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Updated README.

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Felix Delattre 2026-06-11 16:07:29 +02:00
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AGENTS.md
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@ -16,8 +16,6 @@ Worldwide PhenoCam EFAST feasibility screening. Human summary: [`README.md`](REA
| `data/` | Manifests, per-site caches, screening outputs (large; mostly generated) | | `data/` | Manifests, per-site caches, screening outputs (large; mostly generated) |
| `index.html`, `common.js` | Static QA viewer (`make serve` from workspace root) | | `index.html`, `common.js` | Static QA viewer (`make serve` from workspace root) |
Workspace orchestration: [`../AGENTS.md`](../AGENTS.md).
--- ---
## Where to work ## Where to work

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README.md
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# Worldwide PhenoCam EFAST screening and fusion # EFAST fusion with phenocam validation.
Screen the global [PhenoCam Network](https://phenocam.nau.edu/) for sites where EFAST Sentinel-2 / Sentinel-3 fusion is likely to work: enough PhenoCam `gcc_90`, seasonal signal, and S2/S3 coverage for a calendar year. End-to-end pipeline from the global [PhenoCam Network](https://phenocam.nau.edu/) to validated EFAST Sentinel-2 / Sentinel-3 fusion results. The five numbered steps cover site selection, Sentinel data acquisition, BtI/ItB fusion, and accuracy metrics, all feeding a static web QA viewer.
Agent-oriented detail: [`AGENTS.md`](AGENTS.md). ---
## 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 |
--- ---
## Quick start ## Quick start
From `processing/`:
```bash ```bash
uv sync uv sync
uv run python 1-phenocam.py --evaluation-year 2025 uv run python 1-phenocam.py --evaluation-year 2025
```
### Stepped pipeline (resumable)
All steps use `--evaluation-year` (default 2025) and optional `--site`. See each script docstring for inputs/outputs under `data/`.
```bash
uv run python 1-phenocam.py --evaluation-year 2025
uv run python 2-phenocam-screening.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 3-sentinel-data.py --evaluation-year 2025
uv run python 4-fusion.py --evaluation-year 2025 uv run python 4-fusion.py --evaluation-year 2025
uv run python 5-metrics.py --evaluation-year 2025 uv run python 5-metrics.py --evaluation-year 2025
# single site
uv run python 3-sentinel-data.py --evaluation-year 2025 --site innsbruck
uv run python 4-fusion.py --evaluation-year 2025 --site innsbruck
uv run python 5-metrics.py --evaluation-year 2025 --site innsbruck
``` ```
Step 3 S3 uses CDSE OpenEO (`SENTINEL3_SYN_L2_SYN`); S2 uses AWS Earth Search COG range reads (no auth). CDSE credentials live in `../.env` at the workspace root (`CDSE_USER`, `CDSE_PASSWORD`). 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).
--- ---
@ -41,20 +47,19 @@ Step 3 S3 uses CDSE OpenEO (`SENTINEL3_SYN_L2_SYN`); S2 uses AWS Earth Search CO
| Artifact | Step | Role | | Artifact | Step | Role |
|----------|------|------| |----------|------|------|
| `phenocam/{year}.json` | 1 | Site list + `sites_dir` pointer | | `phenocam/{year}.json` | 1 | Site list + `sites_dir` pointer |
| `phenocam/{year}/{site}.json`, `{site}_1day.csv` | 1 | Raw API + GCC CSV | | `phenocam/{year}/{site}.json`, `{site}_1day.csv` | 1 | Raw API payload and GCC CSV |
| `phenocam_screening/{year}.json` / `.csv` | 2 | PhenoCam + SNR gate results | | `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/s2/` | 3 | S2 REFL + DIST_CLOUD GeoTIFFs |
| `sentinel_data/{year}/{site}/prepared/s3/` | 3 | S3 composite GeoTIFFs | | `sentinel_data/{year}/{site}/prepared/s3/` | 3 | S3 composite GeoTIFFs |
| `fusion/{year}/{site}/` | 4 | BtI/ItB fused rasters | | `fusion/{year}/{site}/bti/`, `.../itb/` | 4 | BtI fused reflectance + GCC; ItB fused GCC |
| `metrics/{year}/{site}/`, `metrics/manifest.json` | 5 | Timeseries JSON, covariates, webapp manifest | | `metrics/{year}/{site}/` | 5 | Per-site timeseries, metrics, covariates JSON |
| `metrics/manifest.json` | 5 | Webapp manifest (years + site metadata) |
The 2025 manifest currently lists **739** cameras with archive overlap; most per-site CSV/JSON files are cached under `data/phenocam/2025/`.
--- ---
## Web viewer ## Web viewer
From the workspace root, `make serve` serves `processing/` at [http://localhost:8000/index.html](http://localhost:8000/index.html). Requires step 5 (`data/metrics/manifest.json`). `make serve` (from the workspace root) serves `processing/` at [http://localhost:8000/index.html](http://localhost:8000/index.html). Requires step 5 output (`data/metrics/manifest.json`).
--- ---