EBImage Function Names

Question

Can someone explain what is used to calculate various functions in computeFeatures?

I use the naming convention specified in ? computeFeatures. I do not understand the labels .0., .a.and .Ba..

For instance:

> library(EBImage)
> y = readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1]
> x = thresh(y, 10, 10, 0.05)
> x = opening(x, makeBrush(5, shape='disc'))
> x = bwlabel(x)
> ft = computeFeatures(x, y, xname="nucleus")
> colnames(ft)
 [1] "nucleus.0.m.cx"            "nucleus.0.m.cy"           
 [3] "nucleus.0.m.majoraxis"     "nucleus.0.m.eccentricity" 
<snip>
[11] "nucleus.0.s.radius.max"    "nucleus.a.b.mean"         
[13] "nucleus.a.b.sd"            "nucleus.a.b.mad"          
<snip>
[51] "nucleus.Ba.b.mean"         "nucleus.Ba.b.sd"          
[53] "nucleus.Ba.b.mad"          "nucleus.Ba.b.q001"        
[55] "nucleus.Ba.b.q005"         "nucleus.Ba.b.q05"  
<snip>       

I assume that nucleus.0.*functions only use data from the binary masks contained in x. Thus, nucleus.0.m.cyis the centroid of the y axis calculated using binary data. There are also nucleus.a.m.cyand nucleus.Ba.m.cy, but it is unclear how these calculations are different (they are highly correlated, but not identical).

, .a. .Ba. y, . , nucleus.a.b.mean nucleus.Ba.b.mean, (~.80 .), . , y , x, .

- ?

,

Max

> sessionInfo()
R Under development (unstable) (2014-08-23 r66461)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] EBImage_4.7.16

loaded via a namespace (and not attached):
 [1] abind_1.4-0         BiocGenerics_0.11.4 grid_3.2.0         
 [4] jpeg_0.1-8          lattice_0.20-29     locfit_1.5-9.1     
 [7] parallel_3.2.0      png_0.1-7           tiff_0.1-5         
[10] tools_3.2.0  

Answer 1

: AnalysisWithEBImage

, -, , . Grégoire Pau? , , .

Answer 2

, , , , , . debugonce(computeFeatures), ft = computeFeatures(x, y, xname="nucleus"). ( Q) , .

, :

x.y.f, x - , y       f .

computeFeatures (a, aB 0). , , , , a. , 0 , .

, B_i. , , , expandRef ( ):

# Hard code a filter
blob = gblob(x0 = 15, n = 49, alpha = 0.8, beta = 1.2)
# Filter using the fast 2D FFT convolution product.
bref = lapply(ref, function(r) filter2(r, blob)/2)
# Name it "B" and then the layer name
names(bref) = paste("B", names(ref), sep = "")

, , , . x ( display(x), ):

(y):

:

, y:

, : 0 no reference, a y , aB y.