Package: octavvs
OCTAVVS: Open Chemometrics Toolbox for Analysis and Visualization of Vibrational Spectroscopy dataOCTAVVS 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 two/three separate tools in the current version:preprocessingdeals with atmospheric correction, resonant Mie scattering
correction, baseline correction and normalization.decompositiondecomposes observed spectra into nonnegative concentrations and
spectra using the MCR-ALS algorithm, performs K-means clustering on the MCR-ALS
concentrations (or on the input data), and allows the user to manually annotate
clusters and export the annotated data.The decomposition tool supersedes two earlier tools:mcr_alsdecomposes observed spectra into nonnegative concentrations and
spectra using the MCR-ALS algorithm.clusteringperforms K-means clustering on the concentrations inferred by
MCR-ALS.Installation on Windows, Mac or LinuxOCCTAVS 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 later) version ofMiniconda.
There are some platform-specific differences during installation:OnWindows: The default options are good (no need to have Conda modify your path).After installation, start a Conda console (found in the Start menu).OnMac OS X: The default options are good. (Butifyou choose to not
let Conda modify your path, you can specify the full path to the commands
in the following steps.)After installation, start Terminal.OnLinux: Make the Miniconda .sh package executable and run it. When it asks about
running conda init, it wants to modify your$PATHin .bashrc. This can be fine, but on some
Linux distributions (notably OpenSUSE) it breaks KDE when logging in. A suggested workaround
is to change$PATHmanually when needed. An alias in .bashrc can be convenient:alias startconda='export PATH=~/miniconda3/bin:"$PATH"'From the console, install OCTAVVS and its dependencies:conda install -c ctroein octavvsFinding and using OCTAVVSThe easiest way to access the OCTAVVS tools is through desktop shortcuts
which are created by running theoct_make_iconsscript from the command prompt.
(We are not entirely sure if this works on all Mac OS X versions)Regardless of whether you created icons, the scriptsoct_preprocessingandoct_decompositioncan be run straight from the console (Conda console or terminal window, as described above).The location of the OCTAVVS scripts will depend on where you installed Conda.
Within the Conda directory, the three scripts will be inbinwhereas
the actual Python code will be located inlib/python3.7/site-packages/octavvs.Test dataTest data from two 64x64 images ofPaxillushyphae growing on lignin can bedownloaded here(zip archive, 47 MB).Upgrading to the latest versionInformation about the most recent release of OCTAVVS can be found on itsPyPI page, as well as on itsAnaconda Cloud page.To upgrade to the most recent version, doconda update -c ctroein octavvsin the Conda console / Terminal.Information about released versions can be foundhere.Bug reports and code repositoryThe main project homepage is itsGitHub page,
where developers can access the OCTAVVS code and submit bug reports and patches etc.Questions, bug reports and other feedback may be sent to corresponding author Carl Troeincarl@thep.lu.se.Installation through pipUsers familiar with Python could also install OCTAVVS through pip as an alternative to Anaconda,
as new releases will be made to PyPI in parallel with releases to Anaconda Cloud.
Note that pyqt and opencv sometimes don't work when installed through pip, depending on your system etc.