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Parse OceanOptics JCAMP-DX (.jdx) file

Source: R/parse_jdx.R
lr_parse_jdx.Rd

Parse OceanOptics/OceanInsight JCAMP-DX (.jdx) file. https://www.oceanoptics.com/

Usage

lr_parse_jdx(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 lightr with the function lr_compute_processed().

References

McDonald RS, Wilks PA. JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form. Applied Spectroscopy. 1988;42(1):151-62.

Examples

res_jdx <- lr_parse_jdx(system.file("testdata", "OceanOptics_period.jdx",
                                    package = "lightr"))
head(res_jdx$data)
#>       wl      dark     white     scope processed
#> 1 176.36 32822.795 32822.795 32822.795       NaN
#> 2 176.58 32822.795 32822.795 32822.795       NaN
#> 3 176.80 32822.795 32822.795 32822.795       NaN
#> 4 177.02  1661.312  1606.017  1647.796  24.44344
#> 5 177.24  1654.349  1555.227  1660.083  -5.78479
#> 6 177.47  2568.562  2494.426  2585.356 -22.65296
res_jdx$metadata
#>  [1] "hugo" NA     NA     NA     "400"  "400"  "400"  "5"    "5"    "5"   
#> [11] "0"    "0"    "0"