GetPeakPosFFT (spectrum, xaxis, treshhold)

%GetPeakPosFFT
%
%This function calculates the peak maxima of a complete dataset. The function looks
%for peaks based on the first and second derivative. Peak positions are
%calculated based on fourier interpolation.
%
%Syntax:
%   [pos, intensity] = GetPeakPosFFT (yaxis, xaxis, treshhold)
%
%With:
%   yaxis: the spectrum
%   xaxis: the corresponding xaxis
%   treshhold: a tyhreshold for the second derivative
%   intensity: intensity of the spectrum at the interpolated maximum
%
%This funtion needs the savgol routine from the PLS toolbox.
%
%Examples:
%   peaks = GetPeakPosFFT (dataset, xaxis, 1e-4)

%This software package is dual licensed. You can use it according to the terms
%of either the GPLv3 or the BSD license.
%
%The ShowPeaks toolbox for MATLAB: routines for peaks detection
%C 2004-2008, Kris De Gussem, Raman Spectroscopy Research Group, Department
%of analytical chemistry, Ghent University
%C 2009 Kris De Gussem
%
%This file is part of ShowPeaks. ShowPeaks is used a.o. by the Biodata toolb ox.
%
%ShowPeaks is free software: you can redistribute it and/or modify
%it under the terms of the GNU General Public License as published by
%the Free Software Foundation, either version 3 of the License, or
%(at your option) any later version.
%
%ShowPeaks is distributed in the hope that it will be useful,
%but WITHOUT ANY WARRANTY; without even the implied warranty of
%MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%GNU General Public License for more details.
%
%You should have received a copy of the GNU General Public License
%along with ShowPeaks.  If not, see <http://www.gnu.org/licenses/>.

%Copyright (c) 2004-2009, Kris De Gussem
%All rights reserved.
%
%Redistribution and use in source and binary forms, with or without 
%modification, are permitted provided that the following conditions are 
%met:
%
%    * Redistributions of source code must retain the above copyright 
%      notice, this list of conditions and the following disclaimer.
%    * Redistributions in binary form must reproduce the above copyright 
%      notice, this list of conditions and the following disclaimer in 
%      the documentation and/or other materials provided with the distribution
%    * Neither the name of Raman Spectroscopy Research Group, Department of
%	  analytical chemistry, Ghent University nor the names 
%      of its contributors may be used to endorse or promote products derived 
%      from this software without specific prior written permission.
%      
%THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
%AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
%IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
%ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
%LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
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%CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
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%POSSIBILITY OF SUCH DAMAGE.

function [pos, intensity] = GetPeakPosFFT (spectrum, xaxis, treshhold)
si = size (spectrum, 1);
pos = cell(si,1);
intensity = cell(si,1);
le2 = 0; %to determine the maximum number of detected peaks in a single spectrum
for k=1:si
    p = GetPeakPos (spectrum(k,:), xaxis, treshhold);
    le = length (p);
    if (le > le2)
        le2 = le;
    end
    for i = 1:le
        [pos{k}(i), dummy1, dummy2, intensity{k}(i)] = PeakPosFFT (spectrum(k,:), xaxis, p(i)); %#ok<ASGLU>
        %intensity{k}(i) = interp1 (xaxis, spectrum(k,:), pos{k}(i), 'linear');
    end
end

pos2 = zeros(si, le2);
intensity2 = zeros(si, le2);

for k=1:si
    thislength = length (pos{k});
    pos2(k, 1:thislength) = pos{k};
    intensity2(k, 1:thislength) = intensity{k};
end

clear pos
clear intensity
pos = pos2;
intensity = intensity2;