All Questions
Tagged with euclidean-distance python
355
questions
790
votes
26
answers
1.4m
views
How can the Euclidean distance be calculated with NumPy?
I have two points in 3D space:
a = (ax, ay, az)
b = (bx, by, bz)
I want to calculate the distance between them:
dist = sqrt((ax-bx)^2 + (ay-by)^2 + (az-bz)^2)
How do I do this with NumPy? I have:
...
- 125k
46
votes
9
answers
62k
views
Minimum Euclidean distance between points in two different Numpy arrays, not within
I have two arrays of x-y coordinates, and I would like to find the minimum Euclidean distance between each point in one array with all the points in the other array. The arrays are not necessarily the ...
- 3,243
35
votes
5
answers
109k
views
python numpy euclidean distance calculation between matrices of row vectors
I am new to Numpy and I would like to ask you how to calculate euclidean distance between points stored in a vector.
Let's assume that we have a numpy.array each row is a vector and a single numpy....
- 2,264
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
27
votes
2
answers
38k
views
Is "norm" equivalent to "Euclidean distance"?
I am not sure whether "norm" and "Euclidean distance" mean the same thing. Please could you help me with this distinction.
I have an n by m array a, where m > 3. I want to calculate the Eculidean ...
- 2,702
22
votes
6
answers
38k
views
Find the shortest distance between a point and line segments (not line)
I have set of line segments (not lines), (A1, B1), (A2, B2), (A3, B3), where A,B are ending points of the line segment. Each A and B has (x,y) coordinates.
QUESTION:
I need to know the shortest ...
- 977
21
votes
7
answers
36k
views
Multidimensional Euclidean Distance in Python
I want to calculate the Euclidean distance in multiple dimensions (24 dimensions) between 2 arrays. I'm using numpy-Scipy.
Here is my code:
import numpy,scipy;
A=numpy.array([116.629, 7192.6, 4535....
- 4,733
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
15
votes
3
answers
2k
views
Efficient calculation of euclidean distance
I have a MxN array, where M is the number of observations and N is the dimensionality of each vector. From this array of vectors, I need to calculate the mean and minimum euclidean distance between ...
- 329
14
votes
6
answers
23k
views
Efficient and precise calculation of the euclidean distance
Following some online research (1, 2, numpy, scipy, scikit, math), I have found several ways for calculating the Euclidean Distance in Python:
# 1
numpy.linalg.norm(a-b)
# 2
distance.euclidean(...
user6167676
11
votes
2
answers
18k
views
Find euclidean distance from a point to rows in pandas dataframe
i have a dataframe
id lat long
1 12.654 15.50
2 14.364 25.51
3 17.636 32.53
5 12.334 25.84
9 32.224 15.74
I want to find the euclidean distance of these ...
- 7,562
10
votes
1
answer
13k
views
Compute Euclidean distance between rows of two pandas dataframes
I have two pandas dataframes d1 and d2 that look like these:
d1 looks like:
output value1 value2 value2
1 100 103 87
1 201 97.5 88.9
1 ...
- 1,547
10
votes
5
answers
11k
views
Compute L2 distance with numpy using matrix multiplication
I'm trying to do it by myself the assignments from Stanford CS231n 2017 CNN course.
I'm trying to compute L2 distance using only matrix multiplication and sum broadcasting with Numpy. L2 distance is:
...
- 45.4k
9
votes
7
answers
10k
views
Identifying points with the smallest Euclidean distance
I have a collection of n dimensional points and I want to find which 2 are the closest. The best I could come up for 2 dimensions is:
from numpy import *
myArr = array( [[1, 2],
[3, 4]...
- 2,600
9
votes
2
answers
7k
views
Minimize total distance between two sets of points in Python
Given two sets of points in n-dimensional space, how can one map points from one set to the other, such that each point is only used once and the total euclidean distance between the pairs of points ...
- 4,920
9
votes
4
answers
10k
views
Euclidean distance with weights
I am currently using SciPy to calculate the euclidean distance
dis = scipy.spatial.distance.euclidean(A,B)
where; A, B are 5-dimension bit vectors. It works fine now, but if I add weights for each ...
- 5,963
8
votes
3
answers
14k
views
Memory Efficient L2 norm using Python broadcasting
I am trying to implement a way to cluster points in a test dataset based on their similarity to a sample dataset, using Euclidean distance. The test dataset has 500 points, each point is a N ...
- 133
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
8
votes
1
answer
4k
views
einsum and distance calculations
I have searched for a solution to determine distances using einsum for numpy arrays that are not equal in their number of rows, but equal in columns. I have tried various combinations but the only ...
user1121588
8
votes
2
answers
16k
views
Calculating pairwise Euclidean distance between all the rows of a dataframe
How can I calculate the Euclidean distance between all the rows of a dataframe? I am trying this code, but it is not working:
zero_data = data
distance = lambda column1, column2: pd.np.linalg.norm(...
- 133
8
votes
2
answers
3k
views
Find minimum distances between groups of points in 2D (fast and not too memory consuming)
I have two sets of points in 2D A and B and I need to find the minimum distance for each point in A, to a point in B. So far I've been using SciPy's cdist with the code below
import numpy as np
from ...
- 41.7k
8
votes
1
answer
5k
views
Caffe Iteration loss versus Train Net loss
I'm using caffe to train a CNN with a Euclidean loss layer at the bottom, and my solver.prototxt file configured to display every 100 iterations. I see something like this,
Iteration 4400, loss = 0
...
- 499
8
votes
1
answer
2k
views
Clustering in python(scipy) with space and time variables
The format of my dataset:
[x-coordinate, y-coordinate, hour] with hour an integer value from 0 to 23.
My question now is how can I cluster this data when I need an euclidean distance metric for the ...
- 83
7
votes
2
answers
11k
views
Pycuda Blocks and Grids to work with big datas
I need help to know the size of my blocks and grids.
I'm building a python app to perform metric calculations based on scipy as: Euclidean distance, Manhattan, Pearson, Cosine, joined other.
The ...
7
votes
1
answer
6k
views
Calculating euclidean distance between consecutive points of an array with numpy
I have an array which describes a polyline (ordered list of connected straight segments) as follows:
points = ((0,0),
(1,2),
(3,4),
(6,5),
(10,3),
(...
- 27.2k
7
votes
1
answer
802
views
Euclidean distance, different results between Scipy, pure Python, and Java
I was playing around with different implementations of the Euclidean distance metric and I noticed that I get different results for Scipy, pure Python, and Java.
Here's how I compute the distance ...
- 129
6
votes
4
answers
4k
views
Euclidian Distance Python Implementation
I am playing with the following code from programming collective intelligence, this is a function from the book that calculated eclidian distance between two movie critics.
This function sums the ...
- 49.2k
6
votes
1
answer
4k
views
Calculate the euclidian distance between an array of points to a line segment in Python without for loop
I'm looking for a function to compute the euclidian distance between a numpy array of points with two coordinates (x, y) and a line segment. My goal is to have a result in under 0.01 sec for a line ...
- 152
6
votes
1
answer
6k
views
Why cdist from scipy.spatial.distance is so fast?
I wanted to create a distance proximity matrix for 10060 records/ points, where each record/point has 23 attributes using euclidean distance as metric. I wrote code using nested for loops to calculate ...
- 400
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
6
votes
4
answers
2k
views
Sum of distances from a point to all other points
I have two lists
available_points = [[2,3], [4,5], [1,2], [6,8], [5,9], [51,35]]
and
solution = [[3,5], [2,1]]
I'm trying to pop a point in available_points and append it to solution for which ...
- 143
5
votes
1
answer
9k
views
Calculating Euclidian Norm in Pytorch.. Trouble understanding an implementation
I've seen another StackOverflow thread talking about the various implementations for calculating the Euclidian norm and I'm having trouble seeing why/how a particular implementation works.
The code ...
- 572
5
votes
2
answers
4k
views
Calculate Euclidean Distance within points in numpy array
I have 3D array as
A = [[x1 y1 z1]
[x2 y2 z2]
[x3 y3 z3]]
I have to find euclidean distance between each points so that I'll get output with only 3 distance between (row0,row1),(row1,...
- 425
5
votes
4
answers
589
views
Vectorize mask of squared euclidean distance in Python
I'm running code to generate a mask of locations in B closer than some distance D to locations in A.
N = [[0 for j in range(length_B)] for i in range(length_A)]
dSquared = D*D
for i in range(...
- 489
5
votes
2
answers
4k
views
How to implement callable distance metric in scikit-learn?
I'm using the clustering module in python's scikit learn, and I'd like to use a Normalized Euclidean Distance. There is no built-in distance for this (that i know of) Here's a list.
So, I want to ...
- 9,583
4
votes
3
answers
17k
views
How to calculate euclidean distance between pair of rows of a numpy array
I have a numpy array like:
import numpy as np
a = np.array([[1,0,1,0],
[1,1,0,0],
[1,0,1,0],
[0,0,1,1]])
I would like to calculate euclidian distance between ...
- 529
4
votes
8
answers
4k
views
Python: reduce on tuple of tuples
I am trying to compute in Python the length of the path from a point A to a point B going through a list of intermediary points. I know how to do it but I do want to use the reduce Built-in function.
...
- 3,734
4
votes
3
answers
16k
views
In Numpy, find Euclidean distance between each pair from two arrays
I have two arrays of 2D coordinate points (x,y)
a = [ (x1,y1), (x2,y2), ... (xN,yN) ]
b = [ (X1,Y1), (X2,Y2), ... (XN,YN) ]
How can I find the Euclidean distances between each aligned pairs (xi,yi) ...
- 11.9k
4
votes
2
answers
4k
views
calculating average distance of nearest neighbours in pandas dataframe
I have a set of objects and their positions over time. I would like to get the distance between each car and their nearest neighbour, and calculate an average of this for each time point. An example ...
- 503
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
4
votes
2
answers
1k
views
Euclidean Minimal Spanning Tree and Delaunay Triangulation
I want to calculate the minimal spanning tree based on the euclidean distance between a set of points on a 2D-plane. My current code stores all the edges, and then performs Prim's algorithm in order ...
- 625
4
votes
2
answers
5k
views
Calculate the euclidean distance in scipy csr matrix
I need to calculate the Euclidean Distance between all points that is stored in csr sparse matrix and some lists of points. It would be easier for me to convert the csr to a dense one, but I couldn't ...
- 85
4
votes
4
answers
4k
views
How to apply euclidean distance function to a groupby object in pandas dataframe?
I have a set of objects and their positions over time. I would like to get the average distance between objects for each time point. An example dataframe is as follows:
time = [0, 0, 0, 1, 1, 2, 2]
x ...
- 503
4
votes
1
answer
5k
views
Vectorized implementation for Euclidean distance [duplicate]
I am trying to compute a vectorized implementation of Euclidean distance(between each element in X and Y using inner product). The data as follows:
X = np.random.uniform(low=0, high=1, size=(10000, 5)...
- 857
4
votes
1
answer
3k
views
Calculating Euclidean Distance With Given Lists
def distance(alist, blist):
sum_of = 0
for x in alist:
for y in blist:
ans = (x - y)**2
sum_of += ans
return (sum_of)**(1/2)
print(distance([1, 1, 3], [2, 2,...
- 43
4
votes
1
answer
3k
views
How to find the closest corresponding vectors between two coordinate matrices?
I have the following problem in Python I need to solve:
Given two coordinate matrices (NumPy ndarrays) A and B, find for all coordinate vectors a in A the corresponding coordinate vectors b in B, ...
- 4,313
4
votes
1
answer
3k
views
Find distance to nearest neighbor in 2d array
I have a 2D array and I want to find for each (x, y) point the distance to its nearest neighbor as fast as possible.
I can do this using scipy.spatial.distance.cdist:
import numpy as np
from scipy....
- 41.7k
4
votes
2
answers
4k
views
Error - Calculating Euclidean distance for PCA in python
I am trying to implement face recognition by Principal Component Analysis (PCA) using python. I am following the steps in this tutorial: http://onionesquereality.wordpress.com/2009/02/11/face-...
- 1,559
4
votes
2
answers
5k
views
Can we cluster Multivariate Time Series dataset in Python
I have a dataset with many financial signal values for different stocks at different times.For example
StockName Date Signal1 Signal2
----------------------------------
Stock1 1/1/20 a ...
- 125
4
votes
2
answers
2k
views
Pass coordinates of 2D Numpy pixel array to distance function
I'm working on an image processing program with OpenCV and numpy. For most pixel operations, I'm able to avoid nested for loops by using np.vectorize(), but one of the functions I need to implement ...
- 12.2k