switched from Constraints window to ImageAddon

src/mustic/gui/DataSession.java

@@ -19,6 +19,7 @@ import mustic.gui.panels.data.DataPanel;
 import mustic.io.ImageData;
 import mustic.models.gui.ClassificationModel;
 import mustic.models.gui.panels.ResultPanel;
+import mustic.utils.image.ImageDisplayer;
 import net.infonode.tabbedpanel.TabDragEvent;
 import net.infonode.tabbedpanel.TabEvent;
 import net.infonode.tabbedpanel.TabListener;

src/mustic/gui/ImageSession.java

@@ -15,6 +15,7 @@ import mustic.gui.panels.ImageInformationPanel;
 import mustic.gui.panels.ImagePanel;
 import mustic.gui.segmentation.SegmentationPanel;
 import mustic.io.RawImage;
+import mustic.utils.image.ImageManager;
 import net.infonode.tabbedpanel.TabFactory;
 import net.infonode.tabbedpanel.TabbedPanel;
 import net.infonode.tabbedpanel.titledtab.TitledTab;
@@ -245,7 +246,7 @@ public class ImageSession extends ImageManager {
 
 		if (displayEnable) {
 			((ImagePanel) this.displayer).applyMask(this.rawImage.getMask());
-			((ImagePanel) this.displayer).refresh();
+			((ImagePanel) this.displayer).refresh(true);
 		}
 	}
 

src/mustic/gui/MainFrame.java

@@ -131,7 +131,7 @@ public class MainFrame extends JFrame {
 	private JPanel	               	infosPanel;
 
 	/** boolean pour lier le birdview avec l'image active */
-	private boolean	               	linkToAllImages			= true;
+	private boolean	               	linkToAllImages			= false;
 
 	/** the project root for datas */
 	private DefaultMutableTreeNode	mDataProjectNode;
@@ -429,7 +429,8 @@ public class MainFrame extends JFrame {
 				openZip();
 			}
 		});
-		fileMenu.add(menuItemOpenZip);
+		//TODO regenerate the result import same as imageResultPanel
+		//fileMenu.add(menuItemOpenZip);
 
 		menuItemSave = new JMenuItem(Messages.getString("MainFrame.10")); //$NON-NLS-1$
 		menuItemSave.addActionListener(new ActionListener() {
@@ -493,7 +494,7 @@ public class MainFrame extends JFrame {
 					}
 			}
 		});
-		toolsMenu.add(menuItemClustering);
+//		toolsMenu.add(menuItemClustering);
 
 		menuItemSegmentation = new JMenuItem(Messages.getString("MainFrame.17")); //$NON-NLS-1$
 		menuItemSegmentation.addActionListener(new ActionListener() {
@@ -625,7 +626,7 @@ public class MainFrame extends JFrame {
 				createDistanceMatrix();
 			}
 		});
-		toolsMenu.add(menuDistanceMatrix);
+//		toolsMenu.add(menuDistanceMatrix);
 		
 		/** Menu to generate constraints from current image session */
 		menuConstraints = new JMenuItem(Messages.getString("MainFrame.301"));
@@ -635,7 +636,7 @@ public class MainFrame extends JFrame {
 				createConstraints();
 			}
 		});
-		toolsMenu.add(menuConstraints);
+//		toolsMenu.add(menuConstraints);
 		
 		menuBar.add(toolsMenu);
 
@@ -914,7 +915,8 @@ public class MainFrame extends JFrame {
 			}
 		});
 
-		menuResult.add(menuOpenRes);
+		//TODO regenerate the result import same as imageResultPanel
+		//menuResult.add(menuOpenRes);
 		menuResult.add(menuSaveRes);
 
 		menuRoiEval = new JMenuItem(Messages.getString("MainFrame.52")); //$NON-NLS-1$
@@ -1490,7 +1492,7 @@ public class MainFrame extends JFrame {
 		// =============== Creation of the Desktop ================
 		JPanel panel_desktop = new JPanel(new BorderLayout());
 		panel_desktop.setOpaque(false);
-		panel_desktop.setBorder(Borders.DIALOG_BORDER);
+		panel_desktop.setBorder(Borders.DIALOG);
 		panel_desktop.add(this.desktop);
 
 		sif_desktop = new SimpleInternalFrame(Messages.getString("MainFrame.72")); //$NON-NLS-1$
@@ -1504,7 +1506,7 @@ public class MainFrame extends JFrame {
 
 		JPanel panel = new JPanel(new BorderLayout());
 		panel.setOpaque(false);
-		panel.setBorder(Borders.DIALOG_BORDER);
+		panel.setBorder(Borders.DIALOG);
 		panel.add(pane);
 
 		// =============== Creation of the Progress Panel => South
@@ -1625,7 +1627,7 @@ public class MainFrame extends JFrame {
 		// =============== Creation of the Desktop ================
 		JPanel panel_desktop = new JPanel(new BorderLayout());
 		panel_desktop.setOpaque(false);
-		panel_desktop.setBorder(Borders.DIALOG_BORDER);
+		panel_desktop.setBorder(Borders.DIALOG);
 		panel_desktop.add(this.desktop);
 
 		sif_desktop = new SimpleInternalFrame(Messages.getString("MainFrame.72")); //$NON-NLS-1$
@@ -1639,7 +1641,7 @@ public class MainFrame extends JFrame {
 
 		JPanel panel = new JPanel(new BorderLayout());
 		panel.setOpaque(false);
-		panel.setBorder(Borders.DIALOG_BORDER);
+		panel.setBorder(Borders.DIALOG);
 		panel.add(pane);
 
 		// =============== Creation of the Progress Panel => South
@@ -2167,7 +2169,8 @@ public class MainFrame extends JFrame {
 			}
 		});
 
-		toolBar.add(jbOpen);
+		//TODO regenerate the result import same as imageResultPanel
+		//toolBar.add(jbOpen);
 		toolBar.add(jbSave);
 
 		JButton jbRoiEval = new JButton(new ImageIcon(getClass().getResource("/icons/icon_roi_eval.png"))); //$NON-NLS-1$
@@ -3007,44 +3010,44 @@ public class MainFrame extends JFrame {
 							// seg = segThread.getS();
 							// setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
 
-							Data data = MainFrame.this.currentImageSession.getImageData();
-
-							MainFrame.this.currentImageSession.setData(data);
-							ClassificationImage ci = new ClassificationImage(data, Messages.getString("MainFrame.190") //$NON-NLS-1$
-							        + ImageSession.nbClustering, true);
-
-							SegmentationResultPanel srp = new SegmentationResultPanel(classif, ci, MainFrame.this.currentImageSession.getRawImage(),
-							        seg, imageLabelisee, -1); // ImageSession.getSession(0).getImage(),ImageSession.getSession(0),
-							// scene);
-
-							Tab tabResult = ClassificationModel.createTab(Messages.getString("MainFrame.191") + ResultPanel.nbResult, //$NON-NLS-1$
-							                                              new ImageIcon(getClass()
-							                                                      .getResource("/icons/actions/document-open-result.png")), //$NON-NLS-1$
-							                                              srp, true);
-							ci.tabbedPane.addTab(tabResult);
-							tabResult.setSelected(true);
-
-							SegmentationResultPanel irp = (SegmentationResultPanel) ci.tabbedPane.getTabAt(ci.tabbedPane.getTabCount() - 1)
-							        .getContentComponent();
-							irp.historique.addInfosln("******** Classification apres segmentation *********"); //$NON-NLS-1$
-
-							irp.historique.addInfosln(Messages.getString("MainFrame.0") //$NON-NLS-1$
-							        + classif.getData().getDataName() + "\n"); //$NON-NLS-1$
-
-							// irp.historique.addInfosln(ci.().getParameters().toString());
-
-							final TitledTab tab = new TitledTab(Messages.getString("MainFrame.196") //$NON-NLS-1$
-							        + ImageSession.nbClustering++, null, ci.tabbedPane, new JPanel());
-							tab.setFocusableComponent(null);
-
-							MainFrame.this.currentImageSession.getWorkSpace().addTab(tab);
-							MainFrame.this.currentImageSession.getWorkSpace().setSelectedTab(tab);
-
-							try {
-								MainFrame.this.currentImageSession.associatedFrame.setMaximum(true);
-							} catch (PropertyVetoException e1) {}
-
-							irp.updateImageColors();
+//							Data data = MainFrame.this.currentImageSession.getImageData();
+//
+//							MainFrame.this.currentImageSession.setData(data);
+//							ClassificationImage ci = new ClassificationImage(data, Messages.getString("MainFrame.190") //$NON-NLS-1$
+//							        + DataSession.nbClustering, true);
+//
+//							SegmentationResultPanel srp = new SegmentationResultPanel(classif, ci, MainFrame.this.currentImageSession.getRawImage(),
+//							        seg, imageLabelisee, -1); // ImageSession.getSession(0).getImage(),ImageSession.getSession(0),
+//							// scene);
+//
+//							Tab tabResult = ClassificationModel.createTab(Messages.getString("MainFrame.191") + ResultPanel.nbResult, //$NON-NLS-1$
+//							                                              new ImageIcon(getClass()
+//							                                                      .getResource("/icons/actions/document-open-result.png")), //$NON-NLS-1$
+//							                                              srp, true);
+//							ci.tabbedPane.addTab(tabResult);
+//							tabResult.setSelected(true);
+//
+//							SegmentationResultPanel irp = (SegmentationResultPanel) ci.tabbedPane.getTabAt(ci.tabbedPane.getTabCount() - 1)
+//							        .getContentComponent();
+//							irp.historique.addInfosln("******** Classification apres segmentation *********"); //$NON-NLS-1$
+//
+//							irp.historique.addInfosln(Messages.getString("MainFrame.0") //$NON-NLS-1$
+//							        + classif.getData().getDataName() + "\n"); //$NON-NLS-1$
+//
+//							// irp.historique.addInfosln(ci.().getParameters().toString());
+//
+//							final TitledTab tab = new TitledTab(Messages.getString("MainFrame.196") //$NON-NLS-1$
+//							        + ImageSession.nbClustering++, null, ci.tabbedPane, new JPanel());
+//							tab.setFocusableComponent(null);
+//
+//							MainFrame.this.currentImageSession.getWorkSpace().addTab(tab);
+//							MainFrame.this.currentImageSession.getWorkSpace().setSelectedTab(tab);
+//
+//							try {
+//								MainFrame.this.currentImageSession.associatedFrame.setMaximum(true);
+//							} catch (PropertyVetoException e1) {}
+//
+//							irp.updateImageColors();
 
 						}
 						else {
@@ -3736,8 +3739,8 @@ public class MainFrame extends JFrame {
 		String resultPath = "/home/baptiste/A2CNES/results/";
 		String testResultPath = "/home/baptiste/A2CNES/Train_results/";
 		
-		Data dataTrain = getDataFromFile(dataPath+datasetPath+"/train/"+datasetName+".data", '\t', "train");
-		Data dataTest = getDataFromFile(dataPath+datasetPath+"/test/"+datasetName+".data", '\t', "test");
+		Data dataTrain = getDataFromFile(dataPath+datasetPath+"/train/"+datasetName+".data", '\t', "train", null);
+		Data dataTest = getDataFromFile(dataPath+datasetPath+"/test/"+datasetName+".data", '\t', "test", null);
 		
 
 //		AttributeMultiDimSequence.setMode(AttributeMultiDimSequence.EUCLIDIEN);
@@ -3781,38 +3784,39 @@ public class MainFrame extends JFrame {
 		// we search for all constraints files
 			
 // <<<< START FOR PARAM config
-		for (int i = 0 ; i < 10 ; i++) {
-			HybridClassification classif = (HybridClassification) classification.clone();
-			if (i % 2 == 1 ) {
-				classification.setParameters(nInf, nSup, minC, 0.4, 0.6, pcr);
-			}
-			if (i <= 5)
-				classif.addAgent(new ParametersKmeans(8, 10, weights), dataTrain);
-			if (i <= 7)
-				classif.addAgent(new ParametersKmeans(10, 10, weights), dataTrain);
-			classif.addAgent(new ParametersKmeans(13, 10, weights), dataTrain);
-			classif.addAgent(new ParametersKmeans(16, 10, weights), dataTrain);
-			if (i >= 2)
-				classif.addAgent(new ParametersKmeans(19, 10, weights), dataTrain);
-			if (i >= 4)
-				classif.addAgent(new ParametersKmeans(22, 10, weights), dataTrain);
-//			classif.addAgent(new ParametersKmeans(3, 10, weights), dataTest);
-//			classif.addAgent(new ParametersKmeans(4, 10, weights), dataTest);
-//			classif.addAgent(new ParametersKmeans(6, 10, weights), dataTest);
-
-			classif.setName(testResultPath+datasetName+"/clusteing"+i);
-			classif.setData(dataTrain);
-//// >>>> END FOR PARAM config1
 //		for (int i = 0 ; i < 10 ; i++) {
 //			HybridClassification classif = (HybridClassification) classification.clone();
-////			classif.addAgent(new ParametersKmeans(10, 15, weights), dataTest);
-//			classif.addAgent(new ParametersKmeans(13, 10, weights), dataTest);
-//			classif.addAgent(new ParametersKmeans(16, 10, weights), dataTest);
-//			classif.addAgent(new ParametersKmeans(19, 10, weights), dataTest);
-//			
-//			classif.setName(resultPath+datasetPath+"/clustering"+i);
-//			classif.setData(dataTest);
-//// >>>> REPLACE PARAM
+//			if (i % 2 == 1 ) {
+//				classification.setParameters(nInf, nSup, minC, 0.4, 0.6, pcr);
+//			}
+//			if (i <= 5)
+//				classif.addAgent(new ParametersKmeans(8, 25, weights), dataTrain);
+//			if (i <= 7)
+//				classif.addAgent(new ParametersKmeans(10, 25, weights), dataTrain);
+//			classif.addAgent(new ParametersKmeans(13, 25, weights), dataTrain);
+//			classif.addAgent(new ParametersKmeans(16, 25, weights), dataTrain);
+//			if (i >= 2)
+//				classif.addAgent(new ParametersKmeans(19, 25, weights), dataTrain);
+//			if (i >= 4)
+//				classif.addAgent(new ParametersKmeans(22, 25, weights), dataTrain);
+////			classif.addAgent(new ParametersKmeans(3, 10, weights), dataTest);
+////			classif.addAgent(new ParametersKmeans(4, 10, weights), dataTest);
+////			classif.addAgent(new ParametersKmeans(6, 10, weights), dataTest);
+//
+//			classif.setName(testResultPath+datasetName+"/clusteing"+i);
+//			classif.setData(dataTrain);
+// >>>> END FOR PARAM config1
+		for (int i = 0 ; i < 10 ; i++) {
+			HybridClassification classif = (HybridClassification) classification.clone();
+//			classif.addAgent(new ParametersKmeans(10, 25, weights), dataTest);
+			classif.addAgent(new ParametersKmeans(13, 25, weights), dataTest);
+			classif.addAgent(new ParametersKmeans(16, 25, weights), dataTest);
+			classif.addAgent(new ParametersKmeans(19, 25, weights), dataTest);
+//			classif.addAgent(new ParametersKmeans(22, 25, weights), dataTest);
+			
+			classif.setName(resultPath+datasetPath+"/clustering"+i);
+			classif.setData(dataTest);
+// >>>> REPLACE PARAM
 			Thread t = null;
 
 			ClassificationImage classificationImage = new ClassificationImage(testSession,
@@ -3879,9 +3883,11 @@ public class MainFrame extends JFrame {
 //				Data currentData = (Data) dataTest.clone();
 //				currentData.updateAndSetConstraintsToSample(constraints);
 //				
-//				classif.addAgent(new ParametersKmeans(4, 15, weights), currentData);
-//				classif.addAgent(new ParametersKmeans(6, 15, weights), currentData);
-//				classif.addAgent(new ParametersKmeans(8, 15, weights), currentData);
+//				classif.addAgent(new ParametersKmeans(10, 25, weights), currentData);
+//				classif.addAgent(new ParametersKmeans(13, 25, weights), currentData);
+//				classif.addAgent(new ParametersKmeans(16, 25, weights), currentData);
+//				classif.addAgent(new ParametersKmeans(19, 25, weights), currentData);
+//				classif.addAgent(new ParametersKmeans(22, 25, weights), currentData);
 //				
 //				classif.setName(resultPath+datasetName+"/"+ 
 //						ImageHelper.stripExtension(filename)+ 
@@ -3890,9 +3896,9 @@ public class MainFrame extends JFrame {
 //				
 //				Thread t = null;
 //	
-//				ClassificationImage classificationImage = new ClassificationImage(currentData,
-//				        Messages.getString("ClassifierPanel.73") + DataSession.nbClustering, //$NON-NLS-1$
-//				        true);
+//				ClassificationImage classificationImage = new ClassificationImage(testSession,
+//		        Messages.getString("ClassifierPanel.73") + DataSession.nbClustering, //$NON-NLS-1$
+//		        true);
 //	
 //	
 //				t = new ClassificationThread(classif, classificationImage.getProgressBar(), 
@@ -3908,7 +3914,6 @@ public class MainFrame extends JFrame {
 //				} catch (PropertyVetoException e) {
 //					e.printStackTrace();
 //				}
-//				classificationImage.toFront();
 //				classificationImage.setVisible(true);
 //	
 //				threadList.add(t);
@@ -3946,7 +3951,7 @@ public class MainFrame extends JFrame {
 		ClassificationFrame.getInstance().dispose();
 	}
 	
-	private Data getDataFromFile(String path, char separator, String name) {
+	private Data getDataFromFile(String path, char separator, String name, String mask) {
 
 		Data data = null;
 		// we create the two data session
@@ -3955,12 +3960,20 @@ public class MainFrame extends JFrame {
 			List<DataObject> result = new ArrayList<DataObject>();
 			
 			CSVUtils reader = null;
+			CSVUtils maskReader = null;
 	        try {
 	        	File file = new File(path);
 				reader = new CSVUtils(file, separator);
 				List<String> line;
+				if (mask != null) {
+					maskReader = new CSVUtils(new File(mask), separator);
+				}
+				List<String> maskLine = null;
 				while((line = reader.readNext()) != null) {
-					extractObjectFromLine(result, line, 1);
+					if (mask != null) {
+						maskLine = maskReader.readNext();
+					}
+					extractObjectFromLine(result, line, 3, maskLine);
 				}
 			} catch (FileNotFoundException e) {
 				e.printStackTrace();
@@ -3985,10 +3998,14 @@ public class MainFrame extends JFrame {
 	 * @param line
 	 * 			the line to interpret
 	 */
-	private void extractObjectFromLine(List<DataObject> list, List<String> line, int featureNb) {
+	private void extractObjectFromLine(List<DataObject> list, List<String> line, int featureNb, List<String> maskLine) {
 		DataObject obj = new DataObject(1);	
 		double[][] seq = new double[line.size()/featureNb][];
 		for (int i = 0 ; i < line.size()/featureNb ; i++) {
+			if (maskLine != null) {
+				if(Integer.parseInt(maskLine.get(i)) == 0) 
+					continue;
+			} 
 			seq[i] = new double[featureNb];
 			for (int j = 0 ; j < featureNb ; j++) {
 				seq[i][j] = Double.parseDouble(line.get(i*featureNb + j));

src/mustic/gui/dialog/RgbBandChooserInternalFrame.java

@@ -50,8 +50,8 @@ public class RgbBandChooserInternalFrame extends JInternalFrame {
 	public RgbBandChooserInternalFrame(final RawImage rawImage) {
 		super();
 
-		this.scaledMax = rawImage.getScaledMaxValues();
-		this.scaledMin = rawImage.getScaledMinValues();
+		this.scaledMax = rawImage.getScaledMaxValues().clone();
+		this.scaledMin = rawImage.getScaledMinValues().clone();
 		this.redComboBox = new JComboBox<String>();
 		this.redMin = new JTextArea();
 		this.redMax = new JTextArea();

src/mustic/gui/dialog/SequenceDialog.java

@@ -301,10 +301,10 @@ public class SequenceDialog extends JDialog {
 	 * @throws FormatException 
 	 * 			if the images don't have the same dimensions
 	 */
-	public Vector<String> getSequenceData() throws FormatException {
+	public Vector<RawImage> getSequenceData() throws FormatException {
 		int nb = this.dlmSeq.getSize();
 		Donnee donnee;
-		Vector<String> paths = new Vector<String>();
+		Vector<RawImage> paths = new Vector<RawImage>();
 		
 		if (nb > 0) {
 			ImageDesktopFrame[] desktopFrames = MainFrame.getInstance().getDesktop()
@@ -314,7 +314,7 @@ public class SequenceDialog extends JDialog {
 			for (int i = 0; i < nb; i++) {
 				donnee = (Donnee) this.dlmSeq.getElementAt(i);
 				paths.add(desktopFrames[donnee.index].getImageSession()
-						.getRawImage().getPath());
+						.getRawImage());
 			}
 		}
 		

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

@@ -26,19 +26,19 @@ public class ConstraintsColor extends JDialog {
 	private static final long serialVersionUID = 1L;
 
 	/** constraints colors */
-	private Color 					mustLinkColor 			 			= new Color(124, 252, 0);
-	private Color 					cannotLinkColor 					= new Color(255, 0, 255);
-	private Vector<Color> 			labelConstraintColor 				= new Vector<Color>();
+	private Color 							mustLinkColor 			 			= new Color(124, 252, 0);
+	private Color 							cannotLinkColor 					= new Color(255, 0, 255);
+	private Vector<Color> 					labelConstraintColor 				= new Vector<Color>();
 
 	/** constraints buttons */
-	private JButton 				jb_mustLinkChooseColor 				= new JButton();
-	private JButton 				jb_cannotLinkChooseColor 			= new JButton();
-	private Vector<JButton> 		jb_labelConstraintClassChooseColor	= new Vector<JButton>();
+	private JButton 						jb_mustLinkChooseColor 				= new JButton();
+	private JButton 						jb_cannotLinkChooseColor 			= new JButton();
+	private Vector<JButton> 				jb_labelConstraintClassChooseColor	= new Vector<JButton>();
 
 	/** dynamic JPanel Colors of Label Constraints Classes*/
-	JPanel 									labelColorConstraintPanel			= new JPanel(new GridLayout(0,1));
+	private JPanel							labelColorConstraintPanel			= new JPanel(new GridLayout(0,1));
 
-	private ConstraintsSelectionDialog		dialog = null;
+	private ConstraintsSelectionFrame		dialog = null;
 
 	/**
 	 * @brief Constructor dialog window that allows the user to change the color of the constraints 
@@ -47,7 +47,7 @@ public class ConstraintsColor extends JDialog {
 	 * @param colorCL
 	 * @param colorVectorLabel
 	 */
-	public ConstraintsColor(ConstraintsSelectionDialog d, Color colorML, Color colorCL, Vector<Color> colorVectorLabel) {
+	public ConstraintsColor(ConstraintsSelectionFrame d, Color colorML, Color colorCL, Vector<Color> colorVectorLabel) {
 		this.dialog = d;
 		this.mustLinkColor = colorML;
 		this.cannotLinkColor = colorCL;

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

@@ -24,12 +24,12 @@ import mustic.utils.filters.CSVFileFilter;
  */
 public class ExportConstraintsTask extends SwingWorker<Void, Void> 
 {
-	ConstraintsSelectionDialog dialog = null;
+	ConstraintsSelectionFrame dialog = null;
 	static final private int incrementation = 10;
 	static int progress = 0;	
 	static int jalon = incrementation; // avoid too many progress update
 			
-	public ExportConstraintsTask (ConstraintsSelectionDialog dialog) 
+	public ExportConstraintsTask (ConstraintsSelectionFrame dialog) 
 	{
 		this.dialog = dialog;
 	}

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

@@ -21,12 +21,12 @@ import mustic.utils.io.CSVUtils;
  */
 public class ImportConstraintsTask extends SwingWorker<Void, Void> 
 {
-	ConstraintsSelectionDialog dialog = null;
+	ConstraintsSelectionFrame dialog = null;
 	static final private int incrementation = 10;
 	static int progress = 0;	
 	static int jalon = incrementation; // avoid too many progress update
 			
-	public ImportConstraintsTask (ConstraintsSelectionDialog dialog) 
+	public ImportConstraintsTask (ConstraintsSelectionFrame dialog) 
 	{
 		this.dialog = dialog;
 	}
@@ -108,8 +108,7 @@ public class ImportConstraintsTask extends SwingWorker<Void, Void>
 					}