Merge pull request #197 from ESA-APEx/parceldelineation

Add parcel delineation UDP

Author: HansVRP

algorithm_catalog/vito/parcel_delineation/benchmark_scenarios/parcel_delineation.json

@@ -0,0 +1,28 @@
+[
+    {
+        "id": "parcel_delineation",
+        "type": "openeo",
+        "description": "Parcel Delineation based on ML using Sentinal-2",
+        "backend": "openeo.dataspace.copernicus.eu",
+        "process_graph": {
+            "parcel_delineation1": {
+                "process_id": "parcel_delineation",
+                "namespace": "https://raw.githubusercontent.com/ESA-APEx/apex_algorithms/b828eecc13f1bd4d012576d746329041cf840c61/algorithm_catalog/vito/parcel_delineation/openeo_udp/parcel_delineation.json",
+                "arguments": {
+                    "spatial_extent": {
+			"west": 5.0,
+			"south": 51.2,
+			"east": 5.1,
+			"north": 51.3
+		    },
+                    "temporal_extent": [
+                        "2021-01-01",
+                        "2021-12-31"
+                    ]
+                },
+                "result": true
+            }
+        },
+        "reference_data": {}
+    }
+]

algorithm_catalog/vito/parcel_delineation/openeo_udp/README.md

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+# Parcel delineation
+This is an [openEO](https://openeo.org/) example for delineating agricultural parcels based on a neural network, using Sentinel-2 input data.
+
+[VITO Remote Sensing](https://remotesensing.vito.be)

algorithm_catalog/vito/parcel_delineation/openeo_udp/generate.py

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+import json
+from pathlib import Path
+import openeo
+from openeo.api.process import Parameter
+from openeo.rest.udp import build_process_dict
+
+
+def generate() -> dict:
+    # DEFINE PARAMETERS
+    # define spatial_extent
+    spatial_extent = Parameter.bounding_box(
+        name="spatial_extent", default={"west": 5.0, "south": 51.2, "east": 5.1, "north": 51.3}
+    )
+    # define temporal_extent
+    temporal_extent = Parameter.temporal_interval(name="temporal_extent", default=["2021-01-01", "2021-12-31"])
+
+    # backend to connect and load
+    backend_url = "openeo.dataspace.copernicus.eu/"
+    conn = openeo.connect(backend_url).authenticate_oidc()
+
+    # Compute cloud mask, and filter input data based on cloud mask.
+    # compute cloud mask using the SCL band
+    scl = conn.load_collection(
+        "SENTINEL2_L2A",
+        temporal_extent=temporal_extent,
+        spatial_extent=spatial_extent,
+        bands=["SCL"],
+        max_cloud_cover=10,
+    )
+    cloud_mask = scl.process(
+        "to_scl_dilation_mask",
+        data=scl,
+        kernel1_size=17,
+        kernel2_size=77,
+        mask1_values=[2, 4, 5, 6, 7],
+        mask2_values=[3, 8, 9, 10, 11],
+        erosion_kernel_size=3,
+    )
+
+    # Load s2 bands and set max cloud cover to be less than 10%
+    s2_bands = conn.load_collection(
+        collection_id="SENTINEL2_L2A",
+        spatial_extent=spatial_extent,
+        temporal_extent=temporal_extent,
+        bands=["B04", "B08"],
+        max_cloud_cover=10,
+    )
+    # mask data with cloud mask
+    s2_bands_masked = s2_bands.mask(cloud_mask)
+
+    # The delineation will be estimated based on the NDVI. The `ndvi` process can be used for these calculations.
+    ndviband = s2_bands_masked.ndvi(red="B04", nir="B08")
+
+    # Apply ML algorithm
+    # apply a neural network, requires 128x128 pixel 'chunks' as input.
+    segment_udf = openeo.UDF.from_file("udf_segmentation.py")
+    segmentationband = ndviband.apply_neighborhood(
+        process=segment_udf,
+        size=[{"dimension": "x", "value": 64, "unit": "px"}, {"dimension": "y", "value": 64, "unit": "px"}],
+        overlap=[{"dimension": "x", "value": 32, "unit": "px"}, {"dimension": "y", "value": 32, "unit": "px"}],
+    )
+
+    # Postprocess the output from the neural network using a sobel filter and
+    # Felzenszwalb's algorithm, which are then merged.
+    segment_postprocess_udf = openeo.UDF.from_file("udf_sobel_felzenszwalb.py")
+    sobel_felzenszwalb = segmentationband.apply_neighborhood(
+        process=segment_postprocess_udf,
+        size=[{"dimension": "x", "value": 2048, "unit": "px"}, {"dimension": "y", "value": 2048, "unit": "px"}],
+        overlap=[{"dimension": "x", "value": 0, "unit": "px"}, {"dimension": "y", "value": 0, "unit": "px"}],
+    )
+    job_options = {
+        "udf-dependency-archives": [
+            "https://artifactory.vgt.vito.be/auxdata-public/openeo/onnx_dependencies.zip#onnx_deps",
+            "https://artifactory.vgt.vito.be/artifactory/auxdata-public/openeo/parcelDelination/BelgiumCropMap_unet_3BandsGenerator_Models.zip#onnx_models",
+        ],
+        "driver-memory": "500m",
+        "driver-memoryOverhead": "1000m",
+        "executor-memory": "1000m",
+        "executor-memoryOverhead": "500m",
+        "python-memory": "4200m",
+    }
+
+    # Build the process dictionary
+    return build_process_dict(
+        process_graph=sobel_felzenszwalb,
+        process_id="parcel_delineation",
+        summary="Parcel delineation using Sentinel-2 data retrieved from the CDSE and processed on openEO.",
+        description="Parcel delineation using Sentinel-2",
+        parameters=[spatial_extent, temporal_extent],
+        default_job_options=job_options,
+    )
+
+
+if __name__ == "__main__":
+    # save the generated process to a file
+    output_path = Path(__file__).parent
+    print(output_path)
+    output_path.mkdir(parents=True, exist_ok=True)
+
+    # Save the generated process to a file
+    with open(output_path / "parcel_delineation.json", "w") as f:
+        json.dump(generate(), f, indent=2)