objectTransform: 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
)

Value

the matrix transformed according to input parameters

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.

Details

When 'add_noise' is FALSE and attr(msk, "removal") is "masked" or "MC", background will be automatically set to minimal pixel value.