BinarizeMatrix

binarizeMatrix is a Matlab function that takes as an input one or more normalized time series matrices, Z, and returns up to two transformations of these matrices, BIN and SCALED. A Z-score threshold, thresh is applied to the normalized values: For all values greater than +thresh are set to 1; all values less than -thresh are set to 0. For the SCALED transformation, the intermediate values are scaled so that the columnar mean of the values between 0 and 1 is 0.5. For the BIN transformation, all fractional values are set to NaN. Additionally, a clipping value, clip can be supplied: all values with an absolute value exceeding the clip value are set to NaN. If a threshold is not supplied, 0 is used by default (i.e., all positive values are set to 1, and negative values are set to 0). If a clipping value is not used, no outlier values are filtered.

Defensible Z threshold values

AUC	Z
.66	.44
.75	.68
.80	.84
.90	1.28
.95	1.65
.99	2.33

Function Source Code

function [BIN, SCALED]=binarizeMatrix(Z, varargin)
%function [BIN, SCALED]=binarizeMatrix(Z, thresh, clip) 
%binarizeMatrix takes a normalized matrix, Z, and scales and binarizes its 
%elements: 
%positive values are set to 1 and negative values ar set to 0. If thresh is
%set to a nonzero value, elements with an absolute value less than thresh
%are set to NaN. If a clipping value, clip, is provided, elements with an
%absolute value exceeding clip are first set to NaN before binarizing.
%Required Parameters:
%   Z: a normalized matrix or cell array
%
%Optional Parameters:
%   thresh: the z-score threshold above which the absolute values of the
%       normalized values in Z will be set to 1 (for positive values above the
%       threshold) or 0 (for negative values below the negative threshold)
%   clip:   the z-score above which the absolute values will be set to NaN
%   precision: values are rounded to PRECISION decimal points
%Sample usage:
%thresh=1.96;
%clip=3.0;
%[BIN, SCALED]=binarizeMatrix(Z, 'thresh', thresh, 'clip', clip, 'precision', 2);
%
options = struct('thresh',1, ...
   'clip', inf, ...
   'precision', 1);

% read the acceptable names
optionNames = fieldnames(options);

% count arguments
nArgs = length(varargin);
if (isstruct(varargin))
   options=varargin;
else
   if round(nArgs/2)~=nArgs/2
       error('This function needs propertyName/propertyValue pairs')
   end
   
   for pair = reshape(varargin,2,[]) % pair is {propName;propValue}
       inpName = lower(pair{1}); % make case insensitive
       
       if any(strcmp(inpName,optionNames))
           % overwrite defaults
           options.(inpName) = pair{2};
       else
           error('%s is not a recognized parameter name',inpName)
       end
   end
end

if(options.thresh==0)
   options.thresh=realmin; %workaround to allow a threshold of approx. zero
end
if (~iscell(Z))
   %Z is not a cell array, which is the easiest case
   SCALED=scaleMatrix(Z,options.clip, options.thresh, options.precision);
   BIN=SCALED;
   BIN(0<BIN & BIN<1)=nan;
else
   if(iscell(Z))
       %M is a cell array, so we have to apply droprows and zscore to each
       %cell element
       SCALED=cellfun(@(x) scaleMatrix(x, options.clip, options.thresh, options.precision), Z, 'UniformOutput', false);
       BIN=cellfun(@(x) nanBin(x), SCALED, 'UniformOutput', false);
   end
end

%%Nested utility function scale matrix
   function SM=scaleMatrix(M, clip, thresh, precision)
       M(abs(M)>clip)=nan; %remove items to be clipped
       M=M/thresh;%scale in terms of thresholds
       M(M>1)=1;%anything above +threshold=1
       M(M<-1)=-1; %anything below -threshold=-1
       M=M+1;%shift values from range -1:1 to 0:2
       M=M/2;%now values range from 0:1
       %subtly shift values so that mean value for each column is ~0.5
       meansignal=nanmean(M);%what is the current mean of each column?
       %use log to determine exponent required to shift each mean to 0.5
       centerexp=repmat(power(log10(meansignal),-1).*log10(0.5),size(M,1),1);
       %raise each value to the required exponent. 0s and 1s will be
       %unaffected
       precis=power(10,precision);
       SM=round(precis*M.^centerexp)/precis;
       
   end
%%Nested utility function sets all non 0-1 values to nan
   function BIN=nanBin(M)
       BIN=M;
       BIN(0<BIN & BIN<1)=nan;
   end
end