R/subsetOffsets.R

In IFC: Tools for Imaging Flow Cytometry

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# 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_offset Subsetting
#' @description
#' Subsets `IFC_offset`
#' @param offsets object of class `IFC_offset` to subset.
#' @param objects integer vector, IDEAS objects ids numbers to extract.
#' @param image_type image_type of desired offsets. Default is c("img", "msk"). Allowed are "img" and/or "msk".
#' @examples
#' if(requireNamespace("IFCdata", quietly = TRUE)) {
#'   ## use a cif file
#'   file_cif <- system.file("extdata", "example.cif", package = "IFCdata")
#'   ## extract offsets
#'   offsets <- getOffsets(fileName = file_cif)
#'   ## subset offsets of the 4 first "img" objects
#'   sub_offs <- subsetOffsets(offsets = offsets, objects = 0:3, image_type = "img")
#'   ## show subsetted offsets' structure
#'   str(sub_offs)
#' } else {
#'   message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
#'                   'https://gitdemont.github.io/IFCdata/',
#'                   'to install extra files required to run this example.'))
#' }
#' @return a class `IFC_offset` integer vector or empty integer() if objects are outside of offsets.
#' @export
subsetOffsets <- function(offsets, objects, image_type = c("img", "msk")) {
  if(missing(offsets)) stop("'offsets' can't be missing")
  if(missing(objects)) stop("'objects' can't be missing")
  assert(offsets, cla = "IFC_offset")
  assert(image_type, alw = c("img", "msk"))
  XIF_test = ifelse(length(attr(offsets, "test")) == 0, testXIF(attr(offsets, "fileName_image")), attr(offsets, "test"))
  type = as.integer(XIF_test == 1) + 1L
  objects = as.integer(objects); objects = objects[(objects >= 0) & (objects < attr(offsets, "obj_count")) & (is.finite(objects))]
  if(length(objects) == 0) {
    warning("subsetOffsets: No objects to subset, check the objects you provided.", immediate. = TRUE, call. = FALSE)
    foo = integer()
  } else {
    if(all(c("img", "msk") %in% image_type)) {
      if(type == 1) {
        in_offsets = objects + 1L
        warning("subsetOffsets: There may be no mask to subset.", immediate. = TRUE, call. = FALSE)
      } else {
        in_offsets = unlist(lapply(objects, FUN=function(x) c(2*x+1,2*(x+1)))) 
      }
    } else {
      if("img" %in% image_type) {
        if(type == 1) {
          in_offsets = objects + 1L
        } else {
          in_offsets = 2 * objects + 1
        }
      } else {
        if(type == 1) {
          in_offsets = NULL
          warning("subsetOffsets: There may be no mask to subset.", immediate. = TRUE, call. = FALSE)
        } else {
          in_offsets = 2 * (objects + 1)
        }
      }
    }
    foo = attr(offsets, "all")[in_offsets]
  }
  attr(foo, "all") = attr(offsets, "all")
  attr(foo, "first") = attr(offsets, "first")
  attr(foo, "fileName_image") = attr(offsets, "fileName_image")
  attr(foo, "checksum") = attr(offsets, "checksum")
  attr(foo, "obj_count") = attr(offsets, "obj_count")
  attr(foo, "test") = XIF_test
  class(foo) = c("IFC_offset")
  return(foo)
}