Skip to contents

Extract spectral data from spectra files

Source: R/get_spec.R
lr_get_spec.Rd

Finds and imports reflectance/transmittance/absorbance data from spectra files in a given location.

Usage

lr_get_spec(
  where = getwd(),
  ext = "txt",
  lim = c(300, 700),
  subdir = FALSE,
  subdir.names = FALSE,
  ignore.case = TRUE,
  interpolate = TRUE,
  parser = NULL,
  ...
)

Arguments

where

Folder in which files are located (defaults to current working directory).

ext

File extension to be searched for, without the "." (defaults to txt). You can also use a character vector to specify multiple file extensions.

lim

A vector with two numbers determining the wavelength limits to be considered (defaults to c(300, 700)).

subdir

Should subdirectories within the where folder be included in the search? (defaults to FALSE).

subdir.names

Should subdirectory path be included in the name of the spectra? (defaults to FALSE).

ignore.case

Should the extension search be case insensitive? (defaults to TRUE)

interpolate

Boolean indicated whether spectral data should be interpolated and pruned at every nanometre. Note that this option can only work if all input data samples the same wavelengths. Defaults to TRUE.

parser

Optional function to specify the parser to be used. By default, the parser is automatically selected based on the file extension. This argument can be used to force the use of a specific parser, or to pass a custom parser. See details for more information on custom parsers. Please note that this argument can produce easily produce invalid results if used incorrectly and only advanced users should use it, with extra caution.

...

Arguments passed to individual parsers.

Value

A data.frame, containing the wavelengths in the first column and individual imported spectral files in the subsequent columns.

Details

Parallel processing

You can customise the type of parallel processing used by this function with the future::plan() function. This works on all operating systems, as well as high performance computing (HPC) environment. Similarly, you can customise the way progress is shown with the progressr::handlers() functions (progress bar, acoustic feedback, nothing, etc.)

Custom parsers

To create a custom parser to pass to the parser argument, you need to create with the following signature:

  • input: a file path (string) as a first argument, and optionally, any additional arguments needed to parse the file. These arguments can be passed to the lr_get_spec() function via the ... argument.

  • output: a named list of two elements, as defined in lr_parse_generic().

See also

pavo::getspec()

Examples

spcs <- lr_get_spec(system.file("testdata", package = "lightr"), ext = "jdx")
#> 1 files found; importing spectra:
head(spcs)
#>    wl OceanOptics_period
#> 1 300           154.3030
#> 2 301           129.2981
#> 3 302           115.9120
#> 4 303           122.5818
#> 5 304           125.9307
#> 6 305           152.3136