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makconnstrength.m
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makconnstrength.m
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function J = makconnstrength ( E , n )
%
% J = makconnstrength ( E , n )
%
% MET Analysis Kit, pre-processing. Returns connection-strength matrix J,
% computed from raw interface-energy matrix E and per-cluster spike count
% vector n.
%
% References:
%
% Fee MS, Mitra PP, Kleinfeld D. J Neurosci Methods. 1996 Nov;69(2):175-88.
% Hill DN, Mehta SB, Kleinfeld D. J Neurosci. 2011 Jun 15;31(24):8699-705.
% UltraMegaSort2000, https://neurophysics.ucsd.edu/software.php
%
%
% Written by Jackson Smith - January 2018 - DPAG , University of Oxford
%
% Make sure that spike-count vector is double floating point
if ~ isa ( n , 'double' ) , n = double ( n ) ; end
% Number of clusters
cnum = numel ( n ) ;
% Linear index of diagonal elements
i = find ( eye( cnum ) ) ;
% Compute normalised interface energy
En = n' * n ;
En( i ) = ( En( i ) - n' ) / 2 ;
En = E ./ En ;
% Compute connection strengths
J = 2 * En ./ ...
( repmat( En( i ) , 1 , cnum ) + repmat( En( i )' , cnum , 1 ) ) ;
% When numerical limitations of the computer cause within-cluster energy
% to be zero then we will get 0 / 0 = NaN. A sensible thing seems to set
% the self energy for such clusters to 1.
J( i( E( i ) == 0 ) ) = 1 ;
end % makconnstrength