update constraint format to Orlean format and add distance matrix computation

src/mustic/gui/ImageSession.java

@@ -66,7 +66,7 @@ public class ImageSession {
 	public SSHParameters	          	sshparameters	  	= null;
 	
 	/** enable the image to display the image or not, for a memory usage matter */
-	private boolean						displayEnable		= true;
+	private boolean						displayEnable		= false;
 
 	/**
 	 * @param aImage

src/mustic/gui/MainFrame.java

@@ -569,6 +569,16 @@ public class MainFrame extends JFrame {
 			}
 		});
 		toolsMenu.add(menuTransformationBmp);
+
+		/** Menu to generate constraints from current image session */
+		menuDistanceMatrix= new JMenuItem(Messages.getString("MainFrame.304"));
+		menuDistanceMatrix.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				createDistanceMatrix();
+			}
+		});
+		toolsMenu.add(menuDistanceMatrix);
 		
 		/** Menu to generate constraints from current image session */
 		menuConstraints = new JMenuItem(Messages.getString("MainFrame.301"));
@@ -996,6 +1006,8 @@ public class MainFrame extends JFrame {
 	private Boolean	     actionTransformationBmp;
 	private JMenuItem	 menuConstraints;
 	private Boolean	     actionConstraints;
+	private JMenuItem	 menuDistanceMatrix;
+	private	Boolean		 actionDistanceMatrix;
 	private JMenuItem	 menuItemArff;
 	private Boolean	     actionArff;
 	private JMenuItem	 menuItemRaw;
@@ -1113,6 +1125,7 @@ public class MainFrame extends JFrame {
 		this.actionContratsP = false;
 		this.actionCrop = false;
 		this.actionConstraints = false;
+		this.actionDistanceMatrix = false;
 		this.actionFilter = false;
 		this.actionMask = false;
 		this.actionRefresh = false;
@@ -1143,6 +1156,7 @@ public class MainFrame extends JFrame {
 		this.actionContratsP = true;
 		this.actionCrop = true;
 		this.actionConstraints = true;
+		this.actionDistanceMatrix = true;
 		this.actionFilter = true;
 		this.actionMask = true;
 		this.actionNew = true;
@@ -1181,6 +1195,7 @@ public class MainFrame extends JFrame {
 		menuItemMask.setEnabled(this.actionMask);
 		menuCrop.setEnabled(this.actionCrop);
 		menuConstraints.setEnabled(this.actionConstraints);
+		menuDistanceMatrix.setEnabled(this.actionDistanceMatrix);
 		menuTransformationBmp.setEnabled(this.actionTransformationBmp);
 		menuItemArff.setEnabled(this.actionArff);
 		menuItemRaw.setEnabled(this.actionRaw);
@@ -2172,6 +2187,15 @@ public class MainFrame extends JFrame {
 				                              JOptionPane.WARNING_MESSAGE);
 			}
 	}
+	
+	/**
+	 * Open the dialog window to generate a distance matrix from a data
+	 */
+	protected void createDistanceMatrix() {
+		DistanceMatrixDialog dialog = new DistanceMatrixDialog();
+		this.desktop.add(dialog);
+		dialog.toFront();
+	}
 
 	public void doAfterSegmentation(Segmentation seg, RawImage img) {
 		// fenetre et panel du resultat

src/mustic/gui/dialog/DataToArffDialog.java

@@ -17,13 +17,12 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
-import javax.swing.JSpinner;
 import javax.swing.JTextField;
 
 import jcl.data.Data;
 import mustic.gui.DataDesktopFrame;
 import mustic.gui.MainFrame;
-import mustic.utils.dataExchange.DataArffExchange;
+import mustic.utils.io.dataExchange.DataArffExchange;
 
 /**
  * Fenetre permettant de creer des fichier ARFF à partir d'un image
@@ -36,9 +35,6 @@ public class DataToArffDialog extends JInternalFrame {
 	/** liste des images ouvertes */
 	private JComboBox<String> comboData = new JComboBox<String>();
 
-	/** nombre de divisions */
-	private JSpinner spinner = new JSpinner();
-
 	/** chemin du fichier que l'on va créer */
 	private JTextField textSave = new JTextField();
 
@@ -105,15 +101,15 @@ public class DataToArffDialog extends JInternalFrame {
 		panelData.add(new JLabel(Messages.getString("DataToArffDialog.15"))); //$NON-NLS-1$
 		panelData.add(txtDate);
 
-		panelData.add(new JLabel(Messages.getString("DataToArffDialog.16"))); //$NON-NLS-1$
-		JSpinner.NumberEditor spinnerEditor = new JSpinner.NumberEditor(
-				this.spinner);
-		this.spinner.setEditor(spinnerEditor);
-		spinnerEditor.getModel().setMinimum(1);
-		spinnerEditor.getModel().setMaximum(256);
-		spinnerEditor.getModel().setStepSize(1);
-		spinnerEditor.getModel().setValue(10);
-		panelData.add(this.spinner);
+//		panelData.add(new JLabel(Messages.getString("DataToArffDialog.16"))); //$NON-NLS-1$
+//		JSpinner.NumberEditor spinnerEditor = new JSpinner.NumberEditor(
+//				this.spinner);
+//		this.spinner.setEditor(spinnerEditor);
+//		spinnerEditor.getModel().setMinimum(1);
+//		spinnerEditor.getModel().setMaximum(256);
+//		spinnerEditor.getModel().setStepSize(1);
+//		spinnerEditor.getModel().setValue(10);
+//		panelData.add(this.spinner);
 
 		JPanel panelOk = new JPanel();
 		JButton buttonOk = new JButton(Messages.getString("DataToArffDialog.17")); //$NON-NLS-1$

src/mustic/gui/dialog/DistanceMatrixDialog.java

+package mustic.gui.dialog;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import jcl.data.Data;
+import mustic.gui.DataDesktopFrame;
+import mustic.gui.MainFrame;
+import mustic.utils.io.WriteDistancesPath;
+
+/**
+ * Fenetre permettant de creer des fichier ARFF à partir d'un image
+ * 
+ */
+public class DistanceMatrixDialog extends JInternalFrame {
+
+	private static final long serialVersionUID = 1L;
+
+	/** liste des images ouvertes */
+	private JComboBox<String> comboData = new JComboBox<String>();
+
+	/** chemin du fichier que l'on va créer */
+	private JTextField textSave = new JTextField();
+
+	private JTextField txtDate;
+
+	public DistanceMatrixDialog() {
+		super();
+
+		JPanel mainPanel = new JPanel(new BorderLayout());
+		JPanel panelData = new JPanel(new GridLayout(4, 2));
+		panelData.add(new JLabel(Messages.getString("DistanceMatrixDialog.0"))); //$NON-NLS-1$
+
+		DataDesktopFrame[] desktopFrames = MainFrame.getInstance().getDesktop()
+				.getAllDataDesktopFrames();
+		int nbSession = desktopFrames.length;
+		for (int i = 0; i < nbSession; i++) {
+			String name = desktopFrames[i].getDataSession().getTitle();
+			this.comboData.addItem(name);
+		}
+		if (nbSession == 0) {
+			JOptionPane.showMessageDialog(this, Messages.getString("DistanceMatrixDialog.24"), //$NON-NLS-1$
+					Messages.getString("DistanceMatrixDialog.23"), JOptionPane.WARNING_MESSAGE); //$NON-NLS-1$
+			return;
+		}
+		this.comboData.setPreferredSize(new Dimension(100, 30));
+
+		panelData.add(comboData);
+
+		panelData.add(new JLabel(Messages.getString("DistanceMatrixDialog.12"))); //$NON-NLS-1$
+		JPanel panelSave = new JPanel(new BorderLayout());
+		JButton buttonBrowse = new JButton(Messages.getString("DistanceMatrixDialog.13")); //$NON-NLS-1$
+
+		buttonBrowse.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				JFileChooser fileChooser = new JFileChooser();
+				DataDesktopFrame[] desktopFrames = MainFrame.getInstance()
+						.getDesktop().getAllDataDesktopFrames();
+				int nbSessions = desktopFrames.length;
+				if (nbSessions > 0) {
+					String name = desktopFrames[comboData.getSelectedIndex()]
+							.getDataSession().getData().getDataName();
+					String path = "~/" + name + ".txt"; //$NON-NLS-1$
+					File f = new File(path);
+					fileChooser.setSelectedFile(f);
+				}
+				int returnVal = fileChooser
+						.showSaveDialog(DistanceMatrixDialog.this);
+				if (returnVal == JFileChooser.APPROVE_OPTION) {
+					String path = fileChooser.getSelectedFile().getPath();
+					textSave.setText(path);
+				}
+			}
+
+		});
+
+		panelSave.add(this.textSave, BorderLayout.CENTER);
+		panelSave.add(buttonBrowse, BorderLayout.EAST);
+		panelData.add(panelSave);
+
+		txtDate = new JTextField();
+		DateFormat formatDate=new SimpleDateFormat("ddMMyy");
+		txtDate.setText(formatDate.format(new Date()));
+		panelData.add(new JLabel(Messages.getString("DistanceMatrixDialog.15"))); //$NON-NLS-1$
+		panelData.add(txtDate);
+
+//		panelData.add(new JLabel(Messages.getString("DataToArffDialog.16"))); //$NON-NLS-1$
+//		JSpinner.NumberEditor spinnerEditor = new JSpinner.NumberEditor(
+//				this.spinner);
+//		this.spinner.setEditor(spinnerEditor);
+//		spinnerEditor.getModel().setMinimum(1);
+//		spinnerEditor.getModel().setMaximum(256);
+//		spinnerEditor.getModel().setStepSize(1);
+//		spinnerEditor.getModel().setValue(10);
+//		panelData.add(this.spinner);
+
+		JPanel panelOk = new JPanel();
+		JButton buttonOk = new JButton(Messages.getString("DistanceMatrixDialog.17")); //$NON-NLS-1$
+
+		buttonOk.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				buttonOk_actionPerformed();
+			}
+
+		});
+
+		panelOk.add(buttonOk);
+		mainPanel.add(panelData, BorderLayout.NORTH);
+		mainPanel.add(panelOk, BorderLayout.SOUTH);
+		this.setContentPane(mainPanel);
+		this.setTitle(Messages.getString("DistanceMatrixDialog.18")); //$NON-NLS-1$
+		this.setSize(350, 175);
+		this.setResizable(true);
+		this.setMaximizable(true);
+		this.setIconifiable(true);
+		this.setClosable(true);
+		this.setVisible(true);
+	}
+
+	/**
+	 * lance la création du fichier arff
+	 */
+	protected void buttonOk_actionPerformed() {
+		DataDesktopFrame[] desktopFrames = MainFrame.getInstance().getDesktop()
+				.getAllDataDesktopFrames();
+		int nbSessions = desktopFrames.length;
+		if (nbSessions == 0) {
+			JOptionPane.showMessageDialog(this,
+					Messages.getString("DistanceMatrixDialog.19"), Messages.getString("DataToArffDialog.20"), //$NON-NLS-1$ //$NON-NLS-2$
+					JOptionPane.WARNING_MESSAGE);
+			this.dispose();
+		} else if (this.textSave.getText().equals("")) { //$NON-NLS-1$
+			JOptionPane.showMessageDialog(this, Messages.getString("DataToArffDialog.22"), //$NON-NLS-1$
+					Messages.getString("DistanceMatrixDialog.23"), JOptionPane.WARNING_MESSAGE); //$NON-NLS-1$
+		} else {
+			Data data = desktopFrames[this.comboData.getSelectedIndex()]
+					.getDataSession().getData();
+
+			WriteDistancesPath.write(data, this.textSave.getText());
+			
+			JOptionPane.showMessageDialog(this,
+					Messages.getString("DistanceMatrixDialog.44"), Messages.getString("DataToArffDialog.45"), //$NON-NLS-1$ //$NON-NLS-2$
+					JOptionPane.INFORMATION_MESSAGE);
+			this.dispose();
+		}
+	}
+
+}

src/mustic/gui/dialog/classifier/ConstraintsSelectionDialog.java

@@ -60,8 +60,8 @@ import jcl.clustering.constraints.NbClusterConstraint;
 import jcl.data.Data;
 import jcl.utils.Images.StreamedImageReaderWrapper;
 import mustic.io.RawImage;
-import mustic.utils.CSVUtils;
 import mustic.utils.filters.CSVFileFilter;
+import mustic.utils.io.CSVUtils;
 
 /**
  * Dialog window that allow the user to generate a set of constraints
@@ -393,12 +393,12 @@ public class ConstraintsSelectionDialog extends JInternalFrame {
 	}
 
 	private void addConstraint(List<String> line, boolean isImageRelated) {
-		switch (Integer.parseInt(line.get(0))) {
+		switch (Integer.parseInt(line.get(line.size()-1))) {
 			case Constraint.MUST_LINK_TYPE :
 				try {
 					createMustLinkConstraint();
-					int index1 = getIndex(Integer.parseInt(line.get(1)), isImageRelated);
-					int index2 = getIndex(Integer.parseInt(line.get(2)), isImageRelated);
+					int index1 = getIndex(Integer.parseInt(line.get(0)), isImageRelated);
+					int index2 = getIndex(Integer.parseInt(line.get(1)), isImageRelated);
 					constraints.add(new MustLinkConstraint(index1, index2));
 					currentStep = -1;
 					// we update text fields
@@ -412,8 +412,8 @@ public class ConstraintsSelectionDialog extends JInternalFrame {
 				break;
 			case Constraint.CANNOT_LINK_TYPE :
 				try {
-					int index1 = getIndex(Integer.parseInt(line.get(1)), isImageRelated);
-					int index2 = getIndex(Integer.parseInt(line.get(2)), isImageRelated);
+					int index1 = getIndex(Integer.parseInt(line.get(0)), isImageRelated);
+					int index2 = getIndex(Integer.parseInt(line.get(1)), isImageRelated);
 					createCannotLinkConstraint();
 					constraints.add(new CannotLinkConstraint(index1, index2));
 					currentStep = -1;
@@ -428,7 +428,7 @@ public class ConstraintsSelectionDialog extends JInternalFrame {
 				break;
 			case Constraint.LABEL_TYPE :
 				try {
-					int index = getIndex(Integer.parseInt(line.get(1)), isImageRelated);
+					int index = getIndex(Integer.parseInt(line.get(0)), isImageRelated);
 					createLabelConstraint();
 					constraints.add(new LabelConstraint(index,
 							Integer.parseInt(line.get(2))));

src/mustic/gui/dialog/messages_en.properties

@@ -133,6 +133,21 @@ DataToArffDialog.44=The file was created successfull.
 DataToArffDialog.45=Successful
 DataToArffDialog.6=DataToArffDialog \=> Nr. sesiune 1 \= 
 DataToArffDialog.7=DataToArffDialog \=> Nr. sesiune 2 \= 
+DistanceMatrixDialog.0=Input Data \:
+DistanceMatrixDialog.12=Output file \:
+DistanceMatrixDialog.13=Browse
+DistanceMatrixDialog.15=Date (JJMMAA)\:
+DistanceMatrixDialog.17=OK
+DistanceMatrixDialog.18=Distance Matrix
+DistanceMatrixDialog.19=You must open a data before...
+DistanceMatrixDialog.20=Warning
+DistanceMatrixDialog.22=Select a data to save as.
+DistanceMatrixDialog.23=Warning
+DistanceMatrixDialog.24=There is no Data currently opened
+DistanceMatrixDialog.44=The file was created successfull.
+DistanceMatrixDialog.45=Successful
+DistanceMatrixDialog.6=DistanceMatrixDialog \=> Nr. sesiune 1 \= 
+DistanceMatrixDialog.7=DistanceMatrixDialog \=> Nr. sesiune 2 \= 
 FilterDialog.1=majority
 FilterDialog.2=Filter
 FilterDialog.3=\ Type of filter \: 

src/mustic/gui/messages_en.properties

@@ -161,6 +161,7 @@ MainFrame.30=Create a sub-image...
 MainFrame.301=Constraints
 MainFrame.302=Arff to Data
 MainFrame.303=Data to Arff
+MainFrame.304=Distance Matrix
 MainFrame.31=TransformationBmpToRoi...
 MainFrame.32=Image/Data/ARFF
 MainFrame.33=Image to ARFF...

src/mustic/gui/messages_fr.properties

@@ -161,6 +161,7 @@ MainFrame.30=Cr
 MainFrame.301=Contraintes
 MainFrame.302=Arff en Data
 MainFrame.303=Data en Arff
+MainFrame.304=Matrice des distances
 MainFrame.31=TransformationBmpEnRoi...
 MainFrame.32=Image/Data/ARFF
 MainFrame.33=Image en ARFF...

src/mustic/utils/CSVUtils.java → src/mustic/utils/io/CSVUtils.java

-package mustic.utils;
+package mustic.utils.io;
 
 import java.io.File;
 import java.io.FileNotFoundException;

src/mustic/utils/io/WriteDistancesPath.java

+package mustic.utils.io;
+
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.util.Iterator;
+
+import jcl.data.Data;
+import jcl.data.DataObject;
+
+public class WriteDistancesPath {
+
+	public WriteDistancesPath() {}
+
+
+	public static void write(Data data, String path) {
+		Iterator<DataObject> dataObjectIter_i = data.iterator();
+		DataObject dataObject1;
+		DataObject dataObject2;
+		double distance;
+		int i = 0;
+		PrintWriter writer = null;
+		try {
+			writer = new PrintWriter(path);
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+		}
+
+		writer.println("Number Of DataObjects: " + data.getNbObjects() + "\n\n");
+		
+		while(dataObjectIter_i.hasNext()) {
+			dataObject1 = dataObjectIter_i.next();
+			System.out.println("\t===> i =  " + i);
+			int j= 0;
+			Iterator<DataObject> dataObjectIter_j = data.iterator(i+1, data.getNbObjects());
+			while(dataObjectIter_j.hasNext()) {
+				//System.out.println("\t\t  " + i + " ===> j =  " + (i+1+j));
+				dataObject2 = dataObjectIter_j.next();
+				//distance = DistanceDTWMD.getInstance().compute(attMultiDimSequence1, attMultiDimSequence2, parameterDTW);
+				distance = dataObject1.distance(dataObject2);
+				writer.print(distance);
+				if (j + 1 < data.getNbObjects())
+					writer.print(",");
+				else
+					writer.println();
+				j++;
+			}
+			i++;
+		}
+		writer.flush();
+	}
+
+}

src/mustic/utils/dataExchange/DataArffExchange.java → src/mustic/utils/io/dataExchange/DataArffExchange.java

-package mustic.utils.dataExchange;
+package mustic.utils.io.dataExchange;
 
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -64,6 +64,8 @@ public class DataArffExchange {
 				writer.println("% \""+files+"\"");
 			}
 			writer.println("% >>>");
+			writer.println("% Nb objects : "+data.getNbObjects());
+			writer.println("% ");
 			writer.println(arffData);
 			writer.close();
 			out.close();
@@ -97,7 +99,7 @@ public class DataArffExchange {
 				Instances subSeq = new Instances(sequence.attribute(i).relation(), 0); 
 				double[] subValues = new double[((AttributeMultiDimSequence) attr).sequence[i].length];
 				for(int j = 0 ; j < ((AttributeMultiDimSequence) attr).sequence[i].length ; j++) {
-					subValues[i] = ((AttributeMultiDimSequence) attr).sequence[i][j];
+					subValues[j] = ((AttributeMultiDimSequence) attr).sequence[i][j];
 					subSeq.add(new DenseInstance(1.0, subValues));
 				}
 				values[i] = sequence.attribute(i).addRelation(subSeq);