Generalized Peak and Valley Finding function in Matlab using the Image Processing Toolbox

Driver.m

%% Motivation
% This Matlab function is motivated by http://tonyfast.com/nsf-goali/2014/08/29/Peak-Finding/
%% Example use of Find_Peaks on a 2-D array

N = 100;

% Example Dataset
T = peaks( N );

%% Find Peaks using the default filter

Peaks_default = Find_Peaks( T );

%% Find Valleys using the default filter

Valleys_default = Find_Peaks( T, 'valley', true );

%% Change the size of the neighborhood to find Peaks
% Changing the size of the neighborhood can be effective for noisey datasets.

Peaks_Neighborhood = Find_Peaks( T, 'neighborhood', 11 );

%% Indices of Valleys and Peaks
% Use the ``find`` function to find the positions of the peaks or valleys

id = find( Peaks_Neighborhood );
[x y z] = ind2sub( size( T ), id );

Find_Peaks.m

function P = Find_Peaks( T, varargin )
% Finds Peaks or Valleys in an N-D matrix T.
% Requires the Image Processing Toolbox.
%
% Options
% 'neighborhood', an integer to design a cuboidal filter with edges of length ``r``
%        default: r = 5 
% 'valley', boolean value ``true`` and ``false`` find valleys and peaks respectively.
%        default: false; % Find Peaks
%
% Returns Boolean matrix with dimensions equal to T.  ``true`` entries indicate a peak or valley
%        depending upon the flag used to call this function.


% Finds the peaks or valleys in the spatial correlation functions.
param = setparam( varargin, numel(T),size(T) );

% Design the filter
F = ones( param.neighborhood);
F( ceil(numel(F)./2) ) = 0;


if ~param.valley
    P = T > imdilate( T, F );
else
    P = T < imerode( T, F );
end



function param = setparam( varargin, N, sz )
    if sz(2) == 1 & N == sz(1)
        r = 1;
    else
        r = numel( sz );
    end

    param = struct( 'neighborhood', 5*ones(1,r),...
        'valley', false);
    if numel( varargin ) > 0
        for ii = 1 : 2 :numel( varargin )
            param = setfield( param, varargin{ii}, varargin{ii+1});
        end
    end
end %setparam

end %Find_Peaks