R/cmoments3d.R

In bioimaginggroup/bioimagetools: Tools for Microscopy Imaging

#' Computes moments from image objects
#' 
#' Computes intensity-weighted centers of objects and their mass (sum of intensities) and size.
#' 
#' @param mask a labeled stack as returned from bwlabel3d
#' @param ref the original image stack
#' @return a matrix with the moments of the objects in the stack
#' @author Volker Schmid
#' @export
cmoments3d <- function(mask, ref){
  labels <- 1:max(mask, na.rm=TRUE)
  ret <- t(sapply(labels, function(x){
    ind <- which(mask == x, arr.ind=T)
    w <- ref[ind]
    return(c(x, apply(ind, 2, weighted.mean, w=w), sum(w), length(w)))
  }))
  colnames(ret) <- c("label","m.x","m.y","m.z","w","n")
  return(ret)
}