Cropsar_px process migration #78
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,151 @@ | ||
| { | ||
| "id": "cropsar_px", | ||
| "type": "Feature", | ||
| "conformsTo": [ | ||
| "http://www.opengis.net/spec/ogcapi-records-1/1.0/req/record-core" | ||
| ], | ||
| "geometry": null, | ||
| "properties": { | ||
| "created": "2024-10-03T00:00:00Z", | ||
| "updated": "2024-10-03T00:00:00Z", | ||
| "type": "apex_algorithm", | ||
| "title": "Cloud-free monitoring using Sentinel satellites", | ||
| "description": "The `CropSAR_px` process produces Sentinel-2 data cloud-free with a regularity of five-day intervals. \nIn the current version of the service, the output types supported include:\n\n- NDVI\n- FAPAR\n- FCOVER\n\n> The 'startdate' parameter corresponds to the date of the first image in the result. \n> From this start date, a new image will be generated every five days up to, or beyond, the specified end date.\n\n## Usage\n\nThe following example demonstrates how the 'CropSAR_px' process can be executed using an OpenEO batch job. \nThis batch job produces a netCDF file containing the results. \nAdditionally, the `GeoTIFF` format can be specified to yield separate files for each date. \n\n> Note that generating multiple GeoTIFF files as output is a unique feature available only in a batch job.\n\nBy default, the output variable is set to NDVI.\nHowever, by supplying one of the supported values listed above to the output parameter, a different result can be obtained.", | ||
| "cost_estimate": 50, | ||
| "cost_unit": "platform credits per km²", | ||
| "keywords": [ | ||
| "agriculture", | ||
| "crops" | ||
| ], | ||
| "language": { | ||
| "code": "en-US", | ||
| "name": "English (United States)" | ||
| }, | ||
| "languages": [ | ||
| { | ||
| "code": "en-US", | ||
| "name": "English (United States)" | ||
| } | ||
| ], | ||
| "contacts": [ | ||
| { | ||
| "name": "Stijn Caerts", | ||
| "position": "Researcher", | ||
| "organization": "VITO", | ||
| "links": [ | ||
| { | ||
| "href": "https://www.vito.be/", | ||
| "rel": "about", | ||
| "type": "text/html" | ||
| } | ||
| ], | ||
| "contactInstructions": "Contact via VITO", | ||
| "roles": [ | ||
| "principal investigator" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Bram Janssen", | ||
| "position": "Researcher", | ||
| "organization": "VITO", | ||
| "links": [ | ||
| { | ||
| "href": "https://www.vito.be/", | ||
| "rel": "about", | ||
| "type": "text/html" | ||
| } | ||
| ], | ||
| "contactInstructions": "Contact via VITO", | ||
| "roles": [ | ||
| "service provider" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Pratichhya Sharma", | ||
| "position": "Researcher", | ||
| "organization": "VITO", | ||
| "links": [ | ||
| { | ||
| "href": "https://www.vito.be/", | ||
| "rel": "about", | ||
| "type": "text/html" | ||
| } | ||
| ], | ||
| "contactInstructions": "Contact via VITO", | ||
| "roles": [ | ||
| "service provider" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "VITO", | ||
| "links": [ | ||
| { | ||
| "href": "https://www.vito.be/", | ||
| "rel": "about", | ||
| "type": "text/html" | ||
| } | ||
| ], | ||
| "contactInstructions": "SEE WEBSITE", | ||
| "roles": [ | ||
| "processor" | ||
| ] | ||
| } | ||
| ], | ||
| "themes": [ | ||
| { | ||
| "concepts": [ | ||
| { | ||
| "id": "Leaf Area Index (LAI)" | ||
| }, | ||
| { | ||
| "id": "Fraction of Absorbed Photosynthetic Active Radiation (fAPAR)" | ||
| }, | ||
| { | ||
| "id": "Fraction of Vegetation Coverage (fCOVER)" | ||
| }, | ||
| { | ||
| "id": "Sentinel-2 MSI" | ||
| }, | ||
| { | ||
| "id": "Canopy Water Content (CWC)" | ||
| }, | ||
| { | ||
| "id": "Canopy Chlorophyll Content (CCC)" | ||
| } | ||
| ], | ||
| "scheme": "https://gcmd.earthdata.nasa.gov/kms/concepts/concept_scheme/sciencekeywords" | ||
| } | ||
| ], | ||
| "formats": [ | ||
| { | ||
| "name": "GeoTiff" | ||
| } | ||
| ], | ||
| "license": "other" | ||
| }, | ||
| "linkTemplates": [], | ||
| "links": [ | ||
| { | ||
| "rel": "openeo-process", | ||
| "type": "application/json", | ||
| "title": "openEO Process Definition", | ||
| "href": "https://raw.githubusercontent.com/ESA-APEx/apex_algorithms/3215de22eded7c87c46122f073d15c7258af26b4/openeo_udp/cropsar_px/cropsar_px.json" | ||
| }, | ||
| { | ||
| "rel": "service", | ||
| "type": "application/json", | ||
| "title": "CDSE openEO federation", | ||
| "href": "https://openeofed.dataspace.copernicus.eu" | ||
| }, | ||
| { | ||
| "rel": "license", | ||
| "href": "https://apex.esa.int/license" | ||
| }, | ||
| { | ||
| "rel": "example", | ||
| "type": "application/json", | ||
| "title": "Example output", | ||
| "href": "https://s3.waw3-1.cloudferro.com/swift/v1/apex-examples/cropsar_px/cropsar_px.nc" | ||
| } | ||
| ] | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| [ | ||
| { | ||
| "id": "cropsar_px", | ||
| "type": "openeo", | ||
| "description": "Calculating FAPAR using Cropsar service available in Copernicus Data Space Ecosystem", | ||
| "backend": "openeofed.dataspace.copernicus.eu", | ||
| "process_graph": { | ||
| "cropsarpx1": { | ||
| "arguments": { | ||
| "enddate": "2021-01-20", | ||
| "output": "NDVI", | ||
| "spatial_extent": { | ||
| "coordinates": [ | ||
| [ | ||
| [ | ||
| 5.178303838475193, | ||
| 51.252856237848164 | ||
| ], | ||
| [ | ||
| 5.178003609252369, | ||
| 51.25109194151486 | ||
| ], | ||
| [ | ||
| 5.179280940922463, | ||
| 51.25103833409551 | ||
| ], | ||
| [ | ||
| 5.179565949577788, | ||
| 51.25278555186941 | ||
| ], | ||
| [ | ||
| 5.178303838475193, | ||
| 51.252856237848164 | ||
| ] | ||
| ] | ||
| ], | ||
| "type": "Polygon" | ||
| }, | ||
| "startdate": "2021-01-01" | ||
| }, | ||
| "namespace": "https://raw.githubusercontent.com/ESA-APEx/apex_algorithms/3215de22eded7c87c46122f073d15c7258af26b4/openeo_udp/cropsar_px/cropsar_px.json", | ||
| "process_id": "cropsar_px" | ||
| } | ||
| }, | ||
| "reference_data": { | ||
| "cropsar_px.nx": "https://s3.waw3-1.cloudferro.com/swift/v1/apex-examples/cropsar_px/cropsar_px.nc" | ||
| } | ||
| } | ||
| ] | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| # CropSAR_px | ||
|
|
||
| ## Description | ||
|
|
||
| The `CropSAR_px` process produces Sentinel-2 data cloud-free with a regularity of five-day intervals. | ||
| In the current version of the service, the output types supported include: | ||
|
|
||
| - NDVI | ||
| - FAPAR | ||
| - FCOVER | ||
|
|
||
| > The 'startdate' parameter corresponds to the date of the first image in the result. | ||
| > From this start date, a new image will be generated every five days up to, or beyond, the specified end date. | ||
|
|
||
| ## Usage | ||
|
|
||
| The following example demonstrates how the 'CropSAR_px' process can be executed using an OpenEO batch job. | ||
| This batch job produces a netCDF file containing the results. | ||
| Additionally, the `GeoTIFF` format can be specified to yield separate files for each date. | ||
|
|
||
| ```python | ||
|
|
||
| import openeo | ||
| connection = openeo.connect("openeofed.dataspace.copernicus.eu").authenticate_oidc() | ||
|
|
||
|
There was a problem hiding this comment. Accoring to the documentation: We recommend including these sections: Description: A short description of what the algorithm does. |
||
| spat_ext = { | ||
| "coordinates": [ | ||
| [ | ||
| [ | ||
| 5.178303838475193, | ||
| 51.252856237848164 | ||
| ], | ||
| [ | ||
| 5.178003609252369, | ||
| 51.25109194151486 | ||
| ], | ||
| [ | ||
| 5.179280940922463, | ||
| 51.25103833409551 | ||
| ], | ||
| [ | ||
| 5.179565949577788, | ||
| 51.25278555186941 | ||
| ], | ||
| [ | ||
| 5.178303838475193, | ||
| 51.252856237848164 | ||
| ] | ||
| ] | ||
| ], | ||
| "type": "Polygon" | ||
| } | ||
|
|
||
| startdate = "2021-01-01" | ||
| enddate = "2021-01-20" | ||
| cropsarpx_id = 'cropsar_px' | ||
| namespace = "REPLACE_WITH_NAMESPACE" | ||
|
|
||
| cropsarpx = connection.datacube_from_process( | ||
| process_id=cropsarpx_id, | ||
| namespace=namespace, | ||
| spatial_extent=spat_ext, | ||
| startdate=startdate, | ||
| enddate=enddate, | ||
| output="NDVI" | ||
| ) | ||
|
|
||
| cropsarpx.execute_batch('results/cropsar_px_290125.nc', title=f'cropsar_px', job_options={ | ||
| "executor-memory": "2G", | ||
| "executor-memoryOverhead": "500m", | ||
| "python-memory": "3G" | ||
| }) | ||
|
|
||
| ``` | ||
|
|
||
| ## Parameters | ||
|
|
||
| The `CropSAR_px` process requires the following parameters: | ||
|
|
||
| - `startdate` (string): The start date of the time series. | ||
| - `enddate` (string): The end date of the time series. | ||
| - `spatial_extent` (dict): The spatial extent of the area of interest. | ||
| - `output` (string): The output type of the process. The supported output types are `NDVI`, `FAPAR`, and `FCOVER`. | ||
|
|
||
| When compared with few others processes shared in this repository, the `CropSAR_px` process require temporal extent to be defined using `startdate` and `enddate` parameters. It is due to the nature of the CropSAR_px workflow, which performs the date-shift of 90 days preceeding the start date and postceeding the end date. | ||
|
|
||
|
|
||
| Refer to this [blog post](https://blog.vito.be/remotesensing/cropsar2023) for more information on how to run batch jobs. | ||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
according to the documentation:
Temporal filtering
For openEO processes that support arbitrary temporal ranges, we recommend using temporal_extent as the name of parameter to ensure consistency with other openEO processes, such as load_collection.
Many cases also require a time range with a fixed length. In such a case, you can allow to specify only the start or end date, and use the date_shift process to construct the second date in the temporal interval, ensuring a fixed length. This avoids faulty user input.
https://esa-apex.github.io/apex_documentation/guides/udp_writer_guide.html
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yes, however, in this case, it takes the start and end date separately and has date_shift implemented in the source code itself. So in that scenario I chose to go ahead with the date schema itself.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
sounds good, do make sure it is well documented