In Bisaloo/lightr: Read Spectrometric Data and Metadata

lightr provides three main functions for patch import of spectral data and metadata:

• lr_get_spec()
• lr_get_metadata()
• lr_convert_tocsv()

Those three functions contain an internal loop and can directly be used to import/convert whole folders.

They also allow for recursive search in the folder tree with the argument subdir. In this example, the data that contains a subdirectory named procspec_files, which contains :

└──+ data
   ├── avantes_export.ttt
   ├── avantes_export2.trt
   ├── avantes_export_long.ttt
   └──+ procspec_files
      ├── OceanOptics_badencode.ProcSpec
      ├── OceanOptics_Linux.ProcSpec
      ├── OceanOptics_Windows.ProcSpec
      └── whiteref.ProcSpec

We first demonstrate these features on lr_get_spec() but they work in the same way for lr_get_metadata() and lr_convert_tocsv()

library(lightr)

Import spectral data: lr_get_spec()

lr_get_spec() is one the core functions of lightr. It finds spectral data files, extract the reflectance / transmittance / absorbance data and returns a data.frame where the first column (named wl) contains the wavelengths and the subsequent columns contain the spectral data, interpolated every nanometre:

res <- lr_get_spec(where = "data", ext = "ttt", lim = c(300, 700))
head(res)

lr_get_spec() also supports setting multiple file extensions at once by passing a character vector to ext:

res <- lr_get_spec(where = "data", ext = c("ttt", "trt"), lim = c(300, 700))
head(res)

Finally, lr_get_spec() can also recursively search in your folder tree with the subdir argument:

res <- lr_get_spec(where = "data", ext = "procspec", lim = c(300, 700), subdir = TRUE)
head(res)

As you may have noticed, lr_get_spec() does not care about the file extension case by default. This can be changed by using the ignore.case switch:

res <- lr_get_spec(where = "data", ext = "procspec", subdir = TRUE, ignore.case = FALSE)

If all your input files sample the wavelengths (this would be the case if you use the same spectrometer model and same recording software), you can also get uninterpolated data, by changing the value of the interpolate boolean argument:

res <- lr_get_spec(where = file.path("data", "puffin"), ext = "procspec", interpolate = FALSE)
head(res)

Import spectral metadata: lr_get_metadata()

lr_get_metadata() extracts metadata captured by the spectrophotometer during the recording. This metadata should be reported in your scientific articles to ensure reproducibility of your measurements and ultimately of your findings. The amount of information strongly depends on the brand and model of the spectrometer.

Similarly to lr_get_spec(), it can handle multiple extensions at once and perform recursive searches:

res <- lr_get_metadata(where = "data", ext = c("trt", "procspec"), subdir = TRUE)
head(res)

Convert spectral data to csv: lr_convert_tocsv()

lr_convert_tocsv() is designed for users who want an open format version for each individual input file, possibly allowing them to carry on with their analysis using another programming language or software.

It works in a very similar way to lr_get_spec() and will create csv files with the same file names as the input files (but a different extension).

lr_convert_tocsv(where = "data", ext = "procspec", subdir = TRUE)

Bisaloo/lightr documentation built on March 28, 2024, 8:14 p.m.