Examples with WatchedProcess edu.cmu.tetradapp.util.WatchedProcess used on opensource projects

Example 16 with WatchedProcess

use of edu.cmu.tetradapp.util.WatchedProcess 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 17 with WatchedProcess

use of edu.cmu.tetradapp.util.WatchedProcess in project tetrad by cmu-phil.

the class PathsAction method update.

private void update(final Graph graph, final JTextArea textArea, final List<Node> nodes1, final List<Node> nodes2, final String method) {
    Window owner = (Window) JOptionUtils.centeringComp().getTopLevelAncestor();
    final WatchedProcess process = new WatchedProcess(owner) {

        public void watch() {
            if ("Directed Paths".equals(method)) {
                textArea.setText("");
                allDirectedPaths(graph, textArea, nodes1, nodes2);
            } else if ("Semidirected Paths".equals(method)) {
                textArea.setText("");
                allSemidirectedPaths(graph, textArea, nodes1, nodes2);
            } else if ("Treks".equals(method)) {
                textArea.setText("");
                allTreks(graph, textArea, nodes1, nodes2);
            } else if ("Adjacents".equals(method)) {
                textArea.setText("");
                adjacentNodes(graph, textArea, nodes1, nodes2);
            }
        }
    };
}

Example 18 with WatchedProcess

use of edu.cmu.tetradapp.util.WatchedProcess in project tetrad by cmu-phil.

the class GeneralAlgorithmEditor method doSearch.

private void doSearch(final GeneralAlgorithmRunner runner) {
    new WatchedProcess((Window) getTopLevelAncestor()) {

        @Override
        public void watch() {
            AlgorithmModel algoModel = algorithmList.getSelectedValue();
            if (algoModel != null) {
                String title = String.format("Algorithm: %s", algoModel.getAlgorithm().getAnnotation().name());
                algorithmGraphTitle.setText(title);
                HpcAccount hpcAccount = null;
                if (algoModel.getAlgorithm().getAnnotation().algoType() != AlgType.orient_pairwise && runner.getDataModelList().getModelList().size() == 1) {
                    String algoName = algoModel.getAlgorithm().getAnnotation().name();
                    hpcAccount = showRemoteComputingOptions(algoName);
                }
                if (hpcAccount == null) {
                    graphEditor.saveLayout();
                    runner.execute();
                    // Show graph
                    graphEditor.replace(runner.getGraphs());
                    graphEditor.validate();
                    firePropertyChange("modelChanged", null, null);
                    // Update the graphContainer
                    graphContainer.add(graphEditor);
                    changeCard(GRAPH_CARD);
                } else {
                    try {
                        doRemoteCompute(runner, hpcAccount);
                    } catch (Exception exception) {
                        LOGGER.error("Unable to run algorithm.", exception);
                    }
                }
            }
        }
    };
}

Example 19 with WatchedProcess

use of edu.cmu.tetradapp.util.WatchedProcess in project tetrad by cmu-phil.

the class FgesSearchEditor method calcStats.

private void calcStats() {
    FgesRunner runner = (FgesRunner) getAlgorithmRunner();
    if (runner.getTopGraphs().isEmpty()) {
        throw new IllegalArgumentException("No patterns were recorded. Please adjust the number of " + "patterns to store.");
    }
    Graph resultGraph = runner.getTopGraphs().get(runner.getIndex()).getGraph();
    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 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("");
        // }
        String bayesFactorsReport = ((FgesRunner) getAlgorithmRunner()).getBayesFactorsReport(dag);
        // String bootstrapEdgeCountsReport = ((ImagesRunner) getAlgorithmRunner()).getBootstrapEdgeCountsReport(25);
        JScrollPane dagWorkbenchScroll = dagWorkbenchScroll(dag);
        // modelStatsText = new JTextArea();
        JTextArea logBayesFactorsScroll = new JTextArea();
        // bootstrapEdgeCountsScroll = new JTextArea();
        // modelStatsText.setLineWrap(true);
        // modelStatsText.setWrapStyleWord(true);
        // modelStatsText.setText(report);
        logBayesFactorsScroll.setLineWrap(true);
        logBayesFactorsScroll.setWrapStyleWord(true);
        logBayesFactorsScroll.setText(bayesFactorsReport);
        // bootstrapEdgeCountsScroll.setLineWrap(true);
        // bootstrapEdgeCountsScroll.setWrapStyleWord(true);
        // bootstrapEdgeCountsScroll.setText(bootstrapEdgeCountsReport);
        // JPanel bootstrapPanel = new JPanel();
        // bootstrapPanel.setLayout(new BorderLayout());
        // bootstrapPanel.add(bootstrapEdgeCountsScroll, BorderLayout.CENTER);
        JTextArea modelStatisticsScroll = new JTextArea();
        // bootstrapEdgeCountsScroll = new JTextArea();
        // modelStatsText.setLineWrap(true);
        // modelStatsText.setWrapStyleWord(true);
        // modelStatsText.setText(report);
        modelStatisticsScroll.setLineWrap(true);
        modelStatisticsScroll.setWrapStyleWord(true);
        modelStatisticsScroll.setText(reportIfDiscrete(dag, (DataSet) getDataModel()));
        Box b = Box.createHorizontalBox();
        b.add(new JLabel("# Bootstraps = "));
        final IntTextField numBootstraps = new IntTextField(25, 8);
        numBootstraps.setFilter(new IntTextField.Filter() {

            public int filter(int value, int oldValue) {
                if (value < 0)
                    return oldValue;
                else
                    return value;
            }
        });
        b.add(numBootstraps);
        JButton goButton = new JButton("Go!");
        goButton.addActionListener(new ActionListener() {

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

                    public void watch() {
                        int n = numBootstraps.getValue();
                    // String bootstrapEdgeCountsReport = ((ImagesRunner) getAlgorithmRunner()).getBootstrapEdgeCountsReport(n);
                    // bootstrapEdgeCountsScroll.setText(bootstrapEdgeCountsReport);
                    }
                };
            }
        });
        b.add(Box.createHorizontalGlue());
        b.add(goButton);
        // bootstrapPanel.add(b, BorderLayout.NORTH);
        removeStatsTabs();
        tabbedPane.addTab("DAG in pattern", dagWorkbenchScroll);
        // tabbedPane.addTab("DAG Model Statistics", new JScrollPane(modelStatsText));
        tabbedPane.addTab("Log Bayes Factors", new JScrollPane(logBayesFactorsScroll));
        // tabbedPane.addTab("Edge Bootstraps", new JScrollPane(bootstrapPanel));
        tabbedPane.addTab("Model Stats", new JScrollPane(modelStatisticsScroll));
    }
}

Example 20 with WatchedProcess

use of edu.cmu.tetradapp.util.WatchedProcess in project tetrad by cmu-phil.

the class FgesSearchEditor method getToolbar.

/**
 * Construct the toolbar panel.
 */
protected JPanel getToolbar() {
    JPanel toolbar = new JPanel();
    getExecuteButton().setText("Execute*");
    getExecuteButton().addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            removeStatsTabs();
            execute();
        }
    });
    JButton statsButton = new JButton("Calc Stats");
    statsButton.addActionListener(new ActionListener() {

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

                public void watch() {
                    calcStats();
                }
            };
        }
    });
    Box b1 = Box.createVerticalBox();
    b1.add(getParamsPanel());
    b1.add(Box.createVerticalStrut(10));
    Box b2 = Box.createHorizontalBox();
    b2.add(Box.createGlue());
    b2.add(getExecuteButton());
    b1.add(b2);
    b1.add(Box.createVerticalStrut(10));
    if (!(getAlgorithmRunner().getDataModel() instanceof ICovarianceMatrix)) {
        Box b3 = Box.createHorizontalBox();
        b3.add(Box.createGlue());
        b3.add(statsButton);
        b1.add(b3);
    }
    // if (getAlgorithmRunner().getParameters() instanceof Parameters) {
    // Parameters params = (Parameters) getAlgorithmRunner().getParameters();
    // JCheckBox preventCycles = new JCheckBox("Aggressively Prevent Cycles");
    // preventCycles.setHorizontalTextPosition(AbstractButton.RIGHT);
    // preventCycles.setSelected(params.isAggressivelyPreventCycles());
    // 
    // preventCycles.addActionListener(new ActionListener() {
    // public void actionPerformed(ActionEvent e) {
    // JCheckBox box = (JCheckBox) e.getSource();
    // Parameters params = (Parameters) getAlgorithmRunner().getParameters();
    // params.setAggressivelyPreventCycles(box.isSelected());
    // }
    // });
    // 
    // b1.add(Box.createVerticalStrut(5));
    // Box hBox = Box.createHorizontalBox();
    // hBox.add(Box.createHorizontalGlue());
    // hBox.add(preventCycles);
    // b1.add(hBox);
    // b1.add(Box.createVerticalStrut(5));
    // }
    Box b4 = Box.createHorizontalBox();
    JLabel label = new JLabel("<html>" + "*Please note that some" + "<br>searches may take a" + "<br>long time to complete." + "</html>");
    label.setHorizontalAlignment(SwingConstants.CENTER);
    label.setVerticalAlignment(SwingConstants.CENTER);
    label.setBorder(new TitledBorder(""));
    b4.add(label);
    b1.add(Box.createVerticalStrut(10));
    b1.add(b4);
    toolbar.add(b1);
    return toolbar;
}