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 )
where | Folder in which files are located (defaults to current working directory). |
---|---|
ext | File extension to be searched for, without the "." (defaults to
|
lim | A vector with two numbers determining the wavelength limits to be
considered (defaults to |
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 |
subdir.names | Should subdirectory path be included in the name of the
spectra? (defaults to |
cores | deprecated. See |
ignore.case | Should the extension search be case insensitive? (defaults
to |
A data frame, of class rspec
, containing individual imported
spectral files as columns.
Reflectance values are interpolated to the nearest wavelength integer.
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.)
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 .
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.
Rafael Maia rm72@zips.uakron.edu
Hugo Gruson hugo.gruson+R@normalesup.org
#>#> 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