ooacquire 0.1.2

This is the second release of package ‘ooacquire’. It is an important update as it include bug fixes and enhancements which have some (minor) effect on the calculated spectral values. The update also removes some spurious warnings and has additional documentation, although not yet in final form.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 characterisation and calibration of each individual spectrometer, so as 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 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

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.Continue reading

Packages available

rOmniDriver 0.1.6

This package allows the control of all Ocean Optics spectrometers and the acquisition of spectral data directly from within R code. The current version implements only a subset of the functions available in OmniDriver. Adding other functions should be almost trivial, but not all of them can be tested with the spectrometers we have access to.

It is fully functional  with the installation of the free run-time provided by Ocean Optics, but it is not supported in any way by Ocean Optics, without purchase of a licence. We thank Ocean Optics’ for helping in the development of this package. (The run-time can be installed from the same file as a full installation, but without the need to enter a password.)

MayaCalc 3.2.2

This package implements functions for acquisition of spectral data, application of special correction and calibration algorithms using a Maya2000Pro spectrometer from Ocean Optics. It also implements different radiation measurement protocols. Functions are also provided for estimating calibration constants from measurements of calibration lamps. The algorithms allow in most cases a gain of one order of magnitude in signal to noise ratio, allowing acceptably good measurements of solar ultraviolet radiation with this single-monochromator array instrument. The code is based on algorithms developed by Lasse Ylianttila at the Radiation Safety Authority Finland.

This package can be used as is only with our own Ocean Optics spectrometer unit, a Maya2000Pro. It is made publicly available as an example that could be adapted to other spectrometers. In addition, by making it publicly available, we contribute to making our own research reproducible.

A bugfix update will be released as soon as we have access to the spectrometer for testing it. The bug affects only measurements done under extremely low irradiance levels.

NOTE: Sources, and Windows binaries for R 3.2.x, are now available in the repository.