#' @title AFNI 3dClipLevel function
#' @description Estimates the value at which to clip the anatomical dataset using
#' \code{3dClipLevel} so that background regions are set to zero.
#'
#' @param file nifti object or NIfTI filename. If more than one is given,
#' they are given names of the letters up to \code{z}.
#' @param mfrac Multiplier of the median for clipping (see notes)
#' @note From AFNI docs:
#' Algorithm:
#'
#' (a) Set some initial clip value using wizardry (AKA 'variance').
#'
#' (b) Find the median of all positive values >= clip value.
#'
#' (c) Set the clip value to \code{mfrac} of this median.
#'
#' (d) Loop back to (b) until the clip value doesn't change.
#' @param opts Additional options passed to \code{3dClipLevel}
#' @param ... not used
#'
#' @return Single character string of a nubmer
#' (by default), unless \code{opts = "-doall"}
#' @export
afni_3dClipLevel = function(
file,
mfrac = 0.5,
opts = "") {
func = "3dClipLevel"
file = checkimg(file, allow_array = FALSE)
opts = c(opts, paste0("-mfrac ", mfrac))
opts = trimws(opts)
opts = opts[ opts != "" ]
opts = paste(opts, collapse = " ")
res = afni_cmd(
file = file,
func = func,
opts = opts,
outfile = NULL,
samefile = TRUE,
intern = TRUE,
add_ext = FALSE,
quote_outfile = FALSE,
retimg = FALSE,
quote_file = FALSE
)
attr(res, "afni_version") = afni_version()
return(res)
}
#' @rdname afni_3dClipLevel
#' @export
ClipLevel = function(...) {
afni_3dClipLevel(...)
}
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