octavvs 0.0.19

Open Chemometrics Toolkit for Analysis and Visualization of Vibrational Spectroscopy data

OCTAVVS: Open Chemometrics Toolbox for Analysis and Visualization of Vibrational Spectroscopy data

OCTAVVS is a set of graphical tools for high-throughput preprocessing and analysis of vibrational spectroscopy data. Currently, the preprocessing is primarily geared towards images from infrared absorption spectroscopy with focal plane array detectors.

There are three separate tools in the current version:

preprocessing deals with atmospheric correction, resonant Mie scattering correction, baseline correction and normalization.

mcr_als decomposes observed spectra into nonnegative concentrations and spectra using the MCR-ALS algorithm.

clustering performs K-means clustering on the concentrations inferred by MCR-ALS.

Installation on Windows and Mac

To install OCTAVVS on Windows or Mac, start by downloading Python 3.7 (or newer) from Python.org. (It is also possible to use Conda as described for Linux, below.)

When you have installed Python, get a command prompt:

• On Windows: Windows key + "r", type "cmd"
• On Mac: open Terminal

Then use pip to download and install pyqt5 and octavvs and its requirements:
pip install pyqt5
pip install octavvs

Upgrading to the latest version

Information about the most recent version of OCTAVVS can be found on its PyPI project page. To upgrade to the latest version:
pip install -U octavvs

Installation on Linux (or with Conda on other systems)

Alternatively (and apparently required on at least some Linux distributions because of issues with PyQt5): Install the Python 3.7 (or newer) version of Miniconda or Anaconda. In the last installation step, conda will want to add its path to $PATH in your .bashrc; doing so could potentially break things (on OpenSUSE it's been known to conflict with KDE), so you may want to manually control the $PATH instead.

Then install PyQt5 using conda: conda install pyqt
Install/upgrade Octavvs using pip as above: pip install -U octavvs

If you accidentally install the pip pyqt5 package, the easiest way to get rid of it is to pip uninstall pyqt5 and then conda install --force-reinstall pyqt

Finding and using octavvs

The easiest way to access the Octavvs scripts is through desktop shortcuts which may be created by running the oct_make_icons script in the console.

The location of the octavvs scripts will depend on your operating system and where you installed Python. Within the Python (or Conda) directory, the files will be located in lib/python3.7/site-packages/octavvs but the executable scripts oct_preprocessing, oct_mcr_als and oct_clustering will be located in bin and should be possible to run straight from the console.

Test data

Test data from two 64x64 images of Paxillus hyphae growing on lignin can be downloaded here (zip archive, 47 MB).

Bug reports and code repository

Developers may want to access the OCTAVVS code through the OCTAVVS GitHub page, where bugs and other issues can also be reported.

Non-technical users may prefer to send questions, bug reports and other requests by email to corresponding author Carl Troein [e-mail].