I have multiple grids (numpy arrays [Nk,Ny,Nx]) and would like to use Hausdorff distance as a metric of similarity of these grids. There are several modules in scipy (scipy.spatial.distance.cdist,scipy.spatial.distance.pdist) which allow to calculate Euclidean distance between 2D arrays. Now to compare grids I have to choose some cross-section (e.g. grid1[0,:] & grid2[0,:]) and compare it between each other.
Is it possible to calculate Hausdorff distance between 3D grids directly?
I am newby here, but faced with the same challenge and tried to attack it directly on a 3D level.
So here is the function I did:
def Hausdorff_dist(vol_a,vol_b):
dist_lst = []
for idx in range(len(vol_a)):
dist_min = 1000.0
for idx2 in range(len(vol_b)):
dist= np.linalg.norm(vol_a[idx]-vol_b[idx2])
if dist_min > dist:
dist_min = dist
dist_lst.append(dist_min)
return np.max(dist_lst)
The input needs to be numpy.array, but the rest is working directly.
I have 8000 vs. 5000 3D points and this runs for several minutes, but at the end it gets to the distance you are looking for.
This is however checking the distance between two points, not neccesarily the distance of two curves. (neither mesh).
Edit (on 26/11/2015):
Recenty finished the fine-tuned version of this code. Now it is splitted into two part.
First is taking care of grabbing a box around a given point and taking all the radius. I consider this as a smart way to reduce the number of points required to check.
def bbox(array, point, radius):
a = array[np.where(np.logical_and(array[:, 0] >= point[0] - radius, array[:, 0] <= point[0] + radius))]
b = a[np.where(np.logical_and(a[:, 1] >= point[1] - radius, a[:, 1] <= point[1] + radius))]
c = b[np.where(np.logical_and(b[:, 2] >= point[2] - radius, b[:, 2] <= point[2] + radius))]
return c
And the other code for the distance calculation:
def hausdorff(surface_a, surface_b):
# Taking two arrays as input file, the function is searching for the Hausdorff distane of "surface_a" to "surface_b"
dists = []
l = len(surface_a)
for i in xrange(l):
# walking through all the points of surface_a
dist_min = 1000.0
radius = 0
b_mod = np.empty(shape=(0, 0, 0))
# increasing the cube size around the point until the cube contains at least 1 point
while b_mod.shape[0] == 0:
b_mod = bbox(surface_b, surface_a[i], radius)
radius += 1
# to avoid getting false result (point is close to the edge, but along an axis another one is closer),
# increasing the size of the cube
b_mod = bbox(surface_b, surface_a[i], radius * math.sqrt(3))
for j in range(len(b_mod)):
# walking through the small number of points to find the minimum distance
dist = np.linalg.norm(surface_a[i] - b_mod[j])
if dist_min > dist:
dist_min = dist
dists.append(dist_min)
return np.max(dists)
In case anyone is still looking for the answer to this question years later... since 2016 scipy now includes a function to calculate the Hausdorff distance in 3D:
scipy.spatial.distance.directed_hausdorff
Related
I am facing a problem for computing a large distance matrix. However, this is a specific distance matrix: it is a matrix of points which are in a unit cell. This function gets fractional coordinates (between 0 and 1 in all dimensions) and I would like to calculate the distance matrix accounting for the fact that there is an identical copy of the point in each neighbor of the unit cell, and therefore the correct distance may be with the copy rather than with the other point within the unit cell.
Do you know if anything can be done with scipy or numpy pre-coded C libraries for this? I've done a numba code which works but runs rather slowly. Here I have a list of 13160 points for which I want to calculate a 13160*13160 distance matrix, ie that contains 173185600 elements.
The principle is: for each coordinate, calculate the square fractional distance of the first point with the second point either within the cell, or in one of its two neigbhors (behind and in front). Then get the minimum of the square distance for each coordinate and get the corresponding Euclidian distance from the cartesian coordinates.
The time it currently takes is: 40.82661843299866 seconds
Do you know if I can make it run faster by any means, or is my dataset just large and there is nothing more to be done?
Below is the code:
def getDistInCell(fract, xyz, n_sg, a, b, c): #calculates the distance matrix accounting for symmetry
dist = np.zeros((n_sg, n_sg))
for i in range(n_sg):
for j in range(n_sg):
#we evaluate the closest segment according to translation to neighbouring cells
diff_x = np.zeros((3))
diff_y = np.zeros((3))
diff_z = np.zeros((3))
diff_x[0] = (fract[i][0] - (fract[j][0] - 1))**2
diff_x[1] = (fract[i][0] - (fract[j][0] ))**2
diff_x[2] = (fract[i][0] - (fract[j][0] + 1))**2
diff_y[0] = (fract[i][1] - (fract[j][1] - 1))**2
diff_y[1] = (fract[i][1] - (fract[j][1] ))**2
diff_y[2] = (fract[i][1] - (fract[j][1] + 1))**2
diff_z[0] = (fract[i][2] - (fract[j][2] - 1))**2
diff_z[1] = (fract[i][2] - (fract[j][2] ))**2
diff_z[2] = (fract[i][2] - (fract[j][2] + 1))**2
#get correct shifts
shx = np.argmin(diff_x) - 1
shy = np.argmin(diff_y) - 1
shz = np.argmin(diff_z) - 1
#compute cartesian distance
dist[i][j] = np.sqrt((xyz[i][0] - (xyz[j][0] + shx * a)) ** 2 + (xyz[i][1] - (xyz[j][1] + shy * b)) ** 2 + (xyz[i][2] - (xyz[j][2] + shz * c)) ** 2)
return dist
Here is a sketch of a solution based on BallTree
I create random points, 13160
import numpy as np
n=13160
np.random.seed(1)
points=np.random.uniform(size=(n,3))
Create mirrors/symmetries, e.g.
from itertools import product
def create_symmetries( points ):
symmetries = []
for sym in product([0,-1,1],[0,-1,1],[0,-1,1]):
new_symmetry = points.copy()
diff_x, diff_y, diff_z = sym
new_symmetry[:,0] = new_symmetry[:,0] + diff_x
new_symmetry[:,1] = new_symmetry[:,1] + diff_y
new_symmetry[:,2] = new_symmetry[:,2] + diff_z
symmetries.append(new_symmetry)
return symmetries
and create a larger datasets including symmetries;
all_symmetries = np.concatenate( create_symmetries(points) )
To get the closest one, use, k=2 as the closest one is the point itself, and the 2nd closest is whatever symmetry is the closest (including its own, so be careful there)
%%time
import numpy as np
from sklearn.neighbors import BallTree
tree = BallTree(all_symmetries, leaf_size=15, metric='euclidean')
dist, idx = tree.query(points, k=2, return_distance=True)
This takes < 500ms
CPU times: user 275 ms, sys: 2.77 ms, total: 277 ms
Wall time: 275 ms
I am extremely new to programming but I decided to take on an interesting project as I recently learnt how to represent a sphere in parametric form. When intersecting three spheres, there are two points of intersections that are distinct unless they only overlap at a singular point.
Parametric representation of a sphere:
The code I have is modified from the answer from Python/matplotlib : plotting a 3d cube, a sphere and a vector?, adding the ability to dictate the x, y and z origin and the radius of the sphere. Many similar questions were written in C++, Java, and C#, which I cannot understand at all (I barely know what I am doing so go easy on me).
My Code:
import numpy as np
def make_sphere_x(x, radius):
u, v = np.mgrid[0:2 * np.pi:5000j, 0:np.pi:2500j]
x += radius * np.cos(u) * np.sin(v)
return x
def make_sphere_y(y, radius):
u, v = np.mgrid[0:2 * np.pi:5000j, 0:np.pi:2500j]
y += radius * np.sin(u) * np.sin(v)
return y
def make_sphere_z(z, radius):
u, v = np.mgrid[0:2 * np.pi:5000j, 0:np.pi:2500j]
z += radius * np.cos(v)
return z
#x values
sphere_1_x = make_sphere_x(0, 2)
sphere_2_x = make_sphere_x(1, 3)
sphere_3_x = make_sphere_x(-1, 4)
#y values
sphere_1_y = make_sphere_y(0, 2)
sphere_2_y = make_sphere_y(1, 3)
sphere_3_y = make_sphere_y(0, 4)
#z values
sphere_1_z = make_sphere_z(0, 2)
sphere_2_z = make_sphere_z(1, 3)
sphere_3_z = make_sphere_z(-2, 4)
#intercept of x-values
intercept_x = list(filter(lambda x: x in sphere_1_x, sphere_2_x))
intercept_x = list(filter(lambda x: x in intercept_x, sphere_3_x))
print(intercept_x)
Problems:
Clearly there must be a better way of finding the intercepts. Right now, the code generates points at equal intervals, with the number of intervals I specify under the imaginary number in np.mgrid. If this is increased, the chances of an intersection should increase (I think) but when I try to increase it to 10000j or above, it just spits a memory error.
There are obvious gaps in the array and this method would most likely be erroneous even if I have access to a super computer and can crank up the value to an obscene value. Right now the code results in a null set.
The code is extremely inefficient, not that this is a priority but people like things in threes right?
Feel free to flame me for rookie mistakes in coding or asking questions on Stack Overflow. Your help is greatly valued.
Using scipy.optimize.fsolve you can find the root of a given function, given an initial guess that is somewhere in the range of your solution. I used this approach to solve your problem and it seems to work for me. The only downside is that it only provides you one intersection. To find the second one you would have to tinker with the initial conditions until fsolve finds the second root.
First we define our spheres by defining (arbitrary) radii and centers for each sphere:
a1 = np.array([0,0,0])
r1 = .4
a2 = np.array([.3,0,0])
r2 = .5
a3 = np.array([0,.3,0])
r3 = .5
We then define how to transform back into cartesian coordinates, given angles u,v
def position(a,r,u,v):
return a + r*np.array([np.cos(u)*np.sin(v),np.sin(u)*np.sin(v),np.cos(v)])
Now we think about what equation we need to find the root of. For any intersection point, it holds that for perfect u1,v1,u2,v2,u3,v3 the positions position(a1,r1,u1,v1) = position(a2,r2,u2,v2) = position(a3,r3,u3,v3) are equal. We thus find three equations which must be zeros, namely the differences of two position vectors. In fact, as every vector has 3 components, we have 9 equations which is more than enough to determine our 6 variables.
We find the function to minimize as:
def f(args):
u1,v1,u2,v2,u3,v3,_,_,_ = args
pos1 = position(a1,r1,u1,v1)
pos2 = position(a2,r2,u2,v2)
pos3 = position(a3,r3,u3,v3)
return np.array([pos1 - pos2, pos1 - pos3, pos2 - pos3]).flatten()
fsolve needs the same amount of input and output arguments. As we have 9 equations but only 6 variables I simply used 3 dummy variables so the dimensions match. Flattening the array in the last line is necessary as fsolve only accepts 1D-Arrays.
Now the intersection can be found using fsolve and a (pretty random) guess:
guess = np.array([np.pi/4,np.pi/4,np.pi/4,np.pi/4,np.pi/4,np.pi/4,0,0,0])
x0 = fsolve(f,guess)
u1,v1,u2,v2,u3,v3,_,_,_ = x0
You can check that the result is correct by plugging the angles you received into the position function.
The problem would be better tackled using trigonometry.
Reducing the problem into 2D circles, we could do:
import math
import numpy
class Circle():
def __init__(self, cx, cy, r):
"""initialise Circle and set main properties"""
self.centre = numpy.array([cx, cy])
self.radius = r
def find_intercept(self, c2):
"""find the intercepts between the current Circle and a second c2"""
#Find the distance between the circles
s = c2.centre - self.centre
self.dx, self.dy = s
self.d = math.sqrt(numpy.sum(s**2))
#Test if there is an overlap. Note: this won't detect if one circle completly surrounds the other.
if self.d > (self.radius + c2.radius):
print("no interaction")
else:
#trigonometry
self.theta = math.atan2(self.dy,self.dx)
#cosine rule
self.cosA = (c2.radius**2 - self.radius**2 + self.d**2)/(2*c2.radius*self.d)
self.A = math.acos(self.cosA)
self.Ia = c2.centre - [math.cos(self.A+self.theta)*c2.radius, math.sin(self.A+self.theta)*c2.radius]
self.Ib = c2.centre - [math.cos(self.A-self.theta)*c2.radius,-math.sin(self.A-self.theta)*c2.radius]
print("Interaction points are : ", self.Ia, " and: ", self.Ib)
#define two arbitrary circles
c1 = Circle(2,5,5)
c2 = Circle(1,6,4)
#find the intercepts
c1.find_intercept(c2)
#test results by reversing the operation
c2.find_intercept(c1)
I'm writing a flask application, using some data extracted from a GPS sensor. I am able to draw the route on a Map and I want to calculate the distance the GPS sensor traveled. One way could be to just get the start and end coordinates, however due to the way the sensor travels this is quite inaccurate. Therefore I do sampling of each 50 sensor samples. If the real sensor sample size was 1000 I will now have 20 samples (by extracting each 50 sample).
Now I want to be able to put my list of samples through a function to calculate distance. So far I've been able to use the package geopy, but when I take large gps sample sets I do get "too many requests" errors, not to mention I will have extra processing time from processing the requests, which is not what I want.
Is there a better approach to calculating the cumulative distance of a list element containing latitude and longitude coordinates?
positions = [(lat_1, lng_1), (lat_2, lng_2), ..., (lat_n, lng_n)]
I found methods for lots of different mathematical ways of calculating distance using just 2 coordinates (lat1, lng1 and lat2 and lng2), but none supporting a list of coordinates.
Here's my current code using geopy:
from geopy.distance import vincenty
def calculate_distances(trips):
temp = {}
distance = 0
for trip in trips:
positions = trip['positions']
for i in range(1, len(positions)):
distance += ((vincenty(positions[i-1], positions[i]).meters) / 1000)
if i == len(positions):
temp = {'distance': distance}
trip.update(temp)
distance = 0
trips is a list element containing dictionaries of key-value pairs of information about a trip (duration, distance, start and stop coordinates and so forth) and the positions object inside trips is a list of tuple coordinates as visualized above.
trips = [{data_1}, {data_2}, ..., {data_n}]
Here's the solution I ended up using. It's called the Haversine (distance) function if you want to look up what it does for yourself.
I changed my approach a little as well. My input (positions) is a list of tuple coordinates:
def calculate_distance(positions):
results = []
for i in range(1, len(positions)):
loc1 = positions[i - 1]
loc2 = positions[i]
lat1 = loc1[0]
lng1 = loc1[1]
lat2 = loc2[0]
lng2 = loc2[1]
degreesToRadians = (math.pi / 180)
latrad1 = lat1 * degreesToRadians
latrad2 = lat2 * degreesToRadians
dlat = (lat2 - lat1) * degreesToRadians
dlng = (lng2 - lng1) * degreesToRadians
a = math.sin(dlat / 2) * math.sin(dlat / 2) + math.cos(latrad1) * \
math.cos(latrad2) * math.sin(dlng / 2) * math.sin(dlng / 2)
c = 2 * math.atan2(math.sqrt(a), math.sqrt(1 - a))
r = 6371000
results.append(r * c)
return (sum(results) / 1000) # Converting from m to km
I'd recommend transform your (x, y) coordinates into complex, as it is computational much easier to calculate distances. Thus, the following function should work:
def calculate_distances(trips):
for trip in trips:
positions = trip['positions']
c_pos = [complex(c[0],c[1]) for c in positions]
distance = 0
for i in range(1, len(c_pos)):
distance += abs(c_pos[i] - c_pos[i-1])
trip.update({'distance': distance})
What I'm doing is converting every (lat_1, lng_1) touple into a single complex number c1 = lat_1 + j*lng_1, and creates a list formed by [c1, c2, ... , cn].
A complex number is, all in all, a 2-dimensional number and, therefore, you can make this if you have 2D coordinates, which is perfect for geolocalization, but wouldn't be possible for 3D space coordinates, for instance.
Once you got this, you can easily compute the distance between two complex numbers c1 and c2 as dist12 = abs(c2 - c1). Doing this recursively you obtain the total distance.
Hope this helped!
I have a polygon consists of lots of points. I want to find the intersection of the polygon and a circle. Providing the circle center of [x0,y0] and radius of r0, I have wrote a rough function to simply solve the quadratic equation of the circle and a line. But what about the efficiency of find the intersection of every line segment of the polygon one by one? Is there more efficient way?
I know sympy already provide the feature to get the intersections of different geometry. But also what about the efficiency of external library like sympy compared to calculate it by my own function, if I want to deal with lots of polygons?
def LineIntersectCircle(p,lsp,lep):
# p is the circle parameter, lsp and lep is the two end of the line
x0,y0,r0 = p
x1,y1 = lsp
x2,y2 = esp
if x1 == x2:
if abs(r0) >= abs(x1 - x0):
p1 = x1, y0 - sqrt(r0**2 - (x1-x0)**2)
p2 = x1, y0 + sqrt(r0**2 - (x1-x0)**2)
inp = [p1,p2]
# select the points lie on the line segment
inp = [p for p in inp if p[1]>=min(y1,y2) and p[1]<=max(y1,y2)]
else:
inp = []
else:
k = (y1 - y2)/(x1 - x2)
b0 = y1 - k*x1
a = k**2 + 1
b = 2*k*(b0 - y0) - 2*x0
c = (b0 - y0)**2 + x0**2 - r0**2
delta = b**2 - 4*a*c
if delta >= 0:
p1x = (-b - sqrt(delta))/(2*a)
p2x = (-b + sqrt(delta))/(2*a)
p1y = k*x1 + b0
p2y = k*x2 + b0
inp = [[p1x,p1y],[p2x,p2y]]
# select the points lie on the line segment
inp = [p for p in inp if p[0]>=min(x1,x2) and p[0]<=max(x1,x2)]
else:
inp = []
return inp
I guess maybe your question is about how to in theory do this in the fastest manner. But if you want to do this quickly, you should really use something which is written in C/C++.
I am quite used to Shapely, so I will provide an example of how to do this with this library. There are many geometry libraries for python. I will list them at the end of this answer.
from shapely.geometry import LineString
from shapely.geometry import Point
p = Point(5,5)
c = p.buffer(3).boundary
l = LineString([(0,0), (10, 10)])
i = c.intersection(l)
print i.geoms[0].coords[0]
(2.8786796564403576, 2.8786796564403576)
print i.geoms[1].coords[0]
(7.121320343559642, 7.121320343559642)
What is a little bit counter intuitive in Shapely is that circles are the boundries of points with buffer areas. This is why I do p.buffer(3).boundry
Also the intersection i is a list of geometric shapes, both of them points in this case, this is why I have to get both of them from i.geoms[]
There is another Stackoverflow question which goes into details about these libraries for those interested.
SymPy
CGAL Python bindings
PyEuclid
PythonOCC
Geometry-simple
EDIT because comments:
Shapely is based on GEOS (trac.osgeo.org/geos) which is built in C++ and considerably faster than anything you write natively in python. SymPy seems to be based on mpmath (mpmath.org) which also seems to be python, but seems to have lots of quite complex math integrated into it. Implementing that yourself may require a lot of work, and will probably not be as fast as GEOS C++ implementations.
Here's a solution that computes the intersection of a circle with either a line or a line segment defined by two (x, y) points:
def circle_line_segment_intersection(circle_center, circle_radius, pt1, pt2, full_line=True, tangent_tol=1e-9):
""" Find the points at which a circle intersects a line-segment. This can happen at 0, 1, or 2 points.
:param circle_center: The (x, y) location of the circle center
:param circle_radius: The radius of the circle
:param pt1: The (x, y) location of the first point of the segment
:param pt2: The (x, y) location of the second point of the segment
:param full_line: True to find intersections along full line - not just in the segment. False will just return intersections within the segment.
:param tangent_tol: Numerical tolerance at which we decide the intersections are close enough to consider it a tangent
:return Sequence[Tuple[float, float]]: A list of length 0, 1, or 2, where each element is a point at which the circle intercepts a line segment.
Note: We follow: http://mathworld.wolfram.com/Circle-LineIntersection.html
"""
(p1x, p1y), (p2x, p2y), (cx, cy) = pt1, pt2, circle_center
(x1, y1), (x2, y2) = (p1x - cx, p1y - cy), (p2x - cx, p2y - cy)
dx, dy = (x2 - x1), (y2 - y1)
dr = (dx ** 2 + dy ** 2)**.5
big_d = x1 * y2 - x2 * y1
discriminant = circle_radius ** 2 * dr ** 2 - big_d ** 2
if discriminant < 0: # No intersection between circle and line
return []
else: # There may be 0, 1, or 2 intersections with the segment
intersections = [
(cx + (big_d * dy + sign * (-1 if dy < 0 else 1) * dx * discriminant**.5) / dr ** 2,
cy + (-big_d * dx + sign * abs(dy) * discriminant**.5) / dr ** 2)
for sign in ((1, -1) if dy < 0 else (-1, 1))] # This makes sure the order along the segment is correct
if not full_line: # If only considering the segment, filter out intersections that do not fall within the segment
fraction_along_segment = [(xi - p1x) / dx if abs(dx) > abs(dy) else (yi - p1y) / dy for xi, yi in intersections]
intersections = [pt for pt, frac in zip(intersections, fraction_along_segment) if 0 <= frac <= 1]
if len(intersections) == 2 and abs(discriminant) <= tangent_tol: # If line is tangent to circle, return just one point (as both intersections have same location)
return [intersections[0]]
else:
return intersections
A low cost spacial partition might be to divide the plane into 9 pieces
Here is a crappy diagram. Imagine, if you will, that the lines are just touching the circle.
| |
__|_|__
__|O|__
| |
| |
8 of the areas we are interested in are surrounding the circle. The square in the centre isn't much use for a cheap test, but you can place a square of r/sqrt(2) inside the circle, so it's corners just touch the circle.
Lets label the areas
A |B| C
__|_|__
D_|O|_E
| |
F |G| H
And the square of r/sqrt(2) in the centre we'll call J
We will call the set of points in the centre square shown in the diagram that aren't in J, Z
Label each vertex of the polygon with it's letter code.
Now we can quickly see
AA => Outside
AB => Outside
AC => Outside
...
AJ => Intersects
BJ => Intersects
...
JJ => Inside
This can turned into a lookup table
So depending on your dataset, you may have saved yourself a load of work. Anything with an endpoint in Z will need to be tested however.
I think that the formula you use to find the coordinates of the two intersections cannot be optimized further. The only improvement (which is numerically important) is to distinguish the two cases: |x_2-x_1| >= |y_2-y_1| and |x_2-x1| < |y_2-y1| so that the quantity k is always between -1 and 1 (in your computation you can get very high numerical errors if |x_2-x_1| is very small). You can swap x-s and y-s to reduce one case to the other.
You could also implement a preliminary check: if both endpoints are internal to the circle there are no intersection. By computing the squared distance from the points to the center of the circle this becomes a simple formula which does not use the square root function. The other check: "whether the line is outside the circle" is already implemented in your code and corresponds to delta < 0. If you have a lot of small segments these two check should give a shortcut answer (no intersection) in most cases.
I'm currently trying to simulate many particles in a box bouncing around.
I've taken into account #kalhartt's suggestions and this is the improved code to initialize the particles inside the box:
import numpy as np
import scipy.spatial.distance as d
import matplotlib.pyplot as plt
# 2D container parameters
# Actual container is 50x50 but chose 49x49 to account for particle radius.
limit_x = 20
limit_y = 20
#Number and radius of particles
number_of_particles = 350
radius = 1
def force_init(n):
# equivalent to np.array(list(range(number_of_particles)))
count = np.linspace(0, number_of_particles-1, number_of_particles)
x = (count + 2) % (limit_x-1) + radius
y = (count + 2) / (limit_x-1) + radius
return np.column_stack((x, y))
position = force_init(number_of_particles)
velocity = np.random.randn(number_of_particles, 2)
The initialized positions look like this:
Once I have the particles initialized I'd like to update them at each time-step. The code for updating follows the previous code immediately and is as follows:
# Updating
while np.amax(abs(velocity)) > 0.01:
# Assume that velocity slowly dying out
position += velocity
velocity *= 0.995
#Get pair-wise distance matrix
pair_dist = d.cdist(position, position)
pair_d = pair_dist<=4
#If pdist [i,j] is <=4 then the particles are too close and so treat as collision
for i in range(len(pair_d)):
for j in range(i):
# Only looking at upper triangular matrix (not inc. diagonal)
if pair_d[i,j] ==True:
# If two particles are too close then swap velocities
# It's a bad hack but it'll work for now.
vel_1 = velocity[j][:]
velocity[j] = velocity[i][:]*0.9
velocity[i] = vel_1*0.9
# Masks for particles beyond the boundary
xmax = position[:, 0] > limit_x
xmin = position[:, 0] < 0
ymax = position[:, 1] > limit_y
ymin = position[:, 1] < 0
# flip velocity and assume that it looses 10% of energy
velocity[xmax | xmin, 0] *= -0.9
velocity[ymax | ymin, 1] *= -0.9
# Force maximum positions of being +/- 2*radius from edge
position[xmax, 0] = limit_x-2*radius
position[xmin, 0] = 2*radius
position[ymax, 0] = limit_y-2*radius
position[ymin, 0] = 2*radius
After updating it and letting it run to completion I get this result:
This is infinitely better than before but there are still patches that are too close together - such as:
Too close together. I think the updating works... and thanks to #kalhartt my code is wayyyy better and faster (and I learnt some things about numpy... props #kalhartt) but I still don't know where it's screwing up. I've tried changing the order of the actual updates with the pair-wise distance going last or the position +=velocity going last but to no avail. I added the *0.9 to make the entire thing die down faster and I tried it with 4 to make sure that 2*radius (=2) wasn't too tight a criteria... but nothing seems to work.
Any and all help would be appreciated.
There are just two typos standing in your way. First for i in range(len(positions)/2): only iterates over half of your particles. This is why half the particles stay in the x bounds (if you watch for large iterations its more clear). Second, the second y condition should be a minimum (I assume) position[i][1] < 0. The following block works to bound the particles for me (I didn't test with the collision code so there could be problems there).
for i in range(len(position)):
if position[i][0] > limit_x or position[i][0] < 0:
velocity[i][0] = -velocity[i][0]
if position[i][1] > limit_y or position[i][1] < 0:
velocity[i][1] = -velocity[i][1]
As an aside, try to leverage numpy to eliminate loops when possible. It is faster, more efficient, and in my opinion more readable. For example force_init would look like this:
def force_init(n):
# equivalent to np.array(list(range(number_of_particles)))
count = np.linspace(0, number_of_particles-1, number_of_particles)
x = (count * 2) % limit_x + radius
y = (count * 2) / limit_x + radius
return np.column_stack((x, y))
And your boundary conditions would look like this:
while np.amax(abs(velocity)) > 0.01:
position += velocity
velocity *= 0.995
# Masks for particles beyond the boundary
xmax = position[:, 0] > limit_x
xmin = position[:, 0] < 0
ymax = position[:, 1] > limit_y
ymin = position[:, 1] < 0
# flip velocity
velocity[xmax | xmin, 0] *= -1
velocity[ymax | ymin, 1] *= -1
Final note, it is probably a good idea to hard clip position to the bounding box with something like position[xmax, 0] = limit_x; position[xmin, 0] = 0. There may be cases where velocity is small and a particle outside the box will be reflected but not make it inside in the next iteration. So it will just sit outside the box being reflected forever.
EDIT: Collision
The collision detection is a much harder problem, but lets see what we can do. Lets take a look at your current implementation.
pair_dist = d.cdist(position, position)
pair_d = pair_dist<=4
for i in range(len(pair_d)):
for j in range(i):
# Only looking at upper triangular matrix (not inc. diagonal)
if pair_d[i,j] ==True:
# If two particles are too close then swap velocities
# It's a bad hack but it'll work for now.
vel_1 = velocity[j][:]
velocity[j] = velocity[i][:]*0.9
velocity[i] = vel_1*0.9
Overall a very good approach, cdist will efficiently calculate the distance
between sets of points and you find which points collide with pair_d = pair_dist<=4.
The nested for loops are the first problem. We need to iterate over True values of pair_d where j > i. First your code actually iterate over the lower triangular region by using for j in range(i) so that j < i, not particularly important in this instance as long since i,j pairs are not repeated. However Numpy has two builtins we can use instead, np.triu lets us set all values below a diagonal to 0 and np.nonzero will give us the indices of non-zero elements in a matrix. So this:
pair_dist = d.cdist(position, position)
pair_d = pair_dist<=4
for i in range(len(pair_d)):
for j in range(i+1, len(pair_d)):
if pair_d[i, j]:
...
is equivalent to
pair_dist = d.cdist(position, position)
pair_d = np.triu(pair_dist<=4, k=1) # k=1 to exclude the diagonal
for i, j in zip(*np.nonzero(pair_d)):
...
The second problem (as you noted) is that the velocities are just switched and scaled instead of reflected. What we really want to do is negate and scale the component of each particles velocity along the axis that connects them. Note that to do this we will need the vector connecting them position[j] - position[i] and the length of the vector connecting them (which we already calculated). So unfortunately part of the cdist calculation gets repeated. Lets quit using cdist and do it ourselves instead. The goal here is to make two arrays diff and norm where diff[i][j] is a vector pointing from particle i to j (so diff is a 3D array) and norm[i][j] is the distance between particles i and j. We can do this with numpy like so:
nop = number_of_particles
# Give pos a 3rd index so we can use np.repeat below
# equivalent to `pos3d = np.array([ position ])
pos3d = position.reshape(1, nop, 2)
# 3D arras with a repeated index so we can form combinations
# diff_i[i][j] = position[i] (for all j)
# diff_j[i][j] = position[j] (for all i)
diff_i = np.repeat(pos3d, nop, axis=1).reshape(nop, nop, 2)
diff_j = np.repeat(pos3d, nop, axis=0)
# diff[i][j] = vector pointing from position[i] to position[j]
diff = diff_j - diff_i
# norm[i][j] = sqrt( diff[i][j]**2 )
norm = np.linalg.norm(diff, axis=2)
# check for collisions and take the region above the diagonal
collided = np.triu(norm < radius, k=1)
for i, j in zip(*np.nonzero(collided)):
# unit vector from i to j
unit = diff[i][j] / norm[i][j]
# flip velocity
velocity[i] -= 1.9 * np.dot(unit, velocity[i]) * unit
velocity[j] -= 1.9 * np.dot(unit, velocity[j]) * unit
# push particle j to be radius units from i
# This isn't particularly effective when 3+ points are close together
position[j] += (radius - norm[i][j]) * unit
...
Since this post is long enough already, here is a gist of the code with my modifications.