def test_range_query_flat_to_df(self):
poi_point_rdd = WktReader.readToGeometryRDD(self.sc, bank_csv_path, 1,
False, False)
poi_point_rdd.analyze()
poi_point_rdd.spatialPartitioning(GridType.QUADTREE)
poi_point_rdd.buildIndex(IndexType.QUADTREE, False)
result = RangeQueryRaw.SpatialRangeQuery(
poi_point_rdd, loads("POLYGON((0 0, 0 20, 20 20, 20 0, 0 0))"),
True, True)
rdd = result.to_rdd()
assert rdd.collect().__len__() == 4
df_without_column_names = Adapter.toDf(result, self.spark)
raw_geometries = self.__row_to_list(df_without_column_names.collect())
assert [point[0].wkt for point in raw_geometries] == [
'POINT (9 8)', 'POINT (4 3)', 'POINT (12 1)', 'POINT (11 5)'
]
assert df_without_column_names.count() == 4
assert df_without_column_names.schema == StructType(
[StructField("geometry", GeometryType())])
df = Adapter.toDf(result, self.spark, ["poi_id", "poi_name"])
assert df.count() == 4
assert df.columns == ["geometry", "poi_id", "poi_name"]
def test_spatial_join_query_flat_to_df(self):
poi_point_rdd = WktReader.readToGeometryRDD(self.sc, bank_csv_path, 1,
False, False)
areas_polygon_rdd = WktReader.readToGeometryRDD(
self.sc, areas_csv_path, 1, False, False)
poi_point_rdd.analyze()
areas_polygon_rdd.analyze()
poi_point_rdd.spatialPartitioning(GridType.QUADTREE)
areas_polygon_rdd.spatialPartitioning(poi_point_rdd.getPartitioner())
jvm_sedona_rdd = JoinQueryRaw.SpatialJoinQueryFlat(
poi_point_rdd, areas_polygon_rdd, False, True)
pois_within_areas_with_default_column_names = Adapter.toDf(
jvm_sedona_rdd, self.spark)
assert pois_within_areas_with_default_column_names.count() == 5
pois_within_areas_with_passed_column_names = Adapter.toDf(
jvm_sedona_rdd, ["area_id", "area_name"], ["poi_id", "poi_name"],
self.spark)
assert pois_within_areas_with_passed_column_names.count() == 5
assert pois_within_areas_with_passed_column_names.columns == [
"leftgeometry", "area_id", "area_name", "rightgeometry", "poi_id",
"poi_name"
]
assert pois_within_areas_with_default_column_names.schema == StructType(
[
StructField("leftgeometry", GeometryType()),
StructField("rightgeometry", GeometryType()),
])
left_geometries_raw = pois_within_areas_with_default_column_names. \
selectExpr("ST_AsText(leftgeometry)"). \
collect()
left_geometries = self.__row_to_list(left_geometries_raw)
right_geometries_raw = pois_within_areas_with_default_column_names. \
selectExpr("ST_AsText(rightgeometry)"). \
collect()
right_geometries = self.__row_to_list(right_geometries_raw)
# Ignore the ordering of these
assert set(geom[0] for geom in left_geometries) == set([
'POLYGON ((0 4, -3 3, -8 6, -6 8, -2 9, 0 4))',
'POLYGON ((10 3, 10 6, 14 6, 14 3, 10 3))',
'POLYGON ((2 2, 2 4, 3 5, 7 5, 9 3, 8 1, 4 1, 2 2))',
'POLYGON ((-1 -1, -1 -3, -2 -5, -6 -8, -5 -2, -3 -2, -1 -1))',
'POLYGON ((-1 -1, -1 -3, -2 -5, -6 -8, -5 -2, -3 -2, -1 -1))'
])
assert set(geom[0] for geom in right_geometries) == set([
'POINT (-3 5)', 'POINT (11 5)', 'POINT (4 3)', 'POINT (-1 -1)',
'POINT (-4 -5)'
])
def test_to_spatial_rdd_df_and_geom_field_name(self):
spatial_df = self._create_spatial_point_table()
spatial_rdd = Adapter.toSpatialRdd(spatial_df, "geom")
spatial_rdd = Adapter.toSpatialRdd(spatial_df, "s")
spatial_rdd.analyze()
assert spatial_rdd.approximateTotalCount == 121960
assert spatial_rdd.boundaryEnvelope == Envelope(
-179.147236, 179.475569, -14.548699, 71.35513400000001)
def test_geojson_to_dataframe(self):
spatial_rdd = PolygonRDD(self.spark.sparkContext,
geojson_input_location,
FileDataSplitter.GEOJSON, True)
spatial_rdd.analyze()
Adapter.toDf(spatial_rdd, self.spark).show()
df = Adapter.toDf(spatial_rdd, self.spark)
assert (df.columns[1] == "STATEFP")
def test_read_shapefile_to_dataframe(self):
spatial_rdd = ShapefileReader.readToGeometryRDD(
self.spark.sparkContext, shape_file_input_location)
spatial_rdd.analyze()
logging.info(spatial_rdd.fieldNames)
df = Adapter.toDf(spatial_rdd, self.spark)
df.show()
def test_read_csv_point_into_spatial_rdd(self):
df = self.spark.read.\
format("csv").\
option("delimiter", "\t").\
option("header", "false").\
load(area_lm_point_input_location)
df.show()
df.createOrReplaceTempView("inputtable")
spatial_df = self.spark.sql(
"select ST_PointFromText(inputtable._c0,\",\") as arealandmark from inputtable"
)
spatial_df.show()
spatial_df.printSchema()
spatial_rdd = Adapter.toSpatialRdd(spatial_df, "arealandmark")
spatial_rdd.analyze()
Adapter.toDf(spatial_rdd, self.spark).show()
def test_read_mixed_wkt_geometries_into_spatial_rdd_with_unique_id(self):
df = self.spark.read.format("csv").\
option("delimiter", "\t").\
option("header", "false").\
load(mixed_wkt_geometry_input_location)
df.show()
df.createOrReplaceTempView("inputtable")
spatial_df = self.spark.sql(
"select ST_GeomFromWKT(inputtable._c0) as usacounty, inputtable._c3, inputtable._c5 from inputtable"
)
spatial_df.show()
spatial_df.printSchema()
spatial_rdd = Adapter.toSpatialRdd(spatial_df, "usacounty")
spatial_rdd.analyze()
assert (Adapter.toDf(spatial_rdd, self.spark).columns.__len__() == 3)
Adapter.toDf(spatial_rdd, self.spark).show()
def test_distance_join_result_to_dataframe(self):
point_csv_df = self.spark.\
read.\
format("csv").\
option("delimiter", ",").\
option("header", "false").load(
area_lm_point_input_location
)
point_csv_df.createOrReplaceTempView("pointtable")
point_df = self.spark.sql(
"select ST_Point(cast(pointtable._c0 as Decimal(24,20)),cast(pointtable._c1 as Decimal(24,20))) as arealandmark from pointtable"
)
point_rdd = Adapter.toSpatialRdd(point_df, "arealandmark")
point_rdd.analyze()
polygon_wkt_df = self.spark.read.\
format("csv").\
option("delimiter", "\t").\
option("header", "false").load(
mixed_wkt_geometry_input_location
)
polygon_wkt_df.createOrReplaceTempView("polygontable")
polygon_df = self.spark.\
sql("select ST_GeomFromWKT(polygontable._c0) as usacounty from polygontable")
polygon_rdd = Adapter.toSpatialRdd(polygon_df, "usacounty")
polygon_rdd.analyze()
circle_rdd = CircleRDD(polygon_rdd, 0.2)
point_rdd.spatialPartitioning(GridType.QUADTREE)
circle_rdd.spatialPartitioning(point_rdd.getPartitioner())
point_rdd.buildIndex(IndexType.QUADTREE, True)
join_result_pair_rdd = JoinQuery.\
DistanceJoinQueryFlat(point_rdd, circle_rdd, True, True)
join_result_df = Adapter.toDf(join_result_pair_rdd, self.spark)
join_result_df.printSchema()
join_result_df.show()
def test_geojson_to_dataframe(self):
spatial_rdd = PolygonRDD(self.spark.sparkContext,
geojson_input_location,
FileDataSplitter.GEOJSON, True)
spatial_rdd.analyze()
df = Adapter.toDf(spatial_rdd, self.spark).\
withColumn("geometry", expr("ST_GeomFromWKT(geometry)"))
df.show()
assert (df.columns[1] == "STATEFP")
def test_load_id_column_data_check(self):
spatial_rdd = PolygonRDD(self.spark.sparkContext,
geojson_id_input_location,
FileDataSplitter.GEOJSON, True)
spatial_rdd.analyze()
df = Adapter.toDf(spatial_rdd, self.spark)
df.show()
try:
assert df.columns.__len__() == 3
except AssertionError:
assert df.columns.__len__() == 4
assert df.count() == 1
def test_to_df_srdd_fn_spark(self):
spatial_rdd = PolygonRDD(self.spark.sparkContext,
geojson_input_location,
FileDataSplitter.GEOJSON, True)
spatial_rdd.analyze()
assert spatial_rdd.approximateTotalCount == 1001
spatial_columns = [
"state_id", "county_id", "tract_id", "bg_id", "fips", "fips_short",
"bg_nr", "type", "code1", "code2"
]
spatial_df = Adapter.toDf(spatial_rdd, spatial_columns, self.spark)
spatial_df.show()
assert spatial_df.columns == ["geometry", *spatial_columns]
assert spatial_df.count() == 1001
def get_bdy_rdd(spark, bdy):
# load boundaries from Postgres
sql = """SELECT {}, name as {}, st_astext(geom) as wkt_geom
FROM admin_bdys_202008.{}_analysis""".format(
bdy["id_field"], bdy["name_field"], bdy["name"])
bdy_df = get_dataframe_from_postgres(spark, sql)
# create geometries from WKT strings into new DataFrame
bdy_df2 = bdy_df\
.withColumn("geom", f.expr("st_geomFromWKT(wkt_geom)")) \
.drop("wkt_geom")
# create rdd
output_rdd = Adapter.toSpatialRdd(bdy_df2, "geom")
output_rdd.analyze()
bdy_df2.unpersist()
bdy_df.unpersist()
return output_rdd
def test_distance_join_query_flat_to_df(self):
poi_point_rdd = WktReader.readToGeometryRDD(self.sc, bank_csv_path, 1,
False, False)
circle_rdd = CircleRDD(poi_point_rdd, 2.0)
circle_rdd.analyze()
poi_point_rdd.analyze()
poi_point_rdd.spatialPartitioning(GridType.QUADTREE)
circle_rdd.spatialPartitioning(poi_point_rdd.getPartitioner())
jvm_sedona_rdd = JoinQueryRaw.DistanceJoinQueryFlat(
poi_point_rdd, circle_rdd, False, True)
df_sedona_rdd = Adapter.toDf(jvm_sedona_rdd,
["poi_from_id", "poi_from_name"],
["poi_to_id", "poi_to_name"], self.spark)
assert df_sedona_rdd.count() == 10
assert df_sedona_rdd.columns == [
"leftgeometry", "poi_from_id", "poi_from_name", "rightgeometry",
"poi_to_id", "poi_to_name"
]
def test_spatial_join_to_df(self):
poi_point_rdd = WktReader.readToGeometryRDD(self.sc, bank_csv_path, 1,
False, False)
areas_polygon_rdd = WktReader.readToGeometryRDD(
self.sc, areas_csv_path, 1, False, False)
poi_point_rdd.analyze()
areas_polygon_rdd.analyze()
poi_point_rdd.spatialPartitioning(GridType.QUADTREE)
areas_polygon_rdd.spatialPartitioning(poi_point_rdd.getPartitioner())
jvm_sedona_rdd = JoinQueryRaw.spatialJoin(poi_point_rdd,
areas_polygon_rdd,
JoinParams())
sedona_df = Adapter.toDf(jvm_sedona_rdd, ["area_id", "area_name"],
["poi_id", "poi_name"], self.spark)
assert sedona_df.count() == 5
assert sedona_df.columns == [
"leftgeometry", "area_id", "area_name", "rightgeometry", "poi_id",
"poi_name"
]
def rdd_filesave_join():
logger.info("\t - RDD file save join start")
full_start_time = datetime.now()
# ----------------------------------------------------------
# get spark session and context
# ----------------------------------------------------------
start_time = datetime.now()
spark = create_spark_session()
sc = spark.sparkContext
sedona_version = pkg_resources.get_distribution("sedona").version
logger.info(
"\t - PySpark {} session initiated with Apache Sedona {}: {}".format(
sc.version, sedona_version,
datetime.now() - start_time))
# ----------------------------------------------------------
# create GNAF PointRDD from CSV file
# ----------------------------------------------------------
start_time = datetime.now()
offset = 0 # The point long/lat fields start at column 0
carry_other_attributes = True # include non-geo columns
point_rdd = PointRDD(sc, os.path.join(output_path, gnaf_csv_file_path),
offset, FileDataSplitter.CSV, carry_other_attributes)
point_rdd.analyze()
# add partitioning and indexing
point_rdd.spatialPartitioning(GridType.KDBTREE)
point_rdd.buildIndex(IndexType.RTREE, True)
# set Spark storage type - set to MEMORY_AND_DISK if low on memory
point_rdd.indexedRDD.persist(StorageLevel.MEMORY_ONLY)
logger.info("\t\t - GNAF RDD created: {}".format(datetime.now() -
start_time))
# ----------------------------------------------------------
# get boundary tags using a spatial join
# ----------------------------------------------------------
for bdy in bdy_list:
start_time = datetime.now()
# load boundaries
# create geometries from WKT strings into new DataFrame
bdy_df = spark.read.parquet(os.path.join(output_path, bdy["name"])) \
.withColumn("geom", f.expr("st_geomFromWKT(wkt_geom)")) \
.drop("wkt_geom")
# create bdy rdd
bdy_rdd = Adapter.toSpatialRdd(bdy_df, "geom")
bdy_rdd.analyze()
bdy_df.unpersist()
bdy_rdd.spatialPartitioning(point_rdd.getPartitioner())
bdy_rdd.spatialPartitionedRDD.persist(
StorageLevel.MEMORY_ONLY) # no need to persist(?) - used once
# run the join - returns a PairRDD with 1 boundary to 1-N points
# e.g. [Geometry: Polygon userData: WA32 TANGNEY WA, [Geometry: Point userData: GAWA_146792426 WA, ...]]
result_pair_rdd = JoinQuery.SpatialJoinQueryFlat(
point_rdd, bdy_rdd, True, True)
# jim = result_pair_rdd.take(10)
# for row in jim:
# print(row)
result_pair_rdd.saveAsTextFile(
os.path.join(output_path,
"rdd_file_save_gnaf_with_{}".format(bdy["name"])))
# # flat map values to have one point to bdy matched pair
# flat_mapped_rdd = result_pair_rdd.flatMapValues(lambda x: x)
#
# # map values to create RDD row of gnaf & bdy IDs, plus state data
# mapped_rdd = flat_mapped_rdd.map(
# lambda x: [x[1].getUserData().split("\t")[0],
# x[0].getUserData().split("\t")[0],
# x[0].getUserData().split("\t")[1]]
# )
#
# # convert result to a dataframe of the following shema
# schema = t.StructType([t.StructField("gnaf_pid", t.StringType(), False),
# t.StructField(bdy["id_field"], t.StringType(), False),
# t.StructField(bdy["name_field"], t.StringType(), False)])
#
# join_df = spark.createDataFrame(mapped_rdd, schema)
#
# # save result to disk
# join_df.write \
# .option("compression", "gzip") \
# .mode("overwrite") \
# .parquet(os.path.join(output_path, "rdd_file_save_gnaf_with_{}".format(bdy["name"])))
logger.info("\t\t - GNAF points bdy tagged with {}: {}".format(
bdy["name"],
datetime.now() - start_time))
# cleanup
spark.stop()
logger.info("\t - RDD file save join done: {}".format(datetime.now() -
full_start_time))
def run_test(test_name, num_partitions, max_vertices):
# create spark session object
spark = (
SparkSession.builder.master(
"local[*]").appName("Spatial Join SQL Benchmark").config(
"spark.sql.session.timeZone",
"UTC").config("spark.sql.debug.maxToStringFields",
100).config("spark.serializer",
KryoSerializer.getName).
config("spark.kryo.registrator", SedonaKryoRegistrator.getName).config(
"spark.jars.packages",
'org.apache.sedona:sedona-python-adapter-3.0_2.12:1.0.1-incubating,'
'org.datasyslab:geotools-wrapper:geotools-24.1').config(
"spark.sql.adaptive.enabled",
"true").config("spark.executor.cores",
4).config("spark.driver.memory",
"8g").getOrCreate())
# Add Sedona functions and types to Spark
SedonaRegistrator.registerAll(spark)
start_time = datetime.now()
# load gnaf points and create geoms
point_df = (spark.read.parquet(
os.path.join(input_path, "address_principals")).select(
"gnaf_pid", "state", "geom").withColumnRenamed(
"state", "gnaf_state").repartition(num_partitions,
"gnaf_state"))
# load boundaries and create geoms
if max_vertices is not None:
bdy_vertex_name = "{}_{}".format(bdy_name, max_vertices)
else:
bdy_vertex_name = bdy_name
bdy_df = (spark.read.parquet(os.path.join(
input_path,
bdy_vertex_name)).select(bdy_id, "state",
"geom").repartition(num_partitions,
"state").cache())
bdy_count = bdy_df.count()
# create RDDs - analysed partitioned and indexed
point_rdd = Adapter.toSpatialRdd(point_df, "geom")
bdy_rdd = Adapter.toSpatialRdd(bdy_df, "geom")
point_df.unpersist()
bdy_df.unpersist()
point_rdd.analyze()
bdy_rdd.analyze()
point_rdd.spatialPartitioning(GridType.KDBTREE)
bdy_rdd.spatialPartitioning(point_rdd.getPartitioner())
point_rdd.buildIndex(IndexType.RTREE, True)
bdy_rdd.buildIndex(IndexType.RTREE, True)
# run join query
join_pair_rdd = JoinQueryRaw.SpatialJoinQueryFlat(point_rdd, bdy_rdd, True,
True)
# convert SedonaPairRDD to dataframe
join_df = Adapter.toDf(join_pair_rdd, bdy_rdd.fieldNames,
point_rdd.fieldNames, spark)
# join_df.printSchema()
# | -- leftgeometry: geometry(nullable=true)
# | -- <bdy_id>: string(nullable=true)
# | -- state: string(nullable=true)
# | -- rightgeometry: geometry(nullable=true)
# | -- gnaf_pid: string(nullable=true)
# | -- gnaf_state: string(nullable=true)
join_df2 = (join_df
# .filter((join_df["state"] == join_df["gnaf_state"]))
.select("gnaf_pid", bdy_id, "state")
.dropDuplicates(["gnaf_pid", bdy_id])
.cache()
)
# output to files
if "warmup" in test_name:
name = "gnaf_rdd_{}_{}_{}".format(bdy_id, max_vertices, num_partitions)
(join_df2.repartition(50).write.partitionBy("state").option(
"compression",
"gzip").mode("overwrite").parquet(os.path.join(output_path, name)))
# output vars
join_count = join_df2.count()
time_taken = datetime.now() - start_time
if "warmup" in test_name:
print("{},{},{},{},{},{}".format(test_name, join_count, bdy_count,
max_vertices, num_partitions,
time_taken))
else:
log_file.write("{},{},{},{},{},{}\n".format(test_name, join_count,
bdy_count, max_vertices,
num_partitions,
time_taken))
# cleanup
spark.stop()