SHYFEM Antsiranana Bay Analysis (with xugrid/hvplot trimesh)

README.md

SHYFEM Antsiranana Bay Analysis

Overview

This notebook analyzes SHYFEM ocean model output for Antsiranana Bay, Madagascar (March 31 - April 5, 2021).

It uses xugrid and hvplot (from the OpenScienceComputing fork) for handling unstructured grid data from ocean models.

Installation

Option 1: Conda

conda create -n shyfem python=3.11 -y
conda activate shyfem
conda install -c conda-forge xugrid hvplot holoviews panel bokeh xarray netcdf4 pandas matplotlib

Option 2: Pip

python -m venv shyfem-env
source shyfem-env/bin/activate
pip install -r requirements.txt

Requirements

See requirements.txt for the full list. Key packages:

• xugrid - For handling unstructured UGRID data
• hvplot - Interactive plotting (with xugrid support)
• holoviews - Visualization library
• panel - For interactive dashboards
• xarray - For N-dimensional data arrays
• netcdf4 - For reading NetCDF files

Launch Notebook

jupyter notebook SHYFEM_Analysis.ipynb

Data

The notebook loads data from:

• surf.nos.nc - Raw SHYFEM output
• surf.ous.nc - Processed SHYFEM output

These are loaded directly from the public URL using xugrid.

Features

• Load unstructured grid data with xugrid
• Interactive temperature, salinity, and velocity plots
• Vector field visualization
• Time series analysis
• Summary statistics
• Export to HTML

Credits

Based on the FVCOM notebook by Rich Signell: https://gist.github.com/rsignell/2ee54d379b15be4b8a101c5dec68bd6d

Modified to use xugrid for SHYFEM data.

requirements.txt

SHYFEM_Analysis.ipynb