R/toXML2_regions.R

In gitdemont/IFC: Tools for Imaging Flow Cytometry

################################################################################
# This file is released under the GNU General Public License, Version 3, GPL-3 #
# Copyright (C) 2020 Yohann Demont                                             #
#                                                                              #
# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2020                                                                  #
# -COPYRIGHT HOLDERS: Yohann Demont, Gautier Stoll, Guido Kroemer,             #
#                     Jean-Pierre Marolleau, Loïc Garçon,                      #
#                     INSERM, UPD, CHU Amiens                                  #
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################################################################################

#' @title IFC_regions XML Conversion
#' @description 
#' Helper to convert regions (`IFC_regions` object) to XML nodes.
#' @param regions an `IFC_regions` object.
#' @param verbose whether to display message about current action. Default is FALSE.
#' @return a xml_node.
#' @keywords internal
toXML2_regions = function(regions, verbose = FALSE) {
  assert(verbose, alw = c(TRUE, FALSE))
  if(verbose) message("creating regions node")
  assert(regions, cla = "IFC_regions")
  if(length(regions)==0) return(xml_new_node(name = "Regions", text = ""))
  xml_new_node(name = "Regions", .children = lapply(regions, FUN=function(i_reg) {
    A = attr(i_reg, "sync")
    i_reg = i_reg[sapply(i_reg, length) != 0] # to remove empty values (e.g. xtrans, ytrans)
    i_reg$color = map_color(i_reg$color, FALSE)
    i_reg$lightcolor = map_color(i_reg$lightcolor, FALSE)
    if(length(A) == 1) i_reg$sync = A
    xml_new_node(name = "Region",
               attrs = i_reg[!grepl("^x$|^y$", names(i_reg))],
               .children = lapply(1:length(i_reg[["x"]]), FUN = function(i_coord) {
                 xml_new_node(name = "axy", attrs = list(x = num_to_string(i_reg[["x"]][i_coord]), y = num_to_string(i_reg[["y"]][i_coord])))
               }))
  }))
}