Data Story - Project Pythia Geomorphology Cookbook

Overview¶

This notebook explains the bathymetry datasets used in this cookbook and how they connect to the original Geoscience Australia’s Semi-automated Morphological Mapping Tools (GA-SaMMT) workflow. The goal is to make the data provenance, data transformations, and open-science scope clear before readers start running geomorphology methods.

In this notebook, we will:

Identify the original source of the GA-SaMMT sample data.
Explain why the cookbook uses GeoTIFF rasters instead of ArcGIS File Geodatabases.
Summarize the three bathymetry grids used throughout the examples.
Clarify what this cookbook does and does not attempt to reproduce.
Point readers to the notebooks that inspect, map, characterise, and classify features.

Prerequisites¶

What you should know	Why it matters here
Bathymetry rasters	The methods operate on gridded seabed elevation or depth surfaces.
Coordinate reference systems	Area, distance, and slope measurements require projected coordinates.
Basic Python/Jupyter	The cookbook is written as executable Jupyter notebooks.
GA-SaMMT concept	The notebooks translate an ArcGIS Pro tool workflow into open Python examples.

Source and purpose¶

The data used in this project come from the work presented in (Huang et al., 2023) Rule-based semi-automated tools for mapping seabed morphology from bathymetry data available at Huang et al. (2023).

The original GA-SaMMT package is built around ArcGIS Pro Python toolboxes and sample datasets stored in File Geodatabases. This cookbook keeps the scientific workflow and educational logic, but uses open Python libraries and GeoTIFF inputs so that the methods can be explored without requiring ArcGIS Pro.

Study area¶

Dataset	Why it is useful
`pc_bathy.tif`	Shows how small, dense seabed features respond to radius and area-threshold parameters.
`os_bathy.tif`	Provides a high-resolution shelf example where many raster-derivative methods can be compared.
`gifford_bathy.tif`	Demonstrates that mapping scale changes when the cell size and geomorphic setting change.

They were acquired during ship multibeam echosounder surveys, processed with CARIS HIPS/SIPS, and gridded to metre-scale raster surfaces. The original GA-SaMMT package stores its sample data in three File Geodatabases:

Gifford.gdb
Oceanic_Shoals.gdb
Points_Cloates.gdb

The project uses the GeoTIFF converted version:

gifford_bathy.tif
os_bathy.tif
pc_bathy.tif

Cookbook data	Area	Acquisition and processing summary	Grid resolution
`pc_bathy.tif`	Point Cloates Shelf, offshore Western Australia	Acquired in 2008 during survey SOL4769 using a Kongsberg EM3002 multibeam echosounder; processed with CARIS HIPS/SIPS v6.1	3 m
`os_bathy.tif`	Oceanic Shoals / Bonaparte Basin, Timor Sea	Collected in 2012 during survey GA0339/SOL5650 using a Kongsberg EM3002D multibeam echosounder; processed with CARIS HIPS/SIPS v7.1	2 m
`gifford_bathy.tif`	Gifford Seamounts, Gifford Marine Park, Tasman Sea	Compiled from two multibeam surveys: GA TAN0713 in 2007 using a Kongsberg EM300, and a GA/JAMSTEC survey in 2017 using a Kongsberg 12 kHz deep-water multibeam system; processed with CARIS HIPS/SIPS v7.1	50 m

The Gifford Seamounts grid represents a deeper-water setting than the shelf examples. The case study is centred around 26.79° S, 146.82° E, offshore eastern Australia, and covers water depths from approximately 250 m to 3,500 m. The area contains two seamounts, with ridges and valley-like bedforms on their flat tops and flanks.

Interactive map¶

An interactive folium map is used here to present the data’s geographical position. See the Metadata notebook.

from pathlib import Path
from html import escape
from IPython.display import HTML, display

# Path to the map file
map_path = Path("images/map.html")

if not map_path.exists():
    raise FileNotFoundError(f"Map file not found: {map_path}")

map_html = map_path.read_text(encoding="utf-8")

display(
    HTML(
        f"""
        <iframe
            srcdoc="{escape(map_html, quote=True)}"
            width="100%"
            height="400"
            style="border: none;"
        ></iframe>
        """
    )
)

Original tools and data samples...

The associated ArcGIS Pro tools and dataset samples are available here.

Full dataset with all datalinks...

Scope and limitations¶

This cookbook prioritizes open workflows. That means the first implementation should be judged by clarity, reproducibility, and scientific traceability before it is judged by speed or perfect ArcGIS reproduction.

References and data links¶

Huang, Z., Nanson, R., McNeil, M., Wenderlich, M., Gafeira, J., Post, A., and Nichol, S. (2023). Rule-based semi-automated tools for mapping seabed morphology from bathymetry data. Frontiers in Marine Science, 10, 1236788. Huang et al. (2023)
GA-SaMMT tools and sample data: Z. & Z. (2022)
Dove, D. et al. (2020). A two-part seabed geomorphology classification scheme; Part 1: morphology features glossary. Dove et al. (2020)

Summary¶

The cookbook uses three GeoTIFF bathymetry grids derived from the GA-SaMMT sample-data context. They give readers enough diversity to explore how seabed morphology tools behave across different resolutions and geomorphic settings, while keeping the workflow open and executable in Jupyter.

References¶

Huang, Z., Nanson, R., McNeil, M., Wenderlich, M., Gafeira, J., Post, A., & Nichol, S. (2023). Rule-based semi-automated tools for mapping seabed morphology from bathymetry data. Frontiers in Marine Science, 10. 10.3389/fmars.2023.1236788
Williams, A., Kloser, R., Bax, N., Siwabessy, J., Navidad, C., Taylor, C., & Plunkett, T. (2022). SS200611 Tasman Sea Bathymetry 16m - 64m resolution AusSeabed products. CSIRO. 10.25919/QAN1-QJ27
Z., H., & Z., H. (2022). Geoscience Australia’s Semi-automated Morphological Mapping Tools (GA-SaMMT) for Seabed Characterisation. Commonwealth of Australia (Geoscience Australia). 10.26186/146832
Dove, D., Nanson, R., Bjarnadóttir, L. R., Guinan, J., Gafeira, J., Post, A., Dolan, M. F. J., Stewart, H., Arosio, R., & Scott, G. (2020). A two-part seabed geomorphology classification scheme (v.2); Part 1: morphology features glossary [Techreport]. Zenodo. 10.5281/ZENODO.4075248