better raster-vector extraction

raster-vector-extract.py

@@ -0,0 +1,53 @@
+# +
+from exactextract import exact_extract
+from osgeo import ogr, gdal
+from pathlib import Path
+from joblib import Parallel, delayed
+
+def extract(raster, vector, layer, output = None):
+    if output is None:
+        output = Path(raster).with_suffix('.csv').name
+
+    gdal.UseExceptions()
+    ogr.UseExceptions()
+    rast = gdal.Open(raster)
+    vrt = f"""
+    <OGRVRTDataSource>
+        <OGRVRTWarpedLayer>
+            <OGRVRTLayer name="combined">
+                <SrcDataSource>{vector}</SrcDataSource>
+                <SrcLayer>{layer}</SrcLayer>
+            </OGRVRTLayer>
+            <TargetSRS>{rast.GetSpatialRef().ExportToWkt()}</TargetSRS>
+        </OGRVRTWarpedLayer>
+    </OGRVRTDataSource>
+    """
+    polys = ogr.Open(vrt)
+    exact_extract(rast, polys, 'mean', output='gdal', output_options = {'filename' : output })
+    return output
+    
+
+# -
+
+vector = "/home/rstudio/source.coop/cboettig/pad-us-3/PADUS3_0Geopackage.gpkg"
+layer = "PADUS3_0Combined_DOD_TRIB_Fee_Designation_Easement"
+
+rasters = [
+"/home/rstudio/boettiger-lab/us-pa-policy/hfp_2021_100m_v1-2_cog.tif",
+'/home/rstudio/source.coop/vizzuality/lg-land-carbon-data/deforest_carbon_100m_cog.tif',
+'/home/rstudio/source.coop/vizzuality/lg-land-carbon-data/natcrop_bii_100m_cog.tif',
+'/home/rstudio/source.coop/vizzuality/lg-land-carbon-data/natcrop_fii_100m_cog.tif',
+'/home/rstudio/source.coop/vizzuality/lg-land-carbon-data/natcrop_expansion_100m_cog.tif',
+'/home/rstudio/source.coop/vizzuality/lg-land-carbon-data/natcrop_reduction_100m_cog.tif',
+'/home/rstudio/source.coop/cboettig/carbon/cogs/irrecoverable_c_total_2018.tif',
+'/home/rstudio/source.coop/cboettig/carbon/cogs/manageable_c_total_2018.tif',
+'/home/rstudio/minio/shared-biodiversity/redlist/cog/combined_rwr_2022.tif',
+'/home/rstudio/minio/shared-biodiversity/redlist/cog/combined_sr_2022.tif',
+#'/home/rstudio/source.coop/cboettig/mobi/species-richness-all/SpeciesRichness_All.tif',
+#'/home/rstudio/source.coop/cboettig/mobi/range-size-rarity-all/RSR_All.tif',
+]
+# extract(rasters[0], vector, layer) # just one
+
+parallel_extract = delayed(extract)
+runner = Parallel(n_jobs=-1)
+runner(parallel_extract(i, vector, layer) for i in rasters)