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).

getspec(
  where = getwd(),
  ext = "txt",
  lim = c(300, 700),
  decimal = ".",
  sep = NULL,
  subdir = FALSE,
  subdir.names = FALSE,
  cores = NULL,
  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).
cores	deprecated. See future::plan() for more details on how to customise your parallelisation strategy.
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.

Author

Rafael Maia rm72@zips.uakron.edu

Hugo Gruson hugo.gruson+R@normalesup.org

Examples

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