R/parse_named_map.R

In neuroconductor-devel-releases/cifti: Toolbox for Connectivity Informatics Technology Initiative ('CIFTI') Files

#' @title Parse Named Map from CIFTI
#' @description Extracts information about Named Maps from CIFTI file
#' @param nodeset Set of XML nodes corresponding to \code{NamedMap}
#'
#' @return List of values
#' @export
#'
#' @examples \dontrun{
#' doc = cifti_xml(fname)
#' nodes = xml_find_all(doc, "/CIFTI/Matrix/MatrixIndicesMap")
#' nodeset = xml_find_all(nodes, "./NamedMap")
#' parse_named_map(nodeset)
#' }
parse_named_map = function(nodeset) {
  n_nodes = length(nodeset)
  all_attrs = xml_attrs(nodeset)

  make_num = function(x) {
    as.numeric(as.character(x))
  }
  mn = xml_find_all(nodeset, "./MapName")
  mn = xml_text(mn)

  lt = xml_find_all(nodeset, "./LabelTable")
  lt = lapply(lt, xml_find_all,
              xpath =  "./Label")
  # txt_lt = lapply(lt, xml_text)
  lt = lapply(lt, function(x) {
    att = xml_attrs(x)
    val = xml_text(x)
    att = mapply(function(x, y){
      c(x, "Label" = y)
    }, att, val, SIMPLIFY = FALSE)
    att = do.call("rbind", att)
    att = data.frame(att,
                     stringsAsFactors = FALSE)

    att$Key = make_num(att$Key)
    att$Red = make_num(att$Red)
    att$Green = make_num(att$Green)
    att$Blue = make_num(att$Blue)
    att$Alpha = make_num(att$Alpha)
    return(att)
  })
  L = list(map_names = mn,
           look_up_table = lt)
  if (length(lt) == 0) {
    L$look_up_table = NULL
  }
  return(L)
}


#' @rdname parse_named_map
#' @param fname filename of CIFTI file
#' @export
get_named_map = function(fname) {
  nodes = matrix_ind_map_nodes(fname)
  nodeset = xml_find_all(nodes, "./NamedMap")
  parse_named_map(nodeset)
}