I have two vectors A & B of size 250x4. The first column in each vector has the X values and the second column has the Y values. I want to calculate the euclidean distance between each the X & Y of each row in the two vectors and save the result in a new vector C of size 250x1 which holds the result of the euclidean distance. For example, if the first row in A is A1x, A1y, A1n, A1m and the first row in B is B1x, B1y, B1n, B1m so I want to get the eucledian distance which will be [(A1x-B1x)^2 + (A1y-B1y)^2]^0.5 and the result will be saved in C1 and same will be done for the rest of the 250 rows. So if anyone could please advise how to do this in Matlab.
Like this:
%// First extract on x-y data from A and B
Axy = A(:,1:2);
Bxy = B(:,1:2);
%// Find all euclidean distances (row-wise)
C1 = sqrt(sum((Axy-Bxy).^2,2));
plus it handles higher dimension too
use pdist2:
C1=diag(pdist2(A(:,1:2),B(:,1:2)));
Actually, pdist2 will give you a 250x250 matrix, because it calculate all the distances. You need only the main diagonal, so calling diag on the result (as in the code above) will produce the wanted result.
Related
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 would like to calculate a matrix containing the Euclidean distances between points of type A and type B. Of course, I only need to calculate one half of the matrix, since the other half contains duplicate data.
What is the most efficient way to do that?
When I'm done with that, I want to find the points of type B that are closest to one point of type A. How do I then find the coordinates the closest, second closest, third closest and so on points of type B?
Given a matrix A of size [N,3] and a matrix B of size [M,3], you can use the pdist2 function to get a matrix of size [M,N] containing all the pairwise distances.
If you want to order the points from B by their distance to the rth point in A then you can sort the rth row of the pairwise distance matrix.
% generate some example data
N = 4
M = 7
A = randn(N,3)
B = randn(M,3)
% compute N x M matrix containing pairwise distances
D = pdist2(A, B, 'euclidean')
% sort points in B by their distance to the rth point in A
r = 3
[~, b_idx] = sort(D(r,:))
Then b_idx will contain the indices of the points in B sorted by their distance to the rth point in A. So the actual points in B ordered by b_idx can be obtained with B(b_idx,:), which has the same size as B.
If you want to do this for all r you could use
[~, B_idx] = sort(D, 1)
to sort all the rows of D at the same time. Then the rth row of B_idx will contain b_idx.
If your only objective is to find the closest k points in B for each point in A (for some positive integer k which is less than M), then we would not generally want to compute all the pairwise distances. This is because space-partitioning data structures like K-D-trees can be used to improve the efficiency of searching without explicitly computing all the pairwise distances.
Matlab provides a knnsearch function that uses K-D-trees for this exact purpose. For example, if we do
k = 2
B_kidx = knnsearch(B, A, 'K', k)
then B_kidx will be the first two columns of B_idx, i.e. for each point in A the indices of the nearest two points in B. Also, note that this is only going to be more efficient than the pdist2 method when k is relatively small. If k is too large then knnsearch will automatically use the explicit method from before instead of the K-D-tree approach.
I have a matrix that I generate from a CSV file as follows:
X = xlsread('filename.csv');
I am looping through the matrix based on the number of records and I need to find the Euclidean distance for each of the rows of this matrix :
for i = 1:length(X)
j = X(:, [2:5])
end
The resulting matrix is of 150 X 4. What would be the best way to calculate the Euclidean distance of each row (with 4 columns as the data points) with every row and getting an average of the same?
In order to find the Euclidean distance between any pair of rows, you could use the function pdist.
X = randn(6, 4);
D = pdist(X,'euclidean');
res=mean(D);
The average is stored in res.
I am trying to calculate the distance between nearest neighbours within a nx2 matrix like the one shown below
point_coordinates =
11.4179 103.1400
16.7710 10.6691
16.6068 119.7024
25.1379 74.3382
30.3651 23.2635
31.7231 105.9109
31.8653 36.9388
%for loop going from the top of the vector column to the bottom
for counter = 1:size(point_coordinates,1)
%current point defined selected
current_point = point_coordinates(counter,:);
%math to calculate distance between the current point and all the points
distance_search= point_coordinates-repmat(current_point,[size(point_coordinates,1) 1]);
dist_from_current_point = sqrt(distance_search(:,1).^2+distance_search(:,2).^2);
%line to omit self subtraction that gives zero
dist_from_current_point (dist_from_current_point <= 0)=[];
%gives the shortest distance calculated for a certain vector and current_point
nearest_dist=min(dist_from_current_point);
end
%final line to plot the u,v vectors and the corresponding nearest neighbour
%distances
matnndist = [point_coordinates nearest_dist]
I am not sure how to structure the 'for' loop/nearest_neighbour line to be able to get the nearest neighbour distance for each u,v vector.
I would like to have, for example ;
for the first vector you could have the coordinates and the corresponding shortest distance, for the second vector another its shortest distance, and this goes on till n
Hope someone can help.
Thanks
I understand you want to obtain the minimum distance between different points.
You can compute the distance for each pair of points with bsxfun; remove self-distances; minimize. It's more computationally efficient to work with squared distances, and take the square root only at the end.
n = size(point_coordinates,1);
dist = bsxfun(#minus, point_coordinates(:,1), point_coordinates(:,1).').^2 + ...
bsxfun(#minus, point_coordinates(:,2), point_coordinates(:,2).').^2;
dist(1:n+1:end) = inf; %// remove self-distances
min_dist = sqrt(min(dist(:)));
Alternatively, you could use pdist. This avoids computing each distance twice, and also avoids self-distances:
dist = pdist(point_coordinates);
min_dist = min(dist(:));
If I can suggest a built-in function, use knnsearch from the statistics toolbox. What you are essentially doing is a K-Nearest Neighbour (KNN) algorithm, but you are ignoring self-distances. The way you would call knnsearch is in the following way:
[idx,d] = knnsearch(X, Y, 'k', k);
In simple terms, the KNN algorithm returns the k closest points to your data set given a query point. Usually, the Euclidean distance is the distance metric that is used. For MATLAB's knnsearch, X is a 2D array that consists of your dataset where each row is an observation and each column is a variable. Y would be the query points. Y is also a 2D array where each row is a query point and you need to have the same number of columns as X. We would also specify the flag 'k' to denote how many closest points you want returned. By default, k = 1.
As such, idx would be a N x K matrix, where N is the total number of query points (number of rows of Y) and K would be those k closest points to the dataset for each query point we have. idx indicates the particular points in your dataset that were closest to each query. d is also a N x K matrix that returns the smallest distances for these corresponding closest points.
As such, what you want to do is find the closest point for your dataset to each of the other points, ignoring self-distances. Therefore, you would set both X and Y to be the same, and set k = 2, discarding the first column of both outputs to get the result you're looking for.
Therefore:
[idx,d] = knnsearch(point_coordinates, point_coordinates, 'k', 2)
idx = idx(:,2);
d = d(:,2);
We thus get for idx and d:
>> idx
idx =
3
5
1
1
7
3
5
>> d
d =
17.3562
18.5316
17.3562
31.9027
13.7573
20.4624
13.7573
As such, this tells us that for the first point in your data set, it matched with point #3 the best. This matched with the closest distance of 17.3562. For the second point in your data set, it matched with point #5 the best with the closest distance being 18.5316. You can continue on with the rest of the results in a similar pattern.
If you don't have access to the statistics toolbox, consider reading my StackOverflow post on how I compute KNN from first principles.
Finding K-nearest neighbors and its implementation
In fact, it is very similar to Luis Mendo's post to you earlier.
Good luck!
Say we have a matrix m x n where the number of rows of the matrix is very big. If we assume each row is a vector, then how could one find the maximum/minimum distance between vectors in this matrix?
My suggestion would be to use pdist. This computes pairs of Euclidean distances between unique combinations of observations like #seb has suggested, but this is already built into MATLAB. Your matrix is already formatted nicely for pdist where each row is an observation and each column is a variable.
Once you do apply pdist, apply squareform so that you can display the distance between pairwise entries in a more pleasant matrix form. The (i,j) entry for each value in this matrix tells you the distance between the ith and jth row. Also note that this matrix will be symmetric and the distances along the diagonal will inevitably equal to 0, as any vector's distance to itself must be zero. If your minimum distance between two different vectors were zero, if we were to search this matrix, then it may possibly report a self-distance instead of the actual distance between two different vectors. As such, in this matrix, you should set the diagonals of this matrix to NaN to avoid outputting these.
As such, assuming your matrix is A, all you have to do is this:
distValues = pdist(A); %// Compute pairwise distances
minDist = min(distValues); %// Find minimum distance
maxDist = max(distValues); %// Find maximum distance
distMatrix = squareform(distValues); %// Prettify
distMatrix(logical(eye(size(distMatrix)))) = NaN; %// Ignore self-distances
[minI,minJ] = find(distMatrix == minDist, 1); %// Find the two vectors with min. distance
[maxI,maxJ] = find(distMatrix == maxDist, 1); %// Find the two vectors with max. distance
minI, minJ, maxI, maxJ will return the two rows of A that produced the smallest distance and the largest distance respectively. Note that with the find statement, I have made the second parameter 1 so that it only returns one pair of vectors that have this minimum / maximum distance between each other. However, if you omit this parameter, then it will return all possible pairs of rows that share this same distance, but you will get duplicate entries as the squareform is symmetric. If you want to escape the duplication, set either the upper triangular half, or lower triangular half of your squareform matrix to NaN to tell MATLAB to skip searching in these duplicated areas. You can use MATLAB's tril or triu commands to do that. Take note that either of these methods by default will include the diagonal of the matrix and so there won't be any extra work here. As such, try something like:
distValues = pdist(A); %// Compute pairwise distances
minDist = min(distValues); %// Find minimum distance
maxDist = max(distValues); %// Find maximum distance
distMatrix = squareform(distValues); %// Prettify
distMatrix(triu(true(size(distMatrix)))) = NaN; %// To avoid searching for duplicates
[minI,minJ] = find(distMatrix == minDist); %// Find pairs of vectors with min. distance
[maxI,maxJ] = find(distMatrix == maxDist); %// Find pairs of vectors with max. distance
Judging from your application, you just want to find one such occurrence only, so let's leave it at that, but I'll put that here for you in case you need it.
You mean the max/min distance between any 2 rows? If so, you can try that:
numRows = 6;
A = randn(numRows, 100); %// Example of input matrix
%// Compute distances between each combination of 2 rows
T = nchoosek(1:numRows,2); %// pairs of indexes for all combinations of 2 rows
for k=1:length(T)
d(k) = norm(A(T(k,1),:)-A(T(k,2),:));
end
%// Find min/max distance
[~, minIndex] = min(d);
[~, maxIndex] = max(d);
T(minIndex,:) %// Displays indexes of the 2 rows with minimum distance
T(maxIndex,:) %// Displays indexes of the 2 rows with maximum distance
Which of the following statements will find the minimum difference between any pair of elements (a,b) where a is from the vector A and b is from the vector B.
A. [X,Y] = meshgrid(A,B);
min(abs(X-Y))
B. [X,Y] = meshgrid(A,B);
min(abs(min(Y-X)))
C. min(abs(A-B))
D. [X,Y] = meshgrid(A,B);
min(min(abs(X-Y)))
Can someone please explain to me?
By saying "minimum difference between any pair of elements(a,b)", I presume you mean that you are treating A and B as sets and you intend to find the absolute difference in any possible pair of elements from these two sets. So in this case you should use your option D
[X,Y] = meshgrid(A,B);
min(min(abs(X-Y)))
Explanation: Meshgrid turns a pair of 1-D vectors into 2-D grids. This link can explain what I mean to say:
http://www.mathworks.com/help/matlab/ref/meshgrid.html?s_tid=gn_loc_drop
Hence (X-Y) will give the difference in all possible pairs (a,b) such that a belongs to A and b belongs to B. Note that this will be a 2-D matrix.
abs(X-Y) would return the absolute values of all elements in this matrix (the absolute difference in each pair).
To find the smallest element in this matrix you will have to use min(min(abs(X-Y))). This is because if Z is a matrix, min(Z) treats the columns of Z as vectors, returning a row vector containing the minimum element from each column. So a single min command will give a row vector with each element being the min of the elements of that column. Using min for a second time returns the min of this row vector. This would be the smallest element in the entire matrix.
This can help:
http://www.mathworks.com/help/matlab/ref/min.html?searchHighlight=min
Options C is correct if you treat A and B as vectors and not sets. In this case you won't be considering all possible pairs. You'll end up finding the minimum of (a-b) where a,b are both in the same position in their corresponding vectors (pair-wise difference).
D. [X,Y] = meshgrid(A,B);
min(min(abs(X-Y)))
meshgrid will generate two grids - X and Y - from the vectors, which are arranged so that X-Y will generate all combinations of ax-bx where ax is in a and bx is in b.
The rest of the expression just gets the minimum absolute value from the array resulting from the subtraction, which is the value you want.
CORRECT ANSWER IS D
Let m = size(A) and n = size(B)
You want to subtract each pair of (a,b) such that a is from vector A and b is from vector B.
meshgrid(A,B) creates two matrices X Y both of size nxm where X have rows sames have vector A while Yhas columns same as vector B .
Hence , Z = X-Y will give you a matrix with n*m values corresponding to the difference between each pair of values taken from A and B . Now all you have to do is to find the absolute minimum among all values of Z.
You can do that by
req_min = min(min(abs(z)))
The whole code is
[X Y ] = meshgrid(A,B);
Z= X-Y;
Z = abs(Z);
req_min = min(min(Z));
You could also use bsxfun instead of meshgrid:
min(min(abs(bsxfun(#minus, A(:), B(:).'))))
Or use pdist2:
min(min(pdist2(A(:),B(:))))