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#' BP_DetectBackground detects the background color of an image
#' @title Detects the background color of an image
#' @author Marc Girondot \email{marc.girondot@@gmail.com}
#' @return The orignial bone object with a new attribute for background color
#' @param bone The bone image to be used
#' @param analysis The name or rank of analysis
#' @param show.plot should plot is shown ?
#' @description Detects the background color of an image.
#' @family BoneProfileR
#' @examples
#' \dontrun{
#' # Not run:
#' bone <- BP_OpenImage()
#' bone <- BP_DetectBackground(bone=bone)
#' bone <- BP_DetectForeground(bone=bone)
#' plot(bone)
#' }
#' @export
BP_DetectBackground <- function(bone, analysis=1, show.plot=TRUE) {
red <- bone[c(2:5, dim(bone)[1]-2:5), c(2:5, dim(bone)[2]-2:5), 1, 1]
green <- bone[c(2:5, dim(bone)[1]-2:5), c(2:5, dim(bone)[2]-2:5), 1, 2]
blue <- bone[c(2:5, dim(bone)[1]-2:5), c(2:5, dim(bone)[2]-2:5), 1, 3]
bg <- rgb(red=median(red), green=median(green), blue=median(blue))
bone <- RM_add(x=bone, RMname=analysis,
valuename = "bg", value=bg)
bone <- RM_delete(x=bone, RMname = analysis, valuename="threshold")
bone <- RM_delete(x=bone, RMname = analysis, valuename="contour")
bone <- RM_delete(x=bone, RMname = analysis, valuename="centers")
bone <- RM_delete(x=bone, RMname = analysis, valuename="compactness")
bone <- RM_delete(x=bone, RMname = analysis, valuename="array.compactness")
bone <- RM_delete(x=bone, RMname = analysis, valuename="cut.distance.center")
bone <- RM_delete(x=bone, RMname = analysis, valuename="cut.angle")
bone <- RM_delete(x=bone, RMname = analysis, valuename="compactness.synthesis")
bone <- RM_delete(x=bone, RMname = analysis, valuename="optim")
bone <- RM_delete(x=bone, RMname = analysis, valuename="used.centers")
bone <- RM_delete(x=bone, RMname = analysis, valuename="optimRadial")
if (show.plot) plot(bone, message="Do not forget to check thresholding")
return(bone)
}
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