fix about mask application

src/mustic/gui/ImageSession.java

@@ -269,8 +269,10 @@ public class ImageSession {
 			this.rawImage.setMask(file);
 		}
 
-		this.mImagePanel.applyMask(this.rawImage.getMask());
-		this.mImagePanel.doZoomOp();
+		if (displayEnable) {
+			this.mImagePanel.applyMask(this.rawImage.getMask());
+			this.mImagePanel.doZoomOp();
+		}
 	}
 
 	/**

src/mustic/gui/dialog/SequenceDialog.java

@@ -31,6 +31,7 @@ import javax.swing.event.ListSelectionListener;
 
 import loci.formats.FormatException;
 import mustic.gui.ImageDesktopFrame;
+import mustic.gui.ImageSession;
 import mustic.gui.MainFrame;
 import mustic.io.PictureTool;
 import mustic.io.RawImage;
@@ -305,9 +306,9 @@ public class SequenceDialog extends JDialog {
 	}
 
 	/**
-	 * Renvoie la donnée correspondant à la sequence d'images
+	 * Return the list of image path constituting the selected sequence
 	 * 
-	 * @return data
+	 * @return the list of ordered file path
 	 * 
 	 * @throws FormatException 
 	 * 			if the images don't have the same dimensions
@@ -331,6 +332,33 @@ public class SequenceDialog extends JDialog {
 		
 		return paths;
 	}
+	
+	/**
+	 * Return the list of image sessions constituting the selected sequence
+	 * 
+	 * @return the list of ordered session
+	 * 
+	 * @throws FormatException 
+	 * 			if the images don't have the same dimensions
+	 */
+	public Vector<ImageSession> getSequenceSessions() throws FormatException {
+		int nb = this.dlmSeq.getSize();
+		Donnee donnee;
+		Vector<ImageSession> paths = new Vector<ImageSession>();
+		
+		if (nb > 0) {
+			ImageDesktopFrame[] desktopFrames = MainFrame.getInstance().getDesktop()
+					.getAllImageDesktopFrames();
+			// int nbSessions = desktopFrames.length;			
+
+			for (int i = 0; i < nb; i++) {
+				donnee = (Donnee) this.dlmSeq.getElementAt(i);
+				paths.add(desktopFrames[donnee.index].getImageSession());
+			}
+		}
+		
+		return paths;
+	}
 
 	/**
 	 * Renvoie les indices de chaque image de la sequence

src/mustic/gui/panels/BirdViewPanel.java

@@ -969,6 +969,19 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 			}
 		}
 
+		session.getBirdViewPanel().selArea.x = (int) Math.round(rx / xfact);
+		session.getBirdViewPanel().selArea.y = (int) Math.round(ry / yfact);
+		session.getBirdViewPanel().selArea.width = this.selArea.width;
+		session.getBirdViewPanel().selArea.height = this.selArea.height;
+		
+		session.getBirdViewPanel().xsave = (int) Math.round(rx / xfact);
+		session.getBirdViewPanel().ysave = (int) Math.round(ry / yfact);
+		session.getBirdViewPanel().xxsave = realarea.x;
+		session.getBirdViewPanel().yysave = realarea.y;
+		
+		session.getBirdViewPanel().rxsave = rx;
+		session.getBirdViewPanel().rysave = ry;
+		
 		session.getRawImage().afficheRoi(image, rx, ry);
 		session.getImagePanel().setImage(image);
 
@@ -980,18 +993,6 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 		for (SegmentationPanel segPanel : session.getSegPanels()) {
 			segPanel.setImage(image, rx, ry);
 		}
-		session.getBirdViewPanel().selArea.x = (int) Math.round(rx / xfact);
-		session.getBirdViewPanel().selArea.y = (int) Math.round(ry / yfact);
-		session.getBirdViewPanel().selArea.width = this.selArea.width;
-		session.getBirdViewPanel().selArea.height = this.selArea.height;
-
-		session.getBirdViewPanel().xsave = (int) Math.round(rx / xfact);
-		session.getBirdViewPanel().ysave = (int) Math.round(ry / yfact);
-		session.getBirdViewPanel().xxsave = realarea.x;
-		session.getBirdViewPanel().yysave = realarea.y;
-
-		session.getBirdViewPanel().rxsave = rx;
-		session.getBirdViewPanel().rysave = ry;
 		//
 
 	}

src/mustic/gui/panels/ImagePanel.java

@@ -10,7 +10,6 @@ import javax.swing.*;
 
 import jcl.data.mask.Mask;
 import mustic.gui.*;
-import mustic.io.MusticImageMask;
 import mustic.io.RawImage;
 import mustic.io.roi.RegionOfInterest;
 import mustic.utils.filters.ZipFileFilter;
@@ -105,6 +104,9 @@ public class ImagePanel extends JPanel {
 		this.mImageLabel.addMouseListener(new MouseAdapter() {
 			@Override
 			public void mouseClicked(MouseEvent e) {
+				if(mImageLabel.getIcon() == null)
+					return;
+				
 				double w1 = mImageLabel.getWidth();
 				double w2 = mImageLabel.getIcon().getIconWidth();
 
@@ -742,6 +744,10 @@ public class ImagePanel extends JPanel {
 		@Override
 		public void mouseClicked(MouseEvent e) {
 			if (e.getButton() == MouseEvent.BUTTON1) {
+				// if the display is disabled we don't take it in consideration
+				if (!MainFrame.getInstance().getCurrentImageSession().isDisplayEnable()) {
+					return;
+				}
 
 				// Toute les JInternalFrames afiche sur le MusticDesktop
 				ImageDesktopFrame[] jInternalFrames = MainFrame.getInstance().getDesktop().getAllImageDesktopFrames();
@@ -823,6 +829,9 @@ public class ImagePanel extends JPanel {
 
 		@Override
 		public void mousePressed(MouseEvent e) {
+			if (ImagePanel.this.mScreenImage == null) {
+				return;
+			}
 			// ici on receptionne les evenements de clic de la souris sur
 			// l'image satelitte
 			int x = (int) ((e.getX() - (int) ((ImagePanel.this.mImageLabel.getWidth() - (ImagePanel.this.mScreenImage.getWidth() * ImagePanel.this.mZoomRate)) / 2)) / ImagePanel.this.mZoomRate);

src/mustic/gui/panels/data/DataConstructPanel.java

@@ -4,6 +4,8 @@ import java.awt.BorderLayout;
 import java.awt.FlowLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JButton;
@@ -14,8 +16,10 @@ import com.l2fprod.common.swing.JTaskPane;
 import com.l2fprod.common.swing.JTaskPaneGroup;
 
 import jcl.data.mask.Mask;
+import jcl.data.sampling.ImageSampler;
 import jcl.data.sampling.Sampler;
 import mustic.gui.ImageDesktopFrame;
+import mustic.gui.ImageSession;
 import mustic.gui.MainFrame;
 import mustic.gui.dialog.SequenceDialog;
 import mustic.gui.panels.data.components.SamplingSelectionPanel;
@@ -39,6 +43,8 @@ public class DataConstructPanel extends JPanel implements ToUpdateObject {
 	public static int SEGMENTATION_SOURCE_TYPE = 1;
 	
 	private Vector<String> 			filesPaths		= null;
+
+	private Vector<ImageSession> 	imageSessions	= null;
 	
 	/** Les menus deroulants */
 	private JTaskPane 				taskPane 		= new JTaskPane();
@@ -119,6 +125,21 @@ public class DataConstructPanel extends JPanel implements ToUpdateObject {
 	private void generateData() {
 		ImageData data = null;
 		
+		if (sourcePanel.isSequenceMaskSelected() && sample instanceof ImageSampler 
+				&& imageSessions != null) {
+			List<Mask> maskSequence = new ArrayList<Mask>();
+			boolean containsAtLeastOne = false;
+			for (ImageSession session : imageSessions) {
+				Mask m = session.getRawImage().getMask();
+				maskSequence.add(m);
+				if (m != null) {
+					containsAtLeastOne = true;
+				}
+			}
+			if (containsAtLeastOne) {
+				((ImageSampler) sample).setMaskSequence(maskSequence);
+			}
+		}
 		if (filesPaths.size() > 1) {
 			data = new ImageData(sample, filesPaths);
 		} else {
@@ -134,18 +155,58 @@ public class DataConstructPanel extends JPanel implements ToUpdateObject {
 		samplingPanel.updatedSample();
 	}
 	
+	/**
+	 * Set the list of file path constituting of the current data generated
+	 * 
+	 * @param filesPaths
+	 * 			the list of image's file paths
+	 */
 	public void setFileSources(Vector<String> filesPaths) {
 		this.filesPaths = filesPaths;
 	}
 
+	/**
+	 * Return the list of file path constituting of the current data generated
+	 * 
+	 * @return the list of image's file paths
+	 */
 	public Vector<String> getFilesSources() {
 		return filesPaths;
 	}
+	
+	/**
+	 * Set the list of ImageSessions constituting of the current data generated
+	 * 
+	 * @param imageSessions
+	 * 			the list of ImageSessions
+	 */
+	public void setImageSessions(Vector<ImageSession> imageSessions) {
+		this.imageSessions = imageSessions;
+	}
+
+	/**
+	 * Return the list of ImageSessions constituting of the current data generated
+	 * 
+	 * @return the list of ImageSessions
+	 */
+	public Vector<ImageSession> getImageSessions() {
+		return imageSessions;
+	}
 
+	/**
+	 * Return the subpanel used to select the data source
+	 * 
+	 * @return the panel
+	 */
 	public SourceSelectionPanel getSourceSelectionPanel() {
 		return sourcePanel;
 	}
 
+	/**
+	 * Return the subpanel used to select the sampling parameters
+	 * 
+	 * @return the panel
+	 */
 	public SamplingSelectionPanel getSamplingSelectionPanel() {
 		return samplingPanel;
 	}

src/mustic/gui/panels/data/components/SourceSelectionPanel.java

 package mustic.gui.panels.data.components;
 
 import java.awt.BorderLayout;
+import java.awt.Component;
 import java.awt.FlowLayout;
-import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.File;
@@ -22,6 +22,7 @@ import javax.swing.JRadioButton;
 import jcl.data.sampling.ImageSampler;
 import loci.formats.FormatException;
 import mustic.gui.ImageDesktopFrame;
+import mustic.gui.ImageSession;
 import mustic.gui.MainFrame;
 import mustic.gui.dialog.MaskImportDialog;
 import mustic.gui.panels.data.DataConstructPanel;
@@ -64,7 +65,7 @@ public class SourceSelectionPanel extends JPanel {
 	
 	private JLabel					maskLabel 				= new JLabel("_"); //$NON-NLS-1$
 	
-	private JPanel 					parameterContainer		= null;
+	private JPanel 					parameterContainer		= new JPanel();
 	
 	/** store the sessions used to build the combobox, the order might change
 	 * in the MusticDesktop, so we use it to search by index */
@@ -110,7 +111,9 @@ public class SourceSelectionPanel extends JPanel {
 	}
 	
 	private void updateParametersPanel() {
-		parameterContainer = new JPanel();
+		for (Component c : parameterContainer.getComponents()) {
+			parameterContainer.remove(c);
+		}
 		parameterContainer.setLayout(new BoxLayout(parameterContainer, BoxLayout.Y_AXIS));
 		
 		JPanel addMaskPanel = new JPanel();
@@ -153,11 +156,16 @@ public class SourceSelectionPanel extends JPanel {
 		parameterContainer.add(addMaskPanel);
 		
 		if (multiDateRadioButton.isSelected()) {
+			JPanel useSequenceMaskPanel = new JPanel();
+			useSequenceMaskPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
 			sequenceMaskCheckBox = new JCheckBox(Messages.getString("source.22")); //$NON-NLS-1$
-			parameterContainer.add(sequenceMaskCheckBox);
+			useSequenceMaskPanel.add(sequenceMaskCheckBox);
+			parameterContainer.add(useSequenceMaskPanel);
 		} else {
 			sequenceMaskCheckBox = null;
 		}
+		//parameterContainer.validate();
+		parameterContainer.updateUI();
 		
 	}
 
@@ -320,6 +328,8 @@ public class SourceSelectionPanel extends JPanel {
 				}
 				fatherContainer.setFileSources(fatherContainer
 						.getSequenceDialog().getSequenceData());
+				fatherContainer.setImageSessions(fatherContainer
+						.getSequenceDialog().getSequenceSessions());
 			} catch (FormatException e) {
 				e.printStackTrace();
 			}
@@ -338,6 +348,9 @@ public class SourceSelectionPanel extends JPanel {
 			filesPath.add(allImageDesktopFrames[index]
 					.getImageSession().getImageFilePath());
 			fatherContainer.setFileSources(filesPath);
+			Vector<ImageSession> imageSessions = new Vector<ImageSession>();
+			imageSessions.add(allImageDesktopFrames[index].getImageSession());
+			fatherContainer.setImageSessions(imageSessions);
 		}
 	}
 
@@ -346,7 +359,7 @@ public class SourceSelectionPanel extends JPanel {
 		//TODO we should also initialize the sequenceDialog
 	}
 	
-	public boolean issequenceMaskSelected() {
+	public boolean isSequenceMaskSelected() {
 		if (sequenceMaskCheckBox == null) {
 			return false;
 		}

src/mustic/io/RawImage.java

@@ -825,7 +825,7 @@ public class RawImage implements Serializable, MemoryFlush {
 	 * <p>
 	 * Returns the current mask of this image.
 	 * </p>
-	 * @return the image's mask.
+	 * @return the image's mask, null if none
 	 */
 	public Mask getMask() {
 		return this.mask;