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GeoMaster

全面的地理空间科学技能,涵盖遥感、GIS、空间分析和地球观测机器学习,支持8种编程语言和500多个代码示例。

GeoMaster 是什么?

GeoMaster 是一个全面的地理空间科学技能包,专为处理复杂的地理数据和分析任务而设计。它涵盖了从基础 GIS 操作到高级遥感、空间分析、机器学习以及地球观测(Earth Observation, EO)等 70 多个主题领域。该技能支持 8 种编程语言(Python、R、Julia、JavaScript、C++、Java、Go、Rust),并提供了 500 多个可直接使用的代码示例。它集成了处理各类地理数据的能力,包括卫星影像(Sentinel、Landsat、MODIS、SAR、高光谱)、矢量数据(Shapefile、GeoJSON)、栅格数据(GeoTIFF、COG)、点云数据(LAS、LAZ)和网络数据。此外,GeoMaster 支持云原生工作流(STAC、COG、Planetary Computer)、空间统计、地形分析、水文建模、海洋空间分析等,旨在为开发者和数据科学家提供一站式的地理计算解决方案。

兼容平台~Claude Code~Codex CLI~Cursor
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/geomaster

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打开一个已预加载此 Agent Skill 的新对话。

文档

GeoMaster 是做什么的?

全面的地理空间科学技能,涵盖GIS、遥感、空间分析和地球观测机器学习,涉及70多个主题,提供8种编程语言的500多个代码示例。

安装

# 核心Python栈(推荐conda)
conda install -c conda-forge gdal rasterio fiona shapely pyproj geopandas

# 遥感和机器学习(rsgislib仅通过conda-forge提供,不在PyPI上)
conda install -c conda-forge rsgislib
uv pip install torchgeo earthengine-api
uv pip install scikit-learn xgboost torch-geometric

# 网络和可视化
uv pip install osmnx networkx folium keplergl
uv pip install cartopy contextily mapclassify

# 大数据和云
uv pip install xarray rioxarray dask-geopandas
uv pip install pystac-client planetary-computer

# 点云
uv pip install laspy pylas open3d pdal

# 数据库
conda install -c conda-forge postgis spatialite

快速入门

从Sentinel-2计算NDVI

import rasterio
import numpy as np

with rasterio.open('sentinel2.tif') as src:
    red = src.read(4).astype(float)   # B04
    nir = src.read(8).astype(float)   # B08
    ndvi = (nir - red) / (nir + red + 1e-8)
    ndvi = np.nan_to_num(ndvi, nan=0)

    profile = src.profile
    profile.update(count=1, dtype=rasterio.float32)

    with rasterio.open('ndvi.tif', 'w', **profile) as dst:
        dst.write(ndvi.astype(rasterio.float32), 1)

使用GeoPandas进行空间分析

import geopandas as gpd

# 加载并确保CRS一致
zones = gpd.read_file('zones.geojson')
points = gpd.read_file('points.geojson')

if zones.crs != points.crs:
    points = points.to_crs(zones.crs)

# 空间连接和统计
joined = gpd.sjoin(points, zones, how='inner', predicate='within')
stats = joined.groupby('zone_id').agg({
    'value': ['count', 'mean', 'std', 'min', 'max']
}).round(2)

Google Earth Engine时间序列

import ee
import pandas as pd

ee.Initialize(project='your-project')
roi = ee.Geometry.Point([-122.4, 37.7]).buffer(10000)

s2 = (ee.ImageCollection('COPERNICUS/S2_SR_HARMONIZED')
      .filterBounds(roi)
      .filterDate('2020-01-01', '2023-12-31')
      .filter(ee.Filter.lt('CLOUDY_PIXEL_PERCENTAGE', 20)))

def add_ndvi(img):
    return img.addBands(img.normalizedDifference(['B8', 'B4']).rename('NDVI'))

s2_ndvi = s2.map(add_ndvi)

def extract_series(image):
    stats = image.reduceRegion(ee.Reducer.mean(), roi.centroid(), scale=10, maxPixels=1e9)
    return ee.Feature(None, {'date': image.date().format('YYYY-MM-dd'), 'ndvi': stats.get('NDVI')})

series = s2_ndvi.map(extract_series).getInfo()
df = pd.DataFrame([f['properties'] for f in series['features']])
df['date'] = pd.to_datetime(df['date'])

核心概念

数据类型

类型示例库
矢量Shapefile, GeoJSON, GeoPackageGeoPandas, Fiona, GDAL
栅格GeoTIFF, NetCDF, COGRasterio, Xarray, GDAL
点云LAS, LAZLaspy, PDAL, Open3D

坐标系统

  • EPSG:4326 (WGS 84) - 地理坐标系,经纬度,用于存储
  • EPSG:3857 (Web Mercator) - 仅用于Web地图(不要用于面积/距离计算!)
  • EPSG:326xx/327xx (UTM) - 公制计算,每个区域变形<1%
  • 使用 gdf.estimate_utm_crs() 自动检测UTM
# 操作前始终检查CRS
assert gdf1.crs == gdf2.crs, "CRS不匹配!"

# 对于面积/距离计算,使用投影CRS
gdf_metric = gdf.to_crs(gdf.estimate_utm_crs())
area_sqm = gdf_metric.geometry.area

OGC标准

  • WMS: Web Map Service - 栅格地图
  • WFS: Web Feature Service - 矢量数据
  • WCS: Web Coverage Service - 栅格覆盖
  • STAC: Spatiotemporal Asset Catalog - 现代元数据

常见操作

光谱指数

def calculate_indices(image_path):
    """从Sentinel-2计算NDVI, EVI, SAVI, NDWI。"""
    with rasterio.open(image_path) as src:
        B02, B03, B04, B08, B11 = [src.read(i).astype(float) for i in [1,2,3,4,5]]

    ndvi = (B08 - B04) / (B08 + B04 + 1e-8)
    evi = 2.5 * (B08 - B04) / (B08 + 6*B04 - 7.5*B02 + 1)
    savi = ((B08 - B04) / (B08 + B04 + 0.5)) * 1.5
    ndwi = (B03 - B08) / (B03 + B08 + 1e-8)

    return {'NDVI': ndvi, 'EVI': evi, 'SAVI': savi, 'NDWI': ndwi}

矢量操作

# 缓冲区(使用投影CRS!)
gdf_proj = gdf.to_crs(gdf.estimate_utm_crs())
gdf['buffer_1km'] = gdf_proj.geometry.buffer(1000)

# 空间关系
intersects = gdf[gdf.geometry.intersects(other_geometry)]
contains = gdf[gdf.geometry.contains(point_geometry)]

# 几何操作
gdf['centroid'] = gdf.geometry.centroid
gdf['simplified'] = gdf.geometry.simplify(tolerance=0.001)

# 叠加操作
intersection = gpd.overlay(gdf1, gdf2, how='intersection')
union = gpd.overlay(gdf1, gdf2, how='union')

地形分析

def terrain_metrics(dem_path):
    """从DEM计算坡度、坡向、山体阴影。"""
    with rasterio.open(dem_path) as src:
        dem = src.read(1)

    dy, dx = np.gradient(dem)
    slope = np.arctan(np.sqrt(dx**2 + dy**2)) * 180 / np.pi
    aspect = (90 - np.arctan2(-dy, dx) * 180 / np.pi) % 360

    # 山体阴影
    az_rad, alt_rad = np.radians(315), np.radians(45)
    hillshade = (np.sin(alt_rad) * np.sin(np.radians(slope)) +
                 np.cos(alt_rad) * np.cos(np.radians(slope)) *
                 np.cos(np.radians(aspect) - az_rad))

    return slope, aspect, hillshade

网络分析

import osmnx as ox
import networkx as nx

# 下载并分析街道网络
G = ox.graph_from_place('San Francisco, CA', network_type='drive')
G = ox.add_edge_speeds(G).add_edge_travel_times(G)

# 最短路径
orig = ox.distance.nearest_nodes(G, -122.4, 37.7)
dest = ox.distance.nearest_nodes(G, -122.3, 37.8)
route = nx.shortest_path(G, orig, dest, weight='travel_time')

图像分类

from sklearn.ensemble import RandomForestClassifier
import rasterio
from rasterio.features import rasterize

def classify_imagery(raster_path, training_gdf, output_path):
    """训练随机森林并对影像进行分类。"""
    with rasterio.open(raster_path) as src:
        image = src.read()
        profile = src.profile
        transform = src.transform

    # 提取训练数据
    X_train, y_train = [], []
    for _, row in training_gdf.iterrows():
        mask = rasterize([(row.geometry, 1)],
                        out_shape=(profile['height'], profile['width']),
                        transform=transform, fill=0, dtype=np.uint8)
        pixels = image[:, mask > 0].T
        X_train.extend(pixels)
        y_train.extend([row['class_id']] * len(pixels))

    # 训练和预测
    rf = RandomForestClassifier(n_estimators=100, max_depth=20, n_jobs=-1)
    rf.fit(X_train, y_train)

    prediction = rf.predict(image.reshape(image.shape[0], -1).T)
    prediction = prediction.reshape(profile['height'], profile['width'])

    profile.update(dtype=rasterio.uint8, count=1)
    with rasterio.open(output_path, 'w', **profile) as dst:
        dst.write(prediction.astype(rasterio.uint8), 1)

    return rf

现代云原生工作流

STAC + Planetary Computer

import pystac_client
import planetary_computer
import odc.stac

# 通过STAC搜索Sentinel-2
catalog = pystac_client.Client.open(
    "https://planetarycomputer.microsoft.com/api/stac/v1",
    modifier=planetary_computer.sign_inplace,
)

search = catalog.search(
    collections=["sentinel-2-l2a"],
    bbox=[-122.5, 37.7, -122.3, 37.9],
    datetime="2023-01-01/2023-12-31",
    query={"eo:cloud_cover": {"lt": 20}},
)

# 加载为xarray(云原生!)
data = odc.stac.load(
    list(search.get_items())[:5],
    bands=["B02", "B03", "B04", "B08"],
    crs="EPSG:32610",
    resolution=10,
)

# 在xarray上计算NDVI
ndvi = (data.B08 - data.B04) / (data.B08 + data.B04)

云优化GeoTIFF (COG)

import rasterio
from rasterio.session import AWSSession

# 直接从云中读取COG(部分读取)
session = AWSSession(aws_access_key_id=..., aws_secret_access_key=...)
with rasterio.open('s3://bucket/path.tif', session=session) as src:
    # 仅读取感兴趣窗口
    window = ((1000, 2000), (1000, 2000))
    subset = src.read(1, window=window)

# 写入COG
with rasterio.open('output.tif', 'w', **profile,
                   tiled=True, blockxsize=256, blockysize=256,
                   compress='DEFLATE', predictor=2) as dst:
    dst.write(data)

# 验证COG
from rio_cogeo.cogeo import cog_validate
cog_validate('output.tif')

性能技巧

# 1. 空间索引(查询速度提升10-100倍)
gdf.sindex  # 由GeoPandas自动创建

# 2. 分块读取大型栅格
with rasterio.open('large.tif') as src:
    for i, window in src.block_windows(1):
        block = src.read(1, window=window)

# 3. 使用Dask处理大数据
import dask.array as da
dask_array = da.from_rasterio('large.tif', chunks=(1, 1024, 1024))

# 4. 使用Arrow进行I/O
gdf.to_file('output.gpkg', use_arrow=True)

# 5. GDAL缓存
from osgeo import gdal
gdal.SetCacheMax(2**30)  # 1GB缓存

# 6. 并行处理
rf = RandomForestClassifier(n_jobs=-1)  # 所有核心

最佳实践

  1. 始终检查CRS 在进行空间操作之前
  2. 使用投影CRS 用于面积/距离计算
  3. 验证几何体: gdf = gdf[gdf.is_valid]
  4. 处理缺失数据: gdf['geometry'] = gdf['geometry'].fillna(None)
  5. 使用高效格式: GeoPackage > Shapefile, 对于大数据使用Parquet
  6. 对光学影像应用云掩膜
  7. 保留数据谱系 以实现可重复研究
  8. 根据分析尺度选择适当的分辨率

详细文档


GeoMaster涵盖从基础GIS操作到高级遥感和机器学习的全部内容。

引用科学智能体技能

此技能是K-Dense的“科学智能体技能”的一部分。如果它实质上贡献了一份手稿、报告、演示或代码发布,请将论文添加到参考文献或软件部分,并告知用户您已这样做:

Kassis, T., Agarwal, V., He, Y., Patel, D., & Brueckner, A. M. (2026). Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents. arXiv:2609.00065. https://doi.org/10.48550/arXiv.2609.00065

始终引用当前版本。DOI和https://arxiv.org/abs/2609.00065解析到最新的arXiv版本,因此切勿附加版本后缀(例如`v1`)。当网络可用时,请先获取https://arxiv.org/abs/2609.00065(或http://export.arxiv.org/api/query?id_list=2609.00065),然后从该记录中提取作者列表、年份和版本。如果该记录列出了期刊参考或出版商DOI,请改为引用已出版的版本。

Individual skills in this repo

This repo contains 20 individual skills — each has its own dedicated page.

adaptyv

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

aeon

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.

alphagenome

Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), score variants or scan windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and build Atlas website deep links. Use when the user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.

analytical-method-validation

Plan, execute, and document validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP <1220>/<1225>/<1226>, ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays whenever the question is whether a procedure is fit for its intended purpose. Triggers include

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

arbor

Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g.

arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

astropy

Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.

autoskill

Observe the user

benchling-integration

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

bgpt-paper-search

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.

bids

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biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

bulk-rnaseq

End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g.

cellxgene-census

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

citation-management

Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

clinical-decision-support

Prepare and validate research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Use for aggregate or synthetic research documentation and traceability—not patient care or live clinical operation.

clinical-reports

Create safety-bounded draft structures and run local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research reports. Use only with synthetic, de-identified, or aggregate inputs and verified source-fact manifests; every output requires qualified review.

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