If K is greater than MX, PDIST2 returns an MX-by-MY distance matrix. If instead there is an efficient algorithm for what pdist2 does, you can research it and possibly write your own. Finding faster way to compute a matrix using MATLAB. Learn more about histogram comparison, image comparison, image segmentation, distance comparison, chi-square Image Processing Toolbox. squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. 5 seconds. Find the treasures in MATLAB Central and discover how the community can help you! Start Hunting!This MATLAB function performs k-means clustering to partition the observations of the n-by-p data matrix X into k clusters, and returns an n-by-1 vector (idx) containing cluster indices of each observation. squareform 을 사용하여 관측값 i 와 관측값 j 간의 거리를 쉽게 확인할 수 있습니다. pydist2 is a python library that provides a set of methods for calculating distances between observations. Jim Lehane on 4 Mar 2013. Create distance matrix from the result of pdist. – am304. Q&A for work. % Learning toolbox. Typically I use pdist2 like this D2 = pdist2(x,y). You can use the pdist2 MATLAB / Octave function to calculate pairwise distances between two sets of observations. 计算 X 中各对行向量的相互距离 (X是一个m-by-n的矩阵). Matlab taking too much time in computing mex function for large array. Learn the Essentials, Build Skills. Now, to Minkowski's distance, I want to add this part |-m (i)|^p. close all; % Close all figures (except those of imtool. 1. Learn more about matlab, pdist2, templateknn, fitcecoc, kfoldloss, crossval MATLAB I want a supervised learning on a distance metric. Load 7 more related questions Show fewer related questions Sorted by: Reset to default Know someone who can answer? Share a link. Copy. I am looking for an alternative to this. How to separately compute the Euclidean Distance in different dimension? 2. 'cosine') varies between 0 and 2. I never need the non-squared distances. I am trying to compute the gradient of a Gaussian Process when the training data set is given by N X D in MATLAB. My one-line implementation of both MATLAB's pdist and pdist2 functions which compute the univariate (pdist) or bivariate (pdist2) Euclidean distances between all pairs of input observations. m or remove that directory from your MATLAB path. ^2)); end The result is not. %. Learn more about pdist2 Statistics and Machine Learning ToolboxMar 8, 2021 at 17:55. which -all pdist will list all the pdist MATLAB files in your MATLAB path. I know the distance(lat1,lon1,lat2,lon2) command is the suitable for this but I want to use pdist2 command. A and B should have same no of columns. See the Wikipedia website. mahal() function. D = pdist2 (X,Y,@CalcDist) function D2=CalcDist (ZI,ZJ) % calculation of distance. . 5 single thread - foo3() (see below) - 18. My question is why applying the mean-function over the output of pdist2() in c. mat file if you need more help. index = 1:size (points, 1); In some places you use length (points). Create distance matrix from the result of pdist. Aug 2, 2016 at 13:34. Add the %#codegen compiler directive (or pragma) to the entry. For example, you can find the distance between observations 2 and 3. It uses the same variable names from my answer. GPU Arrays. 6 Why does complex Matlab gpuArray take twice as much memory than it should? 1 Different behaviour for pdist and pdist2. 2954 1. 詳細については、coder. Ask Question Asked 8 years, 5 months ago. Find more on Introduction to Installation and Licensing in Help Center and File Exchange. 2. I'm creating a volume from a very large number of points, created by accumulating a large number of point cloud objects in a box without overlapping any existing points. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. pdist and pdist2 can calculate the city block distance. sir is there any function to reduce row size. This is what I have so far:i am currently doing project on image processing in matlab,. You can import vector and raster data from a wide range of file formats and web map servers. I. %. For assessing the similarity between the histograms, 'cosine' is probably a more meaningful option than 'jaccard' . output D is a 2D matrix with ij entry giving distance between ith row of A and jth row of B. . The function you pass to pdist must take . One matrix has 2 sets of coordinates Copy. Use kmeans to create clusters in MATLAB® and use pdist2 in the generated code to assign new data to existing clusters. Maybe the differences are due to the incorrect use of the indexes i and j. 0. For latitude and longitude, usually the haversine method is used. de 2012 1 Enlazar Traducir Comentada: Ana Gonçalves el 16 de Feb. Learn more about matrix manipulation, distance, pdist2, matlab function, indexing, matrix, arrays MATLAB I was wondering if there is a built in matlab fucntion that calculates the distance between two arrays that don't have the. I know the distance(lat1,lon1,lat2,lon2) command is the suitable for this but I want to use pdist2 command. Categories AI, Data Science, and Statistics Statistics and Machine Learning Toolbox Cluster Analysis k-Means and k-Medoids Clustering. jackknife: Compute jackknife estimates of a parameter taking one or more given samples as parameters. . example [ idx , corepts ] = dbscan( ___ ) also returns a logical vector corepts that contains the core points identified by dbscan , using any of the input argument combinations in the. pdist. 9448. m to avoid conflict with matlab pdist2 function): For calculating the chi-square similarity. y = squareform (Z)The present code is a set of three Matlab functions that provide calculation of six metrics: - Euclidean distance, which vary in the range of [0 : Inf]. Create a matrix with three observations and two. Pass a single point for each of the first two arguments to pdist2 and the result will be a single distance. Neighbors are defined as points whose Voronoi polygons share one or more (finite) vertices. MY-by-N data matrix Y. pdist2 Pairwise distance between two sets of observations. Copy. 0670 0. The distance between each sample in A and each sample in B can be calculated as follows: First, define a matrix D of size 75x50, s. I used this MATLAB function to compute the distance matrix Dists = pdist2(fruchterman_graph(:,:),fruchterman_graph(:,:),'euclidean'); but it fails on large networks for both speed and finally memory. x = [x (1:end-1),x (2:end)]; as mentioned in the research paper I am following. Copy. . . Fully MATLAB compatible. if i go like this the matrix size increase, so I want to reduce minutiae information which is in row. We would like to show you a description here but the site won’t allow us. Mahalanobis distance in matlab: pdist2() vs. For assessing the similarity between the histograms, 'cosine' is probably a more meaningful option than 'jaccard' . Add the contribution due to squared exponential. MATLAB pdist2 WebIf observation i in X or observation j in Y contains NaN values, the function pdist2 returns NaN for the pairwise distance between i. 9448. Anyway, when you have a built-in function in Matlab, it will almost always outperform hardcoded ones so just go with pdist2. if this is the way, any efficient. For the future, try typing edit pdist2 (or whatever other function) in Matlab, in most cases, you will see the Matlab function, which you can then convert to python. [D,I] =. Learn more about for loop, matrix, matlab, pdist MATLAB Hi everybody, i have two 3D matrix A and B with different lengths. Then sqrt() requests the complete arrays again and. You need to rename or delete c: oolboxclassifypdist2. [D,I] =. 3. distances =. Use pdist2 to compute distance matrix of x and y. A and B should have same no of columns. X is a 50*3 matrix, Y is a 60*3 matrix. There are two main classes: pdist1 which calculates the pairwise distances between observations in one matrix and returns a distance matrix. g. pdist2 computes the distances between observations in two matrices and also returns a distance matrix. However i have some coordinates that i cannot remove from the matrix, but that i want pdist to ignore. . For example, you can find the distance between observations 2 and 3. Thread-Based Environment Run code in the background using MATLAB® backgroundPool or accelerate code with Parallel Computing Toolbox™ ThreadPool. Goncalves. 2. Show us your code so we can confirm it. Find a format that’s right for you. Z (2,3) ans = 0. I followed the documentation of MATLAB where in order to calculate Mahalanobis Distance, I have to use pdist2: "D = pdist2 (X,Y,'mahalanobis',C)" A1= [75 87 90]; A2= [99 88 100]; C = nancov (A1,A2); D. Learn more about custom distance function, pdist, pdist2, @distfun, divergence, kl divergenceI have a trajectory like this: We assume that each red star marker can broadcast its coordinate to the green circle markers which are located within a radius of 5 units from its own position. [D,I] = PDIST2. Use kmeans to create clusters in MATLAB® and use pdist2 in the generated code to assign new data to existing clusters. squareform returns a symmetric matrix where Z (i,j) corresponds to the pairwise distance between observations i and j. MATLAB Installation and Licensing Install Products Introduction to Installation and Licensing. Overview of OpenCascade Library [email protected] 摘要Abstract：对OpenCascade 库的功能及其实现做简要介绍。. Learn more about for loop, matrix, matlab, pdist MATLAB Hi everybody, i have two 3D matrix A and B with different lengths. I want the haversine distance to be more specific. D = pdist2 (X,Y,@CalcDist) function D2=CalcDist (ZI,ZJ) % calculation of distance. Let X be an MxP matrix representing m points in P-dimensional space and Y be an NxP matrix representing another set of points in the same space. mahal() function. tic d = sqrt (sum ( (p1-pn). 1. D = pdist2(x, y) < 10; D(1:size(D,1)+1:end) = 0; G = graph(D); C = conncomp(G); The connected components is vector that shows the cluster numbers. and pdist2() where I plotted all 3 of the closest pairs. I know the distance(lat1,lon1,lat2,lon2) command is the suitable for this but I want to use pdist2 command. Use kmeans to create clusters in MATLAB® and use pdist2 in the generated code to assign new data to existing clusters. Learn more about latitude, longitude, closest value, grid, dipole grid, great circle distance. 詳細については、coder. A custom distance function for pdist2 needs two input arguments and the first must specify just a single observation: axa = pdist2(latlon1(1, 1:2), latlon2(:, 1:2), @haversine); % repeat for other values in latlon1Documentation, examples, videos, and other support resources for MathWorks products including MATLAB and Simulink. Add the %#codegen compiler directive (or pragma) to the entry. Copy. My one-line implementation of both MATLAB's pdist and pdist2 functions which compute the univariate (pdist) or bivariate (pdist2) Euclidean distances between all pairs of input observations. Hi, i have two matrices A, of size mx2, and B, of size nx2. Just wanted to let you know that pdist2 in MATLAB uses 'Euclidean' distance by default. Theme. Then pdist returns a [3 x 3] D matrix in which the (i, j) entry represents the distance between the i-th observation in X and the j-th observation. Both represent a number of positions in 3D-space. MY-by-N data matrix Y. 장치의 메모리를 절약하기 위해 각각 kmeans와 pdist2를 사용하여 훈련과 예측을 분리할 수 있습니다. If observation i or j contains NaN values, the function pdist returns NaN for the pairwise distance between i and j. . Attach your data (2 lists of points) in a . Copy. It shows a path (C:\Program Files\MATLAB. x and node(i). Fowzi barznji on 16 Mar 2020. I would like to use the command pdist2 in order to compute distance between two geographical coordinates. Copy. 2711 122. y both form part of multidimensional coordinates for a single multidimensional point node(i) and likewise there is a single multidimensional point designated for node(j) and you want to find the multidimensional distance, then you would need different code (and you would need to. What i want to do is to write a code, that does not involve loops and pdist2,. pdist2 has no problem with the two inputs having different numbers of rows (try for example pdist2 (randn (5,2), randn (7,2)) ). 1 Matlab pdist2 :. Note that if there is a tie for the minimum value in each column, MATLAB chooses the first element in the column. You can use the function pdist2 to measure the Hamming distance between the first and second row of data, the numerical representation of. Thus if you input a matrix with N points and one with M points, you get N*M distances. Now I want to create a mxn matrix such that (i,j) element represents the distance from ith point of mx2 matrix to jth point of nx2 matrix. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and. D = pdist (X) D = 1×3 0. Just wanted to let you know that pdist2 in MATLAB uses 'Euclidean' distance by default. Show 4 older comments Hide 4 older comments. pdist (X): Euclidean distance between pairs of observations in X. @all, thanks a lot. 5 seconds julia 0. Calculating Euclidean distance of pairs of 3D points in matlab Is it possible to write a code in matlab withoutmatlab pdist2,matlab中pdist2函数; windows 10 bash change PS1; linxu中删除指定时间之前的文件shell脚本; react中如何做成 tab 切换的效果; __declspec的英文含义; 从零复现PyTorch版（3） webpack报错:Invalid options object. The distance between each sample in A and each sample in B can be calculated as follows: First, define a matrix D of size 75x50, s. 5 seconds. Learn more about pdist2, error, stats MATLAB Every time I want to use pdist2, I get the following error: Undefined function 'pdist2mex' for input arguments of type 'double'. % accept a matrix ZJ with an arbitrary number of observations. For the future, try typing edit pdist2 (or whatever other function) in Matlab, in most cases, you will see the Matlab function, which you can then convert to python. . Let X be an MxP matrix representing m points in P. Tags matlab; array; Products MATLAB; Community Treasure Hunt. Z = squareform (D) Z = 3×3 0 0. pdist (X): Euclidean distance between pairs of observations in X. This function can do both - it will function like pdist if only one set of observations is provided and will function like pdist2 if two sets of. 2. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. m","path":"MyData. coordinates. 8322 268. This is a very interesting suggestion and comparison. Copy. In this workflow, you must pass training data, which can be of considerable size. To save memory on the device, you can separate training and prediction by using kmeans and pdist2, respectively. For code. example D = pdist2 (X,Y,Distance,DistParameter) returns the. 2种计算方式，一种直接利用pdist计算，另一. computes the distance between objects in the data matrix, , using the method. {"payload":{"allShortcutsEnabled":false,"fileTree":{"":{"items":[{"name":"MyData. Copy. cityblockSimilarity. Let us create a matlab script called speedtest. end. For latitude and longitude, usually the haversine method is used. Sorted by: 4. See squareform for information on how to calculate the index of this entry or to convert the condensed distance matrix to a redundant square matrix. How to find closest Lat/Lon on a grid to an. If you want the cosine, use 1-pdist2 (matrix1,matrix2,'cosine'). Dec 17, 2014 at 14:41. Minkowski's distance equation can be found here. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. If you have to implement the distance yourself (school assignment for instance) this is of absolutely no use to you, but if you just need to calculate the distance as an intermediate step for other calculations I highly recommend d = Pdist2(a,b, distance_measure) the documentation is on matlabs site. Fully MATLAB compatible. I make a calcul between each point : Distance = pdist2 (X,X); But sometimes I have a problem of memory. Copy. ', 'chisq'); pdist2 considers each row as a different sample. In the matlab, the RBF kernel's exponent only # has sigma^2 in the denominator. spatial. % n = norm (v) returns the Euclidean norm of vector v. if you don't have a working pdist2, use the following code. Learn more about matlab, distance, command, haversine, coordinates, km, deggrees, calculation, difference I would like to use the command pdist2 in order to compute distance between two geographical coordinates. train_labels is an N x 1 cell array, where each entry is a. I need to build a for loop to calculate the pdist2 between the first row of A and all the rows of B, the second row of A and all. 使用Matlab计算各种距离. Learn more about mahalanobis, mahal, pdist2, pairwise, difference, versus . cityblockSimilarity. ) Y = pdist (X,'. pairwise distance between rows of matrix A and B. This can be modified as necessary, if one wants to apply distances other than the euclidean. pdist2 (X,Y,Distance): distance between each pair of observations in X and Y using the metric specified by Distance. Generate Code. . This norm is also. pdist2 function. you can also compute the distance between every element and every element of the other array using the function pdist2(). Learn more about distance, matched points, error, pdist2, distance between points Hello, I have two sets of matched points (matchedPoints1 and matchedPoints2, the size is 142x1 and the type is SURFPoints) and I want to. figure. What complicates things even more is the fact, that I have to exclude the current point (to which I'm trying to find the closest one); that's the purpos of my 'others' variable and the 2 pieces of code above and below the for-cycle. tumor,F (i). % ZI is a 1-by-n vector containing a single observation. Hi, So if I have one 102x2 matrix of x,y coordinates, and another 102x2 matrix of x,y coordinates, can pdist be used to compare all the rows in matrix 1 with the rows in matrix 2?. . Could I modify in some manner pdist2 command?I would like to use the command pdist2 in order to compute distance between two geographical coordinates. 1. % accept a matrix ZJ with an arbitrary number of observations. Try pdist2 ( [x, y], [xtrack (:), ytrack (:)]) This MATLAB function returns the distance between each pair of observations in X and Y using the metric specified by Distance. For example instead of @dist(ZI,ZJ) I should send something like @dist(ZI,ZJ,PD) which PD is a parameter (a matrix). m. In this workflow, you must pass training data, which can be of considerable size. Compute the Euclidean distance. Kernel (n)=exp (-0. E=pdist2（X，Y-mean（X），'mahalanobis'，S）. BUT: The code shown here is 10-100 times faster, utilizing the. 🄳. If you look in the matlab documentation for mahal function it says: X and Y must have the same number of columns, but can have different numbers of rows. > In pdist2 (line 253) In ExhaustiveSearcher/knnsearch (line 216) In ClassificationKNN/score (line 428) In ClassificationKNN/predict (line 713) Relevant Code Below: (Any missed out is just the. Output argument "h" (and possibly others) not assigned a value in the execution with "getColorHist"Copy. In human motion analysis, a commond need is the computation of the distance between defferent point sets. Try something like E = pdist2 (X,Y-mean (X),'mahalanobis',S); to see if that gives you the same results as mahal. y = squareform (Z)You can use the function NCHOOSEK to generate a set of indices into X and build your matrix in the following way: >> X = [100 100; 0 100; 100 0; 500 400; 300 600]; %# Your sample data >> D = pdist(X,'euclidean')' %'# Euclidean distance, with result transposed D = 100. t D (i,j) is contains the number of matches between the sample i in A and the sample j in B. Mahalanobis distance has no meaning between two multiple-element vectors. com). Different behaviour for pdist and pdist2. Both represent a number of positions in 3D-space. 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. % ZJ is an m2-by-n matrix containing multiple observations. for low dimensional points (3 in this example) it should be more. 0. I use the pdist2 function to calculate the the distance between the points stored in matricies. . Idx has the same number of rows as Y. Nov 8, 2013 at 9:26. It computes the distances between rows of X. PostCSS Loader. Copy. Generate C code that assigns new data to the existing clusters. where ker_bw is the kernel bandwidth/sigma and x is input of (1000,1) and I have reshaped the input x as. Modified 8 years, 5 months ago. It computes the distances between rows of X. y = squareform (Z)This MATLAB function returns the distance between each pair of observations in X and Y using the metric specified by Distance. Learn more about pdist, matrix, matrix manipulation, distances MATLAB, Statistics and Machine Learning Toolbox. 0670 0. Alternatively, you could avoid computing the 2D histogram by creating a grid covering your scattered points and computing the minimum distance from each grid point to one of your scattered points using pdist2 from the Statistics Toolbox. If you are looking to get 'ChiSquare' distance, please use. Specify the initial values of the kernel parameters (Because you use a custom kernel function, you must provide initial values. m is interfering with use of the pdist2 from the Statistics toolbox. . % Autor: Ana C. I'm having some trouble in calculating the Mahalanobis Distance between a pair of objects. pairwise distance between rows of matrix A and B. In human motion analysis, a commond need is the computation of the distance between defferent point sets. For each observation in Y, PDIST2 finds the K smallest or largest distances by computing and comparing the distance values to all the observations in X. Define an entry-point function named findNearestCentroid that accepts centroid positions and new data, and then find the nearest cluster by using pdist2. It can be calculated as follows: D = A*B' + (1-A)* (1-B)'; The final distance measure can be done by testing for each pair. out = 1×10. I used this MATLAB function to compute the distance matrix Dists = pdist2(fruchterman_graph(:,:),fruchterman_graph(:,:),'euclidean'); but it fails on large networks for both speed and finally memory. t D (i,j) is contains the number of matches between the sample i in A and the sample j in B. distfun must accept a matrix XJ with an arbitrary number of rows. % pairwise mahalanobis distance with pdist2() E = pdist2(X,Y,'mahalanobis',S); % outputs an 50*60 matrix with each ij-th element the pairwise distance between element X(i,:) and Y(j,:) based on the covariance matrix of X: nancov(X) %{ so this is harder to interpret than mahal(), as elements of Y are not just compared to. e the indices of the A. dist = pdist2(d,centroids,distance); % distance between all data points and centroids I'd like to mention that I used matlab in system with windows 8 and following configuration : Mahalanobis Distance with a three variables vector. When I put a comment % on the second plot circle command viscircles([x(i),y(j)],. For a dataset made up of. TagsCompute the Euclidean distance. What i want to do is to write a code, that does not involve loops and pdist2,. 6GB). It was written after reading papers about the topic. The whole kicker is you can simply use the built in MATLAB function pdist2 p1 p2 ‘euclidean MATLAB – Calculate L2 Euclidean distance Programming Tags. The Age values are in years, and the Weight values are in pounds. 9448. If observation i in X or observation j in Y contains NaN values, the function pdist2 returns NaN for the pairwise distance between i and. 2356. Pass Z to the squareform function to reproduce the output of the pdist function. dbscan returns the cluster indices and a vector. You could save half the time by computing each pair only once. Each row of both matrices identifies a point in 2D space. X must have more rows than columns. 9448. 0000 %# Note that I get different results than your example!Very clever - I wouldn't have thought about the pdist2 function (+1). For code generation, define an. Figure out how that file got there or remove that folder from your path so MATLAB can use the correct one. Note that v here in many MATLAB functions can be set by itself, do not necessarily have to take the standard deviation, can be based on the importance of each variable to set different values, such as the Knnsearch function in the Scale property. Specify the origin of the local NED system with the geodetic coordinates lat0, lon0, and h0. x = 177136 x 1 y = 177136 x 1 I have the following query points to which I am trying to find the distance to. Currently avaliable codes in FEX are also insufficient as they can only compute (squared. Viewed 434 times 0 I'm trying to compare the histogram of an image (hsv) with a cell array that contains the histograms of other images in order to find out the closest matches. My question is why applying the mean-function over the output of pdist2() in c. if you don't have a working pdist2, use the following code. pdist (Statistics Toolbox) Y = pdist (X,' Y = pdist (X,distfun,p1,p2,. % ZJ is an m2-by-n matrix containing multiple observations. Ideally it is a distance between a vector (or distances between a set of vectors) and some given distribution defined by means and covariances. From help pdist2: 'cosine' - One minus the cosine of the included angle between observations (treated as vectors) Since the cosine varies between -1 and 1, the result of pdist2 (. See Also. Density-Based Spatial Clustering of Applications with Noise (DBSCAN) identifies arbitrarily shaped clusters and noise (outliers) in data. You can try the following workarounds: 1. You will want the second output of min (combined with ind2sub) to determine the row/column of the pdist2 matrix that corresponds to the minimum distance. 1. m or remove that directory from your MATLAB path. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. I make a calcul between each point : Distance = pdist2 (X,X); But sometimes I have a problem of memory. 2GB) array exceeds maximum array size preference (94. I have two matrices X and Y. % Autor: Ana C. It is much faster than computing the distances using a nested for loop. e. D = pdist2 (X,Y) returns a matrix D containing the Euclidean distances. I want to compute the distance between two vectors by using Jaccard distance measure in matlab program. Sign in to comment. 1. 9448. It is a virtually pleasant drag-and-drop environment. For code generation, define an. computes the Euclidean distance between pairs of objects in . Idx = knnsearch (X,Y) finds the nearest neighbor in X for each query point in Y and returns the indices of the nearest neighbors in Idx, a column vector. 0670 0. workspace; % Make sure the workspace panel is showing. example. matlab中的马氏距离：pdist2（）与mahal（）函数,matlab,Matlab,我有两个矩阵X和Y。它们都代表三维空间中的许多位置。X是一个50*3的矩阵，Y是一个60*3的矩阵 我的问题是：为什么将均值函数与“Mahalanobis”结合应用于pdist2（）的输出上，却不能给出用mahal（）得. Copy. mahal returns the squared Mahalanobis distance. This gave me a m x m matrix of distances. I'm able to get the julia single threaded function running twice as slow as matlab but a multi threaded function running twice as fast as matlab. In a MATLAB code I am using the kullback_leibler_divergence dissimilarity function that can be found here. Along the diagonal are the matching row cases. In Matlab: dist = sqrt(sum((a-b). I have to find the distances between the values in matrix 1 and matrix 2. This function fully supports thread-based environments. This MATLAB function returns the distance between each pair of observations in X and Y using the metric specified by Distance. So, do you know how to make the calcul inside the. Hello, I am using matlab 2019a and I am trying to sort points based on comparing the distance between them. However, I use this matrix in a loop like this : for i:1:n find (Distance (i,:) <= epsilon);. 5. Unfortunately, haversine is not provided as a distance option in pdist2. 0. The biggest distance using pdist2() will be from one end of the line to the opposite end of the other line.