ExtractFromXIF: RIF/CIF File Reader

In IFC: Tools for Imaging Flow Cytometry

RIF/CIF File Reader

Description

Extracts data from RIF or CIF Files.

Usage

ExtractFromXIF(
  fileName,
  extract_features = TRUE,
  extract_images = FALSE,
  extract_offsets = FALSE,
  extract_stats = TRUE,
  pnt_in_poly_algorithm = 1,
  pnt_in_poly_epsilon = 1e-12,
  force_default = TRUE,
  verbose = FALSE,
  verbosity = 1,
  display_progress = TRUE,
  fast = TRUE,
  recursive = FALSE,
  ...
)

Arguments

fileName	path to file.
extract_features	whether to extract features from file. Default is TRUE. If TRUE, ExtractFromXIF will try to export features. It it fails a message will be sent. Otherwise, graphs, pops and regions will be also extracted.
extract_images	whether to extract images information from file. Default is FALSE.
extract_offsets	whether to extract IFDs offsets from corresponding. Default is FALSE. See getOffsets for further details.
extract_stats	whether to extract population statistics. Default is TRUE.
pnt_in_poly_algorithm	algorithm used to determine if object belongs to a polygon region or not. Default is 1. Note that for the moment only 1(Trigonometry) is available.
pnt_in_poly_epsilon	epsilon to determine if object belongs to a polygon region or not. It only applies when algorithm is 1. Default is 1e-12.
force_default	when display information can't be retrieved whether to use default values. Default is TRUE.
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.
display_progress	whether to display a progress bar. Default is TRUE.
fast	whether to fast extract 'objects' or not. Default is TRUE. Meaning that offsets will be extracted expecting that 'objects' are stored in ascending order. if extract_images is FALSE, a message will be thrown since extraction method does not ensure correct mapping between objects and offsets. if extract_images is TRUE, a warning will be sent if an object is found at an unexpected order.
recursive	whether to recursively apply ExtractFromXIF on files defining input fileName when it is a merged. Default is FALSE.
...	Other arguments to be passed.

Details

If extract_stats is TRUE, extract_features will be automatically forced to TRUE.
If extract_images is TRUE, extract_offsets will be automatically forced to TRUE.
If extract_offsets is TRUE, offsets of images and masks IFDs will be extracted.
If extract_images is TRUE, information about images will be extracted.
If the input fileName is a merged of several files and recursive is set to TRUE, then ExtractFromXIF will be applied recursively on these files.
/!\ Note that features extraction is mandatory to correctly extract graphs, pops, regions and statistics values.

Value

A named list of class 'IFC_data', whose members are:
-description, a list of descriptive information,
-fileName, path of fileName input,
-fileName_image, same as fileName,
-features, a data.frame of features,
-features_def, a describing how features are defined,
-graphs, a list of graphical elements found,
-pops, a list describing populations found,
-regions, a list describing how regions are defined,
-images, a data.frame describing information about images,
-offsets, an integer vector of images and masks IFDs offsets,
-stats, a data.frame describing populations count and percentage to parent and total population,
-checksum, current file checksum.
If fileName is a merged of several files returned object will be of class 'IFC_data' and 'Merged'. If recursive is set to "TRUE", ExtractFromXIF will be applied recursively on files defining the merged. and the returned object will be a list of the above-mentionned list for each of these files.

Source

For pnt_in_poly_algorithm, Trigonometry, is an adaptation of Jeremy VanDerWal's code https://github.com/jjvanderwal/SDMTools

Examples

if(requireNamespace("IFCdata", quietly = TRUE)) {
  ## use a cif file, but you can also read rif
  file_cif <- system.file("extdata", "example.cif", package = "IFCdata")
  cif <- ExtractFromXIF(fileName = file_cif)
} else {
  message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
                  'https://gitdemont.github.io/IFCdata/',
                  'to install extra files required to run this example.'))
}

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