@saibolla/ada 0.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.ada/SYSTEM.md +81 -0
- package/.ada/agents/researcher.md +69 -0
- package/.ada/agents/reviewer.md +92 -0
- package/.ada/agents/verifier.md +45 -0
- package/.ada/agents/writer.md +54 -0
- package/.ada/settings.json +32 -0
- package/.ada/themes/ada.json +85 -0
- package/.env.example +31 -0
- package/AGENTS.md +79 -0
- package/LICENSE +191 -0
- package/README.md +188 -0
- package/bin/ada.js +26 -0
- package/dist/bootstrap/sync.js +143 -0
- package/dist/cli.js +404 -0
- package/dist/config/paths.js +32 -0
- package/dist/index.js +10 -0
- package/dist/model/catalog.js +255 -0
- package/dist/model/commands.js +180 -0
- package/dist/pi/launch.js +33 -0
- package/dist/pi/package-presets.js +55 -0
- package/dist/pi/runtime.js +81 -0
- package/dist/pi/settings.js +108 -0
- package/dist/pi/web-access.js +74 -0
- package/dist/search/commands.js +12 -0
- package/dist/setup/doctor.js +126 -0
- package/dist/setup/preview.js +117 -0
- package/dist/setup/prompts.js +34 -0
- package/dist/setup/setup.js +98 -0
- package/dist/setup/update.js +133 -0
- package/dist/system/executables.js +38 -0
- package/dist/system/node-version.js +31 -0
- package/dist/system/open-url.js +35 -0
- package/dist/system/promise-polyfill.js +12 -0
- package/dist/ui/terminal.js +64 -0
- package/dist/web/launch.js +48 -0
- package/dist/web-search.js +1 -0
- package/extensions/docparser/constants.ts +62 -0
- package/extensions/docparser/deps.ts +584 -0
- package/extensions/docparser/doctor.ts +353 -0
- package/extensions/docparser/index.ts +9 -0
- package/extensions/docparser/input.ts +230 -0
- package/extensions/docparser/request.ts +67 -0
- package/extensions/docparser/schema.ts +82 -0
- package/extensions/docparser/tool.ts +305 -0
- package/extensions/docparser/types.ts +99 -0
- package/extensions/research-tools/alpha.ts +107 -0
- package/extensions/research-tools/header.ts +284 -0
- package/extensions/research-tools/help.ts +93 -0
- package/extensions/research-tools/project-scaffold.ts +64 -0
- package/extensions/research-tools/project.ts +123 -0
- package/extensions/research-tools/shared.ts +16 -0
- package/extensions/research-tools.ts +42 -0
- package/logo.d.mts +3 -0
- package/logo.mjs +14 -0
- package/metadata/commands.d.mts +46 -0
- package/metadata/commands.mjs +133 -0
- package/package.json +80 -0
- package/prompts/audit.md +17 -0
- package/prompts/autoresearch.md +66 -0
- package/prompts/compare.md +18 -0
- package/prompts/deepresearch.md +189 -0
- package/prompts/draft.md +19 -0
- package/prompts/jobs.md +16 -0
- package/prompts/litreview.md +18 -0
- package/prompts/log.md +14 -0
- package/prompts/replicate.md +24 -0
- package/prompts/review.md +18 -0
- package/prompts/watch.md +16 -0
- package/scripts/build-native-bundle.mjs +349 -0
- package/scripts/check-node-version.mjs +35 -0
- package/scripts/patch-embedded-pi.mjs +588 -0
- package/scripts/prepare-runtime-workspace.mjs +162 -0
- package/scripts/prune-runtime-deps.mjs +131 -0
- package/scripts/release.sh +152 -0
- package/skills/adaptyv/SKILL.md +112 -0
- package/skills/adaptyv/reference/api_reference.md +308 -0
- package/skills/adaptyv/reference/examples.md +913 -0
- package/skills/adaptyv/reference/experiments.md +360 -0
- package/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/skills/aeon/SKILL.md +372 -0
- package/skills/aeon/references/anomaly_detection.md +154 -0
- package/skills/aeon/references/classification.md +144 -0
- package/skills/aeon/references/clustering.md +123 -0
- package/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/skills/aeon/references/distances.md +256 -0
- package/skills/aeon/references/forecasting.md +140 -0
- package/skills/aeon/references/networks.md +289 -0
- package/skills/aeon/references/regression.md +118 -0
- package/skills/aeon/references/segmentation.md +163 -0
- package/skills/aeon/references/similarity_search.md +187 -0
- package/skills/aeon/references/transformations.md +246 -0
- package/skills/alpha-research/SKILL.md +42 -0
- package/skills/alpha-vantage/SKILL.md +142 -0
- package/skills/alpha-vantage/references/commodities.md +153 -0
- package/skills/alpha-vantage/references/economic-indicators.md +158 -0
- package/skills/alpha-vantage/references/forex-crypto.md +154 -0
- package/skills/alpha-vantage/references/fundamentals.md +223 -0
- package/skills/alpha-vantage/references/intelligence.md +138 -0
- package/skills/alpha-vantage/references/options.md +93 -0
- package/skills/alpha-vantage/references/technical-indicators.md +374 -0
- package/skills/alpha-vantage/references/time-series.md +157 -0
- package/skills/alphafold-database/SKILL.md +511 -0
- package/skills/alphafold-database/references/api_reference.md +423 -0
- package/skills/anndata/SKILL.md +398 -0
- package/skills/anndata/references/best_practices.md +525 -0
- package/skills/anndata/references/concatenation.md +396 -0
- package/skills/anndata/references/data_structure.md +314 -0
- package/skills/anndata/references/io_operations.md +404 -0
- package/skills/anndata/references/manipulation.md +516 -0
- package/skills/arboreto/SKILL.md +241 -0
- package/skills/arboreto/references/algorithms.md +138 -0
- package/skills/arboreto/references/basic_inference.md +151 -0
- package/skills/arboreto/references/distributed_computing.md +242 -0
- package/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/skills/arxiv-database/SKILL.md +362 -0
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- package/skills/arxiv-database/scripts/arxiv_search.py +414 -0
- package/skills/astropy/SKILL.md +329 -0
- package/skills/astropy/references/coordinates.md +273 -0
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- package/skills/autoresearch/SKILL.md +12 -0
- package/skills/benchling-integration/SKILL.md +478 -0
- package/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/skills/benchling-integration/references/authentication.md +379 -0
- package/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/skills/bgpt-paper-search/SKILL.md +81 -0
- package/skills/bindingdb-database/SKILL.md +332 -0
- package/skills/bindingdb-database/references/affinity_queries.md +178 -0
- package/skills/biopython/SKILL.md +441 -0
- package/skills/biopython/references/advanced.md +577 -0
- package/skills/biopython/references/alignment.md +362 -0
- package/skills/biopython/references/blast.md +455 -0
- package/skills/biopython/references/databases.md +484 -0
- package/skills/biopython/references/phylogenetics.md +566 -0
- package/skills/biopython/references/sequence_io.md +285 -0
- package/skills/biopython/references/structure.md +564 -0
- package/skills/biorxiv-database/SKILL.md +481 -0
- package/skills/biorxiv-database/references/api_reference.md +280 -0
- package/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/skills/bioservices/SKILL.md +359 -0
- package/skills/bioservices/references/identifier_mapping.md +685 -0
- package/skills/bioservices/references/services_reference.md +636 -0
- package/skills/bioservices/references/workflow_patterns.md +811 -0
- package/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/skills/brenda-database/SKILL.md +717 -0
- package/skills/brenda-database/references/api_reference.md +537 -0
- package/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/skills/cbioportal-database/SKILL.md +367 -0
- package/skills/cbioportal-database/references/study_exploration.md +128 -0
- package/skills/cellxgene-census/SKILL.md +509 -0
- package/skills/cellxgene-census/references/census_schema.md +182 -0
- package/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/skills/chembl-database/SKILL.md +387 -0
- package/skills/chembl-database/references/api_reference.md +272 -0
- package/skills/chembl-database/scripts/example_queries.py +278 -0
- package/skills/cirq/SKILL.md +344 -0
- package/skills/cirq/references/building.md +307 -0
- package/skills/cirq/references/experiments.md +572 -0
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- package/skills/cirq/references/transformation.md +416 -0
- package/skills/citation-management/SKILL.md +1113 -0
- package/skills/citation-management/assets/bibtex_template.bib +264 -0
- package/skills/citation-management/assets/citation_checklist.md +386 -0
- package/skills/citation-management/references/bibtex_formatting.md +908 -0
- package/skills/citation-management/references/citation_validation.md +794 -0
- package/skills/citation-management/references/google_scholar_search.md +725 -0
- package/skills/citation-management/references/metadata_extraction.md +870 -0
- package/skills/citation-management/references/pubmed_search.md +839 -0
- package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
- package/skills/citation-management/scripts/extract_metadata.py +569 -0
- package/skills/citation-management/scripts/format_bibtex.py +349 -0
- package/skills/citation-management/scripts/search_google_scholar.py +282 -0
- package/skills/citation-management/scripts/search_pubmed.py +398 -0
- package/skills/citation-management/scripts/validate_citations.py +497 -0
- package/skills/clinical-decision-support/SKILL.md +510 -0
- package/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
- package/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
- package/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
- package/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
- package/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
- package/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
- package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
- package/skills/clinical-decision-support/references/README.md +129 -0
- package/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
- package/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
- package/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
- package/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
- package/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
- package/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
- package/skills/clinical-decision-support/scripts/biomarker_classifier.py +384 -0
- package/skills/clinical-decision-support/scripts/build_decision_tree.py +447 -0
- package/skills/clinical-decision-support/scripts/create_cohort_tables.py +524 -0
- package/skills/clinical-decision-support/scripts/generate_survival_analysis.py +422 -0
- package/skills/clinical-decision-support/scripts/validate_cds_document.py +335 -0
- package/skills/clinical-reports/SKILL.md +1131 -0
- package/skills/clinical-reports/assets/case_report_template.md +352 -0
- package/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
- package/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
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- package/skills/clinical-reports/assets/pathology_report_template.md +249 -0
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- package/skills/clinical-reports/scripts/check_deidentification.py +346 -0
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- package/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
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- package/skills/clinical-reports/scripts/generate_report_template.py +163 -0
- package/skills/clinical-reports/scripts/terminology_validator.py +133 -0
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- package/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
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- package/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
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- package/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +756 -0
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- package/skills/treatment-plans/references/treatment_plan_standards.md +485 -0
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- package/skills/uspto-database/scripts/peds_client.py +285 -0
- package/skills/uspto-database/scripts/trademark_client.py +311 -0
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- package/skills/vaex/references/data_processing.md +555 -0
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- package/skills/venue-templates/SKILL.md +688 -0
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- package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
- package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
- package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
- package/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
- package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
- package/skills/venue-templates/assets/journals/nature_article.tex +171 -0
- package/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
- package/skills/venue-templates/assets/journals/plos_one.tex +317 -0
- package/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
- package/skills/venue-templates/references/cell_press_style.md +483 -0
- package/skills/venue-templates/references/conferences_formatting.md +564 -0
- package/skills/venue-templates/references/cs_conference_style.md +463 -0
- package/skills/venue-templates/references/grants_requirements.md +787 -0
- package/skills/venue-templates/references/journals_formatting.md +486 -0
- package/skills/venue-templates/references/medical_journal_styles.md +535 -0
- package/skills/venue-templates/references/ml_conference_style.md +556 -0
- package/skills/venue-templates/references/nature_science_style.md +405 -0
- package/skills/venue-templates/references/posters_guidelines.md +628 -0
- package/skills/venue-templates/references/reviewer_expectations.md +417 -0
- package/skills/venue-templates/references/venue_writing_styles.md +321 -0
- package/skills/venue-templates/scripts/customize_template.py +206 -0
- package/skills/venue-templates/scripts/query_template.py +260 -0
- package/skills/venue-templates/scripts/validate_format.py +255 -0
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- package/skills/what-if-oracle/SKILL.md +168 -0
- package/skills/what-if-oracle/references/scenario-templates.md +137 -0
- package/skills/writing/SKILL.md +414 -0
- package/skills/xlsx/LICENSE.txt +30 -0
- package/skills/xlsx/SKILL.md +292 -0
- package/skills/xlsx/scripts/office/helpers/__init__.py +0 -0
- package/skills/xlsx/scripts/office/helpers/merge_runs.py +199 -0
- package/skills/xlsx/scripts/office/helpers/simplify_redlines.py +197 -0
- package/skills/xlsx/scripts/office/pack.py +159 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/skills/xlsx/scripts/office/soffice.py +183 -0
- package/skills/xlsx/scripts/office/unpack.py +132 -0
- package/skills/xlsx/scripts/office/validate.py +111 -0
- package/skills/xlsx/scripts/office/validators/__init__.py +15 -0
- package/skills/xlsx/scripts/office/validators/base.py +847 -0
- package/skills/xlsx/scripts/office/validators/docx.py +446 -0
- package/skills/xlsx/scripts/office/validators/pptx.py +275 -0
- package/skills/xlsx/scripts/office/validators/redlining.py +247 -0
- package/skills/xlsx/scripts/recalc.py +184 -0
- package/skills/zarr-python/SKILL.md +777 -0
- package/skills/zarr-python/references/api_reference.md +515 -0
- package/skills/zinc-database/SKILL.md +402 -0
- package/skills/zinc-database/references/api_reference.md +692 -0
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# Coordinate Reference Systems (CRS)
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A coordinate reference system defines how coordinates relate to locations on Earth.
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## Understanding CRS
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CRS information is stored as `pyproj.CRS` objects:
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```python
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# Check CRS
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print(gdf.crs)
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# Check if CRS is set
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if gdf.crs is None:
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print("No CRS defined")
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```
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## Setting vs Reprojecting
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### Setting CRS
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Use `set_crs()` when coordinates are correct but CRS metadata is missing:
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```python
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# Set CRS (doesn't transform coordinates)
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gdf = gdf.set_crs("EPSG:4326")
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gdf = gdf.set_crs(4326)
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```
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**Warning**: Only use when CRS metadata is missing. This does not transform coordinates.
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### Reprojecting
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Use `to_crs()` to transform coordinates between coordinate systems:
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```python
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# Reproject to different CRS
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gdf_projected = gdf.to_crs("EPSG:3857") # Web Mercator
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gdf_projected = gdf.to_crs(3857)
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# Reproject to match another GeoDataFrame
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gdf1_reprojected = gdf1.to_crs(gdf2.crs)
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```
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## CRS Formats
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GeoPandas accepts multiple formats via `pyproj.CRS.from_user_input()`:
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```python
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# EPSG code (integer)
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gdf.to_crs(4326)
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# Authority string
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gdf.to_crs("EPSG:4326")
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gdf.to_crs("ESRI:102003")
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# WKT string (Well-Known Text)
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gdf.to_crs("GEOGCS[...]")
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# PROJ string
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gdf.to_crs("+proj=longlat +datum=WGS84")
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# pyproj.CRS object
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from pyproj import CRS
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crs_obj = CRS.from_epsg(4326)
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gdf.to_crs(crs_obj)
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```
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**Best Practice**: Use WKT2 or authority strings (EPSG) to preserve full CRS information.
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## Common EPSG Codes
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### Geographic Coordinate Systems
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```python
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# WGS 84 (latitude/longitude)
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gdf.to_crs("EPSG:4326")
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# NAD83
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gdf.to_crs("EPSG:4269")
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```
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### Projected Coordinate Systems
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```python
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# Web Mercator (used by web maps)
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gdf.to_crs("EPSG:3857")
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# UTM zones (example: UTM Zone 33N)
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gdf.to_crs("EPSG:32633")
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# UTM zones (Southern hemisphere, example: UTM Zone 33S)
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gdf.to_crs("EPSG:32733")
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# US National Atlas Equal Area
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gdf.to_crs("ESRI:102003")
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# Albers Equal Area Conic (North America)
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gdf.to_crs("EPSG:5070")
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```
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## CRS Requirements for Operations
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### Operations Requiring Matching CRS
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These operations require identical CRS:
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```python
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# Spatial joins
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gpd.sjoin(gdf1, gdf2, ...) # CRS must match
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# Overlay operations
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gpd.overlay(gdf1, gdf2, ...) # CRS must match
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# Appending
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pd.concat([gdf1, gdf2]) # CRS must match
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# Reproject first if needed
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gdf2_reprojected = gdf2.to_crs(gdf1.crs)
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result = gpd.sjoin(gdf1, gdf2_reprojected)
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```
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### Operations Best in Projected CRS
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Area and distance calculations should use projected CRS:
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```python
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# Bad: area in degrees (meaningless)
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areas_degrees = gdf.geometry.area # If CRS is EPSG:4326
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# Good: reproject to appropriate projected CRS first
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gdf_projected = gdf.to_crs("EPSG:3857")
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areas_meters = gdf_projected.geometry.area # Square meters
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# Better: use appropriate local UTM zone for accuracy
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gdf_utm = gdf.to_crs("EPSG:32633") # UTM Zone 33N
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accurate_areas = gdf_utm.geometry.area
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```
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## Choosing Appropriate CRS
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### For Area/Distance Calculations
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Use equal-area projections:
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```python
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# Albers Equal Area Conic (North America)
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gdf.to_crs("EPSG:5070")
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# Lambert Azimuthal Equal Area
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gdf.to_crs("EPSG:3035") # Europe
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# UTM zones (for local areas)
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gdf.to_crs("EPSG:32633") # Appropriate UTM zone
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```
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### For Distance-Preserving (Navigation)
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Use equidistant projections:
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```python
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# Azimuthal Equidistant
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gdf.to_crs("ESRI:54032")
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```
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### For Shape-Preserving (Angles)
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Use conformal projections:
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```python
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# Web Mercator (conformal but distorts area)
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gdf.to_crs("EPSG:3857")
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# UTM zones (conformal for local areas)
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gdf.to_crs("EPSG:32633")
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```
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### For Web Mapping
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```python
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# Web Mercator (standard for web maps)
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gdf.to_crs("EPSG:3857")
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```
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## Estimating UTM Zone
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```python
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# Estimate appropriate UTM CRS from data
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utm_crs = gdf.estimate_utm_crs()
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190
|
+
gdf_utm = gdf.to_crs(utm_crs)
|
|
191
|
+
```
|
|
192
|
+
|
|
193
|
+
## Multiple Geometry Columns with Different CRS
|
|
194
|
+
|
|
195
|
+
GeoPandas 0.8+ supports different CRS per geometry column:
|
|
196
|
+
|
|
197
|
+
```python
|
|
198
|
+
# Set CRS for specific geometry column
|
|
199
|
+
gdf = gdf.set_crs("EPSG:4326", allow_override=True)
|
|
200
|
+
|
|
201
|
+
# Active geometry determines operations
|
|
202
|
+
gdf = gdf.set_geometry('other_geom_column')
|
|
203
|
+
|
|
204
|
+
# Check CRS mismatch
|
|
205
|
+
try:
|
|
206
|
+
result = gdf1.overlay(gdf2)
|
|
207
|
+
except ValueError as e:
|
|
208
|
+
print("CRS mismatch:", e)
|
|
209
|
+
```
|
|
210
|
+
|
|
211
|
+
## CRS Information
|
|
212
|
+
|
|
213
|
+
```python
|
|
214
|
+
# Get full CRS details
|
|
215
|
+
print(gdf.crs)
|
|
216
|
+
|
|
217
|
+
# Get EPSG code if available
|
|
218
|
+
print(gdf.crs.to_epsg())
|
|
219
|
+
|
|
220
|
+
# Get WKT representation
|
|
221
|
+
print(gdf.crs.to_wkt())
|
|
222
|
+
|
|
223
|
+
# Get PROJ string
|
|
224
|
+
print(gdf.crs.to_proj4())
|
|
225
|
+
|
|
226
|
+
# Check if CRS is geographic (lat/lon)
|
|
227
|
+
print(gdf.crs.is_geographic)
|
|
228
|
+
|
|
229
|
+
# Check if CRS is projected
|
|
230
|
+
print(gdf.crs.is_projected)
|
|
231
|
+
```
|
|
232
|
+
|
|
233
|
+
## Transforming Individual Geometries
|
|
234
|
+
|
|
235
|
+
```python
|
|
236
|
+
from pyproj import Transformer
|
|
237
|
+
|
|
238
|
+
# Create transformer
|
|
239
|
+
transformer = Transformer.from_crs("EPSG:4326", "EPSG:3857", always_xy=True)
|
|
240
|
+
|
|
241
|
+
# Transform point
|
|
242
|
+
x_new, y_new = transformer.transform(x, y)
|
|
243
|
+
```
|
|
@@ -0,0 +1,165 @@
|
|
|
1
|
+
# Reading and Writing Spatial Data
|
|
2
|
+
|
|
3
|
+
## Reading Files
|
|
4
|
+
|
|
5
|
+
Use `geopandas.read_file()` to import vector spatial data:
|
|
6
|
+
|
|
7
|
+
```python
|
|
8
|
+
import geopandas as gpd
|
|
9
|
+
|
|
10
|
+
# Read from file
|
|
11
|
+
gdf = gpd.read_file("data.shp")
|
|
12
|
+
gdf = gpd.read_file("data.geojson")
|
|
13
|
+
gdf = gpd.read_file("data.gpkg")
|
|
14
|
+
|
|
15
|
+
# Read from URL
|
|
16
|
+
gdf = gpd.read_file("https://example.com/data.geojson")
|
|
17
|
+
|
|
18
|
+
# Read from ZIP archive
|
|
19
|
+
gdf = gpd.read_file("data.zip")
|
|
20
|
+
```
|
|
21
|
+
|
|
22
|
+
### Performance: Arrow Acceleration
|
|
23
|
+
|
|
24
|
+
For 2-4x faster reading, use Arrow:
|
|
25
|
+
|
|
26
|
+
```python
|
|
27
|
+
gdf = gpd.read_file("data.gpkg", use_arrow=True)
|
|
28
|
+
```
|
|
29
|
+
|
|
30
|
+
Requires PyArrow: `uv pip install pyarrow`
|
|
31
|
+
|
|
32
|
+
### Filtering During Read
|
|
33
|
+
|
|
34
|
+
Pre-filter data to load only what's needed:
|
|
35
|
+
|
|
36
|
+
```python
|
|
37
|
+
# Load specific rows
|
|
38
|
+
gdf = gpd.read_file("data.gpkg", rows=100) # First 100 rows
|
|
39
|
+
gdf = gpd.read_file("data.gpkg", rows=slice(10, 20)) # Rows 10-20
|
|
40
|
+
|
|
41
|
+
# Load specific columns
|
|
42
|
+
gdf = gpd.read_file("data.gpkg", columns=['name', 'population'])
|
|
43
|
+
|
|
44
|
+
# Spatial filter with bounding box
|
|
45
|
+
gdf = gpd.read_file("data.gpkg", bbox=(xmin, ymin, xmax, ymax))
|
|
46
|
+
|
|
47
|
+
# Spatial filter with geometry mask
|
|
48
|
+
gdf = gpd.read_file("data.gpkg", mask=polygon_geometry)
|
|
49
|
+
|
|
50
|
+
# SQL WHERE clause (requires Fiona 1.9+ or Pyogrio)
|
|
51
|
+
gdf = gpd.read_file("data.gpkg", where="population > 1000000")
|
|
52
|
+
|
|
53
|
+
# Skip geometry (returns pandas DataFrame)
|
|
54
|
+
df = gpd.read_file("data.gpkg", ignore_geometry=True)
|
|
55
|
+
```
|
|
56
|
+
|
|
57
|
+
## Writing Files
|
|
58
|
+
|
|
59
|
+
Use `to_file()` to export:
|
|
60
|
+
|
|
61
|
+
```python
|
|
62
|
+
# Write to Shapefile
|
|
63
|
+
gdf.to_file("output.shp")
|
|
64
|
+
|
|
65
|
+
# Write to GeoJSON
|
|
66
|
+
gdf.to_file("output.geojson", driver='GeoJSON')
|
|
67
|
+
|
|
68
|
+
# Write to GeoPackage (supports multiple layers)
|
|
69
|
+
gdf.to_file("output.gpkg", layer='layer1', driver="GPKG")
|
|
70
|
+
|
|
71
|
+
# Arrow acceleration for faster writing
|
|
72
|
+
gdf.to_file("output.gpkg", use_arrow=True)
|
|
73
|
+
```
|
|
74
|
+
|
|
75
|
+
### Supported Formats
|
|
76
|
+
|
|
77
|
+
List all available drivers:
|
|
78
|
+
|
|
79
|
+
```python
|
|
80
|
+
import pyogrio
|
|
81
|
+
pyogrio.list_drivers()
|
|
82
|
+
```
|
|
83
|
+
|
|
84
|
+
Common formats: Shapefile, GeoJSON, GeoPackage (GPKG), KML, MapInfo File, CSV (with WKT geometry)
|
|
85
|
+
|
|
86
|
+
## Parquet and Feather
|
|
87
|
+
|
|
88
|
+
Columnar formats preserving spatial information with support for multiple geometry columns:
|
|
89
|
+
|
|
90
|
+
```python
|
|
91
|
+
# Write
|
|
92
|
+
gdf.to_parquet("data.parquet")
|
|
93
|
+
gdf.to_feather("data.feather")
|
|
94
|
+
|
|
95
|
+
# Read
|
|
96
|
+
gdf = gpd.read_parquet("data.parquet")
|
|
97
|
+
gdf = gpd.read_feather("data.feather")
|
|
98
|
+
```
|
|
99
|
+
|
|
100
|
+
Advantages:
|
|
101
|
+
- Faster I/O than traditional formats
|
|
102
|
+
- Better compression
|
|
103
|
+
- Preserves multiple geometry columns
|
|
104
|
+
- Schema versioning support
|
|
105
|
+
|
|
106
|
+
## PostGIS Databases
|
|
107
|
+
|
|
108
|
+
### Reading from PostGIS
|
|
109
|
+
|
|
110
|
+
```python
|
|
111
|
+
from sqlalchemy import create_engine
|
|
112
|
+
|
|
113
|
+
engine = create_engine('postgresql://user:password@host:port/database')
|
|
114
|
+
|
|
115
|
+
# Read entire table
|
|
116
|
+
gdf = gpd.read_postgis("SELECT * FROM table_name", con=engine, geom_col='geometry')
|
|
117
|
+
|
|
118
|
+
# Read with SQL query
|
|
119
|
+
gdf = gpd.read_postgis("SELECT * FROM table WHERE population > 100000", con=engine, geom_col='geometry')
|
|
120
|
+
```
|
|
121
|
+
|
|
122
|
+
### Writing to PostGIS
|
|
123
|
+
|
|
124
|
+
```python
|
|
125
|
+
# Create or replace table
|
|
126
|
+
gdf.to_postgis("table_name", con=engine, if_exists='replace')
|
|
127
|
+
|
|
128
|
+
# Append to existing table
|
|
129
|
+
gdf.to_postgis("table_name", con=engine, if_exists='append')
|
|
130
|
+
|
|
131
|
+
# Fail if table exists
|
|
132
|
+
gdf.to_postgis("table_name", con=engine, if_exists='fail')
|
|
133
|
+
```
|
|
134
|
+
|
|
135
|
+
Requires: `uv pip install psycopg2` or `uv pip install psycopg` and `uv pip install geoalchemy2`
|
|
136
|
+
|
|
137
|
+
## File-like Objects
|
|
138
|
+
|
|
139
|
+
Read from file handles or in-memory buffers:
|
|
140
|
+
|
|
141
|
+
```python
|
|
142
|
+
# From file handle
|
|
143
|
+
with open('data.geojson', 'r') as f:
|
|
144
|
+
gdf = gpd.read_file(f)
|
|
145
|
+
|
|
146
|
+
# From StringIO
|
|
147
|
+
from io import StringIO
|
|
148
|
+
geojson_string = '{"type": "FeatureCollection", ...}'
|
|
149
|
+
gdf = gpd.read_file(StringIO(geojson_string))
|
|
150
|
+
```
|
|
151
|
+
|
|
152
|
+
## Remote Storage (fsspec)
|
|
153
|
+
|
|
154
|
+
Access data from cloud storage:
|
|
155
|
+
|
|
156
|
+
```python
|
|
157
|
+
# S3
|
|
158
|
+
gdf = gpd.read_file("s3://bucket/data.gpkg")
|
|
159
|
+
|
|
160
|
+
# Azure Blob Storage
|
|
161
|
+
gdf = gpd.read_file("az://container/data.gpkg")
|
|
162
|
+
|
|
163
|
+
# HTTP/HTTPS
|
|
164
|
+
gdf = gpd.read_file("https://example.com/data.geojson")
|
|
165
|
+
```
|
|
@@ -0,0 +1,70 @@
|
|
|
1
|
+
# GeoPandas Data Structures
|
|
2
|
+
|
|
3
|
+
## GeoSeries
|
|
4
|
+
|
|
5
|
+
A GeoSeries is a vector where each entry is a set of shapes corresponding to one observation (similar to a pandas Series but with geometric data).
|
|
6
|
+
|
|
7
|
+
```python
|
|
8
|
+
import geopandas as gpd
|
|
9
|
+
from shapely.geometry import Point, Polygon
|
|
10
|
+
|
|
11
|
+
# Create a GeoSeries from geometries
|
|
12
|
+
points = gpd.GeoSeries([Point(1, 1), Point(2, 2), Point(3, 3)])
|
|
13
|
+
|
|
14
|
+
# Access geometric properties
|
|
15
|
+
points.area
|
|
16
|
+
points.length
|
|
17
|
+
points.bounds
|
|
18
|
+
```
|
|
19
|
+
|
|
20
|
+
## GeoDataFrame
|
|
21
|
+
|
|
22
|
+
A GeoDataFrame is a tabular data structure that contains a GeoSeries (similar to a pandas DataFrame but with geographic data).
|
|
23
|
+
|
|
24
|
+
```python
|
|
25
|
+
# Create from dictionary
|
|
26
|
+
gdf = gpd.GeoDataFrame({
|
|
27
|
+
'name': ['Point A', 'Point B'],
|
|
28
|
+
'value': [100, 200],
|
|
29
|
+
'geometry': [Point(1, 1), Point(2, 2)]
|
|
30
|
+
})
|
|
31
|
+
|
|
32
|
+
# Create from pandas DataFrame with coordinates
|
|
33
|
+
import pandas as pd
|
|
34
|
+
df = pd.DataFrame({'x': [1, 2, 3], 'y': [1, 2, 3], 'name': ['A', 'B', 'C']})
|
|
35
|
+
gdf = gpd.GeoDataFrame(df, geometry=gpd.points_from_xy(df.x, df.y))
|
|
36
|
+
```
|
|
37
|
+
|
|
38
|
+
## Key Properties
|
|
39
|
+
|
|
40
|
+
- **geometry**: The active geometry column (can have multiple geometry columns)
|
|
41
|
+
- **crs**: Coordinate reference system
|
|
42
|
+
- **bounds**: Bounding box of all geometries
|
|
43
|
+
- **total_bounds**: Overall bounding box
|
|
44
|
+
|
|
45
|
+
## Setting Active Geometry
|
|
46
|
+
|
|
47
|
+
When a GeoDataFrame has multiple geometry columns:
|
|
48
|
+
|
|
49
|
+
```python
|
|
50
|
+
# Set active geometry column
|
|
51
|
+
gdf = gdf.set_geometry('other_geom_column')
|
|
52
|
+
|
|
53
|
+
# Check active geometry column
|
|
54
|
+
gdf.geometry.name
|
|
55
|
+
```
|
|
56
|
+
|
|
57
|
+
## Indexing and Selection
|
|
58
|
+
|
|
59
|
+
Use standard pandas indexing with spatial data:
|
|
60
|
+
|
|
61
|
+
```python
|
|
62
|
+
# Select by label
|
|
63
|
+
gdf.loc[0]
|
|
64
|
+
|
|
65
|
+
# Boolean indexing
|
|
66
|
+
large_areas = gdf[gdf.area > 100]
|
|
67
|
+
|
|
68
|
+
# Select columns
|
|
69
|
+
gdf[['name', 'geometry']]
|
|
70
|
+
```
|
|
@@ -0,0 +1,221 @@
|
|
|
1
|
+
# Geometric Operations
|
|
2
|
+
|
|
3
|
+
GeoPandas provides extensive geometric manipulation through Shapely integration.
|
|
4
|
+
|
|
5
|
+
## Constructive Operations
|
|
6
|
+
|
|
7
|
+
Create new geometries from existing ones:
|
|
8
|
+
|
|
9
|
+
### Buffer
|
|
10
|
+
|
|
11
|
+
Create geometries representing all points within a distance:
|
|
12
|
+
|
|
13
|
+
```python
|
|
14
|
+
# Buffer by fixed distance
|
|
15
|
+
buffered = gdf.geometry.buffer(10)
|
|
16
|
+
|
|
17
|
+
# Negative buffer (erosion)
|
|
18
|
+
eroded = gdf.geometry.buffer(-5)
|
|
19
|
+
|
|
20
|
+
# Buffer with resolution parameter
|
|
21
|
+
smooth_buffer = gdf.geometry.buffer(10, resolution=16)
|
|
22
|
+
```
|
|
23
|
+
|
|
24
|
+
### Boundary
|
|
25
|
+
|
|
26
|
+
Get lower-dimensional boundary:
|
|
27
|
+
|
|
28
|
+
```python
|
|
29
|
+
# Polygon -> LineString, LineString -> MultiPoint
|
|
30
|
+
boundaries = gdf.geometry.boundary
|
|
31
|
+
```
|
|
32
|
+
|
|
33
|
+
### Centroid
|
|
34
|
+
|
|
35
|
+
Get center point of each geometry:
|
|
36
|
+
|
|
37
|
+
```python
|
|
38
|
+
centroids = gdf.geometry.centroid
|
|
39
|
+
```
|
|
40
|
+
|
|
41
|
+
### Convex Hull
|
|
42
|
+
|
|
43
|
+
Smallest convex polygon containing all points:
|
|
44
|
+
|
|
45
|
+
```python
|
|
46
|
+
hulls = gdf.geometry.convex_hull
|
|
47
|
+
```
|
|
48
|
+
|
|
49
|
+
### Concave Hull
|
|
50
|
+
|
|
51
|
+
Smallest concave polygon containing all points:
|
|
52
|
+
|
|
53
|
+
```python
|
|
54
|
+
# ratio parameter controls concavity (0 = convex hull, 1 = most concave)
|
|
55
|
+
concave_hulls = gdf.geometry.concave_hull(ratio=0.5)
|
|
56
|
+
```
|
|
57
|
+
|
|
58
|
+
### Envelope
|
|
59
|
+
|
|
60
|
+
Smallest axis-aligned rectangle:
|
|
61
|
+
|
|
62
|
+
```python
|
|
63
|
+
envelopes = gdf.geometry.envelope
|
|
64
|
+
```
|
|
65
|
+
|
|
66
|
+
### Simplify
|
|
67
|
+
|
|
68
|
+
Reduce geometric complexity:
|
|
69
|
+
|
|
70
|
+
```python
|
|
71
|
+
# Douglas-Peucker algorithm with tolerance
|
|
72
|
+
simplified = gdf.geometry.simplify(tolerance=10)
|
|
73
|
+
|
|
74
|
+
# Preserve topology (prevents self-intersections)
|
|
75
|
+
simplified = gdf.geometry.simplify(tolerance=10, preserve_topology=True)
|
|
76
|
+
```
|
|
77
|
+
|
|
78
|
+
### Segmentize
|
|
79
|
+
|
|
80
|
+
Add vertices to line segments:
|
|
81
|
+
|
|
82
|
+
```python
|
|
83
|
+
# Add vertices with maximum segment length
|
|
84
|
+
segmented = gdf.geometry.segmentize(max_segment_length=5)
|
|
85
|
+
```
|
|
86
|
+
|
|
87
|
+
### Union All
|
|
88
|
+
|
|
89
|
+
Combine all geometries into single geometry:
|
|
90
|
+
|
|
91
|
+
```python
|
|
92
|
+
# Union all features
|
|
93
|
+
unified = gdf.geometry.union_all()
|
|
94
|
+
```
|
|
95
|
+
|
|
96
|
+
## Affine Transformations
|
|
97
|
+
|
|
98
|
+
Mathematical transformations of coordinates:
|
|
99
|
+
|
|
100
|
+
### Rotate
|
|
101
|
+
|
|
102
|
+
```python
|
|
103
|
+
# Rotate around origin (0, 0) by angle in degrees
|
|
104
|
+
rotated = gdf.geometry.rotate(angle=45, origin='center')
|
|
105
|
+
|
|
106
|
+
# Rotate around custom point
|
|
107
|
+
rotated = gdf.geometry.rotate(angle=45, origin=(100, 100))
|
|
108
|
+
```
|
|
109
|
+
|
|
110
|
+
### Scale
|
|
111
|
+
|
|
112
|
+
```python
|
|
113
|
+
# Scale uniformly
|
|
114
|
+
scaled = gdf.geometry.scale(xfact=2.0, yfact=2.0)
|
|
115
|
+
|
|
116
|
+
# Scale with origin
|
|
117
|
+
scaled = gdf.geometry.scale(xfact=2.0, yfact=2.0, origin='center')
|
|
118
|
+
```
|
|
119
|
+
|
|
120
|
+
### Translate
|
|
121
|
+
|
|
122
|
+
```python
|
|
123
|
+
# Shift coordinates
|
|
124
|
+
translated = gdf.geometry.translate(xoff=100, yoff=50)
|
|
125
|
+
```
|
|
126
|
+
|
|
127
|
+
### Skew
|
|
128
|
+
|
|
129
|
+
```python
|
|
130
|
+
# Shear transformation
|
|
131
|
+
skewed = gdf.geometry.skew(xs=15, ys=0, origin='center')
|
|
132
|
+
```
|
|
133
|
+
|
|
134
|
+
### Custom Affine Transform
|
|
135
|
+
|
|
136
|
+
```python
|
|
137
|
+
from shapely import affinity
|
|
138
|
+
|
|
139
|
+
# Apply 6-parameter affine transformation matrix
|
|
140
|
+
# [a, b, d, e, xoff, yoff]
|
|
141
|
+
transformed = gdf.geometry.affine_transform([1, 0, 0, 1, 100, 50])
|
|
142
|
+
```
|
|
143
|
+
|
|
144
|
+
## Geometric Properties
|
|
145
|
+
|
|
146
|
+
Access geometric properties (returns pandas Series):
|
|
147
|
+
|
|
148
|
+
```python
|
|
149
|
+
# Area
|
|
150
|
+
areas = gdf.geometry.area
|
|
151
|
+
|
|
152
|
+
# Length/perimeter
|
|
153
|
+
lengths = gdf.geometry.length
|
|
154
|
+
|
|
155
|
+
# Bounding box coordinates
|
|
156
|
+
bounds = gdf.geometry.bounds # Returns DataFrame with minx, miny, maxx, maxy
|
|
157
|
+
|
|
158
|
+
# Total bounds for entire GeoSeries
|
|
159
|
+
total_bounds = gdf.geometry.total_bounds # Returns array [minx, miny, maxx, maxy]
|
|
160
|
+
|
|
161
|
+
# Check geometry types
|
|
162
|
+
geom_types = gdf.geometry.geom_type
|
|
163
|
+
|
|
164
|
+
# Check if valid
|
|
165
|
+
is_valid = gdf.geometry.is_valid
|
|
166
|
+
|
|
167
|
+
# Check if empty
|
|
168
|
+
is_empty = gdf.geometry.is_empty
|
|
169
|
+
```
|
|
170
|
+
|
|
171
|
+
## Geometric Relationships
|
|
172
|
+
|
|
173
|
+
Binary predicates testing relationships:
|
|
174
|
+
|
|
175
|
+
```python
|
|
176
|
+
# Within
|
|
177
|
+
gdf1.geometry.within(gdf2.geometry)
|
|
178
|
+
|
|
179
|
+
# Contains
|
|
180
|
+
gdf1.geometry.contains(gdf2.geometry)
|
|
181
|
+
|
|
182
|
+
# Intersects
|
|
183
|
+
gdf1.geometry.intersects(gdf2.geometry)
|
|
184
|
+
|
|
185
|
+
# Touches
|
|
186
|
+
gdf1.geometry.touches(gdf2.geometry)
|
|
187
|
+
|
|
188
|
+
# Crosses
|
|
189
|
+
gdf1.geometry.crosses(gdf2.geometry)
|
|
190
|
+
|
|
191
|
+
# Overlaps
|
|
192
|
+
gdf1.geometry.overlaps(gdf2.geometry)
|
|
193
|
+
|
|
194
|
+
# Covers
|
|
195
|
+
gdf1.geometry.covers(gdf2.geometry)
|
|
196
|
+
|
|
197
|
+
# Covered by
|
|
198
|
+
gdf1.geometry.covered_by(gdf2.geometry)
|
|
199
|
+
```
|
|
200
|
+
|
|
201
|
+
## Point Extraction
|
|
202
|
+
|
|
203
|
+
Extract specific points from geometries:
|
|
204
|
+
|
|
205
|
+
```python
|
|
206
|
+
# Representative point (guaranteed to be within geometry)
|
|
207
|
+
rep_points = gdf.geometry.representative_point()
|
|
208
|
+
|
|
209
|
+
# Interpolate point along line at distance
|
|
210
|
+
points = line_gdf.geometry.interpolate(distance=10)
|
|
211
|
+
|
|
212
|
+
# Interpolate point at normalized distance (0 to 1)
|
|
213
|
+
midpoints = line_gdf.geometry.interpolate(distance=0.5, normalized=True)
|
|
214
|
+
```
|
|
215
|
+
|
|
216
|
+
## Delaunay Triangulation
|
|
217
|
+
|
|
218
|
+
```python
|
|
219
|
+
# Create triangulation
|
|
220
|
+
triangles = gdf.geometry.delaunay_triangles()
|
|
221
|
+
```
|