def test_equals_exact_tolerance():
# specifying tolerance
p1 = pygeos.points(50, 4)
p2 = pygeos.points(50.1, 4.1)
actual = pygeos.equals_exact([p1, p2, None], p1, tolerance=0.05)
np.testing.assert_allclose(actual, [True, False, False])
assert actual.dtype == np.bool
actual = pygeos.equals_exact([p1, p2, None], p1, tolerance=0.2)
np.testing.assert_allclose(actual, [True, True, False])
assert actual.dtype == np.bool
# default value for tolerance
assert pygeos.equals_exact(p1, p1).item() is True
assert pygeos.equals_exact(p1, p2).item() is False
def test_from_wkt():
expected = pygeos.points(1, 1)
actual = pygeos.from_wkt("POINT (1 1)")
assert pygeos.equals(actual, expected)
# also accept bytes
actual = pygeos.from_wkt(b"POINT (1 1)")
assert pygeos.equals(actual, expected)
def boundary_distance(polygon, points):
"""
Find the distance between a polygon's boundary and an
array of points.
Uses either `shapely` or `pygeos` (5-10x faster) as a backend.
Parameters
-------------
polygon : shapely.geometry.Polygon
Polygon to query
points : (n, 2) float
2D points
Returns
------------
distance : (n,) float
Minimum distance from each point to polygon boundary
"""
try:
import pygeos
# the pygeos way is 5-10x faster
pg_points = pygeos.points(*points.T)
pg_boundary = pygeos.boundary(pygeos.Geometry(polygon.wkt))
distance = pygeos.distance(pg_boundary, pg_points)
except BaseException:
# in pure shapely we have to loop
inverse = polygon.boundary
distance = np.array([
inverse.distance(i) for i in MultiPoint(points)])
return distance
def close_gaps(df, tolerance):
"""Close gaps in LineString geometry where it should be contiguous.
Snaps both lines to a centroid of a gap in between.
"""
geom = df.geometry.values.data
coords = pygeos.get_coordinates(geom)
indices = pygeos.get_num_coordinates(geom)
# generate a list of start and end coordinates and create point geometries
edges = [0]
i = 0
for ind in indices:
ix = i + ind
edges.append(ix - 1)
edges.append(ix)
i = ix
edges = edges[:-1]
points = pygeos.points(np.unique(coords[edges], axis=0))
buffered = pygeos.buffer(points, tolerance)
dissolved = pygeos.union_all(buffered)
exploded = [
pygeos.get_geometry(dissolved, i)
for i in range(pygeos.get_num_geometries(dissolved))
]
centroids = pygeos.centroid(exploded)
snapped = pygeos.snap(geom, pygeos.union_all(centroids), tolerance)
return snapped
def test_from_wkb_hex():
# HEX form
expected = pygeos.points(1, 1)
actual = pygeos.from_wkb("0101000000000000000000F03F000000000000F03F")
assert pygeos.equals(actual, expected)
actual = pygeos.from_wkb(b"0101000000000000000000F03F000000000000F03F")
assert pygeos.equals(actual, expected)
def _sample_land_points(self, N_pts):
pt_df = pd.DataFrame(columns=['lon', 'lat'], index=[])
ii_p = 0
while len(pt_df) < N_pts:
pts = np.random.rand(2 * 2 * (N_pts - len(pt_df))).reshape(
(N_pts - len(pt_df)) * 2, 2)
#print ('pts shape',pts.shape)
pts[:, 0] = pts[:, 0] * 360 - 180 # lon
pts[:, 1] = pts[:, 1] * (80 + 70) - 70 # lat between -70 and 80
pts_pygeos = pygeos.points(pts)
Q = self.tree.query_bulk(pts_pygeos, predicate='within').T[:, 0]
#print ('Q-shape',Q.shape)
pt_df = pt_df.append(pd.DataFrame(pts[Q], columns=['lon', 'lat']))
#print ('len pt_df', len(pt_df), 'iter_toc',time.time()-tic)
ii_p += 1
pt_df = pt_df.iloc[0:N_pts]
# reset the index
pt_df.index = range(len(pt_df))
return pt_df
def poly_tree():
# create buffers so that midpoint between two buffers intersects
# each buffer. NOTE: add EPS to help mitigate rounding errors at midpoint.
geoms = pygeos.buffer(pygeos.points(np.arange(10), np.arange(10)),
HALF_UNIT_DIAG + EPS,
quadsegs=32)
yield pygeos.STRtree(geoms)
def setup(self):
# create irregular polygons by merging overlapping point buffers
self.left = pygeos.union_all(
pygeos.buffer(pygeos.points(np.random.random((500, 2)) * 500), 15)
)
# shift this up and right
self.right = pygeos.apply(self.left, lambda x: x + 50)
def intersection(self, coordinates):
# convert bounds to geometry
# the old API uses tuples of bound, but pygeos uses geometries
try:
iter(coordinates)
except TypeError:
# likely not an iterable
# this is a check that rtree does, we mimic it
# to ensure a useful failure message
raise TypeError(
"Invalid coordinates, must be iterable in format "
"(minx, miny, maxx, maxy) (for bounds) or (x, y) (for points). "
"Got `coordinates` = {}.".format(coordinates))
# need to convert tuple of bounds to a geometry object
if len(coordinates) == 4:
indexes = super().query(pygeos.box(*coordinates))
elif len(coordinates) == 2:
indexes = super().query(pygeos.points(*coordinates))
else:
raise TypeError(
"Invalid coordinates, must be iterable in format "
"(minx, miny, maxx, maxy) (for bounds) or (x, y) (for points). "
"Got `coordinates` = {}.".format(coordinates))
return indexes
def test_flush_geometries(tree):
arr = pygeos.points(np.arange(10), np.arange(10))
tree = pygeos.STRtree(arr)
# Dereference geometries
arr[:] = None
# Still it does not lead to a segfault
tree.query(point)
def test_to_wkb_hex():
point = pygeos.points(1, 1)
actual = pygeos.to_wkb(point, hex=True, byte_order=1)
le = "01"
point_type = "01000000"
coord = "000000000000F03F" # 1.0 as double (LE)
assert actual == le + point_type + 2 * coord
def test_to_wkb_3D():
point_z = pygeos.points(1, 1, 1)
actual = pygeos.to_wkb(point_z, byte_order=1)
# fmt: off
assert actual == b"\x01\x01\x00\x00\x80\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\xf0?" # noqa
# fmt: on
actual = pygeos.to_wkb(point_z, output_dimension=2, byte_order=1)
assert actual == POINT11_WKB
def test_to_wkb_byte_order():
point = pygeos.points(1.0, 1.0)
be = b"\x00"
le = b"\x01"
point_type = b"\x01\x00\x00\x00" # 1 as 32-bit uint (LE)
coord = b"\x00\x00\x00\x00\x00\x00\xf0?" # 1.0 as double (LE)
assert pygeos.to_wkb(point, byte_order=1) == le + point_type + 2 * coord
assert pygeos.to_wkb(point, byte_order=0) == be + point_type[::-1] + 2 * coord[::-1]
def test_destroy_prepared():
arr = np.array([pygeos.points(1, 1), None, pygeos.box(0, 0, 1, 1)])
pygeos.prepare(arr)
assert arr[0]._ptr_prepared != 0
assert arr[2]._ptr_prepared != 0
pygeos.destroy_prepared(arr)
assert arr[0]._ptr_prepared == 0
assert arr[1] is None
assert arr[2]._ptr_prepared == 0
pygeos.destroy_prepared(arr) # does not error
def test_to_wkt():
point = pygeos.points(1, 1)
actual = pygeos.to_wkt(point)
assert actual == "POINT (1 1)"
actual = pygeos.to_wkt(point, trim=False)
assert actual == "POINT (1.000000 1.000000)"
actual = pygeos.to_wkt(point, rounding_precision=3, trim=False)
assert actual == "POINT (1.000 1.000)"
def setup(self):
# create irregular polygons by merging overlapping point buffers
self.polygon = pygeos.union_all(
pygeos.buffer(pygeos.points(np.random.random((1000, 2)) * 500),
10))
xmin = np.random.random(100) * 100
xmax = xmin + 100
ymin = np.random.random(100) * 100
ymax = ymin + 100
self.bounds = np.array([xmin, ymin, xmax, ymax]).T
self.boxes = pygeos.box(xmin, ymin, xmax, ymax)
def test_nearest_multi(self, geometry, expected, return_all):
geoms = pygeos.points(np.arange(10), np.arange(10))
df = geopandas.GeoDataFrame({"geometry": geoms})
ps = [Point(p) for p in geometry]
res = df.sindex.nearest(ps, return_all=return_all)
assert_array_equal(res, expected)
ps = pygeos.points(geometry)
res = df.sindex.nearest(ps, return_all=return_all)
assert_array_equal(res, expected)
s = geopandas.GeoSeries(ps)
res = df.sindex.nearest(s, return_all=return_all)
assert_array_equal(res, expected)
x, y = zip(*geometry)
ga = geopandas.points_from_xy(x, y)
res = df.sindex.nearest(ga, return_all=return_all)
assert_array_equal(res, expected)
def intersection(self, coordinates, objects=False):
"""Wrapper for pygeos.query that uses the RTree API.
Parameters
----------
coordinates : sequence or array
Sequence of the form (min_x, min_y, max_x, max_y)
to query a rectangle or (x, y) to query a point.
objects : boolean, default False
If True, return the label based indexes. If False, integer indexes
are returned.
"""
if objects:
warn(
"`objects` is deprecated and will be removed in a future version. "
"Instead, use `iloc` to index your GeoSeries/GeoDataFrame using "
"integer indexes returned by `intersection`.",
FutureWarning,
)
# convert bounds to geometry
# the old API uses tuples of bound, but pygeos uses geometries
try:
iter(coordinates)
except TypeError:
# likely not an iterable
# this is a check that rtree does, we mimic it
# to ensure a useful failure message
raise TypeError(
"Invalid coordinates, must be iterable in format "
"(minx, miny, maxx, maxy) (for bounds) or (x, y) (for points). "
"Got `coordinates` = {}.".format(coordinates))
# need to convert tuple of bounds to a geometry object
if len(coordinates) == 4:
indexes = super().query(pygeos.box(*coordinates))
elif len(coordinates) == 2:
indexes = super().query(pygeos.points(*coordinates))
else:
raise TypeError(
"Invalid coordinates, must be iterable in format "
"(minx, miny, maxx, maxy) (for bounds) or (x, y) (for points). "
"Got `coordinates` = {}.".format(coordinates))
if objects:
objs = self.objects[indexes].values
ids = self.ids[indexes]
return [
self.with_objects(id=id, object=obj)
for id, obj in zip(ids, objs)
]
else:
return indexes
def test_prepare():
arr = np.array([pygeos.points(1, 1), None, pygeos.box(0, 0, 1, 1)])
assert arr[0]._ptr_prepared == 0
assert arr[2]._ptr_prepared == 0
pygeos.prepare(arr)
assert arr[0]._ptr_prepared != 0
assert arr[1] is None
assert arr[2]._ptr_prepared != 0
# preparing again actually does nothing
original = arr[0]._ptr_prepared
pygeos.prepare(arr)
assert arr[0]._ptr_prepared == original
def points_from_xy(x, y, z=None):
x = np.asarray(x, dtype="float64")
y = np.asarray(y, dtype="float64")
if z is not None:
z = np.asarray(z, dtype="float64")
if compat.USE_PYGEOS:
return pygeos.points(x, y, z)
out = _points_from_xy(x, y, z)
aout = np.empty(len(x), dtype=object)
aout[:] = out
return aout
def test_to_wkt_3D():
# 3D points
point_z = pygeos.points(1, 1, 1)
actual = pygeos.to_wkt(point_z)
assert actual == "POINT Z (1 1 1)"
actual = pygeos.to_wkt(point_z, output_dimension=3)
assert actual == "POINT Z (1 1 1)"
actual = pygeos.to_wkt(point_z, output_dimension=2)
assert actual == "POINT (1 1)"
actual = pygeos.to_wkt(point_z, old_3d=True)
assert actual == "POINT (1 1 1)"
def close_gaps(gdf, tolerance):
"""Close gaps in LineString geometry where it should be contiguous.
Snaps both lines to a centroid of a gap in between.
Parameters
----------
gdf : GeoDataFrame, GeoSeries
GeoDataFrame or GeoSeries containing LineString representation of a network.
tolerance : float
nodes within a tolerance will be snapped together
Returns
-------
GeoSeries
See also
--------
momepy.extend_lines
momepy.remove_false_nodes
"""
geom = gdf.geometry.values.data
coords = pygeos.get_coordinates(geom)
indices = pygeos.get_num_coordinates(geom)
# generate a list of start and end coordinates and create point geometries
edges = [0]
i = 0
for ind in indices:
ix = i + ind
edges.append(ix - 1)
edges.append(ix)
i = ix
edges = edges[:-1]
points = pygeos.points(np.unique(coords[edges], axis=0))
buffered = pygeos.buffer(points, tolerance / 2)
dissolved = pygeos.union_all(buffered)
exploded = [
pygeos.get_geometry(dissolved, i)
for i in range(pygeos.get_num_geometries(dissolved))
]
centroids = pygeos.centroid(exploded)
snapped = pygeos.snap(geom, pygeos.union_all(centroids), tolerance)
return gpd.GeoSeries(snapped, crs=gdf.crs)
def test_to_wkb_srid():
# hex representation of POINT (0 0) with SRID=4
ewkb = "01010000200400000000000000000000000000000000000000"
wkb = "010100000000000000000000000000000000000000"
actual = pygeos.from_wkb(ewkb)
assert pygeos.to_wkt(actual, trim=True) == "POINT (0 0)"
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
def points_from_xy(x, y, z=None):
x = np.asarray(x, dtype="float64")
y = np.asarray(y, dtype="float64")
if z is not None:
z = np.asarray(z, dtype="float64")
if compat.USE_PYGEOS:
return pygeos.points(x, y, z)
else:
out = _points_from_xy(x, y, z)
aout = np.empty(len(x), dtype=object)
with compat.ignore_shapely2_warnings():
aout[:] = out
return aout
def test_nearest_max_distance(self, expected, max_distance, return_all,
return_distance):
geoms = pygeos.points(np.arange(10), np.arange(10))
df = geopandas.GeoDataFrame({"geometry": geoms})
ps = [Point(0.5, 0.5), Point(0, 10)]
res = df.sindex.nearest(
ps,
return_all=return_all,
max_distance=max_distance,
return_distance=return_distance,
)
if return_distance:
assert_array_equal(res[0], expected[0])
assert_array_equal(res[1], expected[1])
else:
assert_array_equal(res, expected[0])
def intersection(self, coordinates, objects=False):
"""Wrapper for pygeos.query that uses the RTree API.
Parameters
----------
coordinates : sequence or array
Sequence of the form (min_x, min_y, max_x, max_y)
to query a rectangle or (x, y) to query a point.
objects : True or False
If True, return the label based indexes. If False, integer indexes
are returned.
"""
# convert bounds to geometry
# the old API uses tuples of bound, but pygeos uses geometries
try:
iter(coordinates)
except TypeError:
# likely not an iterable
# this is a check that rtree does, we mimick it
# to ensure a useful failure message
raise TypeError(
"Invalid coordinates, must be iterable in format "
"(minx, miny, maxx, maxy) (for bounds) or (x, y) (for points)."
)
# need to convert tuple of bounds to a geometry object
if len(coordinates) == 4:
indexes = super().query(box(*coordinates))
elif len(coordinates) == 2:
indexes = super().query(points(*coordinates))
else:
raise TypeError(
"Invalid coordinates, must be iterable in format "
"(minx, miny, maxx, maxy) (for bounds) or (x, y) (for points)."
)
if objects:
objs = self.objects[indexes].values
ids = self.ids[indexes]
return [
self.with_objects(id=id, object=obj)
for id, obj in zip(ids, objs)
]
else:
return indexes
def pg_points_wgs84():
size = 1000
x, y = generate_lon_lat(size)
# generate some other fields in the data frame
i = random.randint(-32767, 32767, size=size)
ui = random.randint(0, 65535, size=size).astype("uint64")
df = DataFrame(data={
"x": x,
"y": y,
"i": i,
"ui": ui,
"labels": i.astype("str")
})
df["geometry"] = pg.points(np.array([x, y]).T)
return df
def _geometry_from_latlon(table, lat_field, lon_field, crs):
"""Transforms an arrow to table to spatial arrow table, using lat, lon information.
Extracts the lat, lon information from an arrow table, creates the Point geometry
and writes the geometry information to the arrow table.
Parameters:
table (object): The arrow table.
lat_field (string): The latitude field name.
lon_field (string): The longitude field name.
crs (string): The lat, lon CRS.
Returns:
(object): The arrow spatial table.
"""
lat = table.column(lat_field)
lon = table.column(lon_field)
geometry = pg.to_wkb(pg.points(lon, lat))
field = pa.field('geometry', 'binary', metadata={'crs': crs})
table = table.append_column(field, [geometry])
table = table.drop([lat_field, lon_field])
return table
def convert_to_point(input_array,
trim_invalid_geometry=False,
autocorrect_invalid_geometry=False):
r"""Convert an input array to a Point array.
Args:
input_array (ndarray, list): A ndarray of Point optionally followed by a confidence value and/or a label
where each row is: ``[x, y, (confidence), (label)]``
trim_invalid_geometry (bool): Optional, default to ``False``. If set to ``True`` conversion will ignore invalid
geometries and leave them out of ``output_array``. This means that the function will return an array where
``output_array.shape[0] <= input_array.shape[0]``. If set to ``False``, an invalid geometry will raise an
:exc:`~playground_metrics.utils.geometry_utils.InvalidGeometryError`.
autocorrect_invalid_geometry (Bool): Optional, default to ``False``. Doesn't do anything, introduced to unify
convert functions interfaces.
Returns:
ndarray: A Point ndarray where each row contains a geometry followed by optionally confidence and a label
e.g.: ``[Point, (confidence), (label)]``
Raises:
ValueError: If ``input_array`` have invalid dimensions.
"""
input_array = np.array(input_array, dtype=np.dtype('O'))
if input_array.size == 0:
return 'undefined', input_array
if len(input_array.shape) == 1 or len(input_array.shape) > 2:
raise ValueError('Invalid array number of dimensions: '
'Expected a 2D array, found {}D.'.format(
len(input_array.shape)))
coordinates_array = input_array[:, :2].astype(np.float64)
object_array = np.ndarray((input_array.shape[0], input_array.shape[1] - 1),
dtype=np.dtype('O'))
object_array[:, 0] = points(coordinates_array)
object_array[:, 1:] = input_array[:, 2:]
if trim_invalid_geometry:
object_array = object_array[is_valid(object_array[:, 0]), :]
return object_array
class _TestPolygons(_TestSimilarity):
SIMILAR = [
box(0, 0, 1, 1),
polygons([[0, 0], [0, 1], [1, 1], [1, 0], [0, 0]]),
polygons([[0.5, 0], [1, 0], [1, 1], [0, 1], [0, 0.5], [0, 0]])
]
DISSIMILAR = [
box(10, 10, 11, 11),
polygons([[0, 0], [0, 1], [1, 1], [1, 0], [0, 0]]),
polygons([[8, 8], [8, 13], [13, 13], [13, 8], [8, 8]],
holes=[[[9, 9], [9, 12], [12, 12], [12, 9], [9, 9]]]),
polygons([[4.5, 4], [5, 4], [5, 5], [4, 5], [4, 4.5], [4, 4]]),
points([0.5, 0.5])
]
VALUE_GEOMETRIES = [[
box(0, 0, 2, 2),
polygons([[8, 8], [8, 13], [13, 13], [13, 8], [8, 8]],
holes=[[[9, 9], [9, 12], [12, 12], [12, 9], [9, 9]]])
], [box(-1, -1, 1, 1), box(8, 8, 13, 13)]]
VALUE = [0.14285714285714285, 0.64]