Examples with ExternalAlgorithm edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm used on opensource projects

Example 6 with ExternalAlgorithm

use of edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm in project tetrad by cmu-phil.

the class Comparison 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 7 with ExternalAlgorithm

use of edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm in project tetrad by cmu-phil.

the class Comparison method generateReportFromExternalAlgorithms.

public void generateReportFromExternalAlgorithms(String dataPath, String resultsPath, String outputFileName, Algorithms algorithms, Statistics statistics, Parameters parameters) {
    this.saveGraphs = false;
    this.dataPath = dataPath;
    this.resultsPath = resultsPath;
    for (Algorithm algorithm : algorithms.getAlgorithms()) {
        if (!(algorithm instanceof ExternalAlgorithm))
            throw new IllegalArgumentException("Expecting all algorithms to implement ExternalAlgorithm.");
    }
    Simulations simulations = new Simulations();
    File file = new File(this.dataPath, "save");
    File[] dirs = file.listFiles();
    if (dirs == null) {
        throw new NullPointerException("No files in " + file.getAbsolutePath());
    }
    this.dirs = new ArrayList<String>();
    int count = 0;
    for (File dir : dirs) {
        if (dir.getName().contains("DS_Store"))
            continue;
        count++;
    }
    for (int i = 1; i <= count; i++) {
        File _dir = new File(dataPath, "save/" + i);
        simulations.add(new LoadDataAndGraphs(_dir.getAbsolutePath()));
        this.dirs.add(_dir.getAbsolutePath());
    }
    compareFromSimulations(this.resultsPath, simulations, outputFileName, algorithms, statistics, parameters);
}

Example 8 with ExternalAlgorithm

use of edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm in project tetrad by cmu-phil.

the class Comparison method compareFromFiles.

/**
 * Compares algorithms.
 *
 * @param dataPath    Path to the directory where data and graph files have been saved.
 * @param resultsPath Path to the file where the results should be stored.
 * @param algorithms  The list of algorithms to be compared.
 * @param statistics  The list of statistics on which to compare the algorithm, and their utility weights.
 * @param parameters  The list of parameters and their values.
 */
public void compareFromFiles(String dataPath, String resultsPath, Algorithms algorithms, Statistics statistics, Parameters parameters) {
    for (Algorithm algorithm : algorithms.getAlgorithms()) {
        if (algorithm instanceof ExternalAlgorithm) {
            throw new IllegalArgumentException("Not expecting any implementations of ExternalAlgorithm here.");
        }
    }
    this.dataPath = dataPath;
    this.resultsPath = resultsPath;
    Simulations simulations = new Simulations();
    File file = new File(this.dataPath, "save");
    File[] dirs = file.listFiles();
    if (dirs == null) {
        throw new NullPointerException("No files in " + file.getAbsolutePath());
    }
    this.dirs = new ArrayList<String>();
    int count = 0;
    for (File dir : dirs) {
        if (dir.getName().contains("DS_Store"))
            continue;
        count++;
    }
    for (int i = 1; i <= count; i++) {
        File _dir = new File(dataPath, "save/" + i);
        simulations.add(new LoadDataAndGraphs(_dir.getAbsolutePath()));
        this.dirs.add(_dir.getAbsolutePath());
    }
    compareFromSimulations(this.resultsPath, simulations, algorithms, statistics, parameters);
}

Example 9 with ExternalAlgorithm

use of edu.cmu.tetrad.algcomparison.algorithm.ExternalAlgorithm in project tetrad by cmu-phil.

the class ExternalAlgorithmIntersection method search.

/**
 * Reads in the relevant graph from the file (see above) and returns it.
 */
public Graph search(DataModel dataSet, Parameters parameters) {
    this.elapsed = 0;
    for (ExternalAlgorithm algorithm : algorithms) {
        algorithm.setPath(this.path);
        algorithm.setSimIndex(this.simIndex);
        algorithm.setSimulation(this.simulation);
        elapsed += algorithm.getElapsedTime((DataSet) dataSet, parameters);
    }
    Graph graph0 = algorithms[0].search(dataSet, parameters);
    Set<Edge> edges = graph0.getEdges();
    for (int i = 1; i < algorithms.length; i++) {
        edges.retainAll(algorithms[i].search(dataSet, parameters).getEdges());
    }
    EdgeListGraph intersection = new EdgeListGraph(graph0.getNodes());
    for (Edge edge : edges) {
        intersection.addEdge(edge);
    }
    return intersection;
}