///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below.       //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
// 2007, 2008, 2009, 2010, 2014, 2015 by Peter Spirtes, Richard Scheines, Joseph   //
// Ramsey, and Clark Glymour.                                                //
//                                                                           //
// This program is free software; you can redistribute it and/or modify      //
// it under the terms of the GNU General Public License as published by      //
// the Free Software Foundation; either version 2 of the License, or         //
// (at your option) any later version.                                       //
//                                                                           //
// This program is distributed in the hope that it will be useful,           //
// but WITHOUT ANY WARRANTY; without even the implied warranty of            //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             //
// GNU General Public License for more details.                              //
//                                                                           //
// You should have received a copy of the GNU General Public License         //
// along with this program; if not, write to the Free Software               //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
///////////////////////////////////////////////////////////////////////////////

package edu.cmu.tetrad.sem;

import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.NodeType;
import edu.cmu.tetrad.graph.SemGraph;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradMatrix;
import edu.cmu.tetrad.util.TetradVector;

import java.util.List;

/**
 * Optimizes a DAG SEM with no hidden variables using closed formula
 * regressions. IT SHOULD NOT BE USED WITH SEMs THAT ARE NOT DAGS OR CONTAIN
 * HIDDEN NODES. IT ALSO ASSUMES THAT ALL OBSERVED NODES APPEAR FIRST IN
 * semIm.getSemPm().getDag().getNodes(), I.E., ERROR NODES ARE INSERTED ONLY
 * AFTER MEASURED NODES IN THIS LIST.
 *
 * @author Ricardo Silva
 */

public class SemOptimizerRegression implements SemOptimizer {
    static final long serialVersionUID = 23L;
    private int numRestarts = 1;

    //=============================CONSTRUCTORS============================//

    /**
     * Blank constructor.
     */
    public SemOptimizerRegression() {
    }

    /**
     * Generates a simple exemplar of this class to test serialization.
     */
    public static SemOptimizerRegression serializableInstance() {
        return new SemOptimizerRegression();
    }

    //============================PUBLIC METHODS==========================//

    /**
     * Fit the freeParameters by doing local regressions.
     */
    public void optimize(SemIm semIm) {
        if (numRestarts != 1) {
            throw new IllegalArgumentException("Number of restarts must be 1 for this method.");
        }

        TetradMatrix covar = semIm.getSampleCovar();

        if (covar == null) {
            throw new NullPointerException("Sample covar has not been set.");
        }

        SemGraph graph = semIm.getSemPm().getGraph();
        List<Node> nodes = graph.getNodes();

//        TetradLogger.getInstance().log("info", "FML = " + semIm.getScore());

        for (Node node : nodes) {
            if (node.getNodeType() != NodeType.MEASURED) {
                continue;
            }

            if (!graph.isParameterizable(node)) continue;

            int idx = nodes.indexOf(node);
            List<Node> parents = graph.getParents(node);
//            Node errorParent = node;

            for (int i = 0; i < parents.size(); i++) {
                Node nextParent = parents.get(i);
                if (nextParent.getNodeType() == NodeType.ERROR) {
//                    errorParent = nextParent;
                    parents.remove(nextParent);
                    break;
                }
            }

            double variance = covar.get(idx, idx);

            if (parents.size() > 0) {
                TetradVector nodeParentsCov = new TetradVector(parents.size());
                TetradMatrix parentsCov = new TetradMatrix(parents.size(), parents.size());

                for (int i = 0; i < parents.size(); i++) {
                    int idx2 = nodes.indexOf(parents.get(i));
                    nodeParentsCov.set(i, covar.get(idx, idx2));

                    for (int j = i; j < parents.size(); j++) {
                        int idx3 = nodes.indexOf(parents.get(j));
                        parentsCov.set(i, j, covar.get(idx2, idx3));
                        parentsCov.set(j, i, covar.get(idx2, idx3));
                    }
                }

                TetradVector b = parentsCov.inverse().times(nodeParentsCov);
                variance -= nodeParentsCov.dotProduct(b);

                for (int i = 0; i < b.size(); i++) {
                    int idx2 = nodes.indexOf(parents.get(i));
                    semIm.setParamValue(nodes.get(idx2), node, b.get(i));
                }
            }

            semIm.setParamValue(node, node, variance);
        }

        TetradLogger.getInstance().log("optimization", "FML = " + semIm.getScore());
    }

    @Override
    public void setNumRestarts(int numRestarts) {
        this.numRestarts = numRestarts;
    }

    @Override
    public int getNumRestarts() {
        return numRestarts;
    }

    public String toString() {
        return "Sem Optimizer Regression";
    }
}