New: ooacquire 0.1.1

This is the first release of package ‘ooacquire’ . This package allows the acquisition of spectral data from spectrometers from Ocean Optics connected through the OmniDriver run-time, which is available at no cost from Ocean Optics. The current version implements several corrections and measuring protocols unavailable elsewhere in a single modular framework. Some of these cannot be used off-the-shelf as they require the characterization and calibration of each individual spectrometer, to obtain usable values for constants. However, once these constants are available they can be passed as data arguments without need to modify the package itself. Functions are provided for spectral irradiance, spectral transmittance and spectral reflectance measurements. As transmittance and reflectance measurements are normally done relative to reference objects the calibration requirements are less involved than for  spectral irradiance.

The most advanced corrections have been tested with a Maya2000 Pro spectrometer, especially configured for low stray light, as this is the only instrument we have access to which has been characterised and calibrated to this end. Simpler protocols have been cursorily tested with a Flame-S spectrometer and a two-channel Jaz spectrometer.

The acquisition of raw spectra can be expected to function correctly with any Ocean Optics spectrometer supported by OmniDriver. The same is true for linearization and conversion to counts per second, and correction for dark signal. High dynamic range measurements using integration-time “bracketing” can be expected to also work without problems irrespective of spectrometer model, however how much improvement in the dynamic range is achieved will depend on the noise and stray light characteristics of the spectrometer. The remaining two types of corrections, substraction of measured stray light from a paired long-pass filtered measurement and especially deconvolution of the slit function need detailed characterization of each individual instrument.

Functions are provided both for direct acquisition of spectra and spectrometer control from within R, and for reading raw espectral data files saved by SpectraSuite software, or by Jaz instruments, including reading and decoding of measurement settings and instrument description metadata from the file headers.

This package is at a beta stage of development. The current user interface is unlikely to be subjected to major changes, but enhancements and bug fixes are to be expected. We aim at implementing the control of the Jaz-PX light source for the next release.

This package is built on top of package ‘rOmniDriver’ which is a very thin wrapper used for calling the driver API functions from within R.

The package is available through r4photobiology repository.

Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues

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