MDF DALEC GRASS

Description

This is a python package that implements an ecosystem model of grassland carbon (C) biogeochemistry (DALEC-Grass). DALEC-Grass is integrated into a model-data fusion (MDF) framework. The MDF framework implements DALEC-Grass probabilistically using location-specific (1) weather time-series, (2) soil data and (3) earth observation (EO) time-series on vegetation leaf area, in order to (A) calibrate the model's parameters (B) validate model predictions and (C) estimate field-scale C cycling i.e. C in biomass, roots, soil, C lost to the atmosphere and C removed via grazing/cutting.

The package handles the sourcing and processing of all the necessary data as well as the implementation of the model's code. Its different functions allow the user to :

1. Collect earth observation (EO) data from the ESA Sentinel-1 (SAR) and Sentinel-2 (multispectral) systems
2. Process the EO data into weekly continuous time-series of grass Leaf Area Index (LAI)
3. Implement the MDF algorithm

Requirements

1. Python 3
2. A user account on the Alaska Satellite Facility archive centre
3. A user account on the European Centre for Medium-Range Weather Forecasts
4. A user account on Amazon Web Services
5. The Sentinel Application Platform should be installed on your system

Installation

To install either "git clone https://github.com/vmyrgiotis/MDF_DALEC_GRASS.git" and then run "python setup.py MDF_DALEC_GRASS/install" --OR-- "pip install git+https://github.com/vmyrgiotis/MDF_DALEC_GRASS.git"

Tutorial

To run the tutorial on a local machine :

1. install miniconda on the machine (if not installed) : https://docs.conda.io/en/latest/miniconda.html
2. create a conda environment by running : "conda create -n dalec_grass python=3.9.7"
3. activate the dalec_grass conda environment : "conda activate dalec_grass"
4. install some python packages : "pip install matplotlib jupyter pandas numpy spotpy netCDF4 wand itermplot salem convertbng geopandas motionless joblib xarray"
5. clone the github repo : "git clone https://github.com/vmyrgiotis/MDF_DALEC_GRASS.git"
6. navigate to the location of the github repo that you just cloned : "cd /MDF_DALEC_GRASS"
7. run "jupyter notebook" , your default browser starts , click on dalec_grass_tutorial.ipynb

To run the tutorial on a remote server:

1. open a 1st terminal tab and : "ssh username@remote.server.address"
2. complete steps 1 to 6 from the running-on-local-machine shown above
3. then : "jupyter notebook --no-browser --port=8008"
4. open a 2nd terminal tab and : "ssh -L 8008:localhost:8008 username@remote.server.address"
5. on the local machine open an internet browser and go to http://localhost:8008/

To clean up after running the tutorial

1. conda deactivate
2. conda env remove -n dalec_grass
3. rm -r MDF_DALEC_GRASS