lr_parse_trm: Parse Avantes binary file

In Bisaloo/lightr: Read Spectrometric Data and Metadata

Parse Avantes binary file

Description

Parse Avantes binary file (TRM, ABS, ROH, DRK, REF, RAW8, RFL8 file extensions). https://www.avantes.com/products/spectrometers/

Usage

lr_parse_trm(filename)

lr_parse_abs(filename)

lr_parse_roh(filename)

lr_parse_rfl8(filename, specnum = 1L)

lr_parse_raw8(filename, specnum = 1L)

lr_parse_irr8(filename, specnum = 1L)

Arguments

filename	Path of the file to parse
specnum	Integer representing the position of the spectrum to read in the file. This option only makes sense for AvaSoft8 files and is ignored in the other cases.

Details

'processed' column computed by lightr with the function lr_compute_processed().

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_trm <- lr_parse_trm(
  system.file("testdata", "avantes_trans.TRM", package = "lightr")
)
head(res_trm$data)
res_trm$metadata

res_roh <- lr_parse_roh(
  system.file("testdata", "avantes_reflect.ROH", package = "lightr")
)
head(res_roh$data)
res_roh$metadata

# This parser has a unique `specnum` argument
res_rfl8_1 <- lr_parse_rfl8(
  system.file("testdata", "compare", "Avantes", "feather.RFL8", package = "lightr"),
  specnum = 1
)
head(res_rfl8_1$data)
res_rfl8_1$metadata

res_rfl8_2 <- lr_parse_rfl8(
  system.file("testdata", "compare", "Avantes", "feather.RFL8", package = "lightr"),
  specnum = 2
)
head(res_rfl8_2$data)
res_rfl8_2$metadata

Bisaloo/lightr documentation built on March 28, 2024, 8:14 p.m.