All Questions
Tagged with euclidean-distance matrix
61
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
21
votes
3
answers
42k
views
Distance calculation between rows in Pandas Dataframe using a distance matrix
I have the following Pandas DataFrame:
In [31]:
import pandas as pd
sample = pd.DataFrame({'Sym1': ['a','a','a','d'],'Sym2':['a','c','b','b'],'Sym3':['a','c','b','d'],'Sym4':['b','b','b','a']},index=[...
- 1,545
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
12
votes
3
answers
25k
views
OpenCV euclidean distance between two vectors
I want to calculate the euclidean distance between two vectors (or two Matrx rows, doesn't matter). Is there a good function for that in OpenCV?
- 1,306
10
votes
4
answers
56k
views
How to calculate Euclidian distance between two points defined by matrix containing x, y?
I am very lost in Euclidean distance calculation. I have found functions dist2{SpatialTools} or rdist{fields} to do this, but they doesn´t work as expected.
I suppose that one point has two ...
- 3,980
8
votes
3
answers
23k
views
Python alternative for calculating pairwise distance between two sets of 2d points [duplicate]
In Matlab there exists the pdist2 command. Given the matrix mx2 and the matrix nx2, each row of matrices represents a 2d point. Now I want to create a mxn matrix such that (i,j) element represents the ...
- 903
6
votes
2
answers
5k
views
R - How to get row & column subscripts of matched elements from a distance matrix
I have an integer vector vec1 and I am generating a distant matrix using dist function. I want to get the coordinates (row and column) of element of certain value in the distance matrix. Essentially I ...
- 533
6
votes
3
answers
5k
views
Numpy: find the euclidean distance between two 3-D arrays
Given, two 3-D arrays of dimensions (2,2,2):
A = [[[ 0, 0],
[92, 92]],
[[ 0, 92],
[ 0, 92]]]
B = [[[ 0, 0],
[92, 0]],
[[ 0, 92],
[92, 92]]]
How do you find the Euclidean ...
- 1,418
5
votes
2
answers
4k
views
Distance matrix from two separate data frames
I'd like to create a matrix which contains the euclidean distances of the rows from one data frame versus the rows from another. For example, say I have the following data frames:
a <- c(1,2,3,4,5)...
- 355
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
4
votes
2
answers
13k
views
Optimize performance for calculation of euclidean distance between two images
I implemented the k-nearest-neighbours algorithm in python to classify some randomly picked images from the mnist database. However I found my distance function to be quite slow: An analisys of 10 ...
- 3,112
3
votes
3
answers
12k
views
Euclidean Distance
I have two points
x1 = (a1,b1,c1,d1,e1); //5 dimensional point
x2 = (a2,b2,c2,d2,e2); //5 dimensional point
So is this right way to calculate the euclidean dist?
d = sqrt(sqr(a1-a2)+sqr(...
- 9,424
3
votes
1
answer
657
views
Finding euclidean difference between coordinates in numpy
I am trying to calculate the difference between coordinates using numpy using following code :
X = np.random.random((1000, 3))
# using broadcasting to calculate to find pairwise diffrence
diff = X....
- 1,573
3
votes
1
answer
947
views
How to use apply function to calculate the distance between two matrices
I'm trying to calculate the euclidean distance between two matrices. I have already achieved that using 2 for loops but trying to vectorize the calculation to speed up. I'm using pdist as a benchmark ...
- 59
3
votes
3
answers
3k
views
Calculating Euclidean distance of pairs of 3D points in matlab
I have an Nx3 array that contains N 3D points
a1 b1 c1
a2 b2 c2
....
aN bN cN
I want to calculate Euclidean distance in a NxN array that measures the Euclidean distance between each pair of 3D ...
- 33
3
votes
1
answer
784
views
Making an Euclidean Distance Matrix with Random Points in Python
I wrote a code that produces the desired number of points in a certain width and length range in the coordinate system. How can I calculate and tabulate the distance matrix of these points I produced ...
user16726326
2
votes
5
answers
3k
views
Calculate Euclidean distances between all rows in matrices A and B
I have two matrices, A and B, with N_a and N_b rows, respectively. I need to calculate the Euclidean distance between all pairwise combinations of an element in A (a) and another in B (b), such that ...
2
votes
2
answers
227
views
Compute the difference matrix between a matrix and another matrix in MATLAB
Given a matrix A in matlab with:
3 1
4 5
7 8
and another matrix B which could be referred to as some reference points (each row is reference point that is to be compared to each row of A),
1 ...
2
votes
2
answers
707
views
Remove Elements of matrix by eucledian distance
I have an mxn matrix with E nonzero elements. The coordinates of the nonzeros are already available in an Ex2 vector.
I'd like to check if the minimum Euclidean distance between every pair of ...
- 410
2
votes
1
answer
2k
views
Distance between two cells in a 2D matrix
I have a 2D matrix represented as a vector of values, an index representing the first cell and a pair of coordinate representing the second cell.
vector<double> matrix;
auto index = 10;
auto ...
- 10.4k
2
votes
1
answer
895
views
Calculate distance matrix for 3D points
I have the lists xA, yA, zA and the lists xB, yB, zB in Matlab. The contain the the x,y and z coordinates of points of type A and type B. There may be different numbers of type A and type B points.
I ...
- 288
2
votes
2
answers
1k
views
Adjacency Matrix from Numpy array using Euclidean Distance
Can someone help me please on how to generate a weighted adjacency matrix from a numpy array based on euclidean distance between all rows, i.e 0 and 1, 0 and 2,.. 1 and 2,...?
Given the following ...
- 55
2
votes
1
answer
1k
views
How to find Euclidean Norm of rows of a matrix with BLAS?
I have an matrix M that I need to calculate its Euclidean Norm of its rows. Is it possible to use the efficiency of BLAS library for such purpose?
- 13.4k
2
votes
4
answers
9k
views
How do I create a simliarity matrix in MATLAB?
I am working towards comparing multiple images. I have these image data as column vectors of a matrix called "images." I want to assess the similarity of images by first computing their Eucledian ...
- 1,174
2
votes
2
answers
82
views
How to compute the Euclidean distance between two complex matrix by vectorization?
X=[x_1,x_2,...,x_N] is a [S,N] complex matrix.
For example, S=3 and x_1=[1+2j,2+3j,3+4j]'.
D is the distance matrix of X, which means D(i,j) is the Euclidean distance between x_i and x_j.
my code:
D = ...
- 45
2
votes
1
answer
341
views
Calculate distance between every point of matrix with each other
I want to calculate the euclidean distance between every element of an n-channeled matrix to every other and then apply the function exp(-dist) to it. My matrix is MxN so the output must be (MxN)x(MxN)...
- 79
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
4
answers
126
views
Speed up of the calculation of the sum the point-wise difference in R
Suppose I have two datasets. The first one is:
t1<-sample(1:10,10,replace = T)
t2<-sample(1:10,10,replace = T)
t3<-sample(1:10,10,replace = T)
t4<-sample(11:20,10,replace = T)
t5<-...
- 121
1
vote
2
answers
138
views
Distances from a single point
I'm looking to generate a Euclidean distance matrix from one point [1,1]. This is what I have, however it doesn't work as intended:
a=rand(10,10);
a=sort(a); %sort example matrix it should be visible ...
- 2,059
1
vote
1
answer
2k
views
Euclidean distance between data sets in R using rdist from "fields" package
I am using rdist to compute Euclidean distances between a matrix and itself:
> m = matrix(c(1,1,1,2,2,2,3,4,3),nrow=3, ncol=3)
> m
[,1] [,2] [,3]
[1,] 1 2 3
[2,] 1 2 4
[3,...
- 6,902
1
vote
1
answer
1k
views
A Pure Pythonic Pairwise Euclidean distance of rows of a numpy ndarray
I have a matrix of size (n_classes, n_features) and i want to compute the pairwise euclidean distance of each pair of classes so the output would be a (n_classes, n_classes) matrix where each cell has ...
- 3,480
1
vote
2
answers
2k
views
MATLAB - efficient way of computing distances between points in a graph/network using the adjacency matrix and coordinates
I have the network representation in a 2D coordinate space. I have an adjacency matrix Adj(which is sparse) and a coordinate matrix with the x,y values of all the points/nodes/vertices in the graph ...
- 2,800
1
vote
2
answers
1k
views
How to implement in Python a function to compute the Euclidean distance between two arbitrary points on a torus
Given a 10x10 grid (2d-array) filled randomly with numbers, either 0, 1 or 2. How can I find the Euclidean distance (the l2-norm of the distance vector) between two given points considering periodic ...
- 115
1
vote
1
answer
530
views
Max Euclidean distance between two columns of a matrix in Matlab / Octave
I need to calculate for a program the maximal euclidian distance of vectors that are put together in a matrix A in Octave.
What I have so far:
for i=1:n
for k=i:n+1
C=A(:,i)-A(:,k);
...
user7245782
1
vote
1
answer
5k
views
Calculate Euclidean distance between RGB vectors in a large matrix
I have this RGB matrix of a set of different pixels. (N pixels => n rows, RGB => 3 columns). I have to calculate the minimum RGB distance between any two pixels from this matrix. I tried the loop ...
- 578
1
vote
3
answers
697
views
how to compute the original vector from a distance matrix?
I have a small question about vector and matrix.
Suppose a vector V = {v1, v2, ..., vn}. I generate a n-by-n distance matrix M defined as:
M_ij = | v_i - v_j | such that i,j belong to [1, n].
That ...
- 51
1
vote
1
answer
1k
views
euclidean distance matrix
I'd like to calculate Euclidean distance between two words. First of all, each phoneme was vectorised:
g = (0,1,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0)
a = (0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,1,...
- 37
1
vote
1
answer
255
views
retrieve points based in Euclidean distance and axis values R
I have a dataframe with 11 variables represented by letters a to k, plotted in a bidimentional scatterplot.
cor<-data.frame(X=c(0.36187115, -0.54755904, -0.82417308, -0.70806545, -0.77422866, -0....
- 165
1
vote
1
answer
568
views
Vector Accelerated Euclidean Distance in 3D
I am in need of performing a very common and simple matrix operation.
However I need it fast, really fast...
I am already considering a multi-threaded implementation, however for now I just want to ...
- 676
1
vote
0
answers
25
views
Issue with designing loop in R for calculating Euclidean Distance Matrix and Mod Value
My objective is to calculate the determinant of the Euclidean Distance between each index and store the determinant value in a matrix.
I have data as per the below format where columns B1, B2, ... B10 ...
- 95
1
vote
0
answers
79
views
Bypass conversion of entire dist to matrix (Filter dist object)
I have a very big data frame that looks like this:
> head(df)
X Y Z
0:600000000 193.722 175.733 0.0998975
0:600000001 192.895 176.727 0.0998975
0:600000002 193.828 ...
1
vote
1
answer
161
views
distance between lat and long using a matrix
This is my data in a matrix. It is lat and long. I want the distance between point 1 and 2, 2 and 3, 3 and 4, etc.
> mat<-as.matrix(b)
> mat
buoy.LON buoy.LAT
[1,] -...
- 11
1
vote
1
answer
105
views
How to manipulate matrix addition and multiplication for Euclidean distance computation?
I have the following:
A = [1 2 3; 4 5 6; 7 8 9];
B = [10 11 12; 13 14 15];
[N1, D1] = size(A);
[N2, D2] = size(B);
A_sq = sum(A.^2, 2);
B_sq = sum(B.^2, 2)';
D = A_sq(:,ones(1,N2)) + B_sq(ones(1,...
- 13
0
votes
2
answers
233
views
Eucledian distance matrix between two matrices
I have the following function that calculates the eucledian distance between all combinations of the vectors in Matrix A and Matrix B
def distance_matrix(A,B):
n=A.shape[1]
m=B.shape[1]
C=...
- 1,273
0
votes
1
answer
234
views
How to incorporate elevation into euclidean distance matrix in pandas?
I have the following dataframe in pandas:
import pandas as pd
df = pd.DataFrame({
"CityId": {
"0": 0,
"1": 1,
"2": 2,
"3": 3,
"4": 4
},
"X": {...
- 1,069
0
votes
1
answer
160
views
How to go from a vector to a similarity matrix?
I would like to reconstruct a similarity matrix between two vectors from a vector containing the similarity between each pair of elements in the two vectors. Does anyone know how I could do it?
To ...
- 277
0
votes
3
answers
2k
views
How to compute euclidean distance between all column vector pairs for a given matrix without using loops? (using only numpy) [duplicate]
As titled, I need to calculate the euclidean distance between all possible column vector pairs of a given matrix without using loops and using numpy only.
This produces the output I'm looking for (...
- 23
0
votes
1
answer
481
views
Is there a more efficient way to generate a distance matrix in numpy
I was wondering if there is a more straight forward, more efficient way of generating a distance matrix given the H x W of the matrix, and the starting index location.
For simplicity lets take a 3x3 ...
- 2,803
0
votes
2
answers
2k
views
Python Numpy efficient Polar euclidean distance
I have a list of n polar coordinates, and a distance function which takes in two coordinates.
I want to create an n x n matrix which contains the pairwise distances under my function. I realize I ...
- 577
0
votes
1
answer
1k
views
Is it possible to calculate Euclidean Distance between two varying length matrices?
I have started working on online signature data-set for verification purpose. I have two matrices containing digitized data of two signatures of varying length (the number of rows differ). e.g. one is ...