LI-6800

Copyright © 2019-2023 Luxembourg Institute of Science and Technology. All Rights Reserved.

The code in this repository is distributed under the terms of the GNU General Public License 3.0 or any later version, unless stated otherwise. All other material is licensed under a Creative Commons Attribution 4.0 International license, unless stated otherwise.

This repository contains python scripts to import data files from a LI-COR LI-6800, re-calculate fluxes and plot results. Associated Jupyter notebooks illustrate their use.

This is a renku project available at https://renkulab.io/projects/wave/li-6800, which can be run on renkulab.io or imported from its corresponding gitlab address https://renkulab.io/gitlab/wave/li-6800.

General purpose

This repository contains python scripts to import data files from a LI-COR LI-6800, re-calculate fluxes and plot results. Associated Jupyter notebooks illustrate their use.

This is a renku project available at https://renkulab.io/projects/wave/li-6800, which can be run on renkulab.io or imported from its corresponding gitlab address https://renkulab.io/gitlab/wave/li-6800. To import the scripts into another renku project, execute in the parent folder of your other project:

renku --no-external-storage dataset add --create modules_li_6800 \ --source 'modules/*' git@renkulab.io:wave/li-6800.git

This will save the modules foler in data/modules_li_6800.

See the file README.md for more information.

Repository structure

data: Example data files

notebooks: Jupyter notebooks with code and documentation, demonstrating derivations of equations and use of python scripts.

GC_Fluxes_Computations_equations.ipynb: This jupyter notebook defines variables and derives equations for calculating gas exchange rates from original data collected by a LI-COR Portable Photosynthesis System, the LI-6800.

read_plot.ipynb: This jupyter notebook tests and illustrates the importing and use of the equations and scripts in modules.

modules: Python files (.py) for importing elsewhere.

Mathematical_model_variable_definitions.py: Python module with variable definitions.

Mathematical_model_equations_definitions.py: Python module with equation definitions.

plotting.py: Python module with plotting functions.

read_plot.ipynb: Jupyter notebook with examples for data import, calculations and plotting.