234-refactor-point-extractions

environment.yml

@@ -34,8 +34,8 @@ dependencies:
   - tqdm
   - pip:
     - duckdb==1.1.0
-    - h3==3.7.7
-    - openeo-gfmap==0.2.0
+    - h3==4.1.0
+    - openeo-gfmap==0.3.0
     - git+https://github.com/worldcereal/worldcereal-classification
     - git+https://github.com/WorldCereal/presto-worldcereal.git@croptype
 

pyproject.toml

@@ -37,13 +37,13 @@ dependencies = [
     "cftime",  
     "geojson",  
     "geopandas",  
-    "h3==3.7.7",  
+    "h3==4.1.0",  
     "h5netcdf>=1.1.0",  
     "loguru>=0.7.2",  
     "netcdf4<=1.6.4",  
     "numpy<2.0.0",  
     "openeo==0.31.0",  
-    "openeo-gfmap==0.2.0",  
+    "openeo-gfmap==0.3.0",  
     "pyarrow",  
     "pydantic==2.8.0",  
     "rioxarray>=0.13.0",  

scripts/extractions/extract.py

@@ -103,7 +103,7 @@ def prepare_job_dataframe(
     pipeline_log.info("Preparing the job dataframe.")
 
     # Filter the input dataframe to only keep the locations to extract
-    input_df = input_df[input_df["extract"] == extract_value].copy()
+    input_df = input_df[input_df["extract"] >= extract_value].copy()
 
     # Split the locations into chunks of max_locations
     split_dfs = []
@@ -144,9 +144,9 @@ def prepare_job_dataframe(
 def setup_extraction_functions(
     collection: ExtractionCollection,
     extract_value: int,
-    memory: str,
-    python_memory: str,
-    max_executors: int,
+    memory: typing.Union[str, None],
+    python_memory: typing.Union[str, None],
+    max_executors: typing.Union[int, None],
 ) -> tuple[typing.Callable, typing.Callable, typing.Callable]:
     """Setup the datacube creation, path generation and post-job action
     functions for the given collection. Returns a tuple of three functions:
@@ -158,33 +158,33 @@ def setup_extraction_functions(
     datacube_creation = {
         ExtractionCollection.PATCH_SENTINEL1: partial(
             create_job_patch_s1,
-            executor_memory=memory,
-            python_memory=python_memory,
-            max_executors=max_executors,
+            executor_memory=memory if memory is not None else "1800m",
+            python_memory=python_memory if python_memory is not None else "1900m",
+            max_executors=max_executors if max_executors is not None else 22,
         ),
         ExtractionCollection.PATCH_SENTINEL2: partial(
             create_job_patch_s2,
-            executor_memory=memory,
-            python_memory=python_memory,
-            max_executors=max_executors,
+            executor_memory=memory if memory is not None else "1800m",
+            python_memory=python_memory if python_memory is not None else "1900m",
+            max_executors=max_executors if max_executors is not None else 22,
         ),
         ExtractionCollection.PATCH_METEO: partial(
             create_job_patch_meteo,
-            executor_memory=memory,
-            python_memory=python_memory,
-            max_executors=max_executors,
+            executor_memory=memory if memory is not None else "1800m",
+            python_memory=python_memory if python_memory is not None else "1000m",
+            max_executors=max_executors if max_executors is not None else 22,
         ),
         ExtractionCollection.PATCH_WORLDCEREAL: partial(
             create_job_patch_worldcereal,
-            executor_memory=memory,
-            python_memory=python_memory,
-            max_executors=max_executors,
+            executor_memory=memory if memory is not None else "1800m",
+            python_memory=python_memory if python_memory is not None else "3000m",
+            max_executors=max_executors if max_executors is not None else 22,
         ),
         ExtractionCollection.POINT_WORLDCEREAL: partial(
             create_job_point_worldcereal,
-            executor_memory=memory,
-            python_memory=python_memory,
-            max_executors=max_executors,
+            executor_memory=memory if memory is not None else "1800m",
+            python_memory=python_memory if python_memory is not None else "3000m",
+            max_executors=max_executors if max_executors is not None else 22,
         ),
     }
 
@@ -334,6 +334,102 @@ def manager_main_loop(
             raise e
 
 
+def run_extractions(
+    collection: ExtractionCollection,
+    output_folder: Path,
+    input_df: Path,
+    max_locations_per_job: int = 500,
+    memory: str = "1800m",
+    python_memory: str = "1900m",
+    max_executors: int = 22,
+    parallel_jobs: int = 2,
+    restart_failed: bool = False,
+    extract_value: int = 1,
+    backend=Backend.CDSE,
+) -> None:
+    """Main function responsible for launching point and patch extractions.
+
+    Parameters
+    ----------
+    collection : ExtractionCollection
+        The collection to extract. Most popular: PATCH_WORLDCEREAL, POINT_WORLDCEREAL
+    output_folder : Path
+        The folder where to store the extracted data
+    input_df : Path
+        Path to the input dataframe containing the geometries
+        for which extractions need to be done
+    max_locations_per_job : int, optional
+        The maximum number of locations to extract per job, by default 500
+    memory : str, optional
+        Memory to allocate for the executor, by default "1800m"
+    python_memory : str, optional
+        Memory to allocate for the python processes as well as OrfeoToolbox in the executors,
+        by default "1900m"
+    max_executors : int, optional
+        Number of executors to run, by default 22
+    parallel_jobs : int, optional
+        The maximum number of parallel jobs to run at the same time, by default 10
+    restart_failed : bool, optional
+        Restart the jobs that previously failed, by default False
+    extract_value : int, optional
+        All samples with an "extract" value equal or larger than this one, will be extracted, by default 1
+    backend : openeo_gfmap.Backend, optional
+        cloud backend where to run the extractions, by default Backend.CDSE
+
+    Raises
+    ------
+    ValueError
+        _description_
+    """
+
+    if not output_folder.is_dir():
+        output_folder.mkdir(parents=True)
+
+    tracking_df_path = output_folder / "job_tracking.csv"
+
+    # Load the input dataframe and build the job dataframe
+    input_df = load_dataframe(input_df)
+
+    job_df = None
+    if not tracking_df_path.exists():
+        job_df = prepare_job_dataframe(
+            input_df, collection, max_locations_per_job, extract_value, backend
+        )
+
+    # Setup the extraction functions
+    pipeline_log.info("Setting up the extraction functions.")
+    datacube_fn, path_fn, post_job_fn = setup_extraction_functions(
+        collection, extract_value, memory, python_memory, max_executors
+    )
+
+    # Initialize and setups the job manager
+    pipeline_log.info("Initializing the job manager.")
+
+    job_manager = GFMAPJobManager(
+        output_dir=output_folder,
+        output_path_generator=path_fn,
+        post_job_action=post_job_fn,
+        poll_sleep=60,
+        n_threads=4,
+        restart_failed=restart_failed,
+        stac_enabled=False,
+    )
+
+    job_manager.add_backend(
+        backend.value,
+        cdse_connection,
+        parallel_jobs=parallel_jobs,
+    )
+
+    manager_main_loop(job_manager, collection, job_df, datacube_fn, tracking_df_path)
+
+    pipeline_log.info("Extraction completed successfully.")
+    send_notification(
+        title=f"WorldCereal Extraction {collection.value} - Completed",
+        message="Extractions have been completed successfully.",
+    )
+
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Extract data from a collection")
     parser.add_argument(
@@ -372,8 +468,8 @@ def manager_main_loop(
     parser.add_argument(
         "--parallel_jobs",
         type=int,
-        default=10,
-        help="The maximum number of parrallel jobs to run at the same time.",
+        default=2,
+        help="The maximum number of parallel jobs to run at the same time.",
     )
     parser.add_argument(
         "--restart_failed",
@@ -389,55 +485,16 @@ def manager_main_loop(
 
     args = parser.parse_args()
 
-    # Fetches values and setups hardocded values
-    collection = args.collection
-    extract_value = args.extract_value
-    max_locations_per_job = args.max_locations
-    backend = Backend.CDSE
-
-    if not args.output_folder.is_dir():
-        raise ValueError(f"Output folder {args.output_folder} does not exist.")
-
-    tracking_df_path = Path(args.output_folder) / "job_tracking.csv"
-
-    # Load the input dataframe and build the job dataframe
-    input_df = load_dataframe(args.input_df)
-
-    job_df = None
-    if not tracking_df_path.exists():
-        job_df = prepare_job_dataframe(
-            input_df, collection, max_locations_per_job, extract_value, backend
-        )
-
-    # Setup the extraction functions
-    pipeline_log.info("Setting up the extraction functions.")
-    datacube_fn, path_fn, post_job_fn = setup_extraction_functions(
-        collection, extract_value, args.memory, args.python_memory, args.max_executors
-    )
-
-    # Initialize and setups the job manager
-    pipeline_log.info("Initializing the job manager.")
-
-    job_manager = GFMAPJobManager(
-        output_dir=args.output_folder,
-        output_path_generator=path_fn,
-        post_job_action=post_job_fn,
-        poll_sleep=60,
-        n_threads=4,
-        restart_failed=args.restart_failed,
-        stac_enabled=False,
-    )
-
-    job_manager.add_backend(
-        Backend.CDSE.value,
-        cdse_connection,
+    run_extractions(
+        collection=args.collection,
+        output_folder=args.output_folder,
+        input_df=args.input_df,
+        max_locations_per_job=args.max_locations,
+        memory=args.memory,
+        python_memory=args.python_memory,
+        max_executors=args.max_executors,
         parallel_jobs=args.parallel_jobs,
-    )
-
-    manager_main_loop(job_manager, collection, job_df, datacube_fn, tracking_df_path)
-
-    pipeline_log.info("Extraction completed successfully.")
-    send_notification(
-        title=f"WorldCereal Extraction {collection.value} - Completed",
-        message="Extractions have been completed successfully.",
+        restart_failed=args.restart_failed,
+        extract_value=args.extract_value,
+        backend=Backend.CDSE,
     )

scripts/extractions/patch_extractions/extract_patch_meteo.py

@@ -24,11 +24,11 @@ def create_job_dataframe_patch_meteo(
 def create_job_patch_meteo(
     row: pd.Series,
     connection: openeo.DataCube,
-    provider=None,
-    connection_provider=None,
-    executor_memory: str = "2G",
-    python_memory: str = "1G",
-    max_executors: int = 22,
+    provider,
+    connection_provider,
+    executor_memory: str,
+    python_memory: str,
+    max_executors: int,
 ) -> gpd.GeoDataFrame:
     start_date = row.start_date
     end_date = row.end_date

scripts/extractions/patch_extractions/extract_patch_s1.py

@@ -122,9 +122,9 @@ def create_job_patch_s1(
     connection: openeo.DataCube,
     provider,
     connection_provider,
-    executor_memory: str = "5G",
-    python_memory: str = "2G",
-    max_executors: int = 22,
+    executor_memory: str,
+    python_memory: str,
+    max_executors: int,
 ) -> openeo.BatchJob:
     """Creates an OpenEO BatchJob from the given row information. This job is a
     S1 patch of 32x32 pixels at 20m spatial resolution."""

scripts/extractions/patch_extractions/extract_patch_s2.py

@@ -70,11 +70,11 @@ def create_job_dataframe_patch_s2(
 def create_job_patch_s2(
     row: pd.Series,
     connection: openeo.DataCube,
-    provider=None,
-    connection_provider=None,
-    executor_memory: str = "5G",
-    python_memory: str = "2G",
-    max_executors: int = 22,
+    provider,
+    connection_provider,
+    executor_memory: str,
+    python_memory: str,
+    max_executors: int,
 ) -> gpd.GeoDataFrame:
     start_date = row.start_date
     end_date = row.end_date

scripts/extractions/patch_extractions/extract_patch_worldcereal.py

@@ -124,9 +124,9 @@ def create_job_patch_worldcereal(
     connection: openeo.DataCube,
     provider,
     connection_provider,
-    executor_memory: str = "5G",
-    python_memory: str = "2G",
-    max_executors: int = 22,
+    executor_memory: str,
+    python_memory: str,
+    max_executors: int,
 ) -> openeo.BatchJob:
     """Creates an OpenEO BatchJob from the given row information."""
 
@@ -398,13 +398,16 @@ def post_job_action_patch_worldcereal(
 
 
 def generate_output_path_patch_worldcereal(
-    root_folder: Path, geometry_index: int, row: pd.Series, s2_grid: gpd.GeoDataFrame
+    root_folder: Path,
+    job_index: int,
+    row: pd.Series,
+    asset_id: str,
+    s2_grid: gpd.GeoDataFrame,
 ):
     """Generate the output path for the extracted data, from a base path and
     the row information.
     """
-    features = geojson.loads(row.geometry)
-    sample_id = features[geometry_index].properties.get("sample_id", None)
+    sample_id = asset_id.replace(".nc", "").replace("openEO_", "")
 
     s2_tile_id = row.s2_tile
     epsg = s2_grid[s2_grid.tile == s2_tile_id].iloc[0].epsg