temporary save

src/mustic/gui/MainFrame.java

@@ -3395,7 +3395,7 @@ public class MainFrame extends JFrame {
 	}
 
 	private void toolsMenuArffToData() {
-		DataToArffDialog dialog = new DataToArffDialog();
+		ArffToDataDialog dialog = new ArffToDataDialog();
 		this.desktop.add(dialog);
 		dialog.toFront();
 	}

src/mustic/gui/dialog/ArffToDataDialog.java

@@ -9,6 +9,7 @@ import java.awt.image.BufferedImage;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
+import java.util.List;
 
 import javax.imageio.ImageIO;
 import javax.swing.JButton;
@@ -19,6 +20,11 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTextField;
 
+import jcl.data.Data;
+import jcl.data.DataObject;
+import jcl.data.SimpleData;
+import mustic.utils.io.dataExchange.DataArffExchange;
+
 //import mustic.io.geotiff.GEOTiffImage;
 
 /**
@@ -98,40 +104,20 @@ public class ArffToDataDialog extends JInternalFrame {
 
 	protected void buttonOk_actionPerformed() {
 		try {
-			FileReader fr = new FileReader(new File(this.textFile.getText()));
-
-			BufferedReader br = new BufferedReader(fr);
-			String line = null;
-
-			BufferedImage buff=null;
-			String sdim = Messages.getString("ArffToDataDialog.9"); //$NON-NLS-1$
-			while ((line = br.readLine()) != null) {
-				if (line.startsWith(sdim)) {
-					String dim = line.substring(sdim.length());
-					String dimension[] = dim.split(","); //$NON-NLS-1$
-					int w = Integer.parseInt(dimension[0]);
-					int h = Integer.parseInt(dimension[1]);
-
-					buff=new BufferedImage(w,h,BufferedImage.TYPE_3BYTE_BGR );
-					
-				} else {
-					String val[] = line.split(","); //$NON-NLS-1$
-					if (val.length >= 5) {
-						int x = Integer.parseInt(val[0]);
-						int y = Integer.parseInt(val[1]);
-						buff.setRGB(x, y, (int) (Double.parseDouble(val[2])*256*256+ Double.parseDouble(val[3])*256+ Double.parseDouble(val[4])));
-
-					}
-				}
+			Object[] result = DataArffExchange.arffToData(this.textFile.getText());
+			
+			if(result != null) {
+				Data data = new SimpleData((List<DataObject>) result[1]);
+				
+				JOptionPane.showMessageDialog(this,
+						Messages.getString("ArffToDataDialog.15") + this.textData.getText(), Messages.getString("ArffToDataDialog.16"), //$NON-NLS-1$ //$NON-NLS-2$
+						JOptionPane.INFORMATION_MESSAGE);
+			} else {
+				JOptionPane.showMessageDialog(this,
+						"File selected isn't supported", Messages.getString("ArffToDataDialog.4"), //$NON-NLS-1$ //$NON-NLS-2$
+						JOptionPane.WARNING_MESSAGE);
 			}
 
-			String name = this.textData.getText();
-			File outputfile = new File(name);
-			ImageIO.write(buff, "png", outputfile);
-
-			JOptionPane.showMessageDialog(this,
-					Messages.getString("ArffToDataDialog.15") + this.textData.getText(), Messages.getString("ArffToDataDialog.16"), //$NON-NLS-1$ //$NON-NLS-2$
-					JOptionPane.INFORMATION_MESSAGE);
 			this.dispose();
 		} catch (Exception e) {
 			JOptionPane.showMessageDialog(this,

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

@@ -142,15 +142,12 @@ public class AgentDialog extends JDialog {
 
 			DataDesktopFrame[] desktopFrames = MainFrame.getInstance().getDesktop().getAllDataDesktopFrames();
 			int nbSessions = desktopFrames.length;
-			//TODO
 			if (nbSessions > 0 &&
 					this.classifierPanel.getApproachPanel().getDataComboBox().getSelectedIndex() <= nbSessions
-					//&& this.classifierPanel.getApproachPanel().getMonodateRadioButton().isSelected()
 					) {
 				int index = this.classifierPanel.getApproachPanel().getDataComboBox().getSelectedIndex();
 				if (index < nbSessions) { // choix de données existantes
 
-					
 					DataSession img = desktopFrames
 							[this.classifierPanel.getApproachPanel().getDataComboBox().getSelectedIndex()].getDataSession();
 
@@ -158,18 +155,7 @@ public class AgentDialog extends JDialog {
 					this.imgdata = (ImageData) img.getData();
 					this.imgdata.setDataFilesName(imgdata.getDataFilesName());
 
-				} else if (index == nbSessions) { // séquence d'images TODO : sortir
-
-					
-					DataSession img = desktopFrames[this.classifierPanel.sequenceDialog.getFirstIndex()].getDataSession();
-					this.imgdata = img.getData();
-					try {
-						this.imgdata.setSequence(this.classifierPanel.sequenceDialog.getSequenceData());
-					} catch (FormatException e1) {
-						e1.printStackTrace();
-					}
-
-				}
+				} 
 
 				/*
 				 * 

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

 package mustic.utils.io.dataExchange;
 
+import java.io.BufferedReader;
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
+import java.io.FileReader;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Iterator;
+import java.util.List;
 
 import jcl.data.Data;
 import jcl.data.DataObject;
 import jcl.data.attribute.AttributeMultiDimSequence;
 import jcl.data.attribute.AttributeNumerical;
 import jcl.data.attribute.AttributeSequence;
+import jcl.data.attribute.AttributeSymbolicCategorial;
 import weka.core.Attribute;
 import weka.core.DenseInstance;
+import weka.core.Instance;
 import weka.core.Instances;
+import weka.core.converters.ArffLoader.ArffReader;
 
 /**
- * Class to import/export ARFF files from/to Data objects
+ * Class to import/export ARFF files from/to Data objects.
+ * This implementation is not exhaustive. It is designed to handle images
+ * with multi-mono temporal formats, but it might be used/extended for other cases.
+ * 
+ * The import format is based on the export one, so some incompatibilities might occurs.
  * 
  * @author Baptiste LAFABREGUE
  *
  */
 public class DataArffExchange {
 	
+	/**
+	 * Write a Data into a file in respect of the arff format
+	 * 
+	 * @param path
+	 * 			the path of the file to write
+	 * @param data
+	 * 			the data to write
+	 */
 	public static void dataToArff(String path, Data data) {
 		System.out.println("__________________________________________________________________________________________\n"); //$NON-NLS-1$
 		System.out.println("Write \""+data.getDataName()+"\" to file : " + path); //$NON-NLS-1$
@@ -76,10 +95,86 @@ public class DataArffExchange {
 		}
 	}
 
-	public static DataObject[] arffToData(String path) {
-		return null;		
+	/**
+	 * Return a set of DataObjects that is stored in an arff file.
+	 * The file should respect only one additional format constraint, 
+	 * that the first attribute is the index.
+	 * 
+	 * @param path
+	 * 			the path of the arff file
+	 * @return an Object array of size two :
+	 * 			- at index 0 : the set on indexes (List<Integer>)
+	 * 			- at index 1 : the set of DataObjects (List<DataObject>)
+	 */
+	public static Object[] arffToData(String path) {
+		System.out.println("__________________________________________________________________________________________\n"); //$NON-NLS-1$
+		System.out.println("Read \""+path+"\" to new Data "); //$NON-NLS-1$
+		System.out.println("__________________________________________________________________________________________"); //$NON-NLS-1$
+		
+		Object[] result = new Object[2];
+		List<DataObject> dataObjects = new ArrayList<DataObject>();
+		List<Integer> indexes = new ArrayList<Integer>();
+		try {
+			BufferedReader reader = new BufferedReader(new FileReader(new File(path)));
+			ArffReader arff = new ArffReader(reader, 1000);			
+			Instances data = arff.getStructure();
+			data.setClassIndex(0);
+			
+			Instance inst;
+			while ((inst = arff.readInstance(data)) != null) {
+				DataObject obj = new DataObject(inst.numAttributes() - 1);				
+				// the first attribute is ignored because it is the index
+				for(int i = 1 ; i < inst.numAttributes() ; i++) {
+					obj.setAttribute(i-1, getAttribute(inst, i));
+				}				
+				dataObjects.add(obj);
+				
+				indexes.add((int) inst.value(0));
+			}
+			
+			reader.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		result[0] = indexes;
+		result[1] = dataObjects;
+
+		return result;		
 	}
 	
+
+	private static jcl.data.attribute.Attribute getAttribute(Instance inst, int index) {
+		switch(inst.attribute(index).type()) {
+			case Attribute.NUMERIC :
+				return new AttributeNumerical(inst.value(index));
+			case Attribute.STRING :
+				return new AttributeSymbolicCategorial(inst.stringValue(index));
+			case Attribute.RELATIONAL : 
+				if (inst.attribute(index).relation().numAttributes() > 0 &&
+						inst.attribute(index).relation().attribute(0).isRelationValued()) {
+					// MultiDimSequence case, where we have a sub relation in the relation
+					double[][] seq = new double[inst.attribute(index).relation().numAttributes()][];
+					for (int i = 0 ; i < inst.attribute(index).relation().numAttributes() ; i++) {
+						Instances instances = inst.relationalValue(index);
+						seq[i] = new double[instances.attribute(0).relation().numAttributes()];
+						
+						for(int j = 0 ; j < instances.attribute(0).relation().numAttributes() ; j++) {
+							seq[i][j] = instances.get(j).value(0);
+						}
+					}
+					return new AttributeMultiDimSequence(seq);
+				} else {
+					// Sequence case, where we only one relation layer
+					double[] seq = new double[inst.attribute(index).relation().numAttributes()];
+					for (int i = 0 ; i < inst.attribute(index).relation().numAttributes() ; i++) {
+							seq[i] = inst.value(i);
+					}
+					return new AttributeSequence(seq);
+				}
+		}
+		return null;
+	}
+
 	private static double getArffInstance(jcl.data.attribute.Attribute attr, Instances arffData, int attrIndex) {
 		if (attr instanceof AttributeSequence) {
 			Instances sequence = new Instances(arffData.attribute(attrIndex).relation(), 0);