objectTransform: Object Transformation
In gitdemont/IFC: Tools for Imaging Flow Cytometry

objectTransform

R Documentation

Object Transformation

Description

Function to normalize, colorize and add background to images.

Usage

objectTransform(
  mat,
  msk,
  color,
  input_range,
  mode,
  type,
  add_noise = TRUE,
  random_seed = NULL,
  size = c(0, 0),
  bg_mean = 0,
  bg_sd = 0,
  full_range = FALSE,
  force_range = FALSE,
  gamma = 1
)

Arguments

`mat`	a finite numeric matrix.
`msk`	a finite numeric matrix (mask identifying abnormalities). If missing, the default no cleansing will be done.
`color`	a color.
`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 `[0,4095]`.
`mode`	color mode export. Either `"rgb"`, `"gray"` or `"raw"`.
`type`	image object type.
`add_noise`	whether to add normal noise to background or not. Default is `TRUE`.
`random_seed`	a list of elements to pass to 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 set.seed at all.
`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.
`bg_mean`	mean value of the background added if `'add_noise'` is `TRUE`. Default is `0`.
`bg_sd`	standard deviation of the background added if `'add_noise'` is `TRUE`. Default is `0`.
`full_range`	only apply when `'mode'` is not `"raw"`, if `'full_range'` is `TRUE`, then `'input_range'` will be set to `[0,4095]` and `'gamma'` forced to `1`. Default is `FALSE`.
`force_range`	bool, only apply when `'mode'` is not `"raw"`, if `'force_range'` is `TRUE`, then `'input_range'` will be adjusted to object range in `[-4095,+inf]` and `'gamma'` forced to `1`. Default is `FALSE`. Note that this parameter takes the precedence over `'input_range'` and `'full_range'`.
`gamma`	correction. Default is `1`, for no correction.