/above-ground-carbon-density-estimation

Primary LanguageJupyter Notebook

Above-Ground Carbon Density Estimation

Setup

  1. Using a non-cambridge account and signup for earth engine: https://signup.earthengine.google.com/
  2. Create a Google Earth Engine enabled Google Cloud Project
  3. Install the Earth Engine library pip install earthengine-api
  4. Authenticate yourself. Either the code itself will have ee.Authenticate() which will open a browser window to authenticate yourself. Or you can use the command line to authenticate yourself, using the gcloud CLI. See https://developers.google.com/earth-engine/guides/python_install-conda#authenticate
  5. Emukit appears to use concatenate with empty arrays which is no longer possible in current versions of numpy. To fix this, insert outputs = list(filter(lambda x: x.size > 0, outputs)) in emukit.core.loop.user_function.py:176 above outputs = np.concatenate(outputs, axis=0) outputs = np.concatenate(outputs, axis=0)

Running the code

Install the dependencies using pip install -r requirements.txt.

Run the default bayesian optimization with python src/main.py. This will run the function on default, small subset of data and save a visualization of the estimation vs the ground truth data. To use the local data, run the script from the home directory of the project. The data is stored in data/.

Tinker with the parameters in main.py, or you can modify the bayesian optimization procedure in bayes_opt.py.

Running the basic examples will look like: NDVI NDVI EVI EVI

Known Issues

Our current usage of GPy ends up throwing several warnings. When running NDVI, we get

 .../python3.8/site-packages/GPy/kern/src/rbf.py:52: RuntimeWarning:overflow encountered in square
 .../python3.8/site-packages/paramz/transformations.py:111: RuntimeWarning:overflow encountered in expm1

When running EVI, we get

 .../python3.8/site-packages/GPy/kern/src/stationary.py:168: RuntimeWarning:overflow encountered in divide
 .../python3.8/site-packages/GPy/kern/src/rbf.py:52: RuntimeWarning:overflow encountered in square
 .../python3.8/site-packages/GPy/kern/src/rbf.py:76: RuntimeWarning:invalid value encountered in multiply
 .../python3.8/site-packages/paramz/transformations.py:111: RuntimeWarning:overflow encountered in expm1