution).
>
Are you thinking to some specific examples?
Have you looked at AttributeLabelObject?
> thanks for the useful contributions
Thanks for your comments!
Gaëtan
>
> Best
> David
>
> ----- Original Message ----- From: "Jim Miller" <millerjv at gmail.com>
> To: "Gaëtan Lehmann" <gaetan.lehmann at jouy.inra.fr>
> Cc: "Richard Beare" <Richard.Beare at ieee.org>; "Christian Werner" <christian.werner at rwth-aachen.de
> >; "Neal R. Harvey" <harve at lanl.gov>; "LassiPaavolainen" <lassi.paavolainen at jyu.fi
> >; "Julien Michel" <julien.michel at c-s.fr>; "David Pastor" <david.pastor at die.upm.es
> >; "Blezek, Daniel J., Ph.D." <Blezek.Daniel at mayo.edu>; "kien kieu" <kkieu at jouy.inra.fr
> >; "Pierre Adenot" <pierre.adenot at jouy.inra.fr>; "Mario Ceresa" <mrceresa at gmail.com
> >; "Luis Ibanez" <luis.ibanez at kitware.com>; "ITK Users" <insight-users at itk.org
> >; "ITK Developers" <insight-developers at itk.org>
> Sent: Tuesday, September 28, 2010 1:01 AM
> Subject: Re: LabelObject attributes
>
>
> Gaetan,
>
> In general, I think the original names are good.
>
> I was trying to use Roundness but had robustness issues which I
> traced to issues in the perimeter calculation. I wrote my own filter
> which overwrite the Roundness parameter with the something like the
> ellipsoid maximum radius divided by the feret diameter (or something
> like that, I don't have the code in front of me).
>
> This brings up two points.
>
> 1. There could be lots of ways to define roundness so we may want to
> add a few others.
>
> 2. It would great if users could define their own parameters. Maybe
> a general key/value pair mechanism or a set of User1, User2,
> User3, ... for each of scalars, vectors, matrices, etc.
>
>
>
> On Sep 27, 2010, at 7:26 AM, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr
> > wrote:
>
>>
>> Hi,
>>
>> I think you are active users of the contribution "Label object
>> representation and manipulation", so I'd like to get your opinion
>> on the attribute and on the attribute names used in that code. I
>> know that some of us may not be pleased to change the attribute or
>> their name, but I believe this is a important to make the usage of
>> this contribution more intuitive. This contribution should soon be
>> moved out of the Review directory and its API would then be much
>> more difficult to change.
>>
>> So at this time we have two set of attributes splited in two main
>> classes:
>> * ShapeLabelObject, which stores the attributes computable only
>> with the mask of the object;
>> * StatisticsLabelObject, which stores the attributes computable
>> with the intensities from another image in addition to the mask of
>> the object.
>> StatisticsLabelObject is a subclass of ShapeLabelObject, mostly for
>> practical reason: it is easier to use that way, and the
>> informations needed to compute the attributes of ShapeLabelObject
>> are required (but not suffisant) to compute the attributes of
>> StatisticsLabelObject, so I don't think there is any problem in
>> doing that.
>>
>> Here is the list of attributes available in ShapeLabelObject, with
>> some comments:
>>
>> * Size
>>
>> While "Size" is short, it is also quite ambiguous, as the term
>> "size" can represent many measurements. Also, in ITK, GetSize()
>> tends to return an object of type itk::Size<X>, while here it is an
>> integer. What would you think of NumberOfPixels, as it is in
>> itk::ImageRegion?
>>
>> * PhysicalSize
>>
>> this one is a bit redundant with the previous one, because it is
>> simply Size * voxelSize, but it is quite useful anyway so I think
>> it's worth to keep it.
>> As above, size is quite ambiguous. Volume may be a better name,
>> but is less meaningful in the 2D case. Any opinion?
>>
>> * RegionElongation
>>
>> this one may not be really useful. It is there mostly for
>> historical reason: it was better than nothing at the time when the
>> equivalent ellipsoid wasn't computed. I propose to remove it.
>>
>> * SizeRegionRatio
>>
>> I never use this one either - again, it is there more for
>> historical reason than for a real interest. I also propose to
>> remove it.
>>
>> * Centroid
>>
>> seems ok to me
>>
>> * Region
>>
>> This name is especially badly chosen: Region is the type of the
>> attribute and its name should be BoundingBox in my opinion.
>>
>> * SizeOnBorder
>>
>> still this Size problem - may be NumberOfPixelsOnBorder
>>
>> * PhysicalSizeOnBorder
>>
>> This one is not exactly the previous one, because it gives (for a
>> 3D image) the surface on the border while the other gives the
>> number of pixels on the border - there is a difference in the
>> corner of the image!
>> It's name is not consistent with the name used for the surface. I
>> think it should rather be PerimeterOnBorder, or SurfaceOnBorder
>> (see discussion about the Perimeter attribute).
>>
>> * FeretDiameter
>>
>> seems ok to me
>>
>> * BinaryPrincipalMoments
>>
>> The Binary prefix doesn't make much sense here. I think it should
>> be removed.
>>
>> * BinaryPrincipalAxes
>>
>> The Binary prefix doesn't make much sense here. I think it should
>> be removed.
>>
>> * BinaryElongation
>>
>> The Binary prefix doesn't make much sense here. I think it should
>> be removed.
>>
>> * Perimeter
>>
>> seems ok to me, but correspond better for a 2D object. Surface
>> would be better in 3D and more, but would be quite confusing in the
>> 2D case. Any opinion?
>>
>> * Roundness
>>
>> seems ok to me
>>
>> * EquivalentRadius
>> * EquivalentPerimeter
>>
>> These should be EquivalentSphericalRadius and
>> EquivalentSphericalRadius in 3D, but those names doesn't fit well
>> in 2d. Any better idea?
>>
>> * EquivalentEllipsoidSize
>>
>> EquivalentEllipsoidalDiameter seems better
>>
>> * BinaryFlatness
>>
>> The Binary prefix doesn't make much sense here. I think it should
>> be removed.
>>
>> Also I think that a few attributes are missing there - some can be
>> easily implemented, others may be more difficult and shouldn't be
>> part of the attribute rework:
>>
>> * PerimeterOnBorderRatio, which is the perimeter touching the
>> border of the image divided by the perimeter of the object - very
>> useful to fine tune how a partially observed object is to be
>> removed of an image.
>> * Neighbors, which is the list of neighbors of an object. This one
>> is much harder to implement and shouldn't be part of this attribute
>> rework.
>>
>> So to summarize the proposed changes in ShapeLabelObject attributes:
>>
>> * Size -> NumberOfPixels
>> * PhysicalSize -> Volume
>> * RegionElongation -> removed
>> * SizeRegionRatio -> removed
>> * Centroid (no change)
>> * Region -> BoundingBox
>> * SizeOnBorder -> NumberOfPixelsOnBorder
>> * PhysicalSizeOnBorder -> PerimeterOnBorder
>> * FeretDiameter (no change)
>> * BinaryPrincipalMoments -> PrincipalMoments
>> * BinaryPrincipalAxes -> PrincipalAxes
>> * BinaryElongation -> Elongation
>> * Perimeter (no change)
>> * Roundness (no change)
>> * EquivalentRadius -> EquivalentSphericalRadius
>> * EquivalentPerimeter -> EquivalentSphericalPerimeter
>> * EquivalentEllipsoidSize-> EquivalentEllipsoidDiameter
>> * BinaryFlatness -> Flatness
>> * -> creation of PerimeterOnBorderRatio
>>
>>
>> Now for StatisticsLabelObject:
>>
>> There are some overlaps with the ShapeLabelObject attributes -
>> especially all the attributes which can be computed as for
>> ShapeLabelObject, but with a weighting by the pixel in the feature
>> image. I propose to use the same names as in ShapeLabelObject, but
>> with the prefix Weighted.
>>
>> * CenterOfGravity
>>
>> ok
>>
>> * Elongation
>>
>> it conflicts with ShapeLabelObject's Elongation. I propose
>> WeightedElongation.
>>
>> * Flatness
>>
>> it conflicts with ShapeLabelObject's Flatness. I propose
>> WeightedFlatness.
>>
>> * Histogram
>>
>> seems ok to me
>>
>> * Kurtosis
>>
>> seems ok to me
>>
>> * Maximum
>>
>> seems ok to me
>>
>> * MaximumIndex
>>
>> seems ok to me
>>
>> * Mean
>>
>> seems ok to me
>>
>> * Median
>>
>> seems ok to me
>>
>> * Minimum
>>
>> seems ok to me
>>
>> * MinimumIndex
>>
>> seems ok to me
>>
>> * PrincipalAxes
>>
>> it conflicts with ShapeLabelObject's PrincipalAxes. I propose
>> WeightedPrincipalAxes.
>>
>> * PrincipalMoments
>>
>> it conflicts with ShapeLabelObject's PrincipalMoments. I propose
>> WeightedPrincipalMoments.
>>
>> * Sigma
>>
>> Should be StandardDeviation
>>
>> * Skewness
>>
>> seems ok to me
>>
>> * Sum
>>
>> seems ok to me
>>
>> * Variance
>>
>> Quite redundant with StandardDeviation - maybe it should be removed?
>>
>>
>> So to summarize the proposed changes in ShapeLabelObject attributes:
>>
>> * CenterOfGravity (no change)
>> * Elongation -> WeightedElongation
>> * Flatness -> WeightedFlatness
>> * Histogram (no change)
>> * Kurtosis (no change)
>> * Maximum (no change)
>> * MaximumIndex (no change)
>> * Mean (no change)
>> * Median (no change)
>> * Minimum (no change)
>> * MinimumIndex (no change)
>> * PrincipalAxes -> WeightedPrincipalAxes
>> * PrincipalMoments -> WeightedPrincipalMoments
>> * Sigma -> StandardDeviation
>> * Skewness (no change)
>> * Sum (no change)
>> * Variance (no change)
>>
>>
>> Finally, about the returned values.
>>
>> For the positions, a physical position is returned, as an
>> itk::Point, when the position can be between pixels, excepted when
>> position in between pixels doesn't make sense - namely in
>> GetMinimumIndex() and GetMaximumIndex. Index explicitly appears in
>> the attribute names in this last case.
>> Does that seem relevant?
>>
>> That's all for me - please share any concern you have about those
>> classes API - it may be too late later!
>>
>> Regards,
>>
>> Gaëtan
>>
>> --
>> Gaëtan Lehmann
>> Biologie du Développement et de la Reproduction
>> INRA de Jouy-en-Josas (France)
>> tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
>> http://voxel.jouy.inra.fr http://www.itk.org
>> http://www.mandriva.org http://www.bepo.fr
>>
>
> --
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>
--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr http://www.itk.org
http://www.mandriva.org http://www.bepo.fr
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