@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/domains/geoscience/pangaea-data-api/SKILL.md

@@ -0,0 +1,197 @@
+---
+name: pangaea-data-api
+description: "Access earth and environmental science datasets via PANGAEA API"
+metadata:
+  openclaw:
+    emoji: "🌍"
+    category: "domains"
+    subcategory: "geoscience"
+    keywords: ["PANGAEA", "earth science data", "oceanography", "paleoclimate", "environmental data", "geoscience repository"]
+    source: "https://www.pangaea.de/"
+---
+
+# PANGAEA Data Repository API
+
+## Overview
+
+PANGAEA is the world's leading data repository for earth and environmental sciences, hosting 400K+ datasets with 20B+ data points. It archives research data from oceanography, paleoclimatology, geology, ecology, and atmospheric science. Each dataset has a DOI and is linked to the originating publication. The API provides search, metadata retrieval, and data download. Free, no authentication required.
+
+## API Endpoints
+
+### Search API
+
+```bash
+# Search datasets by keyword
+curl "https://www.pangaea.de/advanced/search.php?q=ocean+temperature&count=20&type=json"
+
+# Search with geographic bounding box
+curl "https://www.pangaea.de/advanced/search.php?\
+q=sediment+core&minlat=-60&maxlat=-30&minlon=-180&maxlon=180&type=json"
+
+# Filter by parameter (measurement type)
+curl "https://www.pangaea.de/advanced/search.php?\
+q=carbon+dioxide&param=Atmospheric+CO2&type=json"
+
+# Filter by date range
+curl "https://www.pangaea.de/advanced/search.php?\
+q=Arctic+ice&mindate=2020-01-01&maxdate=2026-12-31&type=json"
+```
+
+### ElasticSearch API
+
+```bash
+# Full-text search via Elasticsearch
+curl -X POST "https://ws.pangaea.de/es/pangaea/panmd/_search" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "query": {
+      "bool": {
+        "must": [
+          {"match": {"citation.title": "ocean temperature"}}
+        ],
+        "filter": [
+          {"range": {"citation.year": {"gte": 2020}}}
+        ]
+      }
+    },
+    "size": 20
+  }'
+```
+
+### Dataset Access
+
+```bash
+# Get dataset metadata
+curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=metainfo_json"
+
+# Download dataset as tab-delimited text
+curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=textfile"
+
+# Download as CSV
+curl "https://doi.pangaea.de/10.1594/PANGAEA.123456?format=csv"
+```
+
+### OAI-PMH Harvesting
+
+```bash
+# List records
+curl "https://ws.pangaea.de/oai/provider?verb=ListRecords&metadataPrefix=oai_dc"
+
+# Get specific record
+curl "https://ws.pangaea.de/oai/provider?verb=GetRecord&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.123456&metadataPrefix=oai_dc"
+```
+
+### Query Parameters (Search API)
+
+| Parameter | Description | Example |
+|-----------|-------------|---------|
+| `q` | Search query | `q=coral+reef+bleaching` |
+| `count` | Results per page | `count=50` |
+| `offset` | Pagination offset | `offset=20` |
+| `minlat/maxlat` | Latitude bounds | `-90` to `90` |
+| `minlon/maxlon` | Longitude bounds | `-180` to `180` |
+| `mindate/maxdate` | Temporal filter | `2020-01-01` |
+| `param` | Parameter/measurement | `Temperature` |
+| `topic` | Topic filter | `Atmosphere`, `Biosphere` |
+| `type` | Response format | `json`, `xml` |
+
+## Python Usage
+
+```python
+import requests
+import pandas as pd
+from io import StringIO
+
+SEARCH_URL = "https://www.pangaea.de/advanced/search.php"
+ES_URL = "https://ws.pangaea.de/es/pangaea/panmd/_search"
+
+
+def search_pangaea(query: str, count: int = 20,
+                   bbox: dict = None) -> list:
+    """Search PANGAEA for earth science datasets."""
+    params = {"q": query, "count": count, "type": "json"}
+    if bbox:
+        params.update({
+            "minlat": bbox.get("south", -90),
+            "maxlat": bbox.get("north", 90),
+            "minlon": bbox.get("west", -180),
+            "maxlon": bbox.get("east", 180),
+        })
+
+    resp = requests.get(SEARCH_URL, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for item in data.get("results", []):
+        results.append({
+            "doi": item.get("URI", ""),
+            "title": item.get("citation", ""),
+            "year": item.get("year"),
+            "size": item.get("size"),
+            "parameters": item.get("params", []),
+            "score": item.get("score"),
+        })
+    return results
+
+
+def download_dataset(doi: str) -> pd.DataFrame:
+    """Download a PANGAEA dataset as a pandas DataFrame."""
+    url = f"https://doi.pangaea.de/{doi}?format=textfile"
+    resp = requests.get(url, timeout=60)
+    resp.raise_for_status()
+
+    lines = resp.text.split("\n")
+    header_end = next(
+        (i for i, line in enumerate(lines) if line.startswith("*/")),
+        -1,
+    )
+    data_text = "\n".join(lines[header_end + 1:])
+    return pd.read_csv(StringIO(data_text), sep="\t")
+
+
+def search_by_location(query: str, lat: float, lon: float,
+                       radius_deg: float = 5.0) -> list:
+    """Search datasets near a geographic location."""
+    bbox = {
+        "south": lat - radius_deg,
+        "north": lat + radius_deg,
+        "west": lon - radius_deg,
+        "east": lon + radius_deg,
+    }
+    return search_pangaea(query, bbox=bbox)
+
+
+# Example: find ocean temperature datasets
+datasets = search_pangaea("sea surface temperature", count=5)
+for ds in datasets:
+    print(f"[{ds['year']}] {ds['title'][:80]}...")
+    print(f"  DOI: {ds['doi']} | Size: {ds['size']}")
+
+# Example: download a specific dataset
+# df = download_dataset("10.1594/PANGAEA.123456")
+# print(df.head())
+
+# Example: find Arctic research data
+arctic = search_by_location("permafrost", lat=70, lon=25)
+for ds in arctic[:3]:
+    print(f"{ds['title'][:80]}...")
+```
+
+## Data Topics
+
+| Topic | Coverage |
+|-------|----------|
+| Oceans | Temperature, salinity, currents, chemistry |
+| Paleoclimate | Ice cores, sediment cores, tree rings |
+| Atmosphere | CO2, aerosols, weather observations |
+| Lithosphere | Geology, tectonics, geochemistry |
+| Biosphere | Biodiversity, ecology, marine biology |
+| Cryosphere | Sea ice, glaciers, permafrost |
+
+## References
+
+- [PANGAEA](https://www.pangaea.de/)
+- [PANGAEA API](https://wiki.pangaea.de/wiki/PANGAEA_API)
+- [PANGAEA Elasticsearch](https://wiki.pangaea.de/wiki/Elasticsearch_API)
+- Diepenbroek, M. et al. (2002). "PANGAEA — an information system for environmental sciences." *C&G* 28(10).

package/skills/domains/geoscience/satellite-remote-sensing/SKILL.md

@@ -0,0 +1,193 @@
+---
+name: satellite-remote-sensing
+description: "Satellite imagery analysis and remote sensing for earth science research"
+metadata:
+  openclaw:
+    emoji: "satellite"
+    category: "domains"
+    subcategory: "geoscience"
+    keywords: ["remote-sensing", "satellite", "geospatial", "landsat", "sentinel", "gis", "earth-observation"]
+    source: "wentor"
+---
+
+# Satellite Remote Sensing
+
+A skill for processing and analyzing satellite imagery for earth science research. Covers data acquisition from major satellite platforms, preprocessing workflows, spectral index computation, land cover classification, and change detection using Python geospatial tools.
+
+## Satellite Data Sources
+
+### Major Earth Observation Missions
+
+| Mission | Operator | Resolution | Revisit | Key Bands | Access |
+|---------|----------|-----------|---------|-----------|--------|
+| Landsat 8/9 | USGS/NASA | 30m (MS), 15m (pan) | 16 days | 11 bands, OLI+TIRS | Free (USGS EarthExplorer) |
+| Sentinel-2 | ESA | 10m-60m | 5 days | 13 bands, MSI | Free (Copernicus Open Access Hub) |
+| MODIS | NASA | 250m-1km | 1-2 days | 36 bands | Free (NASA LAADS DAAC) |
+| Sentinel-1 | ESA | 5-20m | 6 days | C-band SAR | Free (Copernicus) |
+| GOES-16/17 | NOAA | 0.5-2km | 5-15 min | 16 bands, ABI | Free (NOAA CLASS) |
+
+### Programmatic Data Access
+
+```python
+import planetary_computer
+import pystac_client
+import rioxarray
+
+# Search Sentinel-2 imagery via Microsoft Planetary Computer
+catalog = pystac_client.Client.open(
+    "https://planetarycomputer.microsoft.com/api/stac/v1",
+    modifier=planetary_computer.sign_inplace,
+)
+
+# Search for cloud-free imagery over a region
+search = catalog.search(
+    collections=["sentinel-2-l2a"],
+    bbox=[11.0, 46.0, 12.0, 47.0],  # Tyrol, Austria
+    datetime="2025-06-01/2025-08-31",
+    query={"eo:cloud_cover": {"lt": 10}},
+)
+
+items = search.item_collection()
+print(f"Found {len(items)} scenes with <10% cloud cover")
+
+# Load a specific band as xarray DataArray
+item = items[0]
+red = rioxarray.open_rasterio(item.assets["B04"].href)
+nir = rioxarray.open_rasterio(item.assets["B08"].href)
+```
+
+## Preprocessing Pipeline
+
+### Atmospheric Correction
+
+Raw satellite data (Level-1) must be atmospherically corrected to obtain surface reflectance (Level-2):
+
+- **Sentinel-2**: Use Sen2Cor processor (ESA) or download pre-processed L2A products
+- **Landsat**: Collection 2 Level-2 products include surface reflectance
+- **Custom correction**: Use 6S radiative transfer model via Py6S
+
+```python
+# Cloud masking for Sentinel-2 using the SCL band
+import numpy as np
+
+def mask_clouds_sentinel2(scl_band: np.ndarray) -> np.ndarray:
+    """
+    Create cloud mask from Sentinel-2 Scene Classification Layer.
+    SCL values: 0=no_data, 1=saturated, 2=dark_area, 3=cloud_shadow,
+    4=vegetation, 5=bare_soil, 6=water, 7=unclassified,
+    8=cloud_medium, 9=cloud_high, 10=cirrus, 11=snow
+    """
+    cloud_classes = {0, 1, 3, 8, 9, 10}
+    mask = np.isin(scl_band, list(cloud_classes))
+    return mask  # True where clouds/invalid
+```
+
+### Geometric Correction and Mosaicking
+
+```python
+import rasterio
+from rasterio.merge import merge
+from rasterio.warp import calculate_default_transform, reproject, Resampling
+
+def reproject_raster(src_path: str, dst_path: str, dst_crs: str = "EPSG:4326"):
+    """Reproject a raster to a target coordinate reference system."""
+    with rasterio.open(src_path) as src:
+        transform, width, height = calculate_default_transform(
+            src.crs, dst_crs, src.width, src.height, *src.bounds
+        )
+        kwargs = src.meta.copy()
+        kwargs.update({
+            "crs": dst_crs,
+            "transform": transform,
+            "width": width,
+            "height": height,
+        })
+        with rasterio.open(dst_path, "w", **kwargs) as dst:
+            for i in range(1, src.count + 1):
+                reproject(
+                    source=rasterio.band(src, i),
+                    destination=rasterio.band(dst, i),
+                    src_transform=src.transform,
+                    src_crs=src.crs,
+                    dst_transform=transform,
+                    dst_crs=dst_crs,
+                    resampling=Resampling.bilinear,
+                )
+```
+
+## Spectral Indices
+
+### Vegetation and Water Indices
+
+```python
+def compute_indices(red: np.ndarray, nir: np.ndarray,
+                    green: np.ndarray, swir: np.ndarray) -> dict:
+    """
+    Compute common spectral indices from surface reflectance bands.
+    All inputs should be float arrays with values in [0, 1].
+    """
+    eps = 1e-10  # avoid division by zero
+    ndvi = (nir - red) / (nir + red + eps)
+    ndwi = (green - nir) / (green + nir + eps)
+    nbr = (nir - swir) / (nir + swir + eps)
+    evi = 2.5 * (nir - red) / (nir + 6 * red - 7.5 * 0.0001 + 1 + eps)
+    savi = 1.5 * (nir - red) / (nir + red + 0.5 + eps)
+
+    return {
+        "NDVI": ndvi,   # vegetation vigor [-1, 1]
+        "NDWI": ndwi,   # water bodies [-1, 1]
+        "NBR": nbr,     # burn severity [-1, 1]
+        "EVI": evi,     # enhanced vegetation
+        "SAVI": savi,   # soil-adjusted vegetation
+    }
+```
+
+### Index Interpretation
+
+| Index | Range | Low Values | High Values |
+|-------|-------|-----------|-------------|
+| NDVI | -1 to 1 | Water, bare soil, clouds | Dense green vegetation |
+| NDWI | -1 to 1 | Dry land | Open water bodies |
+| NBR | -1 to 1 | Recently burned areas | Healthy vegetation |
+| EVI | -1 to 1 | Non-vegetated | Dense canopy (less saturated than NDVI) |
+
+## Land Cover Classification
+
+### Supervised Classification with Random Forest
+
+```python
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.model_selection import cross_val_score
+
+# Stack bands into feature array: (n_pixels, n_bands)
+# training_labels: land cover classes from ground truth polygons
+bands = np.stack([blue, green, red, nir, swir1, swir2, ndvi, ndwi], axis=-1)
+n_rows, n_cols, n_bands = bands.shape
+X = bands.reshape(-1, n_bands)
+
+# Train Random Forest classifier
+rf = RandomForestClassifier(n_estimators=200, max_depth=20, n_jobs=-1)
+scores = cross_val_score(rf, X_train, y_train, cv=5, scoring="f1_macro")
+print(f"5-fold F1: {scores.mean():.3f} +/- {scores.std():.3f}")
+
+rf.fit(X_train, y_train)
+classification = rf.predict(X).reshape(n_rows, n_cols)
+```
+
+## Change Detection
+
+Multi-temporal analysis for detecting land cover changes (deforestation, urbanization, flood extent):
+
+1. **Image differencing**: Subtract spectral index values between dates
+2. **Post-classification comparison**: Classify each date independently, compare maps
+3. **Change vector analysis**: Compute magnitude and direction of spectral change
+4. **Time series analysis**: BFAST, LandTrendr for continuous monitoring
+
+## Tools and Libraries
+
+- **Rasterio / GDAL**: Raster I/O and geospatial transformations
+- **xarray + rioxarray**: Labeled multi-dimensional array analysis
+- **Google Earth Engine (GEE)**: Cloud-based planetary-scale analysis
+- **QGIS**: Open-source GIS for visualization and manual digitization
+- **Orfeo ToolBox (OTB)**: Advanced remote sensing processing chain
+- **SentinelHub**: Commercial API for on-the-fly Sentinel processing

package/skills/domains/geoscience/seismology-data-guide/SKILL.md

@@ -0,0 +1,208 @@
+---
+name: seismology-data-guide
+description: "Earthquake data analysis, seismogram processing, and seismic research"
+metadata:
+  openclaw:
+    emoji: "globe-showing-asia-australia"
+    category: "domains"
+    subcategory: "geoscience"
+    keywords: ["seismology", "earthquake", "seismogram", "obspy", "waveform", "geophysics"]
+    source: "wentor"
+---
+
+# Seismology Data Guide
+
+A skill for processing seismic data, analyzing earthquake catalogs, and working with seismograms using standard tools in observational seismology. Covers data retrieval from global networks, waveform processing with ObsPy, magnitude estimation, focal mechanism analysis, and seismic hazard assessment.
+
+## Seismic Data Sources
+
+### Global Data Centers
+
+| Data Center | Abbreviation | Coverage | Access |
+|-------------|-------------|----------|--------|
+| IRIS Data Management Center | IRIS DMC | Global broadband | FDSN Web Services |
+| European Integrated Data Archive | EIDA | European networks | FDSN Web Services |
+| USGS Earthquake Hazards Program | USGS EHP | Global catalog | API + ComCat |
+| International Seismological Centre | ISC | Global bulletin | ISC web services |
+| NIED F-net | F-net | Japan broadband | NIED website |
+
+### Retrieving Earthquake Catalogs
+
+```python
+from obspy.clients.fdsn import Client
+from obspy import UTCDateTime
+
+client = Client("IRIS")
+
+# Fetch earthquake catalog for a region and time window
+catalog = client.get_events(
+    starttime=UTCDateTime("2024-01-01"),
+    endtime=UTCDateTime("2024-12-31"),
+    minmagnitude=5.0,
+    maxmagnitude=9.0,
+    minlatitude=30.0, maxlatitude=45.0,
+    minlongitude=125.0, maxlongitude=150.0,
+    orderby="magnitude",
+)
+
+print(f"Found {len(catalog)} events")
+for event in catalog[:5]:
+    origin = event.preferred_origin()
+    mag = event.preferred_magnitude()
+    print(f"  M{mag.mag:.1f} {origin.time} "
+          f"({origin.latitude:.2f}, {origin.longitude:.2f}) "
+          f"depth={origin.depth/1000:.1f} km")
+```
+
+## Waveform Processing
+
+### Retrieving and Preprocessing Seismograms
+
+```python
+from obspy import UTCDateTime
+from obspy.clients.fdsn import Client
+
+client = Client("IRIS")
+
+# Download waveform data for a specific event
+t = UTCDateTime("2024-01-01T07:10:00")
+st = client.get_waveforms(
+    network="IU", station="ANMO", location="00", channel="BHZ",
+    starttime=t, endtime=t + 600,  # 10 minutes of data
+)
+
+# Standard preprocessing pipeline
+st.detrend("demean")        # Remove mean
+st.detrend("linear")        # Remove linear trend
+st.taper(max_percentage=0.05, type="cosine")  # Taper edges
+st.filter("bandpass", freqmin=0.01, freqmax=5.0, corners=4)
+
+# Remove instrument response to get ground velocity (m/s)
+inv = client.get_stations(
+    network="IU", station="ANMO", location="00", channel="BHZ",
+    starttime=t, endtime=t + 600, level="response",
+)
+st.remove_response(inventory=inv, output="VEL", pre_filt=[0.005, 0.01, 8, 10])
+```
+
+### Spectral Analysis
+
+```python
+import numpy as np
+from scipy.signal import welch
+
+def compute_psd(trace, nperseg=256):
+    """
+    Compute power spectral density of a seismic trace.
+    Returns frequencies (Hz) and PSD (dB relative to 1 (m/s)^2/Hz).
+    """
+    freqs, psd = welch(
+        trace.data,
+        fs=trace.stats.sampling_rate,
+        nperseg=nperseg,
+        noverlap=nperseg // 2,
+    )
+    psd_db = 10 * np.log10(psd + 1e-30)
+    return freqs, psd_db
+```
+
+## Phase Picking and Location
+
+### Automatic Phase Arrival Detection
+
+```python
+from obspy.signal.trigger import recursive_sta_lta, trigger_onset
+
+def pick_arrivals(trace, sta_seconds=1.0, lta_seconds=30.0,
+                  threshold_on=3.5, threshold_off=1.0):
+    """
+    STA/LTA trigger for P-wave arrival detection.
+    sta_seconds: short-term average window
+    lta_seconds: long-term average window
+    Returns list of (on_sample, off_sample) trigger windows.
+    """
+    df = trace.stats.sampling_rate
+    cft = recursive_sta_lta(
+        trace.data,
+        int(sta_seconds * df),
+        int(lta_seconds * df),
+    )
+    triggers = trigger_onset(cft, threshold_on, threshold_off)
+    return triggers, cft
+```
+
+### Earthquake Location
+
+Determining earthquake hypocenter from arrival times:
+
+1. **Grid search**: Evaluate travel-time residuals on a 3D grid
+2. **Geiger's method**: Iterative linearized least-squares inversion
+3. **NonLinLoc**: Probabilistic non-linear location using Oct-tree sampling
+4. **HypoDD**: Double-difference relocation for high-precision relative locations
+
+```python
+# Simplified grid search earthquake location
+def grid_search_locate(stations, arrival_times, velocity_model,
+                       lat_range, lon_range, depth_range, grid_spacing):
+    """
+    Brute-force grid search for earthquake location.
+    Minimizes sum of squared travel-time residuals.
+    """
+    best_misfit = float("inf")
+    best_location = None
+
+    for lat in np.arange(*lat_range, grid_spacing):
+        for lon in np.arange(*lon_range, grid_spacing):
+            for depth in np.arange(*depth_range, grid_spacing):
+                residuals = []
+                for sta, obs_time in zip(stations, arrival_times):
+                    dist = geodetic_distance(lat, lon, sta.lat, sta.lon)
+                    pred_time = velocity_model.get_travel_time(dist, depth)
+                    residuals.append((obs_time - pred_time) ** 2)
+                misfit = sum(residuals)
+                if misfit < best_misfit:
+                    best_misfit = misfit
+                    best_location = (lat, lon, depth)
+
+    return best_location, best_misfit
+```
+
+## Magnitude Estimation
+
+### Common Magnitude Scales
+
+| Scale | Symbol | Measurement | Range |
+|-------|--------|------------|-------|
+| Local (Richter) | ML | Max amplitude on Wood-Anderson | < 6.5 |
+| Body wave | mb | P-wave amplitude at 1 Hz | 4-7 |
+| Surface wave | Ms | Rayleigh wave at 20s period | 5-8.5 |
+| Moment | Mw | Seismic moment from waveform | All sizes |
+
+Moment magnitude is the standard for modern seismology:
+
+```python
+def moment_magnitude(seismic_moment_nm: float) -> float:
+    """
+    Compute moment magnitude from seismic moment (in Newton-meters).
+    Mw = (2/3) * log10(M0) - 6.07  (Hanks and Kanamori, 1979)
+    """
+    return (2.0 / 3.0) * np.log10(seismic_moment_nm) - 6.07
+```
+
+## Focal Mechanisms
+
+Beach ball diagrams represent earthquake source geometry. The fault plane solution requires at least 8-10 well-distributed first-motion polarities (up/down) or full waveform moment tensor inversion.
+
+Tools for focal mechanism determination:
+- **HASH**: First-motion focal mechanism (USGS)
+- **TDMT_INV**: Time-domain moment tensor inversion
+- **ObsPy beachball module**: Plotting focal mechanisms
+
+## Tools and Software
+
+- **ObsPy**: Python framework for seismological data processing
+- **SAC (Seismic Analysis Code)**: Classic command-line waveform tool
+- **GMT (Generic Mapping Tools)**: Map generation and focal mechanism plotting
+- **SeisComP**: Real-time seismic network processing system
+- **SPECFEM3D**: Spectral-element wave propagation simulation
+- **Pyrocko**: Python toolbox for seismology (Green's functions, source inversion)