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Open Chemometrics Toolkit for Analysis and Visualization of Vibrational Spectroscopy data

Project description

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 or Linux

OCCTAVS needs a working Python 3 environment with various packages. The easiest way to get this is through the Conda package management system.

Download and install the Python 3.7 (or newer) version of Miniconda. During the installation, Conda will ask about adding its programs to the path. Say yes to this unless you have reason not to (but see below if you are using Linux).

When you have installed Conda, get a command prompt:

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

Make sure that PyQt5 is installed: conda install pyqt

Then install OCTAVVS using pip: pip install octavvs
If pip isn't found, try pip3 install octavvs instead.

Finding and using OCTAVVS

The easiest way to access the OCTAVVS tools is through desktop shortcuts which may be created by running the oct_make_icons script from the command prompt. This works on Windows and Linux but has been known to fail on some Mac OS X versions (icons may look broken, clicking on them may do nothing).

In any case, the three scripts oct_preprocessing, oct_mcr_als and oct_clustering should be possible to run straight from the command line.

The location of the OCTAVVS scripts will depend on your operating system and where you installed Conda / Python. Within the Conda directory, the files will be located in lib/python3.7/site-packages/octavvs but the scripts mentioned above will be in bin.

Test data

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

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

Bug reports and code repository

Questions, bug reports and other feedback may be sent to corresponding author Carl Troein carl@thep.lu.se.

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

Linux path problem

On some Linux distributions, notably OpenSUSE, allowing Conda to modify your $PATH will cause problems with KDE when logging in. If this applies to you, a suggested workaround is to change the path manually when needed. An alias in .bashrc can be convenient: alias startconda='export PATH=~/miniconda3/bin:"$PATH"'

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