Euclidean distance (ED)calculation in matlab

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In my program, I have a matrix obtained after lexicographic sorting. Its dimensions are 347275x64 double. My question is "how we can find euclidean distances (ED) between pairs of rows in this matrix?" Also, in my research paper, they specify that we don't need to find the ED between all the pairs of rows, but only for those pairs of rows which are close to offset threshold. So how to decide this value of offset threshold? Can anyone share his / her knowledge about this?
Please help me in this euclidean distance problem.
Thanks in advance.
  3 Comments
TUSHAR MURATKAR
TUSHAR MURATKAR on 14 Sep 2017
@image analyst, I am following a published paper and in that they didn't mentioned any thing about offset threshold except this formula. The formula is " abs[index(u)-index(v)] ≤ Offset Threshold. Can you help me with this.

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Accepted Answer

John BG
John BG on 12 Sep 2017
Edited: John BG on 13 Sep 2017
Hi TUSHAR MURATKAR
I have written a scaled solution with only 12 rows
1.
the Euclidean distance function you need can be written in different ways, one of them
distn=@(a,k,p) (sum((a(k,:)-a(p,:)).^2))^.5
testing the distance function
A=randi([-10 10],12,5);
distn =
function_handle with value:
@(a,k,p)(sum((a(k,:)-a(p,:)).^2))^.5
distn(A,1,2)
ans =
20.4450
distn(A,3,7)
ans =
17.8326
2.
Now, how many combinations without repetition pairs do you have?
A=randi([-10 10],12,5);
L=nchoosek([1:1:12],2);
here A is a the test matrix, replace A with your input matrix.
3.
Applying the offset threshold
DE=[0 0 0];
off_thresh=10;
for k=1:1:length(L)
if distn(A,L(k,1),L(k,2))>off_thresh
DE=[DE;L(k,1) L(k,2) distn(A,L(k,1),L(k,2))];
end
end
DE(1,:)=[];
4.
The result is DE, with 1st and 2nd columns defining the pair of rows and the 3rd column is the Euclidean distance.
DE =
1.0000 2.0000 20.4450
1.0000 3.0000 13.8203
1.0000 4.0000 17.3781
1.0000 5.0000 22.0454
1.0000 6.0000 16.8226
1.0000 7.0000 22.6053
1.0000 8.0000 23.7908
..
9.0000 10.0000 17.0587
9.0000 11.0000 19.7231
9.0000 12.0000 14.3178
10.0000 11.0000 24.2487
10.0000 12.0000 18.8149
11.0000 12.0000 23.7065
5.
note that the higher the offset threshold off_thresh is defined, the fewer the amount of pairs collected in DE, which is consistent.
If you find this answer useful would you please be so kind to consider marking my answer as Accepted Answer?
To any other reader, if you find this answer useful please consider clicking on the thumbs-up vote link
thanks in advance
John BG
  3 Comments
Jan
Jan on 15 Sep 2017
Edited: Jan on 15 Sep 2017
@TUSHAR: Accepting an answer means, that the problem is solved. Afterwards the chances are lower that your thread is read. Please select the answer as accepted, which solved your problem.
While creating the output by an iterative growing works for an input with 256 elements, it will run for a very very long time for 347275 elements. The "DE=[DE; ...]" approach reserves a completely new array in each iteration, such that if the threshold let 1e5 elements pass the test (a guess), Matlab needs to allocate sum(1:1e5)*8 bytes = 40 GB, although the final result uses 800 kB only.
General rules:
  1. Do not let arrays grow iteratively.
  2. A function which works for a tiny data set need not be useful for a large data set, if combinations or permutations are part of the problem.

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More Answers (2)

Walter Roberson
Walter Roberson on 12 Sep 2017
See rangesearch() from the Statistics toolbox.
  4 Comments

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Jan
Jan on 15 Sep 2017
Edited: Jan on 15 Sep 2017
Data = rand(347275, 64) * 1000;
nData = size(Data, 1);
L = nchoosek(1:nData, 2); % Not "{1:1:nData}", but a vector
DE = zeros(2, size(L, 1)); % Pre-allocate
iDE = 0;
thresh = 10^2; % Squared distance
for k = 1:size(L, 2) % SIZE(L, 2) is safer than LENGTH(L)
% Using the function directly is much faster than an anonymous function.
% Calculate the expensive SQRT on demand only:
D2 = sum((Data(L(k,1), :) - Data(L(k,2), :)) .^ 2);
if D2 < thresh
iDE = iDE + 1;
DE(1, iDE) = sqrt(D2); % Store value and index
DE(2, iDE) = k;
end
end
DE = DE(:, 1:iDE); % Crop unused pre-allocated data
Now DE(1, :) contains the distances and L(DE(2, :)) the corresponding indices.
Note that nchoosek(1:347273, 2) has 6.03e10*2 elements. Matlab's nchoosek stores this in a double matrix, such that you need 964.8 GB RAM for this matrix. Using the faster FEX: VChooseK can reduce this by 50% using UINT32 indices:
L = VChooseK(uint32(1):uint32(nData), 2);
But a half TB is still a lot of free RAM. It will be cheaper to create the indices dynamically, but the pre-allocation of the output remains a problem.
% [EDITED, UTC 15:42 15-Sep-2017, Typos fixed, indices fixed, transposed Data]
Data = transpose(Data); % Faster to access 1st dimension
nData = size(Data, 2);
nOut = 1e6; % A guess
DE = zeros(3, nOut); % Pre-allocate the output
iDE = 0;
thresh = 10^2; % Squared distance
L = nchoosek(nData, 2); % Number of outputs, not an array
k1 = 1;
k2 = 2;
for k = 1:L
D2 = sum((Data(k1, :) - Data(k2, :)) .^ 2);
if D2 < thresh
iDE = iDE + 1;
if iDE > nOut % Expand the array, a re-allocation
nOut = nOut + 1e6;
DE(:, nOut) = 0;
end
DE(:, iDE) = [sqrt(D2), k1, k2];
end
% Get new indices:
k2 = k2 + 1;
if k2 > nData
k1 = k1 + 1;
k2 = k1 + 1;
end
end
DE = DE(:, 1:iDE); % Crop unused pre-allocated data
This is still a huge problem and needs about 2.5 days to run. It can be accelerated by a vectorization, but I do not have more time currently to implement this. Walter's suggestion rangesearch() seems to be more promising.
[EDITED] A vectorized and leaner version:
function Near = GetNearPoints(X, Thresh)
% Input: X: [nPoint x m] matrix, nPoints with m dimensions
% Thresh: Positive value
% Output: Near: [nOut x 3], The indices of the rows and the distance
% Author: Jan Simon, License: CC BY-SA 3.0
D = transpose(X);
n = size(D, 2);
C = cell(1, n); % Collect output
T2 = Thresh ^ 2; % Squared threshold
for k = 1:n
D2 = sum(bsxfun(@minus, D(:, k), D(:, k+1:n)) .^ 2, 1);
m = (D2 < T2); % Compare squared distances
if any(m)
C{k} = [repmat(k, sum(m), 1), find(m).' + k, sqrt(D2(m)).'];
end
end
Near = cat(1, C{:});
This is a little bit faster. A parfor will be useful, if you have the parallel processing toolbox. With 8 cores, this might take some hours only. This brute force method cannot be much faster.
  3 Comments
Jan
Jan on 16 Sep 2017
I do not think that this brute force method solves the problem efficiently, but Walter's suggestion is much better.
A divide and conquer approach will be smarter also: Searching the complete data set requires nchoosek(347275, 2) = 60.3e9 comparisons. If the volume is split into 2 halves (and considering the an extra interval with the width of the threshold), reduces the problem to 2*nchoosek(347275, 2) + X = 30.1e9 comparisons (plus the small overhead for the margin). This will reduce the processing speed by nearly 50% - and this can be applied repeatedly in X and Y direction.
If this strategy is applied strictly, you come to a k-D tree approach, see e.g. https://www.mathworks.com/matlabcentral/fileexchange/4586-k-d-tree. Unfortunately I cannot get this code to work...

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