cpp_transform: Matrix Transformation
In IFC: Tools for Imaging Flow Cytometry

cpp_transform

R Documentation

Matrix Transformation

Description

Function to normalize, colorize and add background to images.

Arguments

`mat`	NumericMatrix.
`color`	NumericVector, whose members are h,s,v color. This vector has to be named with 1st name being the name of this color.
`msk`	IntegerMatrix.
`size`	a length 2 IntegerVector, of final dimensions (height,width) of the image. Default is `0,0` for no change.
`mode`	string, color mode export. Either `"rgb"`, `"gray"` or `"raw"`. Default is `"raw"`.
`type`	uint16_t image object type. Default is `2`.
`input_range`	a finite NumericVector, only apply when `'mode'` is not `"raw"`, sets the range of the input intensity values. Values outside this range are clipped. Default is `[0.0,4095.0]`.
`add_noise`	bool, whether to add normal noise or not. Default is `true`.
`bg`	double, mean value of the background added if `'add_noise'` is `true`. Default is `0.0`.
`sd`	double, standard deviation of the background added if `'add_noise'` is `true`. Default is `0.0`.
`full_range`	bool, only apply when `'mode'` is not `"raw"`, if `'full_range'` is `true`, then `'input_range'` will be set to `[0.0,4095.0]` and `'gamma'` forced to `1.0`. 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 `[-4095.0, +inf]` and `'gamma'` forced to `1.0`. Default is `false`. Note that this parameter takes the precedence over `'input_range'` and `'full_range'`.
`gamma`	correction. Default is `1.0`, for no correction.
`spatialX`	X offset correction. Default is `0.0` for no change.
`spatialY`	Y offset correction. Default is `0.0` for no change.

Details

When a mask is detected, 'add_noise', 'full_range' and 'force_range' are set to false, 'bg' and 'sd' to 0.0, 'input_range' to [0.0,3.0] and 'gamma' to 1.0.

Experimental (as of v0.2.0.501): when 'mode' is not "raw", if 'input_range' is within ]0,1[, it will be used as 'probs' argument to quantile to determine clipping range from image object, in addition, 'gamma' will be forced to 1.0.