Correcting zonal stats for pyjeo (#27)

benchmarks_zonalstats/_benchmarks_pyjeo.py → benchmarks_zonalstats/benchmarks_pyjeo.py

@@ -2,12 +2,13 @@
 """
 Module to benchmark zonalstats.
 """
-
+import os
 from datetime import datetime
 import logging
 from pathlib import Path
 from typing import List
 
+import pandas as pd
 import geopandas as gpd
 import pyjeo as pj
 
@@ -27,11 +28,15 @@
 
 
 def _get_package() -> str:
-    return "pygeoprocessing"
+    return "pyjeo"
 
 
 def _get_version() -> str:
-    return f"{pj.__version__}".replace("v", "")
+    nproc = os.environ.get("OMP_NUM_THREADS")
+    if nproc is not None:
+        return f"{pj.__version__} {nproc} threads".replace("v", "")
+    else:
+        return f"{pj.__version__}".replace("v", "")
 
 
 def zonalstats_1band(tmp_dir: Path) -> List[RunResult]:
@@ -55,12 +60,13 @@ def zonalstats_1band(tmp_dir: Path) -> List[RunResult]:
     stats = pj.geometry.extract(
         vector_data,
         jim,
-        rule=["mean", "stdev", "count"],
+        # rule=["mean", "stdev", "count"],
+        rule=["mean", "stdev", "sum"],
         output="/vsimem/pj.json",
         oformat="GeoJSON",
     )
 
-    print(stats)
+    print(pd.DataFrame(stats.dict()))
 
     secs_taken = (datetime.now() - start_time).total_seconds()
     results.append(
@@ -76,7 +82,10 @@ def zonalstats_1band(tmp_dir: Path) -> List[RunResult]:
         )
     )
 
-    logger.info(f"took {secs_taken:.2f}s for {nb_poly} polygons, {len(stats)} results")
+    logger.info(
+        f"took {secs_taken:.2f}s for {nb_poly} polygons, "
+        f"{stats.properties.getFeatureCount()} results"
+    )
 
     # Return
     return results

results_zonalstats/benchmark_results.csv

@@ -1,5 +1,9 @@
 run_datetime,package,package_version,operation,operation_descr,secs_taken,run_details
 2023-03-22 22:51:12.810491,pygeoprocessing,2.4.0,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,52.998522,{}
-2023-03-22 22:52:01.739550,rasterstats,0.18.0,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,46.805364,{}
 2023-03-23 15:42:53.890171,geowombat,2.1.6,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,83.593633,{}
-2023-03-23 18:48:59.459963,pyqgis,3.28.2-Firenze,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,4.282287,{}
+2023-11-01 21:32:20.485871,pyjeo,1.1.6 1 threads,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,20.261884,{}
+2023-11-01 21:33:43.207416,pyjeo,1.1.6 2 threads,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,18.131106,{}
+2023-11-01 21:35:01.359175,pyjeo,1.1.6 3 threads,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,16.00101,{}
+2023-11-01 22:05:48.873225,pyjeo,1.1.6 4 threads,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,15.466929,{}
+2023-11-01 22:06:50.164708,rasterstats,0.19.0,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,58.699413,{}
+2023-11-01 22:06:58.247831,pyqgis,3.28.10-Firenze,zonalstats_1band,zonalstats of agri parcels (5000 polygons) + S2 NDVI BEFL,4.808703,{}