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Adding connectivity functions
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@aojeda
aojeda committed Sep 14, 2019
1 parent e0030c2 commit 8a5941b
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Showing 3 changed files with 199 additions and 23 deletions.
159 changes: 159 additions & 0 deletions Connectivity/SourceConnectivity.m
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Original file line number Diff line number Diff line change
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function SourceConnectivity
fig = findall(0,'Name','Source Connectivity');
if ~isempty(fig)
figure(fig);
return;
end
fig = figure('Name','Source Connectivity','NumberTitle',false,'Menu','none','Toolbar','none','Units','normalized');
fig.Position(3:4) = [0.3766 0.5157];
fig.UserData = struct('M',[],'Y',[],'C',[],'L',[]);

p = fileparts(which('headModel.m'));
p = fullfile(p,'+vis','icons');
playIcon = imread([p filesep 'Gnome-media-playback-start.svg.png']);
helpIcon = imread([p filesep 'Gnome-help-browser.svg.png']);
plotIcon = imread([p filesep 'Gnome-emblem-photos.svg.png']);

pnt = uipanel(fig,'Units','normalized','Position',[0 0.9015 1 0.1000]);
uicontrol(pnt,'style','text','String','Data directory','Units','Normalized','Position',[0.0057 0.5 0.2075 0.375]);
uicontrol(pnt,'style','edit','Units','Normalized', 'Position',[0.2095 0.5 0.6188 0.375],'tag','Data directory');
uicontrol(pnt,'style','pushbutton','String','Select','Units','Normalized', 'Position',[0.8302 0.5 0.1472 0.375],'callback',@callback_select1);

uicontrol(pnt,'style','text','String','Results directory','Units','Normalized','Position',[0.0057 0.0542 0.2075 0.375]);
uicontrol(pnt,'style','edit','Units','Normalized', 'Position',[0.2095 0.1015 0.6188 0.375],'tag','Results directory');
uicontrol(pnt,'style','pushbutton','String','Select','Units','Normalized', 'Position',[0.8302 0.0859 0.1472 0.375],'callback',@callback_select2);

ax = axes(fig, 'Units','normalized');
ax.Position = [0.1300 0.2 0.75 0.65];
pn = uipanel(fig,'Units','normalized');
pn.Position = [0 0 1 0.0529];
lb = uicontrol(pn,'style','text','string','Metric','Units','normalized');
lb.Position = [0.0059 0 0.06 0.8000];
tx = uicontrol(pn,'style','popupmenu','string',{'Mutual Information','Transfer Entropy','Correlation'},'Units','normalized');
tx.Position = [0.07 0.0400 0.2 0.8800];

lb = uicontrol(pn,'style','text','string','WinSize (sec)','Units','normalized');
lb.Position = [0.2860 0 0.1322 0.8000];
tx = uicontrol(pn,'style','edit','string','0.5','Units','normalized','tag','winSize');
tx.Position = [0.4178 0.0800 0.0789 0.8000];

lb = uicontrol(pn,'style','text','string','Overlap (%)','Units','normalized');
lb.Position = [0.5078 0 0.1322 0.8000];
tx = uicontrol(pn,'style','edit','string','50','Units','normalized','tag','overlap');
tx.Position = [0.6335 0.0800 0.0626 0.8000];

tx = uicontrol(pn,'style','radiobutton','string','Normalize','Units','normalized','tag','normalize');
tx.Position = [0.7192 0.0800 0.1215 0.8000];

bt1 = uicontrol(pn,'style','pushbutton','CData',playIcon,'TooltipString','Run','Units','normalized','callback',@callback_run, 'Units','normalized');
bt1.Position = [0.8624 0 0.0436 1.0000];
bt2 = uicontrol(pn,'style','pushbutton','CData',plotIcon,'TooltipString','Vualize','callback',@callback_plot,'Units','normalized');
bt2.Position = [0.9084 0 0.0436 1.0000];
bt3 = uicontrol(pn,'style','pushbutton','CData',helpIcon,'TooltipString','Help','callback',@callback_help,'Units','normalized');
bt3.Position = [0.9530 0 0.0436 1.0000];
end

%%
function callback_select1(src,evnt)
fig = src.Parent;
selpath = uigetdir(pwd, 'Select data folder');
if selpath
set(findall(fig,'tag','Data directory'),'String',selpath);
end
end

function callback_select2(src,evnt)
fig = src.Parent;
selpath = uigetdir(pwd, 'Select data folder');
if selpath
set(findall(fig,'tag','Results directory'),'String',selpath);
end
end

function callback_run(src,evnt)
fig = src.Parent.Parent;
src = get(findall(fig,'tag','Data directory'), 'String');
if ~exist(src,'dir')
return;
end
dest = get(findall(fig,'tag','Results directory'), 'String');
h = findall(fig,'style','popupmenu');
metric = lower(h.String{h.Value});
winSize = str2double(get(findall(fig,'tag','winSize'), 'String'));
overlap = str2double(get(findall(fig,'tag','overlap'), 'String'))/100;
normalize = get(findall(fig,'tag','normalize'), 'Value');
dest = fullfile(dest,metric);
mkdir(dest)

if isempty(winSize), error('Invalid value of parameter WinSize');end
if isempty(overlap), error('Invalid value of parameter Overlap');end

files = pickfiles(src, '.set');
n = size(files,1);
jFrame = get(handle(fig),'JavaFrame');
try
jRootPane = jFrame.fHG1Client.getWindow;
catch
jRootPane = jFrame.fHG2Client.getWindow;
end
jStatusBar = com.mathworks.mwswing.MJStatusBar;
javaObjectEDT(jStatusBar);
jProgressBar = javax.swing.JProgressBar;
javaObjectEDT(jProgressBar);
set(jProgressBar, 'Minimum',0, 'Maximum',100, 'Value',0);
jStatusBar.add(jProgressBar,'West');
jRootPane.setStatusBar(jStatusBar);
jStatusBar.setVisible(1);
jStatusBar.setText('Running...');
drawnow
for subject=1:n
file = deblank(files(subject,:));
[~,fileName] = fileparts(file);
EEG = pop_loadset(file);
EEG = srcConnectivityCont(EEG, metric, winSize, overlap, normalize);
pop_saveset(EEG,'filepath',dest,'filename',['conn_' fileName],'savemode','onefile');
jProgressBar.setValue(100*subject/n);
end
jStatusBar.setText('');
jStatusBar.setVisible(0);
jProgressBar.setValue(0);
end

function callback_plot(src,evnt)
fig = src.Parent.Parent;
dest = get(findall(fig,'tag','Results directory'), 'String');
files = pickfiles(dest, '.set');
if ~exist(dest,'dir')
return;
end
n = size(files,1);
C = [];
for subject=1:n
file = deblank(files(subject,:));
EEG = pop_loadset(file);
C = cat(4,C,EEG.etc.conn.C);
end
h = findall(fig,'style','popupmenu');
metric = lower(h.String{h.Value});

ax = findall(fig,'type','axes');
axes(ax)

T = mean(C,4);
T = bsxfun(@minus,T, mean(T,3));
mx = prctile(abs(T(:)),95);
cnn = Connectivity(T(:,:,1), EEG.etc.src.roi, metric);
cnn.image(ax)

for k=2:length(EEG.etc.conn.times)
cnn.C = T(:,:,k);
cnn.image(ax);
xlabel([num2str(EEG.etc.conn.times(k)) ' ms'])
caxis ([-mx mx]);
pause(0.25)
end
end

function callback_help(src,evnt)
web('https://github.com/aojeda/dsi/wiki/How-to-add-new-artifact-scalp-projections-to-the-existing-artifact-dictionary','-browser');
end
55 changes: 35 additions & 20 deletions Connectivity/conditionalTransferEntropy.m
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,9 @@
normalize = 'false';
end
[n,m] = size(X);
if n<m
X = repmat(X,ceil((m-n)/n)+1,1);
end
teCalc=javaObject('infodynamics.measures.continuous.kraskov.ConditionalTransferEntropyCalculatorKraskov');
teCalc.setProperty('k', num2str(k));
teCalc.setProperty('NORMALISE', normalize);
Expand All @@ -102,28 +105,40 @@
fprintf('%i%%',(prc_c)*10)
end
if findLag
for k=1:n
I(k) = mutualInformation(X(:,indJ(c)),circshift(X(:,indI(c)),k-1));
end

% Find a significant delay
z = zscore(I);
d = find(z > norminv(1-(0.005/n)));
if ~isempty(d)
[~,loc] = max(z(d));
d = d(loc)-1;
% for k=1:n
% I(k) = mutualInformation(X(:,indJ(c)),circshift(X(:,indI(c)),k-1));
% end
[acor,lag] = xcorr(X(:,indJ(c)),X(:,indI(c)));
[~,I] = max(abs(acor));
d = -lag(I);
theta(indJ(c),indI(c)) = d;
if theta(indJ(c),indI(c)) > n/2
d = (n-theta(indJ(c),indI(c)));
tmp = indI(c);
indI(c) = indJ(c);
indJ(c) = tmp;
theta(indJ(c),indI(c)) = d;
if theta(indJ(c),indI(c)) > n/2
d = (n-theta(indJ(c),indI(c)));
tmp = indI(c);
indI(c) = indJ(c);
indJ(c) = tmp;
theta(indJ(c),indI(c)) = d;
theta(indI(c),indJ(c)) = 0;
end
else
continue
theta(indI(c),indJ(c)) = 0;
end

% % Find a significant delay
% z = zscore(I);
% d = find(z > norminv(1-(0.005/n)));
% if ~isempty(d)
% [~,loc] = max(z(d));
% d = d(loc)-1;
% theta(indJ(c),indI(c)) = d;
% if theta(indJ(c),indI(c)) > n/2
% d = (n-theta(indJ(c),indI(c)));
% tmp = indI(c);
% indI(c) = indJ(c);
% indJ(c) = tmp;
% theta(indJ(c),indI(c)) = d;
% theta(indI(c),indJ(c)) = 0;
% end
% else
% continue
% end
end
teCalc.initialise(...
1,1, ... % Destination embedding length (Schreiber k=1) and delays
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8 changes: 5 additions & 3 deletions Connectivity/pairwiseMutualInformation.m
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Original file line number Diff line number Diff line change
@@ -1,13 +1,15 @@
function [I,ind,indi,indj] = pairwiseMutualInformation(X,normalize)
function [I,ind,indi,indj] = pairwiseMutualInformation(X,normalize, kneig)
if nargin < 3, kneig=4;end
X = X(:,:);
n = size(X,2);
I = zeros(n);
ind = triu(ones(n),1);
[indi,indj] = ind2sub([n n],find(ind(:)));
nv = length(indi);
Iv = zeros(nv);
Iv = zeros(nv,1);
parfor k=1:nv
Iv(k) = mutualInformation(X(:,indi(k)),X(:,indj(k)),normalize);
Iv(k) = mutualInformation(X(:,indi(k)),X(:,indj(k)),normalize, kneig);
%Iv(k) = mutualInformation_deprecated(X(:,indi(k)),X(:,indj(k)));
end
for k=1:nv
I(indi(k), indj(k)) = Iv(k);
Expand Down

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