www.gusucode.com > 峰值搜索源码程序 > 峰值搜索源码程序/PeakFinder/DemoFindPeaksb3.m
function DemoFindPeaksb3 % Demonstration of the findpeaksb3 function (in line 60) % applied to noisy synthetic data set consisting of a random number of % peaks. Each time you run this, a different set of peaks is generated. % Calls the fundpeaksb3 function, which must be in the Matlab path. % See http://terpconnect.umd.edu/~toh/spectrum/Smoothing.html and % http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm % Tom O'Haver (toh@umd.edu). Version 1, January 2014 % You can change the signal characteristics in lines 13-18 format short g format compact clf % For each simulated peak, compute the amplitude, position, and width increment=10; x=1:increment:8000; pos=300:200:7800; % Positions of the peaks (Change if desired) amp=1+round(5.*randn(1,length(pos))); % Amplitudes of the peaks (Change if desired) wid=100.*ones(size(pos)); % Widths of the peaks (Change if desired) Noise=.1; % Amount of random noise added to the signal. (Change if desired) % Initial values of variable parameters WidthPoints=mean(wid)/increment; % Average number of points in half-width of peaks SlopeThreshold=1e-6; % set low enough to detect all the real peaks AmpThreshold=.8; % set low enough to detect all the real peaks SmoothWidth=3; % set low enough to detect all the real peaks FitWidth=9; % FitWidth should be roughly equal to the peak widths (in points) peakshape=2; % 1-Gaussian, 2=Lorentzian NumTrials=10; autozero=0; ShowPlots=0; % A = matrix containing one of the unit-amplidude peak in each of its rows A = zeros(length(pos),length(x)); ActualPeaks=[0 0 0 0 0]; p=1; for k=1:length(pos) if amp(k)>.1, % Keep only those peaks above a certain amplitude % Create a series of peaks of different x-positions if peakshape==1,A(k,:)=exp(-((x-pos(k))./(0.6005615.*wid(k))).^2);end % Gaussian peaks if peakshape==2,A(k,:)=ones(size(x))./(1+((x-pos(k))./(0.5.*wid(k))).^2);end % Lorentzian peaks % Assembles actual parameters into ActualPeaks matrix: each row = 1 % peak; columns are Peak #, Position, Height, Width, Area ActualPeaks(p,:) = [p pos(k) amp(k) wid(k) 1.0646.*amp(k)*wid(k)]; p=p+1; end; end z=amp*A; % Multiplies each row by the corresponding amplitude and adds them up y=z+Noise.*randn(size(z)); % Adds constant random noise % y=z+Noise.*sqrtnoise(z); % Adds signal-dependent random noise % y=y+5.*gaussian(x,0,4000); % Optionally adds a broad background signal % demodata=[x' y']; % Assembles x and y vectors into data matrix % Label the x-axis with the parameter values xlabel(['SlopeThresh. = ' num2str(SlopeThreshold) ' AmpThresh. = ' num2str(AmpThreshold) ' SmoothWidth = ' num2str(SmoothWidth) ' FitWidth = ' num2str(FitWidth) ]) % Find the peaks figure(1); % Graph the signal in red findpeaksResults=findpeaksplot(x,y,SlopeThreshold,AmpThreshold,SmoothWidth,FitWidth,3); title('findpeaksb3 demo. Detected peaks are numbered. Peak table is printed in Command Window') figure(2); tic; findpeaksb3Results=findpeaksb3(x,y,SlopeThreshold,AmpThreshold,SmoothWidth,FitWidth,3,peakshape,0,NumTrials,autozero,ShowPlots); ElapsedTime=toc; PeaksPerSecond=length(findpeaksb3Results)/ElapsedTime; % Display settings disp('-------------------findpeaksb3.m demo--------------------') disp(['SlopeThreshold = ' num2str(SlopeThreshold) ] ) disp(['AmpThreshold = ' num2str(AmpThreshold) ] ) disp(['SmoothWidth = ' num2str(SmoothWidth) ] ) disp(['FitWidth = ' num2str(FitWidth) ] ) disp(['peakshape = ' num2str(peakshape) ] ) disp(['autozero = ' num2str(autozero) ] ) disp(['Speed = ' num2str(round(PeaksPerSecond)) ' Peaks Per Second' ] ) disp(' Position Height Width Area') ActualPeaks; findpeaksResults; findpeaksb3Results; % Display table of peaks if length(ActualPeaks)==length(findpeaksb3Results), PercentErrors=100.*(ActualPeaks(:,1:5)-findpeaksb3Results(:,1:5))./ActualPeaks(:,1:5); PercentErrors(1:5,1)=findpeaksb3Results(1:5,1); disp(' Peak # Position Height Width Area') AverageAbsolutePercentErrors=mean(abs(100.*(ActualPeaks(:,1:5)-findpeaksb3Results(:,1:5))./ActualPeaks(:,1:5))) end Heights=findpeaksb3Results(:,3)'; Positions=findpeaksb3Results(:,2)'; Widths=findpeaksb3Results(:,4)'; model=modelpeaks(x,length(findpeaksb3Results),peakshape,Heights,Positions,Widths,0); figure(3);plot(x,y,'.');hold on;plot(x,model,'r');hold off function FPB=findpeaksb3(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype,PeakShape,extra,NumTrials,AUTOZERO,ShowPlots) % function P=findpeaksb3(x,y,SlopeThreshold,AmpThreshold,smoothwidth, % peakgroup,smoothtype,PeakShape,extra,NumTrials,AUTOZERO,ShowPlots) % Function to locate and fit the positive peaks in a noisy x-y time series % data set and fit each detected peak with 3 Gaussians, the two flanking % Gaussians taken from the previous and next peaks found by prior % application of findpeaks. Finds peaks by looking for downward % zero-crossings in the first derivative that exceed SlopeThreshold. % Returns a matrix of peak number, peak position, peak height, peak width, % peak area, and the percent fitting error, for each peak detected. % Version 2, March 2015 % % Input arguments: % "SlopeThreshold", "AmpThreshold" and "smoothwidth" control peak % sensitivity. Higher values will neglect smaller features. % % "smoothwidth" is the width of the smooth applied before peak detection; % larger values ignore narrow peaks. If smoothwidth=0, no smoothing. % % "peakgroup" is the number points around the top part of the peak that are % taken for thge initial estimation. If Peakgroup=0 the local maximum is % takes as the peak height and position. % % "smoothtype" determines the smooth algorithm: % If smoothtype=1, rectangular (sliding-average or boxcar) % If smoothtype=2, triangular (2 passes of sliding-average) % If smoothtype=3, pseudo-Gaussian (3 passes of sliding-average) % % "peakshape" specifies the peak shape of the model: 1=Gaussian, % 2=Lorentzian, 3=logistic distribution, 4=Pearson, 5=exponentionally % broadened Gaussian; 6=equal-width Gaussians; 7=Equal-width Lorentzians; % 8=exponentionally broadened equal-width Gaussian, 9=exponential pulse, % 10=up-sigmoid (logistic function), 11=Fixed-width Gaussian, % 12=Fixed-width Lorentzian; 13=Gaussian/ Lorentzian blend; 14=Bifurcated % Gaussian, 15=Breit-Wigner-Fano, 16=Fixed-position Gaussians; % 17=Fixed-position Lorentzians; 18=exponentionally broadened Lorentzian; % 19=alpha function; 20=Voigt profile; 21=triangular; 22=multiple shapes; % 23=down-sigmoid; 25=lognormal; 26=slope; 27=Gaussian first derivative; % 28=polynomial; 29=piecewise linear; 30=variable-alpha Voigt; 31=variable % time constant ExpGaussian; 32=variable Pearson; 33=independently-variable % Gaussian/Lorentzian blend % % "extra" Specifies the value of 'extra', used only in the Voigt, Pearson, % exponentionally broadened Gaussian, Gaussian/Lorentzian blend, and % bifurcated Gaussian and Lorentzian shapes to fine-tune the peak shape. % % "NumTrials" sets the number of trial fits and selects the best one (with % lowest itting error); can be any positive integer (default is 1). % % "AUTOZERO": 0 does not subtract baseline from data segment; 1 subtracts % interpolated linear baseline from data segment; 2 subtracts interpolated % quadratic baseline from data segment; 3 subtracts flat baseline without % reference to the data segment. % % "ShowPlots" 1 displays each fit graphically as it goes; 0 does not plot. % % See http://terpconnect.umd.edu/~toh/spectrum/Smoothing.html and % http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm % % (c) T. C. O'Haver, Version 2, March 2015 % % Example: Four Lorentzians, heights=1, 2, 3, and 4, widths=3 % x=1:.2:100; % y=modelpeaks(x,4,2,[1 2 3 4],[45 50 55 60],[3 3 3 3])+.02*randn(size(x)); % findpeaksresults=findpeaksplot(x,y,.00005,.5,9,12,3); % findpeaksb3results=findpeaksb3(x,y,.00005,.5,9,12,3,2,0,10,0,0); % disp(' Peak Position Height Width Area % error') % findpeaksresults % findpeaksb3results % Copyright (c) 2014, Thomas C. O'Haver % % Permission is hereby granted, free of charge, to any person obtaining a copy % of this software and associated documentation files (the "Software"), to deal % in the Software without restriction, including without limitation the rights % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell % copies of the Software, and to permit persons to whom the Software is % furnished to do so, subject to the following conditions: % % The above copyright notice and this permission notice shall be included in % all copies or substantial portions of the Software. % % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN % THE SOFTWARE. fixedparameters=0; % Used for fixed parameters shapes only (11,16,12,and 17) plots=ShowPlots; if smoothtype>3;smoothtype=3;end if smoothtype<1;smoothtype=1;end smoothwidth=round(smoothwidth); peakgroup=round(peakgroup); if ShowPlots, P=findpeaksplot(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype); drawnow; else P=findpeaks(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype); end NumPeaks=size(P); NumPeaks=NumPeaks(1); PeakX=zeros(size(NumPeaks)); PeakY=zeros(size(NumPeaks)); MeasuredWidth=zeros(size(NumPeaks)); MeasuredArea=zeros(size(NumPeaks)); MeasuredError=zeros(size(NumPeaks)); for peak=1:NumPeaks; % Fit first peak if peak==1, x1=P(peak,2)-P(peak,4); x2=P(peak+1,2); startpoint=val2ind(x,x1); endpoint=val2ind(x,x2); XXX=x((startpoint):(endpoint)); YYY=y((startpoint):(endpoint)); signal=[XXX',YYY']; % Portion of the signal selected for fitting start=[P(peak,2) P(peak,4) P(peak+1,2) P(peak+1,4)]; [FitResults,Error]=peakfit(signal,0,0,2,PeakShape,extra,NumTrials,start,AUTOZERO,fixedparameters,plots); if ShowPlots,drawnow;end end % peak=1 % Fit intermediate peaks if peak>1, if peak<NumPeaks, x1=P(peak-1,2); x2=P(peak+1,2); startpoint=val2ind(x,x1); endpoint=val2ind(x,x2); XXX=x((startpoint):(endpoint)); YYY=y((startpoint):(endpoint)); signal=[XXX',YYY']; % Portion of the signal selected for fitting start=[P(peak-1,2) P(peak-1,4) P(peak,2) P(peak,4) P(peak+1,2) P(peak+1,4)]; [FitResults,Error]=peakfit(signal,P(peak,2),2*(P(peak+1,2)-P(peak-1,2)),3,PeakShape,extra,NumTrials,start,AUTOZERO,fixedparameters,plots); if ShowPlots,drawnow;end end % if peak<NumPeaks, end % if peak>1 % Fit last peak if peak==NumPeaks, x1=P(peak-1,2); x2=P(peak,2)+P(peak,4); startpoint=val2ind(x,x1); endpoint=val2ind(x,x2); XXX=x((startpoint):(endpoint)); YYY=y((startpoint):(endpoint)); signal=[XXX',YYY']; % Portion of the signal selected for fitting start=[P(peak-1,2) P(peak-1,4) P(peak,2) P(peak,4)]; [FitResults,Error]=peakfit(signal,P(peak,2),2*(max(XXX)-P(peak-1)),2,PeakShape,extra,NumTrials,start,AUTOZERO,fixedparameters,plots); if ShowPlots,drawnow;end end % if peak=NumPeaks % Assign FitResults to the result arrays PeakX, PeakY, MeasuredWidth, % MeasuredArea, and MeasuredError. CenterPeak=val2ind(FitResults(:,2),P(peak,2)); % find the peak number of the peak whose position is closest to each peak PeakX(peak)=FitResults(CenterPeak(1),2); % Get the X value of that peak PeakY(peak)=FitResults(CenterPeak(1),3); % and the Y value MeasuredWidth(peak)=FitResults(CenterPeak(1),4); % and the width. MeasuredArea(peak)=FitResults(CenterPeak(1),5); % and the area. MeasuredError(peak)=Error(1); % and the fitting error % PeakNumber=peak % for testing end % for peak=1:NumPeaks; % Assemble result arrays into a matrix and return to calling routine. FPB=[1:NumPeaks;PeakX;PeakY;MeasuredWidth;MeasuredArea;MeasuredError]'; % end of function % -----------------------internal functions-------------------------------- function d=deriv(a) % First derivative of vector using 2-point central difference. % T. C. O'Haver, 1988. n=length(a); d(1)=a(2)-a(1); d(n)=a(n)-a(n-1); for j = 2:n-1; d(j)=(a(j+1)-a(j-1)) ./ 2; end function SmoothY=fastsmooth(Y,w,type,ends) % fastbsmooth(Y,w,type,ends) smooths vector Y with smooth % of width w. Version 2.0, May 2008. % The argument "type" determines the smooth type: % If type=1, rectangular (sliding-average or boxcar) % If type=2, triangular (2 passes of sliding-average) % If type=3, pseudo-Gaussian (3 passes of sliding-average) % The argument "ends" controls how the "ends" of the signal % (the first w/2 points and the last w/2 points) are handled. % If ends=0, the ends are zero. (In this mode the elapsed % time is independent of the smooth width). The fastest. % If ends=1, the ends are smoothed with progressively % smaller smooths the closer to the end. (In this mode the % elapsed time increases with increasing smooth widths). % fastsmooth(Y,w,type) smooths with ends=0. % fastsmooth(Y,w) smooths with type=1 and ends=0. % Example: % fastsmooth([1 1 1 10 10 10 1 1 1 1],3)= [0 1 4 7 10 7 4 1 1 0] % fastsmooth([1 1 1 10 10 10 1 1 1 1],3,1,1)= [1 1 4 7 10 7 4 1 1 1] % T. C. O'Haver, May, 2008. if nargin==2, ends=0; type=1; end if nargin==3, ends=0; end switch type case 1 SmoothY=sa(Y,w,ends); case 2 SmoothY=sa(sa(Y,w,ends),w,ends); case 3 SmoothY=sa(sa(sa(Y,w,ends),w,ends),w,ends); end function SmoothY=sa(Y,smoothwidth,ends) w=round(smoothwidth); SumPoints=sum(Y(1:w)); s=zeros(size(Y)); halfw=round(w/2); L=length(Y); for k=1:L-w, s(k+halfw-1)=SumPoints; SumPoints=SumPoints-Y(k); SumPoints=SumPoints+Y(k+w); end s(k+halfw)=sum(Y(L-w+1:L)); SmoothY=s./w; % Taper the ends of the signal if ends=1. if ends==1, startpoint=(smoothwidth + 1)/2; SmoothY(1)=(Y(1)+Y(2))./2; for k=2:startpoint, SmoothY(k)=mean(Y(1:(2*k-1))); SmoothY(L-k+1)=mean(Y(L-2*k+2:L)); end SmoothY(L)=(Y(L)+Y(L-1))./2; end function P=findpeaks(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype) % function P=findpeaks(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype) % Function to locate the positive peaks in a noisy x-y time series data % set. Detects peaks by looking for downward zero-crossings % in the first derivative that exceed SlopeThreshold. % Returns list (P) containing peak number and position, % height, width, and area of each peak. Arguments "slopeThreshold", % "ampThreshold" and "smoothwidth" control peak sensitivity. % Higher values will neglect smaller features. "Smoothwidth" is % the width of the smooth applied before peak detection; larger % values ignore narrow peaks. If smoothwidth=0, no smoothing % is performed. "Peakgroup" is the number points around the top % part of the peak that are taken for measurement. If Peakgroup=0 % the local maximum is takes as the peak height and position. % The argument "smoothtype" determines the smooth algorithm: % If smoothtype=1, rectangular (sliding-average or boxcar) % If smoothtype=2, triangular (2 passes of sliding-average) % If smoothtype=3, pseudo-Gaussian (3 passes of sliding-average) % See http://terpconnect.umd.edu/~toh/spectrum/Smoothing.html and % http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm % T. C. O'Haver, 1995. Version 5.1, Last revised December, 2012 % Skip peaks if peak measurement results in NaN values % Examples: % findpeaks(0:.01:2,humps(0:.01:2),0,-1,5,5) % x=[0:.01:50];findpeaks(x,cos(x),0,-1,5,5) % x=[0:.01:5]';findpeaks(x,x.*sin(x.^2).^2,0,-1,5,5) % Copyright (c) 2013, Thomas C. O'Haver % % Permission is hereby granted, free of charge, to any person obtaining a copy % of this software and associated documentation files (the "Software"), to deal % in the Software without restriction, including without limitation the rights % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell % copies of the Software, and to permit persons to whom the Software is % furnished to do so, subject to the following conditions: % % The above copyright notice and this permission notice shall be included in % all copies or substantial portions of the Software. % % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN % THE SOFTWARE. % if nargin~=7;smoothtype=1;end % smoothtype=1 if not specified in argument if smoothtype>3;smoothtype=3;end if smoothtype<1;smoothtype=1;end smoothwidth=round(smoothwidth); peakgroup=round(peakgroup); if smoothwidth>1, d=fastsmooth(deriv(y),smoothwidth,smoothtype); else d=y; end n=round(peakgroup/2+1); P=[0 0 0 0 0]; vectorlength=length(y); peak=1; AmpTest=AmpThreshold; for j=2*round(smoothwidth/2)-1:length(y)-smoothwidth, if sign(d(j)) > sign (d(j+1)), % Detects zero-crossing if d(j)-d(j+1) > SlopeThreshold*y(j), % if slope of derivative is larger than SlopeThreshold if y(j) > AmpTest, % if height of peak is larger than AmpThreshold xx=zeros(size(peakgroup));yy=zeros(size(peakgroup)); for k=1:peakgroup, % Create sub-group of points near peak groupindex=j+k-n+1; if groupindex<1, groupindex=1;end if groupindex>vectorlength, groupindex=vectorlength;end xx(k)=x(groupindex);yy(k)=y(groupindex); end if peakgroup>3, [Height, Position, Width]=gaussfit(xx,yy); PeakX=real(Position); % Compute peak position and height of fitted parabola PeakY=real(Height); MeasuredWidth=real(Width); % if the peak is too narrow for least-squares technique to work % well, just use the max value of y in the sub-group of points near peak. else PeakY=max(yy); pindex=val2ind(yy,PeakY); PeakX=xx(pindex(1)); MeasuredWidth=0; end % Construct matrix P. One row for each peak % detected, containing the peak number, peak % position (x-value) and peak height (y-value). % If peak measurements fails and results in NaN, skip this % peak if isnan(PeakX) || isnan(PeakY) || PeakY<AmpThreshold, % Skip this peak else % Otherwiase count this as a valid peak P(peak,:) = [round(peak) PeakX PeakY MeasuredWidth 1.0646.*PeakY*MeasuredWidth]; peak=peak+1; % Move on to next peak end end end end end function [FitResults,GOF,baseline,coeff,BestStart,xi,yi,BootResults]=peakfit(signal,center,window,NumPeaks,peakshape,extra,NumTrials,start,autozero,fixedparameters,plots,bipolar,minwidth,DELTA,clipheight) % A command-line peak fitting program for time-series signals, written as a % Version 7: March, 2015 % For more details, see % http://terpconnect.umd.edu/~toh/spectrum/CurveFittingC.html and % http://terpconnect.umd.edu/~toh/spectrum/InteractivePeakFitter.htm % % Copyright (c) 2015, Thomas C. O'Haver % Permission is hereby granted, free of charge, to any person obtaining a copy % of this software and associated documentation files (the "Software"), to deal % in the Software without restriction, including without limitation the rights % to use, copy, modify, merge, publish, distribute, sublicense, and/or sell % copies of the Software, and to permit persons to whom the Software is % furnished to do so, subject to the following conditions: % % The above copyright notice and this permission notice shall be included in % all copies or substantial portions of the Software. % % THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR % IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, % FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE % AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER % LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, % OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN % THE SOFTWARE. % global AA xxx PEAKHEIGHTS FIXEDPARAMETERS AUTOZERO delta BIPOLAR CLIPHEIGHT % peakfit.m version 5, February 2014 format short g format compact warning off all NumArgOut=nargout; datasize=size(signal); if datasize(1)<datasize(2),signal=signal';end datasize=size(signal); if datasize(2)==1, % Must be isignal(Y-vector) X=1:length(signal); % Create an independent variable vector Y=signal; else % Must be isignal(DataMatrix) X=signal(:,1); % Split matrix argument Y=signal(:,2); end X=reshape(X,1,length(X)); % Adjust X and Y vector shape to 1 x n (rather than n x 1) Y=reshape(Y,1,length(Y)); % If necessary, flip the data vectors so that X increases if X(1)>X(length(X)), disp('X-axis flipped.') X=fliplr(X); Y=fliplr(Y); end % Isolate desired segment from data set for curve fitting if nargin==1 || nargin==2,center=(max(X)-min(X))/2;window=max(X)-min(X);end % Y=Y-min(Y); xoffset=0; n1=val2ind(X,center-window/2); n2=val2ind(X,center+window/2); if window==0,n1=1;n2=length(X);end xx=X(n1:n2)-xoffset; yy=Y(n1:n2); ShapeString='Gaussian'; coeff=0; CLIPHEIGHT=max(Y); LOGPLOT=0; % Define values of any missing arguments % (signal,center,window,NumPeaks,peakshape,extra,NumTrials,start,autozero,fixedparameters,plots,bipolar,minwidth,DELTA) switch nargin case 1 NumPeaks=1; peakshape=1; extra=0; NumTrials=1; xx=X;yy=Y; start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; plots=1; BIPOLAR=0; MINWIDTH=xx(2)-xx(1); delta=1; CLIPHEIGHT=max(Y); case 2 NumPeaks=1; peakshape=1; extra=0; NumTrials=1; xx=signal;yy=center; start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; plots=1; BIPOLAR=0; MINWIDTH=xx(2)-xx(1); delta=1; CLIPHEIGHT=max(Y); case 3 NumPeaks=1; peakshape=1; extra=0; NumTrials=1; start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=xx(2)-xx(1); delta=1; CLIPHEIGHT=max(Y); case 4 % Numpeaks specified in arguments peakshape=1; extra=0; NumTrials=1; start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=xx(2)-xx(1); delta=1; CLIPHEIGHT=max(Y); case 5 % Numpeaks, peakshape specified in arguments extra=zeros(1,NumPeaks); NumTrials=1; start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; CLIPHEIGHT=max(Y); case 6 NumTrials=1; start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; case 7 start=calcstart(xx,NumPeaks,xoffset); AUTOZERO=0; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; CLIPHEIGHT=max(Y); case 8 AUTOZERO=0; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; CLIPHEIGHT=max(Y); case 9 AUTOZERO=autozero; FIXEDPARAMETERS=0; plots=1; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; case 10 AUTOZERO=autozero; FIXEDPARAMETERS=fixedparameters; plots=1; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; case 11 AUTOZERO=autozero; FIXEDPARAMETERS=fixedparameters; BIPOLAR=0; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; CLIPHEIGHT=max(Y); case 12 AUTOZERO=autozero; FIXEDPARAMETERS=fixedparameters; BIPOLAR=bipolar; MINWIDTH=zeros(size(peakshape))+(xx(2)-xx(1)); delta=1; CLIPHEIGHT=max(Y); case 13 AUTOZERO=autozero; FIXEDPARAMETERS=fixedparameters; BIPOLAR=bipolar; MINWIDTH=minwidth; delta=1; case 14 AUTOZERO=autozero; FIXEDPARAMETERS=fixedparameters; BIPOLAR=bipolar; MINWIDTH=minwidth; delta=DELTA; CLIPHEIGHT=max(Y); case 15 AUTOZERO=autozero; FIXEDPARAMETERS=fixedparameters; BIPOLAR=bipolar; MINWIDTH=minwidth; delta=DELTA; CLIPHEIGHT=clipheight; otherwise end % switch nargin % Saturation Code, skips points greater than set maximum if CLIPHEIGHT<max(Y), apnt=1; for pnt=1:length(xx), if yy(pnt)<CLIPHEIGHT, axx(apnt)=xx(pnt); ayy(apnt)=yy(pnt); apnt=apnt+1; end end xx=axx;yy=ayy; end % Default values for placeholder zeros1 if NumTrials==0;NumTrials=1;end if isscalar(peakshape), else % disp('peakshape is vector'); shapesvector=peakshape; NumPeaks=length(peakshape); peakshape=22; end if peakshape==0;peakshape=1;end if NumPeaks==0;NumPeaks=1;end if start==0;start=calcstart(xx,NumPeaks,xoffset);end if FIXEDPARAMETERS==0, FIXEDPARAMETERS=length(xx)/10;end if peakshape==16;FIXEDPOSITIONS=fixedparameters;end if peakshape==17;FIXEDPOSITIONS=fixedparameters;end if AUTOZERO>3,AUTOZERO=3,end if AUTOZERO<0,AUTOZERO=0,end Heights=zeros(1,NumPeaks); FitResults=zeros(NumPeaks,6); % % Remove linear baseline from data segment if AUTOZERO==1 baseline=0; bkgcoef=0; bkgsize=round(length(xx)/10); if bkgsize<2,bkgsize=2;end lxx=length(xx); if AUTOZERO==1, % linear autozero operation XX1=xx(1:round(lxx/bkgsize)); XX2=xx((lxx-round(lxx/bkgsize)):lxx); Y1=yy(1:(round(length(xx)/bkgsize))); Y2=yy((lxx-round(lxx/bkgsize)):lxx); bkgcoef=polyfit([XX1,XX2],[Y1,Y2],1); % Fit straight line to sub-group of points bkg=polyval(bkgcoef,xx); yy=yy-bkg; end % if if AUTOZERO==2, % Quadratic autozero operation XX1=xx(1:round(lxx/bkgsize)); XX2=xx((lxx-round(lxx/bkgsize)):lxx); Y1=yy(1:round(length(xx)/bkgsize)); Y2=yy((lxx-round(lxx/bkgsize)):lxx); bkgcoef=polyfit([XX1,XX2],[Y1,Y2],2); % Fit parabola to sub-group of points bkg=polyval(bkgcoef,xx); yy=yy-bkg; end % if autozero PEAKHEIGHTS=zeros(1,NumPeaks); n=length(xx); newstart=start; % Assign ShapStrings switch peakshape(1) case 1 ShapeString='Gaussian'; case 2 ShapeString='Lorentzian'; case 3 ShapeString='Logistic'; case 4 ShapeString='Pearson'; case 5 ShapeString='ExpGaussian'; case 6 ShapeString='Equal width Gaussians'; case 7 ShapeString='Equal width Lorentzians'; case 8 ShapeString='Exp. equal width Gaussians'; case 9 ShapeString='Exponential Pulse'; case 10 ShapeString='Up Sigmoid (logistic function)'; case 23 ShapeString='Down Sigmoid (logistic function)'; case 11 ShapeString='Fixed-width Gaussian'; case 12 ShapeString='Fixed-width Lorentzian'; case 13 ShapeString='Gaussian/Lorentzian blend'; case 14 ShapeString='BiGaussian'; case 15 ShapeString='Breit-Wigner-Fano'; case 16 ShapeString='Fixed-position Gaussians'; case 17 ShapeString='Fixed-position Lorentzians'; case 18 ShapeString='Exp. Lorentzian'; case 19 ShapeString='Alpha function'; case 20 ShapeString='Voigt (equal alphas)'; case 21 ShapeString='triangular'; case 22 ShapeString=num2str(shapesvector); case 24 ShapeString='Negative Binomial Distribution'; case 25 ShapeString='Lognormal Distribution'; case 26 ShapeString='slope'; case 27 ShapeString='First derivative'; case 28 ShapeString='Polynomial'; case 29 ShapeString='Segmented linear'; case 30 ShapeString='Voigt (variable alphas)'; case 31 ShapeString='ExpGaussian (var. time constant)'; case 32 ShapeString='Pearson (var. shape constant)'; case 33 ShapeString='Variable Gaussian/Lorentzian'; otherwise end % switch peakshape % Perform peak fitting for selected peak shape using fminsearch function options = optimset('TolX',.001,'Display','off','MaxFunEvals',1000 ); LowestError=1000; % or any big number greater than largest error expected FitParameters=zeros(1,NumPeaks.*2); BestStart=zeros(1,NumPeaks.*2); height=zeros(1,NumPeaks); bestmodel=zeros(size(yy)); for k=1:NumTrials, % StartMatrix(k,:)=newstart; % disp(['Trial number ' num2str(k) ] ) % optionally prints the current trial number as progress indicator switch peakshape(1) case 1 TrialParameters=fminsearch(@(lambda)(fitgaussian(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 2 TrialParameters=fminsearch(@(lambda)(fitlorentzian(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 3 TrialParameters=fminsearch(@(lambda)(fitlogistic(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 4 TrialParameters=fminsearch(@(lambda)(fitpearson(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 5 zxx=[zeros(size(xx)) xx zeros(size(xx)) ]; zyy=[zeros(size(yy)) yy zeros(size(yy)) ]; TrialParameters=fminsearch(@(lambda)(fitexpgaussian(lambda,zxx,zyy,-extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 6 cwnewstart(1)=newstart(1); for pc=2:NumPeaks, cwnewstart(pc)=newstart(2.*pc-1); end cwnewstart(NumPeaks+1)=(max(xx)-min(xx))/5; TrialParameters=fminsearch(@(lambda)(fitewgaussian(lambda,xx,yy)),cwnewstart,options); for Peak=1:NumPeaks; if TrialParameters(NumPeaks+1)<MINWIDTH, TrialParameters(NumPeaks+1)=MINWIDTH; end end case 7 cwnewstart(1)=newstart(1); for pc=2:NumPeaks, cwnewstart(pc)=newstart(2.*pc-1); end cwnewstart(NumPeaks+1)=(max(xx)-min(xx))/5; TrialParameters=fminsearch(@(lambda)(fitewlorentzian(lambda,xx,yy)),cwnewstart,options); for Peak=1:NumPeaks; if TrialParameters(NumPeaks+1)<MINWIDTH, TrialParameters(NumPeaks+1)=MINWIDTH; end end case 8 cwnewstart(1)=newstart(1); for pc=2:NumPeaks, cwnewstart(pc)=newstart(2.*pc-1); end cwnewstart(NumPeaks+1)=(max(xx)-min(xx))/5; TrialParameters=fminsearch(@(lambda)(fitexpewgaussian(lambda,xx,yy,-extra)),cwnewstart,options); for Peak=1:NumPeaks; if TrialParameters(NumPeaks+1)<MINWIDTH, TrialParameters(NumPeaks+1)=MINWIDTH; end end case 9 TrialParameters=fminsearch(@(lambda)(fitexppulse(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 10 TrialParameters=fminsearch(@(lambda)(fitupsigmoid(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 23 TrialParameters=fminsearch(@(lambda)(fitdownsigmoid(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 11 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=min(xx)+pc.*(max(xx)-min(xx))./(NumPeaks+1); end TrialParameters=fminsearch(@(lambda)(FitFWGaussian(lambda,xx,yy)),fixedstart,options); case 12 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=min(xx)+pc.*(max(xx)-min(xx))./(NumPeaks+1); end TrialParameters=fminsearch(@(lambda)(FitFWLorentzian(lambda,xx,yy)),fixedstart,options); case 13 TrialParameters=fminsearch(@(lambda)(fitGL(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 14 TrialParameters=fminsearch(@(lambda)(fitBiGaussian(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 15 TrialParameters=fminsearch(@(lambda)(fitBWF(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 16 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=(max(xx)-min(xx))./(NumPeaks+1); fixedstart(pc)=fixedstart(pc)+.1*(rand-.5).*fixedstart(pc); end TrialParameters=fminsearch(@(lambda)(FitFPGaussian(lambda,xx,yy)),fixedstart,options); for Peak=1:NumPeaks; if TrialParameters(Peak)<MINWIDTH, TrialParameters(Peak)=MINWIDTH; end end case 17 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=(max(xx)-min(xx))./(NumPeaks+1); fixedstart(pc)=fixedstart(pc)+.1*(rand-.5).*fixedstart(pc); end TrialParameters=fminsearch(@(lambda)(FitFPLorentzian(lambda,xx,yy)),fixedstart,options); for Peak=1:NumPeaks; if TrialParameters(Peak)<MINWIDTH, TrialParameters(Peak)=MINWIDTH; end end case 18 zxx=[zeros(size(xx)) xx zeros(size(xx)) ]; zyy=[ones(size(yy)).*yy(1) yy zeros(size(yy)).*yy(length(yy)) ]; TrialParameters=fminsearch(@(lambda)(fitexplorentzian(lambda,zxx,zyy,-extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 19 TrialParameters=fminsearch(@(lambda)(fitalphafunction(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 20 TrialParameters=fminsearch(@(lambda)(fitvoigt(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 21 TrialParameters=fminsearch(@(lambda)(fittriangular(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 22 TrialParameters=fminsearch(@(lambda)(fitmultiple(lambda,xx,yy,shapesvector,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH(Peak), TrialParameters(2*Peak)=MINWIDTH(Peak); end end case 24 TrialParameters=fminsearch(@(lambda)(fitnbinpdf(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 25 TrialParameters=fminsearch(@(lambda)(fitlognpdf(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 26 TrialParameters=fminsearch(@(lambda)(fitlinslope(lambda,xx,yy)),polyfit(xx,yy,1),options); coeff=TrialParameters; case 27 TrialParameters=fminsearch(@(lambda)(fitd1gauss(lambda,xx,yy)),newstart,options); case 28 coeff=fitpolynomial(xx,yy,extra); TrialParameters=coeff; case 29 cnewstart(1)=newstart(1); for pc=2:NumPeaks, cnewstart(pc)=newstart(2.*pc-1)+(delta*(rand-.5)/50); end TrialParameters=fminsearch(@(lambda)(fitsegmented(lambda,xx,yy)),cnewstart,options); case 30 nn=max(xx)-min(xx); start=[]; startpos=[nn/(NumPeaks+1):nn/(NumPeaks+1):nn-(nn/(NumPeaks+1))]+min(xx); for marker=1:NumPeaks, markx=startpos(marker)+ xoffset; start=[start markx nn/5 extra]; end % for marker newstart=start; for parameter=1:3:3*NumPeaks, newstart(parameter)=newstart(parameter)*(1+randn/100); newstart(parameter+1)=newstart(parameter+1)*(1+randn/20); newstart(parameter+2)=newstart(parameter+1)*(1+randn/20); end TrialParameters=fminsearch(@(lambda)(fitvoigtv(lambda,xx,yy)),newstart); case 31 nn=max(xx)-min(xx); start=[]; startpos=[nn/(NumPeaks+1):nn/(NumPeaks+1):nn-(nn/(NumPeaks+1))]+min(xx); for marker=1:NumPeaks, markx=startpos(marker)+ xoffset; start=[start markx nn/5 extra]; end % for marker newstart=start; for parameter=1:3:3*NumPeaks, newstart(parameter)=newstart(parameter)*(1+randn/100); newstart(parameter+1)=newstart(parameter+1)*(1+randn/20); newstart(parameter+2)=newstart(parameter+1)*(1+randn/20); end % newstart=newstart zxx=[zeros(size(xx)) xx zeros(size(xx)) ]; zyy=[ones(size(yy)).*yy(1) yy zeros(size(yy)).*yy(length(yy)) ]; TrialParameters=fminsearch(@(lambda)(fitexpgaussianv(lambda,zxx,zyy)),newstart); case 32 nn=max(xx)-min(xx); start=[]; startpos=[nn/(NumPeaks+1):nn/(NumPeaks+1):nn-(nn/(NumPeaks+1))]+min(xx); for marker=1:NumPeaks, markx=startpos(marker)+ xoffset; start=[start markx nn/5 extra]; end % for marker newstart=start; for parameter=1:3:3*NumPeaks, newstart(parameter)=newstart(parameter)*(1+randn/100); newstart(parameter+1)=newstart(parameter+1)*(1+randn/20); newstart(parameter+2)=newstart(parameter+1)*(1+randn/20); end % newstart=newstart TrialParameters=fminsearch(@(lambda)(fitpearsonv(lambda,xx,yy)),newstart); case 33 nn=max(xx)-min(xx); start=[]; startpos=[nn/(NumPeaks+1):nn/(NumPeaks+1):nn-(nn/(NumPeaks+1))]+min(xx); for marker=1:NumPeaks, markx=startpos(marker)+ xoffset; start=[start markx nn/5 extra]; end % for marker newstart=start; for parameter=1:3:3*NumPeaks, newstart(parameter)=newstart(parameter)*(1+randn/100); newstart(parameter+1)=newstart(parameter+1)*(1+randn/20); newstart(parameter+2)=newstart(parameter+1)*(1+randn/20); end % newstart=newstart TrialParameters=fminsearch(@(lambda)(fitGLv(lambda,xx,yy)),newstart); otherwise end % switch peakshape % Construct model from Trial parameters A=zeros(NumPeaks,n); for m=1:NumPeaks, switch peakshape(1) case 1 A(m,:)=gaussian(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 2 A(m,:)=lorentzian(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 3 A(m,:)=logistic(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 4 A(m,:)=pearson(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 5 A(m,:)=expgaussian(xx,TrialParameters(2*m-1),TrialParameters(2*m),-extra)'; case 6 A(m,:)=gaussian(xx,TrialParameters(m),TrialParameters(NumPeaks+1)); case 7 A(m,:)=lorentzian(xx,TrialParameters(m),TrialParameters(NumPeaks+1)); case 8 A(m,:)=expgaussian(xx,TrialParameters(m),TrialParameters(NumPeaks+1),-extra)'; case 9 A(m,:)=exppulse(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 10 A(m,:)=upsigmoid(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 11 A(m,:)=gaussian(xx,TrialParameters(m),FIXEDPARAMETERS); case 12 A(m,:)=lorentzian(xx,TrialParameters(m),FIXEDPARAMETERS); case 13 A(m,:)=GL(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 14 A(m,:)=BiGaussian(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 15 A(m,:)=BWF(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 16 A(m,:)=gaussian(xx,FIXEDPOSITIONS(m),TrialParameters(m)); case 17 A(m,:)=lorentzian(xx,FIXEDPOSITIONS(m),TrialParameters(m)); case 18 A(m,:)=explorentzian(xx,TrialParameters(2*m-1),TrialParameters(2*m),-extra)'; case 19 A(m,:)=alphafunction(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 20 A(m,:)=voigt(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 21 A(m,:)=triangular(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 22 A(m,:)=peakfunction(shapesvector(m),xx,TrialParameters(2*m-1),TrialParameters(2*m),extra(m)); case 23 A(m,:)=downsigmoid(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 24 A(m,:)=nbinpdf(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 25 A(m,:)=lognormal(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 26 A(m,:)=linslope(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 27 A(m,:)=d1gauss(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 28 A(m,:)=polynomial(xx,coeff); case 29 A(m,:)=segmented(xx,yy,PEAKHEIGHTS); case 30 A(m,:)=voigt(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); case 31 A(m,:)=expgaussian(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),-TrialParameters(3*m)); case 32 A(m,:)=pearson(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); case 33 A(m,:)=GL(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); otherwise end % switch for parameter=1:2:2*NumPeaks, newstart(parameter)=newstart(parameter)*(1+delta*(rand-.5)/500); newstart(parameter+1)=newstart(parameter+1)*(1+delta*(rand-.5)/100); end end % for NumPeaks % Multiplies each row by the corresponding amplitude and adds them up if peakshape(1)==29, % Segmented linear model=segmented(xx,yy,PEAKHEIGHTS); TrialParameters=PEAKHEIGHTS; Heights=ones(size(PEAKHEIGHTS)); else if AUTOZERO==3, baseline=PEAKHEIGHTS(1); Heights=PEAKHEIGHTS(2:1+NumPeaks); model=Heights'*A+baseline; else % size(PEAKHEIGHTS) % error check % size(A) model=PEAKHEIGHTS'*A; Heights=PEAKHEIGHTS; baseline=0; end end if peakshape(1)==28, % polynomial; model=polynomial(xx,coeff); TrialParameters=PEAKHEIGHTS; Heights=ones(size(PEAKHEIGHTS)); end % Compare trial model to data segment and compute the fit error MeanFitError=100*norm(yy-model)./(sqrt(n)*max(yy)); % Take only the single fit that has the lowest MeanFitError if MeanFitError<LowestError, if min(Heights)>=-BIPOLAR*10^100, % Consider only fits with positive peak heights LowestError=MeanFitError; % Assign LowestError to the lowest MeanFitError FitParameters=TrialParameters; % Assign FitParameters to the fit with the lowest MeanFitError BestStart=newstart; % Assign BestStart to the start with the lowest MeanFitError height=Heights; % Assign height to the PEAKHEIGHTS with the lowest MeanFitError bestmodel=model; % Assign bestmodel to the model with the lowest MeanFitError end % if min(PEAKHEIGHTS)>0 end % if MeanFitError<LowestError % ErrorVector(k)=MeanFitError; end % for k (NumTrials) Rsquared=1-(norm(yy-bestmodel)./norm(yy-mean(yy))); SStot=sum((yy-mean(yy)).^2); SSres=sum((yy-bestmodel).^2); Rsquared=1-(SSres./SStot); GOF=[LowestError Rsquared]; % Uncomment following 4 lines to monitor trail fit starts and errors. % StartMatrix=StartMatrix; % ErrorVector=ErrorVector; % matrix=[StartMatrix ErrorVector'] % std(StartMatrix) % Construct model from best-fit parameters AA=zeros(NumPeaks,600); xxx=linspace(min(xx),max(xx),600); % xxx=linspace(min(xx)-length(xx),max(xx)+length(xx),200); for m=1:NumPeaks, switch peakshape(1) case 1 AA(m,:)=gaussian(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 2 AA(m,:)=lorentzian(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 3 AA(m,:)=logistic(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 4 AA(m,:)=pearson(xxx,FitParameters(2*m-1),FitParameters(2*m),extra); case 5 AA(m,:)=expgaussian(xxx,FitParameters(2*m-1),FitParameters(2*m),-extra*length(xxx)./length(xx))'; case 6 AA(m,:)=gaussian(xxx,FitParameters(m),FitParameters(NumPeaks+1)); case 7 AA(m,:)=lorentzian(xxx,FitParameters(m),FitParameters(NumPeaks+1)); case 8 AA(m,:)=expgaussian(xxx,FitParameters(m),FitParameters(NumPeaks+1),-extra*length(xxx)./length(xx))'; case 9 AA(m,:)=exppulse(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 10 AA(m,:)=upsigmoid(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 11 AA(m,:)=gaussian(xxx,FitParameters(m),FIXEDPARAMETERS); case 12 AA(m,:)=lorentzian(xxx,FitParameters(m),FIXEDPARAMETERS); case 13 AA(m,:)=GL(xxx,FitParameters(2*m-1),FitParameters(2*m),extra); case 14 AA(m,:)=BiGaussian(xxx,FitParameters(2*m-1),FitParameters(2*m),extra); case 15 AA(m,:)=BWF(xxx,FitParameters(2*m-1),FitParameters(2*m),extra); case 16 AA(m,:)=gaussian(xxx,FIXEDPOSITIONS(m),FitParameters(m)); case 17 AA(m,:)=lorentzian(xxx,FIXEDPOSITIONS(m),FitParameters(m)); case 18 AA(m,:)=explorentzian(xxx,FitParameters(2*m-1),FitParameters(2*m),-extra*length(xxx)./length(xx))'; case 19 AA(m,:)=alphafunction(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 20 AA(m,:)=voigt(xxx,FitParameters(2*m-1),FitParameters(2*m),extra); case 21 AA(m,:)=triangular(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 22 AA(m,:)=peakfunction(shapesvector(m),xxx,FitParameters(2*m-1),FitParameters(2*m),extra(m)); case 23 AA(m,:)=downsigmoid(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 24 AA(m,:)=nbinpdf(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 25 AA(m,:)=lognormal(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 26 AA(m,:)=linslope(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 27 AA(m,:)=d1gauss(xxx,FitParameters(2*m-1),FitParameters(2*m)); case 28 AA(m,:)=polynomial(xxx,coeff); case 29 case 30 AA(m,:)=voigt(xxx,FitParameters(3*m-2),FitParameters(3*m-1),FitParameters(3*m)); case 31 AA(m,:)=expgaussian(xxx,FitParameters(3*m-2),FitParameters(3*m-1),-FitParameters(3*m)*length(xxx)./length(xx)); case 32 AA(m,:)=pearson(xxx,FitParameters(3*m-2),FitParameters(3*m-1),FitParameters(3*m)); case 33 AA(m,:)=GL(xxx,FitParameters(3*m-2),FitParameters(3*m-1),FitParameters(3*m)); otherwise end % switch end % for NumPeaks % Multiplies each row by the corresponding amplitude and adds them up if peakshape(1)==29, % Segmented linear mmodel=segmented(xx,yy,PEAKHEIGHTS); baseline=0; else heightsize=size(height'); AAsize=size(AA); if heightsize(2)==AAsize(1), mmodel=height'*AA+baseline; else mmodel=height*AA+baseline; end end % Top half of the figure shows original signal and the fitted model. if plots, subplot(2,1,1);plot(xx+xoffset,yy,'b.'); % Plot the original signal in blue dots hold on end if peakshape(1)==28, % Polynomial yi=polynomial(xxx,coeff); else for m=1:NumPeaks, if plots, plot(xxx+xoffset,height(m)*AA(m,:)+baseline,'g'),end % Plot the individual component peaks in green lines area(m)=trapz(xxx+xoffset,height(m)*AA(m,:)); % Compute the area of each component peak using trapezoidal method yi(m,:)=height(m)*AA(m,:); % Place y values of individual model peaks into matrix yi end end xi=xxx+xoffset; % Place the x-values of the individual model peaks into xi if plots, % Mark starting peak positions with vertical dashed magenta lines if peakshape(1)==16||peakshape(1)==17 else if peakshape(1)==29, % Segmented linear subplot(2,1,1);plot([PEAKHEIGHTS' PEAKHEIGHTS'],[0 max(yy)],'m--') else for marker=1:NumPeaks, markx=BestStart((2*marker)-1); subplot(2,1,1);plot([markx+xoffset markx+xoffset],[0 max(yy)],'m--') end % for end end % if peakshape % Plot the total model (sum of component peaks) in red lines if peakshape(1)==29, % Segmented linear mmodel=segmented(xx,yy,PEAKHEIGHTS); plot(xx+xoffset,mmodel,'r'); else plot(xxx+xoffset,mmodel,'r'); end hold off; lyy=min(yy); uyy=max(yy)+(max(yy)-min(yy))/10; if BIPOLAR, axis([min(xx) max(xx) lyy uyy]); ylabel('+ - mode') else axis([min(xx) max(xx) 0 uyy]); ylabel('+ mode') end switch AUTOZERO, case 0 title(['peakfit.m Version 7 No baseline correction']) case 1 title(['peakfit.m Version 7 Linear baseline subtraction']) case 2 title(['peakfit.m Version 7 Quadratic subtraction baseline']) case 3 title(['peakfit.m Version 7 Flat baseline correction']) end switch peakshape(1) case {4,20} xlabel(['Peaks = ' num2str(NumPeaks) ' Shape = ' ShapeString ' Min. Width = ' num2str(MINWIDTH) ' Shape Constant = ' num2str(extra) ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(100000*Rsquared)/100000) ] ) case {5,8,18} xlabel(['Peaks = ' num2str(NumPeaks) ' Shape = ' ShapeString ' Min. Width = ' num2str(MINWIDTH) ' Time Constant = ' num2str(extra) ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(100000*Rsquared)/100000) ] ) case 13 xlabel(['Peaks = ' num2str(NumPeaks) ' Shape = ' ShapeString ' Min. Width = ' num2str(MINWIDTH) ' % Gaussian = ' num2str(extra) ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(100000*Rsquared)/100000) ] ) case {14,15,22} xlabel(['Peaks = ' num2str(NumPeaks) ' Shape = ' ShapeString ' Min. Width = ' num2str(MINWIDTH) ' extra = ' num2str(extra) ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(100000*Rsquared)/100000) ] ) case 28 xlabel(['Shape = ' ShapeString ' Order = ' num2str(extra) ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(1000*LowestError)/1000) ] ) otherwise if peakshape(1)==29, % Segmented linear xlabel(['Breakpoints = ' num2str(NumPeaks) ' Shape = ' ShapeString ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(100000*Rsquared)/100000) ] ) else xlabel(['Peaks = ' num2str(NumPeaks) ' Shape = ' ShapeString ' Min. Width = ' num2str(MINWIDTH) ' Error = ' num2str(round(1000*LowestError)/1000) '% R2 = ' num2str(round(100000*Rsquared)/100000) ] ) end % if peakshape(1)==29 end % switch peakshape(1) % Bottom half of the figure shows the residuals and displays RMS error % between original signal and model residual=yy-bestmodel; subplot(2,1,2);plot(xx+xoffset,residual,'r.') axis([min(xx)+xoffset max(xx)+xoffset min(residual) max(residual)]); xlabel('Residual Plot') if NumTrials>1, title(['Best of ' num2str(NumTrials) ' fits']) else title(['Single fit']) end end % if plots % Put results into a matrix FitResults, one row for each peak, showing peak index number, % position, amplitude, and width. FitResults=zeros(NumPeaks,6); switch peakshape(1), case {6,7,8}, % equal-width peak models only for m=1:NumPeaks, if m==1, FitResults=[[round(m) FitParameters(m)+xoffset height(m) abs(FitParameters(NumPeaks+1)) area(m)]]; else FitResults=[FitResults ; [round(m) FitParameters(m)+xoffset height(m) abs(FitParameters(NumPeaks+1)) area(m)]]; end end case {11,12}, % Fixed-width shapes only for m=1:NumPeaks, if m==1, FitResults=[[round(m) FitParameters(m)+xoffset height(m) FIXEDPARAMETERS area(m)]]; else FitResults=[FitResults ; [round(m) FitParameters(m)+xoffset height(m) FIXEDPARAMETERS area(m)]]; end end case {16,17}, % Fixed-position shapes only for m=1:NumPeaks, if m==1, FitResults=[round(m) FIXEDPOSITIONS(m) height(m) FitParameters(m) area(m)]; else FitResults=[FitResults ; [round(m) FIXEDPOSITIONS(m) height(m) FitParameters(m) area(m)]]; end end case 28, % Simple polynomial fit FitResults=PEAKHEIGHTS; case 29, % Segmented linear fit FitResults=PEAKHEIGHTS; case {30,31,32,33} % Special case of shapes with 3 iterated variables for m=1:NumPeaks, if m==1, FitResults=[round(m) FitParameters(3*m-2) height(m) abs(FitParameters(3*m-1)) area(m) FitParameters(3*m)]; else FitResults=[FitResults ; [round(m) FitParameters(3*m-2) height(m) abs(FitParameters(3*m-1)) area(m)] FitParameters(3*m)]; end end otherwise % Normal shapes with 2 iterated variables for m=1:NumPeaks, if m==1, FitResults=[round(m) FitParameters(2*m-1)+xoffset height(m) abs(FitParameters(2*m)) area(m)]; else FitResults=[FitResults ; [round(m) FitParameters(2*m-1)+xoffset height(m) abs(FitParameters(2*m)) area(m)]]; end % if m==1 end % for m=1:NumPeaks, end % switch peakshape(1) % Display Fit Results on lower graph if plots, % Display Fit Results on lower graph subplot(2,1,2); startx=min(xx)+(max(xx)-min(xx))./20; dxx=(max(xx)-min(xx))./10; dyy=((max(residual)-min(residual))./10); starty=max(residual)-dyy; FigureSize=get(gcf,'Position'); switch peakshape(1) case {9,19,11} % Pulse and sigmoid shapes only text(startx,starty+dyy/2,['Peak # tau1 Height tau2 Area'] ); case 28, % Polynomial text(startx,starty+dyy/2,['Polynomial coefficients'] ); case 29 % Segmented linear text(startx,starty+dyy/2,['x-axis breakpoints'] ); case {30,31,32,33} % Special case of shapes with 3 iterated variables text(startx,starty+dyy/2,['Peak # Position Height Width Area Shape factor'] ); otherwise text(startx,starty+dyy/2,['Peak # Position Height Width Area '] ); end % Display FitResults using sprintf if peakshape(1)==28||peakshape(1)==29, % Polynomial or segmented linear for number=1:length(FitResults), column=1; itemstring=sprintf('%0.4g',FitResults(number)); xposition=startx+(1.7.*dxx.*(column-1).*(600./FigureSize(3))); yposition=starty-number.*dyy.*(400./FigureSize(4)); text(xposition,yposition,[' ' itemstring]); end else for peaknumber=1:NumPeaks, for column=1:5, itemstring=sprintf('%0.4g',FitResults(peaknumber,column)); xposition=startx+(1.7.*dxx.*(column-1).*(600./FigureSize(3))); yposition=starty-peaknumber.*dyy.*(400./FigureSize(4)); text(xposition,yposition,itemstring); end end xposition=startx; yposition=starty-(peaknumber+1).*dyy.*(400./FigureSize(4)); if AUTOZERO==3, text(xposition,yposition,[ 'Baseline= ' num2str(baseline) ]); end % if AUTOZERO end % if peakshape(1) if peakshape(1)==30 || peakshape(1)==31 || peakshape(1)==32 || peakshape(1)==33, for peaknumber=1:NumPeaks, column=6; itemstring=sprintf('%0.4g',FitParameters(3*peaknumber)); xposition=startx+(1.7.*dxx.*(column-1).*(600./FigureSize(3))); yposition=starty-peaknumber.*dyy.*(400./FigureSize(4)); text(xposition,yposition,itemstring); end end end % if plots if NumArgOut==8, if plots,disp('Computing bootstrap sampling statistics.....'),end BootstrapResultsMatrix=zeros(6,100,NumPeaks); BootstrapErrorMatrix=zeros(1,100,NumPeaks); clear bx by tic; for trial=1:100, n=1; bx=xx; by=yy; while n<length(xx)-1, if rand>.5, bx(n)=xx(n+1); by(n)=yy(n+1); end n=n+1; end bx=bx+xoffset; [FitResults,BootFitError]=fitpeaks(bx,by,NumPeaks,peakshape,extra,NumTrials,start,AUTOZERO,FIXEDPARAMETERS); for peak=1:NumPeaks, switch peakshape(1) case {30,31,32,33} BootstrapResultsMatrix(1:6,trial,peak)=FitResults(peak,1:6); otherwise BootstrapResultsMatrix(1:5,trial,peak)=FitResults(peak,1:5); end BootstrapErrorMatrix(:,trial,peak)=BootFitError; end end if plots,toc;end for peak=1:NumPeaks, if plots, disp(' ') disp(['Peak #',num2str(peak) ' Position Height Width Area Shape Factor']); end % if plots BootstrapMean=mean(real(BootstrapResultsMatrix(:,:,peak)')); BootstrapSTD=std(BootstrapResultsMatrix(:,:,peak)'); BootstrapIQR=iqr(BootstrapResultsMatrix(:,:,peak)'); PercentRSD=100.*BootstrapSTD./BootstrapMean; PercentIQR=100.*BootstrapIQR./BootstrapMean; BootstrapMean=BootstrapMean(2:6); BootstrapSTD=BootstrapSTD(2:6); BootstrapIQR=BootstrapIQR(2:6); PercentRSD=PercentRSD(2:6); PercentIQR=PercentIQR(2:6); if plots, disp(['Bootstrap Mean: ', num2str(BootstrapMean)]) disp(['Bootstrap STD: ', num2str(BootstrapSTD)]) disp(['Bootstrap IQR: ', num2str(BootstrapIQR)]) disp(['Percent RSD: ', num2str(PercentRSD)]) disp(['Percent IQR: ', num2str(PercentIQR)]) end % if plots BootResults(peak,:)=[BootstrapMean BootstrapSTD PercentRSD BootstrapIQR PercentIQR]; end % peak=1:NumPeaks, end % if NumArgOut==8, if AUTOZERO==3; else baseline=bkgcoef; end % ---------------------------------------------------------------------- function [FitResults,LowestError]=fitpeaks(xx,yy,NumPeaks,peakshape,extra,NumTrials,start,AUTOZERO,fixedparameters) % Based on peakfit Version 3: June, 2012. global PEAKHEIGHTS FIXEDPARAMETERS AUTOZERO BIPOLAR MINWIDTH coeff format short g format compact warning off all FIXEDPARAMETERS=fixedparameters; xoffset=0; if start==0;start=calcstart(xx,NumPeaks,xoffset);end PEAKHEIGHTS=zeros(1,NumPeaks); n=length(xx); newstart=start; coeff=0; LOGPLOT=0; % Perform peak fitting for selected peak shape using fminsearch function options = optimset('TolX',.001,'Display','off','MaxFunEvals',1000 ); LowestError=1000; % or any big number greater than largest error expected FitParameters=zeros(1,NumPeaks.*2); BestStart=zeros(1,NumPeaks.*2); height=zeros(1,NumPeaks); bestmodel=zeros(size(yy)); for k=1:NumTrials, % StartVector=newstart switch peakshape(1) case 1 TrialParameters=fminsearch(@(lambda)(fitgaussian(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 2 TrialParameters=fminsearch(@(lambda)(fitlorentzian(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 3 TrialParameters=fminsearch(@(lambda)(fitlogistic(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 4 TrialParameters=fminsearch(@(lambda)(fitpearson(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 5 zxx=[zeros(size(xx)) xx zeros(size(xx)) ]; zyy=[zeros(size(yy)) yy zeros(size(yy)) ]; TrialParameters=fminsearch(@(lambda)(fitexpgaussian(lambda,zxx,zyy,-extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 6 cwnewstart(1)=newstart(1); for pc=2:NumPeaks, cwnewstart(pc)=newstart(2.*pc-1); end cwnewstart(NumPeaks+1)=(max(xx)-min(xx))/5; TrialParameters=fminsearch(@(lambda)(fitewgaussian(lambda,xx,yy)),cwnewstart,options); for Peak=1:NumPeaks; if TrialParameters(NumPeaks+1)<MINWIDTH, TrialParameters(NumPeaks+1)=MINWIDTH; end end case 7 cwnewstart(1)=newstart(1); for pc=2:NumPeaks, cwnewstart(pc)=newstart(2.*pc-1); end cwnewstart(NumPeaks+1)=(max(xx)-min(xx))/5; TrialParameters=fminsearch(@(lambda)(fitewlorentzian(lambda,xx,yy)),cwnewstart,options); for Peak=1:NumPeaks; if TrialParameters(NumPeaks+1)<MINWIDTH, TrialParameters(NumPeaks+1)=MINWIDTH; end end case 8 cwnewstart(1)=newstart(1); for pc=2:NumPeaks, cwnewstart(pc)=newstart(2.*pc-1); end cwnewstart(NumPeaks+1)=(max(xx)-min(xx))/5; TrialParameters=fminsearch(@(lambda)(fitexpewgaussian(lambda,xx,yy,-extra)),cwnewstart,options); for Peak=1:NumPeaks; if TrialParameters(NumPeaks+1)<MINWIDTH, TrialParameters(NumPeaks+1)=MINWIDTH; end end case 9 TrialParameters=fminsearch(@(lambda)(fitexppulse(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 10 TrialParameters=fminsearch(@(lambda)(fitupsigmoid(lambda,xx,yy)),newstar,optionst); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 11 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=min(xx)+pc.*(max(xx)-min(xx))./(NumPeaks+1); end TrialParameters=fminsearch(@(lambda)(FitFWGaussian(lambda,xx,yy)),fixedstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 12 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=min(xx)+pc.*(max(xx)-min(xx))./(NumPeaks+1); end TrialParameters=fminsearch(@(lambda)(FitFWLorentzian(lambda,xx,yy)),fixedstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 13 TrialParameters=fminsearch(@(lambda)(fitGL(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 14 TrialParameters=fminsearch(@(lambda)(fitBiGaussian(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 15 TrialParameters=fminsearch(@(lambda)(fitBWF(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 16 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=(max(xx)-min(xx))./(NumPeaks+1); end TrialParameters=fminsearch(@(lambda)(FitFPGaussian(lambda,xx,yy)),fixedstart,options); for Peak=1:NumPeaks; if TrialParameters(Peak)<MINWIDTH, TrialParameters(Peak)=MINWIDTH; end end case 17 fixedstart=[]; for pc=1:NumPeaks, fixedstart(pc)=(max(xx)-min(xx))./(NumPeaks+1); end TrialParameters=fminsearch(@(lambda)(FitFPLorentzian(lambda,xx,yy)),fixedstart,options); for Peak=1:NumPeaks; if TrialParameters(Peak)<MINWIDTH, TrialParameters(Peak)=MINWIDTH; end end case 18 zxx=[zeros(size(xx)) xx zeros(size(xx)) ]; zyy=[zeros(size(yy)) yy zeros(size(yy)) ]; TrialParameters=fminsearch(@(lambda)(fitexplorentzian(lambda,zxx,zyy,-extra)),newstart,options); case 19 TrialParameters=fminsearch(@(lambda)(alphafunction(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 20 TrialParameters=fminsearch(@(lambda)(fitvoigt(lambda,xx,yy,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 21 TrialParameters=fminsearch(@(lambda)(fittriangular(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 22 TrialParameters=fminsearch(@(lambda)(fitmultiple(lambda,xx,yy,shapesvector,extra)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH(Peak), TrialParameters(2*Peak)=MINWIDTH(Peak); end end case 23 TrialParameters=fminsearch(@(lambda)(fitdownsigmoid(lambda,xx,yy)),newstar,optionst); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 24 TrialParameters=fminsearch(@(lambda)(fitnbinpdf(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 25 TrialParameters=fminsearch(@(lambda)(fitlognpdf(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 26 TrialParameters=fminsearch(@(lambda)(fitlinslope(lambda,xx,yy)),polyfit(xx,yy,1),options); coeff=TrialParameters; case 27 TrialParameters=fminsearch(@(lambda)(fitd1gauss(lambda,xx,yy)),newstart,options); for Peak=1:NumPeaks; if TrialParameters(2*Peak)<MINWIDTH, TrialParameters(2*Peak)=MINWIDTH; end end case 28 TrialParameters=fitpolynomial(xx,yy,extra); case 29 TrialParameters=fminsearch(@(lambda)(fitsegmented(lambda,xx,yy)),newstart,options); case 30 TrialParameters=fminsearch(@(lambda)(fitvoigtv(lambda,xx,yy)),newstart); case 31 zxx=[zeros(size(xx)) xx zeros(size(xx)) ]; zyy=[zeros(size(yy)) yy zeros(size(yy)) ]; TrialParameters=fminsearch(@(lambda)(fitexpgaussianv(lambda,zxx,zyy)),newstart); case 32 TrialParameters=fminsearch(@(lambda)(fitpearsonv(lambda,xx,yy)),newstart); case 33 TrialParameters=fminsearch(@(lambda)(fitGLv(lambda,xx,yy)),newstart); otherwise end % switch peakshape for peaks=1:NumPeaks, peakindex=2*peaks-1; newstart(peakindex)=start(peakindex)-xoffset; end % Construct model from Trial parameters A=zeros(NumPeaks,n); for m=1:NumPeaks, switch peakshape(1) case 1 A(m,:)=gaussian(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 2 A(m,:)=lorentzian(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 3 A(m,:)=logistic(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 4 A(m,:)=pearson(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 5 A(m,:)=expgaussian(xx,TrialParameters(2*m-1),TrialParameters(2*m),-extra)'; case 6 A(m,:)=gaussian(xx,TrialParameters(m),TrialParameters(NumPeaks+1)); case 7 A(m,:)=lorentzian(xx,TrialParameters(m),TrialParameters(NumPeaks+1)); case 8 A(m,:)=expgaussian(xx,TrialParameters(m),TrialParameters(NumPeaks+1),-extra)'; case 9 A(m,:)=exppulse(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 10 A(m,:)=upsigmoid(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 11 A(m,:)=gaussian(xx,TrialParameters(m),FIXEDPARAMETERS); case 12 A(m,:)=lorentzian(xx,TrialParameters(m),FIXEDPARAMETERS); case 13 A(m,:)=GL(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 14 A(m,:)=BiGaussian(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 15 A(m,:)=BWF(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 16 A(m,:)=gaussian(xx,FIXEDPOSITIONS(m),TrialParameters(m)); case 17 A(m,:)=lorentzian(xx,FIXEDPOSITIONS(m),TrialParameters(m)); case 18 A(m,:)=explorentzian(xx,TrialParameters(2*m-1),TrialParameters(2*m),-extra)'; case 19 A(m,:)=alphafunction(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 20 A(m,:)=voigt(xx,TrialParameters(2*m-1),TrialParameters(2*m),extra); case 21 A(m,:)=triangular(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 22 A(m,:)=peakfunction(shapesvector(m),xx,TrialParameters(2*m-1),TrialParameters(2*m),extra(m)); case 23 A(m,:)=downsigmoid(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 24 A(m,:)=nbinpdf(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 25 A(m,:)=lognormal(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 26 A(m,:)=linslope(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 27 A(m,:)=d1gauss(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 28 A(m,:)=polynomial(xx,TrialParameters(2*m-1),TrialParameters(2*m)); case 29 A(m,:)=segmented(xx,yy,PEAKHEIGHTS); case 30 A(m,:)=voigt(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); case 31 A(m,:)=expgaussian(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); case 32 A(m,:)=pearson(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); case 33 A(m,:)=GL(xx,TrialParameters(3*m-2),TrialParameters(3*m-1),TrialParameters(3*m)); end % switch end % for % Multiplies each row by the corresponding amplitude and adds them up if peakshape(1)==29, % Segmented linear model=segmented(xx,yy,PEAKHEIGHTS); TrialParameters=coeff; Heights=ones(size(coeff)); else if AUTOZERO==3, baseline=PEAKHEIGHTS(1); Heights=PEAKHEIGHTS(2:1+NumPeaks); model=Heights'*A+baseline; else model=PEAKHEIGHTS'*A; Heights=PEAKHEIGHTS; baseline=0; end end % Compare trial model to data segment and compute the fit error MeanFitError=100*norm(yy-model)./(sqrt(n)*max(yy)); % Take only the single fit that has the lowest MeanFitError if MeanFitError<LowestError, if min(Heights)>=-BIPOLAR*10^100, % Consider only fits with positive peak heights LowestError=MeanFitError; % Assign LowestError to the lowest MeanFitError FitParameters=TrialParameters; % Assign FitParameters to the fit with the lowest MeanFitError height=Heights; % Assign height to the PEAKHEIGHTS with the lowest MeanFitError end % if min(PEAKHEIGHTS)>0 end % if MeanFitError<LowestError end % for k (NumTrials) Rsquared=1-(norm(yy-bestmodel)./norm(yy-mean(yy))); SStot=sum((yy-mean(yy)).^2); SSres=sum((yy-bestmodel).^2); Rsquared=1-(SSres./SStot); GOF=[LowestError Rsquared]; for m=1:NumPeaks, area(m)=trapz(xx+xoffset,height(m)*A(m,:)); % Compute the area of each component peak using trapezoidal method end % Put results into a matrix FitResults, one row for each peak, showing peak index number, % position, amplitude, and width. FitResults=zeros(NumPeaks,6); switch peakshape(1), case {6,7,8}, % equal-width peak models only for m=1:NumPeaks, if m==1, FitResults=[[round(m) FitParameters(m)+xoffset height(m) abs(FitParameters(NumPeaks+1)) area(m)]]; else FitResults=[FitResults ; [round(m) FitParameters(m)+xoffset height(m) abs(FitParameters(NumPeaks+1)) area(m)]]; end end case {11,12}, % Fixed-width shapes only for m=1:NumPeaks, if m==1, FitResults=[[round(m) FitParameters(m)+xoffset height(m) FIXEDPARAMETERS area(m)]]; else FitResults=[FitResults ; [round(m) FitParameters(m)+xoffset height(m) FIXEDPARAMETERS area(m)]]; end end case {16,17}, % Fixed-position shapes only for m=1:NumPeaks, if m==1, FitResults=[round(m) FIXEDPOSITIONS(m) height(m) FitParameters(m) area(m)]; else FitResults=[FitResults ; [round(m) FIXEDPOSITIONS(m) height(m) FitParameters(m) area(m)]]; end end case 28, % Simple polynomial fit FitResults=PEAKHEIGHTS; case 29, % Segmented linear fit FitResults=PEAKHEIGHTS; case {30,31,32,33} % Special case of shapes with 3 iterated variables for m=1:NumPeaks, if m==1, FitResults=[round(m) FitParameters(3*m-2) height(m) abs(FitParameters(3*m-1)) area(m) FitParameters(3*m)]; else FitResults=[FitResults ; [round(m) FitParameters(3*m-2) height(m) abs(FitParameters(3*m-1)) area(m) FitParameters(3*m)]]; end end otherwise % Normal shapes with 2 iterated variables for m=1:NumPeaks, if m==1, FitResults=[round(m) FitParameters(2*m-1)+xoffset height(m) abs(FitParameters(2*m)) area(m)]; else FitResults=[FitResults ; [round(m) FitParameters(2*m-1)+xoffset height(m) abs(FitParameters(2*m)) area(m)]]; end % if m==1 end % for m=1:NumPeaks, end % switch peakshape(1) % ---------------------------------------------------------------------- function start=calcstart(xx,NumPeaks,xoffset) n=max(xx)-min(xx); start=[]; startpos=[n/(NumPeaks+1):n/(NumPeaks+1):n-(n/(NumPeaks+1))]+min(xx); for marker=1:NumPeaks, markx=startpos(marker)+ xoffset; start=[start markx n/ (3.*NumPeaks)]; end % for marker % ---------------------------------------------------------------------- function [index,closestval]=val2ind(x,val) % Returns the index and the value of the element of vector x that is closest to val % If more than one element is equally close, returns vectors of indicies and values % Tom O'Haver (toh@umd.edu) October 2006 % Examples: If x=[1 2 4 3 5 9 6 4 5 3 1], then val2ind(x,6)=7 and val2ind(x,5.1)=[5 9] % [indices values]=val2ind(x,3.3) returns indices = [4 10] and values = [3 3] dif=abs(x-val); index=find((dif-min(dif))==0); closestval=x(index); % ---------------------------------------------------------------------- function err = fitgaussian(lambda,t,y) % Fitting function for a Gaussian band signal. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT numpeaks=round(length(lambda)/2); A = zeros(length(t),numpeaks); for j = 1:numpeaks, % if lambda(2*j)<MINWIDTH,lambda(2*j)=MINWIDTH;end A(:,j) = gaussian(t,lambda(2*j-1),lambda(2*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitewgaussian(lambda,t,y) % Fitting function for a Gaussian band signal with equal peak widths. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT numpeaks=round(length(lambda)-1); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = gaussian(t,lambda(j),lambda(numpeaks+1))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = FitFWGaussian(lambda,t,y) % Fitting function for a fixed width Gaussian global PEAKHEIGHTS AUTOZERO FIXEDPARAMETERS BIPOLAR LOGPLOT numpeaks=round(length(lambda)); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = gaussian(t,lambda(j),FIXEDPARAMETERS)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = FitFPGaussian(lambda,t,y) % Fitting function for fixed-position Gaussians global PEAKHEIGHTS AUTOZERO FIXEDPARAMETERS BIPOLAR LOGPLOT numpeaks=round(length(lambda)); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = gaussian(t,FIXEDPARAMETERS(j), lambda(j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = FitFPLorentzian(lambda,t,y) % Fitting function for fixed-position Lorentzians global PEAKHEIGHTS AUTOZERO FIXEDPARAMETERS BIPOLAR numpeaks=round(length(lambda)); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = lorentzian(t,FIXEDPARAMETERS(j), lambda(j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; err = norm(z-y'); % ---------------------------------------------------------------------- function err = FitFWLorentzian(lambda,t,y) % Fitting function for fixed width Lorentzian global PEAKHEIGHTS AUTOZERO FIXEDPARAMETERS BIPOLAR LOGPLOT numpeaks=round(length(lambda)); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = lorentzian(t,lambda(j),FIXEDPARAMETERS)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitewlorentzian(lambda,t,y) % Fitting function for a Lorentzian band signal with equal peak widths. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT numpeaks=round(length(lambda)-1); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = lorentzian(t,lambda(j),lambda(numpeaks+1))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = gaussian(x,pos,wid) % gaussian(X,pos,wid) = gaussian peak centered on pos, half-width=wid % X may be scalar, vector, or matrix, pos and wid both scalar % Examples: gaussian([0 1 2],1,2) gives result [0.5000 1.0000 0.5000] % plot(gaussian([1:100],50,20)) displays gaussian band centered at 50 with width 20. g = exp(-((x-pos)./(0.6005615.*wid)).^2); % ---------------------------------------------------------------------- function err = fitlorentzian(lambda,t,y) % Fitting function for single lorentzian, lambda(1)=position, lambda(2)=width % Fitgauss assumes a lorentzian function global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = lorentzian(t,lambda(2*j-1),lambda(2*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = lorentzian(x,position,width) % lorentzian(x,position,width) Lorentzian function. % where x may be scalar, vector, or matrix % position and width scalar % T. C. O'Haver, 1988 % Example: lorentzian([1 2 3],2,2) gives result [0.5 1 0.5] g=ones(size(x))./(1+((x-position)./(0.5.*width)).^2); % ---------------------------------------------------------------------- function err = fitlogistic(lambda,t,y) % Fitting function for logistic, lambda(1)=position, lambda(2)=width % between the data and the values computed by the current % function of lambda. Fitlogistic assumes a logistic function % T. C. O'Haver, May 2006 global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = logistic(t,lambda(2*j-1),lambda(2*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = logistic(x,pos,wid) % logistic function. pos=position; wid=half-width (both scalar) % logistic(x,pos,wid), where x may be scalar, vector, or matrix % pos=position; wid=half-width (both scalar) % T. C. O'Haver, 1991 n = exp(-((x-pos)/(.477.*wid)) .^2); g = (2.*n)./(1+n); % ---------------------------------------------------------------------- function err = fittriangular(lambda,t,y) % Fitting function for triangular, lambda(1)=position, lambda(2)=width % between the data and the values computed by the current % function of lambda. Fittriangular assumes a triangular function % T. C. O'Haver, May 2006 global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = triangular(t,lambda(2*j-1),lambda(2*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = triangular(x,pos,wid) %triangle function. pos=position; wid=half-width (both scalar) %trianglar(x,pos,wid), where x may be scalar or vector, %pos=position; wid=half-width (both scalar) % T. C. O'Haver, 1991 % Example % x=[0:.1:10];plot(x,trianglar(x,5.5,2.3),'.') g=1-(1./wid) .*abs(x-pos); for i=1:length(x), if g(i)<0,g(i)=0;end end % ---------------------------------------------------------------------- function err = fitpearson(lambda,t,y,shapeconstant) % Fitting functions for a Pearson 7 band signal. % T. C. O'Haver (toh@umd.edu), Version 1.3, October 23, 2006. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = pearson(t,lambda(2*j-1),lambda(2*j),shapeconstant)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitpearsonv(lambda,t,y) % Fitting functions for pearson function with independently variable % percent Gaussian % T. C. O'Haver (toh@umd.edu), 2015. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/3)); for j = 1:length(lambda)/3, A(:,j) = pearson(t,lambda(3*j-2),lambda(3*j-1),lambda(3*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = pearson(x,pos,wid,m) % Pearson VII function. % g = pearson7(x,pos,wid,m) where x may be scalar, vector, or matrix % pos=position; wid=half-width (both scalar) % m=some number % T. C. O'Haver, 1990 g=ones(size(x))./(1+((x-pos)./((0.5.^(2/m)).*wid)).^2).^m; % ---------------------------------------------------------------------- function err = fitexpgaussian(lambda,t,y,timeconstant) % Fitting functions for a exponentially-broadened Gaussian band signal. % T. C. O'Haver, October 23, 2006. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = expgaussian(t,lambda(2*j-1),lambda(2*j),timeconstant); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitexplorentzian(lambda,t,y,timeconstant) % Fitting functions for a exponentially-broadened lorentzian band signal. % T. C. O'Haver, 2013. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = explorentzian(t,lambda(2*j-1),lambda(2*j),timeconstant); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitexpewgaussian(lambda,t,y,timeconstant) % Fitting function for exponentially-broadened Gaussian bands with equal peak widths. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT numpeaks=round(length(lambda)-1); A = zeros(length(t),numpeaks); for j = 1:numpeaks, A(:,j) = expgaussian(t,lambda(j),lambda(numpeaks+1),timeconstant); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitexpgaussianv(lambda,t,y) % Fitting functions for exponentially-broadened Gaussians with % independently variable time constants % T. C. O'Haver (toh@umd.edu), 2015. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/3)); for j = 1:length(lambda)/3, A(:,j) = expgaussian(t,lambda(3*j-2),lambda(3*j-1),-lambda(3*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = expgaussian(x,pos,wid,timeconstant) % Exponentially-broadened gaussian(x,pos,wid) = gaussian peak centered on pos, half-width=wid % x may be scalar, vector, or matrix, pos and wid both scalar % T. C. O'Haver, 2006 g = exp(-((x-pos)./(0.6005615.*wid)) .^2); g = ExpBroaden(g',timeconstant); % ---------------------------------------------------------------------- function g = explorentzian(x,pos,wid,timeconstant) % Exponentially-broadened lorentzian(x,pos,wid) = lorentzian peak centered on pos, half-width=wid % x may be scalar, vector, or matrix, pos and wid both scalar % T. C. O'Haver, 2013 g = ones(size(x))./(1+((x-pos)./(0.5.*wid)).^2); g = ExpBroaden(g',timeconstant); % ---------------------------------------------------------------------- function yb = ExpBroaden(y,t) % ExpBroaden(y,t) zero pads y and convolutes result by an exponential decay % of time constant t by multiplying Fourier transforms and inverse % transforming the result. hly=round(length(y)./2); ey=[y(1).*ones(1,hly)';y;y(length(y)).*ones(1,hly)']; % figure(2);plot(ey);figure(1); fy=fft(ey); a=exp(-(1:length(fy))./t); fa=fft(a); fy1=fy.*fa'; ybz=real(ifft(fy1))./sum(a); yb=ybz(hly+2:length(ybz)-hly+1); % ---------------------------------------------------------------------- function err = fitexppulse(tau,x,y) % Iterative fit of the sum of exponential pulses % of the form Height.*exp(-tau1.*x).*(1-exp(-tau2.*x))) global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = exppulse(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = exppulse(x,t1,t2) % Exponential pulse of the form % g = (x-spoint)./pos.*exp(1-(x-spoint)./pos); e=(x-t1)./t2; p = 4*exp(-e).*(1-exp(-e)); p=p .* (p>0); g = p'; % ---------------------------------------------------------------------- function err = fitalphafunction(tau,x,y) % Iterative fit of the sum of alpha funciton % of the form Height.*exp(-tau1.*x).*(1-exp(-tau2.*x))) global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = alphafunction(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = alphafunction(x,pos,spoint) % alpha function. pos=position; wid=half-width (both scalar) % alphafunction(x,pos,wid), where x may be scalar, vector, or matrix % pos=position; wid=half-width (both scalar) % Taekyung Kwon, July 2013 g = (x-spoint)./pos.*exp(1-(x-spoint)./pos); for m=1:length(x);if g(m)<0;g(m)=0;end;end % ---------------------------------------------------------------------- function err = fitdownsigmoid(tau,x,y) % Fitting function for iterative fit to the sum of % downward moving sigmiods global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = downsigmoid(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitupsigmoid(tau,x,y) % Fitting function for iterative fit to the sum of % upwards moving sigmiods global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = upsigmoid(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g=downsigmoid(x,t1,t2) % down step sigmoid g=.5-.5*erf(real((x-t1)/sqrt(2*t2))); % ---------------------------------------------------------------------- function g=upsigmoid(x,t1,t2) % up step sigmoid g=1/2 + 1/2* erf(real((x-t1)/sqrt(2*t2))); % ---------------------------------------------------------------------- function err = fitGL(lambda,t,y,shapeconstant) % Fitting functions for Gaussian/Lorentzian blend. % T. C. O'Haver (toh@umd.edu), 2012. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = GL(t,lambda(2*j-1),lambda(2*j),shapeconstant)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitGLv(lambda,t,y) % Fitting functions for Gaussian/Lorentzian blend function with % independently variable percent Gaussian % T. C. O'Haver (toh@umd.edu), 2015. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/3)); for j = 1:length(lambda)/3, A(:,j) = GL(t,lambda(3*j-2),lambda(3*j-1),lambda(3*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = GL(x,pos,wid,m) % Gaussian/Lorentzian blend. m = percent Gaussian character % pos=position; wid=half-width % m = percent Gaussian character. % T. C. O'Haver, 2012 % sizex=size(x) % sizepos=size(pos) % sizewid=size(wid) % sizem=size(m) g=2.*((m/100).*gaussian(x,pos,wid)+(1-(m(1)/100)).*lorentzian(x,pos,wid))/2; % ---------------------------------------------------------------------- function err = fitvoigt(lambda,t,y,shapeconstant) % Fitting functions for Voigt profile function % T. C. O'Haver (toh@umd.edu), 2013. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = voigt(t,lambda(2*j-1),lambda(2*j),shapeconstant)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitvoigtv(lambda,t,y) % Fitting functions for Voigt profile function with independently variable % alphas % T. C. O'Haver (toh@umd.edu), 2015. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/3)); for j = 1:length(lambda)/3, A(:,j) = voigt(t,lambda(3*j-2),lambda(3*j-1),lambda(3*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g=voigt(xx,pos,gD,alpha) % Voigt profile function. xx is the independent variable (energy, % wavelength, etc), gD is the Doppler (Gaussian) width, and alpha is the % shape constant (ratio of the Lorentzian width gL to the Doppler width gD. % Based on Chong Tao's "Voigt lineshape spectrum simulation", % File ID: #26707 % alpha=alpha gL=alpha.*gD; gV = 0.5346*gL + sqrt(0.2166*gL.^2 + gD.^2); x = gL/gV; y = abs(xx-pos)/gV; g = 1/(2*gV*(1.065 + 0.447*x + 0.058*x^2))*((1-x)*exp(-0.693.*y.^2) + (x./(1+y.^2)) + 0.016*(1-x)*x*(exp(-0.0841.*y.^2.25)-1./(1 + 0.021.*y.^2.25))); g=g./max(g); % ---------------------------------------------------------------------- function err = fitBiGaussian(lambda,t,y,shapeconstant) % Fitting functions for BiGaussian. % T. C. O'Haver (toh@umd.edu), 2012. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = BiGaussian(t,lambda(2*j-1),lambda(2*j),shapeconstant)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = BiGaussian(x,pos,wid,m) % BiGaussian (different widths on leading edge and trailing edge). % pos=position; wid=width % m determines shape; symmetrical if m=50. % T. C. O'Haver, 2012 lx=length(x); hx=val2ind(x,pos); g(1:hx)=gaussian(x(1:hx),pos,wid*(m/100)); g(hx+1:lx)=gaussian(x(hx+1:lx),pos,wid*(1-m/100)); % ---------------------------------------------------------------------- function err = fitBWF(lambda,t,y,shapeconstant) % Fitting function for Breit-Wigner-Fano. % T. C. O'Haver (toh@umd.edu), 2014. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = BWF(t,lambda(2*j-1),lambda(2*j),shapeconstant)'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = BWF(x,pos,wid,m) % BWF (Breit-Wigner-Fano) http://en.wikipedia.org/wiki/Fano_resonance % pos=position; wid=width; m=Fano factor % T. C. O'Haver, 2014 y=((m*wid/2+x-pos).^2)./(((wid/2).^2)+(x-pos).^2); % y=((1+(x-pos./(m.*wid))).^2)./(1+((x-pos)./wid).^2); g=y./max(y); % ---------------------------------------------------------------------- function err = fitnbinpdf(tau,x,y) % Fitting function for iterative fit to the sum of % Negative Binomial Distributions % (http://www.mathworks.com/help/stats/negative-binomial-distribution.html) global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = nbinpdf(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function err = fitlognpdf(tau,x,y) % Fitting function for iterative fit to the sum of % Lognormal Distributions % (http://www.mathworks.com/help/stats/lognormal-distribution.html) global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = lognormal(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g = lognormal(x,pos,wid) % lognormal function. pos=position; wid=half-width (both scalar) % lognormal(x,pos,wid), where x may be scalar, vector, or matrix % pos=position; wid=half-width (both scalar) % T. C. O'Haver, 1991 g = exp(-(log(x/pos)/(0.01.*wid)) .^2); % ---------------------------------------------------------------------- function err = fitsine(tau,x,y) % Fitting function for iterative fit to the sum of % sine waves (alpha test, NRFPT) global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, A(:,j) = sine(x,tau(2*j-1),tau(2*j)); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function g=sine(x,f,phase) % Sine wave (alpha test) g=sin(2*pi*f*(x+phase)); % ---------------------------------------------------------------------- function err = fitd1gauss(lambda,t,y) % Fitting functions for the first derivative of a Gaussian % T. C. O'Haver, 2014 global PEAKHEIGHTS AUTOZERO BIPOLAR A = zeros(length(t),round(length(lambda)/2)); for j = 1:length(lambda)/2, A(:,j) = d1gauss(t,lambda(2*j-1),lambda(2*j))'; end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; err = norm(z-y'); % ---------------------------------------------------------------------- function y=d1gauss(x,p,w) % First derivative of Gaussian (alpha test) y=-(5.54518.*(x-p).*exp(-(2.77259.*(p-x).^2)./w^2))./w.^2; y=y./max(y); % ---------------------------------------------------------------------- function coeff = fitpolynomial(t,y,order) coeff=polyfit(t,y,order); % order=order % coeff=coeff % ---------------------------------------------------------------------- function y=polynomial(t,coeff) y=polyval(coeff,t); % ---------------------------------------------------------------------- function err = fitsegmented(lambda,t,y) % Fitting functions for articulated segmented linear % T. C. O'Haver, 2014 global LOGPLOT breakpoints=[t(1) lambda max(t)]; z = segmented(t,y,breakpoints); % lengthz=length(z); if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y); end % ---------------------------------------------------------------------- function yi=segmented(x,y,segs) global PEAKHEIGHTS clear yy for n=1:length(segs) yind=val2ind(x,segs(n)); yy(n)=y(yind(1)); end yi=INTERP1(segs,yy,x); PEAKHEIGHTS=segs; % ---------------------------------------------------------------------- function err = fitlinslope(tau,x,y) % Fitting function for iterative fit to linear function global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT A = zeros(length(x),round(length(tau)/2)); for j = 1:length(tau)/2, z = (x.*tau(2*j-1)+tau(2*j))'; A(:,j) = z./max(z); end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function y=linslope(x,slope,intercept) y=x.*slope+intercept; % y=y./max(y); % ---------------------------------------------------------------------- function b=iqr(a) % b = IQR(a) returns the interquartile range of the values in a. For % vector input, b is the difference between the 75th and 25th percentiles % of a. For matrix input, b is a row vector containing the interquartile % range of each column of a. % T. C. O'Haver, 2012 mina=min(a); sizea=size(a); NumCols=sizea(2); for n=1:NumCols,b(:,n)=a(:,n)-mina(n);end Sorteda=sort(b); lx=length(Sorteda); SecondQuartile=round(lx/4); FourthQuartile=3*round(lx/4); b=abs(Sorteda(FourthQuartile,:)-Sorteda(SecondQuartile,:)); % ---------------------------------------------------------------------- function err = fitmultiple(lambda,t,y,shapesvector,m) % Fitting function for a multiple-shape band signal. % The sequence of peak shapes are defined by the vector "shape". % The vector "m" determines the shape of variable-shape peaks. global PEAKHEIGHTS AUTOZERO BIPOLAR LOGPLOT coeff numpeaks=round(length(lambda)/2); A = zeros(length(t),numpeaks); for j = 1:numpeaks, if shapesvector(j)==28, coeff=polyfit(t,y,m(j)); A(:,j) = polyval(coeff,t); else A(:,j) = peakfunction(shapesvector(j),t,lambda(2*j-1),lambda(2*j),m(j))'; end end if AUTOZERO==3,A=[ones(size(y))' A];end if BIPOLAR,PEAKHEIGHTS=A\y';else PEAKHEIGHTS=abs(A\y');end z = A*PEAKHEIGHTS; if LOGPLOT, err = norm(log10(z)-log10(y)'); else err = norm(z-y'); end % ---------------------------------------------------------------------- function p=peakfunction(shape,x,pos,wid,m,coeff) % function that generates any of 20 peak types specified by number. 'shape' % specifies the shape type of each peak in the signal: "peakshape" = 1-20. % 1=Gaussian 2=Lorentzian, 3=logistic, 4=Pearson, 5=exponentionally % broadened Gaussian; 9=exponential pulse, 10=up sigmoid, % 13=Gaussian/Lorentzian blend; 14=BiGaussian, 15=Breit-Wigner-Fano (BWF) , % 18=exponentionally broadened Lorentzian; 19=alpha function; 20=Voigt % profile; 21=triangular; 23=down sigmoid; 25=lognormal. "m" is required % for variable-shape peaks only. switch shape, case 1 p=gaussian(x,pos,wid); case 2 p=lorentzian(x,pos,wid); case 3 p=logistic(x,pos,wid); case 4 p=pearson(x,pos,wid,m); case 5 p=expgaussian(x,pos,wid,m); case 6 p=gaussian(x,pos,wid); case 7 p=lorentzian(x,pos,wid); case 8 p=expgaussian(x,pos,wid,m)'; case 9 p=exppulse(x,pos,wid); case 10 p=upsigmoid(x,pos,wid); case 11 p=gaussian(x,pos,wid); case 12 p=lorentzian(x,pos,wid); case 13 p=GL(x,pos,wid,m); case 14 p=BiGaussian(x,pos,wid,m); case 15 p=BWF(x,pos,wid,m); case 16 p=gaussian(x,pos,wid); case 17 p=lorentzian(x,pos,wid); case 18 p=explorentzian(x,pos,wid,m)'; case 19 p=alphafunction(x,pos,wid); case 20 p=voigt(x,pos,wid,m); case 21 p=triangular(x,pos,wid); case 23 p=downsigmoid(x,pos,wid); case 25 p=lognormal(x,pos,wid); case 26 p=linslope(x,pos,wid); case 27 p=d1gauss(x,pos,wid); case 28 p=polynomial(x,coeff); otherwise end % switch function [Height, Position, Width]=gaussfit(x,y) % Converts y-axis to a log scale, fits a parabola % (quadratic) to the (x,ln(y)) data, then calculates % the position, width, and height of the % Gaussian from the three coefficients of the % quadratic fit. This is accurate only if the data have % no baseline offset (that is, trends to zero far off the % peak) and if there are no zeros or negative values in y. % % Example 1: Simplest Gaussian data set % [Height, Position, Width]=gaussfit([1 2 3],[1 2 1]) % returns Height = 2, Position = 2, Width = 2 % % Example 2: best fit to synthetic noisy Gaussian % x=50:150;y=100.*gaussian(x,100,100)+10.*randn(size(x)); % [Height,Position,Width]=gaussfit(x,y) % returns [Height,Position,Width] clustered around 100,100,100. % % Example 3: plots data set as points and best-fit Gaussian as line % x=[1 2 3 4 5];y=[1 2 2.5 2 1]; % [Height,Position,Width]=gaussfit(x,y); % plot(x,y,'o',linspace(0,8),Height.*gaussian(linspace(0,8),Position,Width)) % Copyright (c) 2012, Thomas C. O'Haver maxy=max(y); for p=1:length(y), if y(p)<(maxy/100),y(p)=maxy/100;end end % for p=1:length(y), z=log(y); coef=polyfit(x,z,2); a=coef(3); b=coef(2); c=coef(1); Height=exp(a-c*(b/(2*c))^2); Position=-b/(2*c); Width=2.35482/(sqrt(2)*sqrt(-c));