import numpy as np
import pygeos
point_polygon_testdata = (
pygeos.points(np.arange(6), np.arange(6)),
pygeos.box(2, 2, 4, 4),
)
point = pygeos.points(2, 3)
line_string = pygeos.linestrings([(0, 0), (1, 0), (1, 1)])
linear_ring = pygeos.linearrings([(0, 0), (1, 0), (1, 1), (0, 1), (0, 0)])
polygon = pygeos.polygons([(0, 0), (2, 0), (2, 2), (0, 2), (0, 0)])
multi_point = pygeos.multipoints([(0, 0), (1, 2)])
multi_line_string = pygeos.multilinestrings([[(0, 0), (1, 2)]])
multi_polygon = pygeos.multipolygons([
[(0, 0), (1, 0), (1, 1), (0, 1), (0, 0)],
[(2.1, 2.1), (2.2, 2.1), (2.2, 2.2), (2.1, 2.2), (2.1, 2.1)],
])
geometry_collection = pygeos.geometrycollections(
[pygeos.points(51, -1),
pygeos.linestrings([(52, -1), (49, 2)])])
point_z = pygeos.points(1.0, 1.0, 1.0)
polygon_with_hole = pygeos.Geometry(
"POLYGON((0 0, 0 10, 10 10, 10 0, 0 0), (2 2, 2 4, 4 4, 4 2, 2 2))")
all_types = (
point,
line_string,
linear_ring,
polygon,
multi_point,
multi_line_string,
@pytest.mark.parametrize(
"geometry,expected",
[
# points do not intersect
(pygeos.points(0.5, 0.5), []),
# points intersect
(pygeos.points(1, 1), [1]),
# box contains points
(box(0, 0, 1, 1), [0, 1]),
# box contains points
(box(5, 5, 15, 15), [5, 6, 7, 8, 9]),
# envelope of buffer contains points
(pygeos.buffer(pygeos.points(3, 3), 1), [2, 3, 4]),
# envelope of points contains points
(pygeos.multipoints([[5, 7], [7, 5]]), [5, 6, 7]),
],
)
def test_query_points(tree, geometry, expected):
assert_array_equal(tree.query(geometry), expected)
@pytest.mark.parametrize(
"geometry,expected",
[
# point intersects first line
(pygeos.points(0, 0), [0]),
(pygeos.points(0.5, 0.5), [0]),
# point within envelope of first line
(pygeos.points(0, 0.5), [0]),
# point at shared vertex between 2 lines
def test_multipoints():
actual = pygeos.multipoints([point], indices=[0])
assert_geometries_equal(actual, pygeos.multipoints([point]))
def test_create_collection_only_none():
actual = pygeos.multipoints(np.array([None], dtype=object))
assert actual.to_wkt() == "MULTIPOINT EMPTY"
def test_create_collection_skips_none():
actual = pygeos.multipoints([point, None, None, point])
assert actual.to_wkt() == "MULTIPOINT (2 3, 2 3)"
def test_repr_multipoint_with_point_empty():
# Test if segfault is prevented
geom = pygeos.multipoints([point, empty_point])
assert repr(geom) == "<pygeos.Geometry Exception in WKT writer>"
def create_network_OD_points(country_network):
"""Create a list of OD points for the specified country
Args:
country ([type]): [description]
Returns:
[type]: [description]
"""
# set paths to data
#data_path = Path(r'/scistor/ivm/data_catalogue/open_street_map/')
data_path = Path(r'C:/data/')
world_pop = data_path.joinpath('worldpop','ppp_2018_1km_Aggregated.tif')
if data_path.joinpath('network_OD_points','{}.csv'.format(country_network)).is_file():
return None
#print("{} already finished!".format(country_network))
try:
#get country ID
print('{} started!'.format(country_network))
# load data
nodes = feather.read_dataframe(data_path.joinpath("percolation_networks","{}-nodes.feather".format(country_network)))
nodes.geometry = pygeos.from_wkb(nodes.geometry)
#create dataframe of country row
geometry = pygeos.convex_hull(pygeos.multipoints(nodes.geometry.values))
df = pd.DataFrame([geometry],columns=['geometry'])
#specify height of cell in the grid and create grid of bbox
def create_final_od_grid(df,height_div):
height = numpy.sqrt(pygeos.area(df.geometry)/height_div).values[0]
grid = pd.DataFrame(create_grid(create_bbox(df),height),columns=['geometry'])
#clip grid of bbox to grid of the actual spatial exterior of the country
clip_grid = pygeos.intersection(grid,df.geometry)
clip_grid = clip_grid.loc[~pygeos.is_empty(clip_grid.geometry)]
# turn to shapely geometries again for zonal stats
clip_grid.geometry = pygeos.to_wkb(clip_grid.geometry)
clip_grid.geometry = clip_grid.geometry.apply(loads)
clip_grid = gpd.GeoDataFrame(clip_grid)
# get total population per grid cell
if height < 0.01:
clip_grid['tot_pop'] = clip_grid.geometry.apply(lambda x: point_query(x,world_pop))
clip_grid['tot_pop'] = clip_grid['tot_pop'].apply(lambda x: np.sum(x))
else:
clip_grid['tot_pop'] = clip_grid.geometry.apply(lambda x: zonal_stats(x,world_pop,stats="sum"))
clip_grid['tot_pop'] = clip_grid['tot_pop'].apply(lambda x: x[0]['sum'])
# remove cells in the grid that have no population data
clip_grid = clip_grid.loc[~pd.isna(clip_grid.tot_pop)]
if len(clip_grid) > 100:
clip_grid = clip_grid.loc[clip_grid.tot_pop > 100]
clip_grid.reset_index(inplace=True,drop=True)
clip_grid.geometry = clip_grid.geometry.centroid
clip_grid['GID_0'] = country_network[:3]
clip_grid['grid_height'] = height
#print(len(clip_grid),height)
return clip_grid
length_clip = 0
height_div = 200
save_lengths = []
while length_clip < 150:
clip_grid = create_final_od_grid(df,height_div)
length_clip = len(clip_grid)
save_lengths.append(length_clip)
height_div += 50
if (len(save_lengths) == 6) & (numpy.mean(save_lengths[3:]) < 150):
break
print('{} finished with {} points!'.format(country_network,len(clip_grid)))
clip_grid.to_csv(data_path.joinpath('network_OD_points','{}.csv'.format(country_network)))
except:
None
assert pygeos.to_wkb(actual, hex=True, byte_order=1) == wkb
assert pygeos.to_wkb(actual, hex=True, include_srid=True,
byte_order=1) == ewkb
point = pygeos.points(1, 1)
point_with_srid = pygeos.set_srid(point, np.int32(4326))
result = pygeos.to_wkb(point_with_srid, include_srid=True, byte_order=1)
assert np.frombuffer(result[5:9], "<u4").item() == 4326
@pytest.mark.skipif(pygeos.geos_version >= (3, 8, 0),
reason="Pre GEOS 3.8.0 has 3D empty points")
@pytest.mark.parametrize("geom,dims,expected", [
(empty_point, 2, POINT_NAN_WKB),
(empty_point, 3, POINTZ_NAN_WKB),
(pygeos.multipoints([empty_point]), 2, MULTIPOINT_NAN_WKB),
(pygeos.multipoints([empty_point]), 3, MULTIPOINTZ_NAN_WKB),
(pygeos.geometrycollections([empty_point]), 2, GEOMETRYCOLLECTION_NAN_WKB),
(pygeos.geometrycollections([empty_point
]), 3, GEOMETRYCOLLECTIONZ_NAN_WKB),
(pygeos.geometrycollections([pygeos.multipoints([empty_point])
]), 2, NESTED_COLLECTION_NAN_WKB),
(pygeos.geometrycollections([pygeos.multipoints([empty_point])
]), 3, NESTED_COLLECTIONZ_NAN_WKB),
])
def test_to_wkb_point_empty_pre_geos38(geom, dims, expected):
actual = pygeos.to_wkb(geom, output_dimension=dims, byte_order=1)
# Use numpy.isnan; there are many byte representations for NaN
assert actual[:-dims * 8] == expected[:-dims * 8]
assert np.isnan(struct.unpack("<{}d".format(dims),
actual[-dims * 8:])).all()
def test_to_wkt_multipoint_with_point_empty_errors():
# Test if segfault is prevented
geom = pygeos.multipoints([empty_point, point])
with pytest.raises(ValueError):
pygeos.to_wkt(geom)
def test_create_collection_only_nan():
actual = pygeos.multipoints(np.array([np.nan], dtype=object))
assert actual.to_wkt() == "GEOMETRYCOLLECTION EMPTY"
def test_create_collection_skips_nan():
actual = pygeos.multipoints([point, np.nan, np.nan, point])
assert actual.to_wkt() == "MULTIPOINT (2 2, 2 2)"
tree = pygeos.STRtree(arr)
# Dereference geometries
arr[:] = None
# Still it does not lead to a segfault
tree.query(point)
def test_query_no_geom(tree):
with pytest.raises(TypeError):
tree.query("I am not a geometry")
def test_query_none(tree):
assert tree.query(None).size == 0
def test_query_empty(tree):
assert tree.query(empty).size == 0
@pytest.mark.parametrize(
"envelope,expected",
[
(pygeos.points(1, 1), [1]),
(box(0, 0, 1, 1), [0, 1]),
(box(5, 5, 15, 15), [5, 6, 7, 8, 9]),
(pygeos.multipoints([[5, 7], [7, 5]]), [5, 6, 7]), # query by envelope
])
def test_query(tree, envelope, expected):
assert_array_equal(tree.query(envelope), expected)
import numpy as np
import pygeos
point_polygon_testdata = (
pygeos.points(np.arange(6), np.arange(6)),
pygeos.box(2, 2, 4, 4),
)
point = pygeos.points(2, 2)
line_string = pygeos.linestrings([[0, 0], [1, 0], [1, 1]])
linear_ring = pygeos.linearrings(((0, 0), (0, 1), (1, 1), (1, 0), (0, 0)))
polygon = pygeos.polygons(
((0.0, 0.0), (0.0, 2.0), (2.0, 2.0), (2.0, 0.0), (0.0, 0.0)))
multi_point = pygeos.multipoints([[0.0, 0.0], [1.0, 2.0]])
multi_line_string = pygeos.multilinestrings([[[0.0, 0.0], [1.0, 2.0]]])
multi_polygon = pygeos.multipolygons([
((0.0, 0.0), (0.0, 1.0), (1.0, 1.0), (1.0, 0.0)),
((0.1, 0.1), (0.1, 0.2), (0.2, 0.2), (0.2, 0.1)),
])
geometry_collection = pygeos.geometrycollections(
[pygeos.points(51, -1),
pygeos.linestrings([(52, -1), (49, 2)])])
point_z = pygeos.points(1.0, 1.0, 1.0)
all_types = (
point,
line_string,
linear_ring,
polygon,
multi_point,
multi_line_string,
multi_polygon,
def create_voronoi(
points: Sequence[pygeos.Geometry]) -> Sequence[pygeos.Geometry]:
mp = pygeos.multipoints(points)
polys = pygeos.get_parts(pygeos.voronoi_polygons(mp))
convex_hull = pygeos.buffer(pygeos.convex_hull(mp), 2)
return pygeos.intersection(convex_hull, polys)
def test_multipoints():
actual = pygeos.multipoints(
np.array([point], dtype=object), indices=np.zeros(1, dtype=np.intp)
)
assert_geometries_equal(actual, pygeos.multipoints([point]))
assert pygeos.to_wkt(actual, trim=True) == "POINT (0 0)"
assert pygeos.to_wkb(actual, hex=True) == wkb
assert pygeos.to_wkb(actual, hex=True, include_srid=True) == ewkb
point = pygeos.points(1, 1)
point_with_srid = pygeos.set_srid(point, np.int32(4326))
result = pygeos.to_wkb(point_with_srid, include_srid=True)
assert np.frombuffer(result[5:9], "<u4").item() == 4326
@pytest.mark.skipif(pygeos.geos_version >= (3, 8, 0), reason="Pre GEOS 3.8.0 has 3D empty points")
@pytest.mark.parametrize("geom,dims,expected", [
(empty_point, 2, POINT_NAN_WKB),
(empty_point, 3, POINTZ_NAN_WKB),
(pygeos.multipoints([empty_point]), 2, MULTIPOINT_NAN_WKB),
(pygeos.multipoints([empty_point]), 3, MULTIPOINTZ_NAN_WKB),
(pygeos.geometrycollections([empty_point]), 2, GEOMETRYCOLLECTION_NAN_WKB),
(pygeos.geometrycollections([empty_point]), 3, GEOMETRYCOLLECTIONZ_NAN_WKB),
(pygeos.geometrycollections([pygeos.multipoints([empty_point])]), 2, NESTED_COLLECTION_NAN_WKB),
(pygeos.geometrycollections([pygeos.multipoints([empty_point])]), 3, NESTED_COLLECTIONZ_NAN_WKB),
])
def test_to_wkb_point_empty_pre_geos38(geom,dims,expected):
actual = pygeos.to_wkb(geom, output_dimension=dims)
# Use numpy.isnan; there are many byte representations for NaN
assert actual[:-dims * 8] == expected[:-dims * 8]
assert np.isnan(struct.unpack("<{}d".format(dims), actual[-dims * 8:])).all()
@pytest.mark.skipif(pygeos.geos_version < (3, 8, 0), reason="Post GEOS 3.8.0 has 2D empty points")
@pytest.mark.parametrize("geom,dims,expected", [
