code: ///////////////////////////////////////////////////////////////////////////////
  // 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.data.CovarianceMatrix;
  import edu.cmu.tetrad.data.DataUtils;
  import edu.cmu.tetrad.graph.SemGraph;
  import edu.cmu.tetrad.util.TetradLogger;
  import edu.cmu.tetrad.util.TetradMatrix;
  
  /**
   * Optimizes a SEM using RICF (see that class).
   *
   * @author Joseph Ramsey
   */
  public class SemOptimizerRicf implements SemOptimizer {
      static final long serialVersionUID = 23L;
      private int numRestarts = 1;
  
      //=============================CONSTRUCTORS=========================//
  
      /**
       * Blank constructor.
       */
      public SemOptimizerRicf() {
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static SemOptimizerRicf serializableInstance() {
          return new SemOptimizerRicf();
      }
  
      //==============================PUBLIC METHODS========================//
  
      /**
       * Optimizes the fitting function of the given Sem using the Powell method
       * from Numerical Recipes by adjusting the freeParameters of the Sem.
       */
      public void optimize(SemIm semIm) {
          if (numRestarts < 1) numRestarts = 1;
  
          if (numRestarts != 1) {
              throw new IllegalArgumentException("Number of restarts must be 1 for this method.");
          }
  
          TetradMatrix sampleCovar = semIm.getSampleCovar();
  
          if (sampleCovar == null) {
              throw new NullPointerException("Sample covar has not been set.");
          }
  
          if (DataUtils.containsMissingValue(sampleCovar)) {
              throw new IllegalArgumentException("Please remove or impute missing values.");
          }
  
          if (DataUtils.containsMissingValue(sampleCovar)) {
              throw new IllegalArgumentException("Please remove or impute missing values.");
          }
  
          TetradLogger.getInstance().log("info", "Trying EM...");
  //        new SemOptimizerEm().optimize(semIm);
  
          CovarianceMatrix cov = new CovarianceMatrix(semIm.getMeasuredNodes(),
                  sampleCovar, semIm.getSampleSize());
  
          SemGraph graph = semIm.getSemPm().getGraph();
          Ricf.RicfResult result = new Ricf().ricf(graph, cov, 0.001);
  
  
  //        Ricf.RicfResult result = null;
  //
  //        for (int t = 0; t < 10; t++) {
  //            Graph graph = semIm.getSemPm().getGraph();
  //            result = new Ricf().ricf(graph, cov, 0.001);
  //
  //            TetradMatrix bHat = result.getBhat();
  //            TetradMatrix lHat = result.getLhat();
  //            TetradMatrix oHat = result.getOhat();
  //            TetradMatrix sHat = result.getShat();
  //
  //            for (Parameter param : semIm.getFreeParameters()) {
  //                if (param.getType() == ParamType.COEF) {
  //                    int i = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeA());
  //                    int j = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeB());
  //                    semIm.setEdgeCoef(param.getNodeA(), param.getNodeB(), -bHat.get(j, i));
  //                }
  //
  //                if (param.getType() == ParamType.VAR) {
  //                    int i = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeA());
  //                    if (lHat.get(i, i) != 0) {
  //                        semIm.setErrVar(param.getNodeA(), lHat.get(i, i));
  //                    } else if (oHat.get(i, i) != 0) {
  //                        semIm.setErrVar(param.getNodeA(), oHat.get(i, i));
  //                    }
  //                }
  //            }
  //
  //            if (t < 9) {
  //                for (Parameter param : semIm.getFreeParameters()) {
  //                    double value = semIm.getParamValue(param);
  //                    double max = Double.NEGATIVE_INFINITY;
  //                    double d;
  //
  //                    for (d = value - .5; d <= value + 0.5; d += 0.001) {
  //                        semIm.setParamValue(param, d);
  //                        double fml = semIm.getFml();
  //                        if (fml > max) max = fml;
  //                    }
  //
  //                    semIm.setParamValue(param, d);
  //                }
  //            }
  //        }
  
          TetradMatrix bHat = new TetradMatrix(result.getBhat().toArray());
          TetradMatrix lHat = new TetradMatrix(result.getLhat().toArray());
          TetradMatrix oHat = new TetradMatrix(result.getOhat().toArray());
  
          for (Parameter param : semIm.getFreeParameters()) {
              if (param.getType() == ParamType.COEF) {
                  int i = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeA());
                  int j = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeB());
                  semIm.setEdgeCoef(param.getNodeA(), param.getNodeB(), -bHat.get(j, i));
              }
  
              if (param.getType() == ParamType.VAR) {
                  int i = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeA());
                  if (lHat.get(i, i) != 0) {
                      semIm.setErrVar(param.getNodeA(), lHat.get(i, i));
                  } else if (oHat.get(i, i) != 0) {
                      semIm.setErrVar(param.getNodeA(), oHat.get(i, i));
                  }
              }
  
              if (param.getType() == ParamType.COVAR) {
                  int i = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeA());
                  int j = semIm.getSemPm().getVariableNodes().indexOf(param.getNodeB());
                  if (lHat.get(i, i) != 0) {
                      semIm.setErrCovar(param.getNodeA(), param.getNodeB(), lHat.get(j, i));
                  } else if (oHat.get(i, i) != 0) {
                      semIm.setErrCovar(param.getNodeA(), param.getNodeB(), oHat.get(j, i));
                  }
              }
          }
  
          System.out.println(result);
          System.out.println(semIm);
      }
  
      @Override
      public void setNumRestarts(int numRestarts) {
          this.numRestarts = numRestarts;
      }
  
      @Override
      public int getNumRestarts() {
          return numRestarts;
      }
  
      public String toString() {
          return "Sem Optimizer RICF";
      }
  }
  
  
  
  