private boolean existsUnblockedSemiDirectedPath(Node from, Node to, List<Node> cond, Graph G) {
Queue<Node> Q = new LinkedList<Node>();
Set<Node> V = new HashSet<Node>();
Q.offer(from);
V.add(from);
while (!Q.isEmpty()) {
Node t = Q.remove();
if (t == to) return true;
for (Node u : G.getAdjacentNodes(t)) {
Edge edge = G.getEdge(t, u);
Node c = Edges.traverseSemiDirected(t, edge);
if (c == null) continue;
if (cond.contains(c)) continue;
if (c == to) return true;
if (!V.contains(c)) {
V.add(c);
Q.offer(c);
}
}
}
return false;
}
void storeLatestWorkbenchGraph() {
Graph latestWorkbenchGraph = workbench.getGraph();
if (latestWorkbenchGraph.getNumNodes() == 0) {
return;
}
SearchParams searchParams = algorithmRunner.getParams();
try {
Graph graph = new MarshalledObject<Graph>(latestWorkbenchGraph).get();
if (graph == null) {
throw new NullPointerException("Null graph");
}
if (searchParams != null) {
searchParams.setSourceGraph(graph);
}
} catch (IOException e) {
e.printStackTrace();
if (searchParams != null) {
searchParams.setSourceGraph(null);
}
} catch (ClassNotFoundException e) {
if (searchParams != null) {
searchParams.setSourceGraph(null);
}
e.printStackTrace();
}
}
public TimeLagGraphWrapper(GraphWrapper graphWrapper) {
if (graphWrapper == null) {
throw new NullPointerException("No graph wrapper.");
}
TimeLagGraph graph = new TimeLagGraph();
Graph _graph = graphWrapper.getGraph();
for (Node node : _graph.getNodes()) {
Node _node = node.like(node.getName() + ":0");
_node.setNodeType(node.getNodeType());
graph.addNode(_node);
}
for (Edge edge : _graph.getEdges()) {
if (!Edges.isDirectedEdge(edge)) {
throw new IllegalArgumentException();
}
Node from = edge.getNode1();
Node to = edge.getNode2();
Node _from = graph.getNode(from.getName(), 1);
Node _to = graph.getNode(to.getName(), 0);
graph.addDirectedEdge(_from, _to);
}
this.graph = graph;
}
/** Initializes the lists of parents and parent dimension for the given variable. */
private void initializeNode(int nodeIndex) {
Node node = nodes[nodeIndex];
// Set up parents array. Should store the parents of
// each node as ints in a particular order.
Graph graph = getBayesPm().getDag();
List<Node> parentList = new ArrayList<Node>(graph.getParents(node));
int[] parentArray = new int[parentList.size()];
for (int i = 0; i < parentList.size(); i++) {
parentArray[i] = getNodeIndex(parentList.get(i));
}
// Sort parent array.
Arrays.sort(parentArray);
parents[nodeIndex] = parentArray;
// Setup dimensions array for parents.
int[] dims = new int[parentArray.length];
for (int i = 0; i < dims.length; i++) {
Node parNode = nodes[parentArray[i]];
dims[i] = getBayesPm().getNumCategories(parNode);
}
parentDims[nodeIndex] = dims;
}
public static Graph erdosRenyiGraph(int n, int e) {
List<Node> nodes = new ArrayList<Node>();
for (int i = 0; i < n; i++) nodes.add(new GraphNode("X" + i));
Graph graph = new EdgeListGraph(nodes);
for (int e0 = 0; e0 < e; e0++) {
int i1 = RandomUtil.getInstance().nextInt(n);
int i2 = RandomUtil.getInstance().nextInt(n);
if (i1 == i2) {
e0--;
continue;
}
Edge edge = Edges.undirectedEdge(nodes.get(i1), nodes.get(i2));
if (graph.containsEdge(edge)) {
e0--;
continue;
}
graph.addEdge(edge);
}
return graph;
}
////////////////////////////////////////////////
// collect in rTupleList all unshielded tuples
////////////////////////////////////////////////
private List<Node[]> getRTuples() {
List<Node[]> rTuples = new ArrayList<Node[]>();
List<Node> nodes = graph.getNodes();
for (Node j : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(j);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node i = adjacentNodes.get(combination[0]);
Node k = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (!graph.isAdjacentTo(i, k)) {
Node[] newTuple = {i, j, k};
rTuples.add(newTuple);
}
}
}
return (rTuples);
}
/** Get a graph and direct only the unshielded colliders. */
public static void basicPattern(Graph graph) {
Set<Edge> undirectedEdges = new HashSet<Edge>();
NEXT_EDGE:
for (Edge edge : graph.getEdges()) {
Node head = null, tail = null;
if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.TAIL) {
head = edge.getNode1();
tail = edge.getNode2();
} else if (edge.getEndpoint2() == Endpoint.ARROW && edge.getEndpoint1() == Endpoint.TAIL) {
head = edge.getNode2();
tail = edge.getNode1();
}
if (head != null) {
for (Node node : graph.getParents(head)) {
if (node != tail && !graph.isAdjacentTo(tail, node)) {
continue NEXT_EDGE;
}
}
undirectedEdges.add(edge);
}
}
for (Edge nextUndirected : undirectedEdges) {
Node node1 = nextUndirected.getNode1(), node2 = nextUndirected.getNode2();
graph.removeEdge(nextUndirected);
graph.addUndirectedEdge(node1, node2);
}
}
public List<Triple> getUnshieldedCollidersFromGraph(Graph graph) {
List<Triple> colliders = new ArrayList<>();
List<Node> nodes = graph.getNodes();
for (Node b : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(b);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node a = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(a, c)) {
continue;
}
if (graph.isDefCollider(a, b, c)) {
colliders.add(new Triple(a, b, c));
}
}
}
return colliders;
}
private Graph changeLatentNames(Graph full, Clusters measurements, List<String> latentVarList) {
Graph g2 = null;
try {
g2 = (Graph) new MarshalledObject(full).get();
} catch (IOException e) {
e.printStackTrace();
} catch (ClassNotFoundException e) {
e.printStackTrace();
}
for (int i = 0; i < measurements.getNumClusters(); i++) {
List<String> d = measurements.getCluster(i);
String latentName = latentVarList.get(i);
for (Node node : full.getNodes()) {
if (!(node.getNodeType() == NodeType.LATENT)) {
continue;
}
List<Node> _children = full.getChildren(node);
_children.removeAll(ReidentifyVariables.getLatents(full));
List<String> childNames = getNames(_children);
if (new HashSet<String>(childNames).equals(new HashSet<String>(d))) {
g2.getNode(node.getName()).setName(latentName);
}
}
}
return g2;
}
public Set<Edge> getNonadjacencies() {
Graph complete = GraphUtils.completeGraph(graph);
Set<Edge> nonAdjacencies = complete.getEdges();
Graph undirected = GraphUtils.undirectedGraph(graph);
nonAdjacencies.removeAll(undirected.getEdges());
return new HashSet<Edge>(nonAdjacencies);
}
/**
* Constructs a new on-the-fly BayesIM that will calculate conditional probabilities on the fly
* from the given discrete data set, for the given Bayes PM.
*
* @param bayesPm the given Bayes PM, which specifies a directed acyclic graph for a Bayes net and
* parametrization for the Bayes net, but not actual values for the parameters.
* @param dataSet the discrete data set from which conditional probabilities should be estimated
* on the fly.
*/
public OnTheFlyMarginalCalculator(BayesPm bayesPm, DataSet dataSet)
throws IllegalArgumentException {
if (bayesPm == null) {
throw new NullPointerException();
}
if (dataSet == null) {
throw new NullPointerException();
}
// Make sure all of the variables in the PM are in the data set;
// otherwise, estimation is impossible.
BayesUtils.ensureVarsInData(bayesPm.getVariables(), dataSet);
// DataUtils.ensureVariablesExist(bayesPm, dataSet);
this.bayesPm = new BayesPm(bayesPm);
// Get the nodes from the BayesPm. This fixes the order of the nodes
// in the BayesIm, independently of any change to the BayesPm.
// (This order must be maintained.)
Graph graph = bayesPm.getDag();
this.nodes = graph.getNodes().toArray(new Node[0]);
// Initialize.
initialize();
// Create a subset of the data set with the variables of the IM, in
// the order of the IM.
List<Node> variables = getVariables();
this.dataSet = dataSet.subsetColumns(variables);
// Create a tautologous proposition for evidence.
this.evidence = new Evidence(Proposition.tautology(this));
}
// ===========================SCORING METHODS===================//
public double scoreDag(Graph graph) {
Graph dag = new EdgeListGraphSingleConnections(graph);
buildIndexing(graph);
double score = 0.0;
for (Node y : dag.getNodes()) {
Set<Node> parents = new HashSet<Node>(dag.getParents(y));
int nextIndex = -1;
for (int i = 0; i < getVariables().size(); i++) {
nextIndex = hashIndices.get(variables.get(i));
}
int parentIndices[] = new int[parents.size()];
Iterator<Node> pi = parents.iterator();
int count = 0;
while (pi.hasNext()) {
Node nextParent = pi.next();
parentIndices[count++] = hashIndices.get(nextParent);
}
if (this.isDiscrete()) {
score += localDiscreteScore(nextIndex, parentIndices);
} else {
score += localSemScore(nextIndex, parentIndices);
}
}
return score;
}
/**
* Step C of PC; orients colliders using specified sepset. That is, orients x *-* y *-* z as x *->
* y <-* z just in case y is in Sepset({x, z}).
*/
public Map<Triple, Double> findCollidersUsingSepsets(
SepsetProducer sepsetProducer, Graph graph, boolean verbose, IKnowledge knowledge) {
TetradLogger.getInstance().log("details", "Starting Collider Orientation:");
Map<Triple, Double> colliders = new HashMap<>();
System.out.println("Looking for colliders");
List<Node> nodes = graph.getNodes();
for (Node b : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(b);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node a = adjacentNodes.get(combination[0]);
Node c = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(a, c)) {
continue;
}
List<Node> sepset = sepsetProducer.getSepset(a, c);
if (sepset == null) continue;
// if (sepsetProducer.getPValue() < 0.5) continue;
if (!sepset.contains(b)) {
if (verbose) {
// boolean dsep = this.dsep.isIndependent(a, c);
// System.out.println("QQQ p = " + independenceTest.getPValue() +
// " " + dsep);
System.out.println(
"\nCollider orientation <" + a + ", " + b + ", " + c + "> sepset = " + sepset);
}
colliders.put(new Triple(a, b, c), sepsetProducer.getPValue());
TetradLogger.getInstance()
.log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(a, b, c, sepset));
}
}
}
TetradLogger.getInstance().log("details", "Finishing Collider Orientation.");
System.out.println("Done finding colliders");
return colliders;
}
private boolean isUndirected(Graph graph, Node x, Node y) {
List<Edge> edges = graph.getEdges(x, y);
if (edges.size() == 1) {
Edge edge = graph.getEdge(x, y);
return Edges.isUndirectedEdge(edge);
}
return false;
}
/**
* Performs step C of the algorithm, as indicated on page xxx of CPS, with the modification that
* X--W--Y is oriented as X-->W<--Y if W is *determined by* the sepset of (X, Y), rather than W
* just being *in* the sepset of (X, Y).
*/
public static void pcdOrientC(
SepsetMap set, IndependenceTest test, Knowledge knowledge, Graph graph) {
TetradLogger.getInstance().log("info", "Staring Collider Orientation:");
List<Node> nodes = graph.getNodes();
for (Node y : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(y);
if (adjacentNodes.size() < 2) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node x = adjacentNodes.get(combination[0]);
Node z = adjacentNodes.get(combination[1]);
// Skip triples that are shielded.
if (graph.isAdjacentTo(x, z)) {
continue;
}
List<Node> sepset = set.get(x, z);
if (sepset == null) {
continue;
}
List<Node> augmentedSet = new LinkedList<Node>(sepset);
augmentedSet.add(y);
if (test.determines(sepset, y)) {
continue;
}
//
if (!test.splitDetermines(sepset, x, z) && test.splitDetermines(augmentedSet, x, z)) {
continue;
}
if (!isArrowpointAllowed(x, y, knowledge) || !isArrowpointAllowed(z, y, knowledge)) {
continue;
}
graph.setEndpoint(x, y, Endpoint.ARROW);
graph.setEndpoint(z, y, Endpoint.ARROW);
TetradLogger.getInstance()
.log("colliderOriented", SearchLogUtils.colliderOrientedMsg(x, y, z));
}
}
TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
}
private boolean localMarkovIndep(Node x, Node y, Graph pattern, IndependenceTest test) {
List<Node> future = pattern.getDescendants(Collections.singletonList(x));
List<Node> boundary = pattern.getAdjacentNodes(x);
boundary.removeAll(future);
List<Node> closure = new ArrayList<>(boundary);
closure.add(x);
closure.remove(y);
if (future.contains(y) || boundary.contains(y)) return false;
return test.isIndependent(x, y, boundary);
}
/**
* Provides methods for estimating a Bayes IM from an existing BayesIM and a discrete dataset
* using EM (Expectation Maximization). The data columns in the given data must be equal to a
* variable in the given Bayes IM but the latter may contain variables which don't occur in the
* dataset (latent variables). The first argument of the constructoris the BayesPm whose graph
* contains latent and observed variables. The second is the dataset of observed variables;
* missing value codes may be present.
*/
public EmBayesEstimator(BayesPm bayesPm, DataSet dataSet) {
if (bayesPm == null) {
throw new NullPointerException();
}
if (dataSet == null) {
throw new NullPointerException();
}
List<Node> observedVars = new ArrayList<Node>();
this.bayesPm = bayesPm;
this.dataSet = dataSet;
// this.variables = Collections.unmodifiableList(vars);
graph = bayesPm.getDag();
this.nodes = new Node[graph.getNumNodes()];
Iterator<Node> it = graph.getNodes().iterator();
for (int i = 0; i < this.nodes.length; i++) {
this.nodes[i] = it.next();
// System.out.println("node " + i + " " + nodes[i]);
}
for (int i = 0; i < this.nodes.length; i++) {
if (nodes[i].getNodeType() == NodeType.MEASURED) {
observedVars.add(bayesPm.getVariable(nodes[i]));
}
}
// Make sure variables in dataset are measured variables in the BayesPM
// for (Node dataSetVariable : this.dataSet.getVariables()) {
// if (!observedVars.contains(dataSetVariable)) {
// throw new IllegalArgumentException(
// "Some var in the dataset is not a " +
// "measured variable in the Bayes net");
// }
// }
// Make sure all measured variables in the BayesPm are in the discrete dataset
for (Node observedVar : observedVars) {
try {
this.dataSet.getVariable(observedVar.getName());
} catch (Exception e) {
throw new IllegalArgumentException(
"Some observed var in the Bayes net " + "is not in the dataset: " + observedVar);
}
}
findBayesNetObserved(); // Sets bayesPmObs
initialize();
}
private void calcStats() {
// Graph resultGraph = getAlgorithmRunner().getResultGraph();
IGesRunner runner = (IGesRunner) getAlgorithmRunner();
if (runner.getTopGraphs().isEmpty()) {
throw new IllegalArgumentException(
"No patterns were recorded. Please adjust the number of " + "patterns to store.");
}
Graph resultGraph = runner.getTopGraphs().get(runner.getIndex()).getGraph();
if (getAlgorithmRunner().getDataModel() instanceof DataSet) {
// resultGraph may be the output of a PC search.
// Such graphs sometimes contain doubly directed edges.
// /We converte such edges to directed edges here.
// For the time being an orientation is arbitrarily selected.
Set<Edge> allEdges = resultGraph.getEdges();
for (Edge edge : allEdges) {
if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.ARROW) {
// Option 1 orient it from node1 to node2
resultGraph.setEndpoint(edge.getNode1(), edge.getNode2(), Endpoint.ARROW);
// Option 2 remove such edges:
resultGraph.removeEdge(edge);
}
}
Pattern pattern = new Pattern(resultGraph);
PatternToDag ptd = new PatternToDag(pattern);
Graph dag = ptd.patternToDagMeekRules();
DataSet dataSet = (DataSet) getAlgorithmRunner().getDataModel();
String report;
if (dataSet.isContinuous()) {
report = reportIfContinuous(dag, dataSet);
} else if (dataSet.isDiscrete()) {
report = reportIfDiscrete(dag, dataSet);
} else {
throw new IllegalArgumentException("");
}
JScrollPane dagWorkbenchScroll = dagWorkbenchScroll(dag);
modelStatsText.setLineWrap(true);
modelStatsText.setWrapStyleWord(true);
modelStatsText.setText(report);
removeStatsTabs();
tabbedPane.addTab("DAG in pattern", dagWorkbenchScroll);
tabbedPane.addTab("DAG Model Statistics", modelStatsText);
}
}
private double getPMulticluster(List<List<Integer>> clusters, int numRestarts) {
if (false) {
Graph g = new EdgeListGraph();
List<Node> latents = new ArrayList<Node>();
for (int i = 0; i < clusters.size(); i++) {
GraphNode latent = new GraphNode("L" + i);
latent.setNodeType(NodeType.LATENT);
latents.add(latent);
g.addNode(latent);
List<Node> cluster = variablesForIndices(clusters.get(i));
for (int j = 0; j < cluster.size(); j++) {
g.addNode(cluster.get(j));
g.addDirectedEdge(latent, cluster.get(j));
}
}
SemPm pm = new SemPm(g);
// pm.fixOneLoadingPerLatent();
SemOptimizerPowell semOptimizer = new SemOptimizerPowell();
semOptimizer.setNumRestarts(numRestarts);
SemEstimator est = new SemEstimator(cov, pm, semOptimizer);
est.setScoreType(SemIm.ScoreType.Fgls);
est.estimate();
return est.getEstimatedSem().getPValue();
} else {
double max = Double.NEGATIVE_INFINITY;
for (int i = 0; i < numRestarts; i++) {
Mimbuild2 mimbuild = new Mimbuild2();
List<List<Node>> _clusters = new ArrayList<List<Node>>();
for (List<Integer> _cluster : clusters) {
_clusters.add(variablesForIndices(_cluster));
}
List<String> names = new ArrayList<String>();
for (int j = 0; j < clusters.size(); j++) {
names.add("L" + j);
}
mimbuild.search(_clusters, names, cov);
double c = mimbuild.getpValue();
if (c > max) max = c;
}
return max;
}
}
/** Meek's rule R3. If a--b, a--c, a--d, c-->b, c-->b, then orient a-->b. */
public static boolean meekR3(Graph graph, Knowledge knowledge) {
List<Node> nodes = graph.getNodes();
boolean changed = false;
for (Node a : nodes) {
List<Node> adjacentNodes = graph.getAdjacentNodes(a);
if (adjacentNodes.size() < 3) {
continue;
}
for (Node b : adjacentNodes) {
List<Node> otherAdjacents = new LinkedList<Node>(adjacentNodes);
otherAdjacents.remove(b);
if (!graph.isUndirectedFromTo(a, b)) {
continue;
}
ChoiceGenerator cg = new ChoiceGenerator(otherAdjacents.size(), 2);
int[] combination;
while ((combination = cg.next()) != null) {
Node c = otherAdjacents.get(combination[0]);
Node d = otherAdjacents.get(combination[1]);
if (graph.isAdjacentTo(c, d)) {
continue;
}
if (!graph.isUndirectedFromTo(a, c)) {
continue;
}
if (!graph.isUndirectedFromTo(a, d)) {
continue;
}
if (graph.isDirectedFromTo(c, b) && graph.isDirectedFromTo(d, b)) {
if (isArrowpointAllowed(a, b, knowledge)) {
graph.setEndpoint(a, b, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Meek R3", graph.getEdge(a, b)));
changed = true;
break;
}
}
}
}
}
return changed;
}
private Graph structure(Graph mim) {
List<Node> latents = new ArrayList<Node>();
for (Node node : mim.getNodes()) {
if (node.getNodeType() == NodeType.LATENT) {
latents.add(node);
}
}
return mim.subgraph(latents);
}
private Graph restrictToEmpiricalLatents(Graph mimStructure, Graph mimbuildStructure) {
Graph _mim = new EdgeListGraph(mimStructure);
for (Node node : mimbuildStructure.getNodes()) {
if (!mimbuildStructure.containsNode(node)) {
_mim.removeNode(node);
}
}
return _mim;
}
public List<Node> findMb(String targetName) {
Node target = getVariableForName(targetName);
Pc search = new Pc(test);
search.setDepth(depth);
Graph graph = search.search();
MbUtils.trimToMbNodes(graph, target, false);
List<Node> mbVariables = graph.getNodes();
mbVariables.remove(target);
return mbVariables;
}
private boolean missingColliders(Graph graph) {
List<Triple> colliders = getUnshieldedCollidersFromGraph(graph);
Graph copy = new EdgeListGraphSingleConnections(graph);
new MeekRules().orientImplied(copy);
if (copy.existsDirectedCycle()) return true;
List<Triple> newColliders = getUnshieldedCollidersFromGraph(copy);
newColliders.removeAll(colliders);
if (!newColliders.isEmpty()) {
return true;
}
return false;
}
public static Graph bestGuessCycleOrientation(Graph graph, IndependenceTest test) {
while (true) {
List<Node> cycle = GraphUtils.directedCycle(graph);
if (cycle == null) {
break;
}
LinkedList<Node> _cycle = new LinkedList<Node>(cycle);
Node first = _cycle.getFirst();
Node last = _cycle.getLast();
_cycle.addFirst(last);
_cycle.addLast(first);
int _j = -1;
double minP = Double.POSITIVE_INFINITY;
for (int j = 1; j < _cycle.size() - 1; j++) {
int i = j - 1;
int k = j + 1;
Node x = test.getVariable(_cycle.get(i).getName());
Node y = test.getVariable(_cycle.get(j).getName());
Node z = test.getVariable(_cycle.get(k).getName());
test.isIndependent(x, z, Collections.singletonList(y));
System.out.println("Testing " + x + " _||_ " + z + " | " + y);
double p = test.getPValue();
System.out.println("p = " + p);
if (p < minP) {
_j = j;
minP = p;
}
}
Node x = _cycle.get(_j - 1);
Node y = _cycle.get(_j);
Node z = _cycle.get(_j + 1);
graph.removeEdge(x, y);
graph.removeEdge(z, y);
graph.addDirectedEdge(x, y);
graph.addDirectedEdge(z, y);
}
return graph;
}
private boolean dConnected(Graph graph, String x, String y, String... z) {
Node _x = graph.getNode(x);
Node _y = graph.getNode(y);
List<Node> _z = new ArrayList<Node>();
for (String name : z) {
_z.add(graph.getNode(name));
}
return graph.isDConnectedTo(_x, _y, _z);
}
// Cannot be done if the graph changes.
public void setInitialGraph(Graph initialGraph) {
initialGraph = GraphUtils.replaceNodes(initialGraph, variables);
out.println("Initial graph variables: " + initialGraph.getNodes());
out.println("Data set variables: " + variables);
if (!new HashSet<Node>(initialGraph.getNodes()).equals(new HashSet<Node>(variables))) {
throw new IllegalArgumentException("Variables aren't the same.");
}
this.initialGraph = initialGraph;
}
private void addColliders(
Graph graph, final SepsetProducer sepsetProducer, IKnowledge knowledge) {
final Map<Triple, Double> collidersPs =
findCollidersUsingSepsets(sepsetProducer, graph, verbose, knowledge);
List<Triple> colliders = new ArrayList<>(collidersPs.keySet());
Collections.shuffle(colliders);
Collections.sort(
colliders,
new Comparator<Triple>() {
public int compare(Triple o1, Triple o2) {
return -Double.compare(collidersPs.get(o1), collidersPs.get(o2));
}
});
if (trueDag != null) {
for (Triple collider : colliders) {
Node a = collider.getX();
Node b = collider.getY();
Node c = collider.getZ();
List<Node> sep = trueDag.getSepset(a, c);
System.out.println(
"JJJ "
+ collider
+ " collider = "
+ (sep != null && !sep.contains(b))
+ " p = "
+ collidersPs.get(collider));
}
}
for (Triple collider : colliders) {
Node a = collider.getX();
Node b = collider.getY();
Node c = collider.getZ();
if (!(isArrowpointAllowed(a, b, knowledge) && isArrowpointAllowed(c, b, knowledge))) {
continue;
}
if (!graph.getEdge(a, b).pointsTowards(a) && !graph.getEdge(b, c).pointsTowards(c)) {
graph.setEndpoint(a, b, Endpoint.ARROW);
graph.setEndpoint(c, b, Endpoint.ARROW);
}
}
}
/** Orients according to background knowledge. */
public static void pcOrientbk(Knowledge bk, Graph graph, List<Node> nodes) {
TetradLogger.getInstance().log("info", "Staring BK Orientation.");
for (Iterator<KnowledgeEdge> it = bk.forbiddenEdgesIterator(); it.hasNext(); ) {
KnowledgeEdge edge = it.next();
// match strings to variables in the graph.
Node from = translate(edge.getFrom(), nodes);
Node to = translate(edge.getTo(), nodes);
if (from == null || to == null) {
continue;
}
if (graph.getEdge(from, to) == null) {
continue;
}
// Orient to-->from
graph.removeEdge(from, to);
graph.addDirectedEdge(from, to);
graph.setEndpoint(from, to, Endpoint.TAIL);
graph.setEndpoint(to, from, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(to, from)));
}
for (Iterator<KnowledgeEdge> it = bk.requiredEdgesIterator(); it.hasNext(); ) {
KnowledgeEdge edge = it.next();
// match strings to variables in this graph
Node from = translate(edge.getFrom(), nodes);
Node to = translate(edge.getTo(), nodes);
if (from == null || to == null) {
continue;
}
if (graph.getEdge(from, to) == null) {
continue;
}
// Orient from-->to
graph.setEndpoint(to, from, Endpoint.TAIL);
graph.setEndpoint(from, to, Endpoint.ARROW);
TetradLogger.getInstance()
.edgeOriented(SearchLogUtils.edgeOrientedMsg("Knowledge", graph.getEdge(from, to)));
}
TetradLogger.getInstance().log("info", "Finishing BK Orientation.");
}
public static void arrangeByKnowledgeTiers(Graph graph, Knowledge knowledge) {
if (knowledge.getNumTiers() == 0) {
throw new IllegalArgumentException("There are no Tiers to arrange.");
}
List<Node> nodes = graph.getNodes();
List<String> varNames = new ArrayList<String>();
int ySpace = 500 / knowledge.getNumTiers();
ySpace = ySpace < 50 ? 50 : ySpace;
for (Node node1 : nodes) {
varNames.add(node1.getName());
}
List<String> notInTier = knowledge.getVarsNotInTier(varNames);
int x = 0;
int y = 50 - ySpace;
if (notInTier.size() > 0) {
y += ySpace;
for (String name : notInTier) {
x += 90;
Node node = graph.getNode(name);
if (node != null) {
node.setCenterX(x);
node.setCenterY(y);
}
}
}
for (int i = 0; i < knowledge.getNumTiers(); i++) {
List<String> tier = knowledge.getTier(i);
y += ySpace;
x = -25;
for (String name : tier) {
x += 90;
Node node = graph.getNode(name);
if (node != null) {
node.setCenterX(x);
node.setCenterY(y);
}
}
}
}