Calculating kernel-density estimate in parallel - parallel-processing

I want to perform kernel-density estimate on a grid in parallel. There is some scaling involved and I can't figure out how to obtain the same results when performing the calculation on different threads.
To illustre this, I'm using an simple example from the scipy documentation.
import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
def measure(n):
"Measurement model, return two coupled measurements."
m1 = np.random.normal(size=n)
m2 = np.random.normal(scale=0.5, size=n)
return m1+m2, m1-m2
m1, m2 = measure(2000)
xmin = m1.min()
xmax = m1.max()
ymin = m2.min()
ymax = m2.max()
kde_bandwith = 0.5
X, Y = np.mgrid[xmin:xmax:100j, ymin:ymax:100j]
positions = np.vstack([X.ravel(), Y.ravel()])
values = np.vstack([m1, m2])
kernel = stats.gaussian_kde(values, bw_method=kde_bandwith)
Z = np.reshape(kernel.evaluate(positions).T, X.shape)
I'm performing the last two lines on n_split subsets of the data (in practice this would be performed on different thread but here I kept a simple loop for simplicity):
## split
n_split = 10
values_split = np.array_split(values, n_split, axis=1)
results = []
for v in values_split:
kernel_n = stats.gaussian_kde(v, bw_method=kde_bandwith)
Z_n = np.reshape(kernel_n.evaluate(positions).T, X.shape)
results.append(Z_n)
Z2 = np.sum(results, axis=0)
here I'm simply recombining the results from each subset of data by summing the Z_n of each subset together into Z2.
Finally, a simple code to compare the results: left is the original version, middle is the result obtain from combining the subsets, and right the difference between the two.
fig = plt.figure(figsize=(9,2), dpi=200)
ax1 = fig.add_subplot(1,3,1)
ax2 = fig.add_subplot(1,3,2)
ax3 = fig.add_subplot(1,3,3)
c1 = ax1.imshow(np.rot90(Z), cmap=plt.cm.gist_earth_r,
extent=[xmin, xmax, ymin, ymax])
#ax1.plot(m1, m2, 'k.', markersize=2)
ax1.set_xlim([xmin, xmax])
ax1.set_ylim([ymin, ymax])
plt.colorbar(c1, shrink=0.6)
c2 = ax2.imshow(np.rot90(Z2), cmap=plt.cm.gist_earth_r,
extent=[xmin, xmax, ymin, ymax])
#ax2.plot(m1, m2, 'k.', markersize=2)
ax2.set_xlim([xmin, xmax])
ax2.set_ylim([ymin, ymax])
plt.colorbar(c2, shrink=0.6)
c3 = ax3.imshow(np.rot90(Z2-Z), cmap=plt.cm.gist_earth_r,
extent=[xmin, xmax, ymin, ymax])
ax3.plot(m1, m2, 'k.', markersize=0.1)
ax3.set_xlim([xmin, xmax])
ax3.set_ylim([ymin, ymax])
plt.colorbar(c3, shrink=0.6)
plt.show()
Notes: It looks like the magnitude of the KDE is n_split larger, but by simply normalizing with 1/n_split or even len(values_split)/len(values) (which in this case is equal), the results are not exactly the same, shown on the next figure as reference.

Related

Fast Radial Symmetry Transform (FRST) implementation (python) results in unusual cross-hair looking artifacts

I am trying to implement FRST on python to detect centroids of elliptical objects (e.g. cells in microscopy images), but my implementation does not find seed points (more or less center points) of elliptical objects. This effort comes from duplicating FRST from Segmentation of Overlapping Elliptical Objects in Silhouette Images (https://ieeexplore.ieee.org/document/7300433). I don't know why I have these artifacts. An interesting thing is that I see these patterns (crosses) all in the same direction per object. Any point in the right direction to generate the same result as in the paper (just to find the seed points) will be most welcome.
Original Paper: A Fast Radial Symmetry Transform for Detecting Points of Interest by Loy and Zelinsky (ECCV 2002)
I have also tried the pre-existing python package for FRST: https://pypi.org/project/frst/. This somehow results in the same artifacts. Weird.
First image: Original Image
Second image: Sobel-operated Image
Third image: Magnitude Projection Image
Fourth image: Magnitude Projection Image with positively affected pixels only
Fifth image: FRST'd image: end-product with original image overlaid (shadowed)
Sixth image: FRST'd image by the pre-existing python package with original image overlaid (shadowed).
from scipy.ndimage import gaussian_filter
import numpy as np
from scipy.signal import convolve
# Get orientation projection image
def get_proj_img(image, radius):
workingDims = tuple((e + 2*radius) for e in image.shape)
h,w = image.shape
ori_img = np.zeros(workingDims) # Orientation Projection Image
mag_img = np.zeros(workingDims) # Magnitutde Projection Image
# Kenels for the sobel operator
a1 = np.matrix([1, 2, 1])
a2 = np.matrix([-1, 0, 1])
Kx = a1.T * a2
Ky = a2.T * a1
# Apply the Sobel operator
sobel_x = convolve(image, Kx)
sobel_y = convolve(image, Ky)
sobel_norms = np.hypot(sobel_x, sobel_y)
# Distances to afpx, afpy (affected pixels)
dist_afpx = np.multiply(np.divide(sobel_x, sobel_norms, out = np.zeros(sobel_x.shape), where = sobel_norms!=0), radius)
dist_afpx = np.round(dist_afpx).astype(int)
dist_afpy = np.multiply(np.divide(sobel_y, sobel_norms, out = np.zeros(sobel_y.shape), where = sobel_norms!=0), radius)
dist_afpy = np.round(dist_afpy).astype(int)
for cords, sobel_norm in np.ndenumerate(sobel_norms):
i, j = cords
pos_aff_pix = (i+dist_afpx[i,j], j+dist_afpy[i,j])
neg_aff_pix = (i-dist_afpx[i,j], j-dist_afpy[i,j])
ori_img[pos_aff_pix] += 1
ori_img[neg_aff_pix] -= 1
mag_img[pos_aff_pix] += sobel_norm
mag_img[neg_aff_pix] -= sobel_norm
ori_img = ori_img[:h, :w]
mag_img = mag_img[:h, :w]
print ("Did it go back to the original image size? ")
print (ori_img.shape == image.shape)
# try normalizing ori and mag img
return ori_img, mag_img
def get_sn(ori_img, mag_img, radius, kn, alpha):
ori_img_limited = np.minimum(ori_img, kn)
fn = np.multiply(np.divide(mag_img,kn), np.power((np.absolute(ori_img_limited)/kn), alpha))
# convolute fn with gaussian filter.
sn = gaussian_filter(fn, 0.25*radius)
return sn
def do_frst(image, radius, kn, alpha, ksize = 3):
ori_img, mag_img = get_proj_img(image, radius)
sn = get_sn(ori_img, mag_img, radius, kn, alpha)
return sn
Parameters:
radius = 50
kn = 10
alpha = 2
beta = 0
stdfactor = 0.25

Visualzing the solution of a differential equation with an animation in Julia

I have solved a system of two second-order differential equations using an implementation of Euler's method in Julia. The below code shows how Euler's method has been called to solve the system in question.
θ1 = 1.1900518004210798; θ2 = 0.3807445263738167
f(t, y) = [y[2], -2(y[1] - θ1) - 4y[2] + 0.5sin(3pi*t),
y[4], -2(y[3] - θ2) - 4(y[4] + abs(y[2])) + 0.5sin(3pi*t)]
y0 = [pi/2, 0, pi/6, 0]; t0 = 0; tFinal = 50; h = 0.001
res = euler(f, y0, t0, tFinal, h)
The result, res, is a vector of four numbers
1.18798735437173
-0.0458294959470722
0.31530569612003573
-0.049213402534541074
The first entry is the angle that the bottom line segment forms with the x-axis while the third entry is the angle that the two line segments form with one another (see below figure).
To create this plot I called plot_robotarm([res[1], res[3]]) which is implemented according to the below code.
function plot_robotarm(thetav)
# Plots a robotarm with angles thetav
R = 1;
xv=zeros(length(thetav)+1)
yv=zeros(length(thetav)+1)
for i in 1:length(thetav)
xv[i+1]=xv[i]+R*cos(thetav[i])
yv[i+1]=yv[i]+R*sin(thetav[i])
end
# Plot with colors
opts = (:circle, 10, 1., :blue, stroke(7, 1., :red))
plt = plot(xv, yv,
marker = opts,
c = :red,
w = 5,
legend = false,
xlims = (0, 2.0),
ylims = (0, 2.0))
display(plt)
end
How can I create an animation that visualizes how consecutive iterations of Euler's method make the robot arm (i.e. the two line segments) move toward the final point at t = 50? (I do not need to plot every iteration, just enough so that it makes for an animation that captures the movement of the robot arm.)
You can use ffmpeg and Luxor.jl's animation features to make an animated GIF. The frame function needs to be modified to reflect graphical display of each step in your program. See the docs for Luxor for more.
using Luxor
using Colors
using BoundaryValueDiffEq
# constants for differential equations and movie
const g = 9.81
const L = 1.0 # pendulum length in meters
const bobd = 0.10 # pendulum bob diameter in meters
const framerate = 50.0 # intended frame rate/sec
const t0 = 0.0 # start time (s)
const tf = 2.3 # end simulation time (s)
const dtframe = 1.0/framerate # time increment per frame
const tspan = LinRange(t0, tf, Int(floor(tf*framerate))) # array of time points in animation
const bgcolor = "black" # gif background
const leaderhue = (0.80, 0.70, 0.20) # gif swing arm hue light gold
const hslcolors = [HSL(col) for col in (distinguishable_colors(
Int(floor(tf*framerate)+3),[RGB(1,1,1)])[2:end])]
const giffilename = "pendulum.gif" # output file
# differential equations copied from docs of DifferentialEquations.jl
simplependulum!(du, u, p, t) = (θ=u[1]; dθ=u[2]; du[1]=dθ; du[2]=-(g/L)*sin(θ))
bc1!(residual, u, p, t) = (residual[1] = u[div(end,2)][1] + pi/2; residual[2] = u[end][1] - pi/2)
bvp1 = TwoPointBVProblem(simplependulum!, bc1!, [pi/2,pi/2], (tspan[1],tspan[end]))
sol2 = solve(bvp1, GeneralMIRK4(), dt=dtframe)
# movie making background
backdrop(scene, framenumber) = background(bgcolor)
function frame(scene, framenumber)
u1, u2 = sol2.u[framenumber]
y, x = L*cos(u1), L*sin(u1)
sethue(leaderhue)
poly([Point(-4.0, 0.0), Point(4.0, 0.0),
Point(160.0x,160.0y)], :fill)
sethue(Colors.HSV(framenumber*4.0, 1, 1))
circle(Point(160.0x,160.0y), 160bobd, :fill)
text(string("frame $framenumber of $(scene.framerange.stop)"),
Point(0.0, -190.0),
halign=:center)
end
muv = Movie(400, 400, "Pendulum Demo", 1:length(tspan))
animate(muv, [Scene(muv, backdrop),
Scene(muv, frame, easingfunction=easeinoutcubic)],
creategif=true, pathname=giffilename)

Matplotlib animate space vs time plot

I'm currently working on traffic jams analysis and was wondering if there's a way to animate the generation of a plot of such jams.
A plot of this things grow from up to the lower end of the figure, each 'row' is a time instance. The horizontal axis is just the road indicating at each point the position of each vehicle and, with a certain numeric value, the velocity of it. So applying different colors to different velocities, you get a plot that shows how a jam evolves through time in a given road.
My question is, how can I use matplotlib to generate an animation of each instance of the road in time to get such a plot?
The plot is something like this:
I'm simulating a road with vehicles with certain velocities through time, so I wish to animate a plot showing how the traffic jams evolve...
EDIT:
I add some code to make clear what I'm already doing
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation, rc
plt.rcParams['animation.ffmpeg_path'] = u'/usr/bin/ffmpeg'
# model params
vmax = 5
lenroad = 50
prob = 0.4
# sim params
numiters = 10
# traffic model
def nasch():
gaps = np.full(road.shape, -1)
road_r4 = np.full(road.shape, -1)
for n,x in enumerate(road):
if x > -1:
d = 1
while road[(n+d) % len(road)] < 0:
d += 1
d -= 1
gaps[n] = d
road_r1 = np.where(road!=-1, np.minimum(road+1, vmax), -1)
road_r2 = np.where(road_r1!=-1, np.minimum(road_r1, gaps), -1)
road_r3 = np.where(road_r2!=-1, np.where(np.random.rand() < prob, np.maximum(road-1, 0), road), -1)
for n,x in enumerate(road_r3):
if x > -1:
road_r4[(n+x) % len(road_r3)] = x
return road_r4
def plot_nasch(*args):
road = nasch()
plot.set_array([road])
return plot,
# init road
road = np.random.randint(-10, vmax+1, [lenroad])
road = np.where(road>-1, road, -1)
# simulate
fig = plt.figure()
plot = plt.imshow([road], cmap='Pastel2', interpolation='nearest')
for i in range(numiters):
ani = animation.FuncAnimation(fig, plot_nasch, frames=100, interval=500, blit=True)
plt.show()
And I get the following figure, just one road instead of each road painted at the bottom of the previous one:
This is possibly what you want, although I'm not sure why you want to animate the time, since time is already one of the axes in the plot.
The idea here is to store the simulation results of a time-step row by row in an array and replot this array. Thereby previous simulation results are not lost.
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation, rc
# model params
vmax = 5
lenroad = 50
prob = 0.4
# sim params
numiters = 25
# traffic model
def nasch():
global road
gaps = np.full(road.shape, -1)
road_r4 = np.full(road.shape, -1)
for n,x in enumerate(road):
if x > -1:
d = 1
while road[(n+d) % len(road)] < 0:
d += 1
d -= 1
gaps[n] = d
road_r1 = np.where(road!=-1, np.minimum(road+1, vmax), -1)
road_r2 = np.where(road_r1!=-1, np.minimum(road_r1, gaps), -1)
road_r3 = np.where(road_r2!=-1, np.where(np.random.rand() < prob, np.maximum(road-1, 0), road), -1)
for n,x in enumerate(road_r3):
if x > -1:
road_r4[(n+x) % len(road_r3)] = x
return road_r4
def plot_nasch(i):
print i
global road
road = nasch()
#store result in array
road_over_time[i+1,:] = road
# plot complete array
plot.set_array(road_over_time)
# init road
road = np.random.randint(-10, vmax+1, [lenroad])
road = np.where(road>-1, road, -1)
# initiate array
road_over_time = np.zeros((numiters+1, lenroad))*np.nan
road_over_time[0,:] = road
fig = plt.figure()
plot = plt.imshow(road_over_time, cmap='Pastel2', interpolation='nearest', vmin=-1.5, vmax=6.5)
plt.colorbar()
ani = animation.FuncAnimation(fig, plot_nasch, frames=numiters, init_func=lambda : 1, interval=400, blit=False, repeat=False)
plt.show()

Speeding up vectorized eye-tracking algorithm in numpy

I'm trying to implement Fabian Timm's eye-tracking algorithm [http://www.inb.uni-luebeck.de/publikationen/pdfs/TiBa11b.pdf] (found here: [http://thume.ca/projects/2012/11/04/simple-accurate-eye-center-tracking-in-opencv/]) in numpy and OpenCV and I've hit a snag. I think I've vectorized my implementation decently enough, but it's still not fast enough to run in real time and it doesn't detect pupils with as much accuracy as I had hoped. This is my first time using numpy, so I'm not sure what I've done wrong.
def find_pupil(eye):
eye_len = np.arange(eye.shape[0])
xx,yy = np.meshgrid(eye_len,eye_len) #coordinates
XX,YY = np.meshgrid(xx.ravel(),yy.ravel()) #all distance vectors
Dx,Dy = [YY-XX, YY-XX] #y2-y1, x2-x1 -- simpler this way because YY = XXT
Dlen = np.sqrt(Dx**2+Dy**2)
Dx,Dy = [Dx/Dlen, Dy/Dlen] #normalized
Gx,Gy = np.gradient(eye)
Gmagn = np.sqrt(Gx**2+Gy**2)
Gx,Gy = [Gx/Gmagn,Gy/Gmagn] #normalized
GX,GY = np.meshgrid(Gx.ravel(),Gy.ravel())
X = (GX*Dx+GY*Dy)**2
eye = cv2.bitwise_not(cv2.GaussianBlur(eye,(5,5),0.005*eye.shape[1])) #inverting and blurring eye for use as w
eyem = np.repeat(eye.ravel()[np.newaxis,:],eye.size,0)
C = (np.nansum(eyem*X, axis=0)/eye.size).reshape(eye.shape)
return np.unravel_index(C.argmax(), C.shape)
and the rest of the code:
def find_eyes(face):
left_x, left_y = [int(floor(0.5 * face.shape[0])), int(floor(0.2 * face.shape[1]))]
right_x, right_y = [int(floor(0.1 * face.shape[0])), int(floor(0.2 * face.shape[1]))]
area = int(floor(0.2 * face.shape[0]))
left_eye = (left_x, left_y, area, area)
right_eye = (right_x, right_y, area, area)
return [left_eye,right_eye]
faceCascade = cv2.CascadeClassifier("haarcascade_frontalface_default.xml")
video_capture = cv2.VideoCapture(0)
while True:
# Capture frame-by-frame
ret, frame = video_capture.read()
gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
faces = faceCascade.detectMultiScale(
gray,
scaleFactor=1.1,
minNeighbors=5,
minSize=(30, 30),
flags=cv2.CASCADE_SCALE_IMAGE
)
# Draw a rectangle around the faces
for (x, y, w, h) in faces:
cv2.rectangle(frame, (x, y), (x+w, y+h), (0, 255, 0), 2)
roi_gray = gray[y:y+h, x:x+w]
roi_color = frame[y:y+h, x:x+w]
eyes = find_eyes(roi_gray)
for (ex,ey,ew,eh) in eyes:
eye_gray = roi_gray[ey:ey+eh,ex:ex+ew]
eye_color = roi_color[ey:ey+eh,ex:ex+ew]
cv2.rectangle(roi_color,(ex,ey),(ex+ew,ey+eh),(255,0,0),2)
px,py = find_pupil(eye_gray)
cv2.rectangle(eye_color,(px,py),(px+1,py+1),(255,0,0),2)
# Display the resulting frame
cv2.imshow('Video', frame)
if cv2.waitKey(1) & 0xFF == ord('q'):
break
# When everything is done, release the capture
video_capture.release()
cv2.destroyAllWindows()
You can perform many of those operations that save replicated elements and then perform some mathematical opertaions by directly performing the mathematical operatrions after creating singleton dimensions that would allow NumPy broadcasting. Thus, there would be two benefits - On the fly operations to save workspace memory and performance boost. Also, at the end, we can replace the nansum calculation with a simplified version. Thus, with all of that philosophy in mind, here's one modified approach -
def find_pupil_v2(face, x, y, w, h):
eye = face[x:x+w,y:y+h]
eye_len = np.arange(eye.shape[0])
N = eye_len.size**2
eye_len_diff = eye_len[:,None] - eye_len
Dlen = np.sqrt(2*((eye_len_diff)**2))
Dxy0 = eye_len_diff/Dlen
Gx0,Gy0 = np.gradient(eye)
Gmagn = np.sqrt(Gx0**2+Gy0**2)
Gx,Gy = [Gx0/Gmagn,Gy0/Gmagn] #normalized
B0 = Gy[:,:,None]*Dxy0[:,None,:]
C0 = Gx[:,None,:]*Dxy0
X = ((C0.transpose(1,0,2)[:,None,:,:]+B0[:,:,None,:]).reshape(N,N))**2
eye1 = cv2.bitwise_not(cv2.GaussianBlur(eye,(5,5),0.005*eye.shape[1]))
C = (np.nansum(X,0)*eye1.ravel()/eye1.size).reshape(eye1.shape)
return np.unravel_index(C.argmax(), C.shape)
There's one repeat still left in it at Dxy. It might be possible to avoid that step and Dxy0 could be fed directly into the step that uses Dxy to give us X, but I haven't worked through it. Everything's converted to broadcasting based!
Runtime test and output verification -
In [539]: # Inputs with random elements
...: face = np.random.randint(0,10,(256,256)).astype('uint8')
...: x = 40
...: y = 60
...: w = 64
...: h = 64
...:
In [540]: find_pupil(face,x,y,w,h)
Out[540]: (32, 63)
In [541]: find_pupil_v2(face,x,y,w,h)
Out[541]: (32, 63)
In [542]: %timeit find_pupil(face,x,y,w,h)
1 loops, best of 3: 4.15 s per loop
In [543]: %timeit find_pupil_v2(face,x,y,w,h)
1 loops, best of 3: 529 ms per loop
It seems we are getting close to 8x speedup!

Algorithm to subdivide a polygon in smaller polygons

I have a polygon made of successive edges on a plane, and would like to subdivide it in sub-polygons being triangles or rectangles.
Where can I find an algorithm to do this ?
Thanks !
In computational geometry, the problem you want to solve is called triangulation.
There are algorithms to solve this problem, giving triangulations with different properties. You will need to decide which one is the best fit.
I was looking for an answer for this myself but couldn't find one. Tried to stitch together several pieces and here's the result.
This is not necessarily the most optimal routine but it did the job for me. If you want to increase performance, try experimenting with the code.
A brief description of the algorithm:
Using the boundaries of the original geometry itself, and the boundaries of its convex hull, and its minimum rotated rectangle, derive all possible rectangles.
Divide all rectangles into smaller squares of specified side length.
Drop duplicates using a rounded off centroid. (r: round off param)
Retain either those squares 'within' the geometry, or those that 'intersect' the geometry, depending on whichever is closer to the total number of required squares.
EDITED
New Solution
#### Python script for dividing any shapely polygon into smaller equal sized polygons
import numpy as np
from shapely.ops import split
import geopandas
from shapely.geometry import MultiPolygon, Polygon
def rhombus(square):
"""
Naively transform the square into a Rhombus at a 45 degree angle
"""
coords = square.boundary.coords.xy
xx = list(coords[0])
yy = list(coords[1])
radians = 1
points = list(zip(xx, yy))
Rhombus = Polygon(
[
points[0],
points[1],
points[3],
((2 * points[3][0]) - points[2][0], (2 * points[3][1]) - points[2][1]),
points[4],
]
)
return Rhombus
def get_squares_from_rect(RectangularPolygon, side_length=0.0025):
"""
Divide a Rectangle (Shapely Polygon) into squares of equal area.
`side_length` : required side of square
"""
rect_coords = np.array(RectangularPolygon.boundary.coords.xy)
y_list = rect_coords[1]
x_list = rect_coords[0]
y1 = min(y_list)
y2 = max(y_list)
x1 = min(x_list)
x2 = max(x_list)
width = x2 - x1
height = y2 - y1
xcells = int(np.round(width / side_length))
ycells = int(np.round(height / side_length))
yindices = np.linspace(y1, y2, ycells + 1)
xindices = np.linspace(x1, x2, xcells + 1)
horizontal_splitters = [
LineString([(x, yindices[0]), (x, yindices[-1])]) for x in xindices
]
vertical_splitters = [
LineString([(xindices[0], y), (xindices[-1], y)]) for y in yindices
]
result = RectangularPolygon
for splitter in vertical_splitters:
result = MultiPolygon(split(result, splitter))
for splitter in horizontal_splitters:
result = MultiPolygon(split(result, splitter))
square_polygons = list(result)
return square_polygons
def split_polygon(G, side_length=0.025, shape="square", thresh=0.9):
"""
Using a rectangular envelope around `G`, creates a mesh of squares of required length.
Removes non-intersecting polygons.
Args:
- `thresh` : Range - [0,1]
This controls - the number of smaller polygons at the boundaries.
A thresh == 1 will only create (or retain) smaller polygons that are
completely enclosed (area of intersection=area of smaller polygon)
by the original Geometry - `G`.
A thresh == 0 will create (or retain) smaller polygons that
have a non-zero intersection (area of intersection>0) with the
original geometry - `G`
- `side_length` : Range - (0,infinity)
side_length must be such that the resultant geometries are smaller
than the original geometry - `G`, for a useful result.
side_length should be >0 (non-zero positive)
- `shape` : {square/rhombus}
Desired shape of subset geometries.
"""
assert side_length>0, "side_length must be a float>0"
Rectangle = G.envelope
squares = get_squares_from_rect(Rectangle, side_length=side_length)
SquareGeoDF = geopandas.GeoDataFrame(squares).rename(columns={0: "geometry"})
Geoms = SquareGeoDF[SquareGeoDF.intersects(G)].geometry.values
if shape == "rhombus":
Geoms = [rhombus(g) for g in Geoms]
geoms = [g for g in Geoms if ((g.intersection(G)).area / g.area) >= thresh]
elif shape == "square":
geoms = [g for g in Geoms if ((g.intersection(G)).area / g.area) >= thresh]
return geoms
# Reading geometric data
geo_filepath = "/data/geojson/pc_14.geojson"
GeoDF = geopandas.read_file(geo_filepath)
# Selecting random shapely-geometry
G = np.random.choice(GeoDF.geometry.values)
squares = split_polygon(G,shape='square',thresh=0.5,side_length=0.025)
rhombuses = split_polygon(G,shape='rhombus',thresh=0.5,side_length=0.025)
Previous Solution:
import numpy as np
import geopandas
from shapely.ops import split
from shapely.geometry import MultiPolygon, Polygon, Point, MultiPoint
def get_rect_from_geom(G, r=2):
"""
Get rectangles from a geometry.
r = rounding factor.
small r ==> more rounding off ==> more rectangles
"""
coordinate_arrays = G.exterior.coords.xy
coordinates = list(
zip(
[np.round(c, r) for c in coordinate_arrays[0]],
[np.round(c, r) for c in coordinate_arrays[1]],
)
)
Rectangles = []
for c1 in coordinates:
Coords1 = [a for a in coordinates if a != c1]
for c2 in Coords1:
Coords2 = [b for b in Coords1 if b != c2]
x1, y1 = c1[0], c1[1]
x2, y2 = c2[0], c2[1]
K1 = [k for k in Coords2 if k == (x1, y2)]
K2 = [k for k in Coords2 if k == (x2, y1)]
if (len(K1) > 0) & (len(K2) > 0):
rect = [list(c1), list(K1[0]), list(c2), list(K2[0])]
Rectangles.append(rect)
return Rectangles
def get_squares_from_rect(rect, side_length=0.0025):
"""
Divide a rectangle into equal area squares
side_length = required side of square
"""
y_list = [r[1] for r in rect]
x_list = [r[0] for r in rect]
y1 = min(y_list)
y2 = max(y_list)
x1 = min(x_list)
x2 = max(x_list)
width = x2 - x1
height = y2 - y1
xcells, ycells = int(np.round(width / side_length)), int(
np.round(height / side_length)
)
yindices = np.linspace(y1, y2, ycells + 1)
xindices = np.linspace(x1, x2, xcells + 1)
horizontal_splitters = [
LineString([(x, yindices[0]), (x, yindices[-1])]) for x in xindices
]
vertical_splitters = [
LineString([(xindices[0], y), (xindices[-1], y)]) for y in yindices
]
result = Polygon(rect)
for splitter in vertical_splitters:
result = MultiPolygon(split(result, splitter))
for splitter in horizontal_splitters:
result = MultiPolygon(split(result, splitter))
square_polygons = list(result)
return [np.stack(SQPOLY.exterior.coords.xy, axis=1) for SQPOLY in square_polygons]
def round_centroid(g, r=10):
"""
Get Centroids.
Round off centroid coordinates to `r` decimal points.
"""
C = g.centroid.coords.xy
return (np.round(C[0][0], r), np.round(C[1][0], r))
def subdivide_polygon(g, side_length=0.0025, r=10):
"""
1. Create all possible rectangles coordinates from the geometry, its minimum rotated rectangle, and its convex hull.
2. Divide all rectangles into smaller squares.
small r ==> more rounding off ==> fewer overlapping squares. (these are dropped as duplicates)
large r ==> may lead to a few overlapping squares.
"""
# Number of squares required.
num_squares_reqd = g.area // (side_length ** 2)
# Some of these combinations can be dropped to improve performance.
Rectangles = []
Rectangles.extend(get_rect_from_geom(g))
Rectangles.extend(get_rect_from_geom(g.minimum_rotated_rectangle))
Rectangles.extend(get_rect_from_geom(g.convex_hull))
Squares = []
for r in range(len(Rectangles)):
rect = Rectangles[r]
Squares.extend(get_squares_from_rect(rect, side_length=side_length))
SquarePolygons = [Polygon(square) for square in Squares]
GDF = geopandas.GeoDataFrame(SquarePolygons).rename(columns={0: "geometry"})
GDF.loc[:, "centroid"] = GDF.geometry.apply(round_centroid, r=r)
GDF = GDF.drop_duplicates(subset=["centroid"])
wgeoms = GDF[GDF.within(g)].geometry.values
igeoms = GDF[GDF.intersects(g)].geometry.values
w = abs(num_squares_reqd - len(wgeoms))
i = abs(num_squares_reqd - len(igeoms))
print(w, i)
if w <= i:
return wgeoms
else:
return igeoms
geoms = subdivide(g)
Stumbled across this after many searches.
Thanks #Aditya Chhabra for your submission, it works great but get_squares_from_rect is very slow for small side lengths due to iterative clips.
We can do this instantaneously if we combine all LineStrings into a single collection, then clip and polygonize in one step, which I found in in this question.
Previously side lengths of 0.0001 (EPSG:4326) took > 1 minute, now it takes no time.
from shapely.ops import unary_union, polygonize, linemerge
from shapely.geometry import LineString
import numpy as np
def get_squares_from_rect_faster(RectangularPolygon, side_length=0.0025):
rect_coords = np.array(RectangularPolygon.boundary.coords.xy)
y_list = rect_coords[1]
x_list = rect_coords[0]
y1 = min(y_list)
y2 = max(y_list)
x1 = min(x_list)
x2 = max(x_list)
width = x2 - x1
height = y2 - y1
xcells = int(np.round(width / side_length))
ycells = int(np.round(height / side_length))
yindices = np.linspace(y1, y2, ycells + 1)
xindices = np.linspace(x1, x2, xcells + 1)
horizontal_splitters = [
LineString([(x, yindices[0]), (x, yindices[-1])]) for x in xindices
]
vertical_splitters = [
LineString([(xindices[0], y), (xindices[-1], y)]) for y in yindices
]
lines = horizontal_splitters + vertical_splitters
lines.append(RectangularPolygon.boundary)
lines = unary_union(lines)
lines = linemerge(lines)
return list(polygonize(lines))

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