Package ooacquire provides a set of high level functions for spectral data acquisition built using package rOmniDriver as a base. It is very flexible with respect to measuring protocols. It caters for all steps involved in the acquisition of spectral data from connecting to the instrument(s) and retrieving information from its/their non-volatile memory, setting and adjusting acquisition parameters, acquiring raw counts and converting them into counts per second. It supports bracketing of the integration time for high dynamic range (HDR) protocols, both with respect to acquisition and merging of the data. It also supports protocols in which the total measuring time is kept constant by adjusting integration time and number of scans averaged in coordination. It works seamlessly together with package photobiology on which it also depends.
The package rOmniDriver makes available in R the functions in OmniDriver SDP from Ocean Optics. OmniDriver allows to change settings and acquire spectra using any Ocean Optics USB-connected spectrometer. It has been tested with our Maya2000Pro, Flame and Jaz instruments under MS-windows 7 and MS-Windows 10, but should also work with any other modern spectrometer from Ocean Optics, and also under OS X, and Linux. However, only a subset of all OmniDriver exported functions are implemented (those functions that write to the instrument EEPROM are not implemented as they require a secret key for activation, and in addition their use without risk requires a profound understanding of the instruments’ hardware and firmware). As currently the API documentation is freely available at Ocean Optics’ support page, adding additional functions using the source code of the functions included in our package as examples is almost trivial.
In addition to directly acquired RAW counts data, raw-counts spectra acquired with OceanView or SpectraSuite programs from Ocean Optics stored in files can be used as the starting point for the computation of spectra expressed as corrected counts-per-second with the same flexibility as for directly acquired spectra.
High level functions in this package and in package photobiology allow the easy conversion of counts-per-second into the physical quantities of interest such as spectral irradiance, spectral transmittance, spectral reflectance and spectral absorbance.
Our package’s functions related to direct data acquisition use the free OmniDriver run-time driver, which can be downloaded from the Ocean Optics web site should also installed, as well as Java, a requirement of the driver itself. There is no other set up needed, just plug your spectrometer to an USB port. The first time you connect an instrument the operating system will install the drivers as they are made available by the OmniDriver installation.
This package does NOT require OceanView or SpectraSuite to be installed. It does not require the purchase of software from Ocean Optics, but it is not supported in any way by Ocean Optics, unless you acquire a licence to the SDP.