FitChoCr.m

    function [FitParams, rejectframe, residCr]  = FitChoCr(freq, FrameData, initx,Larmor)
    warning off;
    %All parameters in initx are in standard units.
    % Conversion factors to FWHM in Hz, delta f0 in Hz, phase in degrees
    conv = [1 2*Larmor Larmor (180/pi) 1 1 1];
    initx=initx./conv;
    
    nlinopts = statset('nlinfit');
    nlinopts = statset(nlinopts, 'MaxIter', 1e5, 'Display','Off');
    nframes = size(FrameData,2);
    
    for jj = 1:nframes
        % [fit_param, resnorm, resid, exitflag ]  = ...
        %     lsqcurvefit(@(xdummy,ydummy) LorentzModel(xdummy, ydummy), initx, ...
        % 		  freq', real(FrameData(:,jj)));
        %120112 cje
        %add lsqcurvefit initialisation here too, keep nlin initialisers
        %separate from LSQ
        
     %   size(real(FrameData(:,jj)))
     %   size(TwoLorentzModel(initx,freq'))
        
        [fit_param, resnorm, resid, exitflag ]  = ...
            lsqcurvefit(@(xdummy,ydummy) TwoLorentzModel(xdummy, ydummy), initx, ...
                         freq', real(FrameData(:,jj)));
              initxLSQ = fit_param;
        
        [fit_param, residCr] = nlinfit(freq', real(FrameData(:,jj)), ...
            @(xdummy, ydummy) TwoLorentzModel(xdummy, ydummy), ...
            initxLSQ, nlinopts);
        FitParams(jj,:) = fit_param;
        fit_plot = TwoLorentzModel(fit_param, freq);
        
        %  figure(3); plot(freq', real(FrameData(:,jj)), 'g', freq', fit_plot,'b');
          %pause(0.8)
        %  set(gca,'XDir','reverse');
        %  input('next')
    end
    
    for kk=1:size(FitParams,1)
        if FitParams(kk,1)<0
            FitParams(kk,4)= FitParams(kk,4)+pi;
        end
    end
    
    % Need to deal with phase wrap:
    % Convert to complex number then recalculate phase within 2*pi range
    phase_wrapped = FitParams(:,4);
    cmplx = cos(phase_wrapped) + 1i * sin(phase_wrapped);
    phase_unwrapped = angle(cmplx);
    

    % then fix to be within -pi..pi
    offsetpos =  pi*lt(phase_unwrapped, -pi/2);
    offsetneg = -pi*gt(phase_unwrapped,  pi/2);
    phase_unwrapped = phase_unwrapped + offsetpos + offsetneg;
    FitParams(:,4) = phase_unwrapped;
    
    % Fix area and linewidth to be positive

    FitParams(:,1) = abs(FitParams(:,1));
    FitParams(:,2) = abs(FitParams(:,2));
    
    % Conversion factors to FWHM in Hz, delta f0 in Hz, phase in degrees
    conv = repmat([1 (2*Larmor) (Larmor) (180/pi) 1 1 1], [nframes 1]);
    
    FitParams = FitParams .* conv;
    
    % Reject any point where the fit params - area, fwhm, phase
    %  or freq are > 3stdev away from the mean
    % set reject criteria for all fit parameters
    MeanFitParams = mean(FitParams, 1);
    UpperLim = repmat(MeanFitParams + 3*std(FitParams,1), [nframes 1]);
    LowerLim = repmat(MeanFitParams - 3*std(FitParams,1), [nframes 1]);
    %but don't reject on linear, const baseline fit vals
    UpperLim(:,5:6) = Inf;
    LowerLim(:,5:6) = -Inf;
    rejectframe = gt(FitParams, UpperLim);
    rejectframe = rejectframe + lt(FitParams, LowerLim);
    rejectframe = max(rejectframe,[],2);
    
    end