All Questions
Tagged with euclidean-distance performance
25
questions
32
votes
5
answers
61k
views
Efficiently Calculating a Euclidean Distance Matrix Using Numpy
I have a set of points in 2-dimensional space and need to calculate the distance from each point to each other point.
I have a relatively small number of points, maybe at most 100. But since I need ...
- 2,074
13
votes
2
answers
5k
views
Efficiently compute pairwise squared Euclidean distance in Matlab
Given two sets of d-dimensional points. How can I most efficiently compute the pairwise squared euclidean distance matrix in Matlab?
Notation:
Set one is given by a (numA,d)-matrix A and set two is ...
- 2,120
9
votes
6
answers
22k
views
Fastest way to calculate Euclidean distance in c
I need to calculate euclidean distance between two points in the fastest way possible.
In C.
My code is this and seems a little bit slow:
float distance(int py, int px, int jy, int jx){
return ...
- 103
4
votes
4
answers
1k
views
(Speed Challenge) Any faster method to calculate distance matrix between rows of two matrices, in terms of Euclidean distance?
First of all, this is NOT the problem of calculating Euclidean distance between two matrices.
Assuming I have two matrices x and y, e.g.,
set.seed(1)
x <- matrix(rnorm(15), ncol=5)
y <- matrix(...
- 89.5k
3
votes
2
answers
5k
views
Finding squared distances beteen n points to m points in numpy
I have 2 numpy arrays (say X and Y) which each row represents a point vector.
I would like to find the squared euclidean distances (will call this 'dist') between each point in X to each point in Y.
I ...
- 797
3
votes
1
answer
3k
views
Calculate euclidean distance in a faster way
I want to calculate the euclidean distances between rows of a dataframe with 30.000 observations. A simple way to do this is the dist function (e.g., dist(data)). However, since my dataframe is large, ...
- 2,077
2
votes
2
answers
344
views
How to improve processing time for euclidean distance calculation
I'm trying to calculate the weighted euclidean distance (squared) between twoo data frames that have the same number of columns (variables) and different number of rows (observations).
The ...
- 43
2
votes
1
answer
4k
views
Numpy operation for euclidean distance between multidimensional arrays
I have two numpy arrays. 'A' of size w,h,2 and 'B' with n,2.
In other words, A is a 2-dimensional array of 2D vectors while B is a 1D array of 2D vectors.
What i want as a result is an array of size w,...
- 843
2
votes
1
answer
200
views
For loop on two arrays of points
I have two arrays of points: list1 with list1.shape = [N, 3] and list2 with list2.shape = [M, 3]. Within N, M: the total number of point, (x, y, z) are 3 coordinates in 3D.
Now I want to check if ...
- 645
2
votes
0
answers
663
views
Minimum euclidean distances and corresponding indices between array and array columns
UPDATE
Just in case this is useful for anyone. As stated below, the Euclidean distance calculation and np.argmin accounted for almost all of the runtime. By rewriting the distance calculation with ...
- 21
1
vote
1
answer
4k
views
R: pairwise Euclidean distance between columns of two matrices
The following loop takes too lonng to run (2mins/iteration)
The tumor_signals is size 950000x422
The normal_signals is size 950000x772
Any ideas for how to speed it up?
for(i in 1:ncol(tumor_signals))...
- 11
1
vote
1
answer
1k
views
Calculating euclidean distances with Python runs too slow
I read to datasets from file into numpy arrays like this:
def read_data(filename):
data = np.empty(shape=[0, 65], dtype=int)
with open(filename) as f:
for line in f:
data = np....
- 662
1
vote
1
answer
77
views
High performance computation of mean 2D-Euclidian-distance
Let's say I have a position matrix P with dimensions 10x2, where the first column contains x values and second column the corresponding y values. I want the mean of the lengths of the positions. The ...
- 231
1
vote
1
answer
97
views
Apply PHP compare function to all elements in MySQL table
I'm building an algorithm that takes an euclidean coordinate—for example (-4, 2)—and searches through a large database table of other coordinates to find the closest coordinates (using euclidean ...
- 4,600
1
vote
3
answers
4k
views
Minimum, mean and maximum distance between points 3-D in Python
I have a list of x,y,z points. Using the formula to find the distance between two points in 3-D
import math
import numpy as np
point0 = x0, y0, z0
point1 = x1, y1, z1
dist = math.sqrt((x0-x1)**...
- 7,406
1
vote
0
answers
47
views
Why broadcasting is slower than for loop in this case?
I wrote a simple code to compare the performance of broadcasting vs for loop. The code is as below:
import numpy as np
D = 3072
num_train = 5000
test = np.random.rand(D)
X_train = np.random.rand(...
- 143
1
vote
1
answer
484
views
find the most efficient path (in term of shortest distance) between a set of 2D points
I have a set of 2D points stored in a dictionary and i need to find the most efficient path to sampling all points (red traingles) in term of the shortest distance from a start-end point (yellow ...
- 7,406
1
vote
0
answers
57
views
Find closest point to another point with NumPy and/or SciPy quickly [duplicate]
I want to know the fastest way in python to calculate the closest point in a list of points to my point. There is already this question, but it does not consider performance and there are the ...
- 10.3k
0
votes
2
answers
2k
views
Efficient euclidean distance calculation in python for millions of rows
I am trying to find the euclidean distance between elements of two data sets. Each has millions of elements. After calculating euclidean distance, I need the closest match. Given the number of ...
- 38
0
votes
3
answers
365
views
Finding nearest pixel in defined color space - quick implementation using numpy
I have been working on a task, where I implemented median cut for image quantization – representing the whole image by only limited set of pixels. I implemented the algorithm and now I am trying to ...
- 455
0
votes
2
answers
1k
views
Calculating Euclidean distance with a lot of pairs of points is too slow in Python
The main goal is to generate the customer similarity based on Euclidean distance, and find the 5 most similar customers for each customer.
I have 400,000 customers data, each of them has 40 attributes....
- 123
0
votes
2
answers
170
views
Python: Improve the speed of Euclidean distance calculation in a class
I have a class component that calculates the Euclidean distance between the last elements in arrays within 2 dictionaries. One dictionary contents the tracking trajectory of blobs (r), and the other ...
- 2,531
0
votes
1
answer
53
views
Speed-up special case euclidean distance in MATLAB
I want to optimize the following code example:
%Example definition
A = rand(40,10000,250);
B = rand(40,10000,250);
%Euclidean
seuc = sum((A-B).^2, 3);
Do you have any idea how to speed this up? Or ...
- 15
-1
votes
3
answers
2k
views
how to define a pow2 macro in C++
I want to have definition for pow2C as follows. But my compiler shows it (__tmpDouble__) is already defined. Please help me define it.
#ifndef pow2C
double __tmpDouble__;
#define pow2C(a) ((...
- 888
-2
votes
2
answers
226
views
How can I speed up my 3D Euclidean distance matrix code [closed]
I have created code to calculate the distance of all objects (tagID) from one another based on x, y, z coordinates (TX, TY, TZ) at each time step (Frame). While this code does work, it is too slow for ...
- 191