photobiologyInOut (version 0.4.32)

read_oo_jazirrad: Read Files Saved by Ocean Optics' Jaz spectrometer.

Description

Reads and parses the header of processed data text files output by Jaz instruments extracting the spectral data from the body of the file and the metadata, including time and date of measurement from the header. Jaz modular spectrometers were manufactured by Ocean Optics.

Usage

read_oo_jazirrad(
  file,
  date = NULL,
  geocode = NULL,
  label = NULL,
  tz = NULL,
  locale = readr::default_locale(),
  unit.in = "energy"
)
read_oo_jazpc(
  file,
  qty.in = "Tpc",
  Tfr.type = c("total", "internal"),
  Rfr.type = c("total", "specular"),
  date = NULL,
  geocode = NULL,
  label = NULL,
  tz = NULL,
  locale = readr::default_locale()
)
read_oo_jazdata(
  file,
  date = NULL,
  geocode = NULL,
  label = NULL,
  tz = NULL,
  locale = readr::default_locale()
)

Value

A source_spct object, a filter_spct object, a reflector_spct object or a raw_spct object.

Arguments

file

character string Path to the file to be read, following R's use of forward slashes as separator for folder names.

date

a POSIXct object to use to set the "when.measured" attribute. If NULL, the default, the date is extracted from the file header.

geocode

A data frame with columns lon and lat, and optionally address used to set attribute "where.measured".

label

character string to which to set the "what.measured" attribute. If NULL the value of basename(file) is used, and if NA the "what.measured" attribute is not set.

tz

character A time zone recognized by R. If NULL, the default, it is extracted from `locale`.

locale

The locale controls defaults that vary from place to place. The default locale is US-centric (like R), but you can use locale to create your own locale that controls things like the default time zone, encoding, decimal mark, big mark, and day/month names. Its value must match that used to write the imported file, which is not necessarily the default one or the local one.

unit.in

character One of "energy", "photon" (or "quantum"), for data in uW cm-2 nm-1 and umol cm-2 nm-1.

qty.in

character string, one of "Tpc" (spectral transmittance, %), "A" (spectral absorbance), or "Rpc" (spectral reflectance, %).

Tfr.type

character string, either "total" or "internal".

Rfr.type

character string, either "total" or "specular".

Details

Function read_oo_jazirrad can read processed irradiance output files. Function read_oo_jazpc can read processed transmittance and reflectance output files (expressed as %s). Function read_oo_jazdata can read raw-counts data.

References

https://www.oceanoptics.com/

Examples

 file.name <- 
   system.file("extdata", "spectrum.jaz", 
               package = "photobiologyInOut", mustWork = TRUE)
                
 jaz.filter_spct <- read_oo_jazpc(file = file.name)
 
 jaz.filter_spct
 getWhenMeasured(jaz.filter_spct)
 getWhatMeasured(jaz.filter_spct)
 cat(comment(jaz.filter_spct))

 file.name <- 
   system.file("extdata", "spectrum.JazIrrad", 
               package = "photobiologyInOut", mustWork = TRUE)
                
 jaz.source_spct <- read_oo_jazirrad(file = file.name, unit.in = "energy")
 
 jaz.source_spct
 getWhenMeasured(jaz.source_spct)
 getWhatMeasured(jaz.source_spct)
 cat(comment(jaz.source_spct))
 q_irrad(jaz.source_spct, waveband(c(400, 700)), scale.factor = 1e6) # mol -> umol