Project GOTECH: Predicting Coral Presence Using LIDAR and Open-Source Coral Data

Contributors: Josh Mattingly, Tina Guo, Dan Schauder

Dependencies

• Linux (Preferably Ubuntu 20.04)
• Anaconda or Miniconda (Available here: https://docs.conda.io/en/latest/miniconda.html#linux-installers)
• Admin/su privileges

Installation

• Download and unzip repo
• Navigate to project root in a command prompt
• Run the following command to create a conda environment with required packages/dependencies

conda env create -f environment.yml

• Activate the conda environment with the following command

conda activate GOTECH_env

Verbose Flag

Include the following flag for detailed output to be printed to the console

python main.py --verbose

Database installation

With the conda environment active, navigate to the project root and run the following command:

python main.py --setup_db

This will instantiate a postgresql database and activate the postgis extensions

Database Commands

Run the following command to start the database instance

python main.py --start_db

Run the following command to stop the database instance

python main.py --stop_db

Run the following command to create spatial indexes in the postgis database (dramatically improves performance)

python main.py --create_indexes

Extractors

With the database instance running, run the following command to download Allen Coral Atlas benthic data and ingest it into the db

python main.py --get_aca_benthic

With the database instance running, run the following command to download Allen Coral Atlas geomorphic data and ingest it into the db

python main.py --get_aca_geomorphic

With the database instance running, run the following command to download CALIPSO data and ingest it into the db

python main.py --get_calipso

The default bounding box for all extractors includes the Florida region. To set a different bounding box, use the full set of flags to specify the corners of a custom bounding box, like so:

python main.py --get_calipso --latitude_min -82.0 --latitude_max -80.0 --longitude_min 24.001 --longitude_max 26.22

Transformers

With the database instance running, run the following command to perform transformations to prepare benthic data to be merged with ACA data

python main.py --transform_aca_benthic

With the database instance running, run the following command to merge data into a unified table

python main.py --merge

Models

To train and test classification models and view the results, run the following command

python main.py --run_models