R/objectResize.R

In gitdemont/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 Object Resizing
#' @description
#' Resizes mat to new dimensions.
#' @param mat a numeric matrix.
#' @param size a length 2 integer vector of final dimensions of the image, height 1st and width 2nd. Default is c(0,0) for no change.
#' @param add_noise if TRUE adds normal noise when size is larger than mat dimensions 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 a resized matrix with padding background if desired size is larger than original mat dimensions.
#' @keywords internal
objectResize <- function(mat, size = c(0,0), add_noise = TRUE, random_seed = NULL, bg = 0, sd = 0) {
  if(length(size) != 2) return(mat)
  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)
    }
  }
  return(f(cpp_resize(mat = mat, new_height = size[1], new_width = size[2], add_noise = add_noise, bg = bg, sd= sd)))
}