buildBatch: Batch Builder
In IFC: Tools for Imaging Flow Cytometry

buildBatch

R Documentation

Batch Builder

Description

Prepares XML node for ExportToBATCH.

Usage

buildBatch(
  files,
  compensation,
  analysis,
  default_batch_dir,
  config_file,
  name = "Batch1",
  use_acquisition = FALSE,
  suffix = "",
  allow_channels_dissimilarity = FALSE,
  overwrite = TRUE,
  segment_rif = "None",
  options
)

Arguments

`files`	path of files to batch.
`compensation`	path to compensation file.
`analysis`	path to analysis file.
`default_batch_dir`	directory where batches are stored. It can be found in IDEAS(R) software, under Options -> Application Defaults -> Directories -> Default Batch Report Files Directory. If missing, the default, it will be deduced from IDEAS(R) config file, However, if it can't be deduced then tempdir(check = TRUE) from base will be used. This argument takes precedence over 'config_file' and filling 'default_batch_dir' prevents the use of 'config_file' argument.
`config_file`	path to IDEAS(R) config file. It may depends on IDEAS(R) software installation but one may use "C:/Users/%USER%/AppData/Roaming/Amnis Corporation/userconfig.xml".
`name`	name of batch. Default is "Batch1".
`use_acquisition`	whether to use acquisition as analysis template. Default is FALSE.
`suffix`	suffix to add to files when batched. Default is "".
`allow_channels_dissimilarity`	whether to allow building batch when all files were not acquired with same channels. Default is FALSE.
`overwrite`	whether to overwrite files or not. Default is TRUE.
`segment_rif`	size of file segmentation. Default is "None", for no segmentation. Allowed are "None", "100", "1K", "5K", "10K", "50K", "100K".
`options`	A list of arguments to be passed. If missing, the default, options will be set to: -"Brightfield compensation"=TRUE, -"EDF deconvolution"=TRUE, -"Camera background"=TRUE, -"Spatial alignment"=TRUE. Allowed are TRUE or FALSE for all, excepted for 'Spatial aligment' which can also be path to .rif file.

Value

a list containing batch information:
-xml, the xml object to be written,
-batch_dir, the directory where xml file is desired to be saved according to 'default_batch_dir' and 'config_file'.

IFC documentation built on Sept. 14, 2023, 1:08 a.m.