[Insight-users] LabelObject attributes

[Christian Werner]

  Hi there,
I just remembered another terminology-issue. One filter is called 
"BinaryShapeOpeningImageFilter", but "opening" is a morphological 
operation on binary images that isn't related to what this Filter does. 
I used your library for the integration of image analysis functionality 
in Paraview and there I called the procedure of removing objects due to 
some geometrical criteria "Binary Classification".
This is what the "BinaryShapeOpeningImageFilter" does. It classifies 
objects into two different classes, "keep" and "don't keep". So what 
about "BinaryShapeClassificationImageFilter"? Or, to make clear that 
objects are being removed, you could also call it 
"BinaryShapeRemovingImageFilter".

"Opening" is misleading in my opinion.

Best regards,
Christian


Am 27.09.2010 13:26, schrieb Gaëtan Lehmann:
>
> 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
>