weka.gui.visualize.plugins.PrefuseTree Maven / Gradle / Ivy
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A visualization component for displaying tree structures from those schemes that can output trees (e.g. decision tree learners, Cobweb clusterer etc.). This component is available from the popup menu in the Explorer's classify and cluster panels. The component uses the prefuse visualization library.
/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see prefuse.demos.TreeView demo class.
*
* @author jeffrey heer (original prefuse demo)
* @author fracpete (fracpete at waikato dot ac dot nz)
* @version $Revision: 8108 $
* @see prefuse.demos.TreeView
*/
public class PrefuseTree
implements Serializable, TreeVisualizePlugin {
/** for serialization. */
private static final long serialVersionUID = 7485599985684890717L;
/**
* Turns the GraphViz dotty
* format into Prefuse's tree XML format (according to the tree.dtd).
*
* @author fracpete (fracpete at waikato dot ac dot nz)
* @version $Revision: 8108 $
*/
public static class DottyToTree {
/**
* Replaces certain characters with their character entities.
*
* @param s the string to process
* @return the processed string
*/
protected String sanitize(String s) {
String result;
result = s;
result = result.replaceAll("&", "&")
.replaceAll("\"", """)
.replaceAll("'", "'")
.replaceAll("<", "<")
.replaceAll(">", ">");
// in addition, replace some other entities as well
result = result.replaceAll("\n", "
")
.replaceAll("\r", "
")
.replaceAll("\t", " ");
return result;
}
/**
* Writes the header of the GraphML file.
*
* @param writer the writer to use
* @throws Exception if an error occurs
*/
protected void writeHeader(BufferedWriter writer) throws Exception {
writer.write(""); writer.newLine();
writer.newLine();
writer.write(""); writer.newLine();
writer.newLine();
writer.write("");
writer.newLine();
writer.write(""); writer.newLine();
writer.write(""); writer.newLine();
writer.write(""); writer.newLine();
writer.write(" "); writer.newLine();
}
/**
* Writes the node as GraphML.
*
* @param writer the writer to use
* @param node the node to write as GraphML
* @throws Exception if an error occurs
*/
protected void writeNode(BufferedWriter writer, Node node) throws Exception {
int i;
String tag;
boolean leaf;
// leaf?
leaf = (node.getChild(0) == null);
if (leaf)
tag = "leaf";
else
tag = "branch";
// the node itself
writer.write("<" + tag + ">"); writer.newLine();
writer.write(""); writer.newLine();
writer.write(" "); writer.newLine();
}
else {
writeNode(writer, edge.getTarget());
}
}
/**
* Writes the footer of the GraphML file.
*
* @param writer the writer to use
* @throws Exception if an error occurs
*/
protected void writeFooter(BufferedWriter writer) throws Exception {
writer.write(" "); writer.newLine();
}
/**
* Parses the incoming data and writes the generated output.
*
* @param dotty the graph in dotty format
* @return the TreeML data
* @throws Exception if parsing or writing fails
*/
public String convert(String dotty) throws Exception {
Node root;
TreeBuild tree;
StringWriter output;
BufferedWriter writer;
// parse dotty format
tree = new TreeBuild();
root = tree.create(new StringReader(dotty));
// generate GraphML output
output = new StringWriter();
writer = new BufferedWriter(output);
writeHeader(writer);
writeNode(writer, root);
writeFooter(writer);
writer.flush();
return output.toString();
}
}
/**
* Displays a tree.
*
* Based on the prefuse.demos.TreeView demo class.
*
* @author fracpete (fracpete at waikato dot ac dot nz)
* @version $Revision: 8108 $
* @see prefuse.demos.TreeView
*/
public static class TreePanel
extends Display {
/** for serialization. */
private static final long serialVersionUID = 8262123080545898882L;
public class OrientAction extends AbstractAction {
private int orientation;
public OrientAction(int orientation) {
this.orientation = orientation;
}
public void actionPerformed(ActionEvent evt) {
setOrientation(orientation);
getVisualization().cancel("orient");
getVisualization().run("treeLayout");
getVisualization().run("orient");
}
}
public class AutoPanAction extends Action {
private Point2D m_start = new Point2D.Double();
private Point2D m_end = new Point2D.Double();
private Point2D m_cur = new Point2D.Double();
private int m_bias = 150;
public void run(double frac) {
TupleSet ts = m_vis.getFocusGroup(Visualization.FOCUS_ITEMS);
if ( ts.getTupleCount() == 0 )
return;
if ( frac == 0.0 ) {
int xbias=0, ybias=0;
switch ( m_orientation ) {
case Constants.ORIENT_LEFT_RIGHT:
xbias = m_bias;
break;
case Constants.ORIENT_RIGHT_LEFT:
xbias = -m_bias;
break;
case Constants.ORIENT_TOP_BOTTOM:
ybias = m_bias;
break;
case Constants.ORIENT_BOTTOM_TOP:
ybias = -m_bias;
break;
}
VisualItem vi = (VisualItem)ts.tuples().next();
m_cur.setLocation(getWidth()/2, getHeight()/2);
getAbsoluteCoordinate(m_cur, m_start);
m_end.setLocation(vi.getX()+xbias, vi.getY()+ybias);
} else {
m_cur.setLocation(m_start.getX() + frac*(m_end.getX()-m_start.getX()),
m_start.getY() + frac*(m_end.getY()-m_start.getY()));
panToAbs(m_cur);
}
}
}
public static class NodeColorAction extends ColorAction {
public NodeColorAction(String group) {
super(group, VisualItem.FILLCOLOR);
}
public int getColor(VisualItem item) {
if ( m_vis.isInGroup(item, Visualization.SEARCH_ITEMS) )
return ColorLib.rgb(255,190,190);
else if ( m_vis.isInGroup(item, Visualization.FOCUS_ITEMS) )
return ColorLib.rgb(198,229,229);
else if ( item.getDOI() > -1 )
return ColorLib.rgb(164,193,193);
else
return ColorLib.rgba(255,255,255,0);
}
} // end of inner class TreeMapColorAction
private static final String tree = "tree";
private static final String treeNodes = "tree.nodes";
private static final String treeEdges = "tree.edges";
private LabelRenderer m_nodeRenderer;
private EdgeRenderer m_edgeRenderer;
private String m_label = "name";
private int m_orientation = Constants.ORIENT_LEFT_RIGHT;
/**
* Initializes the panel.
*
* @param t the tree to visualize
*/
public TreePanel(Tree t) {
super(new Visualization());
m_vis.add(tree, t);
m_nodeRenderer = new LabelRenderer(m_label);
m_nodeRenderer.setRenderType(AbstractShapeRenderer.RENDER_TYPE_FILL);
m_nodeRenderer.setHorizontalAlignment(Constants.LEFT);
m_nodeRenderer.setRoundedCorner(8,8);
m_edgeRenderer = new EdgeRenderer(Constants.EDGE_TYPE_CURVE);
DefaultRendererFactory rf = new DefaultRendererFactory(m_nodeRenderer);
rf.add(new InGroupPredicate(treeEdges), m_edgeRenderer);
m_vis.setRendererFactory(rf);
// colors
ItemAction nodeColor = new NodeColorAction(treeNodes);
ItemAction textColor = new ColorAction(treeNodes,
VisualItem.TEXTCOLOR, ColorLib.rgb(0,0,0));
m_vis.putAction("textColor", textColor);
ItemAction edgeColor = new ColorAction(treeEdges,
VisualItem.STROKECOLOR, ColorLib.rgb(200,200,200));
// quick repaint
ActionList repaint = new ActionList();
repaint.add(nodeColor);
repaint.add(new RepaintAction());
m_vis.putAction("repaint", repaint);
// full paint
ActionList fullPaint = new ActionList();
fullPaint.add(nodeColor);
m_vis.putAction("fullPaint", fullPaint);
// animate paint change
ActionList animatePaint = new ActionList(400);
animatePaint.add(new ColorAnimator(treeNodes));
animatePaint.add(new RepaintAction());
m_vis.putAction("animatePaint", animatePaint);
// create the tree layout action
NodeLinkTreeLayout treeLayout = new NodeLinkTreeLayout(tree,
m_orientation, 50, 0, 8);
treeLayout.setLayoutAnchor(new Point2D.Double(25,300));
m_vis.putAction("treeLayout", treeLayout);
CollapsedSubtreeLayout subLayout =
new CollapsedSubtreeLayout(tree, m_orientation);
m_vis.putAction("subLayout", subLayout);
AutoPanAction autoPan = new AutoPanAction();
// create the filtering and layout
ActionList filter = new ActionList();
filter.add(new FisheyeTreeFilter(tree, 2));
filter.add(new FontAction(treeNodes, FontLib.getFont("Tahoma", 16)));
filter.add(treeLayout);
filter.add(subLayout);
filter.add(textColor);
filter.add(nodeColor);
filter.add(edgeColor);
m_vis.putAction("filter", filter);
// animated transition
ActionList animate = new ActionList(1000);
animate.setPacingFunction(new SlowInSlowOutPacer());
animate.add(autoPan);
animate.add(new QualityControlAnimator());
animate.add(new VisibilityAnimator(tree));
animate.add(new LocationAnimator(treeNodes));
animate.add(new ColorAnimator(treeNodes));
animate.add(new RepaintAction());
m_vis.putAction("animate", animate);
m_vis.alwaysRunAfter("filter", "animate");
// create animator for orientation changes
ActionList orient = new ActionList(2000);
orient.setPacingFunction(new SlowInSlowOutPacer());
orient.add(autoPan);
orient.add(new QualityControlAnimator());
orient.add(new LocationAnimator(treeNodes));
orient.add(new RepaintAction());
m_vis.putAction("orient", orient);
// ------------------------------------------------
// initialize the display
setSize(700,600);
setItemSorter(new TreeDepthItemSorter());
addControlListener(new ZoomToFitControl());
addControlListener(new ZoomControl());
addControlListener(new WheelZoomControl());
addControlListener(new PanControl());
addControlListener(new FocusControl(1, "filter"));
registerKeyboardAction(
new OrientAction(Constants.ORIENT_LEFT_RIGHT),
"left-to-right", KeyStroke.getKeyStroke("ctrl 1"), WHEN_FOCUSED);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_TOP_BOTTOM),
"top-to-bottom", KeyStroke.getKeyStroke("ctrl 2"), WHEN_FOCUSED);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_RIGHT_LEFT),
"right-to-left", KeyStroke.getKeyStroke("ctrl 3"), WHEN_FOCUSED);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_BOTTOM_TOP),
"bottom-to-top", KeyStroke.getKeyStroke("ctrl 4"), WHEN_FOCUSED);
// ------------------------------------------------
// filter graph and perform layout
setOrientation(m_orientation);
m_vis.run("filter");
TupleSet search = new PrefixSearchTupleSet();
m_vis.addFocusGroup(Visualization.SEARCH_ITEMS, search);
search.addTupleSetListener(new TupleSetListener() {
public void tupleSetChanged(TupleSet t, Tuple[] add, Tuple[] rem) {
m_vis.cancel("animatePaint");
m_vis.run("fullPaint");
m_vis.run("animatePaint");
}
});
}
public void setOrientation(int orientation) {
NodeLinkTreeLayout rtl
= (NodeLinkTreeLayout)m_vis.getAction("treeLayout");
CollapsedSubtreeLayout stl
= (CollapsedSubtreeLayout)m_vis.getAction("subLayout");
switch ( orientation ) {
case Constants.ORIENT_LEFT_RIGHT:
m_nodeRenderer.setHorizontalAlignment(Constants.LEFT);
m_edgeRenderer.setHorizontalAlignment1(Constants.RIGHT);
m_edgeRenderer.setHorizontalAlignment2(Constants.LEFT);
m_edgeRenderer.setVerticalAlignment1(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment2(Constants.CENTER);
break;
case Constants.ORIENT_RIGHT_LEFT:
m_nodeRenderer.setHorizontalAlignment(Constants.RIGHT);
m_edgeRenderer.setHorizontalAlignment1(Constants.LEFT);
m_edgeRenderer.setHorizontalAlignment2(Constants.RIGHT);
m_edgeRenderer.setVerticalAlignment1(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment2(Constants.CENTER);
break;
case Constants.ORIENT_TOP_BOTTOM:
m_nodeRenderer.setHorizontalAlignment(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment1(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment2(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment1(Constants.BOTTOM);
m_edgeRenderer.setVerticalAlignment2(Constants.TOP);
break;
case Constants.ORIENT_BOTTOM_TOP:
m_nodeRenderer.setHorizontalAlignment(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment1(Constants.CENTER);
m_edgeRenderer.setHorizontalAlignment2(Constants.CENTER);
m_edgeRenderer.setVerticalAlignment1(Constants.TOP);
m_edgeRenderer.setVerticalAlignment2(Constants.BOTTOM);
break;
default:
throw new IllegalArgumentException(
"Unrecognized orientation value: "+orientation);
}
m_orientation = orientation;
rtl.setOrientation(orientation);
stl.setOrientation(orientation);
}
public int getOrientation() {
return m_orientation;
}
}
/** the constant for "tree". */
public final static String TREE = "tree";
/** the constant for "tree.nodes". */
public final static String TREE_NODES = "tree.nodes";
/** the constant for "tree.edges". */
public final static String TREE_EDGES = "tree.edges";
/** the constant for "label". */
public final static String LABEL = "label";
/**
* Get the minimum version of Weka, inclusive, the class
* is designed to work with. eg: 3.5.0
*
* @return the minimum version
*/
public String getMinVersion() {
return "3.5.9";
}
/**
* Get the maximum version of Weka, exclusive, the class
* is designed to work with. eg: 3.6.0
*
* @return the maximum version
*/
public String getMaxVersion() {
return "3.7.1";
}
/**
* Get the specific version of Weka the class is designed for.
* eg: 3.5.1
*
* @return the version the plugin was designed for
*/
public String getDesignVersion() {
return "3.5.9";
}
/**
* Get a JMenu or JMenuItem which contain action listeners
* that perform the visualization of the tree in GraphViz's dotty format.
* Exceptions thrown because of changes in Weka since compilation need to
* be caught by the implementer.
*
* @see NoClassDefFoundError
* @see IncompatibleClassChangeError
*
* @param dotty the tree in dotty format
* @param name the name of the item (in the Explorer's history list)
* @return menuitem for opening visualization(s), or null
* to indicate no visualization is applicable for the input
*/
public JMenuItem getVisualizeMenuItem(String dotty, String name) {
JMenuItem result;
final String dottyF = dotty;
final String nameF = name;
result = new JMenuItem("Prefuse tree");
result.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
display(dottyF, nameF);
}
});
return result;
}
/**
* Displays the error.
*
* @param msg the error to display
*/
protected void displayError(String msg) {
JOptionPane.showMessageDialog(null, msg, "Error displaying graph", JOptionPane.ERROR_MESSAGE);
}
/**
* Converts the dotty format to GraphML.
*
* @param dotty the graph in dotty format
* @return the graph in tree XML or null in case of an error
*/
protected String convert(String dotty) {
String result;
DottyToTree d2gml;
d2gml = new DottyToTree();
try {
result = d2gml.convert(dotty);
}
catch (Exception e) {
result = null;
e.printStackTrace();
displayError(e.toString());
}
return result;
}
/**
* Parses the graph in GraphML and returns the built graph.
*
* @param graphml the graph in GraphML
* @return the graph or null in case of an error
*/
protected Tree parse(String graphml) {
ByteArrayInputStream inStream;
Tree result;
try {
inStream = new ByteArrayInputStream(graphml.getBytes());
result = (Tree) new TreeMLReader().readGraph(inStream);
}
catch ( Exception e ) {
result = null;
e.printStackTrace();
displayError(e.toString());
}
return result;
}
/**
* Displays the graph.
*
* @param dotty the graph in dotty format
* @param name the name of the graph
*/
protected void display(String dotty, String name) {
String treeml;
Tree tree;
TreePanel panel;
JFrame frame;
// convert dotty graph
treeml = convert(dotty);
if (treeml == null)
return;
// parse graph
tree = parse(treeml);
if (tree == null)
return;
// display graph
panel = new TreePanel(tree);
frame = new JFrame("Prefuse tree [" + name + "]");
frame.setSize(800, 600);
frame.setContentPane(panel);
frame.setVisible(true);
}
/**
* Gets a container for displaying the graph.
*
* @param dotty the graph in dotty format
* @return a java.awt.Container that can be shown in a JFrame
* for example.
*/
public javax.swing.JComponent getDisplay(String dotty)
throws Exception {
String treeml;
Tree tree;
TreePanel panel;
// convert dotty graph
treeml = convert(dotty);
if (treeml == null) {
throw new Exception("Problem parsing dotty.");
}
// parse graph
tree = parse(treeml);
if (tree == null) {
throw new Exception("Problem constructing visualization");
}
// display graph
panel = new TreePanel(tree);
return panel;
}
}
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