R/objectCleanse.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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# DISCLAIMER:                                                                  #
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#' @title Object Cleanser
#' @description
#' Removes abnormalities (clipped/debris) from image.
#' @param mat a numeric matrix (image).
#' @param msk a numeric matrix (mask identifying abnormalities).
#' @param add_noise if TRUE adds normal noise to background using rnorm(), from \pkg{Rcpp}. Default is TRUE.
#' @param random_seed a list of elements to pass to \link[base]{set.seed} or a single value, interpreted as an integer, or NULL to be used when 'add_noise' is set to TRUE. Default is NULL.
#' Note that NA_integer_ or list(seed = NA_integer_) can be used to not call \link[base]{set.seed} at all.
#' @param bg mean value of the background added if add_noise is TRUE. Default is 0.
#' @param sd standard deviation of the background added if add_noise is TRUE. Default is 0.
#' @return According to msk, pixel values in mat are substituted by either bg [add_noise == FALSE] or rnorm(n = prod(dim(mat), mean=bg, sd=sd)) [add_noise == TRUE].
#' @export
objectCleanse = function(mat, msk, add_noise = TRUE, random_seed = NULL, bg = 0, sd = 0) {
  f = function(x) { x }
  if(add_noise) {
    SEED = fetch_seed(random_seed)
    f = function(x) { 
      with_seed(x, SEED$seed, SEED$kind, SEED$normal.kind, SEED$sample.kind)
    }
  }
  foo = f(cpp_cleanse(mat, msk, add_noise = add_noise, bg = bg, sd = sd))
  # attr(foo, "msk_cleanse") <- msk
  return(foo)
}