VBA_dcmMatrices.m

function [A,B,C,D,dim] = VBA_dcmMatrices(out,theta)
%VBA_DCMMATRICES matrices A,B, C D of a DCM


try 
    inF = out.options.inF{1};
catch
    inF = out.options.inF;
end
n = numel(inF.n1);
nu = out.dim.u-1;
try
nr = numel(inF.r);
catch
    nr=0;
end
dim.n=n;
dim.nr=nr;
dim.nu=nu;

% inF=out.options.inF;
% theta = posterior.muTheta;

A = inF.A;
indA = inF.indA;
if ~isempty(indA)
    A(A~=0) = theta(indA);
    A = A - exp(theta(inF.indself)).*eye(n);
else
    A = A - exp(theta(inF.indself)).*eye(n);
end

B = inF.B;
indB = inF.indB;
for i=1:nu
    if ~isempty(indB{i})
        B{i}(B{i}~=0) = theta(indB{i});
    end
end

C = inF.C;
indC = inF.indC;
if ~isempty(indC)
    C(C~=0) = theta(indC);
end

D = inF.D;
indD = inF.indD;
for i=1:n
    if ~isempty(indD{i})
        D{i}(D{i}~=0) = theta(indD{i});
    end
end

return

%% ########################################################################
try
hself = - diag(exp(theta(inF.indhself))) ;


if out.options.extended
hA = inF.hA;
indhA = inF.indhA;
if ~isempty(indhA)
    hA(hA~=0) = theta(indhA);
end

hB = inF.hB;
indhB = inF.indhB;
for i=1:nu
    if ~isempty(indhB{i})
        hB{i}(hB{i}~=0) = theta(indhB{i});
    end
end

hC = inF.hC;
indhC = inF.indhC;
if ~isempty(indhC)
    hC(hC~=0) = theta(indhC);
end

A = [A  zeros(n,nr);
     hA hself*eye(nr)] ;

C = [C ; hC] ;
end

for i=1:nu
    B{i} = [[B{i}; hB{i}] zeros(n+nr,nr)];
end
end

end