analysis/org.eclipse.stem.util.analysis/src/org/eclipse/stem/util/analysis/views/LyapunovControl.java - stem/org.eclipse.stem - Git at Google

 // EstimatorControl.java
 package org.eclipse.stem.util.analysis.views;

 /*******************************************************************************
  * Copyright (c) 2007, 2008 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation
  *******************************************************************************/

 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;

 import org.eclipse.birt.chart.model.attribute.ColorDefinition;
 import org.eclipse.birt.chart.model.attribute.impl.ColorDefinitionImpl;
 import org.eclipse.emf.common.util.EList;
 import org.eclipse.jface.dialogs.ProgressMonitorDialog;
 import org.eclipse.stem.analysis.ScenarioInitializationException;
 import org.eclipse.stem.diseasemodels.Activator;
 import org.eclipse.stem.util.analysis.CSVAnalysisWriter;
 import org.eclipse.stem.util.analysis.PhaseSpaceCoordinate;
 import org.eclipse.stem.util.analysis.ScenarioAnalysisSuite;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.events.SelectionAdapter;
 import org.eclipse.swt.events.SelectionEvent;
 import org.eclipse.swt.layout.FormAttachment;
 import org.eclipse.swt.layout.FormData;
 import org.eclipse.swt.layout.FormLayout;
 import org.eclipse.swt.widgets.Button;
 import org.eclipse.swt.widgets.Composite;
 import org.eclipse.swt.widgets.DirectoryDialog;
 import org.eclipse.swt.widgets.Display;
 import org.eclipse.swt.widgets.Label;
 import org.eclipse.swt.widgets.Shell;
 import org.eclipse.swt.widgets.Text;

 /**
  * This class is a SWT GUI component that uses BIRT to plot
  */
 public class LyapunovControl extends AnalysisControl {


 	/**
 	 * used to identify user preferences for this class
 	 * This String is not human readable so does not need to be NLS'd. It is a key in a map
 	 */
 	private static final String CONSUMER = "LYAPUNOV_CONTROL";

 	/**
 	 * used to remember the primary directory in the user preferences
 	 * This String is not human readable so does not need to be NLS'd. It is a key in a map
 	 */
 	private static final String PRIMARY_FOLDER_KEY = CONSUMER+"_PRIMARY";
 	/**
 	 * used to remember the secondary directory in the user preferences
 	 * This String is not human readable so does not need to be NLS'd. It is a key in a map
 	 */
 	private static final String SECONDARY_FOLDER_KEY = CONSUMER+"_SECONDARY";

 	/**
 	 *  First Scenario Label - indicates number of regions being watched for analysis.
 	 *  There are locations with relative value history providers attached
 	 */
 	Label firstScenarioFolderLabel;

 	/**
 	 *  Second Scenario Label - indicates number of regions being watched for analysis.
 	 *  There are locations with relative value history providers attached
 	 */
 	Label secondScenarioFolderLabel;

 	/**
 	 *  A Label to give feedbak on the computation action
 	 */
 	//Label userFeedbackLabel;

 	/**
 	 * First input text field for the scenario folder of data to use in making the estimation
 	 */
 	Text text1;


 	/**
 	 * Second Input text field for the scenario folder of data to be compared
 	 **/
 	Text text2;


 	/**
 	 * A label to report status (not yet used)
 	 */
 	Label statusLabel;


 	/**
 	 * Results of analysis
 	 */
 	Label resultsLabel;

 	/**
 	 * the chart of two (or more) trajectories in phase space
 	 */
 	LyapunovTrajectoryCanvas lyapunovTrajectoryCanvas;

 	/**
 	 * the time series chart of the divergence of the Lyapunov trajectory(ies) from the reference trajectory
 	 */
 	TimeSeriesCanvas timeSeriesCanvas;
 	/**
 	 * Colors for the time series chart
 	 */
 	static final ColorDefinition foreGround = ColorDefinitionImpl.create(180, 0, 0);
 	static final ColorDefinition backgroundGround = ColorDefinitionImpl.create(255, 255, 225);
 	static final ColorDefinition frameColor = ColorDefinitionImpl.WHITE();

 	/**
 	 * Label for line series Data (legend)
 	 */


 	/**
 	 * the results of various scenario comparisons
 	 * TODO: eventually this might be a map keyed by comparison id
 	 * for now there is only one comparison, the mean square difference.
 	 */
 	List<PhaseSpaceCoordinate[]> comparisonValues = new ArrayList<PhaseSpaceCoordinate[]>();

 	/**
 	 * this is the cumulative deviation between the trajectories (relative to the reference
 	 * trajectory
 	 */
 	List<EList<Double>> cumulativeDeviation = new ArrayList<EList<Double>>();

 	protected static final String LYAPUNOV_FILE_PREFIX = Messages.getString("LYA.TITLE");
 	protected static final String LYAPUNOV_DEVIATION_FILE_PREFIX = Messages.getString("LYA.DEVIATION");
 	protected static final String SELECT_FOLDER_DIALOG_TEXT = Messages.getString("LYA.SELECTFOLDERDIALG");

 	ScenarioAnalysisSuite analyzer = new ScenarioAnalysisSuite(this);

 	Composite parentComposite;

 	/**
 	 *
 	 * @param parent
 	 */
 	public LyapunovControl(final Composite parent) {
 		super(parent, SWT.None);
 		parentComposite = parent;
 		createContents();
 	} // EstimatorControl

 	/**
 	 * Create the contents of the plotter
 	 */
 	private void createContents() {
 		setLayout(new FormLayout());
 		Display display = this.getDisplay();

 		identifiableTitle = new Label(this, SWT.BORDER);
 		identifiableTitle.setText(Messages.getString("LYA.TITLE"));
 		identifiableTitle.setFont(getLargerFont(18, display));


 		statusLabel = new Label(this, SWT.BORDER);
 		statusLabel.setText("");

 		firstScenarioFolderLabel = new Label(this, SWT.NONE);
 		//firstScenarioFolderLabel.setBackground(labelBackground);
 		firstScenarioFolderLabel.setText(Messages.getString("LYA.FOLDER1LABEL"));

 		text1 = new Text(this, SWT.BORDER);
 	    text1.setBounds(10, 10, 100, 20);
 	    String primaryDir=prefs.getRecentFolder(PRIMARY_FOLDER_KEY);
 	    text1.setText(primaryDir);

 	    secondScenarioFolderLabel = new Label(this, SWT.NONE);
 	    // secondScenarioFolderLabel.setBackground(labelBackground);
 	    secondScenarioFolderLabel.setText(Messages.getString("LYA.FOLDER2LABEL"));

 		text2 = new Text(this, SWT.BORDER);
 	    text2.setBounds(10, 10, 100, 20);
 	    String secondaryDir=prefs.getRecentFolder(SECONDARY_FOLDER_KEY);
 	    text2.setText(secondaryDir);

 	    Composite analyzeButtonComposite = getAnalyzeButtonComposite(this,Messages.getString("LYA.COMPARISON"));

 		resultsLabel = new Label(this, SWT.SHADOW_OUT);
 		resultsLabel.setText("");

 		final FormData titleFormData = new FormData();
 		identifiableTitle.setLayoutData(titleFormData);
 		titleFormData.top = new FormAttachment(0, 0);
 		titleFormData.left = new FormAttachment(0, 0);
 		titleFormData.right = new FormAttachment(25, 0);

 		final FormData resultsFormData = new FormData();
 		resultsLabel.setLayoutData(resultsFormData);
 		resultsFormData.top = new FormAttachment(0, 0);
 		resultsFormData.left = new FormAttachment(25, 0);
 		resultsFormData.right = new FormAttachment(75, 0);

 		int spacer = 10;
 		int buttonspacer = 5;

         /////////////////////////////////////////////////////////////////////////
 		// TextField folder label
 		final FormData firstScenarioFolderLabelFormData = new FormData();
 		// propertySelectorFormData.top = new FormAttachment(cSVLoggerCanvas,
 		// 0);
 		firstScenarioFolderLabelFormData.top = new FormAttachment(identifiableTitle, spacer);
 		//firstScenarioFolderLabelFormData.bottom = new FormAttachment(bottom, 0);
 		firstScenarioFolderLabelFormData.left = new FormAttachment(0, 0);
 		firstScenarioFolderLabelFormData.right = new FormAttachment(15, 0);
 		firstScenarioFolderLabel.setLayoutData(firstScenarioFolderLabelFormData);

 		// first text field for parameter Estimator
 		final FormData text1FormData = new FormData();
 		text1FormData.top = new FormAttachment(identifiableTitle, spacer);
 		text1FormData.left = new FormAttachment(firstScenarioFolderLabel, 5);
 		text1FormData.right = new FormAttachment(85, 0);
 		text1.setLayoutData(text1FormData);

 		Button selectFolder1Button = new Button(this, SWT.NONE);
 		selectFolder1Button.setText(Messages.getString("LYA.SELECTFOLDER"));
 		final FormData selectFolder1FormData = new FormData();
 		selectFolder1FormData.top = new FormAttachment(identifiableTitle, buttonspacer);
 		//selectFolder1FormData.bottom = new FormAttachment(bottom, 0);
 		selectFolder1FormData.left = new FormAttachment(text1, 5);
 		selectFolder1Button.setLayoutData(selectFolder1FormData);

 		final Shell shell = this.getShell();

 		selectFolder1Button.addSelectionListener(new SelectionAdapter() {
 			@Override
 			public void widgetSelected(@SuppressWarnings("unused")
 			final SelectionEvent e) {
 				final DirectoryDialog dd = new DirectoryDialog(
 						shell, SWT.OPEN);
 					dd.setText(Messages.getString("LYA.SELECTFOLDERDIALOG")); //$NON-NLS-1$
 					String beginSearch = text1.getText();
 					if((beginSearch==null)||(beginSearch.length()<1)) beginSearch = ROOT_PATH;

 					dd.setFilterPath(beginSearch);
 					final String selected = dd.open();
 					if(selected!=null) text1.setText(selected);
 			}
 		});
         /////////////////////////////////////////////////////////////////////////

 	//	bottom += deltaBottom;

         /////////////////////////////////////////////////////////////////////////
 		// TextField folder label
 		final FormData secondScenarioFolderLabelFormData = new FormData();
 		// propertySelectorFormData.top = new FormAttachment(cSVLoggerCanvas,
 		// 0);
 		secondScenarioFolderLabelFormData.top = new FormAttachment(firstScenarioFolderLabel, spacer);
 		secondScenarioFolderLabelFormData.left = new FormAttachment(0, 0);
 		secondScenarioFolderLabelFormData.right = new FormAttachment(15, 0);
 		secondScenarioFolderLabel.setLayoutData(secondScenarioFolderLabelFormData);

 		// first text field for parameter Estimator
 		final FormData text2FormData = new FormData();
 		text2FormData.top = new FormAttachment(firstScenarioFolderLabel, spacer);
 		text2FormData.left = new FormAttachment(secondScenarioFolderLabel, 5);
 		text2FormData.right = new FormAttachment(85, 0);
 		text2.setLayoutData(text2FormData);

 		Button selectFolder2Button = new Button(this, SWT.NONE);
 		selectFolder2Button.setText(Messages.getString("LYA.SELECTFOLDER"));
 		final FormData selectFolder2FormData = new FormData();
 		selectFolder2FormData.top = new FormAttachment(firstScenarioFolderLabel, buttonspacer);
 		selectFolder2FormData.left = new FormAttachment(text2, 5);
 		selectFolder2Button.setLayoutData(selectFolder2FormData);

 		selectFolder2Button.addSelectionListener(new SelectionAdapter() {
 			@Override
 			public void widgetSelected(@SuppressWarnings("unused")
 			final SelectionEvent e) {
 				final DirectoryDialog dd = new DirectoryDialog(
 						shell, SWT.OPEN);
 					dd.setText(SELECT_FOLDER_DIALOG_TEXT); //$NON-NLS-1$
 					String beginSearch = text2.getText();
 					if((beginSearch==null)||(beginSearch.length()<1)) beginSearch = ROOT_PATH;

 					dd.setFilterPath(beginSearch);
 					final String selected = dd.open();
 					if(selected!=null) text2.setText(selected);
 			}
 		});

 		/////////////////////////////////////////////////////////////////////////

 	//	bottom += deltaBottom;
 		// AnalyzeButton
 		final FormData analysisButtonFormData = new FormData();
 		// propertySelectorFormDataX.top = new FormAttachment(propertySelectorY,
 		// 0);
 		analysisButtonFormData.top = new FormAttachment(secondScenarioFolderLabel, spacer);
 		//analysisButtonFormData.bottom = new FormAttachment(bottom, 0);
 		analysisButtonFormData.left = new FormAttachment(0, 0);
 		analysisButtonFormData.right = new FormAttachment(100, 0);
 		analyzeButtonComposite.setLayoutData(analysisButtonFormData);


 		// Trajectories
 		lyapunovTrajectoryCanvas = new LyapunovTrajectoryCanvas(this);
 		final FormData trajectoryChartFormData = new FormData();
 		lyapunovTrajectoryCanvas.setLayoutData(trajectoryChartFormData);
 		trajectoryChartFormData.top = new FormAttachment(analyzeButtonComposite, 0);
 		trajectoryChartFormData.bottom = new FormAttachment(100, 0);
 		trajectoryChartFormData.left = new FormAttachment(0, 0);
 		trajectoryChartFormData.right = new FormAttachment(50, 0);

 		// divergence graph
 		timeSeriesCanvas = new TimeSeriesCanvas(this,
 													Messages.getString("LYA.DIVERGENCELEGEND"),
 													Messages.getString("LYA.DIVERGENCEYAXIS"),
 													Messages.getString("LYA.DIVERGENCEYAXIS"),
 													foreGround,
 													backgroundGround,
 													frameColor, 0);


 		final FormData analysisChartFormData = new FormData();
 		timeSeriesCanvas.setLayoutData(analysisChartFormData);
 		analysisChartFormData.top = new FormAttachment(analyzeButtonComposite, 0);
 		analysisChartFormData.bottom = new FormAttachment(100, 0);
 		analysisChartFormData.left = new FormAttachment(50, 0);
 		analysisChartFormData.right = new FormAttachment(100, 0);


 		final ProgressMonitorDialog progressDialog = new ProgressMonitorDialog(this.getShell());

 		analyzeButton.addSelectionListener(new SelectionAdapter() {
 			@Override
 			public void widgetSelected(@SuppressWarnings("unused")
 			final SelectionEvent e) {

 				String referenceDirectory  = text1.getText();
 				String comparisonDirectory = text2.getText();
 				Display display = parentComposite.getDisplay();
 				/*
 				 * reset the label text
 				 */
 			    identifiableTitle.setText(Messages.getString("LYA.TITLE"));
 			    resultsLabel.setText(Messages.getString("LYA.WORKING"));
 			    /*
 				 * reinitialize the graph
 				 */
 				comparisonValues.clear();
 				cumulativeDeviation.clear();
 				lyapunovTrajectoryCanvas.reset();

 				/*
 				 * VALIDATE the text input Fields
 				 */
 				if(!analyzer.validate(referenceDirectory)) {
 					identifiableTitle.setText(ScenarioAnalysisSuite.NOT_FOUND_MSG);
 					text1.setText("");
 				}
                 if(!analyzer.validate(comparisonDirectory)) {
                 	identifiableTitle.setText(ScenarioAnalysisSuite.NOT_FOUND_MSG);
                 	text2.setText("");
 				}
                 if((!analyzer.validate(referenceDirectory)) || (!analyzer.validate(comparisonDirectory))) {
                 	return;
                 }

 				try {

 					List<PhaseSpaceCoordinate[]> data = analyzer.getLyapunovTrajectory(referenceDirectory, comparisonDirectory, progressDialog);
 					if(data==null) {
 						resultsLabel.setBackground(display.getSystemColor(SWT.COLOR_RED));
 					    resultsLabel.setText(Messages.getString("LYA.ERROR1"));

 					} else {
 						comparisonValues.addAll(data);
 						//success... remember the users prefs
 						prefs.setRecentFolder(PRIMARY_FOLDER_KEY,referenceDirectory);
 						prefs.setRecentFolder(SECONDARY_FOLDER_KEY,comparisonDirectory);

 						cumulativeDeviation.addAll(ScenarioAnalysisSuite.getCumulativePhaseSpaceDeviation(comparisonValues));

 						//
 						// now udate everything
 						//
 						lyapunovTrajectoryCanvas.draw();
 						// Log the trajectory data
 						String outFileName = LYAPUNOV_FILE_PREFIX+"_"+
 						 getScenarioNameFromDirectoryName(referenceDirectory)+
 						 "_"+
 						 getScenarioNameFromDirectoryName(comparisonDirectory);

 						CSVAnalysisWriter writer = new CSVAnalysisWriter(outFileName);
 						writer.logData(2,comparisonValues);

 						// Log the cumulative deviation data
 						outFileName = LYAPUNOV_DEVIATION_FILE_PREFIX+"_"+
 						 getScenarioNameFromDirectoryName(referenceDirectory)+
 						 "_"+
 						 getScenarioNameFromDirectoryName(comparisonDirectory);
 						 CSVAnalysisWriter writer2 = new CSVAnalysisWriter(outFileName);
 						 writer2.logData(cumulativeDeviation);
 						 timeSeriesCanvas.draw();
 						 resultsLabel.setText(Messages.getString("LYA.COMPLETE"));
 					}

 				} catch(ScenarioInitializationException sie) {
 					Activator.logError("", sie);
 				}

 				// done
 			}
 		});

 	} // createContents


 	/**
 	 * @param dirName
 	 * @return short name of scenario
 	 */
 	public static String getScenarioNameFromDirectoryName(String dirName) {
 		int last = dirName.lastIndexOf("/");
 		int last2 = dirName.lastIndexOf("\\");
 		if (last2 > last)
 			last = last2;
 		if (last <= 0)
 			last = 0;
 		String retVal = dirName.substring(last + 1, dirName.length());
 		return retVal;
 	}

 	/**
 	 * This returns the results of a comparison of type comparisonType
 	 * as an array of double.
 	 *
 	 * @param trajectory the trajectory to return
 	 * @return comparison
 	 */
 	public PhaseSpaceCoordinate[] getPointValues(int trajectory) {

 		return comparisonValues.get(trajectory);
 	}

 	/**
 	 * returns the analysis of lyapunov tractory(ies) relative to reference.
 	 * @param chartIndex not used (only one chart)
 	 * @param trajectory
 	 * @return Cumulative deviation from reference trajectory
 	 */
 	@SuppressWarnings("boxing")
 	@Override
 	public double[] getValues(int chartIndex, int trajectory) {

 		EList<Double> l = cumulativeDeviation.get(trajectory);
 		double [] res = new double[l.size()];
 		for(int i=0;i<res.length;++i) res[i] = l.get(i);
 		return res;
 	}

 	/**
 	 * Not used
 	 * @param chartIndex not used (only one chart)
 	 * @param state
 	 * @return property name
 	 */
 	@Override
 	public String getProperty(int chartIndex, int state) {
 		return Messages.getString("LYA.DIVERGENCEYAXIS");
 	}

 	/**
 	 * Only one property to plot = the RMS difference
 	 * @param chartIndex not used (only one chart)
 	 * @return the number of properties
 	 * @see org.eclipse.stem.util.analysis.views.AnalysisControl#getNumProperties(int chartIndex)
 	 */
 	@Override
 	public int getNumProperties(int chartIndex) {
 		return 1;
 	}


 	/**
 	 * to remove the control e.g. by a remove button event
 	 */
 	@Override
 	public void remove() {
 		updateStatusLabel();
 	}


 	protected void updateStatusLabel() {
 		statusLabel.setText(Messages.getString("COMMON.STATUS"));
 	}


 	/**
 	 * Initialize the header label
 	 *
 	 * @param folderName
 	 */
 	@Override
 	protected void initializeHeader(String folderName) {
 		simulationNameLabel.setText("analyzing "+folderName);

 	} // initializeFromSimulation


 	/**
 	 * @see org.eclipse.swt.widgets.Widget#dispose()
 	 */
 	@Override
 	public void dispose() {

 		super.dispose();

 	} // dispose

 	/**
 	 * Each Control class may add objects to this map
 	 * @return the control parameters maps
 	 */
 	public Map<String, Object> getControlParametersMap() {
 		// add nothing for now
 		return controlParametersMap;
 	}


 } // EstimatorControl
	// EstimatorControl.java
	package org.eclipse.stem.util.analysis.views;

	/*******************************************************************************
	* Copyright (c) 2007, 2008 IBM Corporation and others.
	* All rights reserved. This program and the accompanying materials
	* are made available under the terms of the Eclipse Public License v1.0
	* which accompanies this distribution, and is available at
	* http://www.eclipse.org/legal/epl-v10.html
	*
	* Contributors:
	* IBM Corporation - initial API and implementation
	*******************************************************************************/

	import java.util.ArrayList;
	import java.util.List;
	import java.util.Map;

	import org.eclipse.birt.chart.model.attribute.ColorDefinition;
	import org.eclipse.birt.chart.model.attribute.impl.ColorDefinitionImpl;
	import org.eclipse.emf.common.util.EList;
	import org.eclipse.jface.dialogs.ProgressMonitorDialog;
	import org.eclipse.stem.analysis.ScenarioInitializationException;
	import org.eclipse.stem.diseasemodels.Activator;
	import org.eclipse.stem.util.analysis.CSVAnalysisWriter;
	import org.eclipse.stem.util.analysis.PhaseSpaceCoordinate;
	import org.eclipse.stem.util.analysis.ScenarioAnalysisSuite;
	import org.eclipse.swt.SWT;
	import org.eclipse.swt.events.SelectionAdapter;
	import org.eclipse.swt.events.SelectionEvent;
	import org.eclipse.swt.layout.FormAttachment;
	import org.eclipse.swt.layout.FormData;
	import org.eclipse.swt.layout.FormLayout;
	import org.eclipse.swt.widgets.Button;
	import org.eclipse.swt.widgets.Composite;
	import org.eclipse.swt.widgets.DirectoryDialog;
	import org.eclipse.swt.widgets.Display;
	import org.eclipse.swt.widgets.Label;
	import org.eclipse.swt.widgets.Shell;
	import org.eclipse.swt.widgets.Text;

	/**
	* This class is a SWT GUI component that uses BIRT to plot
	*/
	public class LyapunovControl extends AnalysisControl {


	/**
	* used to identify user preferences for this class
	* This String is not human readable so does not need to be NLS'd. It is a key in a map
	*/
	private static final String CONSUMER = "LYAPUNOV_CONTROL";

	/**
	* used to remember the primary directory in the user preferences
	* This String is not human readable so does not need to be NLS'd. It is a key in a map
	*/
	private static final String PRIMARY_FOLDER_KEY = CONSUMER+"_PRIMARY";
	/**
	* used to remember the secondary directory in the user preferences
	* This String is not human readable so does not need to be NLS'd. It is a key in a map
	*/
	private static final String SECONDARY_FOLDER_KEY = CONSUMER+"_SECONDARY";

	/**
	* First Scenario Label - indicates number of regions being watched for analysis.
	* There are locations with relative value history providers attached
	*/
	Label firstScenarioFolderLabel;

	/**
	* Second Scenario Label - indicates number of regions being watched for analysis.
	* There are locations with relative value history providers attached
	*/
	Label secondScenarioFolderLabel;

	/**
	* A Label to give feedbak on the computation action
	*/
	//Label userFeedbackLabel;

	/**
	* First input text field for the scenario folder of data to use in making the estimation
	*/
	Text text1;


	/**
	* Second Input text field for the scenario folder of data to be compared
	**/
	Text text2;




	/**
	* A label to report status (not yet used)
	*/
	Label statusLabel;


	/**
	* Results of analysis
	*/
	Label resultsLabel;

	/**
	* the chart of two (or more) trajectories in phase space
	*/
	LyapunovTrajectoryCanvas lyapunovTrajectoryCanvas;

	/**
	* the time series chart of the divergence of the Lyapunov trajectory(ies) from the reference trajectory
	*/
	TimeSeriesCanvas timeSeriesCanvas;
	/**
	* Colors for the time series chart
	*/
	static final ColorDefinition foreGround = ColorDefinitionImpl.create(180, 0, 0);
	static final ColorDefinition backgroundGround = ColorDefinitionImpl.create(255, 255, 225);
	static final ColorDefinition frameColor = ColorDefinitionImpl.WHITE();

	/**
	* Label for line series Data (legend)
	*/


	/**
	* the results of various scenario comparisons
	* TODO: eventually this might be a map keyed by comparison id
	* for now there is only one comparison, the mean square difference.
	*/
	List<PhaseSpaceCoordinate[]> comparisonValues = new ArrayList<PhaseSpaceCoordinate[]>();

	/**
	* this is the cumulative deviation between the trajectories (relative to the reference
	* trajectory
	*/
	List<EList<Double>> cumulativeDeviation = new ArrayList<EList<Double>>();

	protected static final String LYAPUNOV_FILE_PREFIX = Messages.getString("LYA.TITLE");
	protected static final String LYAPUNOV_DEVIATION_FILE_PREFIX = Messages.getString("LYA.DEVIATION");
	protected static final String SELECT_FOLDER_DIALOG_TEXT = Messages.getString("LYA.SELECTFOLDERDIALG");

	ScenarioAnalysisSuite analyzer = new ScenarioAnalysisSuite(this);

	Composite parentComposite;

	/**
	*
	* @param parent
	*/
	public LyapunovControl(final Composite parent) {
	super(parent, SWT.None);
	parentComposite = parent;
	createContents();
	} // EstimatorControl

	/**
	* Create the contents of the plotter
	*/
	private void createContents() {
	setLayout(new FormLayout());
	Display display = this.getDisplay();

	identifiableTitle = new Label(this, SWT.BORDER);
	identifiableTitle.setText(Messages.getString("LYA.TITLE"));
	identifiableTitle.setFont(getLargerFont(18, display));




	statusLabel = new Label(this, SWT.BORDER);
	statusLabel.setText("");

	firstScenarioFolderLabel = new Label(this, SWT.NONE);
	//firstScenarioFolderLabel.setBackground(labelBackground);
	firstScenarioFolderLabel.setText(Messages.getString("LYA.FOLDER1LABEL"));

	text1 = new Text(this, SWT.BORDER);
	text1.setBounds(10, 10, 100, 20);
	String primaryDir=prefs.getRecentFolder(PRIMARY_FOLDER_KEY);
	text1.setText(primaryDir);

	secondScenarioFolderLabel = new Label(this, SWT.NONE);
	// secondScenarioFolderLabel.setBackground(labelBackground);
	secondScenarioFolderLabel.setText(Messages.getString("LYA.FOLDER2LABEL"));

	text2 = new Text(this, SWT.BORDER);
	text2.setBounds(10, 10, 100, 20);
	String secondaryDir=prefs.getRecentFolder(SECONDARY_FOLDER_KEY);
	text2.setText(secondaryDir);

	Composite analyzeButtonComposite = getAnalyzeButtonComposite(this,Messages.getString("LYA.COMPARISON"));

	resultsLabel = new Label(this, SWT.SHADOW_OUT);
	resultsLabel.setText("");

	final FormData titleFormData = new FormData();
	identifiableTitle.setLayoutData(titleFormData);
	titleFormData.top = new FormAttachment(0, 0);
	titleFormData.left = new FormAttachment(0, 0);
	titleFormData.right = new FormAttachment(25, 0);

	final FormData resultsFormData = new FormData();
	resultsLabel.setLayoutData(resultsFormData);
	resultsFormData.top = new FormAttachment(0, 0);
	resultsFormData.left = new FormAttachment(25, 0);
	resultsFormData.right = new FormAttachment(75, 0);

	int spacer = 10;
	int buttonspacer = 5;

	/////////////////////////////////////////////////////////////////////////
	// TextField folder label
	final FormData firstScenarioFolderLabelFormData = new FormData();
	// propertySelectorFormData.top = new FormAttachment(cSVLoggerCanvas,
	// 0);
	firstScenarioFolderLabelFormData.top = new FormAttachment(identifiableTitle, spacer);
	//firstScenarioFolderLabelFormData.bottom = new FormAttachment(bottom, 0);
	firstScenarioFolderLabelFormData.left = new FormAttachment(0, 0);
	firstScenarioFolderLabelFormData.right = new FormAttachment(15, 0);
	firstScenarioFolderLabel.setLayoutData(firstScenarioFolderLabelFormData);

	// first text field for parameter Estimator
	final FormData text1FormData = new FormData();
	text1FormData.top = new FormAttachment(identifiableTitle, spacer);
	text1FormData.left = new FormAttachment(firstScenarioFolderLabel, 5);
	text1FormData.right = new FormAttachment(85, 0);
	text1.setLayoutData(text1FormData);

	Button selectFolder1Button = new Button(this, SWT.NONE);
	selectFolder1Button.setText(Messages.getString("LYA.SELECTFOLDER"));
	final FormData selectFolder1FormData = new FormData();
	selectFolder1FormData.top = new FormAttachment(identifiableTitle, buttonspacer);
	//selectFolder1FormData.bottom = new FormAttachment(bottom, 0);
	selectFolder1FormData.left = new FormAttachment(text1, 5);
	selectFolder1Button.setLayoutData(selectFolder1FormData);

	final Shell shell = this.getShell();

	selectFolder1Button.addSelectionListener(new SelectionAdapter() {
	@Override
	public void widgetSelected(@SuppressWarnings("unused")
	final SelectionEvent e) {
	final DirectoryDialog dd = new DirectoryDialog(
	shell, SWT.OPEN);
	dd.setText(Messages.getString("LYA.SELECTFOLDERDIALOG")); //$NON-NLS-1$
	String beginSearch = text1.getText();
	if((beginSearch==null)\|\|(beginSearch.length()<1)) beginSearch = ROOT_PATH;

	dd.setFilterPath(beginSearch);
	final String selected = dd.open();
	if(selected!=null) text1.setText(selected);
	}
	});
	/////////////////////////////////////////////////////////////////////////

	// bottom += deltaBottom;

	/////////////////////////////////////////////////////////////////////////
	// TextField folder label
	final FormData secondScenarioFolderLabelFormData = new FormData();
	// propertySelectorFormData.top = new FormAttachment(cSVLoggerCanvas,
	// 0);
	secondScenarioFolderLabelFormData.top = new FormAttachment(firstScenarioFolderLabel, spacer);
	secondScenarioFolderLabelFormData.left = new FormAttachment(0, 0);
	secondScenarioFolderLabelFormData.right = new FormAttachment(15, 0);
	secondScenarioFolderLabel.setLayoutData(secondScenarioFolderLabelFormData);

	// first text field for parameter Estimator
	final FormData text2FormData = new FormData();
	text2FormData.top = new FormAttachment(firstScenarioFolderLabel, spacer);
	text2FormData.left = new FormAttachment(secondScenarioFolderLabel, 5);
	text2FormData.right = new FormAttachment(85, 0);
	text2.setLayoutData(text2FormData);

	Button selectFolder2Button = new Button(this, SWT.NONE);
	selectFolder2Button.setText(Messages.getString("LYA.SELECTFOLDER"));
	final FormData selectFolder2FormData = new FormData();
	selectFolder2FormData.top = new FormAttachment(firstScenarioFolderLabel, buttonspacer);
	selectFolder2FormData.left = new FormAttachment(text2, 5);
	selectFolder2Button.setLayoutData(selectFolder2FormData);

	selectFolder2Button.addSelectionListener(new SelectionAdapter() {
	@Override
	public void widgetSelected(@SuppressWarnings("unused")
	final SelectionEvent e) {
	final DirectoryDialog dd = new DirectoryDialog(
	shell, SWT.OPEN);
	dd.setText(SELECT_FOLDER_DIALOG_TEXT); //$NON-NLS-1$
	String beginSearch = text2.getText();
	if((beginSearch==null)\|\|(beginSearch.length()<1)) beginSearch = ROOT_PATH;

	dd.setFilterPath(beginSearch);
	final String selected = dd.open();
	if(selected!=null) text2.setText(selected);
	}
	});

	/////////////////////////////////////////////////////////////////////////

	// bottom += deltaBottom;
	// AnalyzeButton
	final FormData analysisButtonFormData = new FormData();
	// propertySelectorFormDataX.top = new FormAttachment(propertySelectorY,
	// 0);
	analysisButtonFormData.top = new FormAttachment(secondScenarioFolderLabel, spacer);
	//analysisButtonFormData.bottom = new FormAttachment(bottom, 0);
	analysisButtonFormData.left = new FormAttachment(0, 0);
	analysisButtonFormData.right = new FormAttachment(100, 0);
	analyzeButtonComposite.setLayoutData(analysisButtonFormData);



	// Trajectories
	lyapunovTrajectoryCanvas = new LyapunovTrajectoryCanvas(this);
	final FormData trajectoryChartFormData = new FormData();
	lyapunovTrajectoryCanvas.setLayoutData(trajectoryChartFormData);
	trajectoryChartFormData.top = new FormAttachment(analyzeButtonComposite, 0);
	trajectoryChartFormData.bottom = new FormAttachment(100, 0);
	trajectoryChartFormData.left = new FormAttachment(0, 0);
	trajectoryChartFormData.right = new FormAttachment(50, 0);

	// divergence graph
	timeSeriesCanvas = new TimeSeriesCanvas(this,
	Messages.getString("LYA.DIVERGENCELEGEND"),
	Messages.getString("LYA.DIVERGENCEYAXIS"),
	Messages.getString("LYA.DIVERGENCEYAXIS"),
	foreGround,
	backgroundGround,
	frameColor, 0);



	final FormData analysisChartFormData = new FormData();
	timeSeriesCanvas.setLayoutData(analysisChartFormData);
	analysisChartFormData.top = new FormAttachment(analyzeButtonComposite, 0);
	analysisChartFormData.bottom = new FormAttachment(100, 0);
	analysisChartFormData.left = new FormAttachment(50, 0);
	analysisChartFormData.right = new FormAttachment(100, 0);


	final ProgressMonitorDialog progressDialog = new ProgressMonitorDialog(this.getShell());

	analyzeButton.addSelectionListener(new SelectionAdapter() {
	@Override
	public void widgetSelected(@SuppressWarnings("unused")
	final SelectionEvent e) {

	String referenceDirectory = text1.getText();
	String comparisonDirectory = text2.getText();
	Display display = parentComposite.getDisplay();
	/*
	* reset the label text
	*/
	identifiableTitle.setText(Messages.getString("LYA.TITLE"));
	resultsLabel.setText(Messages.getString("LYA.WORKING"));
	/*
	* reinitialize the graph
	*/
	comparisonValues.clear();
	cumulativeDeviation.clear();
	lyapunovTrajectoryCanvas.reset();

	/*
	* VALIDATE the text input Fields
	*/
	if(!analyzer.validate(referenceDirectory)) {
	identifiableTitle.setText(ScenarioAnalysisSuite.NOT_FOUND_MSG);
	text1.setText("");
	}
	if(!analyzer.validate(comparisonDirectory)) {
	identifiableTitle.setText(ScenarioAnalysisSuite.NOT_FOUND_MSG);
	text2.setText("");
	}
	if((!analyzer.validate(referenceDirectory)) \|\| (!analyzer.validate(comparisonDirectory))) {
	return;
	}

	try {

	List<PhaseSpaceCoordinate[]> data = analyzer.getLyapunovTrajectory(referenceDirectory, comparisonDirectory, progressDialog);
	if(data==null) {
	resultsLabel.setBackground(display.getSystemColor(SWT.COLOR_RED));
	resultsLabel.setText(Messages.getString("LYA.ERROR1"));

	} else {
	comparisonValues.addAll(data);
	//success... remember the users prefs
	prefs.setRecentFolder(PRIMARY_FOLDER_KEY,referenceDirectory);
	prefs.setRecentFolder(SECONDARY_FOLDER_KEY,comparisonDirectory);

	cumulativeDeviation.addAll(ScenarioAnalysisSuite.getCumulativePhaseSpaceDeviation(comparisonValues));

	//
	// now udate everything
	//
	lyapunovTrajectoryCanvas.draw();
	// Log the trajectory data
	String outFileName = LYAPUNOV_FILE_PREFIX+"_"+
	getScenarioNameFromDirectoryName(referenceDirectory)+
	"_"+
	getScenarioNameFromDirectoryName(comparisonDirectory);

	CSVAnalysisWriter writer = new CSVAnalysisWriter(outFileName);
	writer.logData(2,comparisonValues);

	// Log the cumulative deviation data
	outFileName = LYAPUNOV_DEVIATION_FILE_PREFIX+"_"+
	getScenarioNameFromDirectoryName(referenceDirectory)+
	"_"+
	getScenarioNameFromDirectoryName(comparisonDirectory);
	CSVAnalysisWriter writer2 = new CSVAnalysisWriter(outFileName);
	writer2.logData(cumulativeDeviation);
	timeSeriesCanvas.draw();
	resultsLabel.setText(Messages.getString("LYA.COMPLETE"));
	}

	} catch(ScenarioInitializationException sie) {
	Activator.logError("", sie);
	}

	// done
	}
	});

	} // createContents





	/**
	* @param dirName
	* @return short name of scenario
	*/
	public static String getScenarioNameFromDirectoryName(String dirName) {
	int last = dirName.lastIndexOf("/");
	int last2 = dirName.lastIndexOf("\\");
	if (last2 > last)
	last = last2;
	if (last <= 0)
	last = 0;
	String retVal = dirName.substring(last + 1, dirName.length());
	return retVal;
	}

	/**
	* This returns the results of a comparison of type comparisonType
	* as an array of double.
	*
	* @param trajectory the trajectory to return
	* @return comparison
	*/
	public PhaseSpaceCoordinate[] getPointValues(int trajectory) {

	return comparisonValues.get(trajectory);
	}

	/**
	* returns the analysis of lyapunov tractory(ies) relative to reference.
	* @param chartIndex not used (only one chart)
	* @param trajectory
	* @return Cumulative deviation from reference trajectory
	*/
	@SuppressWarnings("boxing")
	@Override
	public double[] getValues(int chartIndex, int trajectory) {

	EList<Double> l = cumulativeDeviation.get(trajectory);
	double [] res = new double[l.size()];
	for(int i=0;i<res.length;++i) res[i] = l.get(i);
	return res;
	}

	/**
	* Not used
	* @param chartIndex not used (only one chart)
	* @param state
	* @return property name
	*/
	@Override
	public String getProperty(int chartIndex, int state) {
	return Messages.getString("LYA.DIVERGENCEYAXIS");
	}

	/**
	* Only one property to plot = the RMS difference
	* @param chartIndex not used (only one chart)
	* @return the number of properties
	* @see org.eclipse.stem.util.analysis.views.AnalysisControl#getNumProperties(int chartIndex)
	*/
	@Override
	public int getNumProperties(int chartIndex) {
	return 1;
	}




	/**
	* to remove the control e.g. by a remove button event
	*/
	@Override
	public void remove() {
	updateStatusLabel();
	}




	protected void updateStatusLabel() {
	statusLabel.setText(Messages.getString("COMMON.STATUS"));
	}



	/**
	* Initialize the header label
	*
	* @param folderName
	*/
	@Override
	protected void initializeHeader(String folderName) {
	simulationNameLabel.setText("analyzing "+folderName);

	} // initializeFromSimulation






	/**
	* @see org.eclipse.swt.widgets.Widget#dispose()
	*/
	@Override
	public void dispose() {

	super.dispose();

	} // dispose

	/**
	* Each Control class may add objects to this map
	* @return the control parameters maps
	*/
	public Map<String, Object> getControlParametersMap() {
	// add nothing for now
	return controlParametersMap;
	}


	} // EstimatorControl