Examples with PatternToDag edu.cmu.tetrad.search.PatternToDag used on opensource projects

Example 6 with PatternToDag

use of edu.cmu.tetrad.search.PatternToDag in project tetrad by cmu-phil.

the class PcGesSearchEditor method calcStats.

private void calcStats() {
    Graph resultGraph = getAlgorithmRunner().getGraph();
    if (getAlgorithmRunner().getDataModel() instanceof DataSet) {
        // resultGraph may be the output of a PC search.
        // Such graphs sometimes contain doubly directed edges.
        // We convert 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);
            }
        }
        Graph dag = SearchGraphUtils.dagFromPattern(resultGraph);
        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);
    } else if (getAlgorithmRunner().getDataModel() instanceof ICovarianceMatrix) {
        // 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);
            }
        }
        Graph pattern = new EdgeListGraphSingleConnections(resultGraph);
        PatternToDag ptd = new PatternToDag(pattern);
        Graph dag = ptd.patternToDagMeek();
        ICovarianceMatrix dataSet = (ICovarianceMatrix) getAlgorithmRunner().getDataModel();
        String report = reportIfCovMatrix(dag, dataSet);
        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);
    }
}

Example 7 with PatternToDag

use of edu.cmu.tetrad.search.PatternToDag in project tetrad by cmu-phil.

the class PcStableLocalSearchEditor method addSpecialMenus.

protected void addSpecialMenus(JMenuBar menuBar) {
    if (!(getAlgorithmRunner() instanceof IGesRunner)) {
        JMenu test = new JMenu("Independence");
        menuBar.add(test);
        IndTestMenuItems.addIndependenceTestChoices(test, this);
    // test.addSeparator();
    // 
    // AlgorithmRunner algorithmRunner = getAlgorithmRunner();
    // if (algorithmRunner instanceof IndTestProducer) {
    // IndTestProducer p = (IndTestProducer) algorithmRunner;
    // IndependenceFactsAction action =
    // new IndependenceFactsAction(this, p, "Independence Facts...");
    // test.add(action);
    // }
    }
    JMenu graph = new JMenu("Graph");
    JMenuItem showDags = new JMenuItem("Show DAGs in forbid_latent_common_causes");
    // JMenuItem meekOrient = new JMenuItem("Meek Orientation");
    JMenuItem dagInPattern = new JMenuItem("Choose DAG in forbid_latent_common_causes");
    JMenuItem gesOrient = new JMenuItem("Global Score-based Reorientation");
    JMenuItem nextGraph = new JMenuItem("Next Graph");
    JMenuItem previousGraph = new JMenuItem("Previous Graph");
    // graph.add(new LayoutMenu(this));
    graph.add(new GraphPropertiesAction(getWorkbench()));
    graph.add(new PathsAction(getWorkbench()));
    // graph.add(new DirectedPathsAction(getWorkbench()));
    // graph.add(new TreksAction(getWorkbench()));
    // graph.add(new AllPathsAction(getWorkbench()));
    // graph.add(new NeighborhoodsAction(getWorkbench()));
    graph.add(new TriplesAction(getWorkbench().getGraph(), getAlgorithmRunner()));
    graph.addSeparator();
    // graph.add(meekOrient);
    graph.add(dagInPattern);
    graph.add(gesOrient);
    graph.addSeparator();
    graph.add(previousGraph);
    graph.add(nextGraph);
    graph.addSeparator();
    graph.add(showDags);
    graph.addSeparator();
    graph.add(new JMenuItem(new SelectBidirectedAction(getWorkbench())));
    graph.add(new JMenuItem(new SelectUndirectedAction(getWorkbench())));
    menuBar.add(graph);
    showDags.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Window owner = (Window) getTopLevelAncestor();
            new WatchedProcess(owner) {

                public void watch() {
                    // Needs to be a pattern search; this isn't checked
                    // before running the algorithm because of allowable
                    // "slop"--e.g. bidirected edges.
                    AlgorithmRunner runner = getAlgorithmRunner();
                    Graph graph = runner.getGraph();
                    if (graph == null) {
                        JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "No result gaph.");
                        return;
                    }
                    // if (runner instanceof ImagesRunner) {
                    // GraphScorer scorer = ((ImagesRunner) runner).getGraphScorer();
                    // Graph _graph = ((ImagesRunner) runner).getTopGraphs().get(getIndex()).getGraph();
                    // 
                    // ScoredGraphsDisplay display = new ScoredGraphsDisplay(_graph, scorer);
                    // GraphWorkbench workbench = getWorkbench();
                    // 
                    // EditorWindow editorWindow =
                    // new EditorWindow(display, "Independence Facts",
                    // "Close", false, workbench);
                    // DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
                    // editorWindow.setVisible(true);
                    // }
                    // else {
                    PatternDisplay display = new PatternDisplay(graph);
                    GraphWorkbench workbench = getWorkbench();
                    EditorWindow editorWindow = new EditorWindow(display, "Independence Facts", "Close", false, workbench);
                    DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
                    editorWindow.setVisible(true);
                // }
                }
            };
        }
    });
    // meekOrient.addActionListener(new ActionListener() {
    // public void actionPerformed(ActionEvent e) {
    // ImpliedOrientation rules = getAlgorithmRunner().getMeekRules();
    // rules.setKnowledge((IKnowledge) getAlgorithmRunner().getParams().get("knowledge", new Knowledge2()));
    // rules.orientImplied(getGraph());
    // getGraphHistory().add(getGraph());
    // getWorkbench().setGraph(getGraph());
    // firePropertyChange("modelChanged", null, null);
    // }
    // });
    dagInPattern.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph graph = new EdgeListGraph(getGraph());
            // Removing bidirected edges from the pattern before selecting a DAG.                                   4
            for (Edge edge : graph.getEdges()) {
                if (Edges.isBidirectedEdge(edge)) {
                    graph.removeEdge(edge);
                }
            }
            PatternToDag search = new PatternToDag(new EdgeListGraphSingleConnections(graph));
            Graph dag = search.patternToDagMeek();
            getGraphHistory().add(dag);
            getWorkbench().setGraph(dag);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(dag);
            firePropertyChange("modelChanged", null, null);
        }
    });
    gesOrient.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            DataModel dataModel = getAlgorithmRunner().getDataModel();
            final Graph graph = SearchGraphUtils.reorient(getGraph(), dataModel, getKnowledge());
            getGraphHistory().add(graph);
            getWorkbench().setGraph(graph);
            firePropertyChange("modelChanged", null, null);
        }
    });
    nextGraph.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph next = getGraphHistory().next();
            getWorkbench().setGraph(next);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(next);
            firePropertyChange("modelChanged", null, null);
        }
    });
    previousGraph.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            Graph previous = getGraphHistory().previous();
            getWorkbench().setGraph(previous);
            ((AbstractAlgorithmRunner) getAlgorithmRunner()).setResultGraph(previous);
            firePropertyChange("modelChanged", null, null);
        }
    });
    // if (getAlgorithmRunner().supportsKnowledge()) {
    // menuBar.add(new Knowledge2Menu(this));
    // }
    menuBar.add(new LayoutMenu(this));
}

Example 8 with PatternToDag

use of edu.cmu.tetrad.search.PatternToDag in project tetrad by cmu-phil.

the class PcStableLocalSearchEditor method calcStats.

private void calcStats() {
    Graph resultGraph = getAlgorithmRunner().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);
            }
        }
        Graph pattern = new EdgeListGraphSingleConnections(resultGraph);
        PatternToDag ptd = new PatternToDag(pattern);
        Graph dag = ptd.patternToDagMeek();
        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", dag);
        modelStatsText.setLineWrap(true);
        modelStatsText.setWrapStyleWord(true);
        modelStatsText.setText(report);
        removeStatsTabs();
        tabbedPane.addTab("DAG in pattern", dagWorkbenchScroll);
        tabbedPane.addTab("DAG Model Statistics", modelStatsText);
    }
}