matplotlib – Whats the fastest way of checking if a point is inside a polygon in python

matplotlib – Whats the fastest way of checking if a point is inside a polygon in python

You can consider shapely:

from shapely.geometry import Point
from shapely.geometry.polygon import Polygon

point = Point(0.5, 0.5)
polygon = Polygon([(0, 0), (0, 1), (1, 1), (1, 0)])
print(polygon.contains(point))

From the methods youve mentioned Ive only used the second, path.contains_points, and it works fine. In any case depending on the precision you need for your test I would suggest creating a numpy bool grid with all nodes inside the polygon to be True (False if not). If you are going to make a test for a lot of points this might be faster (although notice this relies you are making a test within a pixel tolerance):

from matplotlib import path
import matplotlib.pyplot as plt
import numpy as np

first = -3
size  = (3-first)/100
xv,yv = np.meshgrid(np.linspace(-3,3,100),np.linspace(-3,3,100))
p = path.Path([(0,0), (0, 1), (1, 1), (1, 0)])  # square with legs length 1 and bottom left corner at the origin
flags = p.contains_points(np.hstack((xv.flatten()[:,np.newaxis],yv.flatten()[:,np.newaxis])))
grid = np.zeros((101,101),dtype=bool)
grid[((xv.flatten()-first)/size).astype(int),((yv.flatten()-first)/size).astype(int)] = flags

xi,yi = np.random.randint(-300,300,100)/100,np.random.randint(-300,300,100)/100
vflag = grid[((xi-first)/size).astype(int),((yi-first)/size).astype(int)]
plt.imshow(grid.T,origin=lower,interpolation=nearest,cmap=binary)
plt.scatter(((xi-first)/size).astype(int),((yi-first)/size).astype(int),c=vflag,cmap=Greens,s=90)
plt.show()

, the results is this:

point

If speed is what you need and extra dependencies are not a problem, you maybe find numba quite useful (now it is pretty easy to install, on any platform). The classic ray_tracing approach you proposed can be easily ported to numba by using numba @jit decorator and casting the polygon to a numpy array. The code should look like:

@jit(nopython=True)
def ray_tracing(x,y,poly):
    n = len(poly)
    inside = False
    p2x = 0.0
    p2y = 0.0
    xints = 0.0
    p1x,p1y = poly[0]
    for i in range(n+1):
        p2x,p2y = poly[i % n]
        if y > min(p1y,p2y):
            if y <= max(p1y,p2y):
                if x <= max(p1x,p2x):
                    if p1y != p2y:
                        xints = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
                    if p1x == p2x or x <= xints:
                        inside = not inside
        p1x,p1y = p2x,p2y

    return inside

The first execution will take a little longer than any subsequent call:

%%time
polygon=np.array(polygon)
inside1 = [numba_ray_tracing_method(point[0], point[1], polygon) for 
point in points]

CPU times: user 129 ms, sys: 4.08 ms, total: 133 ms
Wall time: 132 ms

Which, after compilation will decrease to:

CPU times: user 18.7 ms, sys: 320 µs, total: 19.1 ms
Wall time: 18.4 ms

If you need speed at the first call of the function you can then pre-compile the code in a module using pycc. Store the function in a src.py like:

from numba import jit
from numba.pycc import CC
cc = CC(nbspatial)


@cc.export(ray_tracing,  b1(f8, f8, f8[:,:]))
@jit(nopython=True)
def ray_tracing(x,y,poly):
    n = len(poly)
    inside = False
    p2x = 0.0
    p2y = 0.0
    xints = 0.0
    p1x,p1y = poly[0]
    for i in range(n+1):
        p2x,p2y = poly[i % n]
        if y > min(p1y,p2y):
            if y <= max(p1y,p2y):
                if x <= max(p1x,p2x):
                    if p1y != p2y:
                        xints = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
                    if p1x == p2x or x <= xints:
                        inside = not inside
        p1x,p1y = p2x,p2y

    return inside


if __name__ == __main__:
    cc.compile()

Build it with python src.py and run:

import nbspatial

import numpy as np
lenpoly = 100
polygon = [[np.sin(x)+0.5,np.cos(x)+0.5] for x in 
np.linspace(0,2*np.pi,lenpoly)[:-1]]

# random points set of points to test 
N = 10000
# making a list instead of a generator to help debug
points = zip(np.random.random(N),np.random.random(N))

polygon = np.array(polygon)

%%time
result = [nbspatial.ray_tracing(point[0], point[1], polygon) for point in points]

CPU times: user 20.7 ms, sys: 64 µs, total: 20.8 ms
Wall time: 19.9 ms

In the numba code I used:
b1(f8, f8, f8[:,:])

In order to compile with nopython=True, each var needs to be declared before the for loop.

In the prebuild src code the line:

@cc.export(ray_tracing , b1(f8, f8, f8[:,:]))

Is used to declare the function name and its I/O var types, a boolean output b1 and two floats f8 and a two-dimensional array of floats f8[:,:] as input.

Edit Jan/4/2021

For my use case, I need to check if multiple points are inside a single polygon – In such a context, it is useful to take advantage of numba parallel capabilities to loop over a series of points. The example above can be changed to:

from numba import jit, njit
import numba
import numpy as np 

@jit(nopython=True)
def pointinpolygon(x,y,poly):
    n = len(poly)
    inside = False
    p2x = 0.0
    p2y = 0.0
    xints = 0.0
    p1x,p1y = poly[0]
    for i in numba.prange(n+1):
        p2x,p2y = poly[i % n]
        if y > min(p1y,p2y):
            if y <= max(p1y,p2y):
                if x <= max(p1x,p2x):
                    if p1y != p2y:
                        xints = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x
                    if p1x == p2x or x <= xints:
                        inside = not inside
        p1x,p1y = p2x,p2y

    return inside


@njit(parallel=True)
def parallelpointinpolygon(points, polygon):
    D = np.empty(len(points), dtype=numba.boolean) 
    for i in numba.prange(0, len(D)):
        D[i] = pointinpolygon(points[i,0], points[i,1], polygon)
    return D    

Note: pre-compiling the above code will not enable the parallel capabilities of numba (parallel CPU target is not supported by pycc/AOT compilation) see: https://github.com/numba/numba/issues/3336

Test:


import numpy as np
lenpoly = 100
polygon = [[np.sin(x)+0.5,np.cos(x)+0.5] for x in np.linspace(0,2*np.pi,lenpoly)[:-1]]
polygon = np.array(polygon)
N = 10000
points = np.random.uniform(-1.5, 1.5, size=(N, 2))

For N=10000 on a 72 core machine, returns:

%%timeit
parallelpointinpolygon(points, polygon)
# 480 µs ± 8.19 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

Edit 17 Feb 21:

  • fixing loop to start from 0 instead of 1 (thanks @mehdi):

for i in numba.prange(0, len(D))

Edit 20 Feb 21:

Follow-up on the comparison made by @mehdi, I am adding a GPU-based method below. It uses the point_in_polygon method, from the cuspatial library:

    import numpy as np
    import cudf
    import cuspatial

    N = 100000002
    lenpoly = 1000
    polygon = [[np.sin(x)+0.5,np.cos(x)+0.5] for x in 
    np.linspace(0,2*np.pi,lenpoly)]
    polygon = np.array(polygon)
    points = np.random.uniform(-1.5, 1.5, size=(N, 2))


    x_pnt = points[:,0]
    y_pnt = points[:,1]
    x_poly =polygon[:,0]
    y_poly = polygon[:,1]
    result = cuspatial.point_in_polygon(
        x_pnt,
        y_pnt,
        cudf.Series([0], index=[geom]),
        cudf.Series([0], name=r_pos, dtype=int32), 
        x_poly, 
        y_poly,
    )

Following @Mehdi comparison. For N=100000002 and lenpoly=1000 – I got the following results:

 time_parallelpointinpolygon:         161.54760098457336 
 time_mpltPath:                       307.1664695739746 
 time_ray_tracing_numpy_numba:        353.07356882095337 
 time_is_inside_sm_parallel:          37.45389246940613 
 time_is_inside_postgis_parallel:     127.13793849945068 
 time_is_inside_rapids:               4.246025562286377

point

hardware specs:

  • CPU Intel xeon E1240
  • GPU Nvidia GTX 1070

Notes:

  • The cuspatial.point_in_poligon method, is quite robust and powerful, it offers the ability to work with multiple and complex polygons (I guess at the expense of performance)

  • The numba methods can also be ported on the GPU – it will be interesting to see a comparison which includes a porting to cuda of fastest method mentioned by @Mehdi (is_inside_sm).

matplotlib – Whats the fastest way of checking if a point is inside a polygon in python

Your test is good, but it measures only some specific situation:
we have one polygon with many vertices, and long array of points to check them within polygon.

Moreover, I suppose that youre measuring not
matplotlib-inside-polygon-method vs ray-method,
but
matplotlib-somehow-optimized-iteration vs simple-list-iteration

Lets make N independent comparisons (N pairs of point and polygon)?

# ... your code...
lenpoly = 100
polygon = [[np.sin(x)+0.5,np.cos(x)+0.5] for x in np.linspace(0,2*np.pi,lenpoly)[:-1]]

M = 10000
start_time = time()
# Ray tracing
for i in range(M):
    x,y = np.random.random(), np.random.random()
    inside1 = ray_tracing_method(x,y, polygon)
print Ray Tracing Elapsed time:  + str(time()-start_time)

# Matplotlib mplPath
start_time = time()
for i in range(M):
    x,y = np.random.random(), np.random.random()
    inside2 = path.contains_points([[x,y]])
print Matplotlib contains_points Elapsed time:  + str(time()-start_time)

Result:

Ray Tracing Elapsed time: 0.548588991165
Matplotlib contains_points Elapsed time: 0.103765010834

Matplotlib is still much better, but not 100 times better.
Now lets try much simpler polygon…

lenpoly = 5
# ... same code

result:

Ray Tracing Elapsed time: 0.0727779865265
Matplotlib contains_points Elapsed time: 0.105288982391

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