implemntation of the version with bufferedImage

src/mustic/gui/ClassList.java

@@ -223,8 +223,7 @@ public class ClassList {
 					this.imageSession.mImagePanel.supprimePoint(x, y,
 							this.imageSession.getPixelColor(x, y));
 					this.imageSession.mImagePanel
-							.updateImageView(this.imageSession.mImagePanel
-									.getmScreenImage());
+							.updateImageView();
 				}
 			}
 			/** The user choose to create a zone */
@@ -542,8 +541,7 @@ public class ClassList {
 		this.deleteCollectionOfPoints(vp);
 		fillListOfDrawnPoints();
 		this.imageSession.mImagePanel
-				.updateImageView(this.imageSession.mImagePanel
-						.getmScreenImage());
+				.updateImageView();
 	}
 
 	/**
@@ -684,8 +682,7 @@ public class ClassList {
 					this.imageSession.getPixelColor(pt.x, pt.y));
 		}
 		fillListOfDrawnPoints();
-		imageSession.mImagePanel.updateImageView(imageSession.mImagePanel
-				.getmScreenImage());
+		imageSession.mImagePanel.updateImageView();
 	}
 
 	/**
@@ -880,8 +877,7 @@ public class ClassList {
 					this.imageSession.getPixelColor(pt.x, pt.y));
 		}
 		fillListOfDrawnPoints();
-		imageSession.mImagePanel.updateImageView(imageSession.mImagePanel
-				.getmScreenImage());
+		imageSession.mImagePanel.updateImageView();
 	}
 
 	/**
@@ -1051,8 +1047,7 @@ public class ClassList {
 					this.imageSession.getPixelColor(pt.x, pt.y));
 		}
 		fillListOfDrawnPoints();
-		imageSession.mImagePanel.updateImageView(imageSession.mImagePanel
-				.getmScreenImage());
+		imageSession.mImagePanel.updateImageView();
 	}
 
 	/**

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		= false;
+	private boolean						displayEnable		= true;
 
 	/**
 	 * @param aImage
@@ -105,7 +105,7 @@ public class ImageSession {
 		/**
 		 * creation ImagePane
 		 */
-		this.mImagePanel = new ImagePanel(aImage);
+		this.mImagePanel = new ImagePanel(aImage, this);
 		if (MainFrame.DEBUG_MODE)
 			System.out.println(Messages.getString("ImageSession.4")); //$NON-NLS-1$
 
@@ -121,12 +121,11 @@ public class ImageSession {
 		if (MainFrame.DEBUG_MODE)
 			System.out.println(Messages.getString("ImageSession.6")); //$NON-NLS-1$
 		this.mWorskSpace = new TabbedPanel();
-		JScrollPane sp = new JScrollPane(this.mImagePanel);
 		final TitledTab tabImage = TabFactory.createTitledTab(
 				"Image",
 				new ImageIcon(getClass().getResource(
 						"/icons/mimetypes/image-x-generic.png")),
-				sp);
+				this.mImagePanel);
 //		mWorskSpace = new JPanel(new BorderLayout());
 		mWorskSpace.addTab(tabImage);
 		
@@ -271,7 +270,7 @@ public class ImageSession {
 
 		if (displayEnable) {
 			this.mImagePanel.applyMask(this.rawImage.getMask());
-			this.mImagePanel.doZoomOp();
+			this.mImagePanel.refresh();
 		}
 	}
 

src/mustic/gui/ListOfPolygon.java

@@ -89,8 +89,7 @@ public class ListOfPolygon {
 				}
 			}
 			removePolygon(plg);
-			areasLst.getImagePanel().updateImageView(
-					areasLst.getImagePanel().getmScreenImage());
+			areasLst.getImagePanel().updateImageView();
 		}
 	}
 

src/mustic/gui/MainFrame.java

@@ -84,27 +84,27 @@ public class MainFrame extends JFrame {
 	/*
 	 * temporary files directory Always check the directory existence or create it
 	 */
-	private static final String		TMP_DIR_PATH	 = "temporary";
-	private static final File		TMP_DIR_FILE	 = new File(TMP_DIR_PATH);
+	private static final String		TMP_DIR_PATH	 		= "temporary";
+	private static final File		TMP_DIR_FILE	 		= new File(TMP_DIR_PATH);
 	/** l'instance unique de ce singleton */
-	private static MainFrame		instance	     = null;
+	private static MainFrame		instance	     		= null;
 
-	public final static boolean		DEBUG_MODE	     = true;
+	public final static boolean		DEBUG_MODE	     		= true;
 
 	/** La barre de progression */
-	private static JProgressBar		progressBar	     = new JProgressBar();
+	private static JProgressBar		progressBar	     		= new JProgressBar();
 
 	/** */
-	private static final long		serialVersionUID	= 1L;
+	private static final long		serialVersionUID		= 1L;
 
 	/** barre d'etat */
-	private static ProgressStatus		progressStatus	     = new ProgressStatus();
-	private static boolean	    	targetMode	     = true;
+	private static ProgressStatus	progressStatus	     	= new ProgressStatus();
+	private static boolean	    	targetMode	     		= true;
 
 	/** panel pour l'affichage du birdview de l'image selectionnee */
 	private JPanel	               	birdPanel;
 
-	private File	               	currentDirectory	   = null;
+	private File	               	currentDirectory	   	= null;
 
 	/** l'image courante selectionne */
 	private ImageSession	       	currentImageSession;
@@ -114,7 +114,7 @@ public class MainFrame extends JFrame {
 	/**
 	 * bureau pour internal frame (une DesktopFrame (extends JInternalFrame) par image)
 	 */
-	private MusticDesktop	       	desktop	           = null;
+	private MusticDesktop	       	desktop					= null;
 
 	/** repertoire contenant l'aide */
 	private String	               	helpPath	           = "/docs/help";	                             //$NON-NLS-1$
@@ -146,25 +146,25 @@ public class MainFrame extends JFrame {
 	/**
 	 * Nombre de threads
 	 */
-	public int	                   	nbThreads	       = Runtime.getRuntime().availableProcessors();
+	public int	                   	nbThreads	       		= Runtime.getRuntime().availableProcessors();
 
 	/** panel de la toolbar */
-	private JPanel	               	northPanel	       = new JPanel(new BorderLayout());
+	private JPanel	               	northPanel	       		= new JPanel(new BorderLayout());
 
 	/**
 	 * <p>
 	 * Affiche une fenetre permettant de faire une segmentation
 	 * </p>
 	 */
-	private JPanel	               	panelResSave	       = new JPanel();
+	private JPanel	               	panelResSave			= new JPanel();
 
-	private JInternalFrame	       	resultSaveTextField	= new JInternalFrame();
+	private JInternalFrame	       	resultSaveTextField		= new JInternalFrame();
 
 	/**
 	 * Indique si l'orthorectification doit etre lancee par mustic ou non
 	 * Desactive par defaut
 	 */
-	private boolean 				launchOrthoRect = false;
+	private boolean 				launchOrthoRect 		= false;
 
 	/**
 	 * <p>
@@ -2767,7 +2767,7 @@ public class MainFrame extends JFrame {
 			MainFrame.this.currentImageSession.getBirdViewPanel().refresh();
 			this.getProgressBar().setValue(100);
 		}
-		this.currentImageSession.getBirdViewPanel().syncImage(this.currentImageSession);
+		this.currentImageSession.getBirdViewPanel().syncImage();
 		this.getProgressBar().setValue(0);
 		endTime = System.currentTimeMillis();
 		if (MainFrame.DEBUG_MODE)

src/mustic/gui/panels/BirdViewPanel.java

@@ -65,9 +65,7 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 
 	/** Represents the initial selction area. */
 	private Rectangle 			initArea 			= new Rectangle();
-
-	private double 				max[]; // max value for each band
-
+	
 	/** The Image */
 	private BufferedImage 		mBirdImage;
 
@@ -77,6 +75,8 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 	/** Represents the panel which display the selection area */
 	private ImagePanel 			mImagePanel;
 
+	private double 				max[]; // max value for each band
+	
 	private double 				min[]; // min value for each band
 	/** Info */
 	private ImageInformationPanel mInfoPanel;
@@ -718,6 +718,34 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 		// draw the buffer
 		g.drawImage(this.offscreenImage, 0, 0, null);
 	}
+	
+	/**
+	 * Update the selection area in the BirdViewPanel to match a new
+	 * selection
+	 * 
+	 * @param x
+	 * 			X coordinate in the original image
+	 * @param y
+	 * 			Y coordinate in the original image
+	 * @param width
+	 * 			width in the original image
+	 * @param height
+	 * 			height in the original image
+	 */
+	public void updateSelectedArea(int x, int y, int width, int height) {
+		Picture birdview = this.mImage.getBirdview();
+		double xfact = (double) this.mImage.getWidth()
+				/ (double) birdview.getImage().getWidth();
+		double yfact = (double) this.mImage.getHeight()
+				/ (double) birdview.getImage().getHeight();
+
+		int sx = (int) (x / xfact);
+		int sy = (int) (y / yfact);
+		int swidth = (int) Math.ceil(width / xfact);
+		int sheight = (int) Math.ceil(height / yfact);
+		this.selArea = new Rectangle(sx, sy, swidth, sheight);
+		refresh();
+	}
 
 	public void refresh() {
 		if(!session.isDisplayEnable())
@@ -745,6 +773,9 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 		this.bImage = img;
 	}
 
+	/**
+	 * Synchronize the ImagePanel to the BirdViewPanel selection
+	 */
 	public void syncImage() {
 		if(!session.isDisplayEnable())
 			return;
@@ -760,85 +791,7 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 		int width = (int) Math.ceil(this.selArea.width * xfact);
 		int height = (int) Math.ceil(this.selArea.height * yfact);
 
-		Rectangle realarea = new Rectangle(rx, ry, width, height);
-
-		double data[][][] = this.mImage.load(realarea.x, realarea.y,
-				realarea.width, realarea.height);
-		double values[][] = data[0];
-
-		BufferedImage image = new BufferedImage(realarea.width,
-				realarea.height, BufferedImage.TYPE_INT_RGB);
-
-		this.bImage = new BufferedImage(realarea.width, realarea.height,
-				BufferedImage.TYPE_INT_RGB);
-
-		if (this.max == null || this.min == null) {
-			for (int x = 0; x < values.length; x++) {
-				for (int y = 0; y < values[0].length; y++) {
-					int pixel = (int) values[x][y] << 24
-							| (int) data[this.r][x][y] << 16
-							| (int) data[this.g][x][y] << 8
-							| (int) data[this.b][x][y];
-					image.setRGB(x, y, pixel);
-
-					this.bImage.setRGB(x, y, pixel);
-
-				}
-			}
-		} else {
-			short[][][] dataView = new short[data.length][data[0].length][data[0][0].length];
-			; // the values to display
-			int i;
-
-			// r g b
-			int[] bands = new int[3];
-			bands[0] = this.r;
-			bands[1] = this.g;
-			bands[2] = this.b;
-
-			/*
-			 * max contains the max value for r g b, we can create a valid
-			 * representation of data. the data values must be between 0 and 255
-			 * to be valid, so let's convert them if needed
-			 */
-			for (int b = 0; b < bands.length; b++) {
-				i = bands[b];
-				for (int x = 0; x < data[0].length; x++) {
-					for (int y = 0; y < data[0][0].length; y++) {
-						if (data[i][x][y] > 0) {
-							// convert only if needed to avoid color deformation
-							// on 8 bits images
-							if (this.max[i] <= 255 && this.min[i] >= 0) {
-								dataView[i][x][y] = (short) data[i][x][y];
-							} else {
-								dataView[i][x][y] = (short) (255 * (data[i][x][y] - this.min[i]) / (this.max[i] - this.min[i]));
-							}
-						} else {
-							dataView[i][x][y] = 0;
-						}
-					}
-				}
-			}
-
-			// pixels of the image to display
-			for (int x = 0; x < values.length; x++) {
-				for (int y = 0; y < values[0].length; y++) {
-
-					int pixel = (int) values[x][y] << 24
-							| dataView[this.r][x][y] << 16
-							| dataView[this.g][x][y] << 8
-							| dataView[this.b][x][y];
-
-					image.setRGB(x, y, pixel);
-
-					//
-					this.bImage.setRGB(x, y, pixel);
-					//
-				}
-			}
-		}
-		this.mImage.afficheRoi(image, rx, ry);
-		this.mImagePanel.setImage(image);
+		this.mImagePanel.updateImageViewTo(rx, ry, width, height);
 
 		this.rxsave = rx;
 		this.rysave = ry;
@@ -846,6 +799,11 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 
 	}
 
+	/**
+	 * Synchronize an ImagePanel to the BirdViewPanel selection
+	 * 
+	 * @param session the ImageSession to be synchronized
+	 */
 	synchronized public void syncImage(ImageSession session) {
 		
 		if (!session.isDisplayEnable())
@@ -902,88 +860,7 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 		if (ry < 0)
 			ry = 0;
 
-		Rectangle realarea = new Rectangle(rx, ry, width, height);
-
-		double data[][][] = session.getRawImage().load(realarea.x, realarea.y,
-				realarea.width, realarea.height);
-		double values[][] = data[0];
-
-		BufferedImage image = new BufferedImage(realarea.width,
-				realarea.height, BufferedImage.TYPE_INT_RGB);
-
-		this.bImage = new BufferedImage(realarea.width, realarea.height,
-				BufferedImage.TYPE_INT_RGB);
-
-		short[][][] dataView = new short[data.length][data[0].length][data[0][0].length];
-		; // the values to display
-		int i;
-
-		// r g b
-		int[] bands = new int[3];
-		bands[0] = session.getBirdViewPanel().r;
-		bands[1] = session.getBirdViewPanel().g;
-		bands[2] = session.getBirdViewPanel().b;
-
-		/*
-		 * max contains the max value for r g b, we can create a valid
-		 * representation of data. the data values must be between 0 and 255 to
-		 * be valid, so let's convert them if needed
-		 */
-		for (int b = 0; b < bands.length; b++) {
-			i = bands[b];
-			for (int x = 0; x < data[0].length; x++) {
-				for (int y = 0; y < data[0][0].length; y++) {
-					if (data[i][x][y] > 0) {
-						// convert only if needed to avoid color deformation on
-						// 8 bits images
-						if (session.getBirdViewPanel().max[i] <= 255
-								&& session.getBirdViewPanel().min[i] >= 0) {
-							dataView[i][x][y] = (short) data[i][x][y];
-						} else {
-							dataView[i][x][y] = (short) (255 * (data[i][x][y] - session
-									.getBirdViewPanel().min[i]) / (session
-									.getBirdViewPanel().max[i] - session
-									.getBirdViewPanel().min[i]));
-						}
-					} else {
-						dataView[i][x][y] = 0;
-					}
-				}
-			}
-		}
-
-		// pixels of the image to display
-		for (int x = 0; x < values.length; x++) {
-			for (int y = 0; y < values[0].length; y++) {
-
-				int pixel = (int) values[x][y] << 24
-						| dataView[session.getBirdViewPanel().r][x][y] << 16
-						| dataView[session.getBirdViewPanel().g][x][y] << 8
-						| dataView[session.getBirdViewPanel().b][x][y];
-
-				image.setRGB(x, y, pixel);
-
-				//
-				this.bImage.setRGB(x, y, pixel);
-				//
-			}
-		}
-
-		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);
+		this.session.getImagePanel().updateImageViewTo(rx, ry, width, height);
 
 		//TODO do the same for the DataSession
 //		for (ImageResultPanel resultPanel : session.getResultPanels()) {
@@ -991,7 +868,7 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 //		}
 
 		for (SegmentationPanel segPanel : session.getSegPanels()) {
-			segPanel.setImage(image, rx, ry);
+			segPanel.setImage(this.session.getImagePanel().getImage(), rx, ry);
 		}
 		//
 

src/mustic/gui/segmentation/SegmentationPanel.java

@@ -102,7 +102,7 @@ public class SegmentationPanel extends JPanel implements ActionListener, MouseLi
 		this.mZoomRate = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getZoomRate();
 		this.mZoomStep = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getmZoomStep();
 		this.offset = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getBrightnessValue();
-		this.offsetStep = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getOffsetStep();
+		this.offsetStep = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getBrightnessStep();
 		this.scaleFactor = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getScaleFactor();
 		this.scaleFactorStep = MainFrame.getInstance().getCurrentImageSession().getImagePanel().getScaleFactorStep();
 

src/mustic/utils/image/BufferedImageHelper.java

+package mustic.utils.image;
+
+import java.awt.Color;
+import java.awt.Point;
+import java.awt.image.BufferedImage;
+import java.awt.image.ColorModel;
+import java.awt.image.DirectColorModel;
+import java.awt.image.Raster;
+import java.awt.image.SampleModel;
+import java.awt.image.SinglePixelPackedSampleModel;
+import java.awt.image.WritableRaster;
+
+/**
+ * Class that allows buffer manipulation and creation from images.
+ * This class use bio-format library to read images and works only 
+ * with BuffredImage using DirectColorModel and SinglePixelPaxedSampleModel.
+ * There not yet any support for other format, and it is not likely 
+ * to works if the format is different.
+ * 
+ * @author Baptiste LAFABREGUE
+ *
+ */
+public class BufferedImageHelper {
+
+	/**
+	 * Transform an image on short array format into a RGB BufferedImage
+	 * The raster should follow the order bellow :
+	 * short[channel][x][y]
+	 * 
+	 * @param raster
+	 * 			an image raster to convert to bufferImage
+	 * @param r
+	 * 			the index of the red channel
+	 * @param g
+	 * 			the index of the green channel
+	 * @param b
+	 * 			the index of the blue channel
+	 * @return the corresponding BufferdImage
+	 */
+	public static BufferedImage createBufferedImageFromImage(short[][][] raster, int r, int g, int b) {
+		if (r < 0 || r >= raster.length || g < 0 || g >= raster.length 
+				|| b < 0 || b >= raster.length) {
+			throw new IndexOutOfBoundsException("R, G and B index should respect"
+					+ " the number of channels in the image.");
+		}
+		DirectColorModel cm = (DirectColorModel) DirectColorModel.getRGBdefault();
+		WritableRaster ra = cm.createCompatibleWritableRaster(raster[0].length, raster[0][0].length);
+		
+		BufferedImage result = new BufferedImage(cm, ra, false, null);
+		for (int x = 0 ; x < raster[0].length ; x++) {
+			for(int y = 0 ; y < raster[0][0].length ; y++) {
+//				int rgb = (raster[r][x][y] << 16)
+//						& (raster[g][x][y] << 8)
+//						& (raster[b][x][y]);
+				int rgb = new Color(raster[r][x][y],
+									raster[g][x][y],
+									raster[b][x][y]).getRGB();
+				result.setRGB(x, y, rgb);
+			}
+		}
+		return result;
+	}
+	
+	/**
+	 * Return the list of all min/max for each channel in an image raster.
+	 * The raster should follow the order bellow :
+	 * short[channel][x][y]
+	 * The result have the format bellow :
+	 * [channel][0] = min
+	 * [channel][1] = max
+	 * 
+	 * @param raster
+	 * 			the raster to evaluate
+	 * @return the list of min/max per channel
+	 */
+	public static double[][] computeMinMax(double[][][] raster) {
+		double[][] result = new double[raster.length][2];
+		
+		for (int c = 0 ; c < raster.length ; c++) {
+			double min = raster[c][0][0];
+			double max = raster[c][0][0];
+			
+			for(int x = 0 ; x < raster[0].length ; x++) {
+				for (int y = 0 ; y < raster[0][0].length ; y++) {
+					if (raster[c][x][y] < min) {
+						min = raster[c][x][y];
+					} else if (raster[c][x][y] > max) {
+						max = raster[c][x][y];
+					}
+				}
+			}
+			
+			result[c][0] = min;
+			result[c][1] = max;
+		}
+		return result;
+	}
+	
+	/**
+	 * Change the order of the channels, this function is only available
+	 * for BufferedImage using DirectColorModel and SinglePixelPaxedSampleModel.
+	 * Channels indexes should go from 0 to 2.
+	 * 
+	 * @param buffer 
+	 * 			the BufferedImage used to get the DataBuffer of the new BufferedImage
+	 * @param nr
+	 * 			the red channel position in the new BufferedImage
+	 * @param ng
+	 * 			the green channel position in the new BufferedImage
+	 * @param nb
+	 * 			the blue channel position in the new BufferedImage
+	 * @return the new BufferedImage
+	 */
+	public static BufferedImage swapChannels(BufferedImage buffer, int nr, int ng, int nb) {
+		int bits = ((DirectColorModel) buffer.getColorModel()).getPixelSize();
+		int[] rgb = new int[3];
+		rgb[nr] = ((DirectColorModel) buffer.getColorModel()).getRedMask();
+		rgb[ng] = ((DirectColorModel) buffer.getColorModel()).getGreenMask();
+		rgb[nb] = ((DirectColorModel) buffer.getColorModel()).getBlueMask();
+		
+		ColorModel cm = new DirectColorModel(bits, rgb[0], rgb[1], rgb[2]); 
+		SampleModel sm = new SinglePixelPackedSampleModel(buffer.getSampleModel().getDataType(),
+				buffer.getWidth(), buffer.getHeight(), rgb);
+		WritableRaster ra = (WritableRaster) Raster.createRaster(sm, buffer.getRaster()
+				.getDataBuffer(), new Point(0,0));
+		
+		return new BufferedImage(cm, ra, false, null);
+	}
+}

src/mustic/utils/image/BufferedImageViewer.java

 package mustic.utils.image;
 
+import java.awt.geom.AffineTransform;
+import java.awt.image.AffineTransformOp;
 import java.awt.image.BufferedImage;
+import java.awt.image.RescaleOp;
+import java.io.IOException;
 
 import jcl.data.mask.Mask;