continuous search of the closest rows in a matrix

Question

pavlos 2013-1-15

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https://ww2.mathworks.cn/matlabcentral/answers/58856-continuous-search-of-the-closest-rows-in-a-matrix

Hello,

Consider a 100x10 matrix and a random row of it, let be "row1".

I want to calculate the Euclidean distance between "row1" and the rest of the rows and I want to find the closest row to "row1", let be "row2".

Then I want to find the closest row to "row2", let be "row3" (the "row1" has been excluded from the matrix) and so on.

I use the "pdist2" for the Euclidean distance.

How you please help me?

Thank you.

Best,

Pavlos

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José-Luis 2013-1-15

Please post what you have done so we can help you accordingly.

pavlos 2013-1-15

Here is the code:

%extract a random row from the matrix M 100x10

T = randperm(100);

row1 = M(T(1:1),:);

%remove the row from the matrix

M(T(1),:)=[];

%calculate the distances between M and row1

d1=pdist2(M,row1);

%find the closest row to row1 and the corresponding distance between them

[min_dis ind_min_dis]=min(d1);

row2=T(ind_min_dis,:);

%remove row2 from the matrix

M(ind_min_dis,:)=[];

%continue the same process with a loop

for k=1:length(M)

d(k)=pdist2(M,row(k));

[min_dis(k) ind_min_dis(k)]=min(d(k));

row(k)=M(ind_min_dis(k),:);

M(ind_min_dis(k),:)=[];

end

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Answer 1

Matt J 2013-1-15

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https://ww2.mathworks.cn/matlabcentral/answers/58856-continuous-search-of-the-closest-rows-in-a-matrix#answer_71231

编辑：Matt J 2013-1-15

在 MATLAB Online 中打开

Here's what I use. There are others like it on the FEX, some of them fancier.

function Graph=interdists(A,B)
%Finds the graph of distances between point coordinates
%
% (1) Graph=interdists(A,B)
%
% in:
% 
% A:  matrix whose columns are coordinates of points, for example 
%          [[x1;y1;z1], [x2;y2;z2] ,..., [xM;yM;zM]]
%     but the columns may be points in a space of any dimension, not just 3D.
% 
% B:  A second matrix whose columns are coordinates of points in the same
%     Euclidean space. Default B=A.
% 
% 
% out:
% 
% Graph: The MxN  matrix of separation distances in l2 norm between the coordinates. 
%        Namely, Graph(i,j) will be the distance between A(:,i) and B(:,j).
%
%
% (2) interdists(A,'noself') is the same as interdists(A), except the output 
%     diagonals will be NaN instead of zero. Hence, for example, operations
%     like min(interdists(A,'noself')) will ignore self-distances.
%
% See also getgraph
noself=false;
if nargin<2  
    B=A; 
elseif ischar(B)&&strcmpi(B,'noself')
    noself=true;
    B=A;
end
N=size(A,1);
B=reshape(B,N,1,[]);
Graph=l2norm(bsxfun(@minus, A, B),1);
Graph=squeeze(Graph);
if noself
    n=length(Graph);
   Graph(linspace(1,n^2,n))=nan;

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pavlos 2013-1-15

My mistake.

It works.

Thank you very much.

José-Luis 2013-1-15

Please accept an answer if it helped you.

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Answer 2

Teja Muppirala 2013-1-16

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https://ww2.mathworks.cn/matlabcentral/answers/58856-continuous-search-of-the-closest-rows-in-a-matrix#answer_71262

在 MATLAB Online 中打开

If you have the Statistics Toolbox installed, instead of using PDIST2, use PDIST (along with SQUAREFORM) instead. It is designed to find all interpoint distances for a single matrix very efficiently. Then your entire problem could be reduced to this:

M = randn(100,10);
L = size(R,1);
D = squareform(pdist(M));
D(1:L+1:L^2) = nan;
startrow = 1; % Starting Row
row = [startrow; zeros(L-1,1)];
for n = 2:L
    oldrow = startrow;
    [val,startrow] = min(D(:,startrow));
    D(oldrow,:) = nan;
    row(n) = startrow;
end
row