diff --git a/README.md b/README.md index 18a6a9d..cb1241f 100644 --- a/README.md +++ b/README.md @@ -31,9 +31,11 @@ Requirements: ----------- OpenMPI >= 4.0.1. -datacube_stats on the refactor branch: https://github.com/opendatacube/datacube-stats/tree/refactor +datacube_stats https://github.com/opendatacube/datacube-stats/ -A database with postgis enabled. +dea_tools to retrieve the waterbody polygons + +A database with postgis enabled Other auxilliary data/scripts/shapefiles... @@ -57,7 +59,7 @@ How To: One'll need four steps. -- Collect all the polygons interact with/contained by the landsat path/row and ouput the results as `txt` in `$out`. +- Collect all the polygons intersect with/contained by the landsat path/row and ouput the results as `txt` in `$out`. Two reasons: 1. Aggregate by time if the polygon(s) would cover more than one path/row; 2. See `Secondly` in Section `Why` `mpirun python -m mpi4py.futures wetland_brutal.py wit-pathrow --output-location $out $shapefile` @@ -70,7 +72,15 @@ mpirun python -m mpi4py.futures wetland_brutal.py wit-pathrow --output-location with `$out = /g/data1a/u46/users/ea6141/wlinsight/sadew/new`, -and `$shapefile=/g/data1a/u46/users/ea6141/wlinsight/shapefiles/waterfowlandwetlands_3577.shp` +and `$shapefile=/g/data1a/u46/users/ea6141/wlinsight/shapefiles/waterfowlandwetlands_3577.shp`. + +Or specially for the polygons from DEA waterbodies + +`mpirun python -m mpi4py.futures wetland_brutal.py wit-pathrow --geo-hash $hashlist --output-location $out` + +where `$hashlist` is a file of geohash list of the waterbody polygons. + +Note: in this case, `$shapefile` has to be left as `default = None`. The results in your output folder would look like: ``` @@ -130,7 +140,12 @@ Here `$in` is `$out` from the last step Example: -`mpirun python -m mpi4py.futures wetland_brutal.py wit-query --input-folder /g/data1a/u46/users/ea6141/wlinsight/sadew/new --output-location /g/data1a/u46/users/ea6141/wlinsight/sadew/query --union True --product-yaml /g/data1a/u46/users/ea6141/wlinsight/fc_pd.yaml /g/data1a/u46/users/ea6141/wlinsight/shapefiles/waterfowlandwetlands_3577.shp` +`mpirun python -m mpi4py.futures wetland_brutal.py wit-query --input-folder /g/data1a/u46/users/ea6141/wlinsight/sadew/new --output-location /g/data1a/u46/users/ea6141/wlinsight/sadew/query --union True --product-yaml /g/data1a/u46/users/ea6141/wlinsight/fc_pd.yaml /g/data1a/u46/users/ea6141/wlinsight/shapefiles/waterfowlandwetlands_3577.shp`. + +Or for the polygons from DEA waterbodies + +`mpirun python -m mpi4py.futures wetland_brutal.py wit-query --geo-hash $hashlist --input-folder $in --output-location $out --union True --product-yaml $pd_yaml` + The result would look like ``` @@ -162,6 +177,10 @@ Example Or deal with the large polygons not contained by a single path/row, set `--aggregate 15` typically, i.e., `mpirun python -m mpi4py.futures wetland_brutal.py wit-cal --feature-list /g/data1a/u46/users/ea6141/wlinsight/anae/intersect_16_17_18_739_740_741.txt --datasets /g/data1a/u46/users/ea6141/wlinsight/anane/query/16_17_18_739_740_741.pkl --aggregate 15 --product-yaml /g/data1a/u46/users/ea6141/wlinsight/fc_pd.yaml /g/data1a/u46/users/ea6141/wlinsight/shapefiles/waterfowlandwetlands_3577.shp` +For the polygons in DEA waterbodies, do + +`mpirun python -m mpi4py.futures wetland_brutal.py wit-cal --geo-hash $hashlist --feature-list $feature --datasets $datasets --aggregate $aggregate --product-yaml $pd_yaml` + - Plot the data `python wetland_brutal.py wit-plot --output-location $folder --feature $id -n $property_1 -n $property_2 $shapefile` @@ -177,6 +196,12 @@ Example: `python wetland_brutal.py wit-plot --output-location sadew/results -n Site_Name shapefiles/waterfowlandwetlands_3577.shp` , where `Site_Name` is an entry under `properties` for each polygon in the shapefile. +For the polygons in DEA waterbodies, do + +`python wetland_brutal.py wit-plot --geo-hash $hashlist --output-location $folder --feature $id -n hash`, + +where `-n hash` is to specify the output file named by the geohash of the waterbody polygon. + The results look like: ``` [ea6141@vdi-n24 wlinsight]$ ls sadew/results/ diff --git a/examples/wit/wetland_brutal.py b/examples/wit/wetland_brutal.py index e7f100d..c192651 100644 --- a/examples/wit/wetland_brutal.py +++ b/examples/wit/wetland_brutal.py @@ -35,13 +35,6 @@ from wit_tooling import poly_wkt, convert_shape_to_polygon, query_wit_data, plot_to_png, query_wit_metrics, load_timeslice, generate_raster from dea_tools import waterbodies -try: - # this need to be fixed - sys.path.append(os.environ['HOME'] + "/datafile/dea-notebooks/Scripts/") - import dea_waterbodies -except: - print("tmp solution fix the water body lib properly please") - _LOG = logging.getLogger('wit_tool') stdout_hdlr = logging.StreamHandler(sys.stdout) formatter = logging.Formatter('[%(asctime)s.%(msecs)03d - %(levelname)s] %(message)s')