Gannetplotnoalign.m

function Gannetplotnoalign(MRS_struct, specno)
%function MRSplotprepostalign(MRS_struct, specno)
% Plots pre and post alignment spectra in MRSLoadPfiles
% 110214:  Scale spectra by the peak _height_ of water
%          Plot multiple spectra as a stack - baselines offset
%            by mean height of GABA

numspec = 2;
SpectraToPlot = [MRS_struct.spec.diff(specno,:)];

% Estimate baseline from between Glx and GABA
z=abs(MRS_struct.spec.freq-3.6);
Glx_right=find(min(z)==z);
z=abs(MRS_struct.spec.freq-3.3);
GABA_left=find(min(z)==z);
z=abs(MRS_struct.spec.freq-2.8);
GABA_right=find(min(z)==z);
specbaseline = mean(real(SpectraToPlot(1,Glx_right:GABA_left)),2);
% averaged gaba height across all scans - to estimate stack spacing
gabaheight = abs(max(SpectraToPlot(1,Glx_right:GABA_right),[],2));
gabaheight = mean(gabaheight);

plot(MRS_struct.spec.freq, real(SpectraToPlot));
legendtxt = {'no align'};
hl=legend(legendtxt);
set(hl,'EdgeColor',[1 1 1]);
set(gca,'XDir','reverse');
oldaxis = axis;
yaxismax = (numspec + 2) *gabaheight; % top spec + 2* height of gaba
yaxismin =  - 2* gabaheight; % extend 2* gaba heights below zero
axis([0 5  yaxismin yaxismax])