Reads the spectral data and in addition parses the header of a energy irradiance data file as output by SpectraSuite. SpectraSuite is a program from Ocean Optics used to measure UV, visible and NIR radiation with array spectrometers from the same company. OceanView replaces the no longer supported SpectraSuite program.
Usage
read_oo_ssirrad(
file,
date = NULL,
geocode = NULL,
label = NULL,
tz = NULL,
locale = readr::default_locale(),
range = NULL
)
read_oo_ssdata(
file,
date = NULL,
geocode = NULL,
label = NULL,
tz = NULL,
locale = readr::default_locale()
)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
POSIXctobject to use to set the"when.measured"attribute. IfNULL, the default, the date is extracted from the file header.- geocode
A data frame with columns
lonandlat, and optionallyaddressused to set attribute"where.measured".- label
character string to which to set the
"what.measured"attribute. IfNULLthe value ofbasename(file)is used, and ifNAthe"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
localeto 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.- range
a numeric vector of length two, or any other object for which function
range()will return a range of wavelengths expressed in nanometres.
Details
The header of the file is first decoded and parsed to extract the
time of data acquisition and serial number of the spectrometer, and to
locate the start of the spectral data. The fields are located by name.
The spectral irradiance is re-expressed in \(W m^{-2} nm^{-1}\) and
returned as an object of class source_spct
with metadata stored in attributes when.measured,
what.measured, and how.measured set to values extracted from
the header. The value stored in the how.measured attribute includes
the User: and Serial Number: values extracted from the file header.
If an argument is passed to parameter geocode, its value is
saved in attribute where.measured. The file header in whole
is copied to attribute file.header. The object's comment
always gives a text that includes the file name, time of import, function
name and the version of packages 'photobiology' and 'photobiologyInOut'
used.
Examples
file.name <-
system.file("extdata", "spectrum.SSIrrad",
package = "photobiologyInOut", mustWork = TRUE)
ooss.spct <- read_oo_ssirrad(file = file.name)
ooss.spct
#> Object: source_spct [1,044 x 2]
#> Wavelength range 199.08-998.61 nm, step 0.72-0.81 nm
#> Label: File: spectrum.SSIrrad
#> Measured on 2013-05-06 15:13:40 UTC
#> Variables:
#> w.length: Wavelength [nm]
#> s.e.irrad: Spectral energy irradiance [W m-2 nm-1]
#> --
#> # A tibble: 1,044 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 199. 0
#> 2 200. 0
#> 3 201. 0
#> 4 202. 1.37
#> 5 202. 1.25
#> 6 203. 1.13
#> 7 204. 1.11
#> 8 205. 1.09
#> 9 206. 0.902
#> 10 206. 0.739
#> # ℹ 1,034 more rows
getWhenMeasured(ooss.spct)
#> [1] "2013-05-06 15:13:40 UTC"
getWhatMeasured(ooss.spct)
#> [1] "File: spectrum.SSIrrad"
getHowMeasured(ooss.spct)
#> [1] "Measured by user User with Ocean Optics spectrometer with s.n. QEB1523 and SpectraSuite software."
cat(comment(ooss.spct))
#> Ocean Optics SpectraSuite irradiance file 'spectrum.SSIrrad' imported on 2025-10-02 21:42:56 UTC with function 'read_oo_ssirrad()'.
#> R packages 'photobiologyInOut' 0.4.32.9000 and 'photobiology' 0.14.0 were used.