Project: Topological Skeletonization Scripts
Last updated: 13 May 2025
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1. Purpose
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This repository contains two Jupyter notebooks that extract skeletons from EEMS contour outputs.


2. Repository contents
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| File/Folder                            | Type | Description                                        |
|----------------------------------------|------|----------------------------------------------------|
| `topo_ske_cam.ipynb`                   | code | Pipeline that generate topological skeletons for   |
|                                        |      | Cambodia dataset, and also convert the results to  |
|                                        |      | GeoTIFF/GeoJSON outputs.                           |
| `topo_ske3spots.ipynb`                 | code | Pipeline that generate topological skeletons for   |
|                                        |      | simulated dataset, and also convert the results to |
|                                        |      | GeoTIFF/GeoJSON outputs.                           |
| `sim_barrierhexagon_unrel_pfrecomrate/`| data | Folder for the simulated dataset.                  |



3. Computing environment
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The notebooks were developed and tested on the following stack:

| Component            | Version / Build                      |
|----------------------|--------------------------------------|
| Operating system     | macOS 10.15.7 (Catalina) × 64‑bit    |
| Python interpreter   | 3.9.13 (IPython kernel)              |
| JupyterLab/Notebook  | 4.1.*                                |
| Conda distribution   | Miniconda 23.11                      |

Required Python packages

| Package        | Minimum Version | Purpose                           |
|----------------|-----------------|-----------------------------------|
| numpy          | 1.24            | array manipulation                |
| rasterio       | 1.3             | raster I/O and affine transforms  |
| GDAL           | 3.7             | low‑level geospatial operations   |
| geopandas      | 0.14            | vector I/O and reprojection       |
| shapely        | 2.0             | geometry construction             |
| scikit‑image   | 0.23            | skeletonisation & filtering       |
| opencv‑python  | 4.9             | binary morphology & thresholding  |
| matplotlib     | 3.8             | diagnostic plots                  |
| Pillow         | 10.0            | ancillary image handling          |


4. License
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The code is released under the Creative Commons License.

5. Funding source and grant number
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The funding source is the National Science Foundation under Grant No. BCS2049805

6. Contact information
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PI: Kathleen Stewart
Email:stewartk@umd.edu
Developer: Yao Li
Email: yao.li@charlotte.edu