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Parse OceanOptics ProcSpec file

Source: R/parse_procspec.R
lr_parse_oceanoptics_procspec.Rd

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

Usage

lr_parse_oceanoptics_procspec(filename, verify_checksum = FALSE, ...)

lr_parse_procspec(filename, verify_checksum = FALSE, ...)

Arguments

filename

Path of the file to parse

verify_checksum

Logical (defaults to FALSE). Should we check if the file has been modified since its creation by the spectrometer? An error will be returned if the check fails.

...

ignored

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_oceanoptics_procspec(system.file("testdata", "procspec_files",
                                     "OceanOptics_Linux.ProcSpec",
                                     package = "lightr"),
                         verify_checksum = TRUE)
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"