Import spectra files

Finds and imports spectra files from a folder. Currently works for reflectance files generated in Ocean Optics SpectraSuite (USB2000, USB4000 and Jaz spectrometers), CRAIC software (after exporting) and Avantes (before or after exporting).

Usage

getspec(
  where = getwd(),
  ext = "txt",
  lim = c(300, 700),
  decimal = ".",
  sep = NULL,
  subdir = FALSE,
  subdir.names = FALSE,
  ignore.case = TRUE
)

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)).

decimal

Character to be used to identify decimal plates (defaults to .).

sep

Column delimiting characters to be considered in addition to the default (which are: tab, space, and ";")

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)

Value

A data frame, of class rspec, containing individual imported spectral files as columns. Reflectance values are interpolated to the nearest wavelength integer.

Details

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.)

References

Gruson H, White TE, Maia R (2019) lightr: import spectral data and metadata in R. Journal of Open Source Software, 4(43), 1857, doi:10.21105/joss.01857 .

See also

lightr::lr_get_spec() for a more flexible version of this function (e.g. uninterpolated wavelengths), and lightr::lr_get_metadata() for the retrieval and import of spectral metadata. See https://docs.ropensci.org/lightr/ for the complete, and up-to-date, list of supported file formats.

Author

Rafael Maia rm72@zips.uakron.edu

Hugo Gruson hugo.gruson+R@normalesup.org

Examples

# Import and inspect example spectral data with a range of set to 400-700nm.
rspecdata <- getspec(system.file("testdata", package = "lightr"), ext = "ttt", lim = c(400, 700))
#> 2 files found; importing spectra:
head(rspecdata)
#>    wl avantes_export avantes_export_long
#> 1 400         4.0899            5.639232
#> 2 401         3.9514            6.342615
#> 3 402         4.1269            6.147300
#> 4 403         4.2617            6.010692
#> 5 404         4.1683            6.333537
#> 6 405         4.0871            6.490569