dnamaca.java

Petri网分析工具PIPE is open-source

package pipe.modules.dnamaca;

import java.awt.Container;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Iterator;

import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JDialog;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.ProgressMonitor;
import javax.swing.SwingUtilities;
import javax.swing.Timer;
import javax.swing.border.EtchedBorder;
import javax.swing.border.TitledBorder;

import pipe.dataLayer.Arc;
import pipe.dataLayer.DataLayer;
import pipe.dataLayer.Place;
import pipe.dataLayer.Transition;
import pipe.gui.CreateGui;
import pipe.gui.widgets.ButtonBar;
import pipe.gui.widgets.GraphPanelPane;
import pipe.gui.widgets.ResultsHTMLPane;
import pipe.modules.Module;

public class Dnamaca implements Module {
	  private static final String MODULE_NAME = "DNAmaca";
	  private Place places[];
	  private Transition transitions[];
	  private DataLayer pnmldata;
	  private String modString = "";
	  private final static String urtaStrings[] = {"Parsing input file", "Generating state-space",
	  		"Peforming functional analysis", "Computing steady-state probabilities",
			"Identifying target states", "Compiling response-time analyser", "Initialising Uniformiser",
			"Running uniformise", "calculating answers for each t_point", "powered down"};
	  private File modFile;
	  private JDialog guiDialog;
	  private JButton resultsButton;
	  private ArrayList resultsX = new ArrayList();
	  private ArrayList resultsY = new ArrayList();
	  private ResultsHTMLPane resultText;
	  private GraphPanelPane resultsGraph;
	  private String urtaExecutablePath; 
	  
	  private JTextField jtfTargetCondition;
	  private JTextField jtfSourceCondition;
	  private JTextField jtfTStart;
	  private JTextField jtfTStop;
	  private JTextField jtfTStep;
    
    private JCheckBox jcbCumulative;
   
	/* (non-Javadoc)
	 * @see pipe.modules.Module#getName()
	 */
	public String getName() {
		return MODULE_NAME;
	}

	/* (non-Javadoc)
	 * @see pipe.modules.Module#run(pipe.dataLayer.DataLayer)
	 */
	public void run(DataLayer _pnmldata) {
		pnmldata = _pnmldata;
		places = pnmldata.getPlaces();
		transitions = pnmldata.getTransitions();
		
		// Build interface
		guiDialog = new JDialog(CreateGui.getApp(),MODULE_NAME,true);
		
		Container contentPane=guiDialog.getContentPane();
		contentPane.setLayout(new BoxLayout(contentPane,BoxLayout.PAGE_AXIS));

		resultText = new ResultsHTMLPane();
		contentPane.add(resultText);
		resultsGraph = new GraphPanelPane();
		guiDialog.getContentPane().add(resultsGraph,0);
		resultsGraph.setVisible(false);
		
    JPanel optionsPanel=new JPanel();
    optionsPanel.setLayout(new BoxLayout(optionsPanel,BoxLayout.PAGE_AXIS));
    optionsPanel.setBorder(new TitledBorder(new EtchedBorder(),"Conditions"));
    JPanel topPanel=new JPanel();
    topPanel.setLayout(new BoxLayout(topPanel,BoxLayout.LINE_AXIS));
		topPanel.add(new JLabel("Source condition:"));
		topPanel.add(Box.createHorizontalStrut(5));
		topPanel.add(jtfSourceCondition=new JTextField(5));
		topPanel.add(Box.createHorizontalStrut(10));
		topPanel.add(new JLabel("Target condition:"));
		topPanel.add(Box.createHorizontalStrut(5));
		topPanel.add(jtfTargetCondition=new JTextField(5));
    JPanel bottomPanel=new JPanel();
    bottomPanel.setLayout(new BoxLayout(bottomPanel,BoxLayout.LINE_AXIS));
		bottomPanel.add(new JLabel("T Start:"));
		bottomPanel.add(Box.createHorizontalStrut(5));
		bottomPanel.add(jtfTStart=new JTextField(5));
    bottomPanel.add(Box.createHorizontalStrut(10));
		bottomPanel.add(new JLabel("T Stop:"));
		bottomPanel.add(Box.createHorizontalStrut(5));
		bottomPanel.add(jtfTStop=new JTextField(5));
    bottomPanel.add(Box.createHorizontalStrut(10));
		bottomPanel.add(new JLabel("T Step:"));
    bottomPanel.add(Box.createHorizontalStrut(5));
    bottomPanel.add(jtfTStep=new JTextField(5));
    bottomPanel.add(Box.createHorizontalStrut(5));
    bottomPanel.add(jcbCumulative=new JCheckBox("Cumulative",false));
    
    optionsPanel.add(topPanel);
    optionsPanel.add(Box.createVerticalStrut(5));
    optionsPanel.add(bottomPanel);

    
    
    // TODO: remove these since they're not generally applicable
		jtfSourceCondition.setText("P4 == 1");
		jtfTargetCondition.setText("P4 == 3");
		jtfTStart.setText("0.1");
		jtfTStop.setText("30");
		jtfTStep.setText("0.1");
		
		
		optionsPanel.setMaximumSize(new Dimension(Integer.MAX_VALUE,optionsPanel.getPreferredSize().height));
		contentPane.add(optionsPanel);
		
		String buttonLabels[] = {"Run DNAmaca", "Toggle graph"};
		ActionListener buttonHandlers[] = {runDnamacaAction, runResultsAction};
		ButtonBar buttons;
		contentPane.add(buttons = new ButtonBar(buttonLabels, buttonHandlers));
		resultsButton = ((JButton)buttons.getComponent(1));
		resultsButton.setEnabled(false);
		
		guiDialog.pack();
		guiDialog.setLocationRelativeTo(null);    
	  guiDialog.setVisible(true);
	}
	
	ActionListener runDnamacaAction=new ActionListener() {
		public void actionPerformed(ActionEvent arg0) {
			if (!getUrtaPath()) {
				resultText.setText("The command 'urta' was not found on your system path.");	
			} else if (pnmldata.getPlaces().length==0) {
				resultText.setText("You cannot run DNAmaca on a net without places.");
			} else if (!hasTimed()) {
				resultText.setText("You cannot run DNAmaca on a net without a timed transition.");				
			} else {
				try {
					modFile = File.createTempFile("dnamaca", ".mod");
					FileWriter out = new FileWriter(modFile);
					generateMod();
					out.write(modString);
					out.close();
					DnamacaRun dnamaca = new DnamacaRun();
				} catch (IOException e3) {
					System.out.println("Could not write to temporary file!");
					e3.printStackTrace();
				}
			}
		}
	};

	ActionListener runResultsAction=new ActionListener() {
		public void actionPerformed(ActionEvent arg0) {
			if (!resultText.isVisible()) {
				resultsGraph.setVisible(false);
				resultText.setVisible(true);
//				resultsButton.setText("View Graph");
			} else {
				resultText.setVisible(false);
				resultsGraph.setVisible(true);
//				resultsButton.setText("View Results");
			}
			guiDialog.validate();
		}
	};
	
	public void displayResults() {
		ArrayList resultList = new ArrayList();
		resultList.add("x"); resultList.add("y");

		for(int i=0; i<resultsX.size(); i++) {
			resultList.add(resultsX.get(i));
			resultList.add(resultsY.get(i));			
		}
		resultText.setText("Passage Time Analysis<br>" + ResultsHTMLPane.makeTable(resultList.toArray(), 2, false,true, true, false));
	}
	private void generateMod() {
		modString = "";
		model();
//		performance();
		passageTime();
	}
	
	private void model() {
		modString += "\\model{\n";
		stateVector();
		initial();
		transitions();
		modString += "}\n\n";		
	}
	
	private void stateVector() {
		modString += "\t\\statevector{\n";
		modString += "\t\t\\type{short}{";
		
		modString += places[0].getId();
		for(int i=1; i<places.length; i++) {
			modString += ", "+places[i].getId();
		}
		
		modString += "}\n";
		modString += "\t}\n\n";
	}
	
	private void initial() {
		modString += "\t\\initial{\n";
		
		modString += "\t\t";
		for(int i=0; i<places.length; i++) {
			modString += places[i].getId()+" = " + places[i].getCurrentMarking()+"; ";
		}
		
		modString += "\n\t}\n";		
	}
	
	private void transitions() {
		for(int i=0; i<transitions.length; i++) {
			modString += "\t\\transition{"+transitions[i].getId()+"}{\n";
		  	modString += "\t\t\\condition{" + getTransitionConditions(i) + "}\n";
		  	modString += "\t\t\\action{\n";
		  	Iterator arcsTo = transitions[i]. getConnectToIterator();
		  	while (arcsTo.hasNext()) {
		  		String currentId = ((Arc)arcsTo.next()).getSource().getId();
		  		modString += "\t\t\tnext->"+currentId;
		  		modString += " = "+currentId+" - 1;\n";
		  	}
		  	Iterator arcsFrom = transitions[i]. getConnectFromIterator();
		  	while (arcsFrom.hasNext()) {
		  		String currentId = ((Arc)arcsFrom.next()).getTarget().getId();
		  		modString += "\t\t\tnext->"+currentId;
		  		modString += " = "+currentId+" + 1;\n";
		  	}
		  	
		  	modString += "\t\t}\n";
		  	
		  	if (transitions[i].getTimed()) {
		  		modString += "\t\t\\rate{" + transitions[i].getRate() + "}\n";
		  	} else {
		  		modString += "\t\t\\weight{" + transitions[i].getRate() + "}\n";
		  	}
		  	modString += "\t}\n";
		}
	}
	
	private void performance() {
		modString += "\\performance{\n";
		tokenDistribution();
		transitionMeasures();
		modString += "}\n";		
		
	}
	
	private void tokenDistribution() {
		for(int i=0; i<places.length; i++) {
			modString += "\t\\statemeasure{Mean tokens on place " + places[i].getId() + "}{\n";
			modString += "\t\t\\estimator{mean variance distribution}\n";
			modString += "\t\t\\expression{" + places[i].getId() + "}\n";
			modString += "\t}\n";
		}
	}
	
	private void transitionMeasures() {
		for(int i=0; i<transitions.length; i++) {
			modString += "\t\\statemeasure{Enabled probability for transition " + transitions[i].getId() + "}{\n";
			modString += "\t\t\\estimator{mean}\n";
			modString += "\t\t\\expression{(" + getTransitionConditions(i) + ") ? 1 : 0}\n";
			modString += "\t}\n";
			
			modString += "\t\\countmeasure{Throughput for transition " + transitions[i].getId() + "}{\n";
			modString += "\t\t\\estimator{mean}\n";
			modString += "\t\t\\precondition{1}\n";
			modString += "\t\t\\postcondition{1}\n";
			modString += "\t\t\\transition{" + transitions[i].getId() + "}\n";
			modString += "\t}\n";
		}
	}
	
	private void passageTime() {
		modString += "\\passage{\n";
		modString += "\t\\targetcondition{" + jtfTargetCondition.getText() + "}\n";
		modString += "\t\\sourcecondition{" + jtfSourceCondition.getText() + "}\n";		
		modString += "\t\\t_start{" + jtfTStart.getText() + "}\n";
		modString += "\t\\t_stop{" + jtfTStop.getText() + "}\n";
		modString += "\t\\t_step{" + jtfTStep.getText() + "}\n";
		modString += "}\n";
	}
	
	private String getTransitionConditions(int transitionNum) {
		String condition = new String();
	  	Iterator arcsTo = transitions[transitionNum]. getConnectToIterator();
	  	if (arcsTo.hasNext())
	  		condition += ((Arc)arcsTo.next()).getSource().getId()+" > 0";
	  	while (arcsTo.hasNext())
	  		condition += " && "+((Arc)arcsTo.next()).getSource().getId()+" > 0";
	  	return condition;
	}
	
	private boolean hasTimed() {
		for(int i=0; i<transitions.length; i++) {
			if (transitions[i].getTimed()) return true;
		}
		return false;
	}
	
	private boolean getUrtaPath() {
		Runtime r = Runtime.getRuntime();
		try {
			Process p = r.exec("urta");
			p.waitFor();
		} catch (Exception e) {
			return false;
		}
		try {
			Process p = r.exec("which urta");
			p.waitFor();
			InputStreamReader stdout = new InputStreamReader(p.getInputStream());
			int ch=0;
			String currentLine="";
			while (((ch = stdout.read()) != -1) && (ch != 10)) {
				currentLine += (char)ch;
			}

			urtaExecutablePath = currentLine.substring(0, currentLine.indexOf("urta"));
		} catch (Exception e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
		return true;
	}
	
	class DnamacaRun {
	    private ProgressMonitor progressMonitor;
	    private Timer timer;
	    private ExternalTask task;
		
		public DnamacaRun() {
	        //Create a timer.
	        timer = new Timer(100, new TimerListener());
            progressMonitor = new ProgressMonitor(guiDialog,
                    "Running DNAmaca",
                    "", 0, urtaStrings.length);
            progressMonitor.setProgress(0);
            progressMonitor.setMillisToDecideToPopup(0);
            progressMonitor.setMillisToPopup(0);
            
            task = new ExternalTask();
            task.go();
            timer.start();
		}

	    class TimerListener implements ActionListener {
	        public void actionPerformed(ActionEvent evt) {
	        	if (progressMonitor.isCanceled() || task.done()) {
	        		progressMonitor.close();
	        		task.stop();
	        		timer.stop();
	        		resultsButton.setEnabled(true);
	        		SwingUtilities.invokeLater(new Runnable() {
	        			public void run() {
	        				displayResults();
	        				resultsGraph.getGraph().setValues(resultsX, resultsY);
	        			}
	        		});
	        	} else {
	        		progressMonitor.setNote(task.getMessage());
	        		progressMonitor.setProgress(task.getCurrent());
	        	}
	        }
	    }
	
	class ExternalTask {
			private int lengthOfTask;
			private int current = 0;
			private String statMessage;
			
			ExternalTask() {
				lengthOfTask = urtaStrings.length-1;
			}

			void go() {
				current = 0;
				final SwingWorker worker = new SwingWorker() {
					public Object construct() {
						return new ActualTask();
                        }
				};
				worker.start();
			}

			int getCurrent() {
				return current;
			}

			void stop() {
				current = lengthOfTask;
			}

			boolean done() {
				if (current >= lengthOfTask)
					return true;
				else
					return false;
			}
			
			String getMessage() {
				return statMessage;
			}
			
			class ActualTask {
				ActualTask () {
					Runtime r = Runtime.getRuntime();
					try {
						Process p = r.exec(urtaExecutablePath + "urta "+modFile.getAbsolutePath());
						InputStreamReader stdout = new InputStreamReader(p.getInputStream());
						int ch=0;
						String currentLine="";
						while (ch != -1) {
							while (((ch = stdout.read()) != -1) && (ch != 10)) {
								currentLine += (char)ch;
							}
							for(int i=0; i<urtaStrings.length; i++) {
								if (currentLine.indexOf(urtaStrings[i])>=0){
									current = i;
									statMessage = currentLine;
								}
							}
//							System.out.println(currentLine);
							currentLine = "";
						}
						p = r.exec(urtaExecutablePath + "uniform"+(jcbCumulative.isSelected()?" -cdf":""));
						stdout = new InputStreamReader(p.getInputStream());
						resultsX.clear(); resultsY.clear();
						ch=0;
						while (ch != -1) {
							while (((ch = stdout.read()) != -1) && (ch != 10)) {
								currentLine += (char)ch;
							}
							for(int i=0; i<urtaStrings.length; i++) {
								if (currentLine.indexOf(urtaStrings[i])>=0){
									current = i;
									statMessage = currentLine;
								}
							}
							if ((currentLine.indexOf("DATA0")>=0) && (currentLine.indexOf("elapsed")==-1)) {
								String results[] = currentLine.split("\\s+");
								resultsX.add(new Double(results[0]));
								resultsY.add(new Double(results[1]));
							}
//							System.out.println(currentLine);
							currentLine = "";
						}
					} catch (IOException e) {
						// TODO Auto-generated catch block
						e.printStackTrace();
					}
				}
			}
		}	
	}
}