Gannet2plotprepostalign.m

function Gannet2plotprepostalign(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 = length(MRS_struct.spec.diff(:,1));
numspec = 2;

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

%Water scaling is touhg if we have no water scans! Comment out
% % Find Water amplitude max, across all Pfiles
% waterheight = abs(max(MRS_struct.waterspec(specno,:),[],2));
% waterheight = repmat(waterheight, [2 1]);
% heightrescale = repmat((1./waterheight), [1 length(MRS_struct.spec.diff(1,:))]);
% SpectraToPlot = SpectraToPlot .* heightrescale;

% Estimate baseline from between Glx and GABA
%specbaseline = mean(real(SpectraToPlot(1,17250:17650)),2);
z=abs(MRS_struct.freq-3.6);
Glx_right=find(min(z)==z);
z=abs(MRS_struct.freq-3.3);
GABA_left=find(min(z)==z);
z=abs(MRS_struct.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);

plotstackoffset = [ 0 : (numspec-1) ]';
plotstackoffset = plotstackoffset * gabaheight;
plotstackoffset = plotstackoffset - specbaseline;

SpectraToPlot = SpectraToPlot + ...
    repmat(plotstackoffset, [ 1  length(MRS_struct.spec.diff(1,:))]);

%figure(99)
plot(MRS_struct.freq, real(SpectraToPlot));
%legendtxt = regexprep(MRS_struct.pfile{specno}, '_','-');
legendtxt = {'post', 'pre'};
hl=legend(legendtxt);
set(hl,'EdgeColor',[1 1 1]);
set(gca,'XDir','reverse');
oldaxis = axis;
% yaxis max = top spec baseline + 2*meangabaheight
yaxismax = (numspec + 2) *gabaheight; % top spec + 2* height of gaba
yaxismin =  - 2* gabaheight; % extend 2* gaba heights below zero

axis([0 5  yaxismin yaxismax])