Metadata-Version: 2.4
Name: aquamatch
Version: 0.1.4
Summary: Python package and script to validate, model water quality parameters with remote sensing data
License: MIT
Keywords: remote sensing,water quality,sentinel-2,acolite
Author: Felipe Sodré
Author-email: felipe.b4rros@gmail.com
Requires-Python: >=3.12,<4.0
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: GIS
Requires-Dist: boto3 (>=1.40.42,<2.0.0)
Requires-Dist: dask (>=2026.3.0,<2027.0.0)
Requires-Dist: geopandas (>=1.1.1,<2.0.0)
Requires-Dist: matplotlib (>=3.10.9,<4.0.0)
Requires-Dist: mgrs (>=1.5.4,<2.0.0)
Requires-Dist: netcdf4 (>=1.7.4,<2.0.0)
Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
Requires-Dist: pandas (>=2.3.3,<3.0.0)
Requires-Dist: pystac-client (>=0.9.0,<0.10.0)
Requires-Dist: python-dotenv (>=1.2.2,<2.0.0)
Requires-Dist: rasterio (>=1.4.3,<2.0.0)
Requires-Dist: requests (>=2.32.5,<3.0.0)
Requires-Dist: rioxarray (>=0.22.0,<0.23.0)
Requires-Dist: sentinelhub (>=3.11.2,<4.0.0)
Requires-Dist: shapely (>=2.1.2,<3.0.0)
Requires-Dist: xarray (>=2024.1.0)
Requires-Dist: zarr (>=3.2.1,<4.0.0)
Project-URL: Homepage, https://github.com/FelipeSBarros/aquamatch
Project-URL: Repository, https://github.com/FelipeSBarros/aquamatch
Description-Content-Type: text/markdown

# Aquamatch

Bridging the gap between satellite observations and field data for water quality monitoring.

Aquamatch is a Python package for discovering and downloading Sentinel-2 imagery based on field sampling events, applies atmospheric correction and extracts water quality parameters via ACOLITE, and exports to multiple formats, including data cube and Cloud Optimized GeoTIFF.
Designed for reproducible, automated environmental monitoring workflows — from a single Python call, CLI command, or YAML config.

## Overview

![](./Workflow.png)

**Color coding**: teal for the five pipeline steps, gray/neutral for data artifacts (CSVs, SAFE folders, outputs), amber for the YAML orchestration layer, and purple for the SCL/datacube components.  
**Dashed arrows**: used for two relationships that are optional or indirect: the SCL polygon clip path (only when use_scl=True), and the Step 5 orchestration edges back to Steps 1–4 (since the YAML config drives the others rather than receiving data from them).

---

## Installation

**Requirements:** Python ≥ 3.12

Clone the repository and install dependencies with [Poetry](https://python-poetry.org/):

```bash
git clone https://github.com/FelipeSBarros/aquamatch.git
cd aquamatch
poetry install
```

Or with pip (using the lock file for reproducibility):

```bash
pip install .
```

> `pyyaml` is required for the pipeline config system. It is included in the project dependencies.

---

## Environment Setup

Create a `.env` file in the project root with your API credentials before running any step:  
* `SH` for SentinelHub (see [documentation](https://sentinelhub-py.readthedocs.io/en/latest/configure.html))  
* `DATASPACE` for Copernicus Dataspace (see [documentation](https://documentation.dataspace.copernicus.eu/APIs/S3.html#example-script-to-download-product-using-boto3))   

```env
SH_CLIENT_ID=your_sentinelhub_client_id    # SentinelHub
SH_CLIENT_SECRET=your_sentinelhub_client_secret    # SentinelHub
DATASPACE_ACCESS_KEY=your_copernicus_dataspace_access_key
DATASPACE_SECRET_KEY=your_copernicus_dataspace_secret_key
```

---

### Passing credentials explicitly (e.g. Colab, shared notebooks)

The `.env` file above works well for a persistent local project, but some  environments — Google Colab, CI jobs, notebooks shared between people —  don't have a persistent `.env` file, or need different credentials per run. 
For these cases, credentials can be passed explicitly instead of (or alongside) environment variables.

#### `SentinelCredentials`

```python
from aquamatch.credentials import SentinelCredentials

creds = SentinelCredentials(
    sh_client_id="...",
    sh_client_secret="...",
    dataspace_access_key="...",
    dataspace_secret_key="...",
)
```

Any field left unset defaults to `None`. `SentinelCredentials.from_env()` builds the same object by reading `SH_CLIENT_ID`, `SH_CLIENT_SECRET`, `DATASPACE_ACCESS_KEY`, `DATASPACE_SECRET_KEY` from the environment — this is what happens automatically whenever no explicit credentials are given anywhere in the call chain.

#### Passing credentials to the full pipeline

`run_sentinel_pipeline()` accepts `credentials` as either a `SentinelCredentials` instance or a plain dict:

```python
from aquamatch import run_sentinel_pipeline

run_sentinel_pipeline(
    mode="all",
    credentials={
        "sh_client_id": "...",
        "sh_client_secret": "...",
        "dataspace_access_key": "...",
        "dataspace_secret_key": "...",
    },
)
```

When `credentials` is passed, it's used to build a fresh SentinelHub catalog client, EarthSearch STAC client, and S3 resource for that call — bypassing whatever `.env`/module-level defaults would otherwise apply.
When omitted (the default, `None`), behaviour is unchanged: the module-level clients built once at import time (from `.env`, if present) are used, exactly as before this feature existed.

#### Lower-level functions

The same `credentials` parameter is available on the individual building blocks, for finer control:

```python
from aquamatch.sentinel_data import build_catalog, run_download
from aquamatch.credentials import SentinelCredentials

creds = SentinelCredentials(
    sh_client_id="...",
    sh_client_secret="...",
    dataspace_access_key="...",
    dataspace_secret_key="...",
)

build_catalog(csv_file="...", output_json="...", credentials=creds)
run_download(catalog_json="...", output_dir="...", credentials=creds)
```

`run_download()` also accepts a plain boto3 `s3` resource directly (`run_download(..., s3=my_s3_resource)`), which takes precedence over `credentials` if both are given — useful if you already have an authenticated S3 session managed elsewhere (e.g. an IAM role in a managed notebook environment).

> **Note:** `run_download()` only needs S3 access, so passing
> `credentials` there builds *just* the S3 resource — it never opens a
> connection to the SentinelHub or EarthSearch catalogs. This means
> `run_download(..., credentials=...)` works even in network-restricted
> environments where only the Copernicus Dataspace S3 endpoint is
> reachable.

#### CLI

The same overrides are available from the command line:

```bash
python aquamatch/sentinel_data.py --mode all \
  --sh-client-id "..." \
  --sh-client-secret "..." \
  --dataspace-access-key "..." \
  --dataspace-secret-key "..."
```

Any of the four flags can be given individually — unset ones fall back to `.env`/environment variables rather than being blanked out. So overriding just `--sh-client-id` on the command line while keeping the Dataspace keys in `.env` works as expected.

#### Precedence summary

From highest to lowest priority:

1. An explicit client object passed directly (`s3=...` on `run_download()`, or `catalog=...`/`client=...` on lower-level search functions).
2. `credentials` passed explicitly — as a `SentinelCredentials` instance, a plain dict, or CLI flags (partial CLI flags merge with `.env` for any field not overridden).
3. Environment variables via `.env` — the original, still-default behaviour.

## Step-by-step Workflow

### Step 1 — Prepare in situ data

This package was developed to work with in-situ data from the [OAN](https://www.ambiente.gub.uy/iSIA_OAN/). 
You are therefore expected to save your campaign and station datasets in the './data/original_data' folder.
This step involves reading field campaign data, cleaning measurement values and, if specified, assigning each station its Sentinel-2 tile. Two outputs are produced:

- `campaigns_organized.csv` — full cleaned dataset for analysis
- `campaigns_unique_data.csv` — one row per unique (date, tile) pair, used to drive the satellite search

```python
from aquamatch import run_insitu_pipeline

run_insitu_pipeline(
    stations="data/original_data/my_stations.xlsx",
    campaigns="data/original_data/my_export.xlsx",
)
```

> Pass skip_clean=True if the OAN export was already cleaned before download. [See OAN's documention](https://www.ambiente.gub.uy/iSIA_OAN/guia.html)

**CLI equivalent:**
```bash
python aquamatch/insitu_data.py --mode campaigns \
  --stations your_path/my_stations.xlsx \
  --campaigns your_path/my_export.xlsx
```

---

### Step 2 — Build the satellite catalog

Searches for Sentinel-2 L1C scenes that match each field date and location from `campaigns_unique_data.csv`. Only scenes whose MGRS tile matches the station's assigned tile are kept. For each L1C scene, the corresponding L2A scene is looked up to retrieve the SCL (Scene Classification) asset URL.

```python
from aquamatch import run_sentinel_pipeline

run_sentinel_pipeline(
    csv="data/monitoring_data/campaigns_unique_data.csv",
    time_delta=2,
    cloud_cover=20,
    mode="catalog"
)
```

The result is a `sentinel_catalog.json` file listing matched scenes per field date. Scenes are grouped into three temporal buckets relative to the field date — `same_day`, `previous` (acquired before), and `posterior` (acquired after) — each sorted by `delta_days` then `cloud_cover` ascending so the best candidate is always `bucket[0]`:

```json
[
  {
    "field_date": "2025-11-05",
    "images_found": {
      "same_day": [],
      "previous": [
        {
          "id": "S2B_MSIL1C_20251103T134659_N0511_R024_T21HVD_20251103T170338.SAFE",
          "datetime": "2025-11-03T14:01:38.729Z",
          "cloud_cover": 0.0,
          "href": "s3://eodata/Sentinel-2/MSI/L1C/2025/11/03/S2B_MSIL1C_20251103T134659_N0511_R024_T21HVD_20251103T170338.SAFE/",
          "delta_days": 2,
          "l2a_scl": "https://sentinel-cogs.s3.us-west-2.amazonaws.com/sentinel-s2-l2a-cogs/21/H/VD/2025/11/S2B_21HVD_20251103_0_L2A/SCL.tif"
        }
      ],
      "posterior": []
    }
  }
]
```

**CLI equivalent:**

```bash
python aquamatch/sentinel_data.py --mode catalog \
  --csv data/monitoring_data/campaigns_unique_data.csv \
  --time-delta 2 \
  --cloud-cover 20
```

---

### Step 3 — Download imagery

Download the SAFE products and SCL assets listed in the catalogue. Any scenes that have already been downloaded are skipped automatically.

The `strategy` parameter controls which scenes are downloaded per field date:

| Strategy | Behaviour |
|----------|-----------|
| `best` (default) | Prefer `same_day`, fall back to `previous`, then `posterior`. Picks up to `max_per_date` scenes. |
| `same_day` | Only download scenes acquired on the exact field date. |
| `previous` | Prefer `same_day`, fall back to `previous` only. Never uses `posterior`. |
| `posterior` | Prefer `same_day`, fall back to `posterior` only. Never uses `previous`. |
| `all` | Download every scene found across all buckets. |

```python
from aquamatch import run_sentinel_pipeline

# Download best matching scene per date (default)
run_sentinel_pipeline(
    strategy="best",
    max_per_date=1,
    download_scl=True,
    mode="download",
)

# Download only same-day scenes, up to 2 per date, cloud cover ≤ 15 %
run_sentinel_pipeline(
    strategy="same_day",
    max_per_date=2,
    max_cloud_cover=15,
    download_scl=True,
    mode="download",
)

# Download everything found
run_sentinel_pipeline(strategy="all", mode="download")
```

> Steps 2 and 3 can also be run together by passing `mode="all"`.

**CLI equivalent:**

```bash
python aquamatch/sentinel_data.py --mode download \
  --strategy best \
  --max-per-date 1 \
  --download-scl
```

---

### Step 4 — Atmospheric correction

Runs [ACOLITE](https://github.com/acolite/acolite) on the downloaded SAFE folders to produce surface reflectance and water quality products (turbidity, SPM, chlorophyll-a, and others) as NetCDF files.

```python
from aquamatch import run_acolite_pipeline

run_acolite_pipeline(
    acolite_executable="/path/to/acolite",
    safe_dir="data/sentinel_downloads/S2A_MSIL1C_20170713T135111_N0500_R024_T21HUD.SAFE",
    output="data/acolite_output",
    limit = [-33.25, -58.45, -33.17, -58.33])
```

A GeoJson's path can also be passed:

```python
run_acolite_pipeline(
    acolite_executable="/path/to/acolite",
    polygon = "/path/polygon.json")
```

For SCL-based water masking, use `with_scl_polygon()` to restrict processing to water pixels only:

```python
run_acolite_pipeline(
    acolite_executable="/path/to/acolite",
    use_scl=True,
    scl_dir="data/sentinel_downloads/scl",
    scl_kwargs={"min_area_m2": 5000},
)
```

To also aggregate the per-scene water masks into a single water polygon GeoPackage datacube after processing — the same output produced by `build_polygon_datacube: true` in the YAML pipeline (see below) — pass `build_polygon_datacube=True`:

```python
result = run_acolite_pipeline(
    acolite_executable="/path/to/acolite",
    safe_dir="data/sentinel_downloads",
    output="data/acolite_output",
    use_scl=True,
    scl_dir="data/sentinel_downloads/scl",
    build_polygon_datacube=True,
    polygon_datacube_path="data/water_polygons.gpkg",
)

result["outputs"]["polygon_datacube"]
# {"status": "ok", "output_path": "data/water_polygons.gpkg", "n_records": 3}
```

`polygon_datacube_path` defaults to `data/water_polygons.gpkg` and `polygon_datacube_overwrite` defaults to `False` (append/skip-duplicates) when omitted — matching `SclSection`'s defaults in the YAML config. The `min_area_m2`/`simplify_tolerance`/`buffer_m` values passed via `scl_kwargs` are reused for the datacube build as well, so there's no separate parameter surface to configure twice.

For batch processing across multiple scenes with per-tile spatial restrictions:

```python
from aquamatch import run_acolite_pipeline
from aquamatch.pipeline_config import TilesSection

# Per-tile restrictions (different polygon or limit per MGRS tile)
tiles = TilesSection.from_dict({
    "21HUD": {"polygon": "data/polygons/21HUD.geojson"},
    "21HVD": {"limit": [-34.2, -56.8, -33.0, -55.1]},
})

result = run_acolite_pipeline(
    acolite_executable="/path/to/acolite",
    safe_dir="data/sentinel_downloads",
    output="data/acolite_output",
    tile_config=tiles,
)
```

> If `tile_config` is omitted, a 0.1° bounding box is derived automatically from `row["latitud"]`/`row["longitud"]`.

**CLI equivalent:**

```bash
python -m aquamatch.acolite_spec \
    --executable /path/to/acolite \
    --safe-dir data/sentinel_downloads/S2A_MSIL1C_20170713T135111_N0500_R024_T21HUD.SAFE \
    --output data/acolite_output
```

> To run acolite with `limit` or `polygon` parameters, used YAML config. [see "Run the full pipeline from a YAML config"](#Run-the-full-pipeline-from-a-YAML-config)

---

## Run the full pipeline from a YAML config

For automated or version-controlled campaigns, the entire workflow can be driven from a single YAML file rather than calling each step individually. This is the recommended approach for production runs and shared projects.

### Generate a template with all parameters at their defaults:

```bash
python -m aquamatch.pipeline_config --generate campaign_2025.yaml
```

### Running from YAML

The generated file includes every parameter at its default value, with inline comments documenting units and valid options. Edit it for your campaign, then run:

```bash
python -m aquamatch.pipeline_config --run campaign_2025.yaml
```

Individual steps can be disabled by setting `enabled: false`:

```yaml
insitu:
  enabled: false   # skip — already prepared

sentinel:
  enabled: true
  time_delta: 2
  cloud_cover: 20

download:
  enabled: true
  # Download selection strategy. One of: best | same_day | previous | posterior | all
  # best: prefer same_day, fall back to previous then posterior (default)
  strategy: best
  # Maximum scenes to download per field date (ignored for strategy: all)
  max_per_date: 1
  # Optional secondary cloud cover ceiling applied at download time
  max_cloud_cover: null
  download_scl: true

acolite:
  enabled: true
  acolite_executable: /path/to/acolite/acolite.py
  scl:
    use_scl: true
    min_area_m2: 5000

tiles:
  21HUD:
    polygon: data/polygons/21HUD.geojson
  21HVD:
    limit: [-34.2, -56.8, -33.0, -55.1]
```

### Dry-run 

Validate config and log steps without executing:

```bash
python -m aquamatch.pipeline_config --run campaign_2025.yaml --dry-run
```

### Force process

Force reprocess — ignore existing outputs and reprocess all scenes:

```bash
python -m aquamatch.pipeline_config --run campaign_2025.yaml --force
```

### Per-tile spatial restrictions

The `tiles`: section assigns a spatial restriction to each Sentinel-2 MGRS tile. The same boundary is then applied consistently across every scene processed for that tile. Restrictions are resolved in this precedence order:

1. **Static polygon** from `tiles:` — highest priority. If a tile has a polygon configured, it is applied directly to ACOLITE and SCL-based clipping (`use_scl`) is suppressed for that tile, since the static polygon already defines the water boundary precisely.
2. **SCL-derived polygon** (`use_scl: true`) — used when the tile has no static polygon. A water mask is extracted from the SCL asset and applied as the processing boundary.
3. **Static limit** from `tiles:` — applied when no polygon is available from either source above.
4. **No restriction** — full scene is processed when the tile is not listed in `tiles:` and SCL clipping is disabled or unavailable.

```yaml
tiles:
  21HUD:
    polygon: data/polygons/21HUD.geojson   # hand-drawn or pre-processed boundary
  21HVD:
    limit: [-34.2, -56.8, -33.0, -55.1]   # bounding box [S, W, N, E]
  21HWD:
    # no entry — full scene processed
```

> The tile ID is extracted automatically from the SAFE folder filename (e.g. `T21HUD` in `S2A_MSIL1C_20250801T101031_N0500_R024_T21HUD_...SAFE`), so no manual mapping between files and tiles is needed.

> The same precedence logic applies when using run_batch() programmatically — see Step 4 above.

---

## Utilities

### Temporal opportunity cost analysis

Before committing to a temporal tolerance for your campaign, it is useful to understand how many field dates will have a valid Sentinel-2 acquisition available and what cloud cover to expect at each tolerance level. `analyze_temporal_opportunity` quantifies this directly from the catalog produced by Step 2.

For every tolerance `d` from 0 to `max_delta_days` the function:

1. Determines whether at least one image exists with `delta_days <= d` for each field date.
2. Computes **availability** (% of field dates with a valid image) and **opportunity cost** (`1 - availability`).
3. Selects the best image per date (minimum `delta_days`, then minimum `cloud_cover`) and reports mean and median cloud cover of the selected set.

A publication-quality three-panel PNG figure is saved to `output_figure`:

| Panel | Content |
|-------|---------|
| Left | Availability (%) vs temporal tolerance (days) |
| Centre | Opportunity cost (%) vs temporal tolerance (days) |
| Right | Mean and median cloud cover (%) vs temporal tolerance (days) |

```python
from aquamatch.utils import analyze_temporal_opportunity

df = analyze_temporal_opportunity(
    catalog_json="data/sentinel_downloads/sentinel_catalog.json",
    output_figure="reports/temporal_opportunity.png",
    max_delta_days=7,
)

print(df[["delta_days", "availability", "opportunity_cost", "mean_cloud_cover"]])
```

```
   delta_days  availability  opportunity_cost  mean_cloud_cover
0           0          42.9              57.1               3.2
1           1          71.4              28.6               4.8
2           2          85.7              14.3               5.1
3           3          92.9               7.1               6.3
4           4          92.9               7.1               6.3
5           5         100.0               0.0               7.0
6           6         100.0               0.0               7.0
7           7         100.0               0.0               7.0
```

The returned DataFrame contains one row per tolerance value with columns `delta_days`, `n_dates`, `n_available`, `availability`, `opportunity_cost`, `mean_cloud_cover`, and `median_cloud_cover`. Pass `return_dataframe=False` if only the figure is needed.

**What to consider when choosing a tolerance**
The table frames a trade-off between temporal fidelity and spatial coverage:

A strict same-day requirement (d=0) gives the most scientifically defensible matchups but leaves 57% of your field dates unmatched — a significant loss of usable data.
d=1 or d=2 is usually the pragmatic sweet spot for water quality remote sensing, where surface conditions can change meaningfully over days but same-day coverage is rare.
If your target variable changes slowly (e.g. long-term turbidity trends in a large reservoir), d=3 or d=5 may be acceptable and recovers nearly all dates.
If your variable is highly dynamic (e.g. algal bloom events, flood pulses), even d=1 may introduce unacceptable temporal mismatch and you should be cautious about any row beyond d=0.

The cloud cover column is a sanity check — if mean cloud cover were climbing sharply with tolerance (say, above 20–30%), it would signal that the additional scenes being recovered are systematically cloudy and may not produce usable retrievals even after atmospheric correction.
