Version 0.2.6 is a maintenance update, fixing compatibility with recent versions of ‘dplyr’ and the just reelased ‘photobiology’ 0.10.14. It also includes minor enhancements to the interactive user interface (UI) of function acq_irrad_interactive() . OceanInsight recently released version 2.70 of OmniDriver, and removed some functions from the API. For the time being, keep using version 2.56 that is known to work.
Category: Data analysis
ooacquire 0.2.4 and 0.2.5
The main new feature in version 0.2.5 is that the package can be installed and used in an off-line mode without need to install what were previously system requirements and required packages. In this mode data acquisition and communication with spectrometers is disabled, but processing of spectral data previously acquired or acquired with a different computer or using other software remains available unchanged.
Version 0.2.4 brings some improvements to the user interface for interactive data acquisition. It also fixes problems caused by code-breaking changes in package ‘readr’.
ooacquire 0.2.3
Main changes since version 0.2.2 are:
- Implement support for on-the-fly retrieval of instrument descriptor and calibration data from EEPROM when calibration is not available as R objects: update
acq_irrad_interactive() and the functions it uses to retrieve and save calibration data. (Similar updates are pending for the other data acquisition functions).
- Update calibration data for MAYP11278 and MAYP112785.
- Test with old USB2000 spectrometer.
Full change history is available at: https://docs.r4photobiology.info/ooacquire/news/index.html
NOTE: This package is NOT available through CRAN.
This package is available through the r4photobiology repository and through GitHub.
INSTALLATION:
Note: this version needs the recently released ‘rOmniDriver’ version 0.1.14 or later, so if this package is already installed it may need to be updated before updating or installing ‘ooacquire’ 0.2.3.
- From the binary or source packages of the released version from the CRAN-compatible repository at http://r.r4photobiology.info/.
- From sources of the under development version retrieved from the Git repository at GitHub.
devtools::install_github("aphalo/romnidriver")
devtools::install_github("aphalo/ooacquire")
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ooacquire/issues
ooacquire 0.2.2
During the last two years development has continued at a slow pace. Most changes are to the functions for interactive acquisition of spectra, correction of bugs and tracking to changes in packages from which imports are made. Testing was done with new OmniDriver releases. Some data examples have been added and also replaced. Some progress with the vignettes has been done. However, the documentation still needs work.
One visible change is the move of the Git repository from Bitbucket to GitHub. Package ‘rOmniDriver’ has also been moved to GitHub and its documentation updated to reflect this.
Starting from this release, the changelog is included in the online documentation at http://docs.r4photobiology.info/ooacquire/.
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ooacquire/issues
NOTE: This package is NOT available through CRAN.
This package is available through the r4photobiology repository and through GitHub.
INSTALLATION:
- From the binary or source packages of the released version from the CRAN-compatible repository at http://r.r4photobiology.info/.
- From sources of the under development version retrieved from the Git repository at GitHub.
devtools::install_github("aphalo/romnidriver")
devtools::install_github("aphalo/ooacquire")
ooacquire 0.1.6
Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of additional measurement methods.
- Update
acq_irrad_interactive() adding alternative user-interface modes, allowing users to set comment and what.measured attributes, and to construct collections of spectra.
- Add pre-built calibrations and methods for additional FLAME-S instruments.
- Improve algorithm for automatic tuning of integration time to achieve faster convergence.
- Fix various minor bugs.
- Update vignettes.
- Test against OmniDriver 1.2.56
- Update
read_ooov_files() for compatibility with ‘readr’ >= 1.2.0 which is now required
Add support for measurement of pulsed light sources (under development)
The new features described below are under development, subject to change without previous notice and not yet well tested!! (double-check any results and please report any bugs by raising an issue!)
Implement support for measuring output from xenon flashes, including use of such flashes as light sources for measurement of spectral transmittance and reflectance. Use of multiple exposures per integration is also supported and the number of exposures stored as metadata is used during later processing. In the case of pulsed light sources the first conversion of RAW spectra is into counts per exposure, and instead of spectral irradiance spectral fluence per exposure is computed. All changes are backwards compatible with raw data acquired with earlier versions of ‘ooacquire’ and the user interface remains unaltered for the measurement of continuous light sources.
- Add function
acq_fluence_interactive() for measuring spectral fluence of pulsed light sources.
- Add
acq_fraction_pulsed_interactive() for measuring transmittance and reflectance using a pulsed light source.
Documentation website is at http://docs.r4photobiology.info/ooacquire/.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues
NOTE: This package is NOT available through CRAN.
This version of the package is available through the r4photobiology repository and through Bitbucket.
INSTALLATION:
- from the binary or source packages from the CRAN-compatible repository at http://r.r4photobiology.info/
- from sources retrieved from the Git repository at Bitbucket.
devtools::install_github("tidyverse/ggplot2")
devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.6")
devtools::install_bitbucket("aphalo/photobiology") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/photobiologyWavebands") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/ggspectra") # only if not automatically installed/updated
Using the Quick TUV Calculator
As our package ‘photobiologyInOut’ (versions >= 0.4.15) supports the automatic import of the files returned by the Quick TUV Calculator, we show here how to produce such files, and link to an example showing how to import and plot them in R.
from Data to Viz (external link)
from data to Viz is a new web site related to data analysis and R. Its aim is to make it easier to choose among different types of data visualisations. It looks beautiful, is easy to navigate, includes “trees” displaying a classification of visualizations and multiple individual examples with the corresponding R code. Highly recommended!
To access the website and/or to buy the printed poster visit from Data to Viz.
ooacquire 0.1.5
Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of additional calibration methods.
- Support use of irradiance calibrations supplied by Ocean Optics
- Add pre-built calibrations and methods for two Flame-S instruments.
Documentation website is at http://docs.r4photobiology.info/ooacquire/.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues
NOTE: This package is NOT available through CRAN. In addition, this version of package ‘ooacquire’ depends on versions of packages ‘photobiology’, ‘photobiologyWavebands’, ‘ggspectra’, and ‘ggplot2’ not yet available through CRAN.
This version of the package is available through the r4photobiology repository and through Bitbucket.
INSTALLATION:
- from the binary or source packages from the CRAN-compatible repository at http://r.r4photobiology.info/
- from sources retrieved from the Git repository at Bitbucket.
devtools::install_github("tidyverse/ggplot2")
devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.5")
devtools::install_bitbucket("aphalo/photobiology") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/photobiologyWavebands") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/ggspectra") # only if not automatically installed/updated
ooacquire 0.1.4.9003
Fix “breaking” bug causing fatal errors after package ‘Rcpp’ was updated, and many non-breaking but important bugs.
Several improvements aiming at continuing the expanding the support to different Ocean Optics spectrometers, and to the documentation.
- Fix serious bug that triggered a fatal error with current version of ‘Rcpp’.
- Add functions
choose_sr_interactive() and choose_ch_interactive() and revise acq_irrad_interactive() and acq_fraction_interactive() to make use of them.
- Add fields to the instrument descriptor to store the numeric coefficients in addition to functions for non-linearity and wavelength calibrations.
- Add pre-built calibrations and methods for our Jaz instrument.
- Update and expand the vignettes and examples.
This version of the package is available through the r4photobiology repository and through Bitbucket.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues
Talk at NOG2017
I gave today a talk on one possible way of using R package ‘ooacquire’. I used for the presentation a video with programmed pauses. The pauses are missing from this exported MP4 video file.
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
A manuscript from 1987
Yesterday I found a copy of one of the first manuscripts I ever submitted. It was never published, so it is time for it to be made available. Ideas discussed are nowadays common place. The manuscript, I think, is still mostly valid almost 30 years after I wrote it… I should have tried harder to get it published then.
Click on the image to read the full manuscript.
ooacquire 0.2.4 and 0.2.5
The main new feature in version 0.2.5 is that the package can be installed and used in an off-line mode without need to install what were previously system requirements and required packages. In this mode data acquisition and communication with spectrometers is disabled, but processing of spectral data previously acquired or acquired with a different computer or using other software remains available unchanged.
Version 0.2.4 brings some improvements to the user interface for interactive data acquisition. It also fixes problems caused by code-breaking changes in package ‘readr’.
ooacquire 0.2.3
Main changes since version 0.2.2 are:
- Implement support for on-the-fly retrieval of instrument descriptor and calibration data from EEPROM when calibration is not available as R objects: update
acq_irrad_interactive()and the functions it uses to retrieve and save calibration data. (Similar updates are pending for the other data acquisition functions). - Update calibration data for MAYP11278 and MAYP112785.
- Test with old USB2000 spectrometer.
Full change history is available at: https://docs.r4photobiology.info/ooacquire/news/index.html
NOTE: This package is NOT available through CRAN.
This package is available through the r4photobiology repository and through GitHub.
INSTALLATION:
Note: this version needs the recently released ‘rOmniDriver’ version 0.1.14 or later, so if this package is already installed it may need to be updated before updating or installing ‘ooacquire’ 0.2.3.
- From the binary or source packages of the released version from the CRAN-compatible repository at http://r.r4photobiology.info/.
- From sources of the under development version retrieved from the Git repository at GitHub.
devtools::install_github("aphalo/romnidriver")
devtools::install_github("aphalo/ooacquire")
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ooacquire/issues
ooacquire 0.2.2
During the last two years development has continued at a slow pace. Most changes are to the functions for interactive acquisition of spectra, correction of bugs and tracking to changes in packages from which imports are made. Testing was done with new OmniDriver releases. Some data examples have been added and also replaced. Some progress with the vignettes has been done. However, the documentation still needs work.
One visible change is the move of the Git repository from Bitbucket to GitHub. Package ‘rOmniDriver’ has also been moved to GitHub and its documentation updated to reflect this.
Starting from this release, the changelog is included in the online documentation at http://docs.r4photobiology.info/ooacquire/.
Please raise issues concerning bugs or enhancements to this package through GitHub at https://github.com/aphalo/ooacquire/issues
NOTE: This package is NOT available through CRAN.
This package is available through the r4photobiology repository and through GitHub.
INSTALLATION:
- From the binary or source packages of the released version from the CRAN-compatible repository at http://r.r4photobiology.info/.
- From sources of the under development version retrieved from the Git repository at GitHub.
devtools::install_github("aphalo/romnidriver")
devtools::install_github("aphalo/ooacquire")
ooacquire 0.1.6
Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of additional measurement methods.
- Update
acq_irrad_interactive()adding alternative user-interface modes, allowing users to set comment and what.measured attributes, and to construct collections of spectra. - Add pre-built calibrations and methods for additional FLAME-S instruments.
- Improve algorithm for automatic tuning of integration time to achieve faster convergence.
- Fix various minor bugs.
- Update vignettes.
- Test against OmniDriver 1.2.56
- Update
read_ooov_files()for compatibility with ‘readr’ >= 1.2.0 which is now required
Add support for measurement of pulsed light sources (under development)
The new features described below are under development, subject to change without previous notice and not yet well tested!! (double-check any results and please report any bugs by raising an issue!)
Implement support for measuring output from xenon flashes, including use of such flashes as light sources for measurement of spectral transmittance and reflectance. Use of multiple exposures per integration is also supported and the number of exposures stored as metadata is used during later processing. In the case of pulsed light sources the first conversion of RAW spectra is into counts per exposure, and instead of spectral irradiance spectral fluence per exposure is computed. All changes are backwards compatible with raw data acquired with earlier versions of ‘ooacquire’ and the user interface remains unaltered for the measurement of continuous light sources.
- Add function
acq_fluence_interactive()for measuring spectral fluence of pulsed light sources. - Add
acq_fraction_pulsed_interactive()for measuring transmittance and reflectance using a pulsed light source.
Documentation website is at http://docs.r4photobiology.info/ooacquire/.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues
NOTE: This package is NOT available through CRAN.
This version of the package is available through the r4photobiology repository and through Bitbucket.
INSTALLATION:
- from the binary or source packages from the CRAN-compatible repository at http://r.r4photobiology.info/
- from sources retrieved from the Git repository at Bitbucket.
devtools::install_github("tidyverse/ggplot2")
devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.6")
devtools::install_bitbucket("aphalo/photobiology") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/photobiologyWavebands") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/ggspectra") # only if not automatically installed/updated
Using the Quick TUV Calculator
As our package ‘photobiologyInOut’ (versions >= 0.4.15) supports the automatic import of the files returned by the Quick TUV Calculator, we show here how to produce such files, and link to an example showing how to import and plot them in R.
from Data to Viz (external link)
from data to Viz is a new web site related to data analysis and R. Its aim is to make it easier to choose among different types of data visualisations. It looks beautiful, is easy to navigate, includes “trees” displaying a classification of visualizations and multiple individual examples with the corresponding R code. Highly recommended!
To access the website and/or to buy the printed poster visit from Data to Viz.
ooacquire 0.1.5
Improvements aiming at continuing the expansion of the support of different Ocean Optics spectrometers and of additional calibration methods.
- Support use of irradiance calibrations supplied by Ocean Optics
- Add pre-built calibrations and methods for two Flame-S instruments.
Documentation website is at http://docs.r4photobiology.info/ooacquire/.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues
NOTE: This package is NOT available through CRAN. In addition, this version of package ‘ooacquire’ depends on versions of packages ‘photobiology’, ‘photobiologyWavebands’, ‘ggspectra’, and ‘ggplot2’ not yet available through CRAN.
This version of the package is available through the r4photobiology repository and through Bitbucket.
INSTALLATION:
- from the binary or source packages from the CRAN-compatible repository at http://r.r4photobiology.info/
- from sources retrieved from the Git repository at Bitbucket.
devtools::install_github("tidyverse/ggplot2")
devtools::install_bitbucket("aphalo/ooacquire", ref = "0.1.5")
devtools::install_bitbucket("aphalo/photobiology") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/photobiologyWavebands") # only if not automatically installed/updated
devtools::install_bitbucket("aphalo/ggspectra") # only if not automatically installed/updated
ooacquire 0.1.4.9003
Fix “breaking” bug causing fatal errors after package ‘Rcpp’ was updated, and many non-breaking but important bugs.
Several improvements aiming at continuing the expanding the support to different Ocean Optics spectrometers, and to the documentation.
- Fix serious bug that triggered a fatal error with current version of ‘Rcpp’.
- Add functions
choose_sr_interactive()andchoose_ch_interactive()and reviseacq_irrad_interactive()andacq_fraction_interactive()to make use of them. - Add fields to the instrument descriptor to store the numeric coefficients in addition to functions for non-linearity and wavelength calibrations.
- Add pre-built calibrations and methods for our Jaz instrument.
- Update and expand the vignettes and examples.
This version of the package is available through the r4photobiology repository and through Bitbucket.
Please raise issues concerning bugs or enhancements to this package through Bitbucket at https://bitbucket.org/aphalo/ooacquire/issues
Talk at NOG2017
I gave today a talk on one possible way of using R package ‘ooacquire’. I used for the presentation a video with programmed pauses. The pauses are missing from this exported MP4 video file.
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
A manuscript from 1987
Yesterday I found a copy of one of the first manuscripts I ever submitted. It was never published, so it is time for it to be made available. Ideas discussed are nowadays common place. The manuscript, I think, is still mostly valid almost 30 years after I wrote it… I should have tried harder to get it published then.
Click on the image to read the full manuscript.
