* Tc is a nstates x nstates coarse-grained transition matrix
* and Pout is a nstates x n output probability matrix.
*/
public IDoubleArray[] coarseGrain(IDoubleArray T, int nstates)
{
MetastableSubspace ms = new MetastableSubspace(T);
ms.coarseGrain(nstates);
IDoubleArray[] res = {ms.getCoarseGrainedTransitionMatrix(), ms.getObservationProbabilities()};
return res;
}