read_oo_pidata: Read File Saved by Ocean Optics' Raspberry Pi software.

In photobiologyInOut: Read Spectral and Logged Data from Foreign Files

Read File Saved by Ocean Optics' Raspberry Pi software.

Description

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
 getWhenMeasured(oopi.spct)
 getWhatMeasured(oopi.spct)
 cat(comment(oopi.spct))

photobiologyInOut documentation built on Sept. 14, 2024, 5:06 p.m.