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///////////////////////////////////////////////////////////////////////////////
// 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, 2022 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.search.utils;
import edu.cmu.tetrad.algcomparison.statistic.BicEst;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.graph.Edge;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.GraphTransforms;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.search.score.Score;
import edu.cmu.tetrad.util.NumberFormatUtil;
import org.jetbrains.annotations.NotNull;
import java.text.NumberFormat;
import java.util.*;
/**
* Contains utilities for logging search steps.
*
* @author josephramsey
*/
public class LogUtilsSearch {
public static String edgeOrientedMsg(String reason, Edge edge) {
return "Orienting edge (" + reason + "): " + edge;
}
public static String colliderOrientedMsg(String note, Node x, Node y, Node z) {
return "Orienting collider (" + note + "): " + x.getName() + " *-> " +
y.getName() + " <-* " + z.getName();
}
public static String colliderOrientedMsg(Node x, Node y, Node z) {
return "Orienting collider: " + x.getName() + " *-> " +
y.getName() + " <-* " + z.getName();
}
public static String colliderOrientedMsg(Node x, Node y, Node z, Set sepset) {
return "Orienting collider: " + x.getName() + " *-> " +
y.getName() + " <-* " + z.getName() + "\t(Sepset = " + sepset +
")";
}
public static String determinismDetected(Set sepset, Node x) {
return "Determinism detected: " + sepset + " -> " + x.getName();
}
public static String independenceFactMsg(Node x, Node y, Set condSet, double pValue) {
StringBuilder sb = new StringBuilder();
NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
sb.append("Independence accepted: ");
sb.append(LogUtilsSearch.independenceFact(x, y, condSet));
if (!Double.isNaN(pValue)) {
sb.append("\tp = ").append(nf.format(pValue));
}
return sb.toString();
}
public static String dependenceFactMsg(Node x, Node y, Set condSet, double pValue) {
StringBuilder sb = new StringBuilder();
NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
sb.append("Dependent: ");
sb.append(LogUtilsSearch.independenceFact(x, y, condSet));
if (!Double.isNaN(pValue)) {
sb.append("\tp = ").append(nf.format(pValue));
}
return sb.toString();
}
public static String independenceFact(Node x, Node y, Set condSet) {
StringBuilder sb = new StringBuilder();
sb.append(x.getName());
sb.append(" _||_ ");
sb.append(y.getName());
Iterator it = condSet.iterator();
if (it.hasNext()) {
sb.append(" | ");
sb.append(it.next());
}
while (it.hasNext()) {
sb.append(", ");
sb.append(it.next());
}
return sb.toString();
}
public static String getScoreFact(int i, int[] parents, List variables) {
StringBuilder fact = new StringBuilder(variables.get(i) + " | ");
for (int j = 0; j < parents.length; j++) {
int p = parents[j];
fact.append(variables.get(p));
if (j < parents.length - 1) {
fact.append(", ");
}
}
return fact.toString();
}
public static String getScoreFact(Node i, List parents) {
StringBuilder fact = new StringBuilder(i + " | ");
for (int p = 0; p < parents.size(); p++) {
fact.append(parents.get(p));
if (p < parents.size() - 1) {
fact.append(", ");
}
}
return fact.toString();
}
public static Map buildIndexing(List nodes) {
Map hashIndices = new HashMap<>();
int i = -1;
for (Node n : nodes) {
hashIndices.put(n, ++i);
}
return hashIndices;
}
@NotNull
public static void stampWithScores(Graph graph, DataModel dataModel, Score score) {
if (!graph.getAllAttributes().containsKey("Score")) {
Graph dag = GraphTransforms.dagFromCPDAG(graph);
Map hashIndices = buildIndexing(dag.getNodes());
double _score = 0.0;
for (Node node : dag.getNodes()) {
List x = dag.getParents(node);
int[] parentIndices = new int[x.size()];
int count = 0;
for (Node parent : x) {
parentIndices[count++] = hashIndices.get(parent);
}
_score += score.localScore(hashIndices.get(node), parentIndices);
}
graph.addAttribute("Score", _score);
}
stampWithBic(graph, dataModel);
}
public static void stampWithBic(Graph graph, DataModel dataModel) {
if (!graph.getAllAttributes().containsKey("BIC")) {
graph.addAttribute("BIC", new BicEst().getValue(null, graph, dataModel));
}
}
}
