Example #1
0
  /**
   * <<<<<<< HEAD ���ߵ�valueֵ���й��� ======= 按边的value值进行过滤 >>>>>>> seuvislogwws/master
   *
   * @param filter
   * @return
   */
  public SankeyGraph FilterByEdgeValue(double filter) {
    Set<Integer> nodeset = new HashSet<Integer>();
    Iterator<? extends Edge> iterator_links = this.links.iterator();
    while (iterator_links.hasNext()) {
      Edge edge = iterator_links.next();
      double value = ((StreamEdge) edge).getValue();
      if (value < filter) iterator_links.remove(); // �Ƴ��
      else {
        nodeset.add(edge.getSource());
        nodeset.add(edge.getTarget());
      }
    }
    Iterator<? extends Node> iterator_nodes = this.nodes.iterator();
    while (iterator_nodes.hasNext()) {
      Node node = iterator_nodes.next();

      if (!nodeset.contains(node.getName())) { // ����nodes��
        iterator_nodes.remove();
      }
    }
    // System.out.println( "���˺�nodes�Ĵ�С�� "+this.nodes.size());
    // �����˹���json����ٴΰ�node��name��0��ʼ�ź�
    int index = 0;
    for (Node n : this.nodes) {
      int old_name = n.getName();
      int new_name = index++;
      n.setName(new_name);

      for (Edge e : this.links) {
        if (e.getSource() == old_name) e.setSource(new_name);
        if (e.getTarget() == old_name) e.setTarget(new_name);
      }
    }
    return this;
  }
Example #2
0
  private void calculateArrowsForward(Node x, Node y, Graph graph) {
    clearArrow(x, y);

    if (!knowledgeEmpty()) {
      if (getKnowledge().isForbidden(x.getName(), y.getName())) {
        return;
      }
    }

    List<Node> naYX = getNaYX(x, y, graph);
    List<Node> t = getTNeighbors(x, y, graph);

    DepthChoiceGenerator gen = new DepthChoiceGenerator(t.size(), t.size());
    int[] choice;

    while ((choice = gen.next()) != null) {
      List<Node> s = GraphUtils.asList(choice, t);

      if (!knowledgeEmpty()) {
        if (!validSetByKnowledge(y, s)) {
          continue;
        }
      }

      double bump = insertEval(x, y, s, naYX, graph);

      if (bump > 0.0) {
        Arrow arrow = new Arrow(bump, x, y, s, naYX);
        sortedArrows.add(arrow);
        addLookupArrow(x, y, arrow);
      }
    }
  }
Example #3
0
  private Graph condense(Graph mimStructure, Graph mimbuildStructure) {
    //        System.out.println("Uncondensed: " + mimbuildStructure);

    Map<Node, Node> substitutions = new HashMap<Node, Node>();

    for (Node node : mimbuildStructure.getNodes()) {
      for (Node _node : mimStructure.getNodes()) {
        if (node.getName().startsWith(_node.getName())) {
          substitutions.put(node, _node);
          break;
        }

        substitutions.put(node, node);
      }
    }

    HashSet<Node> nodes = new HashSet<Node>(substitutions.values());
    Graph graph = new EdgeListGraph(new ArrayList<Node>(nodes));

    for (Edge edge : mimbuildStructure.getEdges()) {
      Node node1 = substitutions.get(edge.getNode1());
      Node node2 = substitutions.get(edge.getNode2());

      if (node1 == node2) continue;

      if (graph.isAdjacentTo(node1, node2)) continue;

      graph.addEdge(new Edge(node1, node2, edge.getEndpoint1(), edge.getEndpoint2()));
    }

    //        System.out.println("Condensed: " + graph);

    return graph;
  }
Example #4
0
 /**
  * Use background knowledge to decide if an insert or delete operation does not orient edges in a
  * forbidden direction according to prior knowledge. If some orientation is forbidden in the
  * subset, the whole subset is forbidden.
  */
 private boolean validSetByKnowledge(Node y, List<Node> subset) {
   for (Node node : subset) {
     if (getKnowledge().isForbidden(node.getName(), y.getName())) {
       return false;
     }
   }
   return true;
 }
  /**
   * Transforms a maximally directed pattern (PDAG) represented in graph <code>g</code> into an
   * arbitrary DAG by modifying <code>g</code> itself. Based on the algorithm described in
   * Chickering (2002) "Optimal structure identification with greedy search" Journal of Machine
   * Learning Research. R. Silva, June 2004
   */
  public static void pdagToDag(Graph g) {
    Graph p = new EdgeListGraph(g);
    List<Edge> undirectedEdges = new ArrayList<Edge>();

    for (Edge edge : g.getEdges()) {
      if (edge.getEndpoint1() == Endpoint.TAIL
          && edge.getEndpoint2() == Endpoint.TAIL
          && !undirectedEdges.contains(edge)) {
        undirectedEdges.add(edge);
      }
    }
    g.removeEdges(undirectedEdges);
    List<Node> pNodes = p.getNodes();

    do {
      Node x = null;

      for (Node pNode : pNodes) {
        x = pNode;

        if (p.getChildren(x).size() > 0) {
          continue;
        }

        Set<Node> neighbors = new HashSet<Node>();

        for (Edge edge : p.getEdges()) {
          if (edge.getNode1() == x || edge.getNode2() == x) {
            if (edge.getEndpoint1() == Endpoint.TAIL && edge.getEndpoint2() == Endpoint.TAIL) {
              if (edge.getNode1() == x) {
                neighbors.add(edge.getNode2());
              } else {
                neighbors.add(edge.getNode1());
              }
            }
          }
        }
        if (neighbors.size() > 0) {
          Collection<Node> parents = p.getParents(x);
          Set<Node> all = new HashSet<Node>(neighbors);
          all.addAll(parents);
          if (!GraphUtils.isClique(all, p)) {
            continue;
          }
        }

        for (Node neighbor : neighbors) {
          Node node1 = g.getNode(neighbor.getName());
          Node node2 = g.getNode(x.getName());

          g.addDirectedEdge(node1, node2);
        }
        p.removeNode(x);
        break;
      }
      pNodes.remove(x);
    } while (pNodes.size() > 0);
  }
Example #6
0
  private double pValue(Node node, List<Node> parents) {
    List<Double> _residuals = new ArrayList<Double>();

    Node _target = node;
    List<Node> _regressors = parents;
    Node target = getVariable(variables, _target.getName());
    List<Node> regressors = new ArrayList<Node>();

    for (Node _regressor : _regressors) {
      Node variable = getVariable(variables, _regressor.getName());
      regressors.add(variable);
    }

    DATASET:
    for (int m = 0; m < dataSets.size(); m++) {
      RegressionResult result = regressions.get(m).regress(target, regressors);
      TetradVector residualsSingleDataset = result.getResiduals();

      for (int h = 0; h < residualsSingleDataset.size(); h++) {
        if (Double.isNaN(residualsSingleDataset.get(h))) {
          continue DATASET;
        }
      }

      DoubleArrayList _residualsSingleDataset =
          new DoubleArrayList(residualsSingleDataset.toArray());

      double mean = Descriptive.mean(_residualsSingleDataset);
      double std =
          Descriptive.standardDeviation(
              Descriptive.variance(
                  _residualsSingleDataset.size(),
                  Descriptive.sum(_residualsSingleDataset),
                  Descriptive.sumOfSquares(_residualsSingleDataset)));

      for (int i2 = 0; i2 < _residualsSingleDataset.size(); i2++) {
        //                _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2) - mean) /
        // std);
        if (isMeanCenterResiduals()) {
          _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2) - mean));
        }
        //                _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2)));
      }

      for (int k = 0; k < _residualsSingleDataset.size(); k++) {
        _residuals.add(_residualsSingleDataset.get(k));
      }
    }

    double[] _f = new double[_residuals.size()];

    for (int k = 0; k < _residuals.size(); k++) {
      _f[k] = _residuals.get(k);
    }

    return new AndersonDarlingTest(_f).getP();
  }
Example #7
0
 public void printSiblings() {
   if (parent == null) System.out.println("Siblings: " + parent);
   else {
     System.out.print("Siblings: ");
     ArrayList<Node> siblings = parent.getChildren();
     if (siblings.isEmpty()) System.out.print("null");
     else {
       for (int i = 0; i < siblings.size(); ++i) {
         Node child = siblings.get(i);
         if (!child.getName().equals(name)) System.out.print(child.getName() + "\t");
       }
     }
     System.out.println();
   }
 }
Example #8
0
  public boolean isViolatedBy(Graph graph) {
    for (Edge edge : graph.getEdges()) {
      if (!edge.isDirected()) {
        continue;
      }

      Node from = Edges.getDirectedEdgeTail(edge);
      Node to = Edges.getDirectedEdgeHead(edge);

      if (isForbidden(from.getName(), to.getName())) {
        return true;
      }
    }

    return false;
  }
Example #9
0
  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;
  }
Example #10
0
 private List<String> getNames(List<Node> nodes) {
   List<String> names = new ArrayList<String>();
   for (Node node : nodes) {
     names.add(node.getName());
   }
   return names;
 }
Example #11
0
  private Node getVariable(List<Node> variables, String name) {
    for (Node node : variables) {
      if (name.equals(node.getName())) {
        return node;
      }
    }

    return null;
  }
  /** Returns the string in nodelist which matches string in BK. */
  public static Node translate(String a, List<Node> nodes) {
    for (Node node : nodes) {
      if ((node.getName()).equals(a)) {
        return node;
      }
    }

    return null;
  }
Example #13
0
  /**
   * Helper method. Appears to check if an arrowpoint is permitted by background knowledge.
   *
   * @param x The possible other node.
   * @param y The possible point node.
   * @return Whether the arrowpoint is allowed.
   */
  private boolean isArrowpointAllowed(Node x, Node y) {
    if (graph.getEndpoint(x, y) == Endpoint.ARROW) {
      return true;
    }

    if (graph.getEndpoint(x, y) == Endpoint.TAIL) {
      return false;
    }

    if (graph.getEndpoint(y, x) == Endpoint.ARROW) {
      if (!knowledge.isForbidden(x.getName(), y.getName())) return true;
    }

    if (graph.getEndpoint(y, x) == Endpoint.TAIL) {
      if (!knowledge.isForbidden(x.getName(), y.getName())) return true;
    }

    return graph.getEndpoint(y, x) == Endpoint.CIRCLE;
  }
Example #14
0
  private String reportIfDiscrete(Graph dag, DataSet dataSet) {
    List vars = dataSet.getVariables();
    Map<String, DiscreteVariable> nodesToVars = new HashMap<String, DiscreteVariable>();
    for (int i = 0; i < dataSet.getNumColumns(); i++) {
      DiscreteVariable var = (DiscreteVariable) vars.get(i);
      String name = var.getName();
      Node node = new GraphNode(name);
      nodesToVars.put(node.getName(), var);
    }

    BayesPm bayesPm = new BayesPm(new Dag(dag));
    List<Node> nodes = bayesPm.getDag().getNodes();

    for (Node node : nodes) {
      Node var = nodesToVars.get(node.getName());

      if (var instanceof DiscreteVariable) {
        DiscreteVariable var2 = nodesToVars.get(node.getName());
        int numCategories = var2.getNumCategories();
        List<String> categories = new ArrayList<String>();
        for (int j = 0; j < numCategories; j++) {
          categories.add(var2.getCategory(j));
        }
        bayesPm.setCategories(node, categories);
      }
    }

    BayesProperties properties = new BayesProperties(dataSet, dag);
    properties.setGraph(dag);

    NumberFormat nf = NumberFormat.getInstance();
    nf.setMaximumFractionDigits(4);

    StringBuilder buf = new StringBuilder();
    buf.append("\nP-value = ").append(properties.getLikelihoodRatioP());
    buf.append("\nDf = ").append(properties.getPValueDf());
    buf.append("\nChi square = ").append(nf.format(properties.getPValueChisq()));
    buf.append("\nBIC score = ").append(nf.format(properties.getBic()));
    buf.append("\n\nH0: Completely disconnected graph.");

    return buf.toString();
  }
Example #15
0
 public void printChildren() {
   System.out.print("Children: ");
   if (children.isEmpty()) System.out.print("null");
   else {
     for (int i = 0; i < children.size(); ++i) {
       Node child = children.get(i);
       System.out.print(child.getName() + "\t");
     }
   }
   System.out.println();
 }
Example #16
0
  // Invalid if then nodes or graph changes.
  private void calculateArrowsBackward(Node x, Node y, Graph graph) {
    if (x == y) {
      return;
    }

    if (!graph.isAdjacentTo(x, y)) {
      return;
    }

    if (!knowledgeEmpty()) {
      if (!getKnowledge().noEdgeRequired(x.getName(), y.getName())) {
        return;
      }
    }

    List<Node> naYX = getNaYX(x, y, graph);

    clearArrow(x, y);

    List<Node> _naYX = new ArrayList<Node>(naYX);
    DepthChoiceGenerator gen = new DepthChoiceGenerator(_naYX.size(), _naYX.size());
    int[] choice;

    while ((choice = gen.next()) != null) {
      List<Node> H = GraphUtils.asList(choice, _naYX);

      if (!knowledgeEmpty()) {
        if (!validSetByKnowledge(y, H)) {
          continue;
        }
      }

      double bump = deleteEval(x, y, H, naYX, graph);

      if (bump > 0.0) {
        Arrow arrow = new Arrow(bump, x, y, H, naYX);
        sortedArrows.add(arrow);
        addLookupArrow(x, y, arrow);
      }
    }
  }
Example #17
0
  /**
   * Constructs a new FCI search for the given independence test and background knowledge and a list
   * of variables to search over.
   */
  public Rfci(IndependenceTest independenceTest, List<Node> searchVars) {
    if (independenceTest == null || knowledge == null) {
      throw new NullPointerException();
    }

    this.independenceTest = independenceTest;
    this.variables.addAll(independenceTest.getVariables());

    Set<Node> remVars = new HashSet<Node>();
    for (Node node1 : this.variables) {
      boolean search = false;
      for (Node node2 : searchVars) {
        if (node1.getName().equals(node2.getName())) {
          search = true;
        }
      }
      if (!search) {
        remVars.add(node1);
      }
    }
    this.variables.removeAll(remVars);
  }
Example #18
0
  private void initializeArrowsBackward(Graph graph) {
    sortedArrows.clear();
    lookupArrows.clear();

    for (Edge edge : graph.getEdges()) {
      Node x = edge.getNode1();
      Node y = edge.getNode2();

      if (!knowledgeEmpty()) {
        if (!getKnowledge().noEdgeRequired(x.getName(), y.getName())) {
          continue;
        }
      }

      if (Edges.isDirectedEdge(edge)) {
        calculateArrowsBackward(x, y, graph);
      } else {
        calculateArrowsBackward(x, y, graph);
        calculateArrowsBackward(y, x, graph);
      }
    }
  }
  private void buildNameToNodeListTable(Node curNode) throws IOException {
    String fullName = curNode.getName();
    String parent = curNode.getParent();
    String separator = System.getProperty("file.separator");

    if (parent != null) {
      if (!fullName.startsWith(parent)) {
        throw new RuntimeException(
            "Internal error: parent of file name \""
                + fullName
                + "\" does not match file name \""
                + parent
                + "\"");
      }

      int len = parent.length();
      if (!parent.endsWith(separator)) {
        len += separator.length();
      }

      String fileName = fullName.substring(len);

      if (fileName == null) {
        throw new RuntimeException("Internal error: file name was empty");
      }

      List nodeList = (List) nameToNodeListTable.get(fileName);
      if (nodeList == null) {
        nodeList = new Vector();
        nameToNodeListTable.put(fileName, nodeList);
      }

      nodeList.add(curNode);
    } else {
      if (curNode != rootNode) {
        throw new RuntimeException(
            "Internal error: parent of file + \"" + fullName + "\"" + " was null");
      }
    }

    if (curNode.isDirectory()) {
      Iterator iter = curNode.getChildren();
      if (iter != null) {
        while (iter.hasNext()) {
          buildNameToNodeListTable((Node) iter.next());
        }
      }
    }
  }
  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);
        }
      }
    }
  }
 public static void buildDefinitions(Session session) {
   log.info("started building node definitions");
   String nodeName = "";
   try {
     allNodes = new HashMap<String, VNodeDefinition>();
     Node rootNode = session.getNode("/jcr:system/jcr:nodeTypes");
     NodeIterator nodeIterator = rootNode.getNodes();
     while (nodeIterator.hasNext()) {
       Node node = nodeIterator.nextNode();
       nodeName = node.getName();
       VNodeDefinition vNodeDefinition = new VNodeDefinition(node);
       customizeDefinition(vNodeDefinition); // possibly customize this definition
       allNodes.put(nodeName, vNodeDefinition);
     }
     log.info("finished building nodes");
   } catch (RepositoryException re) {
     log.warn("Could not build node definitions, died at " + nodeName, re);
   } finally {
     if (session != null) session.logout();
   }
 }
 private JCRNodeWrapper dereference(JCRNodeWrapper parent, String refPath)
     throws RepositoryException {
   JCRStoreProvider provider = parent.getProvider();
   JCRNodeWrapper wrapper;
   Node referencedNode = parent.getRealNode().getProperty("j:node").getNode();
   String fullPath = parent.getPath() + DEREF_SEPARATOR + refPath;
   if (parent.getPath().startsWith(referencedNode.getPath())) {
     throw new PathNotFoundException(fullPath);
   }
   String refRootName = StringUtils.substringBefore(refPath, "/");
   if (!referencedNode.getName().equals(refRootName)) {
     throw new PathNotFoundException(fullPath);
   }
   refPath = StringUtils.substringAfter(refPath, "/");
   if (refPath.equals("")) {
     wrapper = provider.getNodeWrapper(referencedNode, fullPath, parent, this);
   } else {
     Node node = referencedNode.getNode(refPath);
     wrapper = provider.getNodeWrapper(node, fullPath, null, this);
   }
   sessionCacheByPath.put(fullPath, wrapper);
   return wrapper;
 }
Example #23
0
  /** Do an actual deletion (Definition 13 from Chickering, 2002). */
  private void delete(Node x, Node y, List<Node> subset, Graph graph, double bump) {

    Edge trueEdge = null;

    if (trueGraph != null) {
      Node _x = trueGraph.getNode(x.getName());
      Node _y = trueGraph.getNode(y.getName());
      trueEdge = trueGraph.getEdge(_x, _y);
    }

    if (log && verbose) {
      Edge oldEdge = graph.getEdge(x, y);

      String label = trueGraph != null && trueEdge != null ? "*" : "";
      TetradLogger.getInstance()
          .log(
              "deletedEdges",
              (graph.getNumEdges() - 1)
                  + ". DELETE "
                  + oldEdge
                  + " "
                  + subset
                  + " ("
                  + bump
                  + ") "
                  + label);
      out.println(
          (graph.getNumEdges() - 1)
              + ". DELETE "
              + oldEdge
              + " "
              + subset
              + " ("
              + bump
              + ") "
              + label);
    } else {
      int numEdges = graph.getNumEdges() - 1;
      if (numEdges % 50 == 0) out.println(numEdges);
    }

    graph.removeEdge(x, y);

    for (Node h : subset) {
      Edge oldEdge = graph.getEdge(y, h);

      graph.removeEdge(y, h);
      graph.addDirectedEdge(y, h);

      if (log) {
        TetradLogger.getInstance()
            .log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(y, h));
      }

      if (verbose) {
        out.println("--- Directing " + oldEdge + " to " + graph.getEdge(y, h));
      }

      if (Edges.isUndirectedEdge(graph.getEdge(x, h))) {
        if (!graph.isAdjacentTo(x, h))
          throw new IllegalArgumentException("Not adjacent: " + x + ", " + h);
        oldEdge = graph.getEdge(x, h);

        graph.removeEdge(x, h);
        graph.addDirectedEdge(x, h);

        if (log) {
          TetradLogger.getInstance()
              .log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(x, h));
        }

        if (verbose) {
          out.println("--- Directing " + oldEdge + " to " + graph.getEdge(x, h));
        }
      }
    }
  }
Example #24
0
  private double localScoreB(Node node, List<Node> parents) {

    double score = 0.0;
    double maxScore = Double.NEGATIVE_INFINITY;

    Node _target = node;
    List<Node> _regressors = parents;
    Node target = getVariable(variables, _target.getName());
    List<Node> regressors = new ArrayList<Node>();

    for (Node _regressor : _regressors) {
      Node variable = getVariable(variables, _regressor.getName());
      regressors.add(variable);
    }

    DATASET:
    for (int m = 0; m < dataSets.size(); m++) {
      RegressionResult result = regressions.get(m).regress(target, regressors);
      TetradVector residualsSingleDataset = result.getResiduals();
      DoubleArrayList _residualsSingleDataset =
          new DoubleArrayList(residualsSingleDataset.toArray());

      for (int h = 0; h < residualsSingleDataset.size(); h++) {
        if (Double.isNaN(residualsSingleDataset.get(h))) {
          continue DATASET;
        }
      }

      double mean = Descriptive.mean(_residualsSingleDataset);
      double std =
          Descriptive.standardDeviation(
              Descriptive.variance(
                  _residualsSingleDataset.size(),
                  Descriptive.sum(_residualsSingleDataset),
                  Descriptive.sumOfSquares(_residualsSingleDataset)));

      for (int i2 = 0; i2 < _residualsSingleDataset.size(); i2++) {
        _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2) - mean) / std);
      }

      double[] _f = new double[_residualsSingleDataset.size()];

      for (int k = 0; k < _residualsSingleDataset.size(); k++) {
        _f[k] = _residualsSingleDataset.get(k);
      }

      DoubleArrayList f = new DoubleArrayList(_f);

      for (int k = 0; k < f.size(); k++) {
        f.set(k, Math.abs(f.get(k)));
      }

      double _mean = Descriptive.mean(f);
      double diff = _mean - Math.sqrt(2.0 / Math.PI);
      score += diff * diff;

      if (score > maxScore) {
        maxScore = score;
      }
    }

    double avg = score / dataSets.size();

    return avg;
  }
Example #25
0
  /* Print the current type graph to the dotfile */
  public void printDot(String title, Call call) {
    boolean printUnifications = false;
    PrintStream ps = PointsToAnalysis.v().file;
    if (ps == null) return;

    ps.println("\ndigraph F {");
    ps.println("   size = \"7,7\"; rankdir = LR;");
    ps.println("   orientation = landscape;");

    ps.println("   subgraph cluster1 {");
    ps.println("   \"Method: " + method.getName() + "\" [color=white];");

    if (nodes.isEmpty()) {
      ps.println("   \"empty graph\" [color = white];");
      ps.println("   }");
      ps.println("}");
      return;
    }

    for (Node node : nodes) {
      if (!printUnifications && !node.isRep()) continue;
      String color = "style=filled,fillcolor=";
      if (node.isheap && node.hasallocs) color += "red,";
      else if (node.isheap) color += "orange,";
      else if (node.hasallocs) color += "grey,";
      else color += "white,";
      // if (node.istouched) color = "khaki";
      // if (node.hassync) color = "khaki";
      String shape = "shape=";
      if (node.istouched) shape += "box";
      else shape += "ellipse";

      ps.println("   o" + node.id + "[label = \"" + node.getName() + "\"," + color + shape + "];");
    }
    ps.println("   }");

    Map<Integer, Map<Integer, String>> labels = new HashMap<Integer, Map<Integer, String>>();
    for (Field f : fedges.keySet())
      for (FieldEdge e : fedges.get(f)) {
        if (labels.containsKey(e.src.id)) {
          if (labels.get(e.src.id).containsKey(e.dst.id)) {
            labels.get(e.src.id).put(e.dst.id, "*");
            //                            labels.get(e.src.id).get(e.dst.id) + ", " +
            //                            e.field.getName());
          } else labels.get(e.src.id).put(e.dst.id, e.field.getName());

        } else {
          Map<Integer, String> is = new HashMap<Integer, String>();
          is.put(e.dst.id, e.field.getName());
          labels.put(e.src.id, is);
        }
      }
    for (Integer i : labels.keySet())
      for (Integer j : labels.get(i).keySet())
        ps.print(
            "   o"
                + i
                + " -> o"
                + j
                + "[label=\""
                + labels.get(i).get(j)
                + "\",style=solid,color=black];");

    for (Call ce : cedges.keySet())
      for (CallEdge e : cedges.get(ce)) {
        if (!(e.call instanceof VirtualCallExpr)) continue;
        // if (!e.call.equals(call)) continue;
        ps.print(
            "   o"
                + e.src.id
                + " -> o"
                + e.dst.id
                + "[label=\""
                + e.call
                + "\",style=solid,color=red];");
      }

    if (printUnifications)
      for (Node node : nodes)
        if (node.parent != null)
          ps.println("   o" + node.id + " -> o" + node.parent.id + " [color = blue];");

    ps.println("}");
  }
Example #26
0
  private double andersonDarlingPASquareStarB(Node node, List<Node> parents) {
    List<Double> _residuals = new ArrayList<Double>();

    Node _target = node;
    List<Node> _regressors = parents;
    Node target = getVariable(variables, _target.getName());
    List<Node> regressors = new ArrayList<Node>();

    for (Node _regressor : _regressors) {
      Node variable = getVariable(variables, _regressor.getName());
      regressors.add(variable);
    }

    double sum = 0.0;

    DATASET:
    for (int m = 0; m < dataSets.size(); m++) {
      RegressionResult result = regressions.get(m).regress(target, regressors);
      TetradVector residualsSingleDataset = result.getResiduals();

      for (int h = 0; h < residualsSingleDataset.size(); h++) {
        if (Double.isNaN(residualsSingleDataset.get(h))) {
          continue DATASET;
        }
      }

      DoubleArrayList _residualsSingleDataset =
          new DoubleArrayList(residualsSingleDataset.toArray());

      double mean = Descriptive.mean(_residualsSingleDataset);
      double std =
          Descriptive.standardDeviation(
              Descriptive.variance(
                  _residualsSingleDataset.size(),
                  Descriptive.sum(_residualsSingleDataset),
                  Descriptive.sumOfSquares(_residualsSingleDataset)));

      // By centering the individual residual columns, all moments of the mixture become weighted
      // averages of the moments
      // of the individual columns.
      // http://en.wikipedia.org/wiki/Mixture_distribution#Finite_and_countable_mixtures
      for (int i2 = 0; i2 < _residualsSingleDataset.size(); i2++) {
        //                _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2) - mean) /
        // std);
        //                _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2)) / std);
        if (isMeanCenterResiduals()) {
          _residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2) - mean));
        }
      }

      double[] _f = new double[_residuals.size()];

      for (int k = 0; k < _residuals.size(); k++) {
        _f[k] = _residuals.get(k);
      }

      sum += new AndersonDarlingTest(_f).getASquaredStar();
    }

    return sum / dataSets.size();
  }
Example #27
0
  // serial.
  private void insert(Node x, Node y, List<Node> t, Graph graph, double bump) {
    if (graph.isAdjacentTo(x, y)) {
      return; // The initial graph may already have put this edge in the graph.
      //            throw new IllegalArgumentException(x + " and " + y + " are already adjacent in
      // the graph.");
    }

    Edge trueEdge = null;

    if (trueGraph != null) {
      Node _x = trueGraph.getNode(x.getName());
      Node _y = trueGraph.getNode(y.getName());
      trueEdge = trueGraph.getEdge(_x, _y);
    }

    graph.addDirectedEdge(x, y);

    if (log) {
      String label = trueGraph != null && trueEdge != null ? "*" : "";
      TetradLogger.getInstance()
          .log(
              "insertedEdges",
              graph.getNumEdges()
                  + ". INSERT "
                  + graph.getEdge(x, y)
                  + " "
                  + t
                  + " "
                  + bump
                  + " "
                  + label);
    } else {
      int numEdges = graph.getNumEdges() - 1;
      if (verbose) {
        if (numEdges % 50 == 0) out.println(numEdges);
      }
    }

    if (verbose) {
      String label = trueGraph != null && trueEdge != null ? "*" : "";
      out.println(
          graph.getNumEdges()
              + ". INSERT "
              + graph.getEdge(x, y)
              + " "
              + t
              + " "
              + bump
              + " "
              + label);
    } else {
      int numEdges = graph.getNumEdges() - 1;
      if (verbose) {
        if (numEdges % 50 == 0) out.println(numEdges);
      }
    }

    for (Node _t : t) {
      Edge oldEdge = graph.getEdge(_t, y);

      if (oldEdge == null) throw new IllegalArgumentException("Not adjacent: " + _t + ", " + y);

      graph.removeEdge(_t, y);
      graph.addDirectedEdge(_t, y);

      if (log && verbose) {
        TetradLogger.getInstance()
            .log("directedEdges", "--- Directing " + oldEdge + " to " + graph.getEdge(_t, y));
        out.println("--- Directing " + oldEdge + " to " + graph.getEdge(_t, y));
      }
    }
  }
  /**
   * Transforms a DAG represented in graph <code>graph</code> into a maximally directed pattern
   * (PDAG) by modifying <code>g</code> itself. Based on the algorithm described in Chickering
   * (2002) "Optimal structure identification with greedy search" Journal of Machine Learning
   * Research. It works for both BayesNets and SEMs. R. Silva, June 2004
   */
  public static void dagToPdag(Graph graph) {
    // do topological sort on the nodes
    Graph graphCopy = new EdgeListGraph(graph);
    Node orderedNodes[] = new Node[graphCopy.getNodes().size()];
    int count = 0;
    while (graphCopy.getNodes().size() > 0) {
      Set<Node> exogenousNodes = new HashSet<Node>();

      for (Node next : graphCopy.getNodes()) {
        if (graphCopy.isExogenous(next)) {
          exogenousNodes.add(next);
          orderedNodes[count++] = graph.getNode(next.getName());
        }
      }

      graphCopy.removeNodes(new ArrayList<Node>(exogenousNodes));
    }
    // ordered edges - improvised, inefficient implementation
    count = 0;
    Edge edges[] = new Edge[graph.getNumEdges()];
    boolean edgeOrdered[] = new boolean[graph.getNumEdges()];
    Edge orderedEdges[] = new Edge[graph.getNumEdges()];

    for (Edge edge : graph.getEdges()) {
      edges[count++] = edge;
    }

    for (int i = 0; i < edges.length; i++) {
      edgeOrdered[i] = false;
    }

    while (count > 0) {
      for (Node orderedNode : orderedNodes) {
        for (int k = orderedNodes.length - 1; k >= 0; k--) {
          for (int q = 0; q < edges.length; q++) {
            if (!edgeOrdered[q]
                && edges[q].getNode1() == orderedNodes[k]
                && edges[q].getNode2() == orderedNode) {
              edgeOrdered[q] = true;
              orderedEdges[orderedEdges.length - count] = edges[q];
              count--;
            }
          }
        }
      }
    }

    // label edges
    boolean compelledEdges[] = new boolean[graph.getNumEdges()];
    boolean reversibleEdges[] = new boolean[graph.getNumEdges()];
    for (int i = 0; i < graph.getNumEdges(); i++) {
      compelledEdges[i] = false;
      reversibleEdges[i] = false;
    }
    for (int i = 0; i < graph.getNumEdges(); i++) {
      if (compelledEdges[i] || reversibleEdges[i]) {
        continue;
      }
      Node x = orderedEdges[i].getNode1();
      Node y = orderedEdges[i].getNode2();
      for (int j = 0; j < orderedEdges.length; j++) {
        if (orderedEdges[j].getNode2() == x && compelledEdges[j]) {
          Node w = orderedEdges[j].getNode1();
          if (!graph.isParentOf(w, y)) {
            for (int k = 0; k < orderedEdges.length; k++) {
              if (orderedEdges[k].getNode2() == y) {
                compelledEdges[k] = true;
                break;
              }
            }
          } else {
            for (int k = 0; k < orderedEdges.length; k++) {
              if (orderedEdges[k].getNode1() == w && orderedEdges[k].getNode2() == y) {
                compelledEdges[k] = true;
                break;
              }
            }
          }
        }
        if (compelledEdges[i]) {
          break;
        }
      }
      if (compelledEdges[i]) {
        continue;
      }
      boolean foundZ = false;

      for (Edge orderedEdge : orderedEdges) {
        Node z = orderedEdge.getNode1();
        if (z != x && orderedEdge.getNode2() == y && !graph.isParentOf(z, x)) {
          compelledEdges[i] = true;
          for (int k = i + 1; k < graph.getNumEdges(); k++) {
            if (orderedEdges[k].getNode2() == y && !reversibleEdges[k]) {
              compelledEdges[k] = true;
            }
          }
          foundZ = true;
          break;
        }
      }

      if (!foundZ) {
        reversibleEdges[i] = true;

        for (int j = i + 1; j < orderedEdges.length; j++) {
          if (!compelledEdges[j] && orderedEdges[j].getNode2() == y) {
            reversibleEdges[j] = true;
          }
        }
      }
    }

    // undirect edges that are reversible
    for (int i = 0; i < reversibleEdges.length; i++) {
      if (reversibleEdges[i]) {
        graph.setEndpoint(orderedEdges[i].getNode1(), orderedEdges[i].getNode2(), Endpoint.TAIL);
        graph.setEndpoint(orderedEdges[i].getNode2(), orderedEdges[i].getNode1(), Endpoint.TAIL);
      }
    }
  }
Example #29
0
  private void addRequiredEdges(Graph graph) {
    if (true) return;
    if (knowledgeEmpty()) return;

    for (Iterator<KnowledgeEdge> it = getKnowledge().requiredEdgesIterator(); it.hasNext(); ) {
      KnowledgeEdge next = it.next();

      Node nodeA = graph.getNode(next.getFrom());
      Node nodeB = graph.getNode(next.getTo());

      if (!graph.isAncestorOf(nodeB, nodeA)) {
        graph.removeEdges(nodeA, nodeB);
        graph.addDirectedEdge(nodeA, nodeB);
        TetradLogger.getInstance()
            .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeA, nodeB));
      }
    }
    for (Edge edge : graph.getEdges()) {
      final String A = edge.getNode1().getName();
      final String B = edge.getNode2().getName();

      if (knowledge.isForbidden(A, B)) {
        Node nodeA = edge.getNode1();
        Node nodeB = edge.getNode2();

        if (nodeA != null
            && nodeB != null
            && graph.isAdjacentTo(nodeA, nodeB)
            && !graph.isChildOf(nodeA, nodeB)) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
        if (!graph.isChildOf(nodeA, nodeB)
            && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
      } else if (knowledge.isForbidden(B, A)) {
        Node nodeA = edge.getNode2();
        Node nodeB = edge.getNode1();

        if (nodeA != null
            && nodeB != null
            && graph.isAdjacentTo(nodeA, nodeB)
            && !graph.isChildOf(nodeA, nodeB)) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
        if (!graph.isChildOf(nodeA, nodeB)
            && getKnowledge().isForbidden(nodeA.getName(), nodeB.getName())) {
          if (!graph.isAncestorOf(nodeA, nodeB)) {
            graph.removeEdges(nodeA, nodeB);
            graph.addDirectedEdge(nodeB, nodeA);
            TetradLogger.getInstance()
                .log("insertedEdges", "Adding edge by knowledge: " + graph.getEdge(nodeB, nodeA));
          }
        }
      }
    }
  }
Example #30
0
 public void printParent() {
   if (parent == null) System.out.println("Parent: " + parent);
   else System.out.println("Parent: " + parent.getName());
 }