finished pyramid iamge implementation

src/mustic/gui/MainFrame.java

@@ -123,7 +123,7 @@ public class MainFrame extends JFrame {
 	private JPanel	               	infosPanel;
 
 	/** boolean pour lier le birdview avec l'image active */
-	private boolean	               	lierBirdView	       = false;
+	private boolean	               	linkToAllImages	       = false;
 
 	/** the project root for datas */
 	private DefaultMutableTreeNode	mDataProjectNode;
@@ -1310,8 +1310,8 @@ public class MainFrame extends JFrame {
 		menuBrightM.setEnabled(this.actionBrightM);
 		menuContrastP.setEnabled(this.actionContratsP);
 		menuContrastM.setEnabled(this.actionContrastM);
-		menuConnectActiv.setEnabled(!this.isLierBirdView());
-		menuConnectAll.setEnabled(this.isLierBirdView());
+		menuConnectActiv.setEnabled(!this.isLinkToAllBirdView());
+		menuConnectAll.setEnabled(this.isLinkToAllBirdView());
 		menuResetAll.setEnabled(this.actionResetAll);
 		menuChooseRgb.setEnabled(this.actionChooseRgb);
 		menuRefresh.setEnabled(this.actionRefresh);
@@ -1480,7 +1480,7 @@ 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);
+		panel_desktop.setBorder(Borders.DIALOG_BORDER);
 		panel_desktop.add(this.desktop);
 
 		sif_desktop = new SimpleInternalFrame(Messages.getString("MainFrame.72")); //$NON-NLS-1$
@@ -1494,7 +1494,7 @@ public class MainFrame extends JFrame {
 
 		JPanel panel = new JPanel(new BorderLayout());
 		panel.setOpaque(false);
-		panel.setBorder(Borders.DIALOG);
+		panel.setBorder(Borders.DIALOG_BORDER);
 		panel.add(pane);
 
 		// =============== Creation of the Progress Panel => South
@@ -1530,36 +1530,6 @@ public class MainFrame extends JFrame {
 		this.birdPanel.requestFocus();
 	}
 
-	//TODO to remove	
-	// method for resizing an image while keeping aspect ratio
-	private static BufferedImage resizeImage(BufferedImage originalImage, int type, int frameWidth, int frameHeight) {
-
-		double height = originalImage.getHeight();
-		double width = originalImage.getWidth();
-		int newWidth, newHeight;
-
-		// if image size smaller than window size, do not resize
-		if (height < frameHeight && width < frameWidth) {
-			newWidth = (int) width;
-			newHeight = (int) height;
-		}
-		// else resize
-		else {
-			double scaleX = (frameWidth / width);
-			double scaleY = (frameHeight / height);
-			double scale = Math.min(scaleX, scaleY);
-			newWidth = (int) (width * scale);
-			newHeight = (int) (height * scale);
-		}
-
-		BufferedImage resizedImage = new BufferedImage(newWidth, newHeight, type);
-		Graphics2D g = resizedImage.createGraphics();
-		g.drawImage(originalImage, 0, 0, newWidth, newHeight, null);
-		g.dispose();
-
-		return resizedImage;
-	}
-
 	
 	// 20120309_MBH-Test-Fin
 	/**
@@ -1647,7 +1617,7 @@ 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);
+		panel_desktop.setBorder(Borders.DIALOG_BORDER);
 		panel_desktop.add(this.desktop);
 
 		sif_desktop = new SimpleInternalFrame(Messages.getString("MainFrame.72")); //$NON-NLS-1$
@@ -1661,7 +1631,7 @@ public class MainFrame extends JFrame {
 
 		JPanel panel = new JPanel(new BorderLayout());
 		panel.setOpaque(false);
-		panel.setBorder(Borders.DIALOG);
+		panel.setBorder(Borders.DIALOG_BORDER);
 		panel.add(pane);
 
 		// =============== Creation of the Progress Panel => South
@@ -2494,8 +2464,8 @@ public class MainFrame extends JFrame {
 		return mDataTreeModel;
 	}
 
-	public boolean isLierBirdView() {
-		return lierBirdView;
+	public boolean isLinkToAllBirdView() {
+		return linkToAllImages;
 	}
 
 	/**
@@ -3461,7 +3431,7 @@ public class MainFrame extends JFrame {
 	}
 
 	public void setLierBirdView(boolean lierBirdView) {
-		this.lierBirdView = lierBirdView;
+		this.linkToAllImages = lierBirdView;
 		setEnabledMenu();
 	}
 //

src/mustic/gui/panels/BirdViewPanel.java

@@ -288,29 +288,7 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 
 	@Override
 	public void mouseClicked(MouseEvent e) {
-		// Test if an image is loaded
-		if (!session.isDisplayEnable() || this.mImage == null) {
-			return;
-		}
-
-		// Test if the mouse is over the image
-		if (e.getPoint().x >= this.mBirdImage.getWidth()
-				|| e.getPoint().y >= this.mBirdImage.getHeight()) {
-			return;
-		}
-
-		// Zoom factor of the image
-		double xfact = (double) this.mImage.getWidth()
-				/ (double) this.mBirdImage.getWidth();
-		double yfact = (double) this.mImage.getHeight()
-				/ (double) this.mBirdImage.getHeight();
-
-		double x = e.getX() * xfact;
-		double y = e.getY() * yfact;
-
-		this.mInfoPanel.setPixel((int) (x), (int) (y));
-
-		repaint();
+		
 	}
 
 	/**
@@ -631,7 +609,7 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 		this.repaint();
 		this.action = BirdViewPanel.ACT_NONE;
 
-		if (!MainFrame.getInstance().isLierBirdView()) {
+		if (!MainFrame.getInstance().isLinkToAllBirdView()) {
 			ImageDesktopFrame[] desktopFrames = MainFrame.getInstance().getDesktop()
 					.getAllImageDesktopFrames();
 			int nbSessions = desktopFrames.length;
@@ -653,28 +631,13 @@ public class BirdViewPanel extends JPanel implements MouseListener,
 										.getBirdViewPanel().rysave);
 			}
 		} else {
-			if (MainFrame.getInstance().getDesktop().getActiveFrame() instanceof ImageDesktopFrame) {
-				syncImage(((ImageDesktopFrame) MainFrame.getInstance().getDesktop().getActiveFrame())
-						.getImageSession());
-				((ImageDesktopFrame) MainFrame
-						.getInstance()
-						.getDesktop()
-						.getActiveFrame())
-						.getImageSession()
-						.getImagePanel()
-						.reloadPoint(
-								((ImageDesktopFrame) MainFrame.getInstance().getDesktop()
-										.getActiveFrame()).getImageSession()
-										.getBirdViewPanel().xxsave,
-										((ImageDesktopFrame) MainFrame.getInstance().getDesktop()
-										.getActiveFrame()).getImageSession()
-										.getBirdViewPanel().yysave,
-										((ImageDesktopFrame) MainFrame.getInstance().getDesktop()
-										.getActiveFrame()).getImageSession()
-										.getBirdViewPanel().rxsave,
-										((ImageDesktopFrame) MainFrame.getInstance().getDesktop()
-										.getActiveFrame()).getImageSession()
-										.getBirdViewPanel().rysave);
+			if (session != null) {
+				syncImage(session);
+				session.getImagePanel().reloadPoint(
+								session.getBirdViewPanel().xxsave,
+								session.getBirdViewPanel().yysave,
+								session.getBirdViewPanel().rxsave,
+								session.getBirdViewPanel().rysave);
 			}
 		}
 

src/mustic/gui/panels/ImageInformationPanel.java

@@ -406,11 +406,13 @@ public class ImageInformationPanel extends JPanel {
 	 * </p>
 	 * 
 	 * @param x
-	 *            the x position of the pixel
+	 * 			the x position of the pixel
 	 * @param y
-	 *            the y position of the pixel
+	 * 			the y position of the pixel
+	 * @param value
+	 * 			the pixel value
 	 */
-	public void setPixel(int x, int y) {
+	public void setPixel(int x, int y, double value[]) {
 		this.mPixel.setText("Pixel: " + (x + 1) + " - " + (y + 1));
 		try {
 			double posGeo[] = this.mImage.getLatLon(x, y);
@@ -425,19 +427,12 @@ public class ImageInformationPanel extends JPanel {
 			this.mPixelGeo.setText("Lat: " + myFormatter.format(xgeo)
 					+ " Lon: " + myFormatter.format(ygeo));
 		} catch (Exception ex) {
-			if(MainFrame.DEBUG_MODE)
-				ex.printStackTrace();
+//			if(MainFrame.DEBUG_MODE)
+//				ex.printStackTrace();
 			this.mPixelGeo.setText("no georeferencing");
 		}
 
-		double data[][][] = this.mImage.load(x, y, 1, 1);
-
-		double realdata[] = new double[data.length];
-
-		for (int i = 0; i < data.length; i++)
-			realdata[i] = data[i][0][0];
-
-		setPixelVal(this.mImage.getWavelength(), realdata);
+		setPixelVal(this.mImage.getWavelength(), value);
 	}
 
 	/**

src/mustic/gui/panels/ImageResultPanel.java

@@ -19,11 +19,8 @@ import jcl.Classification;
 import jcl.clustering.Cluster;
 import jcl.clustering.ClusteringResult;
 import jcl.data.Data;
-import jcl.data.DataObject;
 import jcl.data.SimpleData;
 import jcl.data.attribute.AttributeMultiDimSequence;
-import jcl.data.attribute.AttributeNumerical;
-import jcl.data.mask.Mask;
 import jcl.evaluation.clustering.ResultsComparison;
 import jcl.learning.*;
 import jcl.learning.methods.monostrategy.SingleClassification;
@@ -643,7 +640,7 @@ public class ImageResultPanel extends ResultPanel implements TreeSelectionListen
 		}
 		MainFrame.getInstance().getCurrentDataSession().addResultPanel(this);
 		this.result = classification.getClusteringResult();
-		//TODO remove comments to allow display again
+		//TODO comment line bellow to disable display
 		this.colored = new BufferedImage(imgData.getResultWidth(), imgData.getResultHeight(), BufferedImage.TYPE_INT_RGB);
 		if (imgData.getAssociatedImageSessions() != null && imgData.getAssociatedImageSessions().size() > 0) {
 			this.setData(imgData.getAssociatedImageSessions().get(0).getImagePanel().getImage());

src/mustic/io/RawImage.java

@@ -20,6 +20,7 @@ import com.l2fprod.common.propertysheet.Property;
 
 import jcl.data.mask.Mask;
 import jcl.utils.MemoryFlush;
+import jcl.utils.Images.StreamedImageReaderWrapper;
 import jcl.utils.exceptions.MethodNotImplementedException;
 
 /**
@@ -129,33 +130,39 @@ public class RawImage implements Serializable, MemoryFlush
 	 * Represents the maximum possible value in the image format
 	 * </p>
 	 */
-	private double maxValue = 0;
+	private double 					maxValue 			= 0;
+	
+	/** min values for each channels */
+	protected double[]				minValues 			= null;
+
+	/** max values for each channels */
+	protected double[]				maxValues 			= null;
 	
 	/**
 	 * <p>
 	 * Represents number of bands in the image.
 	 * </p>
 	 */
-	private int nbBands = 0;
+	private int						nbBands 			= 0;
 	
 	/**
 	 * <p>
 	 * Represents the maximum representative number of bit in the image
 	 * </p>
 	 */
-	private short nBitPerPixel = 0;
+	private short 					nBitPerPixel 		= 0;
 	
 	/**
 	 * Proprietes de l'image
 	 */
-	public Vector<Property> properties = new Vector<Property>();
+	public Vector<Property> 		properties 			= new Vector<Property>();
 	
 	/**
 	 * <p>
 	 * Represents the resolution (in meters/pixel) of the image (0 = X, 1 = Y).
 	 * </p>
 	 */
-	private double[] resolution = null;
+	private double[] 				resolution 			= null;
 	
 	/**
 	 * <p>
@@ -1192,7 +1199,7 @@ public class RawImage implements Serializable, MemoryFlush
 	 */
 	private double[][][] load(ImageReadParam param)
 	{
-		
+		System.out.println(">>>>>>>>>>>>>>>>>>> IN ><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<");
 		int x;
 		int y;
 		int w;
@@ -2095,6 +2102,64 @@ public class RawImage implements Serializable, MemoryFlush
 	{
 		this.workfilename = workfilename;
 	}
+
+	/**
+	 * Return the minimum value for each channel
+	 * @return the minimums 
+	 */
+	public double[] getMinValues() {
+		if(minValues == null) {
+			computeMinMax();
+		}
+		return minValues;
+	}
+
+	/**
+	 * Set the minimum value for each channel
+	 * @param minValues
+	 * 			the minimums
+	 */
+	public void setMinValues(double[] minValues) {
+		this.minValues = minValues;
+	}
+
+	/**
+	 * Return the maximum value for each channel
+	 * @return the maximums 
+	 */
+	public double[] getMaxValues() {
+		if(maxValues == null) {
+			computeMinMax();
+		}
+		return maxValues;
+	}
+
+	/**
+	 * Set the maximum value for each channel
+	 * @param maxValues
+	 * 			the maximums
+	 */
+	public void setMaxValues(double[] maxValues) {
+		this.maxValues = maxValues;
+	}
+	
+	/**
+	 * Compute teh min/max values per channel
+	 */
+	private void computeMinMax() {
+		StreamedImageReaderWrapper reader = new StreamedImageReaderWrapper(filename);
+		long allocatedMemory = (Runtime.getRuntime().totalMemory()-Runtime.getRuntime().freeMemory());
+		long presumableFreeMemory = Runtime.getRuntime().maxMemory() - allocatedMemory;
+		// we just tack the 2/3rd of the memory available;
+		presumableFreeMemory *= 0.05;
+		try {
+			reader.setMaxRAM(presumableFreeMemory);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+		minValues = reader.getMinValues();
+		maxValues = reader.getMaxValues();
+	}
 	
 	@Override
 	public void flushMemory() throws MethodNotImplementedException

src/mustic/utils/image/BufferedImageHelper.java

@@ -178,13 +178,13 @@ public class BufferedImageHelper {
 			for(int x = 0 ; x < imageWidth ; x++) {
 				
 				double[] pixel = null;
-				try {
+//				try {
 					pixel = reader.getPixel(x+imageX, y+imageY);
-				} catch (ArrayIndexOutOfBoundsException e) {
-					System.out.println(x+","+y+" in : "+imageX+","+imageY+" - "+imageWidth+","+imageHeight);
-					e.printStackTrace();
-					
-				}
+//				} catch (ArrayIndexOutOfBoundsException e) {
+//					System.out.println(x+","+y+" in : "+imageX+","+imageY+" - "+imageWidth+","+imageHeight);
+//					e.printStackTrace();
+//					
+//				}
 				int rgb = 0;
 				if (maxValues != null && minValues != null) {
 					rgb = new Color(rescaleColor(pixel[r], 0, maxValues[r]),
@@ -201,6 +201,16 @@ public class BufferedImageHelper {
 		return result;
 	}
 	
+	/**
+	 * Rescale a value from a given range to 0-255
+	 * @param value
+	 * 			the value to recale
+	 * @param min
+	 * 			the min value of the range
+	 * @param max
+	 * 			the max value of the range
+	 * @return the rescaled value
+	 */
 	private static int rescaleColor(double value, double min, double max) {
 		if (value < min) {
 			value = min;
@@ -209,4 +219,51 @@ public class BufferedImageHelper {
 		}
 		return (int) ((255 * (value - min)) / (max - min));
 	}
+	
+	/**
+	 * Clone a bufferedImage. 
+	 * @param bi
+	 * 			the bufferedImage to copy
+	 * @return	the copy of the bufferedImage
+	 */
+	public static BufferedImage deepCopy(BufferedImage bi) {
+		if (bi == null)
+			return null;
+	    ColorModel cm = bi.getColorModel();
+	    boolean isAlphaPremultiplied = cm.isAlphaPremultiplied();
+	    WritableRaster raster = bi.copyData(bi.getRaster().createCompatibleWritableRaster());
+	    return new BufferedImage(cm, raster, isAlphaPremultiplied, null);
+	}
+	
+	/**
+	 * Compute the average image from two images
+	 * For each pixel it's channels values is the average of 
+	 * the channel value of the two images.
+	 * The two image have to have the same dimensions
+	 * @param image1
+	 * 			the first image
+	 * @param image2
+	 * 			the second image
+	 * @return the average of image1 and image2
+	 */
+	public static BufferedImage averagedBufferedImage(BufferedImage image1, BufferedImage image2) {
+		if (image1.getHeight() != image2.getHeight() ||
+			image1.getWidth() != image2.getWidth()) {
+			throw new IndexOutOfBoundsException("the BufferedImage shouyld have the same dimensions");
+		}
+		BufferedImage result = new BufferedImage(image1.getWidth(), image1.getHeight(),
+				BufferedImage.TYPE_INT_RGB);
+		for(int x = 0 ; x < image1.getWidth() ; x++) {
+			for(int y = 0 ; y < image1.getHeight() ; y++) {
+				Color c1 = new Color(image1.getRGB(x, y));
+				Color c2 = new Color(image2.getRGB(x, y));
+				Color c = new Color((c1.getRed()+c2.getRed())/2, 
+									(c1.getGreen()+c2.getGreen())/2,
+									(c1.getBlue()+c2.getBlue())/2);
+				result.setRGB(x, y, c.getRGB());
+			}
+		}
+		
+		return result;
+	}
 }

src/mustic/utils/image/BufferedImageViewer.java

@@ -49,6 +49,8 @@ public class BufferedImageViewer extends ImageViewer {
 	 * - not used if instantiate directly with a BufferedImage */
 	private short[][][]				raster						= null;
 	
+	BufferedImageViewer				comparedImage				= null;
+	
 	
 	/**
 	 * Construct a viewer from a raw BufferedImage.
@@ -190,6 +192,10 @@ public class BufferedImageViewer extends ImageViewer {
 					+ mask.getOverallCarinality() + " != " 
 					+ (this.getRealImageWidth() + "x" + this.getRealImageHeight()) + ")");
 		}
+		
+		if (comparedImage != null) {
+			comparedImage.addMask(mask);
+		}
 	}
 	
 	private void applyMask() {
@@ -211,16 +217,15 @@ public class BufferedImageViewer extends ImageViewer {
 		rgbBands[1] = 1;
 		rgbBands[2] = 2;
 		rescale = null;
+		comparedImage = null;
 		
 	}
 
 	@Override
-	public BufferedImage getScreenImage(int x, int y, int width, int height, double zoomRate) {
+	public BufferedImage getScreenImage(int x, int y, int width, int height, double zoomRate, boolean saved) {
 		if(width <= 0 || height <= 0) {
 			return null;
 		}
-		realX = x;
-		realY = y;
 		// we reverse compute the coordinates in the original image
 		int updatedWidth = (int) Math.ceil(width / zoomRate);
 		int updatedHeight = (int) Math.ceil(height / zoomRate);
@@ -232,11 +237,11 @@ public class BufferedImageViewer extends ImageViewer {
 		if (updatedHeight + y > mSourceImage.getHeight()) {
 			updatedHeight = mSourceImage.getHeight() - y;
 		}
-		mScreenImage = mSourceImage.getSubimage(x, y, updatedWidth, updatedHeight);
+		BufferedImage screen = mSourceImage.getSubimage(x, y, updatedWidth, updatedHeight);
 		
 		// we apply the rescale operation
 		if (rescale != null) {
-			mScreenImage = this.rescale.filter(mScreenImage, null);
+			screen = this.rescale.filter(screen, null);
 		}
 		// we apply the mask to image
 		if (mask != null) {
@@ -245,14 +250,30 @@ public class BufferedImageViewer extends ImageViewer {
 		// we update the source image to crop to the screen size
 		AffineTransform trans = AffineTransform.getScaleInstance(zoomRate, zoomRate);
 		AffineTransformOp op = new AffineTransformOp(trans, AffineTransformOp.TYPE_NEAREST_NEIGHBOR);
-		mScreenImage = op.filter(this.mScreenImage, null);
+		screen = op.filter(screen, null);
 		//mScreenImage = op.filter(this.mScreenImage, null).getSubimage(0, 0, width, height); 
 		
-		return mScreenImage;
+		if (saved) {
+			realX = x;
+			realY = y;
+			mScreenImage = screen;
+		}
+		
+		if (comparedImage != null) {
+			BufferedImage scr2 = comparedImage.getScreenImage(x, y, width, height, zoomRate, saved);
+			return BufferedImageHelper.averagedBufferedImage(screen, scr2);
+		}
+		
+		return screen;
 	}
 
 	@Override
 	public BufferedImage getScreenImage() {
+		if (comparedImage != null) {
+			BufferedImage scr2 = comparedImage.getScreenImage();
+			return BufferedImageHelper.averagedBufferedImage(mScreenImage, scr2);
+		}
+		
 		return mScreenImage;
 	}
 
@@ -274,7 +295,31 @@ public class BufferedImageViewer extends ImageViewer {
 		this.rescale = new RescaleOp(this.getContrastValue(), this.getBrightnessValue(), null);
 		this.mScreenImage = this.rescale.filter(this.mScreenImage, null);
 	}
-	
+
+
+	@Override
+	public double[] getPixelValue(int x, int y) {
+		StreamedImageReaderWrapper reader = new StreamedImageReaderWrapper(imagePath);
+		reader.setBoundries(x, y, x, y);
+		try {
+			return reader.getPixel(x, y);
+		} catch (FormatException | IOException e) {
+			e.printStackTrace();
+		}
+		
+		return null;
+	}
+
+	// TODO this not support images with different dimensions, it should be based on georeferences
+	@Override
+	public void addComparedImage(RawImage image) {
+		if (image == null) {
+			comparedImage = null;
+		} else {
+			comparedImage = new BufferedImageViewer(image, true);
+		}
+		
+	}
 	
 
 }

src/mustic/utils/image/ImageViewer.java

@@ -3,6 +3,7 @@ package mustic.utils.image;
 import java.awt.image.BufferedImage;
 
 import jcl.data.mask.Mask;
+import mustic.io.RawImage;
 
 /**
  * Abstract class that manage the read operations as BufferedImage
@@ -31,6 +32,12 @@ public abstract class ImageViewer {
 	/** max values for each channels */
 	protected double[]				maxValues 					= null;
 	
+	/**	transparency of the image */
+	protected float					transparency				= 1;
+	
+	/** transparency of the compared image */
+	protected float					comparedImageTransparency	= 0.5f;
+	
 	/**
 	 * Decrease the brightness of the image.
 	 */
@@ -171,6 +178,9 @@ public abstract class ImageViewer {
 		this.maxValues = maxValues;
 	}
 	
+	public void adjustTransparency(float firstImage, float secondImage) {
+		
+	}
 	/**
 	 * Rescale the image to take in account the modification of the parameters
 	 * 
@@ -209,10 +219,13 @@ public abstract class ImageViewer {
 	 * 			the height of the output BufferedImage
 	 * @param zoomRate
 	 * 			the zoomRate between the screen and the originImage
+	 * @param saved
+	 * 			specify if the parameters should replace the ones currently saved
+	 * 			this is used to not interfere with getScreenImage() calls
 	 * 
 	 * @return the BufferedImage, null the dimension are not valid
 	 */
-	public abstract BufferedImage getScreenImage(int x, int y, int width, int height, double zoomRate);
+	public abstract BufferedImage getScreenImage(int x, int y, int width, int height, double zoomRate, boolean saved);
 	
 	/**
 	 * Request for the BufferedImage representation of an area in the origin image
@@ -234,4 +247,18 @@ public abstract class ImageViewer {
 	 * @return the height
 	 */
 	public abstract int getRealImageHeight();
+	
+	/**
+	 * Return the value of a specific pixel