# EFAST fusion with phenocam validation.

End-to-end pipeline from selecting sites from the global [PhenoCam Network](https://phenocam.nau.edu/) to run [EFAST](https://github.com/DHI-GRAS/efast) spatio-temporal fusion with Sentinel-2 / Sentinel-3 and validate GCCs accross sensors. The five numbered steps cover site selection, Sentinel data acquisition, different fusion orders, and accuracy metrics, all feeding a static web QA viewer.

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## Pipeline overview

| Step | Script | What it does |
|------|--------|--------------|
| 1 | `1-phenocam.py` | Download PhenoCam metadata and `one_day_summary` GCC CSVs |
| 2 | `2-phenocam-screening.py` | Apply PhenoCam count, SNR, and proximity gates to select feasible sites |
| 3 | `3-sentinel-data.py` | Acquire S2 (Earth Search COG) and S3 OLCI SYN L2 (CDSE OpenEO); prepare REFL, DIST_CLOUD, and composite GeoTIFFs |
| 4 | `4-fusion.py` | Run EFAST BtI (fuse reflectance → GCC) and ItB (fuse GCC directly) for each screened site |
| 5 | `5-metrics.py` | Extract PhenoCam-matched timeseries, compute NSE/RMSE/r baselines and fusion metrics, emit per-site JSON and webapp manifest |

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## Quick start

```bash
uv sync
uv run python 1-phenocam.py --evaluation-year 2025
uv run python 2-phenocam-screening.py --evaluation-year 2025
uv run python 3-sentinel-data.py --evaluation-year 2025
uv run python 4-fusion.py --evaluation-year 2025
uv run python 5-metrics.py --evaluation-year 2025
```

All steps accept `--evaluation-year` (default `2025`) and `--site` (optional, for single-site runs). Steps 3–5 are resumable — existing output files are skipped.

```bash
# single site
uv run python 3-sentinel-data.py --evaluation-year 2025 --site ICOSFR-Fon1
uv run python 4-fusion.py --evaluation-year 2025 --site ICOSFR-Fon1
uv run python 5-metrics.py --evaluation-year 2025 --site ICOSFR-Fon1
```

### Credentials

Step 3 S3 download uses CDSE OpenEO (`SENTINEL3_SYN_L2_SYN`). Set `CDSE_USER` and `CDSE_PASSWORD` in `../.env` at the workspace root. S2 uses AWS Earth Search COG range reads (no auth required).

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## Outputs (under `data/`)

| Artifact | Step | Role |
|----------|------|------|
| `phenocam/{year}.json` | 1 | Site list + `sites_dir` pointer |
| `phenocam/{year}/{site}.json`, `{site}_1day.csv` | 1 | Raw API payload and GCC CSV |
| `phenocam_screening/{year}.json` / `.csv` | 2 | Gate results (pass/fail per site) |
| `sentinel_data/{year}/{site}/prepared/s2/` | 3 | S2 REFL + DIST_CLOUD GeoTIFFs |
| `sentinel_data/{year}/{site}/prepared/s3/` | 3 | S3 composite GeoTIFFs |
| `fusion/{year}/{site}/bti/`, `.../itb/` | 4 | BtI fused reflectance + GCC; ItB fused GCC |
| `metrics/{year}/{site}/` | 5 | Per-site timeseries, metrics, covariates JSON |
| `metrics/manifest.json` | 5 | Webapp manifest (years + site metadata) |

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## Web viewer



`python3 -m http.server 8080` runs the webapp on [http://localhost:8000/index.html](http://localhost:8000/index.html). Requires step 5 output (`data/metrics/manifest.json`).

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## License

[MIT](LICENSE)