Overview

Toolbox for Biology-Informed data-assimilation to solve the inverse problem solution of pheromone propagation, i.e. to identify sources of pheromone emission, in particular insect pests. A specific focus is put on adding prior biological knowledge on insect behavior in the inference process.

The target audience is academic researchers interested in epidemiosurveillance for crops.

• Free software: GNU Lesser General Public License v3 or later (LGPLv3+)

Installation

To install the package:

pip install pherosensor

Alternatively, you can download the sources with:

git clone https://forgemia.inra.fr/pherosensor/pherosensor-toolbox.git

and install them with:

pip install .

You can also install the in-development version with:

pip install git+ssh://git@forgemia.inra.fr/pherosensor/pherosensor-toolbox.git@main

Example usage

A complete example of use can be found here or alternatively can be cloned with:

git clone https://forgemia.inra.fr/pherosensor/companion-code-bi-da.git

These examples are the companion codes of the publication found here.

Automated tests

To run all the tests, install tox with:

pip install tox

and run:

tox

Contributions

Issues or merge requests can be made in the gitlab repository here and here.

Documentation

Documentations are available at ReadTheDocs.

Building the docs

Alternatively, you can compile the documentation of the current code version.

Install sphinx and sphinx-rtd-theme with:

pip install sphinx sphinx-rtd-theme

Additionally install nbsphinx to render the tutorial notebooks:

pip install nbsphinx sphinx-gallery

Nbsphinx needs pandoc that can be installed with:

conda install -c conda-forge pandoc

Then, you can do:

cd docs

and:

make html

The documentations (in html) are then stored in the folder ‘build/html’

Citation

Please cite the paper Biology-Informed inverse problems for insect pests detection using pheromone sensors by T.Malou et al..