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Parse OceanOptics ProcSpec file

Source: R/parse_procspec.R
lr_parse_procspec.Rd

Parse OceanOptics/OceanInsight ProcSpec file. https://www.oceanoptics.com/

Usage

lr_parse_procspec(filename)

Arguments

filename

Path of the file to parse

Value

A named list of two elements:

  • data: a dataframe with columns "wl", "dark", "white", "scope" and "processed", in this order.

  • metadata: a character vector with metadata including:

    • user: Name of the spectrometer operator

    • datetime: Timestamp of the recording in format '%Y-%m-%d %H:%M:%S' and UTC timezone. If timezone is missing in source file, UTC time will be assumed (for reproducibility purposes across computers with different localtimes).

    • spec_model: Model of the spectrometer

    • spec_ID: Unique ID of the spectrometer

    • white_inttime: Integration time of the white reference (in ms)

    • dark_inttime: Integration time of the dark reference (in ms)

    • sample_inttime: Integration time of the sample (in ms)

    • white_avgs: Number of averaged measurements for the white reference

    • dark_avgs: Number of averaged measurements for the dark reference

    • sample_avgs: Number of averaged measurements for the sample

    • white_boxcar: Boxcar width for the white reference

    • dark_boxcar: Boxcar width for the dark reference

    • sample_boxcar: Boxcar width for the sample reference

Details

'processed' column computed by official software and provided as is.

References

https://www.oceanoptics.com/software/

Examples

res <- lr_parse_procspec(system.file("testdata", "procspec_files",
                                     "OceanOptics_Linux.ProcSpec",
                                     package = "lightr"))
head(res$data)
#>         wl      dark     white     scope processed
#> 1 176.3604 32822.795 32822.795 32822.795   0.00000
#> 2 176.5816 32822.795 32822.795 32822.795   0.00000
#> 3 176.8027 32822.795 32822.795 32822.795   0.00000
#> 4 177.0238  1483.549  1517.545  1496.656  38.55422
#> 5 177.2449  1492.150  1506.486  1510.991 131.42857
#> 6 177.4660  1965.640  1934.102  1976.290 -33.76623
res$metadata
#>  [1] "hugo"                "2016-03-16 13:18:31" "USB4000"            
#>  [4] "USB4C00008"          "200"                 "200"                
#>  [7] "200"                 "5"                   "5"                  
#> [10] "5"                   "0"                   "0"                  
#> [13] "0"