[BioC] EBImage: filtering in the presence of NAs

[Arnaud Duranel]

Hello

None of the EBImage filtering functions seems to work when there are NAs 
in the image:

library(EBImage)
lenac = readImage(system.file("images", "lena-color.png", 
package="EBImage"))
lenag<-channel(lenac, 'gray')
lenag[1:50, ]<-NA
flo = makeBrush(21, shape='disc', step=FALSE)^2
flo = flo/sum(flo)
lenaflo = filter2(lenag, flo)
display(lenaflo)
any(!is.na(lenaflo))

Is there a way to process an image that includes NAs, with some kind of 
na.rm=TRUE?

I am working with pictures of irregularly-shaped objects, and the pixels 
between the picture margins and the object were set to NA using a mask. 
I want to apply filters to the object itself, not to the whole image. Is 
there another way to do this?

Many thanks for your help.

Best regards

A. Duranel, UCL Department of Geography