bug fix: in getJ2.m, matrices were not reshape right when containing …

…multiple trials

refactor: plotSpec.m and plotSpecGram.m now replace the various plotPsd....m and plotCoh....m

addWin.m

@@ -13,22 +13,34 @@ function addWin(H,gram,x,y)
 Fs = gram.param.Fs;
 winSz = gram.win(1) + 0.5/Fs;
 if contains(H.Title.String,'timeseries')
-    yLim = ylim;
-    xLim = xlim;
-    if isempty(x)
-        x = xLim(1); x = x.*[1 1];
-        xx = x + [0 1].*winSz;
+    if size(gram.t,2)>1
+        y = ylim;
+        xx = gram.t(:,:,:,:,:,:,1);
+        yy = repmat(y(1),[size(xx,1) 1]);
+        line(xx,yy,'Color','m','linewidth',3)
+
+        xx = gram.t(:,:,:,:,:,:,end);
+        yy = repmat(y(2),[size(xx,1) 1]);
+        line(xx,yy,'Color','m','linewidth',3)
     else
-        x = x.*[1 1];
-        xx = x + [-0.5 0.5].*winSz;
-    end
-    if isempty(y) || y==-inf
-        y = yLim(1);
-    elseif y==inf
-        y = yLim(2);
+        yLim = ylim;
+        xLim = xlim;
+        if isempty(x)
+            x = xLim(1); x = x.*[1 1];
+            xx = x + [0 1].*winSz;
+        else
+            x = x.*[1 1];
+            xx = x + [-0.5 0.5].*winSz;
+        end
+        if isempty(y) || y==-inf
+            y = yLim(1);
+        elseif y==inf
+            y = yLim(2);
+        end
+        y = y.*[1 1];
+        line(xx,y,'Color','m','linewidth',3)
     end
-    y = y.*[1 1];
-    line(xx,y,'Color','m','linewidth',3)
+
 elseif contains(H.Title.String,'spectrogram') || contains(H.Title.String,'coherogram')
     im = findobj(H.Children,'type','image');
     if isempty(x)

getJ2.m

@@ -12,10 +12,16 @@
 
 
 tp2 = reshape(  tp .* exp(-f.*t*2*pi*1i)  ,[N Et*R*K*F*1*Wt]);
-d2  = reshape(  d - mean(d,1)             ,[N  E*R*1*1*V*W ]); % removing the mean here
+d2  = reshape(  d - mean(d,1)             ,[N E*R*1*1*V*W]); % removing the mean here
 
 d2 = permute(d2,[2 1]);
 J = d2*tp2; % [V E*R*K*F*1*W]
+% [E*R*1*1*V*W Et*R*K*F*1*Wt]
 
-J = reshape(J,[V E R K F 1 W]); % [V E R K F 1 W]
-J = permute(J,[6 2 3 4 5 1 7]); % [N E R K F V W]
+J = reshape(J,[E*R*1*1*V*W Et R K F 1 Wt]);
+J = permute(J,[2 3 4 5 6 7 1]);
+J = reshape(J,[Et R K F 1 Wt E R 1 1 V W]);
+J = permute(J,[13 7 2 3 4 11 6 1 5 8 9 10 12]); %[N ,E ,R ,K,F,V,W]
+if any(size(J,9:15)~=1); dbstack; error('X'); end
+% J = reshape(J,[V E R K F 1 W]); % [V E R K F 1 W]
+% J = permute(J,[6 2 3 4 5 1 7]); % [N E R K F V W]

plotPsd2.m

@@ -1,7 +1,9 @@
 function [ax,F] = plotPsd2(volPsd,H,tWin)
 if ~exist('H','var'); H = [];                             end
 if isempty(H);        H = figure('WindowStyle','docked'); end
-if ~exist('tWin','var'); tWin = [];                             end
+if ~exist('tWin','var'); tWin = [];                       end
+if isfield(volPsd,'dsgn') && isfield(volPsd.dsgn,'f0'); f0 = volPsd.dsgn.f0; else; f0 = []; end
+
 
 switch class(H)
     case 'matlab.graphics.layout.TiledChartLayout'
@@ -52,6 +54,10 @@
     addFreq([],volPsd.psdTrialGram.onsetList,volPsd.psdTrialGram.durList)
 end
 
+if ~isempty(f0)
+    xline(f0,'--b')
+end
+
 if isfield(volPsd,'psdTrialGramMD') && ~isempty(volPsd.psdTrialGramMD) && ~isempty(tWin)
     t   = volPsd.psdTrialGramMD.t(1,1,1,1,1,1,:,1);
     f   = volPsd.psdTrialGramMD.f(1,1,1,1,:,1,1,1);

plotSpec.m

@@ -0,0 +1,104 @@
+function [ax,F] = plotSpec(volPsd,metricLabel,H,tWin)
+if ~exist('H','var'); H = [];                             end
+if isempty(H);        H = figure('WindowStyle','docked'); end
+
+if isfield(volPsd,'dsgn') && isfield(volPsd.dsgn,'f0'); f0 = volPsd.dsgn.f0; else; f0 = []; end
+
+if ~exist('tWin','var'); tWin = [];                       end
+if ~exist('metricLabel','var'); metricLabel = [];                             end
+if isempty(metricLabel);        metricLabel = 'psd'; end % 'psd' 'coh'
+
+
+switch class(H)
+    case 'matlab.graphics.layout.TiledChartLayout'
+        F = H.Parent;
+    case 'matlab.ui.Figure'
+        F = H;
+    otherwise
+end
+
+figure(F);
+ax = {};
+ax{end+1} = nexttile;
+
+
+%% Select approrpiate data
+switch metricLabel
+    case 'psd'
+        mt    = volPsd.psd;
+        vec   = mt.PSD;
+        label = 'spatially averaged spectrum';
+    case 'coh'
+        mt    = volPsd.svd;
+        vec   = mt.COH;
+        label = 'coherence spectrum';
+    otherwise
+        dbstack; error('code trhat')
+end
+
+
+
+
+%%% average across space
+vec = squeeze(mean(vec,6));
+f = squeeze(mt.f);
+% f   = squeeze(volPsd.f);
+% psd = squeeze(mean(volPsd.vec,2));
+plot(f,vec,'k')
+grid on
+axis tight
+xlabel('f (Hz)')
+switch metricLabel
+    case 'psd'
+        ylabel('psd')
+        ax{end}.YScale = 'log';
+    case 'coh'
+        ylabel('coherence')
+    otherwise
+        dbstack; error('code trhat')
+end
+
+
+K = mt.K;
+T = mt.T;
+[TW,W] = K2W(T,K,0);
+
+paramStr = ['(K=' num2str(K) '; 2W=' num2str(W*2,'%0.4f') 'Hz; T=' num2str(T,'%0.2f') 'sec); TW=' num2str(TW)];
+title(['spatially averaged spectrum ' paramStr])
+
+yLim = vec(f>0.01);
+yLim = [min(yLim) max(yLim)];
+ylim(yLim)
+xlim([0 f(end)])
+
+addW([],volPsd.psd)
+
+
+
+if isfield(volPsd,'psdTrialGram') && ~isempty(volPsd.psdTrialGram)
+    addFreq([],volPsd.psdTrialGram.onsetList,volPsd.psdTrialGram.durList)
+end
+
+if ~isempty(f0)
+    xline(f0,'--b')
+end
+
+if isfield(volPsd,'psdTrialGramMD') && ~isempty(volPsd.psdTrialGramMD) && ~isempty(tWin)
+    dbstack; error('double-check that');
+    t   = volPsd.psdTrialGramMD.t(1,1,1,1,1,1,:,1);
+    f   = volPsd.psdTrialGramMD.f(1,1,1,1,:,1,1,1);
+    if tWin==inf
+        psd = mean(mean(volPsd.psdTrialGramMD.vec.psdPC(:,:,:,:,:,:,:,:),6),7);
+    else
+        [~,wInd] = min(abs(t-tWin));
+        psd = mean(volPsd.psdTrialGramMD.vec.psdPC(:,:,:,:,:,:,wInd,:),6);
+    end
+    plot(squeeze(f),squeeze(psd),'--k')
+end
+
+
+ax = [ax{:}];
+
+
+
+