Take one set of spectral readings

Take readings according to parameters from a list of settings and a protocol defined by a vector of names.

Usage

acq_raw_mspct(
  descriptor,
  acq.settings,
  f.trigger.on = f.trigger.message,
  f.trigger.off = NULL,
  triggers.enabled = character(),
  seq.settings = list(initial.delay = 0, start.boundary = "none", step.delay = 0,
    num.steps = 1L),
  protocol = c("light", "filter", "dark"),
  user.label = "",
  where.measured = data.frame(lon = NA_real_, lat = NA_real_),
  pause.fun = NULL,
  verbose = TRUE,
  ...
)

Arguments

descriptor

list as returned by function get_oo_descriptor().

acq.settings

list as returned by functions tune_acq_settings() or retune_acq_settings() or acq_settings().

f.trigger.on, f.trigger.off

function Functions to be called immediately before and immediately after a measurement. See acq_raw_spct for details.

triggers.enabled

character vector Names of protocol steps during which trigger functions should be called.

seq.settings

list with members "initial.delay", "step,delay" numeric values in seconds, "num.steps" integer.

protocol

vector of character strings.

user.label

character string to set as label.

where.measured

data.frame with at least columns "lon" and "lat" compatible with value returned by ggmap::geocode().

pause.fun

function used for handling protocol transitions.

verbose

ogical to enable or disable warnings.

...

passed to pause.fun (ignored by the default function).

Value

A raw_mspct object. The names and number of member spectra are determined by protocol, and the number of columns in each member spectrum is determined by acq.settings.

Details

Function acq_raw_mspct acquires directly from a spectrometer a collection of spectra. The settings used for the acquisition of each member spectrum are the same, and are given by the argument passed to acq.settings. The number of numbers and their names are given by the argument passed to protocol.

Two types of light sources can be measured, for continuous-emission light sources, the integration time can at later steps used to compute irradiance. In the case of flashes, the duration of the exposure is unknown and irradiance cannot be computed, while spectral energy per flash can be computed if the number of flashes is known. The argument to num.exposures must be set to the number of flashes.

Two parameters accept functions as arguments, and default to functions that request the operator to trigger the flash or change the light conditions according to the names of the steps in the argument to protocol.

Sequences of light measurements using single "dark" and "filter" measurements are scheduled by setting the four members of the named list passed as argument to seq.settings. The member initial.delay is numeric and gives a minimum delay in seconds before the start of measurements with a default of 0s. Member step.delay is numeric and gives the delay in seconds between successive "light" measurements. In most cases a vector of length one is used as time delta in seconds. Any vector shorter than the number of steps will be extended with rep_len(), and the values interpreted as the time increment in seconds between the start of successive measurements. If the length is the same as "num.steps", and the values are monotonically increasing, they are interpreted as time offsets from the start of the sequence. Member start.boundary can take one of "none", "second", "minute" or "hour" indicating the unit to which the start of the series should be scheduled, e.g. the next minute and 0s, for "minute". Member num.steps must be an integer between 1 and small thousands indicating the number of time steps in the series.

Note

Obviously the duration of the time steps must be longer than the time that a measurement takes. This time can be significantly more than the sum of integration times, as there is considerable overhead in both the OmniDriver Java code, in USB communication, in the spectrometer itself and in R. The overhead depends strongly on the model of spectrometer.

No multitasking is used or supported, so R waits for the spectrometer to answer. The operating system and other programs are not blocked, but the current R instance is.

See also

acq_raw_spct which is used to acquire each member spectrum. Computations on date times are done with lubridate.

Other raw-counts-spectra acquisition functions: acq_raw_spct(), hs_acq_raw_mspct()