gpnddisimUpdateKernels.m

function model = gpnddisimUpdateKernels(model)

% GPSIMUPDATEKERNELS Updates the kernel representations in the GPSIM structure.
% FORMAT
% DESC updates any representations of the kernel in the model
% structure, such as invK, logDetK or K.
% ARG model : the model structure for which kernels are being
% updated.
% RETURN model : the model structure with the kernels updated.
%
% SEEALSO gpsimExpandParam, gpsimCreate
%
% COPYRIGHT Neil D. Lawrence, 2006
%  
% MODIFIED : Pei Gao, 2008

% GPSIM
  
eps = 1e-6;                             % minimum noise variance for the
                                        % RBF kernel of TF.

if isfield(model, 'proteinPrior') && isfield(model, 'timesCell')
  k = real(kernCompute(model.kern, model.timesCell));
  if model.includeNoise
    noiseVar = [zeros(model.kern.comp{1}.diagBlockDim{1}, 1); model.yvar];
  else
    noiseVar = [eps*ones(model.kern.diagBlockDim{1}, 1); model.yvar];
  end
else
  k = real(kernCompute(model.kern, model.t));
  noiseVar = model.yvar;
end

model.K = k + diag(noiseVar);
%model.K
%figure;imagesc(model.K)
%trace(model.K)
%rcond(model.K)
%eig(model.K)
%pause

%model.K

%model.K
%tempdiag=diag(model.K);
%tempK=model.K./sqrt(tempdiag*tempdiag')
% imagesc(log(abs(model.K./sqrt(tempdiag*tempdiag'))))
% pause

%model.K
%pause

[model.invK, U, jitter] = pdinv(model.K);
if jitter>1e-4 && isfield(model, 'debug') && model.debug,
  warning('gpsimUpdateKernels added jitter of %2.4f\n', jitter)
end
model.logDetK = logdet(model.K, U);