that's too much!

This commit is contained in:
2024-12-19 20:22:56 -08:00
parent 0020a609dd
commit 32cd60e92b
8443 changed files with 1446950 additions and 42 deletions

View File

@@ -0,0 +1,15 @@
from .geocoding import geocode, reverse_geocode
from .overlay import overlay
from .sjoin import sjoin, sjoin_nearest
from .util import collect
from .clip import clip
__all__ = [
"collect",
"geocode",
"overlay",
"reverse_geocode",
"sjoin",
"sjoin_nearest",
"clip",
]

View File

@@ -0,0 +1,83 @@
from warnings import warn
import numpy
from shapely.geometry import MultiPoint
from geopandas.array import from_shapely, points_from_xy
from geopandas.geoseries import GeoSeries
def uniform(geom, size, rng=None):
"""
Sample uniformly at random from a geometry.
For polygons, this samples uniformly within the area of the polygon. For lines,
this samples uniformly along the length of the linestring. For multi-part
geometries, the weights of each part are selected according to their relevant
attribute (area for Polygons, length for LineStrings), and then points are
sampled from each part uniformly.
Any other geometry type (e.g. Point, GeometryCollection) are ignored, and an
empty MultiPoint geometry is returned.
Parameters
----------
geom : any shapely.geometry.BaseGeometry type
the shape that describes the area in which to sample.
size : integer
an integer denoting how many points to sample
Returns
-------
shapely.MultiPoint geometry containing the sampled points
Examples
--------
>>> from shapely.geometry import box
>>> square = box(0,0,1,1)
>>> uniform(square, size=102) # doctest: +SKIP
"""
generator = numpy.random.default_rng(seed=rng)
if geom is None or geom.is_empty:
return MultiPoint()
if geom.geom_type in ("Polygon", "MultiPolygon"):
return _uniform_polygon(geom, size=size, generator=generator)
if geom.geom_type in ("LineString", "MultiLineString"):
return _uniform_line(geom, size=size, generator=generator)
warn(
f"Sampling is not supported for {geom.geom_type} geometry type.",
UserWarning,
stacklevel=8,
)
return MultiPoint()
def _uniform_line(geom, size, generator):
"""
Sample points from an input shapely linestring
"""
fracs = generator.uniform(size=size)
return from_shapely(geom.interpolate(fracs, normalized=True)).unary_union()
def _uniform_polygon(geom, size, generator):
"""
Sample uniformly from within a polygon using batched sampling.
"""
xmin, ymin, xmax, ymax = geom.bounds
candidates = []
while len(candidates) < size:
batch = points_from_xy(
x=generator.uniform(xmin, xmax, size=size),
y=generator.uniform(ymin, ymax, size=size),
)
valid_samples = batch[batch.sindex.query(geom, predicate="contains")]
candidates.extend(valid_samples)
return GeoSeries(candidates[:size]).unary_union

View File

@@ -0,0 +1,176 @@
import importlib
import platform
import sys
def _get_sys_info():
"""System information
Returns
-------
sys_info : dict
system and Python version information
"""
python = sys.version.replace("\n", " ")
blob = [
("python", python),
("executable", sys.executable),
("machine", platform.platform()),
]
return dict(blob)
def _get_C_info():
"""Information on system PROJ, GDAL, GEOS
Returns
-------
c_info: dict
system PROJ information
"""
try:
import pyproj
proj_version = pyproj.proj_version_str
except Exception:
proj_version = None
try:
import pyproj
proj_dir = pyproj.datadir.get_data_dir()
except Exception:
proj_dir = None
try:
import shapely._buildcfg
geos_version = "{}.{}.{}".format(*shapely._buildcfg.geos_version)
geos_dir = shapely._buildcfg.geos_library_path
except Exception:
try:
from shapely import geos_version_string
geos_version = geos_version_string
geos_dir = None
except Exception:
geos_version = None
geos_dir = None
try:
import fiona
gdal_version = fiona.env.get_gdal_release_name()
except Exception:
gdal_version = None
try:
import fiona
gdal_dir = fiona.env.GDALDataFinder().search()
except Exception:
gdal_dir = None
if gdal_version is None:
try:
import pyogrio
gdal_version = pyogrio.__gdal_version_string__
gdal_dir = None
except Exception:
pass
try:
# get_gdal_data_path is only available in pyogrio >= 0.4.2
from pyogrio import get_gdal_data_path
gdal_dir = get_gdal_data_path()
except Exception:
pass
blob = [
("GEOS", geos_version),
("GEOS lib", geos_dir),
("GDAL", gdal_version),
("GDAL data dir", gdal_dir),
("PROJ", proj_version),
("PROJ data dir", proj_dir),
]
return dict(blob)
def _get_deps_info():
"""Overview of the installed version of main dependencies
Returns
-------
deps_info: dict
version information on relevant Python libraries
"""
deps = [
"geopandas",
# required deps
"numpy",
"pandas",
"pyproj",
"shapely",
# optional deps
"fiona",
"geoalchemy2",
"geopy",
"matplotlib",
"mapclassify",
"pygeos",
"pyogrio",
"psycopg2",
"pyarrow",
"rtree",
]
def get_version(module):
return module.__version__
deps_info = {}
for modname in deps:
try:
if modname in sys.modules:
mod = sys.modules[modname]
else:
mod = importlib.import_module(modname)
ver = get_version(mod)
deps_info[modname] = ver
except Exception:
deps_info[modname] = None
return deps_info
def show_versions():
"""
Print system information and installed module versions.
Examples
--------
::
$ python -c "import geopandas; geopandas.show_versions()"
"""
sys_info = _get_sys_info()
deps_info = _get_deps_info()
proj_info = _get_C_info()
maxlen = max(len(x) for x in deps_info)
tpl = "{{k:<{maxlen}}}: {{stat}}".format(maxlen=maxlen)
print("\nSYSTEM INFO")
print("-----------")
for k, stat in sys_info.items():
print(tpl.format(k=k, stat=stat))
print("\nGEOS, GDAL, PROJ INFO")
print("---------------------")
for k, stat in proj_info.items():
print(tpl.format(k=k, stat=stat))
print("\nPYTHON DEPENDENCIES")
print("-------------------")
for k, stat in deps_info.items():
print(tpl.format(k=k, stat=stat))

View File

@@ -0,0 +1,246 @@
"""
geopandas.clip
==============
A module to clip vector data using GeoPandas.
"""
import warnings
import numpy as np
import pandas.api.types
from shapely.geometry import Polygon, MultiPolygon, box
from geopandas import GeoDataFrame, GeoSeries
from geopandas.array import _check_crs, _crs_mismatch_warn
def _mask_is_list_like_rectangle(mask):
return pandas.api.types.is_list_like(mask) and not isinstance(
mask, (GeoDataFrame, GeoSeries, Polygon, MultiPolygon)
)
def _clip_gdf_with_mask(gdf, mask):
"""Clip geometry to the polygon/rectangle extent.
Clip an input GeoDataFrame to the polygon extent of the polygon
parameter.
Parameters
----------
gdf : GeoDataFrame, GeoSeries
Dataframe to clip.
mask : (Multi)Polygon, list-like
Reference polygon/rectangle for clipping.
Returns
-------
GeoDataFrame
The returned GeoDataFrame is a clipped subset of gdf
that intersects with polygon/rectangle.
"""
clipping_by_rectangle = _mask_is_list_like_rectangle(mask)
if clipping_by_rectangle:
intersection_polygon = box(*mask)
else:
intersection_polygon = mask
gdf_sub = gdf.iloc[gdf.sindex.query(intersection_polygon, predicate="intersects")]
# For performance reasons points don't need to be intersected with poly
non_point_mask = gdf_sub.geom_type != "Point"
if not non_point_mask.any():
# only points, directly return
return gdf_sub
# Clip the data with the polygon
if isinstance(gdf_sub, GeoDataFrame):
clipped = gdf_sub.copy()
if clipping_by_rectangle:
clipped.loc[
non_point_mask, clipped._geometry_column_name
] = gdf_sub.geometry.values[non_point_mask].clip_by_rect(*mask)
else:
clipped.loc[
non_point_mask, clipped._geometry_column_name
] = gdf_sub.geometry.values[non_point_mask].intersection(mask)
else:
# GeoSeries
clipped = gdf_sub.copy()
if clipping_by_rectangle:
clipped[non_point_mask] = gdf_sub.values[non_point_mask].clip_by_rect(*mask)
else:
clipped[non_point_mask] = gdf_sub.values[non_point_mask].intersection(mask)
if clipping_by_rectangle:
# clip_by_rect might return empty geometry collections in edge cases
clipped = clipped[~clipped.is_empty]
return clipped
def clip(gdf, mask, keep_geom_type=False):
"""Clip points, lines, or polygon geometries to the mask extent.
Both layers must be in the same Coordinate Reference System (CRS).
The ``gdf`` will be clipped to the full extent of the clip object.
If there are multiple polygons in mask, data from ``gdf`` will be
clipped to the total boundary of all polygons in mask.
If the ``mask`` is list-like with four elements ``(minx, miny, maxx, maxy)``, a
faster rectangle clipping algorithm will be used. Note that this can lead to
slightly different results in edge cases, e.g. if a line would be reduced to a
point, this point might not be returned.
The geometry is clipped in a fast but possibly dirty way. The output is not
guaranteed to be valid. No exceptions will be raised for topological errors.
Parameters
----------
gdf : GeoDataFrame or GeoSeries
Vector layer (point, line, polygon) to be clipped to mask.
mask : GeoDataFrame, GeoSeries, (Multi)Polygon, list-like
Polygon vector layer used to clip ``gdf``.
The mask's geometry is dissolved into one geometric feature
and intersected with ``gdf``.
If the mask is list-like with four elements ``(minx, miny, maxx, maxy)``,
``clip`` will use a faster rectangle clipping (:meth:`~GeoSeries.clip_by_rect`),
possibly leading to slightly different results.
keep_geom_type : boolean, default False
If True, return only geometries of original type in case of intersection
resulting in multiple geometry types or GeometryCollections.
If False, return all resulting geometries (potentially mixed-types).
Returns
-------
GeoDataFrame or GeoSeries
Vector data (points, lines, polygons) from ``gdf`` clipped to
polygon boundary from mask.
See also
--------
GeoDataFrame.clip : equivalent GeoDataFrame method
GeoSeries.clip : equivalent GeoSeries method
Examples
--------
Clip points (grocery stores) with polygons (the Near West Side community):
>>> import geodatasets
>>> chicago = geopandas.read_file(
... geodatasets.get_path("geoda.chicago_health")
... )
>>> near_west_side = chicago[chicago["community"] == "NEAR WEST SIDE"]
>>> groceries = geopandas.read_file(
... geodatasets.get_path("geoda.groceries")
... ).to_crs(chicago.crs)
>>> groceries.shape
(148, 8)
>>> nws_groceries = geopandas.clip(groceries, near_west_side)
>>> nws_groceries.shape
(7, 8)
"""
if not isinstance(gdf, (GeoDataFrame, GeoSeries)):
raise TypeError(
"'gdf' should be GeoDataFrame or GeoSeries, got {}".format(type(gdf))
)
mask_is_list_like = _mask_is_list_like_rectangle(mask)
if (
not isinstance(mask, (GeoDataFrame, GeoSeries, Polygon, MultiPolygon))
and not mask_is_list_like
):
raise TypeError(
"'mask' should be GeoDataFrame, GeoSeries,"
f"(Multi)Polygon or list-like, got {type(mask)}"
)
if mask_is_list_like and len(mask) != 4:
raise TypeError(
"If 'mask' is list-like, it must have four values (minx, miny, maxx, maxy)"
)
if isinstance(mask, (GeoDataFrame, GeoSeries)):
if not _check_crs(gdf, mask):
_crs_mismatch_warn(gdf, mask, stacklevel=3)
if isinstance(mask, (GeoDataFrame, GeoSeries)):
box_mask = mask.total_bounds
elif mask_is_list_like:
box_mask = mask
else:
# Avoid empty tuple returned by .bounds when geometry is empty. A tuple of
# all nan values is consistent with the behavior of
# {GeoSeries, GeoDataFrame}.total_bounds for empty geometries.
# TODO(shapely) can simpely use mask.bounds once relying on Shapely 2.0
box_mask = mask.bounds if not mask.is_empty else (np.nan,) * 4
box_gdf = gdf.total_bounds
if not (
((box_mask[0] <= box_gdf[2]) and (box_gdf[0] <= box_mask[2]))
and ((box_mask[1] <= box_gdf[3]) and (box_gdf[1] <= box_mask[3]))
):
return gdf.iloc[:0]
if isinstance(mask, (GeoDataFrame, GeoSeries)):
combined_mask = mask.geometry.unary_union
else:
combined_mask = mask
clipped = _clip_gdf_with_mask(gdf, combined_mask)
if keep_geom_type:
geomcoll_concat = (clipped.geom_type == "GeometryCollection").any()
geomcoll_orig = (gdf.geom_type == "GeometryCollection").any()
new_collection = geomcoll_concat and not geomcoll_orig
if geomcoll_orig:
warnings.warn(
"keep_geom_type can not be called on a "
"GeoDataFrame with GeometryCollection.",
stacklevel=2,
)
else:
polys = ["Polygon", "MultiPolygon"]
lines = ["LineString", "MultiLineString", "LinearRing"]
points = ["Point", "MultiPoint"]
# Check that the gdf for multiple geom types (points, lines and/or polys)
orig_types_total = sum(
[
gdf.geom_type.isin(polys).any(),
gdf.geom_type.isin(lines).any(),
gdf.geom_type.isin(points).any(),
]
)
# Check how many geometry types are in the clipped GeoDataFrame
clip_types_total = sum(
[
clipped.geom_type.isin(polys).any(),
clipped.geom_type.isin(lines).any(),
clipped.geom_type.isin(points).any(),
]
)
# Check there aren't any new geom types in the clipped GeoDataFrame
more_types = orig_types_total < clip_types_total
if orig_types_total > 1:
warnings.warn(
"keep_geom_type can not be called on a mixed type GeoDataFrame.",
stacklevel=2,
)
elif new_collection or more_types:
orig_type = gdf.geom_type.iloc[0]
if new_collection:
clipped = clipped.explode(index_parts=False)
if orig_type in polys:
clipped = clipped.loc[clipped.geom_type.isin(polys)]
elif orig_type in lines:
clipped = clipped.loc[clipped.geom_type.isin(lines)]
return clipped

View File

@@ -0,0 +1,184 @@
from collections import defaultdict
import time
import pandas as pd
from shapely.geometry import Point
import geopandas
def _get_throttle_time(provider):
"""
Amount of time to wait between requests to a geocoding API, for providers
that specify rate limits in their terms of service.
"""
import geopy.geocoders
# https://operations.osmfoundation.org/policies/nominatim/
if provider == geopy.geocoders.Nominatim:
return 1
else:
return 0
def geocode(strings, provider=None, **kwargs):
"""
Geocode a set of strings and get a GeoDataFrame of the resulting points.
Parameters
----------
strings : list or Series of addresses to geocode
provider : str or geopy.geocoder
Specifies geocoding service to use. If none is provided,
will use 'photon' (see the Photon's terms of service at:
https://photon.komoot.io).
Either the string name used by geopy (as specified in
geopy.geocoders.SERVICE_TO_GEOCODER) or a geopy Geocoder instance
(e.g., geopy.geocoders.Photon) may be used.
Some providers require additional arguments such as access keys
See each geocoder's specific parameters in geopy.geocoders
Notes
-----
Ensure proper use of the results by consulting the Terms of Service for
your provider.
Geocoding requires geopy. Install it using 'pip install geopy'. See also
https://github.com/geopy/geopy
Examples
--------
>>> df = geopandas.tools.geocode( # doctest: +SKIP
... ["boston, ma", "1600 pennsylvania ave. washington, dc"]
... )
>>> df # doctest: +SKIP
geometry address
0 POINT (-71.05863 42.35899) Boston, MA, United States
1 POINT (-77.03651 38.89766) 1600 Pennsylvania Ave NW, Washington, DC 20006...
"""
if provider is None:
provider = "photon"
throttle_time = _get_throttle_time(provider)
return _query(strings, True, provider, throttle_time, **kwargs)
def reverse_geocode(points, provider=None, **kwargs):
"""
Reverse geocode a set of points and get a GeoDataFrame of the resulting
addresses.
The points
Parameters
----------
points : list or Series of Shapely Point objects.
x coordinate is longitude
y coordinate is latitude
provider : str or geopy.geocoder (opt)
Specifies geocoding service to use. If none is provided,
will use 'photon' (see the Photon's terms of service at:
https://photon.komoot.io).
Either the string name used by geopy (as specified in
geopy.geocoders.SERVICE_TO_GEOCODER) or a geopy Geocoder instance
(e.g., geopy.geocoders.Photon) may be used.
Some providers require additional arguments such as access keys
See each geocoder's specific parameters in geopy.geocoders
Notes
-----
Ensure proper use of the results by consulting the Terms of Service for
your provider.
Reverse geocoding requires geopy. Install it using 'pip install geopy'.
See also https://github.com/geopy/geopy
Examples
--------
>>> from shapely.geometry import Point
>>> df = geopandas.tools.reverse_geocode( # doctest: +SKIP
... [Point(-71.0594869, 42.3584697), Point(-77.0365305, 38.8977332)]
... )
>>> df # doctest: +SKIP
geometry address
0 POINT (-71.05941 42.35837) 29 Court Sq, Boston, MA 02108, United States
1 POINT (-77.03641 38.89766) 1600 Pennsylvania Ave NW, Washington, DC 20006...
"""
if provider is None:
provider = "photon"
throttle_time = _get_throttle_time(provider)
return _query(points, False, provider, throttle_time, **kwargs)
def _query(data, forward, provider, throttle_time, **kwargs):
# generic wrapper for calls over lists to geopy Geocoders
from geopy.geocoders.base import GeocoderQueryError
from geopy.geocoders import get_geocoder_for_service
if forward:
if not isinstance(data, pd.Series):
data = pd.Series(data)
else:
if not isinstance(data, geopandas.GeoSeries):
data = geopandas.GeoSeries(data)
if isinstance(provider, str):
provider = get_geocoder_for_service(provider)
coder = provider(**kwargs)
results = {}
for i, s in data.items():
try:
if forward:
results[i] = coder.geocode(s)
else:
results[i] = coder.reverse((s.y, s.x), exactly_one=True)
except (GeocoderQueryError, ValueError):
results[i] = (None, None)
time.sleep(throttle_time)
df = _prepare_geocode_result(results)
return df
def _prepare_geocode_result(results):
"""
Helper function for the geocode function
Takes a dict where keys are index entries, values are tuples containing:
(address, (lat, lon))
"""
# Prepare the data for the DataFrame as a dict of lists
d = defaultdict(list)
index = []
for i, s in results.items():
if s is None:
p = Point()
address = None
else:
address, loc = s
# loc is lat, lon and we want lon, lat
if loc is None:
p = Point()
else:
p = Point(loc[1], loc[0])
d["geometry"].append(p)
d["address"].append(address)
index.append(i)
df = geopandas.GeoDataFrame(d, index=index, crs="EPSG:4326")
return df

View File

@@ -0,0 +1,188 @@
import numpy as np
def _hilbert_distance(geoms, total_bounds=None, level=16):
"""
Calculate the distance along a Hilbert curve.
The distances are calculated for the midpoints of the geometries in the
GeoDataFrame.
Parameters
----------
geoms : GeometryArray
total_bounds : 4-element array
Total bounds of geometries - array
level : int (1 - 16), default 16
Determines the precision of the curve (points on the curve will
have coordinates in the range [0, 2^level - 1]).
Returns
-------
np.ndarray
Array containing distances along the Hilbert curve
"""
if geoms.is_empty.any() | geoms.isna().any():
raise ValueError(
"Hilbert distance cannot be computed on a GeoSeries with empty or "
"missing geometries.",
)
# Calculate bounds as numpy array
bounds = geoms.bounds
# Calculate discrete coords based on total bounds and bounds
x, y = _continuous_to_discrete_coords(bounds, level, total_bounds)
# Compute distance along hilbert curve
distances = _encode(level, x, y)
return distances
def _continuous_to_discrete_coords(bounds, level, total_bounds):
"""
Calculates mid points & ranges of geoms and returns
as discrete coords
Parameters
----------
bounds : Bounds of each geometry - array
p : The number of iterations used in constructing the Hilbert curve
total_bounds : Total bounds of geometries - array
Returns
-------
Discrete two-dimensional numpy array
Two-dimensional array Array of hilbert distances for each geom
"""
# Hilbert Side length
side_length = (2**level) - 1
# Calculate mid points for x and y bound coords - returns array
x_mids = (bounds[:, 0] + bounds[:, 2]) / 2.0
y_mids = (bounds[:, 1] + bounds[:, 3]) / 2.0
# Calculate x and y range of total bound coords - returns array
if total_bounds is None:
total_bounds = (
np.nanmin(x_mids),
np.nanmin(y_mids),
np.nanmax(x_mids),
np.nanmax(y_mids),
)
xmin, ymin, xmax, ymax = total_bounds
# Transform continuous value to discrete integer for each dimension
x_int = _continuous_to_discrete(x_mids, (xmin, xmax), side_length)
y_int = _continuous_to_discrete(y_mids, (ymin, ymax), side_length)
return x_int, y_int
def _continuous_to_discrete(vals, val_range, n):
"""
Convert a continuous one-dimensional array to discrete integer values
based their ranges
Parameters
----------
vals : Array of continuous values
val_range : Tuple containing range of continuous values
n : Number of discrete values
Returns
-------
One-dimensional array of discrete ints
"""
width = val_range[1] - val_range[0]
if width == 0:
return np.zeros_like(vals, dtype=np.uint32)
res = (vals - val_range[0]) * (n / width)
np.clip(res, 0, n, out=res)
return res.astype(np.uint32)
# Fast Hilbert curve algorithm by http://threadlocalmutex.com/
# From C++ https://github.com/rawrunprotected/hilbert_curves
# (public domain)
MAX_LEVEL = 16
def _interleave(x):
x = (x | (x << 8)) & 0x00FF00FF
x = (x | (x << 4)) & 0x0F0F0F0F
x = (x | (x << 2)) & 0x33333333
x = (x | (x << 1)) & 0x55555555
return x
def _encode(level, x, y):
x = np.asarray(x, dtype="uint32")
y = np.asarray(y, dtype="uint32")
if level > MAX_LEVEL:
raise ValueError("Level out of range")
x = x << (16 - level)
y = y << (16 - level)
# Initial prefix scan round, prime with x and y
a = x ^ y
b = 0xFFFF ^ a
c = 0xFFFF ^ (x | y)
d = x & (y ^ 0xFFFF)
A = a | (b >> 1)
B = (a >> 1) ^ a
C = ((c >> 1) ^ (b & (d >> 1))) ^ c
D = ((a & (c >> 1)) ^ (d >> 1)) ^ d
a = A.copy()
b = B.copy()
c = C.copy()
d = D.copy()
A = (a & (a >> 2)) ^ (b & (b >> 2))
B = (a & (b >> 2)) ^ (b & ((a ^ b) >> 2))
C ^= (a & (c >> 2)) ^ (b & (d >> 2))
D ^= (b & (c >> 2)) ^ ((a ^ b) & (d >> 2))
a = A.copy()
b = B.copy()
c = C.copy()
d = D.copy()
A = (a & (a >> 4)) ^ (b & (b >> 4))
B = (a & (b >> 4)) ^ (b & ((a ^ b) >> 4))
C ^= (a & (c >> 4)) ^ (b & (d >> 4))
D ^= (b & (c >> 4)) ^ ((a ^ b) & (d >> 4))
# Final round and projection
a = A.copy()
b = B.copy()
c = C.copy()
d = D.copy()
C ^= (a & (c >> 8)) ^ (b & (d >> 8))
D ^= (b & (c >> 8)) ^ ((a ^ b) & (d >> 8))
# Undo transformation prefix scan
a = C ^ (C >> 1)
b = D ^ (D >> 1)
# Recover index bits
i0 = x ^ y
i1 = b | (0xFFFF ^ (i0 | a))
return ((_interleave(i1) << 1) | _interleave(i0)) >> (32 - 2 * level)

View File

@@ -0,0 +1,399 @@
import warnings
from functools import reduce
import numpy as np
import pandas as pd
from geopandas import _compat as compat
from geopandas import GeoDataFrame, GeoSeries
from geopandas.array import _check_crs, _crs_mismatch_warn
def _ensure_geometry_column(df):
"""
Helper function to ensure the geometry column is called 'geometry'.
If another column with that name exists, it will be dropped.
"""
if not df._geometry_column_name == "geometry":
if "geometry" in df.columns:
df.drop("geometry", axis=1, inplace=True)
df.rename(
columns={df._geometry_column_name: "geometry"}, copy=False, inplace=True
)
df.set_geometry("geometry", inplace=True)
def _overlay_intersection(df1, df2):
"""
Overlay Intersection operation used in overlay function
"""
# Spatial Index to create intersections
idx1, idx2 = df2.sindex.query(df1.geometry, predicate="intersects", sort=True)
# Create pairs of geometries in both dataframes to be intersected
if idx1.size > 0 and idx2.size > 0:
left = df1.geometry.take(idx1)
left.reset_index(drop=True, inplace=True)
right = df2.geometry.take(idx2)
right.reset_index(drop=True, inplace=True)
intersections = left.intersection(right)
poly_ix = intersections.geom_type.isin(["Polygon", "MultiPolygon"])
intersections.loc[poly_ix] = intersections[poly_ix].buffer(0)
# only keep actual intersecting geometries
pairs_intersect = pd.DataFrame({"__idx1": idx1, "__idx2": idx2})
geom_intersect = intersections
# merge data for intersecting geometries
df1 = df1.reset_index(drop=True)
df2 = df2.reset_index(drop=True)
dfinter = pairs_intersect.merge(
df1.drop(df1._geometry_column_name, axis=1),
left_on="__idx1",
right_index=True,
)
dfinter = dfinter.merge(
df2.drop(df2._geometry_column_name, axis=1),
left_on="__idx2",
right_index=True,
suffixes=("_1", "_2"),
)
return GeoDataFrame(dfinter, geometry=geom_intersect, crs=df1.crs)
else:
result = df1.iloc[:0].merge(
df2.iloc[:0].drop(df2.geometry.name, axis=1),
left_index=True,
right_index=True,
suffixes=("_1", "_2"),
)
result["__idx1"] = None
result["__idx2"] = None
return result[
result.columns.drop(df1.geometry.name).tolist() + [df1.geometry.name]
]
def _overlay_difference(df1, df2):
"""
Overlay Difference operation used in overlay function
"""
# spatial index query to find intersections
idx1, idx2 = df2.sindex.query(df1.geometry, predicate="intersects", sort=True)
idx1_unique, idx1_unique_indices = np.unique(idx1, return_index=True)
idx2_split = np.split(idx2, idx1_unique_indices[1:])
sidx = [
idx2_split.pop(0) if idx in idx1_unique else []
for idx in range(df1.geometry.size)
]
# Create differences
new_g = []
for geom, neighbours in zip(df1.geometry, sidx):
new = reduce(
lambda x, y: x.difference(y), [geom] + list(df2.geometry.iloc[neighbours])
)
new_g.append(new)
differences = GeoSeries(new_g, index=df1.index, crs=df1.crs)
poly_ix = differences.geom_type.isin(["Polygon", "MultiPolygon"])
if compat.USE_PYGEOS:
differences.loc[poly_ix] = differences[poly_ix].make_valid()
else:
differences.loc[poly_ix] = differences[poly_ix].buffer(0)
geom_diff = differences[~differences.is_empty].copy()
dfdiff = df1[~differences.is_empty].copy()
dfdiff[dfdiff._geometry_column_name] = geom_diff
return dfdiff
def _overlay_symmetric_diff(df1, df2):
"""
Overlay Symmetric Difference operation used in overlay function
"""
dfdiff1 = _overlay_difference(df1, df2)
dfdiff2 = _overlay_difference(df2, df1)
dfdiff1["__idx1"] = range(len(dfdiff1))
dfdiff2["__idx2"] = range(len(dfdiff2))
dfdiff1["__idx2"] = np.nan
dfdiff2["__idx1"] = np.nan
# ensure geometry name (otherwise merge goes wrong)
_ensure_geometry_column(dfdiff1)
_ensure_geometry_column(dfdiff2)
# combine both 'difference' dataframes
dfsym = dfdiff1.merge(
dfdiff2, on=["__idx1", "__idx2"], how="outer", suffixes=("_1", "_2")
)
geometry = dfsym.geometry_1.copy()
geometry.name = "geometry"
# https://github.com/pandas-dev/pandas/issues/26468 use loc for now
geometry.loc[dfsym.geometry_1.isnull()] = dfsym.loc[
dfsym.geometry_1.isnull(), "geometry_2"
]
dfsym.drop(["geometry_1", "geometry_2"], axis=1, inplace=True)
dfsym.reset_index(drop=True, inplace=True)
dfsym = GeoDataFrame(dfsym, geometry=geometry, crs=df1.crs)
return dfsym
def _overlay_union(df1, df2):
"""
Overlay Union operation used in overlay function
"""
dfinter = _overlay_intersection(df1, df2)
dfsym = _overlay_symmetric_diff(df1, df2)
dfunion = pd.concat([dfinter, dfsym], ignore_index=True, sort=False)
# keep geometry column last
columns = list(dfunion.columns)
columns.remove("geometry")
columns.append("geometry")
return dfunion.reindex(columns=columns)
def overlay(df1, df2, how="intersection", keep_geom_type=None, make_valid=True):
"""Perform spatial overlay between two GeoDataFrames.
Currently only supports data GeoDataFrames with uniform geometry types,
i.e. containing only (Multi)Polygons, or only (Multi)Points, or a
combination of (Multi)LineString and LinearRing shapes.
Implements several methods that are all effectively subsets of the union.
See the User Guide page :doc:`../../user_guide/set_operations` for details.
Parameters
----------
df1 : GeoDataFrame
df2 : GeoDataFrame
how : string
Method of spatial overlay: 'intersection', 'union',
'identity', 'symmetric_difference' or 'difference'.
keep_geom_type : bool
If True, return only geometries of the same geometry type as df1 has,
if False, return all resulting geometries. Default is None,
which will set keep_geom_type to True but warn upon dropping
geometries.
make_valid : bool, default True
If True, any invalid input geometries are corrected with a call to `buffer(0)`,
if False, a `ValueError` is raised if any input geometries are invalid.
Returns
-------
df : GeoDataFrame
GeoDataFrame with new set of polygons and attributes
resulting from the overlay
Examples
--------
>>> from shapely.geometry import Polygon
>>> polys1 = geopandas.GeoSeries([Polygon([(0,0), (2,0), (2,2), (0,2)]),
... Polygon([(2,2), (4,2), (4,4), (2,4)])])
>>> polys2 = geopandas.GeoSeries([Polygon([(1,1), (3,1), (3,3), (1,3)]),
... Polygon([(3,3), (5,3), (5,5), (3,5)])])
>>> df1 = geopandas.GeoDataFrame({'geometry': polys1, 'df1_data':[1,2]})
>>> df2 = geopandas.GeoDataFrame({'geometry': polys2, 'df2_data':[1,2]})
>>> geopandas.overlay(df1, df2, how='union')
df1_data df2_data geometry
0 1.0 1.0 POLYGON ((2.00000 2.00000, 2.00000 1.00000, 1....
1 2.0 1.0 POLYGON ((2.00000 2.00000, 2.00000 3.00000, 3....
2 2.0 2.0 POLYGON ((4.00000 4.00000, 4.00000 3.00000, 3....
3 1.0 NaN POLYGON ((2.00000 0.00000, 0.00000 0.00000, 0....
4 2.0 NaN MULTIPOLYGON (((3.00000 4.00000, 3.00000 3.000...
5 NaN 1.0 MULTIPOLYGON (((2.00000 3.00000, 2.00000 2.000...
6 NaN 2.0 POLYGON ((3.00000 5.00000, 5.00000 5.00000, 5....
>>> geopandas.overlay(df1, df2, how='intersection')
df1_data df2_data geometry
0 1 1 POLYGON ((2.00000 2.00000, 2.00000 1.00000, 1....
1 2 1 POLYGON ((2.00000 2.00000, 2.00000 3.00000, 3....
2 2 2 POLYGON ((4.00000 4.00000, 4.00000 3.00000, 3....
>>> geopandas.overlay(df1, df2, how='symmetric_difference')
df1_data df2_data geometry
0 1.0 NaN POLYGON ((2.00000 0.00000, 0.00000 0.00000, 0....
1 2.0 NaN MULTIPOLYGON (((3.00000 4.00000, 3.00000 3.000...
2 NaN 1.0 MULTIPOLYGON (((2.00000 3.00000, 2.00000 2.000...
3 NaN 2.0 POLYGON ((3.00000 5.00000, 5.00000 5.00000, 5....
>>> geopandas.overlay(df1, df2, how='difference')
geometry df1_data
0 POLYGON ((2.00000 0.00000, 0.00000 0.00000, 0.... 1
1 MULTIPOLYGON (((3.00000 4.00000, 3.00000 3.000... 2
>>> geopandas.overlay(df1, df2, how='identity')
df1_data df2_data geometry
0 1.0 1.0 POLYGON ((2.00000 2.00000, 2.00000 1.00000, 1....
1 2.0 1.0 POLYGON ((2.00000 2.00000, 2.00000 3.00000, 3....
2 2.0 2.0 POLYGON ((4.00000 4.00000, 4.00000 3.00000, 3....
3 1.0 NaN POLYGON ((2.00000 0.00000, 0.00000 0.00000, 0....
4 2.0 NaN MULTIPOLYGON (((3.00000 4.00000, 3.00000 3.000...
See also
--------
sjoin : spatial join
GeoDataFrame.overlay : equivalent method
Notes
-----
Every operation in GeoPandas is planar, i.e. the potential third
dimension is not taken into account.
"""
# Allowed operations
allowed_hows = [
"intersection",
"union",
"identity",
"symmetric_difference",
"difference", # aka erase
]
# Error Messages
if how not in allowed_hows:
raise ValueError(
"`how` was '{0}' but is expected to be in {1}".format(how, allowed_hows)
)
if isinstance(df1, GeoSeries) or isinstance(df2, GeoSeries):
raise NotImplementedError(
"overlay currently only implemented for GeoDataFrames"
)
if not _check_crs(df1, df2):
_crs_mismatch_warn(df1, df2, stacklevel=3)
if keep_geom_type is None:
keep_geom_type = True
keep_geom_type_warning = True
else:
keep_geom_type_warning = False
polys = ["Polygon", "MultiPolygon"]
lines = ["LineString", "MultiLineString", "LinearRing"]
points = ["Point", "MultiPoint"]
for i, df in enumerate([df1, df2]):
poly_check = df.geom_type.isin(polys).any()
lines_check = df.geom_type.isin(lines).any()
points_check = df.geom_type.isin(points).any()
if sum([poly_check, lines_check, points_check]) > 1:
raise NotImplementedError(
"df{} contains mixed geometry types.".format(i + 1)
)
if how == "intersection":
box_gdf1 = df1.total_bounds
box_gdf2 = df2.total_bounds
if not (
((box_gdf1[0] <= box_gdf2[2]) and (box_gdf2[0] <= box_gdf1[2]))
and ((box_gdf1[1] <= box_gdf2[3]) and (box_gdf2[1] <= box_gdf1[3]))
):
result = df1.iloc[:0].merge(
df2.iloc[:0].drop(df2.geometry.name, axis=1),
left_index=True,
right_index=True,
suffixes=("_1", "_2"),
)
return result[
result.columns.drop(df1.geometry.name).tolist() + [df1.geometry.name]
]
# Computations
def _make_valid(df):
df = df.copy()
if df.geom_type.isin(polys).all():
mask = ~df.geometry.is_valid
col = df._geometry_column_name
if make_valid:
df.loc[mask, col] = df.loc[mask, col].buffer(0)
elif mask.any():
raise ValueError(
"You have passed make_valid=False along with "
f"{mask.sum()} invalid input geometries. "
"Use make_valid=True or make sure that all geometries "
"are valid before using overlay."
)
return df
df1 = _make_valid(df1)
df2 = _make_valid(df2)
with warnings.catch_warnings(): # CRS checked above, suppress array-level warning
warnings.filterwarnings("ignore", message="CRS mismatch between the CRS")
if how == "difference":
result = _overlay_difference(df1, df2)
elif how == "intersection":
result = _overlay_intersection(df1, df2)
elif how == "symmetric_difference":
result = _overlay_symmetric_diff(df1, df2)
elif how == "union":
result = _overlay_union(df1, df2)
elif how == "identity":
dfunion = _overlay_union(df1, df2)
result = dfunion[dfunion["__idx1"].notnull()].copy()
if how in ["intersection", "symmetric_difference", "union", "identity"]:
result.drop(["__idx1", "__idx2"], axis=1, inplace=True)
if keep_geom_type:
geom_type = df1.geom_type.iloc[0]
# First we filter the geometry types inside GeometryCollections objects
# (e.g. GeometryCollection([polygon, point]) -> polygon)
# we do this separately on only the relevant rows, as this is an expensive
# operation (an expensive no-op for geometry types other than collections)
is_collection = result.geom_type == "GeometryCollection"
if is_collection.any():
geom_col = result._geometry_column_name
collections = result[[geom_col]][is_collection]
exploded = collections.reset_index(drop=True).explode(index_parts=True)
exploded = exploded.reset_index(level=0)
orig_num_geoms_exploded = exploded.shape[0]
if geom_type in polys:
exploded.loc[~exploded.geom_type.isin(polys), geom_col] = None
elif geom_type in lines:
exploded.loc[~exploded.geom_type.isin(lines), geom_col] = None
elif geom_type in points:
exploded.loc[~exploded.geom_type.isin(points), geom_col] = None
else:
raise TypeError(
"`keep_geom_type` does not support {}.".format(geom_type)
)
num_dropped_collection = (
orig_num_geoms_exploded - exploded.geometry.isna().sum()
)
# level_0 created with above reset_index operation
# and represents the original geometry collections
# TODO avoiding dissolve to call unary_union in this case could further
# improve performance (we only need to collect geometries in their
# respective Multi version)
dissolved = exploded.dissolve(by="level_0")
result.loc[is_collection, geom_col] = dissolved[geom_col].values
else:
num_dropped_collection = 0
# Now we filter all geometries (in theory we don't need to do this
# again for the rows handled above for GeometryCollections, but filtering
# them out is probably more expensive as simply including them when this
# is typically about only a few rows)
orig_num_geoms = result.shape[0]
if geom_type in polys:
result = result.loc[result.geom_type.isin(polys)]
elif geom_type in lines:
result = result.loc[result.geom_type.isin(lines)]
elif geom_type in points:
result = result.loc[result.geom_type.isin(points)]
else:
raise TypeError("`keep_geom_type` does not support {}.".format(geom_type))
num_dropped = orig_num_geoms - result.shape[0]
if (num_dropped > 0 or num_dropped_collection > 0) and keep_geom_type_warning:
warnings.warn(
"`keep_geom_type=True` in overlay resulted in {} dropped "
"geometries of different geometry types than df1 has. "
"Set `keep_geom_type=False` to retain all "
"geometries".format(num_dropped + num_dropped_collection),
UserWarning,
stacklevel=2,
)
result.reset_index(drop=True, inplace=True)
return result

View File

@@ -0,0 +1,553 @@
from typing import Optional
import warnings
import numpy as np
import pandas as pd
from geopandas import GeoDataFrame
from geopandas import _compat as compat
from geopandas.array import _check_crs, _crs_mismatch_warn
def sjoin(
left_df,
right_df,
how="inner",
predicate="intersects",
lsuffix="left",
rsuffix="right",
**kwargs,
):
"""Spatial join of two GeoDataFrames.
See the User Guide page :doc:`../../user_guide/mergingdata` for details.
Parameters
----------
left_df, right_df : GeoDataFrames
how : string, default 'inner'
The type of join:
* 'left': use keys from left_df; retain only left_df geometry column
* 'right': use keys from right_df; retain only right_df geometry column
* 'inner': use intersection of keys from both dfs; retain only
left_df geometry column
predicate : string, default 'intersects'
Binary predicate. Valid values are determined by the spatial index used.
You can check the valid values in left_df or right_df as
``left_df.sindex.valid_query_predicates`` or
``right_df.sindex.valid_query_predicates``
Replaces deprecated ``op`` parameter.
lsuffix : string, default 'left'
Suffix to apply to overlapping column names (left GeoDataFrame).
rsuffix : string, default 'right'
Suffix to apply to overlapping column names (right GeoDataFrame).
Examples
--------
>>> import geodatasets
>>> chicago = geopandas.read_file(
... geodatasets.get_path("geoda.chicago_health")
... )
>>> groceries = geopandas.read_file(
... geodatasets.get_path("geoda.groceries")
... ).to_crs(chicago.crs)
>>> chicago.head() # doctest: +SKIP
ComAreaID ... geometry
0 35 ... POLYGON ((-87.60914 41.84469, -87.60915 41.844...
1 36 ... POLYGON ((-87.59215 41.81693, -87.59231 41.816...
2 37 ... POLYGON ((-87.62880 41.80189, -87.62879 41.801...
3 38 ... POLYGON ((-87.60671 41.81681, -87.60670 41.816...
4 39 ... POLYGON ((-87.59215 41.81693, -87.59215 41.816...
[5 rows x 87 columns]
>>> groceries.head() # doctest: +SKIP
OBJECTID Ycoord ... Category geometry
0 16 41.973266 ... NaN MULTIPOINT (-87.65661 41.97321)
1 18 41.696367 ... NaN MULTIPOINT (-87.68136 41.69713)
2 22 41.868634 ... NaN MULTIPOINT (-87.63918 41.86847)
3 23 41.877590 ... new MULTIPOINT (-87.65495 41.87783)
4 27 41.737696 ... NaN MULTIPOINT (-87.62715 41.73623)
[5 rows x 8 columns]
>>> groceries_w_communities = geopandas.sjoin(groceries, chicago)
>>> groceries_w_communities.head() # doctest: +SKIP
OBJECTID Ycoord Xcoord ... GonorrF GonorrM Tuberc
0 16 41.973266 -87.657073 ... 170.8 468.7 13.6
87 365 41.961707 -87.654058 ... 170.8 468.7 13.6
90 373 41.963131 -87.656352 ... 170.8 468.7 13.6
140 582 41.969131 -87.674882 ... 170.8 468.7 13.6
1 18 41.696367 -87.681315 ... 800.5 741.1 2.6
[5 rows x 95 columns]
See also
--------
overlay : overlay operation resulting in a new geometry
GeoDataFrame.sjoin : equivalent method
Notes
-----
Every operation in GeoPandas is planar, i.e. the potential third
dimension is not taken into account.
"""
if "op" in kwargs:
op = kwargs.pop("op")
deprecation_message = (
"The `op` parameter is deprecated and will be removed"
" in a future release. Please use the `predicate` parameter"
" instead."
)
if predicate != "intersects" and op != predicate:
override_message = (
"A non-default value for `predicate` was passed"
f' (got `predicate="{predicate}"`'
f' in combination with `op="{op}"`).'
" The value of `predicate` will be overridden by the value of `op`,"
" , which may result in unexpected behavior."
f"\n{deprecation_message}"
)
warnings.warn(override_message, UserWarning, stacklevel=4)
else:
warnings.warn(deprecation_message, FutureWarning, stacklevel=4)
predicate = op
if kwargs:
first = next(iter(kwargs.keys()))
raise TypeError(f"sjoin() got an unexpected keyword argument '{first}'")
_basic_checks(left_df, right_df, how, lsuffix, rsuffix)
indices = _geom_predicate_query(left_df, right_df, predicate)
joined = _frame_join(indices, left_df, right_df, how, lsuffix, rsuffix)
return joined
def _basic_checks(left_df, right_df, how, lsuffix, rsuffix):
"""Checks the validity of join input parameters.
`how` must be one of the valid options.
`'index_'` concatenated with `lsuffix` or `rsuffix` must not already
exist as columns in the left or right data frames.
Parameters
------------
left_df : GeoDataFrame
right_df : GeoData Frame
how : str, one of 'left', 'right', 'inner'
join type
lsuffix : str
left index suffix
rsuffix : str
right index suffix
"""
if not isinstance(left_df, GeoDataFrame):
raise ValueError(
"'left_df' should be GeoDataFrame, got {}".format(type(left_df))
)
if not isinstance(right_df, GeoDataFrame):
raise ValueError(
"'right_df' should be GeoDataFrame, got {}".format(type(right_df))
)
allowed_hows = ["left", "right", "inner"]
if how not in allowed_hows:
raise ValueError(
'`how` was "{}" but is expected to be in {}'.format(how, allowed_hows)
)
if not _check_crs(left_df, right_df):
_crs_mismatch_warn(left_df, right_df, stacklevel=4)
index_left = "index_{}".format(lsuffix)
index_right = "index_{}".format(rsuffix)
# due to GH 352
if any(left_df.columns.isin([index_left, index_right])) or any(
right_df.columns.isin([index_left, index_right])
):
raise ValueError(
"'{0}' and '{1}' cannot be names in the frames being"
" joined".format(index_left, index_right)
)
def _geom_predicate_query(left_df, right_df, predicate):
"""Compute geometric comparisons and get matching indices.
Parameters
----------
left_df : GeoDataFrame
right_df : GeoDataFrame
predicate : string
Binary predicate to query.
Returns
-------
DataFrame
DataFrame with matching indices in
columns named `_key_left` and `_key_right`.
"""
with warnings.catch_warnings():
# We don't need to show our own warning here
# TODO remove this once the deprecation has been enforced
warnings.filterwarnings(
"ignore", "Generated spatial index is empty", FutureWarning
)
original_predicate = predicate
if predicate == "within":
# within is implemented as the inverse of contains
# contains is a faster predicate
# see discussion at https://github.com/geopandas/geopandas/pull/1421
predicate = "contains"
sindex = left_df.sindex
input_geoms = right_df.geometry
else:
# all other predicates are symmetric
# keep them the same
sindex = right_df.sindex
input_geoms = left_df.geometry
if sindex:
l_idx, r_idx = sindex.query(input_geoms, predicate=predicate, sort=False)
indices = pd.DataFrame({"_key_left": l_idx, "_key_right": r_idx})
else:
# when sindex is empty / has no valid geometries
indices = pd.DataFrame(columns=["_key_left", "_key_right"], dtype=float)
if original_predicate == "within":
# within is implemented as the inverse of contains
# flip back the results
indices = indices.rename(
columns={"_key_left": "_key_right", "_key_right": "_key_left"}
)
return indices
def _frame_join(join_df, left_df, right_df, how, lsuffix, rsuffix):
"""Join the GeoDataFrames at the DataFrame level.
Parameters
----------
join_df : DataFrame
Indices and join data returned by the geometric join.
Must have columns `_key_left` and `_key_right`
with integer indices representing the matches
from `left_df` and `right_df` respectively.
Additional columns may be included and will be copied to
the resultant GeoDataFrame.
left_df : GeoDataFrame
right_df : GeoDataFrame
lsuffix : string
Suffix to apply to overlapping column names (left GeoDataFrame).
rsuffix : string
Suffix to apply to overlapping column names (right GeoDataFrame).
how : string
The type of join to use on the DataFrame level.
Returns
-------
GeoDataFrame
Joined GeoDataFrame.
"""
# the spatial index only allows limited (numeric) index types, but an
# index in geopandas may be any arbitrary dtype. so reset both indices now
# and store references to the original indices, to be reaffixed later.
# GH 352
index_left = "index_{}".format(lsuffix)
left_df = left_df.copy(deep=True)
try:
left_index_name = left_df.index.name
left_df.index = left_df.index.rename(index_left)
except TypeError:
index_left = [
"index_{}".format(lsuffix + str(pos))
for pos, ix in enumerate(left_df.index.names)
]
left_index_name = left_df.index.names
left_df.index = left_df.index.rename(index_left)
left_df = left_df.reset_index()
index_right = "index_{}".format(rsuffix)
right_df = right_df.copy(deep=True)
try:
right_index_name = right_df.index.name
right_df.index = right_df.index.rename(index_right)
except TypeError:
index_right = [
"index_{}".format(rsuffix + str(pos))
for pos, ix in enumerate(right_df.index.names)
]
right_index_name = right_df.index.names
right_df.index = right_df.index.rename(index_right)
right_df = right_df.reset_index()
# perform join on the dataframes
if how == "inner":
join_df = join_df.set_index("_key_left")
joined = (
left_df.merge(join_df, left_index=True, right_index=True)
.merge(
right_df.drop(right_df.geometry.name, axis=1),
left_on="_key_right",
right_index=True,
suffixes=("_{}".format(lsuffix), "_{}".format(rsuffix)),
)
.set_index(index_left)
.drop(["_key_right"], axis=1)
)
if isinstance(index_left, list):
joined.index.names = left_index_name
else:
joined.index.name = left_index_name
elif how == "left":
join_df = join_df.set_index("_key_left")
joined = (
left_df.merge(join_df, left_index=True, right_index=True, how="left")
.merge(
right_df.drop(right_df.geometry.name, axis=1),
how="left",
left_on="_key_right",
right_index=True,
suffixes=("_{}".format(lsuffix), "_{}".format(rsuffix)),
)
.set_index(index_left)
.drop(["_key_right"], axis=1)
)
if isinstance(index_left, list):
joined.index.names = left_index_name
else:
joined.index.name = left_index_name
else: # how == 'right':
joined = (
left_df.drop(left_df.geometry.name, axis=1)
.merge(
join_df.merge(
right_df, left_on="_key_right", right_index=True, how="right"
),
left_index=True,
right_on="_key_left",
how="right",
suffixes=("_{}".format(lsuffix), "_{}".format(rsuffix)),
)
.set_index(index_right)
.drop(["_key_left", "_key_right"], axis=1)
.set_geometry(right_df.geometry.name)
)
if isinstance(index_right, list):
joined.index.names = right_index_name
else:
joined.index.name = right_index_name
return joined
def _nearest_query(
left_df: GeoDataFrame,
right_df: GeoDataFrame,
max_distance: float,
how: str,
return_distance: bool,
exclusive: bool,
):
if not (compat.USE_SHAPELY_20 or (compat.USE_PYGEOS and compat.PYGEOS_GE_010)):
raise NotImplementedError(
"Currently, only PyGEOS >= 0.10.0 or Shapely >= 2.0 supports "
"`nearest_all`. " + compat.INSTALL_PYGEOS_ERROR
)
# use the opposite of the join direction for the index
use_left_as_sindex = how == "right"
if use_left_as_sindex:
sindex = left_df.sindex
query = right_df.geometry
else:
sindex = right_df.sindex
query = left_df.geometry
if sindex:
res = sindex.nearest(
query,
return_all=True,
max_distance=max_distance,
return_distance=return_distance,
exclusive=exclusive,
)
if return_distance:
(input_idx, tree_idx), distances = res
else:
(input_idx, tree_idx) = res
distances = None
if use_left_as_sindex:
l_idx, r_idx = tree_idx, input_idx
sort_order = np.argsort(l_idx, kind="stable")
l_idx, r_idx = l_idx[sort_order], r_idx[sort_order]
if distances is not None:
distances = distances[sort_order]
else:
l_idx, r_idx = input_idx, tree_idx
join_df = pd.DataFrame(
{"_key_left": l_idx, "_key_right": r_idx, "distances": distances}
)
else:
# when sindex is empty / has no valid geometries
join_df = pd.DataFrame(
columns=["_key_left", "_key_right", "distances"], dtype=float
)
return join_df
def sjoin_nearest(
left_df: GeoDataFrame,
right_df: GeoDataFrame,
how: str = "inner",
max_distance: Optional[float] = None,
lsuffix: str = "left",
rsuffix: str = "right",
distance_col: Optional[str] = None,
exclusive: bool = False,
) -> GeoDataFrame:
"""Spatial join of two GeoDataFrames based on the distance between their geometries.
Results will include multiple output records for a single input record
where there are multiple equidistant nearest or intersected neighbors.
Distance is calculated in CRS units and can be returned using the
`distance_col` parameter.
See the User Guide page
https://geopandas.readthedocs.io/en/latest/docs/user_guide/mergingdata.html
for more details.
Parameters
----------
left_df, right_df : GeoDataFrames
how : string, default 'inner'
The type of join:
* 'left': use keys from left_df; retain only left_df geometry column
* 'right': use keys from right_df; retain only right_df geometry column
* 'inner': use intersection of keys from both dfs; retain only
left_df geometry column
max_distance : float, default None
Maximum distance within which to query for nearest geometry.
Must be greater than 0.
The max_distance used to search for nearest items in the tree may have a
significant impact on performance by reducing the number of input
geometries that are evaluated for nearest items in the tree.
lsuffix : string, default 'left'
Suffix to apply to overlapping column names (left GeoDataFrame).
rsuffix : string, default 'right'
Suffix to apply to overlapping column names (right GeoDataFrame).
distance_col : string, default None
If set, save the distances computed between matching geometries under a
column of this name in the joined GeoDataFrame.
exclusive : bool, default False
If True, the nearest geometries that are equal to the input geometry
will not be returned, default False.
Requires Shapely >= 2.0.
Examples
--------
>>> import geodatasets
>>> groceries = geopandas.read_file(
... geodatasets.get_path("geoda.groceries")
... )
>>> chicago = geopandas.read_file(
... geodatasets.get_path("geoda.chicago_health")
... ).to_crs(groceries.crs)
>>> chicago.head() # doctest: +SKIP
ComAreaID ... geometry
0 35 ... POLYGON ((-87.60914 41.84469, -87.60915 41.844...
1 36 ... POLYGON ((-87.59215 41.81693, -87.59231 41.816...
2 37 ... POLYGON ((-87.62880 41.80189, -87.62879 41.801...
3 38 ... POLYGON ((-87.60671 41.81681, -87.60670 41.816...
4 39 ... POLYGON ((-87.59215 41.81693, -87.59215 41.816...
[5 rows x 87 columns]
>>> groceries.head() # doctest: +SKIP
OBJECTID Ycoord ... Category geometry
0 16 41.973266 ... NaN MULTIPOINT (-87.65661 41.97321)
1 18 41.696367 ... NaN MULTIPOINT (-87.68136 41.69713)
2 22 41.868634 ... NaN MULTIPOINT (-87.63918 41.86847)
3 23 41.877590 ... new MULTIPOINT (-87.65495 41.87783)
4 27 41.737696 ... NaN MULTIPOINT (-87.62715 41.73623)
[5 rows x 8 columns]
>>> groceries_w_communities = geopandas.sjoin_nearest(groceries, chicago)
>>> groceries_w_communities[["Chain", "community", "geometry"]].head(2)
Chain community geometry
0 VIET HOA PLAZA UPTOWN MULTIPOINT (1168268.672 1933554.350)
87 JEWEL OSCO UPTOWN MULTIPOINT (1168837.980 1929246.962)
To include the distances:
>>> groceries_w_communities = geopandas.sjoin_nearest(groceries, chicago, \
distance_col="distances")
>>> groceries_w_communities[["Chain", "community", \
"distances"]].head(2) # doctest: +SKIP
Chain community distances
0 VIET HOA PLAZA UPTOWN 0.0
87 JEWEL OSCO UPTOWN 0.0
In the following example, we get multiple groceries for Uptown because all
results are equidistant (in this case zero because they intersect).
In fact, we get 4 results in total:
>>> chicago_w_groceries = geopandas.sjoin_nearest(groceries, chicago, \
distance_col="distances", how="right")
>>> uptown_results = \
chicago_w_groceries[chicago_w_groceries["community"] == "UPTOWN"]
>>> uptown_results[["Chain", "community"]] # doctest: +SKIP
Chain community
30 VIET HOA PLAZA UPTOWN
30 JEWEL OSCO UPTOWN
30 TARGET UPTOWN
30 Mariano's UPTOWN
See also
--------
sjoin : binary predicate joins
GeoDataFrame.sjoin_nearest : equivalent method
Notes
-----
Since this join relies on distances, results will be inaccurate
if your geometries are in a geographic CRS.
Every operation in GeoPandas is planar, i.e. the potential third
dimension is not taken into account.
"""
_basic_checks(left_df, right_df, how, lsuffix, rsuffix)
left_df.geometry.values.check_geographic_crs(stacklevel=1)
right_df.geometry.values.check_geographic_crs(stacklevel=1)
return_distance = distance_col is not None
join_df = _nearest_query(
left_df, right_df, max_distance, how, return_distance, exclusive
)
if return_distance:
join_df = join_df.rename(columns={"distances": distance_col})
else:
join_df.pop("distances")
joined = _frame_join(join_df, left_df, right_df, how, lsuffix, rsuffix)
if return_distance:
columns = [c for c in joined.columns if c != distance_col] + [distance_col]
joined = joined[columns]
return joined

View File

@@ -0,0 +1,462 @@
"""Tests for the clip module."""
import numpy as np
import shapely
from shapely.geometry import (
Polygon,
Point,
LineString,
LinearRing,
GeometryCollection,
MultiPoint,
box,
)
import geopandas
from geopandas import GeoDataFrame, GeoSeries, clip
from geopandas.testing import assert_geodataframe_equal, assert_geoseries_equal
import pytest
from geopandas.tools.clip import _mask_is_list_like_rectangle
pytestmark = pytest.mark.skip_no_sindex
mask_variants_single_rectangle = [
"single_rectangle_gdf",
"single_rectangle_gdf_list_bounds",
"single_rectangle_gdf_tuple_bounds",
"single_rectangle_gdf_array_bounds",
]
mask_variants_large_rectangle = [
"larger_single_rectangle_gdf",
"larger_single_rectangle_gdf_bounds",
]
@pytest.fixture
def point_gdf():
"""Create a point GeoDataFrame."""
pts = np.array([[2, 2], [3, 4], [9, 8], [-12, -15]])
gdf = GeoDataFrame([Point(xy) for xy in pts], columns=["geometry"], crs="EPSG:3857")
return gdf
@pytest.fixture
def pointsoutside_nooverlap_gdf():
"""Create a point GeoDataFrame. Its points are all outside the single
rectangle, and its bounds are outside the single rectangle's."""
pts = np.array([[5, 15], [15, 15], [15, 20]])
gdf = GeoDataFrame([Point(xy) for xy in pts], columns=["geometry"], crs="EPSG:3857")
return gdf
@pytest.fixture
def pointsoutside_overlap_gdf():
"""Create a point GeoDataFrame. Its points are all outside the single
rectangle, and its bounds are overlapping the single rectangle's."""
pts = np.array([[5, 15], [15, 15], [15, 5]])
gdf = GeoDataFrame([Point(xy) for xy in pts], columns=["geometry"], crs="EPSG:3857")
return gdf
@pytest.fixture
def single_rectangle_gdf():
"""Create a single rectangle for clipping."""
poly_inters = Polygon([(0, 0), (0, 10), (10, 10), (10, 0), (0, 0)])
gdf = GeoDataFrame([1], geometry=[poly_inters], crs="EPSG:3857")
gdf["attr2"] = "site-boundary"
return gdf
@pytest.fixture
def single_rectangle_gdf_tuple_bounds(single_rectangle_gdf):
"""Bounds of the created single rectangle"""
return tuple(single_rectangle_gdf.total_bounds)
@pytest.fixture
def single_rectangle_gdf_list_bounds(single_rectangle_gdf):
"""Bounds of the created single rectangle"""
return list(single_rectangle_gdf.total_bounds)
@pytest.fixture
def single_rectangle_gdf_array_bounds(single_rectangle_gdf):
"""Bounds of the created single rectangle"""
return single_rectangle_gdf.total_bounds
@pytest.fixture
def larger_single_rectangle_gdf():
"""Create a slightly larger rectangle for clipping.
The smaller single rectangle is used to test the edge case where slivers
are returned when you clip polygons. This fixture is larger which
eliminates the slivers in the clip return.
"""
poly_inters = Polygon([(-5, -5), (-5, 15), (15, 15), (15, -5), (-5, -5)])
gdf = GeoDataFrame([1], geometry=[poly_inters], crs="EPSG:3857")
gdf["attr2"] = ["study area"]
return gdf
@pytest.fixture
def larger_single_rectangle_gdf_bounds(larger_single_rectangle_gdf):
"""Bounds of the created single rectangle"""
return tuple(larger_single_rectangle_gdf.total_bounds)
@pytest.fixture
def buffered_locations(point_gdf):
"""Buffer points to create a multi-polygon."""
buffered_locs = point_gdf
buffered_locs["geometry"] = buffered_locs.buffer(4)
buffered_locs["type"] = "plot"
return buffered_locs
@pytest.fixture
def donut_geometry(buffered_locations, single_rectangle_gdf):
"""Make a geometry with a hole in the middle (a donut)."""
donut = geopandas.overlay(
buffered_locations, single_rectangle_gdf, how="symmetric_difference"
)
return donut
@pytest.fixture
def two_line_gdf():
"""Create Line Objects For Testing"""
linea = LineString([(1, 1), (2, 2), (3, 2), (5, 3)])
lineb = LineString([(3, 4), (5, 7), (12, 2), (10, 5), (9, 7.5)])
gdf = GeoDataFrame([1, 2], geometry=[linea, lineb], crs="EPSG:3857")
return gdf
@pytest.fixture
def multi_poly_gdf(donut_geometry):
"""Create a multi-polygon GeoDataFrame."""
multi_poly = donut_geometry.unary_union
out_df = GeoDataFrame(geometry=GeoSeries(multi_poly), crs="EPSG:3857")
out_df["attr"] = ["pool"]
return out_df
@pytest.fixture
def multi_line(two_line_gdf):
"""Create a multi-line GeoDataFrame.
This GDF has one multiline and one regular line."""
# Create a single and multi line object
multiline_feat = two_line_gdf.unary_union
linec = LineString([(2, 1), (3, 1), (4, 1), (5, 2)])
out_df = GeoDataFrame(geometry=GeoSeries([multiline_feat, linec]), crs="EPSG:3857")
out_df["attr"] = ["road", "stream"]
return out_df
@pytest.fixture
def multi_point(point_gdf):
"""Create a multi-point GeoDataFrame."""
multi_point = point_gdf.unary_union
out_df = GeoDataFrame(
geometry=GeoSeries(
[multi_point, Point(2, 5), Point(-11, -14), Point(-10, -12)]
),
crs="EPSG:3857",
)
out_df["attr"] = ["tree", "another tree", "shrub", "berries"]
return out_df
@pytest.fixture
def mixed_gdf():
"""Create a Mixed Polygon and LineString For Testing"""
point = Point(2, 3)
line = LineString([(1, 1), (2, 2), (3, 2), (5, 3), (12, 1)])
poly = Polygon([(3, 4), (5, 2), (12, 2), (10, 5), (9, 7.5)])
ring = LinearRing([(1, 1), (2, 2), (3, 2), (5, 3), (12, 1)])
gdf = GeoDataFrame(
[1, 2, 3, 4], geometry=[point, poly, line, ring], crs="EPSG:3857"
)
return gdf
@pytest.fixture
def geomcol_gdf():
"""Create a Mixed Polygon and LineString For Testing"""
point = Point(2, 3)
poly = Polygon([(3, 4), (5, 2), (12, 2), (10, 5), (9, 7.5)])
coll = GeometryCollection([point, poly])
gdf = GeoDataFrame([1], geometry=[coll], crs="EPSG:3857")
return gdf
@pytest.fixture
def sliver_line():
"""Create a line that will create a point when clipped."""
linea = LineString([(10, 5), (13, 5), (15, 5)])
lineb = LineString([(1, 1), (2, 2), (3, 2), (5, 3), (12, 1)])
gdf = GeoDataFrame([1, 2], geometry=[linea, lineb], crs="EPSG:3857")
return gdf
def test_not_gdf(single_rectangle_gdf):
"""Non-GeoDataFrame inputs raise attribute errors."""
with pytest.raises(TypeError):
clip((2, 3), single_rectangle_gdf)
with pytest.raises(TypeError):
clip(single_rectangle_gdf, "foobar")
with pytest.raises(TypeError):
clip(single_rectangle_gdf, (1, 2, 3))
with pytest.raises(TypeError):
clip(single_rectangle_gdf, (1, 2, 3, 4, 5))
def test_non_overlapping_geoms():
"""Test that a bounding box returns empty if the extents don't overlap"""
unit_box = Polygon([(0, 0), (0, 1), (1, 1), (1, 0), (0, 0)])
unit_gdf = GeoDataFrame([1], geometry=[unit_box], crs="EPSG:3857")
non_overlapping_gdf = unit_gdf.copy()
non_overlapping_gdf = non_overlapping_gdf.geometry.apply(
lambda x: shapely.affinity.translate(x, xoff=20)
)
out = clip(unit_gdf, non_overlapping_gdf)
assert_geodataframe_equal(out, unit_gdf.iloc[:0])
out2 = clip(unit_gdf.geometry, non_overlapping_gdf)
assert_geoseries_equal(out2, GeoSeries(crs=unit_gdf.crs))
@pytest.mark.parametrize("mask_fixture_name", mask_variants_single_rectangle)
class TestClipWithSingleRectangleGdf:
@pytest.fixture
def mask(self, mask_fixture_name, request):
return request.getfixturevalue(mask_fixture_name)
def test_returns_gdf(self, point_gdf, mask):
"""Test that function returns a GeoDataFrame (or GDF-like) object."""
out = clip(point_gdf, mask)
assert isinstance(out, GeoDataFrame)
def test_returns_series(self, point_gdf, mask):
"""Test that function returns a GeoSeries if GeoSeries is passed."""
out = clip(point_gdf.geometry, mask)
assert isinstance(out, GeoSeries)
def test_clip_points(self, point_gdf, mask):
"""Test clipping a points GDF with a generic polygon geometry."""
clip_pts = clip(point_gdf, mask)
pts = np.array([[2, 2], [3, 4], [9, 8]])
exp = GeoDataFrame(
[Point(xy) for xy in pts], columns=["geometry"], crs="EPSG:3857"
)
assert_geodataframe_equal(clip_pts, exp)
def test_clip_points_geom_col_rename(self, point_gdf, mask):
"""Test clipping a points GDF with a generic polygon geometry."""
point_gdf_geom_col_rename = point_gdf.rename_geometry("geometry2")
clip_pts = clip(point_gdf_geom_col_rename, mask)
pts = np.array([[2, 2], [3, 4], [9, 8]])
exp = GeoDataFrame(
[Point(xy) for xy in pts],
columns=["geometry2"],
crs="EPSG:3857",
geometry="geometry2",
)
assert_geodataframe_equal(clip_pts, exp)
def test_clip_poly(self, buffered_locations, mask):
"""Test clipping a polygon GDF with a generic polygon geometry."""
clipped_poly = clip(buffered_locations, mask)
assert len(clipped_poly.geometry) == 3
assert all(clipped_poly.geom_type == "Polygon")
def test_clip_poly_geom_col_rename(self, buffered_locations, mask):
"""Test clipping a polygon GDF with a generic polygon geometry."""
poly_gdf_geom_col_rename = buffered_locations.rename_geometry("geometry2")
clipped_poly = clip(poly_gdf_geom_col_rename, mask)
assert len(clipped_poly.geometry) == 3
assert "geometry" not in clipped_poly.keys()
assert "geometry2" in clipped_poly.keys()
def test_clip_poly_series(self, buffered_locations, mask):
"""Test clipping a polygon GDF with a generic polygon geometry."""
clipped_poly = clip(buffered_locations.geometry, mask)
assert len(clipped_poly) == 3
assert all(clipped_poly.geom_type == "Polygon")
def test_clip_multipoly_keep_geom_type(self, multi_poly_gdf, mask):
"""Test a multi poly object where the return includes a sliver.
Also the bounds of the object should == the bounds of the clip object
if they fully overlap (as they do in these fixtures)."""
clipped = clip(multi_poly_gdf, mask, keep_geom_type=True)
expected_bounds = (
mask if _mask_is_list_like_rectangle(mask) else mask.total_bounds
)
assert np.array_equal(clipped.total_bounds, expected_bounds)
# Assert returned data is a not geometry collection
assert (clipped.geom_type.isin(["Polygon", "MultiPolygon"])).all()
def test_clip_multiline(self, multi_line, mask):
"""Test that clipping a multiline feature with a poly returns expected
output."""
clipped = clip(multi_line, mask)
assert clipped.geom_type[0] == "MultiLineString"
def test_clip_multipoint(self, multi_point, mask):
"""Clipping a multipoint feature with a polygon works as expected.
should return a geodataframe with a single multi point feature"""
clipped = clip(multi_point, mask)
assert clipped.geom_type[0] == "MultiPoint"
assert hasattr(clipped, "attr")
# All points should intersect the clip geom
assert len(clipped) == 2
clipped_mutltipoint = MultiPoint(
[
Point(2, 2),
Point(3, 4),
Point(9, 8),
]
)
assert clipped.iloc[0].geometry.wkt == clipped_mutltipoint.wkt
shape_for_points = (
box(*mask) if _mask_is_list_like_rectangle(mask) else mask.unary_union
)
assert all(clipped.intersects(shape_for_points))
def test_clip_lines(self, two_line_gdf, mask):
"""Test what happens when you give the clip_extent a line GDF."""
clip_line = clip(two_line_gdf, mask)
assert len(clip_line.geometry) == 2
def test_mixed_geom(self, mixed_gdf, mask):
"""Test clipping a mixed GeoDataFrame"""
clipped = clip(mixed_gdf, mask)
assert (
clipped.geom_type[0] == "Point"
and clipped.geom_type[1] == "Polygon"
and clipped.geom_type[2] == "LineString"
)
def test_mixed_series(self, mixed_gdf, mask):
"""Test clipping a mixed GeoSeries"""
clipped = clip(mixed_gdf.geometry, mask)
assert (
clipped.geom_type[0] == "Point"
and clipped.geom_type[1] == "Polygon"
and clipped.geom_type[2] == "LineString"
)
def test_clip_with_line_extra_geom(self, sliver_line, mask):
"""When the output of a clipped line returns a geom collection,
and keep_geom_type is True, no geometry collections should be returned."""
clipped = clip(sliver_line, mask, keep_geom_type=True)
assert len(clipped.geometry) == 1
# Assert returned data is a not geometry collection
assert not (clipped.geom_type == "GeometryCollection").any()
def test_clip_no_box_overlap(self, pointsoutside_nooverlap_gdf, mask):
"""Test clip when intersection is empty and boxes do not overlap."""
clipped = clip(pointsoutside_nooverlap_gdf, mask)
assert len(clipped) == 0
def test_clip_box_overlap(self, pointsoutside_overlap_gdf, mask):
"""Test clip when intersection is empty and boxes do overlap."""
clipped = clip(pointsoutside_overlap_gdf, mask)
assert len(clipped) == 0
def test_warning_extra_geoms_mixed(self, mixed_gdf, mask):
"""Test the correct warnings are raised if keep_geom_type is
called on a mixed GDF"""
with pytest.warns(UserWarning):
clip(mixed_gdf, mask, keep_geom_type=True)
def test_warning_geomcoll(self, geomcol_gdf, mask):
"""Test the correct warnings are raised if keep_geom_type is
called on a GDF with GeometryCollection"""
with pytest.warns(UserWarning):
clip(geomcol_gdf, mask, keep_geom_type=True)
def test_clip_line_keep_slivers(sliver_line, single_rectangle_gdf):
"""Test the correct output if a point is returned
from a line only geometry type."""
clipped = clip(sliver_line, single_rectangle_gdf)
# Assert returned data is a geometry collection given sliver geoms
assert "Point" == clipped.geom_type[0]
assert "LineString" == clipped.geom_type[1]
def test_clip_multipoly_keep_slivers(multi_poly_gdf, single_rectangle_gdf):
"""Test a multi poly object where the return includes a sliver.
Also the bounds of the object should == the bounds of the clip object
if they fully overlap (as they do in these fixtures)."""
clipped = clip(multi_poly_gdf, single_rectangle_gdf)
assert np.array_equal(clipped.total_bounds, single_rectangle_gdf.total_bounds)
# Assert returned data is a geometry collection given sliver geoms
assert "GeometryCollection" in clipped.geom_type[0]
def test_warning_crs_mismatch(point_gdf, single_rectangle_gdf):
with pytest.warns(UserWarning, match="CRS mismatch between the CRS"):
clip(point_gdf, single_rectangle_gdf.to_crs(4326))
def test_clip_with_polygon(single_rectangle_gdf):
"""Test clip when using a shapely object"""
polygon = Polygon([(0, 0), (5, 12), (10, 0), (0, 0)])
clipped = clip(single_rectangle_gdf, polygon)
exp_poly = polygon.intersection(
Polygon([(0, 0), (0, 10), (10, 10), (10, 0), (0, 0)])
)
exp = GeoDataFrame([1], geometry=[exp_poly], crs="EPSG:3857")
exp["attr2"] = "site-boundary"
assert_geodataframe_equal(clipped, exp)
def test_clip_with_multipolygon(buffered_locations, single_rectangle_gdf):
"""Test clipping a polygon with a multipolygon."""
multi = buffered_locations.dissolve(by="type").reset_index()
clipped = clip(single_rectangle_gdf, multi)
assert clipped.geom_type[0] == "Polygon"
@pytest.mark.parametrize(
"mask_fixture_name",
mask_variants_large_rectangle,
)
def test_clip_single_multipoly_no_extra_geoms(
buffered_locations, mask_fixture_name, request
):
"""When clipping a multi-polygon feature, no additional geom types
should be returned."""
masks = request.getfixturevalue(mask_fixture_name)
multi = buffered_locations.dissolve(by="type").reset_index()
clipped = clip(multi, masks)
assert clipped.geom_type[0] == "Polygon"
@pytest.mark.filterwarnings("ignore:All-NaN slice encountered")
@pytest.mark.parametrize(
"mask",
[
Polygon(),
(np.nan,) * 4,
(np.nan, 0, np.nan, 1),
GeoSeries([Polygon(), Polygon()], crs="EPSG:3857"),
GeoSeries([Polygon(), Polygon()], crs="EPSG:3857").to_frame(),
GeoSeries([], crs="EPSG:3857"),
GeoSeries([], crs="EPSG:3857").to_frame(),
],
)
def test_clip_empty_mask(buffered_locations, mask):
"""Test that clipping with empty mask returns an empty result."""
clipped = clip(buffered_locations, mask)
assert_geodataframe_equal(
clipped,
GeoDataFrame([], columns=["geometry", "type"], crs="EPSG:3857"),
check_index_type=False,
)
clipped = clip(buffered_locations.geometry, mask)
assert_geoseries_equal(clipped, GeoSeries([], crs="EPSG:3857"))

View File

@@ -0,0 +1,75 @@
import numpy as np
from shapely.geometry import Point
from shapely.wkt import loads
import geopandas
import pytest
from pandas.testing import assert_series_equal
def test_hilbert_distance():
# test the actual Hilbert Code algorithm against some hardcoded values
geoms = geopandas.GeoSeries.from_wkt(
[
"POINT (0 0)",
"POINT (1 1)",
"POINT (1 0)",
"POLYGON ((0 0, 0 1, 1 1, 1 0, 0 0))",
]
)
result = geoms.hilbert_distance(total_bounds=(0, 0, 1, 1), level=2)
assert result.tolist() == [0, 10, 15, 2]
result = geoms.hilbert_distance(total_bounds=(0, 0, 1, 1), level=3)
assert result.tolist() == [0, 42, 63, 10]
result = geoms.hilbert_distance(total_bounds=(0, 0, 1, 1), level=16)
assert result.tolist() == [0, 2863311530, 4294967295, 715827882]
@pytest.fixture
def geoseries_points():
p1 = Point(1, 2)
p2 = Point(2, 3)
p3 = Point(3, 4)
p4 = Point(4, 1)
return geopandas.GeoSeries([p1, p2, p3, p4])
def test_hilbert_distance_level(geoseries_points):
with pytest.raises(ValueError):
geoseries_points.hilbert_distance(level=20)
def test_specified_total_bounds(geoseries_points):
result = geoseries_points.hilbert_distance(
total_bounds=geoseries_points.total_bounds
)
expected = geoseries_points.hilbert_distance()
assert_series_equal(result, expected)
@pytest.mark.parametrize(
"empty",
[
None,
loads("POLYGON EMPTY"),
],
)
def test_empty(geoseries_points, empty):
s = geoseries_points
s.iloc[-1] = empty
with pytest.raises(
ValueError, match="cannot be computed on a GeoSeries with empty"
):
s.hilbert_distance()
def test_zero_width():
# special case of all points on the same line -> avoid warnings because
# of division by 0 and introducing NaN
s = geopandas.GeoSeries([Point(0, 0), Point(0, 2), Point(0, 1)])
with np.errstate(all="raise"):
result = s.hilbert_distance()
assert np.array(result).argsort().tolist() == [0, 2, 1]

View File

@@ -0,0 +1,57 @@
import pytest
import numpy
import geopandas
import geopandas._compat as compat
from geopandas.tools._random import uniform
multipolygons = geopandas.read_file(geopandas.datasets.get_path("nybb")).geometry
polygons = multipolygons.explode(ignore_index=True).geometry
multilinestrings = multipolygons.boundary
linestrings = polygons.boundary
points = multipolygons.centroid
@pytest.mark.skipif(
not (compat.USE_PYGEOS or compat.USE_SHAPELY_20),
reason="array input in interpolate not implemented for shapely<2",
)
@pytest.mark.parametrize("size", [10, 100])
@pytest.mark.parametrize(
"geom", [multipolygons[0], polygons[0], multilinestrings[0], linestrings[0]]
)
def test_uniform(geom, size):
sample = uniform(geom, size=size, rng=1)
sample_series = geopandas.GeoSeries(sample).explode().reset_index(drop=True)
assert len(sample_series) == size
sample_in_geom = sample_series.buffer(0.00000001).sindex.query(
geom, predicate="intersects"
)
assert len(sample_in_geom) == size
@pytest.mark.skipif(
not (compat.USE_PYGEOS or compat.USE_SHAPELY_20),
reason="array input in interpolate not implemented for shapely<2",
)
def test_uniform_unsupported():
with pytest.warns(UserWarning, match="Sampling is not supported"):
sample = uniform(points[0], size=10, rng=1)
assert sample.is_empty
@pytest.mark.skipif(
not (compat.USE_PYGEOS or compat.USE_SHAPELY_20),
reason="array input in interpolate not implemented for shapely<2",
)
def test_uniform_generator():
sample = uniform(polygons[0], size=10, rng=1)
sample2 = uniform(polygons[0], size=10, rng=1)
assert sample.equals(sample2)
generator = numpy.random.default_rng(seed=1)
gen_sample = uniform(polygons[0], size=10, rng=generator)
gen_sample2 = uniform(polygons[0], size=10, rng=generator)
assert sample.equals(gen_sample)
assert not sample.equals(gen_sample2)

View File

@@ -0,0 +1,960 @@
import math
from typing import Sequence
import numpy as np
import pandas as pd
import shapely
from shapely.geometry import Point, Polygon, GeometryCollection
import geopandas
import geopandas._compat as compat
from geopandas import GeoDataFrame, GeoSeries, read_file, sjoin, sjoin_nearest
from geopandas.testing import assert_geodataframe_equal, assert_geoseries_equal
from pandas.testing import assert_frame_equal, assert_series_equal
import pytest
TEST_NEAREST = compat.USE_SHAPELY_20 or (compat.PYGEOS_GE_010 and compat.USE_PYGEOS)
pytestmark = pytest.mark.skip_no_sindex
@pytest.fixture()
def dfs(request):
polys1 = GeoSeries(
[
Polygon([(0, 0), (5, 0), (5, 5), (0, 5)]),
Polygon([(5, 5), (6, 5), (6, 6), (5, 6)]),
Polygon([(6, 0), (9, 0), (9, 3), (6, 3)]),
]
)
polys2 = GeoSeries(
[
Polygon([(1, 1), (4, 1), (4, 4), (1, 4)]),
Polygon([(4, 4), (7, 4), (7, 7), (4, 7)]),
Polygon([(7, 7), (10, 7), (10, 10), (7, 10)]),
]
)
df1 = GeoDataFrame({"geometry": polys1, "df1": [0, 1, 2]})
df2 = GeoDataFrame({"geometry": polys2, "df2": [3, 4, 5]})
if request.param == "string-index":
df1.index = ["a", "b", "c"]
df2.index = ["d", "e", "f"]
if request.param == "named-index":
df1.index.name = "df1_ix"
df2.index.name = "df2_ix"
if request.param == "multi-index":
i1 = ["a", "b", "c"]
i2 = ["d", "e", "f"]
df1 = df1.set_index([i1, i2])
df2 = df2.set_index([i2, i1])
if request.param == "named-multi-index":
i1 = ["a", "b", "c"]
i2 = ["d", "e", "f"]
df1 = df1.set_index([i1, i2])
df2 = df2.set_index([i2, i1])
df1.index.names = ["df1_ix1", "df1_ix2"]
df2.index.names = ["df2_ix1", "df2_ix2"]
# construction expected frames
expected = {}
part1 = df1.copy().reset_index().rename(columns={"index": "index_left"})
part2 = (
df2.copy()
.iloc[[0, 1, 1, 2]]
.reset_index()
.rename(columns={"index": "index_right"})
)
part1["_merge"] = [0, 1, 2]
part2["_merge"] = [0, 0, 1, 3]
exp = pd.merge(part1, part2, on="_merge", how="outer")
expected["intersects"] = exp.drop("_merge", axis=1).copy()
part1 = df1.copy().reset_index().rename(columns={"index": "index_left"})
part2 = df2.copy().reset_index().rename(columns={"index": "index_right"})
part1["_merge"] = [0, 1, 2]
part2["_merge"] = [0, 3, 3]
exp = pd.merge(part1, part2, on="_merge", how="outer")
expected["contains"] = exp.drop("_merge", axis=1).copy()
part1["_merge"] = [0, 1, 2]
part2["_merge"] = [3, 1, 3]
exp = pd.merge(part1, part2, on="_merge", how="outer")
expected["within"] = exp.drop("_merge", axis=1).copy()
return [request.param, df1, df2, expected]
class TestSpatialJoin:
@pytest.mark.parametrize(
"how, lsuffix, rsuffix, expected_cols",
[
("left", "left", "right", {"col_left", "col_right", "index_right"}),
("inner", "left", "right", {"col_left", "col_right", "index_right"}),
("right", "left", "right", {"col_left", "col_right", "index_left"}),
("left", "lft", "rgt", {"col_lft", "col_rgt", "index_rgt"}),
("inner", "lft", "rgt", {"col_lft", "col_rgt", "index_rgt"}),
("right", "lft", "rgt", {"col_lft", "col_rgt", "index_lft"}),
],
)
def test_suffixes(self, how: str, lsuffix: str, rsuffix: str, expected_cols):
left = GeoDataFrame({"col": [1], "geometry": [Point(0, 0)]})
right = GeoDataFrame({"col": [1], "geometry": [Point(0, 0)]})
joined = sjoin(left, right, how=how, lsuffix=lsuffix, rsuffix=rsuffix)
assert set(joined.columns) == expected_cols | {"geometry"}
@pytest.mark.parametrize("dfs", ["default-index", "string-index"], indirect=True)
def test_crs_mismatch(self, dfs):
index, df1, df2, expected = dfs
df1.crs = "epsg:4326"
with pytest.warns(UserWarning, match="CRS mismatch between the CRS"):
sjoin(df1, df2)
@pytest.mark.parametrize("dfs", ["default-index"], indirect=True)
@pytest.mark.parametrize("op", ["intersects", "contains", "within"])
def test_deprecated_op_param(self, dfs, op):
_, df1, df2, _ = dfs
with pytest.warns(FutureWarning, match="`op` parameter is deprecated"):
sjoin(df1, df2, op=op)
@pytest.mark.parametrize("dfs", ["default-index"], indirect=True)
@pytest.mark.parametrize("op", ["intersects", "contains", "within"])
@pytest.mark.parametrize("predicate", ["contains", "within"])
def test_deprecated_op_param_nondefault_predicate(self, dfs, op, predicate):
_, df1, df2, _ = dfs
match = "use the `predicate` parameter instead"
if op != predicate:
warntype = UserWarning
match = (
"`predicate` will be overridden by the value of `op`" # noqa: ISC003
+ r"(.|\s)*"
+ match
)
else:
warntype = FutureWarning
with pytest.warns(warntype, match=match):
sjoin(df1, df2, predicate=predicate, op=op)
@pytest.mark.parametrize("dfs", ["default-index"], indirect=True)
def test_unknown_kwargs(self, dfs):
_, df1, df2, _ = dfs
with pytest.raises(
TypeError,
match=r"sjoin\(\) got an unexpected keyword argument 'extra_param'",
):
sjoin(df1, df2, extra_param="test")
@pytest.mark.filterwarnings("ignore:The `op` parameter:FutureWarning")
@pytest.mark.parametrize(
"dfs",
[
"default-index",
"string-index",
"named-index",
"multi-index",
"named-multi-index",
],
indirect=True,
)
@pytest.mark.parametrize("predicate", ["intersects", "contains", "within"])
@pytest.mark.parametrize("predicate_kw", ["predicate", "op"])
def test_inner(self, predicate, predicate_kw, dfs):
index, df1, df2, expected = dfs
res = sjoin(df1, df2, how="inner", **{predicate_kw: predicate})
exp = expected[predicate].dropna().copy()
exp = exp.drop("geometry_y", axis=1).rename(columns={"geometry_x": "geometry"})
exp[["df1", "df2"]] = exp[["df1", "df2"]].astype("int64")
if index == "default-index":
exp[["index_left", "index_right"]] = exp[
["index_left", "index_right"]
].astype("int64")
if index == "named-index":
exp[["df1_ix", "df2_ix"]] = exp[["df1_ix", "df2_ix"]].astype("int64")
exp = exp.set_index("df1_ix").rename(columns={"df2_ix": "index_right"})
if index in ["default-index", "string-index"]:
exp = exp.set_index("index_left")
exp.index.name = None
if index == "multi-index":
exp = exp.set_index(["level_0_x", "level_1_x"]).rename(
columns={"level_0_y": "index_right0", "level_1_y": "index_right1"}
)
exp.index.names = df1.index.names
if index == "named-multi-index":
exp = exp.set_index(["df1_ix1", "df1_ix2"]).rename(
columns={"df2_ix1": "index_right0", "df2_ix2": "index_right1"}
)
exp.index.names = df1.index.names
assert_frame_equal(res, exp)
@pytest.mark.parametrize(
"dfs",
[
"default-index",
"string-index",
"named-index",
"multi-index",
"named-multi-index",
],
indirect=True,
)
@pytest.mark.parametrize("predicate", ["intersects", "contains", "within"])
def test_left(self, predicate, dfs):
index, df1, df2, expected = dfs
res = sjoin(df1, df2, how="left", predicate=predicate)
if index in ["default-index", "string-index"]:
exp = expected[predicate].dropna(subset=["index_left"]).copy()
elif index == "named-index":
exp = expected[predicate].dropna(subset=["df1_ix"]).copy()
elif index == "multi-index":
exp = expected[predicate].dropna(subset=["level_0_x"]).copy()
elif index == "named-multi-index":
exp = expected[predicate].dropna(subset=["df1_ix1"]).copy()
exp = exp.drop("geometry_y", axis=1).rename(columns={"geometry_x": "geometry"})
exp["df1"] = exp["df1"].astype("int64")
if index == "default-index":
exp["index_left"] = exp["index_left"].astype("int64")
# TODO: in result the dtype is object
res["index_right"] = res["index_right"].astype(float)
elif index == "named-index":
exp[["df1_ix"]] = exp[["df1_ix"]].astype("int64")
exp = exp.set_index("df1_ix").rename(columns={"df2_ix": "index_right"})
if index in ["default-index", "string-index"]:
exp = exp.set_index("index_left")
exp.index.name = None
if index == "multi-index":
exp = exp.set_index(["level_0_x", "level_1_x"]).rename(
columns={"level_0_y": "index_right0", "level_1_y": "index_right1"}
)
exp.index.names = df1.index.names
if index == "named-multi-index":
exp = exp.set_index(["df1_ix1", "df1_ix2"]).rename(
columns={"df2_ix1": "index_right0", "df2_ix2": "index_right1"}
)
exp.index.names = df1.index.names
assert_frame_equal(res, exp)
def test_empty_join(self):
# Check joins resulting in empty gdfs.
polygons = geopandas.GeoDataFrame(
{
"col2": [1, 2],
"geometry": [
Polygon([(0, 0), (1, 0), (1, 1), (0, 1)]),
Polygon([(1, 0), (2, 0), (2, 1), (1, 1)]),
],
}
)
not_in = geopandas.GeoDataFrame({"col1": [1], "geometry": [Point(-0.5, 0.5)]})
empty = sjoin(not_in, polygons, how="left", predicate="intersects")
assert empty.index_right.isnull().all()
empty = sjoin(not_in, polygons, how="right", predicate="intersects")
assert empty.index_left.isnull().all()
empty = sjoin(not_in, polygons, how="inner", predicate="intersects")
assert empty.empty
@pytest.mark.parametrize(
"predicate",
[
"contains",
"contains_properly",
"covered_by",
"covers",
"crosses",
"intersects",
"touches",
"within",
],
)
@pytest.mark.parametrize(
"empty",
[
GeoDataFrame(geometry=[GeometryCollection(), GeometryCollection()]),
GeoDataFrame(geometry=GeoSeries()),
],
)
def test_join_with_empty(self, predicate, empty):
# Check joins with empty geometry columns/dataframes.
polygons = geopandas.GeoDataFrame(
{
"col2": [1, 2],
"geometry": [
Polygon([(0, 0), (1, 0), (1, 1), (0, 1)]),
Polygon([(1, 0), (2, 0), (2, 1), (1, 1)]),
],
}
)
result = sjoin(empty, polygons, how="left", predicate=predicate)
assert result.index_right.isnull().all()
result = sjoin(empty, polygons, how="right", predicate=predicate)
assert result.index_left.isnull().all()
result = sjoin(empty, polygons, how="inner", predicate=predicate)
assert result.empty
@pytest.mark.parametrize("dfs", ["default-index", "string-index"], indirect=True)
def test_sjoin_invalid_args(self, dfs):
index, df1, df2, expected = dfs
with pytest.raises(ValueError, match="'left_df' should be GeoDataFrame"):
sjoin(df1.geometry, df2)
with pytest.raises(ValueError, match="'right_df' should be GeoDataFrame"):
sjoin(df1, df2.geometry)
@pytest.mark.parametrize(
"dfs",
[
"default-index",
"string-index",
"named-index",
"multi-index",
"named-multi-index",
],
indirect=True,
)
@pytest.mark.parametrize("predicate", ["intersects", "contains", "within"])
def test_right(self, predicate, dfs):
index, df1, df2, expected = dfs
res = sjoin(df1, df2, how="right", predicate=predicate)
if index in ["default-index", "string-index"]:
exp = expected[predicate].dropna(subset=["index_right"]).copy()
elif index == "named-index":
exp = expected[predicate].dropna(subset=["df2_ix"]).copy()
elif index == "multi-index":
exp = expected[predicate].dropna(subset=["level_0_y"]).copy()
elif index == "named-multi-index":
exp = expected[predicate].dropna(subset=["df2_ix1"]).copy()
exp = exp.drop("geometry_x", axis=1).rename(columns={"geometry_y": "geometry"})
exp["df2"] = exp["df2"].astype("int64")
if index == "default-index":
exp["index_right"] = exp["index_right"].astype("int64")
res["index_left"] = res["index_left"].astype(float)
elif index == "named-index":
exp[["df2_ix"]] = exp[["df2_ix"]].astype("int64")
exp = exp.set_index("df2_ix").rename(columns={"df1_ix": "index_left"})
if index in ["default-index", "string-index"]:
exp = exp.set_index("index_right")
exp = exp.reindex(columns=res.columns)
exp.index.name = None
if index == "multi-index":
exp = exp.set_index(["level_0_y", "level_1_y"]).rename(
columns={"level_0_x": "index_left0", "level_1_x": "index_left1"}
)
exp.index.names = df2.index.names
if index == "named-multi-index":
exp = exp.set_index(["df2_ix1", "df2_ix2"]).rename(
columns={"df1_ix1": "index_left0", "df1_ix2": "index_left1"}
)
exp.index.names = df2.index.names
if predicate == "within":
exp = exp.sort_index()
assert_frame_equal(res, exp, check_index_type=False)
class TestSpatialJoinNYBB:
def setup_method(self):
nybb_filename = geopandas.datasets.get_path("nybb")
self.polydf = read_file(nybb_filename)
self.crs = self.polydf.crs
N = 20
b = [int(x) for x in self.polydf.total_bounds]
self.pointdf = GeoDataFrame(
[
{"geometry": Point(x, y), "pointattr1": x + y, "pointattr2": x - y}
for x, y in zip(
range(b[0], b[2], int((b[2] - b[0]) / N)),
range(b[1], b[3], int((b[3] - b[1]) / N)),
)
],
crs=self.crs,
)
def test_geometry_name(self):
# test sjoin is working with other geometry name
polydf_original_geom_name = self.polydf.geometry.name
self.polydf = self.polydf.rename(columns={"geometry": "new_geom"}).set_geometry(
"new_geom"
)
assert polydf_original_geom_name != self.polydf.geometry.name
res = sjoin(self.polydf, self.pointdf, how="left")
assert self.polydf.geometry.name == res.geometry.name
def test_sjoin_left(self):
df = sjoin(self.pointdf, self.polydf, how="left")
assert df.shape == (21, 8)
for i, row in df.iterrows():
assert row.geometry.geom_type == "Point"
assert "pointattr1" in df.columns
assert "BoroCode" in df.columns
def test_sjoin_right(self):
# the inverse of left
df = sjoin(self.pointdf, self.polydf, how="right")
df2 = sjoin(self.polydf, self.pointdf, how="left")
assert df.shape == (12, 8)
assert df.shape == df2.shape
for i, row in df.iterrows():
assert row.geometry.geom_type == "MultiPolygon"
for i, row in df2.iterrows():
assert row.geometry.geom_type == "MultiPolygon"
def test_sjoin_inner(self):
df = sjoin(self.pointdf, self.polydf, how="inner")
assert df.shape == (11, 8)
def test_sjoin_predicate(self):
# points within polygons
df = sjoin(self.pointdf, self.polydf, how="left", predicate="within")
assert df.shape == (21, 8)
assert df.loc[1]["BoroName"] == "Staten Island"
# points contain polygons? never happens so we should have nulls
df = sjoin(self.pointdf, self.polydf, how="left", predicate="contains")
assert df.shape == (21, 8)
assert np.isnan(df.loc[1]["Shape_Area"])
def test_sjoin_bad_predicate(self):
# AttributeError: 'Point' object has no attribute 'spandex'
with pytest.raises(ValueError):
sjoin(self.pointdf, self.polydf, how="left", predicate="spandex")
def test_sjoin_duplicate_column_name(self):
pointdf2 = self.pointdf.rename(columns={"pointattr1": "Shape_Area"})
df = sjoin(pointdf2, self.polydf, how="left")
assert "Shape_Area_left" in df.columns
assert "Shape_Area_right" in df.columns
@pytest.mark.parametrize("how", ["left", "right", "inner"])
def test_sjoin_named_index(self, how):
# original index names should be unchanged
pointdf2 = self.pointdf.copy()
pointdf2.index.name = "pointid"
polydf = self.polydf.copy()
polydf.index.name = "polyid"
res = sjoin(pointdf2, polydf, how=how)
assert pointdf2.index.name == "pointid"
assert polydf.index.name == "polyid"
# original index name should pass through to result
if how == "right":
assert res.index.name == "polyid"
else: # how == "left", how == "inner"
assert res.index.name == "pointid"
def test_sjoin_values(self):
# GH190
self.polydf.index = [1, 3, 4, 5, 6]
df = sjoin(self.pointdf, self.polydf, how="left")
assert df.shape == (21, 8)
df = sjoin(self.polydf, self.pointdf, how="left")
assert df.shape == (12, 8)
@pytest.mark.xfail
def test_no_overlapping_geometry(self):
# Note: these tests are for correctly returning GeoDataFrame
# when result of the join is empty
df_inner = sjoin(self.pointdf.iloc[17:], self.polydf, how="inner")
df_left = sjoin(self.pointdf.iloc[17:], self.polydf, how="left")
df_right = sjoin(self.pointdf.iloc[17:], self.polydf, how="right")
expected_inner_df = pd.concat(
[
self.pointdf.iloc[:0],
pd.Series(name="index_right", dtype="int64"),
self.polydf.drop("geometry", axis=1).iloc[:0],
],
axis=1,
)
expected_inner = GeoDataFrame(expected_inner_df)
expected_right_df = pd.concat(
[
self.pointdf.drop("geometry", axis=1).iloc[:0],
pd.concat(
[
pd.Series(name="index_left", dtype="int64"),
pd.Series(name="index_right", dtype="int64"),
],
axis=1,
),
self.polydf,
],
axis=1,
)
expected_right = GeoDataFrame(expected_right_df).set_index("index_right")
expected_left_df = pd.concat(
[
self.pointdf.iloc[17:],
pd.Series(name="index_right", dtype="int64"),
self.polydf.iloc[:0].drop("geometry", axis=1),
],
axis=1,
)
expected_left = GeoDataFrame(expected_left_df)
assert expected_inner.equals(df_inner)
assert expected_right.equals(df_right)
assert expected_left.equals(df_left)
@pytest.mark.skip("Not implemented")
def test_sjoin_outer(self):
df = sjoin(self.pointdf, self.polydf, how="outer")
assert df.shape == (21, 8)
def test_sjoin_empty_geometries(self):
# https://github.com/geopandas/geopandas/issues/944
empty = GeoDataFrame(geometry=[GeometryCollection()] * 3)
df = sjoin(pd.concat([self.pointdf, empty]), self.polydf, how="left")
assert df.shape == (24, 8)
df2 = sjoin(self.pointdf, pd.concat([self.polydf, empty]), how="left")
assert df2.shape == (21, 8)
@pytest.mark.parametrize("predicate", ["intersects", "within", "contains"])
def test_sjoin_no_valid_geoms(self, predicate):
"""Tests a completely empty GeoDataFrame."""
empty = GeoDataFrame(geometry=[], crs=self.pointdf.crs)
assert sjoin(self.pointdf, empty, how="inner", predicate=predicate).empty
assert sjoin(self.pointdf, empty, how="right", predicate=predicate).empty
assert sjoin(empty, self.pointdf, how="inner", predicate=predicate).empty
assert sjoin(empty, self.pointdf, how="left", predicate=predicate).empty
def test_empty_sjoin_return_duplicated_columns(self):
nybb = geopandas.read_file(geopandas.datasets.get_path("nybb"))
nybb2 = nybb.copy()
nybb2.geometry = nybb2.translate(200000) # to get non-overlapping
result = geopandas.sjoin(nybb, nybb2)
assert "BoroCode_right" in result.columns
assert "BoroCode_left" in result.columns
class TestSpatialJoinNaturalEarth:
def setup_method(self):
world_path = geopandas.datasets.get_path("naturalearth_lowres")
cities_path = geopandas.datasets.get_path("naturalearth_cities")
self.world = read_file(world_path)
self.cities = read_file(cities_path)
def test_sjoin_inner(self):
# GH637
countries = self.world[["geometry", "name"]]
countries = countries.rename(columns={"name": "country"})
cities_with_country = sjoin(
self.cities, countries, how="inner", predicate="intersects"
)
assert cities_with_country.shape == (213, 4)
@pytest.mark.skipif(
TEST_NEAREST,
reason=("This test can only be run _without_ PyGEOS >= 0.10 installed"),
)
def test_no_nearest_all():
df1 = geopandas.GeoDataFrame({"geometry": []})
df2 = geopandas.GeoDataFrame({"geometry": []})
with pytest.raises(
NotImplementedError,
match="Currently, only PyGEOS >= 0.10.0 or Shapely >= 2.0 supports",
):
sjoin_nearest(df1, df2)
@pytest.mark.skipif(
not TEST_NEAREST,
reason=(
"PyGEOS >= 0.10.0"
" must be installed and activated via the geopandas.compat module to"
" test sjoin_nearest"
),
)
class TestNearest:
@pytest.mark.parametrize(
"how_kwargs", ({}, {"how": "inner"}, {"how": "left"}, {"how": "right"})
)
def test_allowed_hows(self, how_kwargs):
left = geopandas.GeoDataFrame({"geometry": []})
right = geopandas.GeoDataFrame({"geometry": []})
sjoin_nearest(left, right, **how_kwargs) # no error
@pytest.mark.parametrize("how", ("outer", "abcde"))
def test_invalid_hows(self, how: str):
left = geopandas.GeoDataFrame({"geometry": []})
right = geopandas.GeoDataFrame({"geometry": []})
with pytest.raises(ValueError, match="`how` was"):
sjoin_nearest(left, right, how=how)
@pytest.mark.parametrize("distance_col", (None, "distance"))
def test_empty_right_df_how_left(self, distance_col: str):
# all records from left and no results from right
left = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
right = geopandas.GeoDataFrame({"geometry": []})
joined = sjoin_nearest(
left,
right,
how="left",
distance_col=distance_col,
)
assert_geoseries_equal(joined["geometry"], left["geometry"])
assert joined["index_right"].isna().all()
if distance_col is not None:
assert joined[distance_col].isna().all()
@pytest.mark.parametrize("distance_col", (None, "distance"))
def test_empty_right_df_how_right(self, distance_col: str):
# no records in joined
left = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
right = geopandas.GeoDataFrame({"geometry": []})
joined = sjoin_nearest(
left,
right,
how="right",
distance_col=distance_col,
)
assert joined.empty
if distance_col is not None:
assert distance_col in joined
@pytest.mark.parametrize("how", ["inner", "left"])
@pytest.mark.parametrize("distance_col", (None, "distance"))
def test_empty_left_df(self, how, distance_col: str):
right = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
left = geopandas.GeoDataFrame({"geometry": []})
joined = sjoin_nearest(left, right, how=how, distance_col=distance_col)
assert joined.empty
if distance_col is not None:
assert distance_col in joined
@pytest.mark.parametrize("distance_col", (None, "distance"))
def test_empty_left_df_how_right(self, distance_col: str):
right = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
left = geopandas.GeoDataFrame({"geometry": []})
joined = sjoin_nearest(
left,
right,
how="right",
distance_col=distance_col,
)
assert_geoseries_equal(joined["geometry"], right["geometry"])
assert joined["index_left"].isna().all()
if distance_col is not None:
assert joined[distance_col].isna().all()
@pytest.mark.parametrize("how", ["inner", "left"])
def test_empty_join_due_to_max_distance(self, how):
# after applying max_distance the join comes back empty
# (as in NaN in the joined columns)
left = geopandas.GeoDataFrame({"geometry": [Point(0, 0)]})
right = geopandas.GeoDataFrame({"geometry": [Point(1, 1), Point(2, 2)]})
joined = sjoin_nearest(
left,
right,
how=how,
max_distance=1,
distance_col="distances",
)
expected = left.copy()
expected["index_right"] = [np.nan]
expected["distances"] = [np.nan]
if how == "inner":
expected = expected.dropna()
expected["index_right"] = expected["index_right"].astype("int64")
assert_geodataframe_equal(joined, expected)
def test_empty_join_due_to_max_distance_how_right(self):
# after applying max_distance the join comes back empty
# (as in NaN in the joined columns)
left = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
right = geopandas.GeoDataFrame({"geometry": [Point(2, 2)]})
joined = sjoin_nearest(
left,
right,
how="right",
max_distance=1,
distance_col="distances",
)
expected = right.copy()
expected["index_left"] = [np.nan]
expected["distances"] = [np.nan]
expected = expected[["index_left", "geometry", "distances"]]
assert_geodataframe_equal(joined, expected)
@pytest.mark.parametrize("how", ["inner", "left"])
def test_max_distance(self, how):
left = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
right = geopandas.GeoDataFrame({"geometry": [Point(1, 1), Point(2, 2)]})
joined = sjoin_nearest(
left,
right,
how=how,
max_distance=1,
distance_col="distances",
)
expected = left.copy()
expected["index_right"] = [np.nan, 0]
expected["distances"] = [np.nan, 0]
if how == "inner":
expected = expected.dropna()
expected["index_right"] = expected["index_right"].astype("int64")
assert_geodataframe_equal(joined, expected)
def test_max_distance_how_right(self):
left = geopandas.GeoDataFrame({"geometry": [Point(1, 1), Point(2, 2)]})
right = geopandas.GeoDataFrame({"geometry": [Point(0, 0), Point(1, 1)]})
joined = sjoin_nearest(
left,
right,
how="right",
max_distance=1,
distance_col="distances",
)
expected = right.copy()
expected["index_left"] = [np.nan, 0]
expected["distances"] = [np.nan, 0]
expected = expected[["index_left", "geometry", "distances"]]
assert_geodataframe_equal(joined, expected)
@pytest.mark.parametrize("how", ["inner", "left"])
@pytest.mark.parametrize(
"geo_left, geo_right, expected_left, expected_right, distances",
[
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1)],
[0, 1],
[0, 0],
[math.sqrt(2), 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0, 0)],
[0, 1],
[1, 0],
[0, 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0, 0), Point(0, 0)],
[0, 0, 1],
[1, 2, 0],
[0, 0, 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0, 0), Point(2, 2)],
[0, 1],
[1, 0],
[0, 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0.25, 1)],
[0, 1],
[1, 0],
[math.sqrt(0.25**2 + 1), 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(-10, -10), Point(100, 100)],
[0, 1],
[0, 0],
[math.sqrt(10**2 + 10**2), math.sqrt(11**2 + 11**2)],
),
(
[Point(0, 0), Point(1, 1)],
[Point(x, y) for x, y in zip(np.arange(10), np.arange(10))],
[0, 1],
[0, 1],
[0, 0],
),
(
[Point(0, 0), Point(1, 1), Point(0, 0)],
[Point(1.1, 1.1), Point(0, 0)],
[0, 1, 2],
[1, 0, 1],
[0, np.sqrt(0.1**2 + 0.1**2), 0],
),
],
)
def test_sjoin_nearest_left(
self,
geo_left,
geo_right,
expected_left: Sequence[int],
expected_right: Sequence[int],
distances: Sequence[float],
how,
):
left = geopandas.GeoDataFrame({"geometry": geo_left})
right = geopandas.GeoDataFrame({"geometry": geo_right})
expected_gdf = left.iloc[expected_left].copy()
expected_gdf["index_right"] = expected_right
# without distance col
joined = sjoin_nearest(left, right, how=how)
# inner / left join give a different row order
check_like = how == "inner"
assert_geodataframe_equal(expected_gdf, joined, check_like=check_like)
# with distance col
expected_gdf["distance_col"] = np.array(distances, dtype=float)
joined = sjoin_nearest(left, right, how=how, distance_col="distance_col")
assert_geodataframe_equal(expected_gdf, joined, check_like=check_like)
@pytest.mark.parametrize(
"geo_left, geo_right, expected_left, expected_right, distances",
[
([Point(0, 0), Point(1, 1)], [Point(1, 1)], [1], [0], [0]),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0, 0)],
[1, 0],
[0, 1],
[0, 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0, 0), Point(0, 0)],
[1, 0, 0],
[0, 1, 2],
[0, 0, 0],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0, 0), Point(2, 2)],
[1, 0, 1],
[0, 1, 2],
[0, 0, math.sqrt(2)],
),
(
[Point(0, 0), Point(1, 1)],
[Point(1, 1), Point(0.25, 1)],
[1, 1],
[0, 1],
[0, 0.75],
),
(
[Point(0, 0), Point(1, 1)],
[Point(-10, -10), Point(100, 100)],
[0, 1],
[0, 1],
[math.sqrt(10**2 + 10**2), math.sqrt(99**2 + 99**2)],
),
(
[Point(0, 0), Point(1, 1)],
[Point(x, y) for x, y in zip(np.arange(10), np.arange(10))],
[0, 1] + [1] * 8,
list(range(10)),
[0, 0] + [np.sqrt(x**2 + x**2) for x in np.arange(1, 9)],
),
(
[Point(0, 0), Point(1, 1), Point(0, 0)],
[Point(1.1, 1.1), Point(0, 0)],
[1, 0, 2],
[0, 1, 1],
[np.sqrt(0.1**2 + 0.1**2), 0, 0],
),
],
)
def test_sjoin_nearest_right(
self,
geo_left,
geo_right,
expected_left: Sequence[int],
expected_right: Sequence[int],
distances: Sequence[float],
):
left = geopandas.GeoDataFrame({"geometry": geo_left})
right = geopandas.GeoDataFrame({"geometry": geo_right})
expected_gdf = right.iloc[expected_right].copy()
expected_gdf["index_left"] = expected_left
expected_gdf = expected_gdf[["index_left", "geometry"]]
# without distance col
joined = sjoin_nearest(left, right, how="right")
assert_geodataframe_equal(expected_gdf, joined)
# with distance col
expected_gdf["distance_col"] = np.array(distances, dtype=float)
joined = sjoin_nearest(left, right, how="right", distance_col="distance_col")
assert_geodataframe_equal(expected_gdf, joined)
@pytest.mark.filterwarnings("ignore:Geometry is in a geographic CRS")
def test_sjoin_nearest_inner(self):
# check equivalency of left and inner join
countries = read_file(geopandas.datasets.get_path("naturalearth_lowres"))
cities = read_file(geopandas.datasets.get_path("naturalearth_cities"))
countries = countries[["geometry", "name"]].rename(columns={"name": "country"})
# default: inner and left give the same result
result1 = sjoin_nearest(cities, countries, distance_col="dist")
assert result1.shape[0] == cities.shape[0]
result2 = sjoin_nearest(cities, countries, distance_col="dist", how="inner")
assert_geodataframe_equal(result2, result1)
result3 = sjoin_nearest(cities, countries, distance_col="dist", how="left")
assert_geodataframe_equal(result3, result1, check_like=True)
# with max_distance: rows that go above are dropped in case of inner
result4 = sjoin_nearest(cities, countries, distance_col="dist", max_distance=1)
assert_geodataframe_equal(
result4, result1[result1["dist"] < 1], check_like=True
)
result5 = sjoin_nearest(
cities, countries, distance_col="dist", max_distance=1, how="left"
)
assert result5.shape[0] == cities.shape[0]
result5 = result5.dropna()
result5["index_right"] = result5["index_right"].astype("int64")
assert_geodataframe_equal(result5, result4, check_like=True)
expected_index_uncapped = (
[1, 3, 3, 1, 2] if compat.PANDAS_GE_22 else [1, 1, 3, 3, 2]
)
@pytest.mark.skipif(
not (compat.USE_SHAPELY_20),
reason=(
"shapely >= 2.0 is required to run sjoin_nearest"
"with parameter `exclusive` set"
),
)
@pytest.mark.parametrize(
"max_distance,expected", [(None, expected_index_uncapped), (1.1, [3, 3, 1, 2])]
)
def test_sjoin_nearest_exclusive(self, max_distance, expected):
geoms = shapely.points(np.arange(3), np.arange(3))
geoms = np.append(geoms, [Point(1, 2)])
df = geopandas.GeoDataFrame({"geometry": geoms})
result = df.sjoin_nearest(
df, max_distance=max_distance, distance_col="dist", exclusive=True
)
assert_series_equal(
result["index_right"].reset_index(drop=True),
pd.Series(expected),
check_names=False,
)
if max_distance:
assert result["dist"].max() <= max_distance

View File

@@ -0,0 +1,51 @@
from shapely.geometry import LineString, MultiPoint, Point
from geopandas import GeoSeries
from geopandas.tools import collect
import pytest
class TestTools:
def setup_method(self):
self.p1 = Point(0, 0)
self.p2 = Point(1, 1)
self.p3 = Point(2, 2)
self.mpc = MultiPoint([self.p1, self.p2, self.p3])
self.mp1 = MultiPoint([self.p1, self.p2])
self.line1 = LineString([(3, 3), (4, 4)])
def test_collect_single(self):
result = collect(self.p1)
assert self.p1.equals(result)
def test_collect_single_force_multi(self):
result = collect(self.p1, multi=True)
expected = MultiPoint([self.p1])
assert expected.equals(result)
def test_collect_multi(self):
result = collect(self.mp1)
assert self.mp1.equals(result)
def test_collect_multi_force_multi(self):
result = collect(self.mp1)
assert self.mp1.equals(result)
def test_collect_list(self):
result = collect([self.p1, self.p2, self.p3])
assert self.mpc.equals(result)
def test_collect_GeoSeries(self):
s = GeoSeries([self.p1, self.p2, self.p3])
result = collect(s)
assert self.mpc.equals(result)
def test_collect_mixed_types(self):
with pytest.raises(ValueError):
collect([self.p1, self.line1])
def test_collect_mixed_multi(self):
with pytest.raises(ValueError):
collect([self.mpc, self.mp1])

View File

@@ -0,0 +1,45 @@
import pandas as pd
from shapely.geometry import MultiLineString, MultiPoint, MultiPolygon
from shapely.geometry.base import BaseGeometry
_multi_type_map = {
"Point": MultiPoint,
"LineString": MultiLineString,
"Polygon": MultiPolygon,
}
def collect(x, multi=False):
"""
Collect single part geometries into their Multi* counterpart
Parameters
----------
x : an iterable or Series of Shapely geometries, a GeoSeries, or
a single Shapely geometry
multi : boolean, default False
if True, force returned geometries to be Multi* even if they
only have one component.
"""
if isinstance(x, BaseGeometry):
x = [x]
elif isinstance(x, pd.Series):
x = list(x)
# We cannot create GeometryCollection here so all types
# must be the same. If there is more than one element,
# they cannot be Multi*, i.e., can't pass in combination of
# Point and MultiPoint... or even just MultiPoint
t = x[0].geom_type
if not all(g.geom_type == t for g in x):
raise ValueError("Geometry type must be homogeneous")
if len(x) > 1 and t.startswith("Multi"):
raise ValueError("Cannot collect {0}. Must have single geometries".format(t))
if len(x) == 1 and (t.startswith("Multi") or not multi):
# If there's only one single part geom and we're not forcing to
# multi, then just return it
return x[0]
return _multi_type_map[t](x)