octavvs 0.0.16

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/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 tell pip to download and install octavvs and its requirements: pip install -U octavvs[noconda]

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.

Thus to install the PyQt5 package: PATH=~/miniconda3/bin:$PATH conda install pyqt

Then install Octavvs with pip (without pulling in the incompatible pyqt5 package): 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 will 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. The files will be located in the directory 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.