use of edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm in project tetrad by cmu-phil.
the class GeneralAlgorithmRunner method execute.
// ============================PUBLIC METHODS==========================//
@Override
public void execute() {
List<Graph> graphList = new ArrayList<>();
int i = 0;
if (getDataModelList().isEmpty()) {
if (getSourceGraph() != null) {
Algorithm algo = getAlgorithm();
if (algo instanceof HasKnowledge) {
((HasKnowledge) algo).setKnowledge(getKnowledge());
}
graphList.add(algo.search(null, parameters));
} else {
throw new IllegalArgumentException("The parent boxes did not include any datasets or graphs. Try opening\n" + "the editors for those boxes and loading or simulating them.");
}
} else {
if (getAlgorithm() instanceof MultiDataSetAlgorithm) {
for (int k = 0; k < parameters.getInt("numRuns"); k++) {
List<DataSet> dataSets = getDataModelList().stream().map(e -> (DataSet) e).collect(Collectors.toCollection(ArrayList::new));
if (dataSets.size() < parameters.getInt("randomSelectionSize")) {
throw new IllegalArgumentException("Sorry, the 'random selection size' is greater than " + "the number of data sets.");
}
Collections.shuffle(dataSets);
List<DataModel> sub = new ArrayList<>();
for (int j = 0; j < parameters.getInt("randomSelectionSize"); j++) {
sub.add(dataSets.get(j));
}
Algorithm algo = getAlgorithm();
if (algo instanceof HasKnowledge) {
((HasKnowledge) algo).setKnowledge(getKnowledge());
}
graphList.add(((MultiDataSetAlgorithm) algo).search(sub, parameters));
}
} else if (getAlgorithm() instanceof ClusterAlgorithm) {
for (int k = 0; k < parameters.getInt("numRuns"); k++) {
getDataModelList().forEach(dataModel -> {
if (dataModel instanceof ICovarianceMatrix) {
ICovarianceMatrix dataSet = (ICovarianceMatrix) dataModel;
graphList.add(algorithm.search(dataSet, parameters));
} else if (dataModel instanceof DataSet) {
DataSet dataSet = (DataSet) dataModel;
if (!dataSet.isContinuous()) {
throw new IllegalArgumentException("Sorry, you need a continuous dataset for a cluster algorithm.");
}
graphList.add(algorithm.search(dataSet, parameters));
}
});
}
} else {
getDataModelList().forEach(data -> {
IKnowledge knowledgeFromData = data.getKnowledge();
if (!(knowledgeFromData == null || knowledgeFromData.getVariables().isEmpty())) {
this.knowledge = knowledgeFromData;
}
Algorithm algo = getAlgorithm();
if (algo instanceof HasKnowledge) {
((HasKnowledge) algo).setKnowledge(getKnowledge());
}
DataType algDataType = algo.getDataType();
if (data.isContinuous() && (algDataType == DataType.Continuous || algDataType == DataType.Mixed)) {
graphList.add(algo.search(data, parameters));
} else if (data.isDiscrete() && (algDataType == DataType.Discrete || algDataType == DataType.Mixed)) {
graphList.add(algo.search(data, parameters));
} else if (data.isMixed() && algDataType == DataType.Mixed) {
graphList.add(algo.search(data, parameters));
} else {
throw new IllegalArgumentException("The type of data changed; try opening up the search editor and " + "running the algorithm there.");
}
});
}
}
if (getKnowledge().getVariablesNotInTiers().size() < getKnowledge().getVariables().size()) {
for (Graph graph : graphList) {
SearchGraphUtils.arrangeByKnowledgeTiers(graph, getKnowledge());
}
} else {
for (Graph graph : graphList) {
GraphUtils.circleLayout(graph, 225, 200, 150);
}
}
this.graphList = graphList;
}
use of edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm 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;
}
}
}
}
use of edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm 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;
}
}
}
}
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