R/objectNormalize.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                                             #
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# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2020                                                                  #
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#                     Jean-Pierre Marolleau, Loïc Garçon,                      #
#                     INSERM, UPD, CHU Amiens                                  #
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#' @title Object Intensity Normalization
#' @description
#' Normalizes a matrix to [0,1].
#' @param mat a finite numeric matrix.
#' @param input_range a finite numeric vector of 2 values, sets the range of the input intensity values. Values outside this range are clipped. Default is \code{[0,4095]}.
#' @param full_range if '\code{full_range}' is \code{TRUE}, then '\code{input_range}' will be set to \code{[0,4095]} and '\code{gamma}' forced to \code{1}. Default is \code{FALSE}.
#' @param force_range if '\code{force_range}' is \code{TRUE}, then '\code{input_range}' will be adjusted to '\code{mat}' range in \code{[-4095,+inf]} and '\code{gamma}' forced to \code{1}. Default is \code{FALSE}.\cr
#' Note that this parameter takes the precedence over \code{input_range}' and \code{full_range}'.
#' @param gamma '\code{gamma}' correction. Default is \code{1}, for no correction.
#' @details Note that negative values are used internally for removal of unmasked objects.
#' @return a [0,1] normalized matrix
#' @keywords internal
objectNormalize <- function(mat, input_range=c(0,4095), full_range=FALSE, force_range=FALSE, gamma=1) {
  cpp_normalize(mat = mat, input_range = input_range, full_range = full_range, force_range = force_range, gamma = gamma)
}