lr_parse_jaz {lightr}

Parse OceanInsight converted file

Description

Parse OceanInsight (formerly OceanOptics) converted file. https://www.oceaninsight.com/

Usage

lr_parse_jaz(filename)

lr_parse_jazirrad(filename)

Arguments

filename

Path of the file to parse

Details

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

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

Examples

res_jaz <- lr_parse_jaz(system.file("testdata", "jazspec.jaz",
                        package = "lightr"))
head(res_jaz$data)
res_jaz$metadata

res_jazirrad <- lr_parse_jazirrad(system.file("testdata", "irrad.JazIrrad",
                                  package = "lightr"))
head(res_jazirrad$data)
res_jazirrad$metadata

res_usb4000 <- lr_parse_jaz(system.file("testdata", "OOusb4000.txt",
                            package = "lightr"))
head(res_usb4000$data)
res_usb4000$metadata

res_transmission <- lr_parse_jaz(
  system.file("testdata", "FMNH6834.00000001.Master.Transmission",
               package = "lightr")
)
head(res_transmission$data)
res_transmission$metadata