Package stallone.api.hmm

Examples of stallone.api.hmm.IHMM


            System.exit(0);
        }

        if (cmd.singlePointEstimate)
        {
            IHMM pmm = hmm.pmm(cmd.discreteTrajectories, cmd.nhidden, cmd.tau, cmd.timeshift, cmd.hmmNIter, cmd.hmmDecTol, null, null);
           
            IDoubleArray hmmTC = pmm.getTransitionMatrix();
            io.writeString(cmd.outdir+"/hmmTc.dat", doubles.toString(hmmTC,"\t","\n"));
            IDoubleArray hmmChi = pmm.getOutputParameters();
            io.writeString(cmd.outdir+"/hmmChi.dat", doubles.toString(hmmChi,"\t","\n"));
        }
        else if (cmd.hmmTimescalesEstimate)
        {
            IIntList lagtimes = intsNew.list(0);
            lagtimes.append(cmd.taumin);
            for (double tau = cmd.taumin; tau <= cmd.taumax; tau *= cmd.taumult)
            {
                int lag = (int)tau;
                if (lag != lagtimes.get(lagtimes.size()-1))
                    lagtimes.append(lag);
            }

            PrintStream itsout = new PrintStream(cmd.outdir+"/hmm-its.dat");
           
            IDoubleArray lastTC = cmd.init_T;
            IDoubleArray lastChi = cmd.init_Chi;
           
            for (int i=0; i<lagtimes.size(); i++)
            {
                //set lag and timeshift
                int lag = lagtimes.get(i);
                System.out.println("\ntau = "+lag+"\n");

                // in direct mode, erase the results from last lag. Otherwise use as initialization.
                if (cmd.direct)
                {
                    lastTC = null;
                    lastChi = null;
                }

                System.out.println("Hidden state: "+cmd.nhidden);
                IHMM pmm = hmm.pmm(cmd.discreteTrajectories, cmd.nhidden, lag, cmd.timeshift, cmd.hmmNIter, cmd.hmmDecTol, lastTC, lastChi);
               
                // remember estimation results and use them as a next initializer.
                lastTC = pmm.getTransitionMatrix();
                lastChi = pmm.getOutputParameters();
                //double[] logL = cmd.ninja.getHMMLikelihoodHistory();
                double lastLogL = pmm.getLogLikelihood();

                // output timescales
                IDoubleArray hmmTimescales = msm.timescales(lastTC, lag);
                itsout.println(lag+"\t"+lastLogL+"\t"+doubles.toString(hmmTimescales,""," "));
               
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