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Commit 5b0f182c authored by lafabregue's avatar lafabregue
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implemntation of the version with bufferedImage

parent 11dbff3d
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Showing with 807 additions and 500 deletions
src/mustic/gui/ClassList.java
View file @ 5b0f182c
......@@ -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
View file @ 5b0f182c
......@@ -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
View file @ 5b0f182c
......@@ -89,8 +89,7 @@ public class ListOfPolygon {
}
}
removePolygon(plg);
areasLst.getImagePanel().updateImageView(
areasLst.getImagePanel().getmScreenImage());
areasLst.getImagePanel().updateImageView();
}
}
......
src/mustic/gui/MainFrame.java
View file @ 5b0f182c
......@@ -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
View file @ 5b0f182c
......@@ -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/panels/ImagePanel.java
View file @ 5b0f182c
This diff is collapsed.
src/mustic/gui/segmentation/SegmentationPanel.java
View file @ 5b0f182c
......@@ -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 0 → 100644
View file @ 5b0f182c
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/ImageViewer.java
View file @ 5b0f182c
......@@ -5,75 +5,178 @@ import java.awt.image.BufferedImage;
import jcl.data.mask.Mask;
/**
* Interface that manage the read operations as for an image source
* Abstract class that manage the read operations as BufferedImage
* from an image source.
*
* @author Baptiste LAFABREGUE
*
*/
public interface ImageViewer {
public abstract class ImageViewer {
/** brightness step */
protected float offsetStep = 5.0f;
/** brightness value */
protected float offsetValue = 10;
/** contrast value */
protected float scaleFactor = 1.0f;
/** contrast step */
protected float scaleFactorStep = 0.1f;
/**
* Decrease the brightness of the image.
*/
public void decreaseBrightness();
public void decreaseBrightness() {
if (offsetValue > 0) {
offsetValue = offsetValue - offsetStep;
if (offsetValue < 0) {
offsetStep = 0;
}
rescale();
}
else
System.out.println("Offset is at it's minimum...");
}
/**
* Increase the brightness of the image.
*/
public void increaseBrightness() ;
public void increaseBrightness() {
if (offsetValue < 255) {
offsetValue = offsetValue + offsetStep;
if (offsetValue > 255) {
offsetValue = 255;
}
rescale();
}
else
System.out.println("Offset is at it's maximum...");
}
/**
* @return the brightnessValue
*/
public float getBrightnessValue() ;
public float getBrightnessValue() {
return offsetValue;
}
/**
* @param brightnessValue
* the brightnessValue to set
*/
public void setBrightnessValue(float brightnessValue) ;
public void setBrightnessValue(float brightnessValue) {
offsetValue = brightnessValue;
}
/**
* @return the contrastValue
*/
public float getContrastValue() ;
public float getContrastValue() {
return scaleFactor;
}
/**
* @param brightnessValue
* the brightnessValue to set
*/
public void setContrastValue(float contrastValue) ;
public void setContrastValue(float contrastValue) {
scaleFactor = contrastValue;
}
/**
* Decrease the contrast of the image.
*/
public void decreaseContrast() ;
public void decreaseContrast() {
if (scaleFactor > 0) {
scaleFactor = scaleFactor - scaleFactorStep;
if (scaleFactor < 0)
scaleFactor = 0;
rescale();
}
else
System.out.println("Scale factor is at it's minimum...");
}
/**
* Increase the contrast of the image.
*/
public void increaseContrast();
public void increaseContrast(){
if (scaleFactor < 2) {
scaleFactor = scaleFactor - scaleFactorStep;
if (scaleFactor > 2) {
scaleFactor = 2;
}
rescale();
}
else
System.out.println("Scale factor is at it's maximum...");
}
/**
* Set the contrast step