Read File Saved by Ocean Optics' Raspberry Pi software. — read_oo

Reads and parses the header of a raw data file as output by the server running on a Raspberry Pi board to extract the whole header remark field. The time field is retrieved and decoded. The company formerly named Ocean Optics is now called Ocean Insight.

Usage

read_oo_pidata(
  file,
  date = NULL,
  geocode = NULL,
  label = NULL,
  tz = NULL,
  locale = readr::default_locale(),
  npixels = Inf,
  spectrometer.sn = "FLMS00673"
)

Arguments

file: character string
date: a POSIXct object to use to set the "when.measured" attribute. If NULL, the default, the date is set to the file modification date.
geocode: A data frame with columns lon and lat used to set attribute "where.measured".
label: character string, but if NULL the value of file is used, and if NA the "what.measured" attribute is not set.
tz: character Time zone is not saved to the file.
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.
npixels: integer Number of pixels in spectral data.
spectrometer.sn: character The serial number of the spectrometer needs to be supplied by the user as it is not included in the file header.

Value

A raw_spct object.

Note

The header in these files has very little information. The file contains a time in milliseconds but as the Raspberry Pi board contains no real-time clock, it seems to default to number of milliseconds since the Pi was switched on. The user may wish to supply the date-time as an argument, but if no argument is passed to date this attribute is set to the file modification date obtained with file.mtime(). This date-time gives an upper limit to the real time of measurement as in some operating systems it is reset when the file is copied or even without any good apparent reason. The user may need to supply the number of pixels in the array although the default of npixels = Inf usually works and triggers no warnings.

References

https://www.oceanoptics.com/ https://www.raspberrypi.org/

Examples


 file.name <- 
   system.file("extdata", "spectrum.pi", 
               package = "photobiologyInOut", mustWork = TRUE)
                
 oopi.spct <- read_oo_pidata(file = file.name)
 
 oopi.spct
#> Object: raw_spct [2,048 x 2]
#> Wavelength range 188.41408-1035.613 nm, step 0.3603105-0.4672823 nm 
#> Label: File: spectrum.pi 
#> Measured on 2025-10-02 21:42:33.632242 UTC 
#> Data acquired with 'OO with Raspberry Pi' s.n. FLMS00673
#> grating 'NA', slit 'NA'
#> diffuser 'unknown'
#> integ. time (s): 0.01
#> total time (s): 0.01
#> counts @ peak (% of max): 
#> Variables:
#>  w.length: Wavelength [nm]
#>  counts: Raw detector counts [number] 
#> --
#> # A tibble: 2,048 × 2
#>    w.length  counts
#>       <dbl>   <dbl>
#>  1     188.    16.4
#>  2     189. 27476. 
#>  3     189.  2064. 
#>  4     190.  1994. 
#>  5     190.  2001. 
#>  6     191.  1954. 
#>  7     191.  1950. 
#>  8     192.  2083. 
#>  9     192.  1980. 
#> 10     193.  1980. 
#> # ℹ 2,038 more rows
 getWhenMeasured(oopi.spct)
#> [1] "2025-10-02 21:42:33 UTC"
 getWhatMeasured(oopi.spct)
#> [1] "File: spectrum.pi"
 cat(comment(oopi.spct))
#> Ocean Optics Raspeberry Pi raw counts file 'spectrum.pi' imported on 2025-10-02 21:42:55.313734 UTC
#> Saved at time: 612027 milliseconds
#> Integration time: 10000
#> Scans to average: 0
#> Boxcar smoothing: 0