MATLAB: Optimizing Clustering of Array Elements

array manipulationsclusteringoptimizationion

The Task: a 1-D column array of coordinates exists. Most of those coordinates repeat more than once.
1. look for the most repeated element; 2. assign a cluster id to it; 3. include coordinates that lie in +/-10 units to the same cluster 4. remove clustered values from the array 5. proceed with the second most repeated element and loop the same steps as above 6. do the procedure until coordinates are not repeated
Here is a sample code:
 function [clusterArray,frequencyArray] = ClusterWithModeSeed(inputArray)
    % Cluster vector elements to seeds determined by elements frequency
    % element should be repeated at least two times to be considered in
    % a cluster
    % Function Input
    inputSize=size(inputArray,1);
    index=(1:inputSize)';
    clusterArray=zeros(inputSize,1);
    cluster=0;
    frequencyArray=zeros(inputSize,1);
    freq=2;
    while freq>1
        % Update cluster ID
        cluster=cluster+1;
        % Calculate Mode And Frequency
        [mfv,freq]=mode(inputArray);
        % All Elements In +/-10 range of the most frequent value
        tfCluster=inputArray>=mfv-10&inputArray<=mfv+10;
        % Set Cluster % Frequency Outputs
        clusterArray(index(tfCluster))=cluster;
        frequencyArray(cluster)=sum(tfCluster);
        % Update Index And Data
        inputArray(tfCluster)=[];
        index(tfCluster)=[];
    end
    % Remove Empty Frequency
    frequencyArray(frequencyArray==0)=[];
 end
Example Input Array : ans =
      193974
     2140429
     2140432
     2140437
     2140442
     2249750
     2253106
     2253106
     2269479
     2269980
     2276359
     2276359
     2276365
     2276365
     2276359
     2276359
     2276365
     2276359
     2276359
     2276359
     2276359
     2276359
     2278750
     2282743
     2282756
How can I optimize the above algorithm? It uses arrays with around 1E6 Elements and takes around 15-20sec. Any comments are appreciated, thank you for your time!

Best Answer

Don't do this:
% Update Index And Data
      inputArray(tfCluster)=[];
      index(tfCluster)=[];
Changing the size of a big array takes time. Lots of it. So save the parts you need to get rid of and get rid of them at the end. Or set them to nan or something else your program can ignore.
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