lightr provides three main functions for patch import of spectral data and metadata:
lr_get_spec()lr_get_metadata()lr_spec2csv()Those three functions contain a 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.ProcSpecWe first demonstrate these features on lr_get_spec() but they work in the same way for lr_get_metadata() and lr_spec2csv()
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:
## 2 files found; importing spectra:## wl avantes_export avantes_export_long
## 1 300 3.1487 13.624678
## 2 301 3.1589 5.276307
## 3 302 3.5700 11.023560
## 4 303 3.9215 10.307208
## 5 304 3.4034 8.980705
## 6 305 3.7878 8.278200lr_get_spec() also supports setting multiple file extensions at once by passing a character vector to ext:
## 3 files found; importing spectra:## Warning: Could not import one or more files:
## data/avantes_export2.trt## wl avantes_export avantes_export_long
## 1 300 3.1487 13.624678
## 2 301 3.1589 5.276307
## 3 302 3.5700 11.023560
## 4 303 3.9215 10.307208
## 5 304 3.4034 8.980705
## 6 305 3.7878 8.278200Finally, lr_get_spec() can also recursively search in your folder tree with the subdir argument:
## 6 files found; importing spectra:## wl OceanOptics_Linux OceanOptics_Windows OceanOptics_badencode whiteref
## 1 300 126.5502 3.199635 -6.905214 98.30193
## 2 301 125.3005 3.420500 -7.034905 98.67972
## 3 302 127.0825 3.224495 -7.656868 98.10391
## 4 303 128.0483 3.320803 -8.577880 101.34410
## 5 304 128.9909 3.407551 -9.182934 99.86908
## 6 305 127.4218 3.492118 -9.367868 101.32638
## BR_PF26_1 BR_PF27_3
## 1 19.35800 16.81450
## 2 19.40243 16.69849
## 3 19.42713 16.54195
## 4 19.47335 16.47455
## 5 19.48856 16.38495
## 6 19.41967 16.31837As 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:
## Warning: No files found. Try a different value for argument "ext".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 valu of the interpolate boolean argument:
## Warning: No files found. Try a different value for argument "ext".## NULLlr_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:
## name user date spec_model spec_ID
## 1 avantes_export2 <NA> 2585261312 <NA> 1305084U1
## 2 OceanOptics_Linux hugo 1458134311936 USB4000 USB4C00008
## 3 OceanOptics_Windows doutrelant 1449224954221 JazUSB JAZA2982
## 4 OceanOptics_badencode user 1480711152080 USB2000Plus USB2+H06330
## 5 whiteref gomez 1533225379360 USB4000 USB4C00008
## 6 BR_PF26_1 Adminlocal 1151138946593 USB4000 USB4C00008
## white_inttime dark_inttime sample_inttime white_avgs dark_avgs sample_avgs
## 1 95 95 95 20 20 20
## 2 200 200 200 5 5 5
## 3 60 60 60 15 15 15
## 4 20 20 20 100 100 100
## 5 500 500 500 5 5 5
## 6 10 10 10 40 40 40
## white_boxcar dark_boxcar sample_boxcar
## 1 1 1 1
## 2 0 0 0
## 3 0 0 0
## 4 5 5 5
## 5 0 0 0
## 6 10 10 10lr_convert_tocsv()lr_convert_tocsv() is designed for people that want to a machine readable 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).