Examples with EdgeListGraph edu.cmu.tetrad.graph.EdgeListGraph used on opensource projects

Example 21 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class GraphHistory method add.

public void add(Graph graph) {
    if (graph == null) {
        throw new NullPointerException();
    }
    for (int i = graphs.size() - 1; i > index; i--) {
        graphs.remove(i);
    }
    graphs.addLast(new EdgeListGraph(graph));
    index++;
}

Example 22 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class PcStable method search.

/**
 * Runs PC starting with a commplete graph over the given list of nodes, using the given independence test and
 * knowledge and returns the resultant graph. The returned graph will be a pattern if the independence information
 * is consistent with the hypothesis that there are no latent common causes. It may, however, contain cycles or
 * bidirected edges if this assumption is not born out, either due to the actual presence of latent common causes,
 * or due to statistical errors in conditional independence judgments.
 * <p>
 * All of the given nodes must be in the domain of the given conditional independence test.
 */
public Graph search(List<Node> nodes) {
    this.logger.log("info", "Starting PC algorithm");
    this.logger.log("info", "Independence test = " + getIndependenceTest() + ".");
    // this.logger.log("info", "Variables " + independenceTest.getVariable());
    long startTime = System.currentTimeMillis();
    if (getIndependenceTest() == null) {
        throw new NullPointerException();
    }
    List allNodes = getIndependenceTest().getVariables();
    if (!allNodes.containsAll(nodes)) {
        throw new IllegalArgumentException("All of the given nodes must " + "be in the domain of the independence test provided.");
    }
    graph = new EdgeListGraph(nodes);
    IFas fas = new FasStable(initialGraph, getIndependenceTest());
    fas.setKnowledge(getKnowledge());
    fas.setDepth(getDepth());
    fas.setVerbose(verbose);
    graph = fas.search();
    sepsets = fas.getSepsets();
    SearchGraphUtils.pcOrientbk(knowledge, graph, nodes);
    // SearchGraphUtils.orientCollidersUsingSepsets(this.sepsets, knowledge, graph, initialGraph, verbose);
    // SearchGraphUtils.orientCollidersUsingSepsets(this.sepsets, knowledge, graph, verbose);
    // SearchGraphUtils.orientColeelidersLocally(knowledge, graph, independenceTest, depth);
    SearchGraphUtils.orientCollidersUsingSepsets(this.sepsets, knowledge, graph, verbose, false);
    MeekRules rules = new MeekRules();
    rules.setAggressivelyPreventCycles(this.aggressivelyPreventCycles);
    rules.setKnowledge(knowledge);
    rules.orientImplied(graph);
    this.logger.log("graph", "\nReturning this graph: " + graph);
    this.elapsedTime = System.currentTimeMillis() - startTime;
    this.logger.log("info", "Elapsed time = " + (elapsedTime) / 1000. + " s");
    this.logger.log("info", "Finishing PC Algorithm.");
    this.logger.flush();
    return graph;
}

Example 23 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TimeoutComparison method getSubgraph.

private Graph getSubgraph(Graph graph, boolean discrete1, boolean discrete2, DataModel DataModel) {
    if (discrete1 && discrete2) {
        Graph newGraph = new EdgeListGraph(graph.getNodes());
        for (Edge edge : graph.getEdges()) {
            Node node1 = DataModel.getVariable(edge.getNode1().getName());
            Node node2 = DataModel.getVariable(edge.getNode2().getName());
            if (node1 instanceof DiscreteVariable && node2 instanceof DiscreteVariable) {
                newGraph.addEdge(edge);
            }
        }
        return newGraph;
    } else if (!discrete1 && !discrete2) {
        Graph newGraph = new EdgeListGraph(graph.getNodes());
        for (Edge edge : graph.getEdges()) {
            Node node1 = DataModel.getVariable(edge.getNode1().getName());
            Node node2 = DataModel.getVariable(edge.getNode2().getName());
            if (node1 instanceof ContinuousVariable && node2 instanceof ContinuousVariable) {
                newGraph.addEdge(edge);
            }
        }
        return newGraph;
    } else {
        Graph newGraph = new EdgeListGraph(graph.getNodes());
        for (Edge edge : graph.getEdges()) {
            Node node1 = DataModel.getVariable(edge.getNode1().getName());
            Node node2 = DataModel.getVariable(edge.getNode2().getName());
            if (node1 instanceof DiscreteVariable && node2 instanceof ContinuousVariable) {
                newGraph.addEdge(edge);
            }
            if (node1 instanceof ContinuousVariable && node2 instanceof DiscreteVariable) {
                newGraph.addEdge(edge);
            }
        }
        return newGraph;
    }
}

Example 24 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class TimeoutComparison method doRun.

private void doRun(List<AlgorithmSimulationWrapper> algorithmSimulationWrappers, List<AlgorithmWrapper> algorithmWrappers, List<SimulationWrapper> simulationWrappers, Statistics statistics, int numGraphTypes, double[][][][] allStats, Run run) {
    System.out.println();
    System.out.println("Run " + (run.getRunIndex() + 1));
    System.out.println();
    AlgorithmSimulationWrapper algorithmSimulationWrapper = algorithmSimulationWrappers.get(run.getAlgSimIndex());
    AlgorithmWrapper algorithmWrapper = algorithmSimulationWrapper.getAlgorithmWrapper();
    SimulationWrapper simulationWrapper = algorithmSimulationWrapper.getSimulationWrapper();
    DataModel data = simulationWrapper.getDataModel(run.getRunIndex());
    Graph trueGraph = simulationWrapper.getTrueGraph(run.getRunIndex());
    System.out.println((run.getAlgSimIndex() + 1) + ". " + algorithmWrapper.getDescription() + " simulationWrapper: " + simulationWrapper.getDescription());
    long start = System.currentTimeMillis();
    Graph out;
    try {
        Algorithm algorithm = algorithmWrapper.getAlgorithm();
        Simulation simulation = simulationWrapper.getSimulation();
        if (algorithm instanceof HasKnowledge && simulation instanceof HasKnowledge) {
            ((HasKnowledge) algorithm).setKnowledge(((HasKnowledge) simulation).getKnowledge());
        }
        if (algorithmWrapper.getAlgorithm() instanceof ExternalAlgorithm) {
            ExternalAlgorithm external = (ExternalAlgorithm) algorithmWrapper.getAlgorithm();
            external.setSimulation(simulationWrapper.getSimulation());
            external.setPath(resultsPath);
            external.setSimIndex(simulationWrappers.indexOf(simulationWrapper));
        }
        if (algorithm instanceof MultiDataSetAlgorithm) {
            List<Integer> indices = new ArrayList<>();
            int numDataModels = simulationWrapper.getSimulation().getNumDataModels();
            for (int i = 0; i < numDataModels; i++) {
                indices.add(i);
            }
            Collections.shuffle(indices);
            List<DataModel> dataModels = new ArrayList<>();
            int randomSelectionSize = algorithmWrapper.getAlgorithmSpecificParameters().getInt("randomSelectionSize");
            for (int i = 0; i < Math.min(numDataModels, randomSelectionSize); i++) {
                dataModels.add(simulationWrapper.getSimulation().getDataModel(indices.get(i)));
            }
            Parameters _params = algorithmWrapper.getAlgorithmSpecificParameters();
            out = ((MultiDataSetAlgorithm) algorithm).search(dataModels, _params);
        } else {
            DataModel dataModel = copyData ? data.copy() : data;
            Parameters _params = algorithmWrapper.getAlgorithmSpecificParameters();
            out = algorithm.search(dataModel, _params);
        }
    } catch (Exception e) {
        System.out.println("Could not run " + algorithmWrapper.getDescription());
        e.printStackTrace();
        return;
    }
    int simIndex = simulationWrappers.indexOf(simulationWrapper) + 1;
    int algIndex = algorithmWrappers.indexOf(algorithmWrapper) + 1;
    long stop = System.currentTimeMillis();
    long elapsed = stop - start;
    saveGraph(resultsPath, out, run.getRunIndex(), simIndex, algIndex, algorithmWrapper, elapsed);
    if (trueGraph != null) {
        out = GraphUtils.replaceNodes(out, trueGraph.getNodes());
    }
    if (algorithmWrapper.getAlgorithm() instanceof ExternalAlgorithm) {
        ExternalAlgorithm extAlg = (ExternalAlgorithm) algorithmWrapper.getAlgorithm();
        extAlg.setSimIndex(simulationWrappers.indexOf(simulationWrapper));
        extAlg.setSimulation(simulationWrapper.getSimulation());
        extAlg.setPath(resultsPath);
        elapsed = extAlg.getElapsedTime(data, simulationWrapper.getSimulationSpecificParameters());
    }
    Graph[] est = new Graph[numGraphTypes];
    Graph comparisonGraph;
    if (this.comparisonGraph == ComparisonGraph.true_DAG) {
        comparisonGraph = new EdgeListGraph(trueGraph);
    } else if (this.comparisonGraph == ComparisonGraph.Pattern_of_the_true_DAG) {
        comparisonGraph = SearchGraphUtils.patternForDag(new EdgeListGraph(trueGraph));
    } else if (this.comparisonGraph == ComparisonGraph.PAG_of_the_true_DAG) {
        comparisonGraph = new DagToPag(new EdgeListGraph(trueGraph)).convert();
    } else {
        throw new IllegalArgumentException("Unrecognized graph type.");
    }
    // Graph comparisonGraph = trueGraph == null ? null : algorithmSimulationWrapper.getComparisonGraph(trueGraph);
    est[0] = out;
    graphTypeUsed[0] = true;
    if (data.isMixed()) {
        est[1] = getSubgraph(out, true, true, data);
        est[2] = getSubgraph(out, true, false, data);
        est[3] = getSubgraph(out, false, false, data);
        graphTypeUsed[1] = true;
        graphTypeUsed[2] = true;
        graphTypeUsed[3] = true;
    }
    Graph[] truth = new Graph[numGraphTypes];
    truth[0] = comparisonGraph;
    if (data.isMixed() && comparisonGraph != null) {
        truth[1] = getSubgraph(comparisonGraph, true, true, data);
        truth[2] = getSubgraph(comparisonGraph, true, false, data);
        truth[3] = getSubgraph(comparisonGraph, false, false, data);
    }
    if (comparisonGraph != null) {
        for (int u = 0; u < numGraphTypes; u++) {
            if (!graphTypeUsed[u]) {
                continue;
            }
            int statIndex = -1;
            for (Statistic _stat : statistics.getStatistics()) {
                statIndex++;
                if (_stat instanceof ParameterColumn) {
                    continue;
                }
                double stat;
                if (_stat instanceof ElapsedTime) {
                    stat = elapsed / 1000.0;
                } else {
                    stat = _stat.getValue(truth[u], est[u]);
                }
                allStats[u][run.getAlgSimIndex()][statIndex][run.getRunIndex()] = stat;
            }
        }
    }
}

Example 25 with EdgeListGraph

use of edu.cmu.tetrad.graph.EdgeListGraph in project tetrad by cmu-phil.

the class PngWriter method writePng.

public static void writePng(Graph graph, File file) {
    // circleLayout(graph, 200, 200, 175);
    JPanel panel = new JPanel();
    panel.setLayout(new BorderLayout());
    // Remove self-loops.
    graph = new EdgeListGraph(graph);
    for (Node node : graph.getNodes()) {
        for (Edge edge : new ArrayList<>(graph.getEdges(node, node))) {
            graph.removeEdge(edge);
        }
    }
    final GraphWorkbench workbench = new GraphWorkbench(graph);
    int maxx = 0;
    int maxy = 0;
    for (Node node : graph.getNodes()) {
        if (node.getCenterX() > maxx) {
            maxx = node.getCenterX();
        }
        if (node.getCenterY() > maxy) {
            maxy = node.getCenterY();
        }
    }
    workbench.setSize(new Dimension(maxx + 50, maxy + 50));
    panel.add(workbench, BorderLayout.CENTER);
    JDialog dialog = new JDialog();
    dialog.add(workbench);
    dialog.pack();
    Dimension size = workbench.getSize();
    BufferedImage image = new BufferedImage(size.width, size.height, BufferedImage.TYPE_BYTE_INDEXED);
    Graphics2D graphics = image.createGraphics();
    workbench.paint(graphics);
    image.flush();
    // Write the image to resultFile.
    try {
        ImageIO.write(image, "PNG", file);
    } catch (IOException e1) {
        throw new RuntimeException("Could not write to " + file, e1);
    }
}