objectParam: Object Extraction Parameters Definition
In IFC: Tools for Imaging Flow Cytometry

objectParam

R Documentation

Object Extraction Parameters Definition

Description

Defines 'IFC_object' object extraction parameters.

Usage

objectParam(
  ...,
  info,
  mode = c("rgb", "gray", "raw")[3],
  export = c("file", "matrix", "base64")[2],
  write_to,
  base64_id = FALSE,
  base64_att = "",
  overwrite = FALSE,
  composite = "",
  selection = "all",
  size = c(0, 0),
  force_width = TRUE,
  random_seed = NULL,
  removal = "none",
  add_noise = TRUE,
  full_range = FALSE,
  force_range = FALSE,
  spatial_correction = FALSE
)

Arguments

`...`	arguments to be passed to `getInfo`, only if `'info'` is not provided.
`info`	object of class 'IFC_info', rich information extracted by `getInfo`. This argument is not mandatory but it may allow to save time for repeated image export on same file. If missing, the default, `'info'` will be extracted thanks to `'...'`.
`mode`	color mode export. Either `"rgb"`, `"gray"` or `"raw"`. Default is `"raw"`. Note that `"raw"` is only possible when `'export'` is `"matrix"`.
`export`	format mode export. Either `"file"`, `"matrix"`, `"base64"`. Default is `"matrix"`.
`write_to`	used when export is `"file"` or `"base64"` to compute respectively exported file name or base64 id attribute. Exported file extension and base64 MIME type will be deduced from this pattern. Allowed export are `".bmp"`, `".jpg"`, `".jpeg"`, `".png"`, `".tif"`, `".tiff"`. Note that `".bmp"` are faster but not compressed producing bigger data. Placeholders, if found, will be substituted: -`%d`: with full path directory, -`%p`: with first parent directory, -`%e`: with extension (without leading .), -`%s`: with shortname (i.e. basename without extension), -`%o`: with object_id, -`%c`: with channel_id. A good trick is to use: -`"%d/%s/%s_%o_%c.tiff"`, when `'export'` is `"file"`, -`"%o_%c.bmp"`, when `'export'` is `"base64"`. Note that if missing and `'export'` is not `"file"`, `'write_to'` will be set to `"%o_%c.bmp"`.
`base64_id`	whether to add id attribute to base64 exported object. Default is `FALSE`. Only applied when export is `"base64"`.
`base64_att`	attributes to add to base64 exported object. Default is `""`. Only applied when export is `"base64"`. For example, use `"class='draggable'"`. Note that `id` (if `'base64_id'` is `TRUE`) and `width` and `height` are already used.
`overwrite`	only apply when `'export'` is `"file"` whether to overwrite file or not. Default is `FALSE`.
`composite`	character vector of image composite. Default is `""`, for no image composite. Should be like `"1.05/2.4/4.55"` for a composition of 5 perc. of channel 1, 40 perc. of channel 2 and 50 perc. of channel 55. Note that channels should have been acquired and final image composition should be 100 perc., otherwise an error is thrown. Note that each composite will be appended after `'selection'`.
`selection`	physical channels to extract. Note that this parameter will be ordered. Default is `"all"` to extract all acquired channels. Use `"none"` to only extract composite.
`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.
`force_width`	whether to use information in `'info'` to fill size. Default is `TRUE`. When set to `TRUE`, width of `'size'` argument will be overwritten.
`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.
`removal`	removal method: Either `"none"`, `"raw"`, `"clipped"`, `"masked"`, `"MC"`. -`"none"`, to keep image as is, no mask extraction will be performed resulting in faster extraction, -`"raw"`, to keep image as is, it provides a convenient way to retrieve `"raw"` value for the mask, -`"clipped"`, to remove clipped object from image, -`"masked"`, to only keep masked object from image, -`"MC"`, to keep MC masked object from image. This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to `'selection'` and `'composite'` parameters.
`add_noise`	if `TRUE` adds normal noise to background using Rcpp. Default is `TRUE`. Note that it is better to set it to `FALSE` when `'removal'` is `"masked"` or `"MC"`. Doing so will allow to place masked object in a zero filled background, otherwise background will still be filled with noise. This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to `'selection'` and `'composite'` parameters.
`full_range`	only apply when `'mode'` is not `"raw"`, if `'full_range'` is `TRUE`, then object range will be considered as 0 to 4095, it is like `"raw"` `'mode'` but resulting in [0,4095] normalization to [0,1]. Default is `FALSE`. This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to `'selection'` and `'composite'` parameters.
`force_range`	only apply when `'mode'` is not `"raw"`, if `'force_range'` is `TRUE`, then range will be adjusted to object range in `[-4095,+inf]` resulting in normalization to [0,1]. Default is `FALSE`. This parameter will be repeated with rep_len() from base for every physical channel that needs to be extracted according to `'selection'` and `'composite'` parameters. Note that this parameter takes the precedence over `'full_range'`.
`spatial_correction`	only apply on RIF file, whether to apply spatial correction. Default is `FALSE`.

Details

When a mask is detected, 'add_noise', 'full_range' and 'force_range' are set to FALSE and range used will be forced to [0,3].

Range of image is controlled by 'Images' information from supplied 'info' or as extracted by getInfo and will be returned as 'channels' by objectParam. In case 'mode' is not "raw", 'channels$xmin', 'channels$xmax', 'channels$gamma' will be used for object extraction by objectExtract unless any of 'force_range' or 'full_range' is TRUE.

Experimental (as of v0.2.0.501): once returned by objectParam, those 'channels$xmin' and 'channels$xmax' can be manually adjusted to ]0,1[ so as to be used as 'probs' argument to quantile to allow quantile normalization during object extraction (objectExtract) afterwards.