subsetXIF: RIF/CIF File Subsetting

In IFC: Tools for Imaging Flow Cytometry

RIF/CIF File Subsetting

Description

Subsets RIF or CIF files.

Usage

subsetXIF(
  fileName,
  write_to,
  objects,
  offsets,
  fast = TRUE,
  extract_features = FALSE,
  endianness = .Platform$endian,
  verbose = FALSE,
  verbosity = 1,
  overwrite = FALSE,
  display_progress = TRUE,
  add_tracking = TRUE,
  ...
)

Arguments

fileName	path of file to subset. It has to be a '.rif' or '.cif' file.
write_to	pattern used to export file. Placeholders, like "%d/%s_fromR.%e", will be substituted: -%d: with full path directory of 'fileName' -%p: with first parent directory of 'fileName' -%e: with extension of 'fileName' (without leading .) -%s: with shortname from 'fileName' (i.e. basename without extension). Exported file extension will be deduced from this pattern. It has to be the same as 'fileName', i.e. .cif or .rif.
objects	integer vector, IDEAS objects ids numbers to use. If missing, the default, all objects will be used.
offsets	object of class ‘IFC_offset'. If missing, the default, offsets will be extracted from ’fileName'. This param is not mandatory but it may allow to save time for repeated XIF export on same file.
fast	whether to fast extract 'objects' or not. Default is TRUE. Meaning that 'objects' will be extracted expecting that 'objects' are stored in ascending order. Note that a warning will be sent if an 'object' is found at an unexpected order. In such a case you may need to rerun function with 'fast' = FALSE. If set to FALSE, all raw object_ids will be scanned from 'fileName' to ensure extraction of desired 'objects'. IMPORTANT: whatever this argument is, features are extracted assuming an ascending order of storage in file.
extract_features	whether to try to extract features. Default is FALSE. IMPORTANT: it is not clear if how features are stored and which objects they rely to when input file is already a merge or a subset. For this reason it should be carefully checked.
endianness	The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian. Endianness describes the bytes order of data stored within the files. This parameter may not be modified.
verbose	whether to display information (use for debugging purpose). Default is FALSE.
verbosity	quantity of information displayed when verbose is TRUE; 1: normal, 2: rich. Default is 1.
overwrite	whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite exported file if path of 'fileName' and deduced from 'write_to' arguments are different. Otherwise, you will get an error saying that overwriting source file is not allowed. Note also that an original file, i.e. generated by IDEAS(R) or INSPIRE(R), will never be overwritten. Otherwise, you will get an error saying that overwriting original file is not allowed.
display_progress	whether to display a progress bar. Default is TRUE.
add_tracking	whether to register files' paths and objects' ids in the exported file. Default is TRUE.
...	other arguments to be passed.

Details

when 'extract_features' is set TRUE, only features stored in binary format will be extracted if found.
If the input 'fileName' is a merged of several files then features will be extracted from these files.
If these files can't be found, Warning(s) will be thrown and input 'fileName' will be extracted without features values.

Value

It invisibly returns full path of exported file.

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