private void addCovMatrixTestMenuItems(JMenu test) {
IndTestType testType = getTestType();
if (testType != IndTestType.FISHER_Z
// && testType != IndTestType.CORRELATION_T
) {
setTestType(IndTestType.FISHER_Z);
}
ButtonGroup group = new ButtonGroup();
JCheckBoxMenuItem fishersZ = new JCheckBoxMenuItem("Fisher's Z");
group.add(fishersZ);
test.add(fishersZ);
// JCheckBoxMenuItem tTest = new JCheckBoxMenuItem("Cramer's T");
// group.add(tTest);
// test.add(tTest);
testType = getTestType();
if (testType == IndTestType.FISHER_Z) {
fishersZ.setSelected(true);
}
// else if (testType == IndTestType.CORRELATION_T) {
// tTest.setSelected(true);
// }
fishersZ.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
setTestType(IndTestType.FISHER_Z);
JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "Using Fisher's Z.");
}
});
// tTest.addActionListener(new ActionListener() {
// public void actionPerformed(ActionEvent e) {
// setTestType(IndTestType.CORRELATION_T);
// JOptionPane.showMessageDialog(JOptionUtils.centeringComp(),
// "Using Cramer's T.");
// }
// });
}
private JMenu createGraphMenu() {
JMenu graph = new JMenu("Graph");
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.addSeparator();
JMenuItem correlateExogenous = new JMenuItem("Correlate Exogenous Variables");
JMenuItem uncorrelateExogenous = new JMenuItem("Uncorrelate Exogenous Variables");
graph.add(correlateExogenous);
graph.add(uncorrelateExogenous);
graph.addSeparator();
correlateExogenous.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
correlateExogenousVariables();
getWorkbench().invalidate();
getWorkbench().repaint();
}
});
uncorrelateExogenous.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
uncorrelationExogenousVariables();
getWorkbench().invalidate();
getWorkbench().repaint();
}
});
JMenuItem randomGraph = new JMenuItem("Random Graph");
graph.add(randomGraph);
randomGraph.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
RandomGraphEditor editor = new RandomGraphEditor(workbench.getGraph(), true);
int ret =
JOptionPane.showConfirmDialog(
TimeLagGraphEditor.this,
editor,
"Edit Random DAG Parameters",
JOptionPane.PLAIN_MESSAGE);
if (ret == JOptionPane.OK_OPTION) {
Graph graph = null;
Graph dag = new Dag();
int numTrials = 0;
while (graph == null && ++numTrials < 100) {
if (editor.isRandomForward()) {
dag =
GraphUtils.randomGraphRandomForwardEdges(
getGraph().getNodes(), editor.getNumLatents(), editor.getMaxEdges());
GraphUtils.arrangeBySourceGraph(dag, getWorkbench().getGraph());
HashMap<String, PointXy> layout =
GraphUtils.grabLayout(workbench.getGraph().getNodes());
GraphUtils.arrangeByLayout(dag, layout);
} else if (editor.isUniformlySelected()) {
if (getGraph().getNumNodes() == editor.getNumNodes()) {
HashMap<String, PointXy> layout =
GraphUtils.grabLayout(workbench.getGraph().getNodes());
dag =
GraphUtils.randomGraph(
getGraph().getNodes(),
editor.getNumLatents(),
editor.getMaxEdges(),
editor.getMaxDegree(),
editor.getMaxIndegree(),
editor.getMaxOutdegree(),
editor.isConnected());
GraphUtils.arrangeBySourceGraph(dag, getWorkbench().getGraph());
GraphUtils.arrangeByLayout(dag, layout);
} else {
dag =
GraphUtils.randomGraph(
editor.getNumNodes(),
editor.getNumLatents(),
editor.getMaxEdges(),
editor.getMaxDegree(),
editor.getMaxIndegree(),
editor.getMaxOutdegree(),
editor.isConnected());
}
} else {
do {
if (getGraph().getNumNodes() == editor.getNumNodes()) {
HashMap<String, PointXy> layout =
GraphUtils.grabLayout(workbench.getGraph().getNodes());
dag =
GraphUtils.randomDag(
getGraph().getNodes(),
editor.getNumLatents(),
editor.getMaxEdges(),
30,
15,
15,
editor.isConnected());
GraphUtils.arrangeByLayout(dag, layout);
} else {
dag =
GraphUtils.randomGraph(
editor.getNumNodes(),
editor.getNumLatents(),
editor.getMaxEdges(),
30,
15,
15,
editor.isConnected());
}
} while (dag.getNumEdges() < editor.getMaxEdges());
}
boolean addCycles = editor.isAddCycles();
if (addCycles) {
int minNumCycles = editor.getMinNumCycles();
int minCycleLength = editor.getMinCycleLength();
// graph = DataGraphUtils.addCycles2(dag, minNumCycles,
// minCycleLength);
graph = GraphUtils.cyclicGraph4(editor.getNumNodes(), editor.getMaxEdges());
GraphUtils.addTwoCycles(graph, editor.getMinNumCycles());
} else {
graph = new EdgeListGraph(dag);
}
}
if (graph == null) {
JOptionPane.showMessageDialog(
TimeLagGraphEditor.this, "Could not find a graph that fits those constrains.");
getWorkbench().setGraph(new EdgeListGraph(dag));
} else {
getWorkbench().setGraph(graph);
}
// getWorkbench().setGraph(new EdgeListGraph(dag));
// getWorkbench().setGraph(graph);
}
}
});
JMenuItem randomIndicatorModel = new JMenuItem("Random Multiple Indicator Model");
graph.add(randomIndicatorModel);
randomIndicatorModel.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
RandomMimParamsEditor editor = new RandomMimParamsEditor();
int ret =
JOptionPane.showConfirmDialog(
JOptionUtils.centeringComp(),
editor,
"Edit Random MIM Parameters",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.PLAIN_MESSAGE);
if (ret == JOptionPane.OK_OPTION) {
int numStructuralNodes = Preferences.userRoot().getInt("numStructuralNodes", 3);
int maxStructuralEdges = Preferences.userRoot().getInt("numStructuralEdges", 3);
int measurementModelDegree =
Preferences.userRoot().getInt("measurementModelDegree", 3);
int numLatentMeasuredImpureParents =
Preferences.userRoot().getInt("latentMeasuredImpureParents", 0);
int numMeasuredMeasuredImpureParents =
Preferences.userRoot().getInt("measuredMeasuredImpureParents", 0);
int numMeasuredMeasuredImpureAssociations =
Preferences.userRoot().getInt("measuredMeasuredImpureAssociations", 0);
Graph graph =
DataGraphUtils.randomSingleFactorModel(
numStructuralNodes,
maxStructuralEdges,
measurementModelDegree,
numLatentMeasuredImpureParents,
numMeasuredMeasuredImpureParents,
numMeasuredMeasuredImpureAssociations);
getWorkbench().setGraph(graph);
}
}
});
graph.addSeparator();
graph.add(new JMenuItem(new SelectBidirectedAction(getWorkbench())));
graph.add(new JMenuItem(new SelectUndirectedAction(getWorkbench())));
// graph.addSeparator();
// IndependenceFactsAction action = new IndependenceFactsAction(
// JOptionUtils.centeringComp(), this, "D Separation Facts...");
// graph.add(action);
return graph;
}
/**
* Creates the "file" menu, which allows the user to load, save, and post workbench models.
*
* @return this menu.
*/
private JMenu createEditMenu() {
JMenu edit = new JMenu("Edit");
// JMenuItem copy = new JMenuItem(new CopySubgraphAction(this));
// JMenuItem paste = new JMenuItem(new PasteSubgraphAction(this));
//
// copy.setAccelerator(
// KeyStroke.getKeyStroke(KeyEvent.VK_C, ActionEvent.CTRL_MASK));
// paste.setAccelerator(
// KeyStroke.getKeyStroke(KeyEvent.VK_V, ActionEvent.CTRL_MASK));
//
// edit.add(copy);
// edit.add(paste);
edit.addSeparator();
JMenuItem configuration = new JMenuItem("Configuration...");
edit.add(configuration);
configuration.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
final TimeLagGraph graph = (TimeLagGraph) getLayoutEditable().getGraph();
class ConfigurationEditor extends JPanel {
private int maxLag;
private int numInitialLags;
public ConfigurationEditor(final TimeLagGraph graph) {
maxLag = graph.getMaxLag();
numInitialLags = graph.getNumInitialLags();
final SpinnerModel maxLagSpinnerModel =
new SpinnerNumberModel(graph.getMaxLag(), 0, 300, 1);
JSpinner maxLagSpinner = new JSpinner(maxLagSpinnerModel);
maxLagSpinner.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
JSpinner spinner = (JSpinner) e.getSource();
SpinnerNumberModel model = (SpinnerNumberModel) spinner.getModel();
int value = (Integer) model.getValue();
setMaxLag(value);
}
});
final SpinnerModel initialLagsSpinnerModel =
new SpinnerNumberModel(graph.getNumInitialLags(), 1, 300, 1);
JSpinner initialLagsSpinner = new JSpinner(initialLagsSpinnerModel);
initialLagsSpinner.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
JSpinner spinner = (JSpinner) e.getSource();
SpinnerNumberModel model = (SpinnerNumberModel) spinner.getModel();
int value = (Integer) model.getValue();
setNumInitialLags(value);
}
});
setLayout(new BorderLayout());
Box box = Box.createVerticalBox();
Box b1 = Box.createHorizontalBox();
b1.add(new JLabel("Time lag graph configuration:"));
b1.add(Box.createHorizontalGlue());
box.add(b1);
Box b2 = Box.createHorizontalBox();
b2.add(new JLabel("Maximum Lag = "));
b2.add(Box.createHorizontalGlue());
b2.add(maxLagSpinner);
box.add(b2);
Box b3 = Box.createHorizontalBox();
b3.add(new JLabel("# Initial Lags = "));
b3.add(Box.createHorizontalGlue());
b3.add(initialLagsSpinner);
box.add(b3);
box.setBorder(new EmptyBorder(10, 10, 10, 10));
add(box, BorderLayout.CENTER);
}
public int getMaxLag() {
return maxLag;
}
public void setMaxLag(int maxLag) {
this.maxLag = maxLag;
}
public int getNumInitialLags() {
return numInitialLags;
}
public void setNumInitialLags(int numInitialLags) {
this.numInitialLags = numInitialLags;
}
}
final ConfigurationEditor editor = new ConfigurationEditor((TimeLagGraph) getGraph());
EditorWindow editorWindow =
new EditorWindow(editor, "Configuration...", "Save", true, TimeLagGraphEditor.this);
DesktopController.getInstance()
.addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
editorWindow.pack();
editorWindow.setVisible(true);
editorWindow.addInternalFrameListener(
new InternalFrameAdapter() {
public void internalFrameClosed(InternalFrameEvent e) {
EditorWindow window = (EditorWindow) e.getSource();
if (window.isCanceled()) {
return;
}
graph.setMaxLag(editor.getMaxLag());
graph.setNumInitialLags(editor.getNumInitialLags());
LayoutUtils.lastLayout(getLayoutEditable());
}
});
}
});
return edit;
}
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 Pattern");
JMenuItem meekOrient = new JMenuItem("Meek Orientation");
JMenuItem dagInPattern = new JMenuItem("Choose DAG in Pattern");
JMenuItem gesOrient = new JMenuItem("Global Score-based Reorientation");
JMenuItem nextGraph = new JMenuItem("Next Graph");
JMenuItem previousGraph = new JMenuItem("Previous Graph");
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(), 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.getResultGraph();
if (graph == null) {
JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "No result gaph.");
return;
}
if (runner instanceof GesRunner) {
GraphScorer scorer = ((GesRunner) runner).getGraphScorer();
Graph _graph = ((GesRunner) 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(getAlgorithmRunner().getParams().getKnowledge());
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 Pattern(graph));
Graph dag = search.patternToDagMeekRules();
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);
}
});
menuBar.add(new LayoutMenu(this));
}