Water bodies detection workflow v1.1.0

Water bodies detection based on NDWI and Otsu threshold applied to Sentinel-2 COG STAC items

This software is licensed under the terms of the license - SPDX short identifier:

2026-03-19 - 2026-03-20T21:28:32.321 Copyright EOAP -

Project Team

Authors

Name	Email	Organization	Role	Identifier
Brito, Fabrice	info@terradue.com	Terradue

Contributors

The are no contributors for this project.

Zarr Cloud-Native Format documentation

Zarr Cloud-Native Format documentation can be found on https://eoap.github.io/zarr-cloud-native-format/.

Runtime environment

Supported Operating Systems

Requirements

Software Source code

• Browsable version of the source repository;
• Continuous integration system used by the project;
• Issues, bugs, and feature requests should be submitted to the following issue management system for this project

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water-bodies

CWL Class

Workflow

Requirements

• ScatterFeatureRequirement
• SubworkflowFeatureRequirement
• SchemaDefRequirement

Inputs

Id	Type	Label	Doc
stac_api_endpoint	Any	STAC API endpoint	STAC API endpoint
collection	string	STAC collection	STAC collection identifier
bbox	array of double	Bounding box	Bounding box as [minx, miny, maxx, maxy]
start-datetime	One of: null string DateTime: value: string	Start time	Start time
end-datetime	One of: null string DateTime: value: string	End time	End time
limit	int	limit	limit
max-items	int	max-items	max-items
filter-lang	One of: null enum: cql2-json	Filter language	Filter language
filter	One of: null Any	Filter	Filter
bands	array of string	bands used for the NDWI	bands used for the NDWI
overview_levels	int	Number of Zarr overview levels	Number of multiscale overview levels generated by stac-zarr
continuous_overview_reducer	enum: mean max median nearest	Overview reducer for continuous variables	Reducer used for continuous variables when generating overviews (mean, max, median, nearest)
categorical_overview_reducer	enum: mean max median nearest	Overview reducer for categorical variables	Reducer used for categorical variables when generating overviews (mean, max, median, nearest)

Steps

Id	Runs	Label	Doc
build_search_request	#build_search_request	Build STAC search request	Build STACSearchSettings from bbox and query inputs
build_api_endpoint	#build_api_endpoint	Build STAC API endpoint	Normalize endpoint to APIEndpoint schema expected by discovery step
discovery	#stac-client	STAC API discovery	Discover STAC items from a STAC API endpoint based on a search request
convert_search	#convert-search	Convert Search	Convert Search results to get the item self hrefs and the area of interest
water_bodies	#detect_water_body	Water bodies detection	Water bodies detection based on NDWI and otsu threshold applied to each STAC item (sub-workflow)
stac-collection	#stac-collection	Create a STAC catalog with COG outputs	Create a STAC catalog with the detected water bodies COG outputs
stac_eopf_product	#stac-eopf-product	Create a EOPF Zarr store from a STAC catalog	Create a EOPF Zarr store from a STAC catalog with COG products
stac_zarr	#stac-zarr	Create a STAC Catalog for the Zarr store	Create a STAC Catalog for the Zarr store from the STAC catalog with COG outputs

Outputs

Id	Type	Label	Doc
zarr_stac_catalog	Directory	None	None
stac_catalog	Directory	None	None
eopf_product_stac_catalog	Directory	None	None

UML Diagrams

Activity diagram

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Component diagram

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Class diagram

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Sequence diagram

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State diagram

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build_search_request

build_search_request

CWL Class

ExpressionTool

Inputs

Id	Option	Type
collection	--collection	string
bbox	--bbox	array of double
start-datetime	--start-datetime	One of: null string DateTime: value: string
end-datetime	--end-datetime	One of: null string DateTime: value: string
limit	--limit	int
max-items	--max-items	int
filter-lang	--filter-lang	One of: null enum: cql2-json
filter	--filter	One of: null Any

Run in step

build_api_endpoint

build_api_endpoint

CWL Class

ExpressionTool

Inputs

Id	Option	Type
api_endpoint	--api_endpoint	Any

Run in step

discovery

stac-client

CWL Class

CommandLineTool

Inputs

Id	Option	Type
api_endpoint	--api_endpoint	APIEndpoint: url: URI: value: string headers: One of: null array of KeyValuePair: key: string value: string
search_request	--search_request	STACSearchSettings: bbox: One of: null array of double datetime: One of: null DateTime: value: string datetime-interval: One of: null DatetimeInterval: start: DateTime: value: string end: DateTime: value: string intersects: One of: null Point: type: enum: Point coordinates: array of double bbox: array of double MultiPoint: type: enum: MultiPoint coordinates: array of array of double bbox: array of double LineString: type: enum: LineString coordinates: array of double bbox: array of double MultiLineString: type: enum: MultiLineString coordinates: array of array of array of double bbox: array of double Polygon: type: enum: Polygon coordinates: array of array of array of double bbox: array of double MultiPolygon: type: enum: MultiPolygon coordinates: array of array of array of array of double bbox: array of double GeometryCollection: type: enum: GeometryCollection geometries: array of One of: Point: type: enum: Point coordinates: array of double bbox: array of double LineString: type: enum: LineString coordinates: array of double bbox: array of double Polygon: type: enum: Polygon coordinates: array of array of array of double bbox: array of double MultiPoint: type: enum: MultiPoint coordinates: array of array of double bbox: array of double MultiLineString: type: enum: MultiLineString coordinates: array of array of array of double bbox: array of double MultiPolygon: type: enum: MultiPolygon coordinates: array of array of array of array of double bbox: array of double bbox: array of double collections: One of: null array of string ids: One of: null array of string limit: One of: null int max-items: One of: null int fields: One of: null Fields: include: One of: null array of string exclude: One of: null array of string filter: One of: null Any filter-lang: One of: null enum: cql2-text cql2-json filter-crs: One of: null array of URI: value: string sortby: One of: null array of SortBy: field: string direction: enum: asc desc

Execution usage example:

stac-client search $(inputs.api_endpoint.url.value) ${ const args = []; const collections = inputs.search_request.collections; args.push('--collections', collections.join(",")); return args; } ${ const args = []; const bbox = inputs.search_request?.bbox; if (Array.isArray(bbox) && bbox.length >= 4) { args.push('--bbox', ...bbox.map(String)); } return args; } ${ const args = []; const limit = inputs.search_request?.limit; args.push("--limit", (limit ?? 10).toString()); return args; } ${ const maxItems = inputs.search_request?.['max-items']; return ['--max-items', (maxItems ?? 20).toString()]; } ${ const args = []; const filter = inputs.search_request?.filter; const filterLang = inputs.search_request?.['filter-lang']; if (filterLang) { args.push('--filter-lang', filterLang); } if (filter) { args.push('--filter', JSON.stringify(filter)); } return args; } ${ const datetime = inputs.search_request?.datetime; const datetimeInterval = inputs.search_request?.datetime_interval; if (datetime) { return ['--datetime', datetime]; } else if (datetimeInterval) { const start = datetimeInterval.start?.value || '..'; const end = datetimeInterval.end?.value || '..'; return ['--datetime', `${start}/${end}`]; } return []; } ${ const ids = inputs.search_request?.ids; const args = []; if (Array.isArray(ids) && ids.length > 0) { args.push('--ids', ...ids.map(String)); } return args; } ${ const intersects = inputs.search_request?.intersects; if (intersects) { return ['--intersects', JSON.stringify(intersects)]; } return []; } --save discovery-output.json \
--api_endpoint <API_ENDPOINT> \
--search_request <SEARCH_REQUEST>

Run in step

convert_search

convert-search

CWL Class

CommandLineTool

Inputs

Id	Option	Type
search_request	--search_request	STACSearchSettings: bbox: One of: null array of double datetime: One of: null DateTime: value: string datetime-interval: One of: null DatetimeInterval: start: DateTime: value: string end: DateTime: value: string intersects: One of: null Point: type: enum: Point coordinates: array of double bbox: array of double MultiPoint: type: enum: MultiPoint coordinates: array of array of double bbox: array of double LineString: type: enum: LineString coordinates: array of double bbox: array of double MultiLineString: type: enum: MultiLineString coordinates: array of array of array of double bbox: array of double Polygon: type: enum: Polygon coordinates: array of array of array of double bbox: array of double MultiPolygon: type: enum: MultiPolygon coordinates: array of array of array of array of double bbox: array of double GeometryCollection: type: enum: GeometryCollection geometries: array of One of: Point: type: enum: Point coordinates: array of double bbox: array of double LineString: type: enum: LineString coordinates: array of double bbox: array of double Polygon: type: enum: Polygon coordinates: array of array of array of double bbox: array of double MultiPoint: type: enum: MultiPoint coordinates: array of array of double bbox: array of double MultiLineString: type: enum: MultiLineString coordinates: array of array of array of double bbox: array of double MultiPolygon: type: enum: MultiPolygon coordinates: array of array of array of array of double bbox: array of double bbox: array of double collections: One of: null array of string ids: One of: null array of string limit: One of: null int max-items: One of: null int fields: One of: null Fields: include: One of: null array of string exclude: One of: null array of string filter: One of: null Any filter-lang: One of: null enum: cql2-text cql2-json filter-crs: One of: null array of URI: value: string sortby: One of: null array of SortBy: field: string direction: enum: asc desc
search_results	--search_results	File

Execution usage example:

/bin/sh run.sh \
--search_request <SEARCH_REQUEST> \
--search_results <SEARCH_RESULTS>

Run in step

water_bodies

detect_water_body

CWL Class

Workflow

Requirements

• ScatterFeatureRequirement

Inputs

Id	Type	Label	Doc
aoi	string	None	area of interest as a bounding box
epsg	string	None	EPSG code
bands	array of string	None	bands used for the NDWI
item	string	None	STAC item

Steps

Id	Runs	Label	Doc
crop	#crop	None	None
normalized_difference	#norm_diff	None	None
otsu	#otsu	None	None

Outputs

Id	Type	Label	Doc
detected_water_body	File	None	None
ndwi	File	None	None

UML Diagrams

Activity diagram

Learn more about the Activity diagram below.

Component diagram

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Class diagram

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Sequence diagram

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State diagram

Learn more about the State diagram below.

Run in step

crop

crop

CWL Class

CommandLineTool

Inputs

Id	Option	Type
item	--input-item	string
aoi	--aoi	string
epsg	--epsg	string
band	--band	string

Execution usage example:

python -m app \
--input-item <ITEM> \
--aoi <AOI> \
--epsg <EPSG> \
--band <BAND>

Run in step

normalized_difference

norm_diff

CWL Class

CommandLineTool

Inputs

Id	Option	Type
rasters	--rasters	array of File

Execution usage example:

python -m app \
--rasters <RASTERS>

Run in step

otsu

otsu

CWL Class

CommandLineTool

Inputs

Id	Option	Type
raster	--raster	File

Execution usage example:

python -m app \
--raster <RASTER>

Run in step

stac-collection

stac-collection

CWL Class

CommandLineTool

Inputs

Id	Option	Type
item	--item	array of string
rasters	--rasters	array of File
ndwis	--ndwis	array of File

Execution usage example:

stac-collection \
--item <ITEM> \
--rasters <RASTERS> \
--ndwis <NDWIS>

Run in step

stac_eopf_product

stac-eopf-product

CWL Class

CommandLineTool

Inputs

Id	Option	Type
stac_catalog	--stac-catalog	Directory
resolution	--resolution	One of: null float
chunks	--chunks	enum: manual auto
chunk_x	--chunk-x	int
chunk_y	--chunk-y	int
chunk_time	--chunk-time	int

Execution usage example:

stac-eopf-product \
--stac-catalog <STAC_CATALOG> \
(--resolution <RESOLUTION>) \
--chunks <CHUNKS> \
--chunk-x <CHUNK_X> \
--chunk-y <CHUNK_Y> \
--chunk-time <CHUNK_TIME>

Run in step

stac_zarr

stac-zarr

CWL Class

CommandLineTool

Inputs

Id	Option	Type
stac_catalog	--stac-catalog	Directory
overview_levels	--overview-levels	int
continuous_overview_reducer	--continuous-overview-reducer	enum: mean max median nearest
categorical_overview_reducer	--categorical-overview-reducer	enum: mean max median nearest
resolution	--resolution	One of: null float
chunks	--chunks	enum: manual auto
chunk_x	--chunk-x	int
chunk_y	--chunk-y	int
chunk_time	--chunk-time	int
consolidate	--consolidate	boolean
titiler_eopf_compatible	--titiler-eopf-compatible	boolean
stac_object_type	--stac-object-type	enum: collection item

Execution usage example:

stac-zarr \
--stac-catalog <STAC_CATALOG> \
--overview-levels <OVERVIEW_LEVELS> \
--continuous-overview-reducer <CONTINUOUS_OVERVIEW_REDUCER> \
--categorical-overview-reducer <CATEGORICAL_OVERVIEW_REDUCER> \
(--resolution <RESOLUTION>) \
--chunks <CHUNKS> \
--chunk-x <CHUNK_X> \
--chunk-y <CHUNK_Y> \
--chunk-time <CHUNK_TIME> \
--consolidate <CONSOLIDATE> \
--titiler-eopf-compatible <TITILER_EOPF_COMPATIBLE> \
--stac-object-type <STAC_OBJECT_TYPE>