com.actelion.research.orbit.imageAnalysis.components.RecognitionFrame Maven / Gradle / Ivy
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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see
* Attention: This class still holds a ClassShape list, even if the classShapes are stored in the model. So far this
* is necessary because the drawn class regions (connected to a shapePaintListener) are stored here. This causes problems
* e.g. in the NucleiSegmentationWorker which needs the classShapes of the (nested) segmentation model, so it first sets the
* classShapes of the recognitionFrame to the segmentation model classShapes and later sets it back.
* This should be refactored!!!
*
*/
public class RecognitionFrame extends JComponent implements PropertyChangeListener {
private static final long serialVersionUID = 1L;
public static int maxClassShapesToPaint = 10000;
private static final Logger logger = LoggerFactory.getLogger(RecognitionFrame.class);
private int windowSize = 4;
private double targetRadius = 3.0d; // just for drawing
private double segmentationClassSize = 12.0d;
private int boundaryClass = -1;
private boolean contextClassificationEnabled = false;
private TiledImageWriter classImage = null;
@Deprecated
private RecognitionFrame negativeChannel = null;
private String picName = "";
private String originalName = "";
private final List classShapes = Collections.synchronizedList(new ArrayList());
private final List annotations = Collections.synchronizedList(new ArrayList());
private IScaleableShape ROI = null;
private final HashMap colorClassLookup = new HashMap();
private float opacity = 0f;
private boolean drawMarkup = true;
private double[] ratio = null; // has to be initialized to classShapeList.size
private final List classList = new ArrayList();
private final ReentrantReadWriteLock classListLock = new ReentrantReadWriteLock();
private List objectSegmentationList = null;
private List secondaryObjectSegmentationList = null;
private List objectSegmentationColors = null; // used for heatmap
private int[] objectClassificationList = null;
private List centerList = null;
private List centroidList = null;
@Deprecated
private Arc2D.Double classBounds = null;
private static final Color[] colors = new Color[]{Color.red, Color.blue, Color.green, Color.yellow, Color.cyan, Color.orange, Color.magenta, Color.pink, Color.lightGray};
private static Random rand = new Random();
private static Font toolTipFont = new Font("Arial", Font.PLAIN, 12);
//private boolean fromResource = false;
private double scale = 100d;
private double oldScale = 100d;
private double muMeterPerPixel = 0d;
private Color gaugeColor = Color.black;
private Point2D viewPortOffset = new Point2D.Double(0, 0);
private Dimension2D viewPortSize = new Dimension2D_Double(0d, 0d);
public enum Tools {magneticLasso, brush, rectangle, cell, circle, delete, finger, roi, moveAnnotation, rotateAnnotation}
;
private Tools selectedTool = Tools.finger;
private ShapePainterListener myListener = null;
@Deprecated
public List pathList = new ArrayList();
private String toolTip = null;
private Point toolTipPosition = null;
private double toolTipCurrentScale = 100d;
private boolean showObjectToolTip = false;
private MixtureStatistics mixStats = null;
public TiledImagePainter bimg = new TiledImagePainter();
private List> taskList = null;
private Hashtable threadProgress = null;
private long startTime = 0L;
private FeatureDescription featureDescription = new FeatureDescription(); // with default values
private float classImageScale = 1.0f; // additional scaleFactor, e.g. if classification has been done on MIP image.
private transient RenderThread _renderThread = null;
private static final Color annotationBackgroundColor = new Color(1f, 1f, 1f, 0.6f);
private boolean displayAnnotationLabels = true;
// private ExclusionMapGen exMapGen = null;
private double mipScale = 1d;
private static final boolean ignoreRepaint = true;
private static final boolean opaque = false;
private static final boolean doubleBuffered = false;
private static final AtomicInteger activeAnnotationGroup = new AtomicInteger(0); // annotation group -> see annotationPanel
private BufferedImage screenImage = null;
private BufferedImage lastImage = null;
// private Image smallImage = null;
private ScreenProps screenProps = null;
private AtomicBoolean forceRepaint = new AtomicBoolean(true);
/**
* @param picObj can ob url or orbitId
* @throws OrbitImageServletException
*/
public RecognitionFrame(Object picObj) throws OrbitImageServletException {
this(picObj, false);
}
public RecognitionFrame(Object picName, boolean fromResource) throws OrbitImageServletException {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
//this.fromResource = fromResource;
classShapes.clear();
classShapes.addAll(OrbitUtils.buildDefaultClassShapes());
ratio = new double[classShapes.size()];
if (picName != null)
loadImage(picName, fromResource);
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
myListener = new ShapePainterListener(this.getClassShapes().get(0).getShapeList(), this.getClassShapes().get(0).getName(), this); // at least one class has to exist!
this.addMouseListener(myListener);
this.addMouseMotionListener(myListener);
this.addMouseWheelListener(myListener);
}
public RecognitionFrame(Object picName, boolean fromResource, List classShapes, FeatureDescription featureDescription) {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
//this.fromResource = fromResource;
this.classShapes.clear();
this.classShapes.addAll(classShapes);
this.featureDescription = featureDescription;
this.windowSize = featureDescription.getWindowSize();
ratio = new double[classShapes.size()];
if (picName != null)
try {
loadImage(picName, fromResource);
} catch (OrbitImageServletException e) {
e.printStackTrace();
}
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
myListener = new ShapePainterListener(this.getClassShapes().get(0).getShapeList(), this.getClassShapes().get(0).getName(), this); // at least one class has to exist!
addMouseListeners();
}
/**
* Creates a recognitionframe based on a MIP image of a parent recognition frame.
* Sets classShapes (copy), featureDescription, ratio and picName according to the parent.
* MouseListeners (ShapePainterListener) will be set if addMouseListeners is true.
* No check if requested MIP exists will be performed!
*
* @param parent
* @param mipNum
*/
public RecognitionFrame(RecognitionFrame parent, int mipNum, boolean addMouseListeners) {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
this.classShapes.clear();
this.classShapes.addAll(OrbitUtils.cloneClassShapes(parent.getClassShapes()));
this.featureDescription = parent.getFeatureDescription();
this.windowSize = parent.getWindowSize();
this.ratio = parent.getRatio();
this.picName = parent.getPicName();
this.bimg = parent.bimg.getMipMaps()[mipNum];
this.muMeterPerPixel = parent.getMuMeterPerPixel() * (parent.bimg.getWidth() / (double) this.bimg.getWidth());
this.setGaugeColor(parent.getGaugeColor());
if (parent != null) {
this.mipScale = (double) this.bimg.getWidth() / (double) parent.bimg.getWidth();
// copy scaled roi
if (parent.getROI() != null) {
IScaleableShape roiScaled = (IScaleableShape) parent.getROI().getScaledInstance(((mipScale) * 100d), new Point(0, 0));
roiScaled = roiScaled.clone();
roiScaled.setScale(100d);
this.setROI(roiScaled);
}
}
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
if (addMouseListeners) {
myListener = new ShapePainterListener(this.getClassShapes().get(0).getShapeList(), this.getClassShapes().get(0).getName(), this); // at least one class has to exist!
this.addMouseListener(myListener);
this.addMouseMotionListener(myListener);
try {
this.addMouseWheelListener(myListener);
} catch (Exception e) {
}
}
}
public RecognitionFrame(TiledImagePainter tip) {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
this.classShapes.clear();
this.classShapes.addAll(OrbitUtils.buildDefaultClassShapes());
ratio = new double[classShapes.size()];
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
if (tip != null) {
bimg = tip;
}
}
public RecognitionFrame(IOrbitImage orbitImage, String imageName) throws Exception {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
this.classShapes.clear();
this.classShapes.addAll(OrbitUtils.buildDefaultClassShapes());
ratio = new double[classShapes.size()];
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
OrbitTiledImageIOrbitImage img = new OrbitTiledImageIOrbitImage(orbitImage);
TiledImagePainter tip = new TiledImagePainter(img,imageName);
if (tip != null) {
bimg = tip;
}
}
public RecognitionFrame(RecognitionFrame parent, RawDataFile rdf, int level) {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
this.classShapes.clear();
if (parent != null) {
this.classShapes.addAll(OrbitUtils.cloneClassShapes(parent.getClassShapes()));
this.featureDescription = parent.getFeatureDescription();
this.windowSize = parent.getWindowSize();
this.ratio = parent.getRatio();
} else {
classShapes.clear();
classShapes.addAll(OrbitUtils.buildDefaultClassShapes());
ratio = new double[classShapes.size()];
}
this.picName = rdf.getFileName() + " [" + level + "]";
try {
TiledImagePainter tip = new TiledImagePainter();
tip.loadImageSpecial(rdf, level);
if (tip == null) {
logger.error("Special image not available");
}
if (true) {
myListener = new ShapePainterListener(this.getClassShapes().get(0).getShapeList(), this.getClassShapes().get(0).getName(), this); // at least one class has to exist!
this.addMouseListener(myListener);
this.addMouseMotionListener(myListener);
try {
this.addMouseWheelListener(myListener);
} catch (Exception e) {
}
}
this.bimg = tip;
if (parent != null)
this.mipScale = (double) this.bimg.getWidth() / (double) parent.bimg.getWidth();
logger.trace("loading level {} image with width {}", level, this.bimg.getWidth());
if (parent != null) {
this.muMeterPerPixel = parent.getMuMeterPerPixel() * (parent.bimg.getWidth() / (double) this.bimg.getWidth());
this.setGaugeColor(parent.getGaugeColor());
// copy scaled roi
if (parent.getROI() != null) {
IScaleableShape roiScaled = (IScaleableShape) parent.getROI().getScaledInstance(((mipScale) * 100d), new Point(0, 0));
roiScaled = roiScaled.clone();
roiScaled.setScale(100d);
this.setROI(roiScaled);
}
this.bimg.getImage().setAnalysisHues(parent.bimg.getImage().getAnalysisHues());
this.bimg.getImage().setChannelContributionsClassification(parent.bimg.getImage().getChannelContributionsClassification());
if (parent.getObjectSegmentationList() != null) {
// copy parent segmentations (important for object classification)
double originalCurrentFrameRatioInverse = parent.bimg.getImage().getWidth() / (double) this.bimg.getImage().getWidth();
if (this.getObjectSegmentationList() == null)
this.setObjectSegmentationList(new ArrayList(parent.getObjectSegmentationList().size()));
this.getObjectSegmentationList().clear();
for (Shape shape : parent.getObjectSegmentationList()) {
this.getObjectSegmentationList().add(((IScaleableShape) shape).getScaledInstance(originalCurrentFrameRatioInverse * 100d, new Point(0, 0)));
}
}
}
} catch (Exception e) {
logger.error("error loading special image", e);
}
}
public RecognitionFrame(RecognitionFrame parent, RawDataFile rdf, double scaleFactor) {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
this.classShapes.clear();
if (parent != null) {
this.classShapes.addAll(OrbitUtils.cloneClassShapes(parent.getClassShapes()));
this.featureDescription = parent.getFeatureDescription();
this.windowSize = parent.getWindowSize();
this.ratio = parent.getRatio();
} else {
classShapes.clear();
classShapes.addAll(OrbitUtils.buildDefaultClassShapes());
ratio = new double[classShapes.size()];
}
this.picName = rdf.getFileName() + " [" + scaleFactor + "]";
try {
TiledImagePainter tip = new TiledImagePainter();
tip.loadImageScaleFactor(rdf, scaleFactor, parent.bimg.getImage().getWidth());
if (tip == null) {
logger.error("Special image not available");
}
if (true) {
myListener = new ShapePainterListener(this.getClassShapes().get(0).getShapeList(), this.getClassShapes().get(0).getName(), this); // at least one class has to exist!
this.addMouseListener(myListener);
this.addMouseMotionListener(myListener);
try {
this.addMouseWheelListener(myListener);
} catch (Exception e) {
}
}
this.bimg = tip;
if (parent != null)
this.mipScale = (double) this.bimg.getWidth() / (double) parent.bimg.getWidth();
logger.trace("loading targetWidth {} image by scaleFactor {}", scaleFactor, this.bimg.getWidth());
if (parent != null) {
this.muMeterPerPixel = parent.getMuMeterPerPixel() * (parent.bimg.getWidth() / (double) this.bimg.getWidth());
this.setGaugeColor(parent.getGaugeColor());
// copy scaled roi
if (parent.getROI() != null) {
IScaleableShape roiScaled = (IScaleableShape) parent.getROI().getScaledInstance(((mipScale) * 100d), new Point(0, 0));
roiScaled = roiScaled.clone();
roiScaled.setScale(100d);
this.setROI(roiScaled);
}
this.bimg.getImage().setAnalysisHues(parent.bimg.getImage().getAnalysisHues());
this.bimg.getImage().setChannelContributionsClassification(parent.bimg.getImage().getChannelContributionsClassification());
// System.out.println("channelContribs: "+Arrays.toString(this.bimg.getImage().getChannelContributionsClassification()));
if (parent.getObjectSegmentationList() != null) {
// copy parent segmentations (important for object classification)
double originalCurrentFrameRatioInverse = parent.bimg.getImage().getWidth() / (double) this.bimg.getImage().getWidth();
if (this.getObjectSegmentationList() == null)
this.setObjectSegmentationList(new ArrayList(parent.getObjectSegmentationList().size()));
this.getObjectSegmentationList().clear();
for (Shape shape : parent.getObjectSegmentationList()) {
this.getObjectSegmentationList().add(((IScaleableShape) shape).getScaledInstance(originalCurrentFrameRatioInverse * 100d, new Point(0, 0)));
}
}
}
} catch (Exception e) {
logger.error("error loading special image", e);
}
}
/**
* clones the parent RecognitionFrame. The TiledImagePainter (bimg) will be referenced (not really cloned)!!!
*
* @param parent
* @param addMouseListeners
*/
public RecognitionFrame(RecognitionFrame parent, boolean addMouseListeners) {
this.setOpaque(opaque);
this.setIgnoreRepaint(ignoreRepaint);
this.setDoubleBuffered(doubleBuffered);
this.classShapes.clear();
this.classShapes.addAll(OrbitUtils.cloneClassShapes(parent.getClassShapes()));
this.featureDescription = parent.getFeatureDescription();
this.windowSize = parent.getWindowSize();
this.ratio = parent.getRatio();
this.picName = parent.getPicName();
this.bimg = parent.bimg;
this.muMeterPerPixel = parent.muMeterPerPixel;
this.gaugeColor = parent.getGaugeColor();
// copy scaled roi
if (parent.getROI() != null) {
IScaleableShape roiScaled = (IScaleableShape) parent.getROI().getScaledInstance((((double) this.bimg.getWidth() / parent.bimg.getWidth()) * 100d), new Point(0, 0));
roiScaled = roiScaled.clone();
roiScaled.setScale(100d);
this.setROI(roiScaled);
}
setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
if (addMouseListeners) {
myListener = new ShapePainterListener(this.getClassShapes().get(0).getShapeList(), this.getClassShapes().get(0).getName(), this); // at least one class has to exist!
this.addMouseListener(myListener);
this.addMouseMotionListener(myListener);
try {
this.addMouseWheelListener(myListener);
} catch (Exception e) {
}
}
}
/**
* Constructs and sets a TiledImageWriter-based new classification image.
*/
public void constructClassificationImage() {
setClassImage(new TiledImageWriter(bimg.getWidth(), bimg.getHeight(), bimg.getTileWidth(), bimg.getTileHeight()));
}
public Point[] getTiles() {
return bimg.getImage().getTileIndices(null);
}
public Point[] getTiles(Rectangle rectangle) {
return bimg.getImage().getTileIndices(rectangle);
}
public WritableRaster getWritableClassificationTile(int tileX, int tileY) {
return classImage.getImage().getWritableTile(tileX, tileY);
}
public void releaseWritableClassificationTile(int tileX, int tileY) {
classImage.getImage().releaseWritableTile(tileX, tileY);
}
public Raster getTile(int tileX, int tileY) {
return bimg.getImage().getTile(tileX, tileY);
}
/**
* singleton factory for renderThread
*
* @return
*/
private synchronized RenderThread getRenderThread() {
if (_renderThread == null) {
_renderThread = new RenderThread(this);
_renderThread.setName("renderThread");
_renderThread.addPropertyChangeListener(this);
_renderThread.start();
}
return _renderThread;
}
/**
* returns the renderthread without instantiation.
* This might return null if the private getRenderThread (singleton) has never been called (for small images).
*
* @return
*/
public RenderThread getRenderThreadOriginal() {
return _renderThread;
}
public void addMouseListeners() {
try {
addMouseListener(myListener);
addMouseMotionListener(myListener);
addMouseWheelListener(myListener); // >= Java 1.6
} catch (Exception ex) {
}
}
public void removeMouseListeners() {
try {
removeMouseListener(myListener);
removeMouseMotionListener(myListener);
removeMouseWheelListener(myListener); // >= Java 1.6
} catch (Exception ex) {
}
}
/**
* Obsolete since version 1.90i (no setPreferredSize done anymore)
*/
@Deprecated
public void scaleImage(double percentage) {
scale = percentage;
double scaleFactor = scale / 100d;
double sizeX = bimg.getWidth() * scaleFactor;
double sizeY = bimg.getHeight() * scaleFactor;
this.setPreferredSize(new Dimension((int) sizeX, (int) sizeY));
}
public void loadImage(Object picNameOrUrl, boolean fromResource) throws OrbitImageServletException {
loadImage(picNameOrUrl, fromResource, 0, 0, true);
}
public void loadImage(Object picNameOrUrl, boolean fromResource, int width, int height, boolean scaleIs100) throws OrbitImageServletException {
if (picNameOrUrl == null) return;
//this.fromResource= fromResource;
if (picNameOrUrl instanceof RawDataFile) {
this.picName = ((RawDataFile) picNameOrUrl).getFileName();
this.originalName = ((RawDataFile) picNameOrUrl).getRawDataFileId() + "";
} else {
this.picName = picNameOrUrl.toString();
this.originalName = picNameOrUrl.toString();
if (picNameOrUrl instanceof String) {
String[] splitStr = picNameOrUrl.toString().split("\\\\");
if (splitStr != null && splitStr.length > 0)
this.picName = splitStr[splitStr.length - 1]; // just the filename without the path before
}
}
try {
if (fromResource) picNameOrUrl = this.getClass().getResource(picName);
if (picNameOrUrl == null) picNameOrUrl = picName; // first load might be also a string
bimg.loadImage(picNameOrUrl);
//System.out.println("image: "+bimg.image);
//System.gc();
} catch (Exception e) {
logger.error("Error loading image. Probably the Orbit image server down or not accessible.\nError Details: ", e);
if (e instanceof OrbitImageServletException) {
throw new OrbitImageServletException(e.getMessage());
}
}
this.setPreferredSize(new Dimension(bimg.getWidth(), bimg.getHeight()));
}
public void paintComponent(Graphics g) {
if (bimg == null) return;
ScreenProps currentScreenprops = new ScreenProps(viewPortOffset.getX(),viewPortOffset.getY(),viewPortSize.getWidth(),viewPortSize.getHeight(),scale);
if (screenImage==null || g.getClipBounds().width!=screenImage.getWidth() || g.getClipBounds().height!=screenImage.getHeight()) {
GraphicsConfiguration gconf = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice().getDefaultConfiguration();
screenImage = gconf.createCompatibleImage(g.getClipBounds().width, g.getClipBounds().height);
forceRepaint.set(true);
}
//Graphics2D g2d = (Graphics2D) g;
Graphics2D g2d = screenImage.createGraphics();
try {
// "viewPort"
//System.out.println("vpSize: "+viewPortSize+" vpOffs: "+viewPortOffset+" image: "+bimg.image);
// GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice().getDefaultConfiguration().createCompatibleImage(height, width, Transparency.OPAQUE);
if (viewPortSize.getWidth() <= 0 || viewPortSize.getHeight() <= 0) return;
if (forceRepaint.get() || screenProps==null || !currentScreenprops.equals(screenProps)) {
g2d.setColor(this.getBackground());
g2d.fillRect(0, 0, screenImage.getWidth(), screenImage.getHeight());
}
g2d.translate(-viewPortOffset.getX(), -viewPortOffset.getY());
g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g2d.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_SPEED);
g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR);
g2d.setRenderingHint(RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_SPEED);
//g2d.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
AffineTransform oldTransform = g2d.getTransform();
double sc = getScale() / 100d;
double cx = getParent().getBounds().getCenterX();
double cy = getParent().getBounds().getCenterY();
double vpWidth = viewPortSize.getWidth();
double vpHeight = viewPortSize.getHeight();
if (forceRepaint.get() || screenProps==null || !currentScreenprops.equals(screenProps)) {
forceRepaint.set(false);
if (bimg.hasMipMaps()) {
// for TiledImagePainter rendering scale before drawing the image, for rendering from buffer scale after drawing the image
// if (smallImage==null) {
// smallImage = bimg.getMipMaps()[bimg.getMipMaps().length-1].getImage().getAsBufferedImage();
// VolatileImage vi = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice().getDefaultConfiguration().createCompatibleVolatileImage(smallImage.getWidth(this), smallImage.getHeight(this));
// smallImage = vi;
// //System.out.println("small image: "+smallImage);
// }
if (!getRenderThread().isBufferReady()) {
g2d.scale(sc, sc);
if (scale >= 100)
bimg.drawImage(g2d, viewPortOffset.getX(), viewPortOffset.getY(), vpWidth, vpHeight, getScale(), 0); // bimg.getMipMaps().length - 1 was: 0
//else if (scale>30) bimg.drawImage(g2d, viewPortOffset.getX(),viewPortOffset.getY(),vpWidth,vpHeight,getScale(),bimg.getMipMaps().length-2);
else
bimg.drawImage(g2d, viewPortOffset.getX(), viewPortOffset.getY(), vpWidth, vpHeight, getScale(), bimg.getMipMaps().length - 1);
} else {
Image image = getRenderThread().getImageBuffer();
int vpX = (int) viewPortOffset.getX();
int vpY = (int) viewPortOffset.getY();
g2d.drawImage(image, vpX, vpY, this);
g2d.scale(sc, sc);
}
} else // no mipMaps, so normal rendering
{
g2d.scale(sc, sc);
bimg.drawImage(g2d, viewPortOffset.getX(), viewPortOffset.getY(), vpWidth, vpHeight, getScale(), -1);
}
}
screenProps = currentScreenprops;
// g2d.scale(sc, sc);
// bimg.drawImage(g2d, viewPortOffset.x,viewPortOffset.y,vpWidth,vpHeight,getScale(),-1);
// pathList
if (pathList != null) {
g2d.setColor(Color.red);
//pathList.drawPolygon(g2d);
for (Point p : pathList) {
g2d.fillRect(p.x, p.y, 1, 1);
}
}
if ((toolTip != null) && (toolTipPosition != null)) {
Color oldFront = g2d.getColor();
g2d.setColor(Color.yellow);
g2d.setFont(toolTipFont);
g2d.drawString(toolTip, toolTipPosition.x, toolTipPosition.y);
g2d.setColor(oldFront);
}
if (classBounds != null) {
g2d.setColor(Color.black);
g2d.drawArc((int) classBounds.x, (int) classBounds.y, (int) classBounds.width, (int) classBounds.height, 0, 360);
}
// TODO
/*
if ((exMapGen!=null && exMapGen.getRecognitionFrame()!=null && exMapGen.getRecognitionFrame().getClassImage()!=null) && (opacity>0))
{
AffineTransform af = g2d.getTransform();
g2d.scale(classImageScale, classImageScale);
Rectangle rbb = new Rectangle(viewPortOffset.x, viewPortOffset.y, vpWidth, vpHeight);
if (ROI!=null) {
Rectangle roiBB = ROI.getScaledInstance(getScale(), new Point((int)cx,(int)cy)).getBounds();
if (rbb.intersects(roiBB))
rbb = rbb.intersection(roiBB);
}
exMapGen.getRecognitionFrame().getClassImage().drawImage(g2d, rbb.x,rbb.y,rbb.width,rbb.height,getScale()*classImageScale,opacity);
//classImage.drawImage(g2d, viewPortOffset.x,viewPortOffset.y,viewPortSize.width,viewPortSize.height,getScale()*classImageScale,opacity);
g2d.setTransform(af);
}
*/
TiledImageWriter.timeOut.set(System.currentTimeMillis());
if ((classImage != null) && (opacity > 0) && classImage.getPainting().get() == false) {
AffineTransform af = g2d.getTransform();
g2d.scale(classImageScale, classImageScale);
Rectangle rbb = new Rectangle((int) viewPortOffset.getX(), (int) viewPortOffset.getY(), (int) vpWidth, (int) vpHeight);
if (ROI != null) {
Rectangle roiBB = ROI.getScaledInstance(getScale(), new Point((int) cx, (int) cy)).getBounds();
if (roiBB != null /*&& rbb.intersects(roiBB)*/) {
rbb = rbb.intersection(roiBB);
}
}
Composite composite = g2d.getComposite();
g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, opacity));
classImage.drawImage(g2d, rbb.x, rbb.y, rbb.width, rbb.height, getScale() * classImageScale); // opacity
//classImage.drawImage(g2d, viewPortOffset.x,viewPortOffset.y,viewPortSize.width,viewPortSize.height,getScale()*classImageScale,opacity);
g2d.setComposite(composite);
g2d.setTransform(af);
}
if (classImage != null) {
if (drawMarkup) // draw found regions/objects
{
if (classList != null && classList.size() > 0) {
g2d.setColor(Color.white);
if (classListLock.readLock().tryLock()) {
try {
for (Polygon poly : classList) {
Rectangle rec = poly.getBounds();
g2d.drawArc((int) rec.getCenterX() - (int) segmentationClassSize / 2, (int) rec.getCenterY() - (int) segmentationClassSize / 2, (int) segmentationClassSize, (int) segmentationClassSize, 0, 360);
}
} finally {
classListLock.readLock().unlock();
}
}
}
if (objectSegmentationList != null) {
try {
double scaleFactor = (getScale() / 100d);
int segSize = objectSegmentationList.size();
for (int i = 0; i < segSize; i++) {
Shape shape = objectSegmentationList.get(i);
if (shape == null) continue;
Point pos = null;
// try {
pos = new Point((int) (myListener.getMousePosition().x / scaleFactor), (int) (myListener.getMousePosition().y / scaleFactor));
// } catch (NullPointerException ex) {
// }
if ((objectClassificationList != null) && (objectClassificationList.length == objectSegmentationList.size()) && (objectClassificationList[i] >= 0)) { // draw classification of objects (e.g. cells)
g2d.setColor(classShapes.get(objectClassificationList[i]).getColor());
if (shape instanceof Polygon)
g2d.fillPolygon((Polygon) shape);
}
if (pos != null && shape.contains(pos)) g2d.setColor(Color.red);
else {
g2d.setColor(Color.yellow);
if (objectSegmentationColors != null && objectSegmentationColors.size() == segSize) {
g2d.setColor(objectSegmentationColors.get(i));
}
}
if (shape instanceof Polygon) {
if (objectSegmentationColors != null && objectSegmentationColors.size() == segSize)
g2d.fillPolygon((Polygon) shape);
else drawPolygonLine((Polygon) shape, g2d);
}
}
} catch (Exception e) {
// might fail because objectSegmentationList is null -> better use a final synchronized list
}
}
if (secondaryObjectSegmentationList != null) {
try {
double scaleFactor = (getScale() / 100d);
int segSize = secondaryObjectSegmentationList.size();
for (int i = 0; i < segSize; i++) {
Shape shape = secondaryObjectSegmentationList.get(i);
if (shape == null) continue;
Point pos = null;
pos = new Point((int) (myListener.getMousePosition().x / scaleFactor), (int) (myListener.getMousePosition().y / scaleFactor));
if (pos != null && shape.contains(pos)) g2d.setColor(Color.red);
else g2d.setColor(Color.green);
if (shape instanceof Polygon) {
drawPolygonLine((Polygon) shape, g2d);
}
}
} catch (Exception e) {
// might fail because objectSegmentationList is null -> better use a final synchronized list
}
}
if (centerList != null) {
for (Point center : centerList) {
g2d.setColor(Color.red);
g2d.drawRect(center.x - 1, center.y - 1, 3, 3);
}
}
/*
if (centroidList!=null) {
for (Point centroid: centroidList) {
g2d.setColor(Color.green);
g2d.drawRect(centroid.x-1,centroid.y-1,3,3);
}
}
*/
}
}
g2d.setTransform(oldTransform);
g2d.setColor(Color.white);
// draw arc or fixed rectangle if in arc mode at mouse position
MouseListener listener = myListener;
if (listener instanceof ShapePainterListener) {
// arc
if (((ShapePainterListener) listener).getShapeMode() == ClassShape.SHAPETYPE_ARC &&
(!((ShapePainterListener) listener).isDeleteMode())) {
Point mp = ((ShapePainterListener) listener).getMousePosition();
if (mp != null) {
int r = (int) getTargetRadius();
Arc2D p = new Arc2D.Double(Arc2D.CHORD);
p.setArcByCenter(mp.getX(), mp.getY(), r, 0d, 360d, Arc2D.CHORD);
g2d.drawArc((int) p.getX(), (int) p.getY(), (int) p.getWidth(), (int) p.getHeight(), 0, 360);
}
}
// fixed rectangle
if (((ShapePainterListener) listener).getShapeMode() == ClassShape.SHAPETYPE_RECTANGLE &&
((ShapePainterListener) listener).isFixedRectangle() == true &&
(!((ShapePainterListener) listener).isDeleteMode())) {
Point mp = ((ShapePainterListener) listener).getMousePosition();
if (mp != null) {
int r = (int) getTargetRadius();
double fixedRectangleRatio = ((ShapePainterListener) listener).getFixedRectangleRatio();
//int w = r/2;
int w = (int) ((r / 2) * (getScale() / 100d));
int h = (int) ((double) w * fixedRectangleRatio);
g2d.drawRect(mp.x - w, mp.y - h, w * 2, h * 2);
}
}
} else logger.error("error: MouseListener is not a ShapePainterListener");
// toolTip
if ((showObjectToolTip == true) && (toolTipPosition != null) && (mixStats != null) && (objectSegmentationList != null)) {
String tip = null;
double scaleFactor = (getScale() / 100d);
Point pos = new Point((int) (toolTipPosition.x / scaleFactor), (int) (toolTipPosition.y / scaleFactor));
for (int i = 0; i < objectSegmentationList.size(); i++) {
if (objectSegmentationList.get(i).contains(pos)) {
tip = mixStats.getObjDescription(i);
break;
}
}
if (tip != null) {
//Color oldFront = g2d.getColor();
g2d.setFont(toolTipFont);
Rectangle2D r = toolTipFont.getStringBounds(tip, g2d.getFontRenderContext());
g2d.setColor(Color.white);
g2d.fillRoundRect((int) r.getX() + toolTipPosition.x - 3, (int) r.getY() + toolTipPosition.y - 3, (int) r.getWidth() + 6, (int) r.getHeight() + 6, 12, 12);
g2d.setColor(Color.black);
g2d.drawString(tip, toolTipPosition.x, toolTipPosition.y);
//g2d.setColor(oldFront);
}
}
// draw ploygons
Point currentOffs = new Point((int) cx, (int) cy);
if (drawMarkup) {
int csCnt = 0;
synchronized (classShapes) {
for (ClassShape classShape : classShapes) {
csCnt++;
if (csCnt > maxClassShapesToPaint) break;
if (classShape.getShapeList() != null) {
g2d.setColor(classShape.getColor());
for (Shape p : classShape.getShapeList()) {
//AffineTransform af = AffineTransform.getScaleInstance(0.9d, 0.9d);
//Path2D p2 = (Path2D)af.createTransformedShape(p);
if (p instanceof PolygonExt) {
drawPolygonLine(((PolygonExt) p).getScaledInstance(getScale(), currentOffs), g2d);
} else if (p instanceof Arc2DExt) {
if (p instanceof Arc2DExt)
p = ((Arc2DExt) p).getScaledInstance(getScale(), currentOffs);
g2d.drawArc((int) ((Arc2DExt) p).getX(), (int) ((Arc2DExt) p).getY(), (int) ((Arc2DExt) p).getWidth(), (int) ((Arc2DExt) p).getHeight(), 0, 360);
} else if (p instanceof RectangleExt) {
RectangleExt re = ((RectangleExt) p).getScaledInstance(getScale(), currentOffs);
g2d.drawRect((int) re.getX(), (int) re.getY(), (int) re.getWidth(), (int) re.getHeight());
}
}
}
}
} // synchronized(classShapes)
// draw Annotations
Stroke oldStroke = g2d.getStroke();
g2d.setStroke(new BasicStroke(2));
synchronized (annotations) {
OrbitModel model = null;
if (annotations != null && annotations.size() > 0) {
model = OrbitImageAnalysis.getInstance().getModel();
}
for (ImageAnnotation annotation : annotations) {
if (getActiveAnnotationGroup().get() > 0) { // filter annotations by group
if (getActiveAnnotationGroup().get() != annotation.getGroup()) {
continue; // skip displaying annotation (group not active)
}
}
Point jitterOffs = (Point) currentOffs.clone();
ClassShape classShape = annotation.getShape();
if (classShape != null && classShape.getShapeList() != null) {
double addscale = 1d;
g2d.setColor(classShape.getColor());
if (annotation.isSelected()) { // highlight selected annotation
g2d.setColor(Color.magenta);
}
if (annotation instanceof SpotAnnotation) {
SpotAnnotation sa = (SpotAnnotation) annotation;
if (sa.isSelected()) {
g2d.setColor(Color.yellow);
} else {
// set class color
if (sa.getClassNum() >= 0 && model != null && model.getClassShapes().size() > sa.getClassNum()) {
g2d.setColor(model.getClassShapes().get(sa.getClassNum()).getColor());
}
}
}
for (Shape p : classShape.getShapeList()) {
if (p instanceof PolygonExt) {
drawPolygonLine(((PolygonExt) p).getScaledInstance(getScale(), currentOffs), g2d);
} else if (p instanceof Arc2DExt) {
if (p instanceof Arc2DExt)
p = ((Arc2DExt) p).getScaledInstance(getScale(), currentOffs);
g2d.drawArc((int) ((Arc2DExt) p).getX(), (int) ((Arc2DExt) p).getY(), (int) ((Arc2DExt) p).getWidth(), (int) ((Arc2DExt) p).getHeight(), 0, 360);
} else if (p instanceof RectangleExt) {
RectangleExt re = ((RectangleExt) p).getScaledInstance(getScale(), currentOffs);
g2d.drawRect((int) re.getX(), (int) re.getY(), (int) re.getWidth(), (int) re.getHeight());
}
if (displayAnnotationLabels && (p instanceof PolygonExt) && (((PolygonExt) p).isClosed())) {
Rectangle br = p.getBounds();
Point uppRight = getUppedRightPoint((PolygonExt) p);
int ax = br.x + br.width;
int ay = br.y;
double scaleFactor = (getScale() / ((IScaleableShape) p).getScale());
ax = (int) (ax * scaleFactor);
ay = (int) (ay * scaleFactor);
int dx = (int) (uppRight.x * scaleFactor);
int dy = (int) (uppRight.y * scaleFactor);
g2d.setFont(toolTipFont);
String text = annotation.getDescription();
if (text.length() > 40) text = text.subSequence(0, 40) + "...";
Rectangle2D r = toolTipFont.getStringBounds(text, g2d.getFontRenderContext());
g2d.setColor(annotationBackgroundColor);
g2d.fillRoundRect((int) r.getX() + ax - 3, (int) r.getY() + ay - 3, (int) r.getWidth() + 6, (int) r.getHeight() + 6, 12, 12);
g2d.drawLine(dx, dy, ax, ay);
g2d.setColor(Color.black);
g2d.drawString(text, ax, ay);
}
}
}
} // annotations
} // synchronized annotations
g2d.setStroke(oldStroke);
// drow ROI
if (ROI != null && (ROI instanceof PolygonExt)) {
g2d.setColor(Color.yellow);
//g2d.setXORMode(Color.white);
drawPolygonLine(((PolygonExt) ROI).getScaledInstance(getScale(), currentOffs), g2d);
}
} // drawMarkup
// without vieportOffset
g2d.translate(viewPortOffset.getX(), viewPortOffset.getY());
if (muMeterPerPixel > 0 && OrbitImageAnalysis.getInstance().isShowGauge()) {
final int gaugeLen = 100;
// Component c = getParent().getParent().getParent().getParent().getParent(); // imageFrame
// int gaugeY = c.getHeight()-100+viewPortOffset.y;
// int gaugeX = 20+viewPortOffset.x;
//
int gaugeY = getHeight() - 40; // was -80
int gaugeX = 20;
double gaugeVal = (double) gaugeLen * muMeterPerPixel * (1d / sc);
//g.setColor(Color.white);
//g.fillRect(gaugeX, gaugeY, gaugeLen, 15);
g2d.setColor(gaugeColor);
g2d.drawLine(gaugeX, gaugeY, gaugeX + gaugeLen, gaugeY);
g2d.drawLine(gaugeX, gaugeY - 10, gaugeX, gaugeY + 10);
g2d.drawLine(gaugeX + gaugeLen, gaugeY - 10, gaugeX + gaugeLen, gaugeY + 10);
g2d.drawString(String.format("%1$.2f µm", gaugeVal), gaugeX + 5, gaugeY + 13);
}
} catch (Exception e) {
e.printStackTrace();
} finally {
g.drawImage(screenImage,0,0,null);
g2d.dispose();
}
}
public void prepareBuffer() {
if (bimg != null && bimg.hasMipMaps()) {
getRenderThread().setValuesDirty(true);
//if (renderThread.isScheduleUpdate()) return;
//renderThread.stop();
//renderThread = new RenderThread();
//renderThread.addPropertyChangeListener(this);
getRenderThread().setScale(getScale());
getRenderThread().setViewPortWidth(getViewPortSize().getWidth());
getRenderThread().setViewPortHeight(getViewPortSize().getHeight());
getRenderThread().setViewPortOffsetX(getViewPortOffset().getX());
getRenderThread().setViewPortOffsetY(getViewPortOffset().getY());
getRenderThread().setTiledImagePainter(bimg);
getRenderThread().setScheduleUpdate(true);
//renderThread.start();
}
}
@Override
public void repaint() {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
super.repaint();
}
@Override
public void repaint(long tm, int x, int y, int width, int height) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
super.repaint(tm, x, y, width, height);
}
@Override
public void repaint(Rectangle r) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
super.repaint(r);
}
@Override
public void repaint(int x, int y, int width, int height) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
super.repaint(x, y, width, height);
}
@Override
public void repaint(long tm) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
super.repaint(tm);
}
@Override
public void update(Graphics g) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
super.update(g);
}
/**
* set all pixels in classImage with class label in oldClasses to the newClass label (for two class sets, e.g. set inclusion and exclusion at once)
*/
public void changeClassLabels(List oldClasses1, Byte newClass1, List oldClasses2, Byte newClass2) {
if (classImage == null)
throw new IllegalArgumentException("classImage is null, please perform a classification first.");
initializeClassColors();
Color c1 = classShapes.get(newClass1).getColor();
Color c2 = classShapes.get(newClass2).getColor();
Byte classVal;
Shape roi = null;
if (getROI() != null) roi = getROI().getScaledInstance(100d, new Point(0, 0));
Point[] tileList = classImage.getImage().getTileIndices(null);
for (Point tile : tileList) {
WritableRaster writeRaster = classImage.getImage().getWritableTile(tile.x, tile.y);
for (int x = classImage.getImage().tileXToX(tile.x); x < classImage.getImage().tileXToX(tile.x) + classImage.getImage().getTileWidth(); x++)
for (int y = classImage.getImage().tileYToY(tile.y); y < classImage.getImage().tileYToY(tile.y) + classImage.getImage().getTileHeight(); y++) {
if ((roi == null) || (roi.contains(x, y))) {
classVal = getClass(x, y, writeRaster);
if (classVal != null) {
for (Byte cv : oldClasses1) {
if (cv == classVal) {
writeRaster.setPixel(x, y, new int[]{c1.getRed(), c1.getGreen(), c1.getBlue(), 255});
break;
}
}
for (Byte cv : oldClasses2) {
if (cv == classVal) {
writeRaster.setPixel(x, y, new int[]{c2.getRed(), c2.getGreen(), c2.getBlue(), 255});
break;
}
}
}
} // ROI check
} // x,y
classImage.getImage().releaseWritableTile(tile.x, tile.y);
//DiskMemImage.getCommonTileCache().flush(); // really needed?
} // tile
}
public void makeImageSnapshot() {
if (((long) bimg.getWidth() * bimg.getHeight()) > (8000L * 8000L)) {
JOptionPane.showMessageDialog(this, "In the current version this feature can only be used for images where width*height <= 8000*8000.\nHowever, you can use the Orbit Agent to download the file.", "Image too large", JOptionPane.ERROR_MESSAGE);
return;
}
JFileChooser fc = new JFileChooser();
FileNameExtensionFilter filter = new FileNameExtensionFilter("*.tif", "tif");
fc.setFileFilter(filter);
String snapShotFileName = getPicName();
snapShotFileName = snapShotFileName.replaceAll(RawUtilsCommon.getExtension(snapShotFileName, false), "tif");
fc.setSelectedFile(new File(snapShotFileName));
int returnVal = fc.showSaveDialog(this);
if (returnVal == JFileChooser.APPROVE_OPTION) {
logger.debug("begin making image snapshot");
String fn = fc.getSelectedFile().getAbsolutePath();
if (!fn.toLowerCase().endsWith(".tif")) fn += ".tif";
Dimension2D oldVPSize = viewPortSize;
Point2D oldVPOffs = getViewPortOffset();
double sc = getScale();
setScale(100d);
setViewPortOffset(new Point(0, 0));
viewPortSize = new Dimension(bimg.getWidth(), bimg.getHeight());
/*
ColorModel colorModel = new ComponentColorModel(
ColorSpace.getInstance(ColorSpace.CS_sRGB),
new int[]{8,8,8}, false, false,
Transparency.OPAQUE,
DataBuffer.TYPE_BYTE);
SampleModel sampleModel = colorModel.createCompatibleSampleModel(256, 256);
DiskMemImage tiledImage = new DiskMemImage(0, 0, bimg.getWidth(), bimg.getHeight(), 0, 0, sampleModel, colorModel);
Graphics2D g2d = (Graphics2D)tiledImage.createGraphics();
((DiskMemImageGraphics)g2d).overwriteRenderingHint((((Graphics2D)getGraphics()).getRenderingHints()));
*/
// Update 1.7.2010: Fallback to normal bufferedImage (only up to 30kx30k pixel!)
// due to rendering problems with class image (only first tile problem)
BufferedImage buffImg = new BufferedImage(bimg.getWidth(), bimg.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D g2d = buffImg.createGraphics();
buffImg.flush();
paint(g2d);
setScale(sc);
setViewPortOffset(oldVPOffs);
viewPortSize = oldVPSize;
logger.info("finished painting");
TIFFEncodeParam param = new TIFFEncodeParam();
param.setTileSize(128, 128);
param.setWriteTiled(true);
param.setCompression(TIFFEncodeParam.COMPRESSION_JPEG_TTN2);
JPEGEncodeParam jpgParam = new JPEGEncodeParam();
jpgParam.setQuality(0.85f);
param.setJPEGEncodeParam(jpgParam);
// TODO: extraImages (Iterator where .next() returns further (low-res) RenderedImages
//param.setExtraImages(extraImages)
JAI.create("filestore", /*tiledImage*/buffImg, fn, "TIFF", param);
logger.info("finished writing");
JOptionPane.showMessageDialog(null, "Image successfully saved to " + fn, "Image saved", JOptionPane.INFORMATION_MESSAGE);
//tiledImage = null;
//DiskMemImage.getCommonTileCache().flush();
Runtime.getRuntime().gc();
Runtime.getRuntime().gc();
Runtime.getRuntime().gc();
logger.debug("cleaning up finished");
}
}
public BufferedImage getImageSnapshot() {
if (((long) bimg.getWidth() * bimg.getHeight()) > (30000 * 30000)) {
JOptionPane.showMessageDialog(this, "In the current version this feature can only be used for images where width*height <= 30000*30000.", "Image too large", JOptionPane.ERROR_MESSAGE);
return null;
}
Dimension2D oldVPSize = viewPortSize;
Point2D oldVPOffs = getViewPortOffset();
double sc = getScale();
setScale(100d);
setViewPortOffset(new Point(0, 0));
viewPortSize = new Dimension(bimg.getWidth(), bimg.getHeight());
BufferedImage buffImg = new BufferedImage(bimg.getWidth(), bimg.getHeight(), BufferedImage.TYPE_INT_RGB);
Graphics2D g2d = buffImg.createGraphics();
buffImg.flush();
paint(g2d);
setScale(sc);
setViewPortOffset(oldVPOffs);
viewPortSize = oldVPSize;
logger.debug("finished painting");
return buffImg;
}
/**
* (re)init of colorClassLookup
*/
public void initializeClassColors() {
//colorClassLookup = new HashMap(classShapes.size());
colorClassLookup.clear();
synchronized (classShapes) {
for (byte i = 0; i < classShapes.size(); i++) {
ClassShape cs = classShapes.get(i);
colorClassLookup.put(cs.getColor().getRGB(), i);
//System.out.println("init color: "+cs.getColor().toString()+" -> "+i+" ("+cs.getColor().getRGB()+")");
}
}
// System.out.println("CS: ");
// for (Integer i: colorClassLookup.keySet()) {
// System.out.println(i+":"+colorClassLookup.get(i));
// }
}
/**
* requires getObjectSegmentation to be called first
*
* @return
*/
public List getMixtures() {
if (objectSegmentationList == null) throw new RuntimeException("Error: call getObjectSegmentations first!");
if (classImage == null) throw new RuntimeException("Error: call classifyImage first!");
List mixList = new ArrayList(objectSegmentationList.size());
for (Shape shape : objectSegmentationList) {
int sum = 0;
double[] mix = new double[classShapes.size()];
for (int i = 0; i < mix.length; i++) mix[i] = 0d;
for (int x = (int) shape.getBounds().getMinX(); x < shape.getBounds().getMaxX(); x++)
for (int y = (int) shape.getBounds().getMinY(); y < shape.getBounds().getMaxY(); y++) {
if (shape.contains(x, y)) {
mix[getClass(x, y)]++;
sum++;
}
}
for (int i = 0; i < mix.length; i++) mix[i] = mix[i] / (double) sum;
mixList.add(mix);
}
return mixList;
}
private void drawPolygonLine(Polygon poly, Graphics g) {
if (poly instanceof PolygonExt) {
((PolygonExt) poly).drawPolygon(g);
} else {
g.drawPolygon(poly);
}
}
private Point getUppedRightPoint(Polygon poly) {
int x = poly.getBounds().x;
int y = poly.getBounds().y + poly.getBounds().height;
for (int i = 0; i < poly.npoints; i++) {
if (poly.xpoints[i] > x && poly.ypoints[i] < y) {
x = poly.xpoints[i];
y = poly.ypoints[i];
}
}
return new Point(x, y);
}
public static Color getColorByNum(int num) {
if (num < colors.length) return colors[num];
else return new Color((num * 10000) + rand.nextInt());
}
/**
* returns the class number (in byte) of a position (calls classImage.getPixel(x,y))
*
* @param x
* @param y
* @return
*/
public byte getClass(int x, int y) {
// TODO: performance! (but currently not so bad)
Byte b = colorClassLookup.get(classImage.getPixel(x, y));
if (b == null) return 0;
else return b;
}
/**
* returns the class number (in byte) of a position (calls classImage.getPixel(x,y))
* here the classImage can be specified (used by cell segmentation).
*
* @param x
* @param y
* @return
*/
public byte getClass(int x, int y, TiledImageWriter classImage2) {
Byte b = colorClassLookup.get(classImage2.getPixel(x, y));
if (b == null) {
return 0;
} else return b;
}
/**
* returns the class number (in byte) of a position (calls classImage.getPixel(x,y,raster))
* here the classImage can be specified (used by cell segmentation).
*
* @param x
* @param y
* @return
*/
public byte getClass(int x, int y, TiledImageWriter classImage2, Raster raster) {
Byte b = colorClassLookup.get(classImage2.getPixel(x, y, raster));
if (b == null) {
return 0;
} else return b;
}
/**
* returns the class number (in byte) of a position (calls classImage.getPixel(x,y,r))
* This is the more performant method where the raster is already available.
* Returns nullVal if x,y is outside ROI !
*
* @param x
* @param y
* @return
*/
public byte getClass(int x, int y, final Raster r, final byte nullVal) {
int i = classImage.getPixel(x, y, r);
if (i == OrbitUtils.UNDEF_COLOR) return nullVal; // black / undef
byte b = colorClassLookup.get(i);
return b;
}
/**
* returns the class number (in byte) of a position (calls classImage.getPixel(x,y,r))
* Can return null if x,y is outsite ROI !
* This is the more performant method where the raster is already available.
*
* @param x
* @param y
* @return
*/
public Byte getClass(int x, int y, final Raster r) {
int i = classImage.getPixel(x, y, r);
if (i == OrbitUtils.UNDEF_COLOR) return null; // black / undef
Byte b = colorClassLookup.get(i);
//if (b==null) System.out.println(i);
return b;
}
public List getClassShapes() {
return classShapes;
}
public void setClassShapes(List classShapes) {
synchronized (this.classShapes) {
this.classShapes.clear();
this.classShapes.addAll(classShapes);
ratio = new double[classShapes.size()];
}
}
public void setClassShapes(final List classShapes, int segmentationSize) {
synchronized (this.classShapes) {
this.classShapes.clear();
this.classShapes.addAll(classShapes);
this.segmentationClassSize = segmentationSize;
ratio = new double[classShapes.size()];
}
}
public void setModel(OrbitModel model) {
setClassShapes(model.getClassShapes());
setWindowSize(model.getFeatureDescription().getWindowSize());
setBoundaryClass(model.getBoundaryClass());
}
/**
* annotationGroup -1 means ignore, 0 means use all, otherwise the specific group
*
* @param rdfID
* @param annotationGroup
*/
public void loadAnnotationROI(int rdfID, int annotationGroup) {
loadAnnotationROI(rdfID, annotationGroup, false);
}
/**
* annotationGroup -1 means ignore, 0 means use all, otherwise the specific group
*
* @param rdfID
* @param annotationGroup
*/
public void loadAnnotationROI(int rdfID, int annotationGroup, boolean otherGroupROIAsExclusion) {
loadAnnotationROI(rdfID, annotationGroup, otherGroupROIAsExclusion, false);
}
/**
* annotationGroup -1 means ignore, 0 means use all, otherwise the specific group
*
* @param rdfID
* @param annotationGroup
*/
public void loadAnnotationROI(int rdfID, int annotationGroup, boolean otherGroupROIAsExclusion, boolean exclusionsForAllGroups) {
if (annotationGroup < 0) {
setROI(null);
return; // ignore
}
try {
IScaleableShape roi = OrbitUtils.loadAnnotationROI(rdfID, annotationGroup, otherGroupROIAsExclusion, exclusionsForAllGroups);
if ((roi != null) && Math.abs(mipScale - 1d) > OrbitUtils.EPSILON) {
roi = (IScaleableShape) roi.getScaledInstance(((mipScale) * 100d), new Point(0, 0));
roi.setScale(100d);
}
setROI(roi);
} catch (Exception e) {
logger.error("cannot load raw annotations", e);
}
}
/**
* load image annotations according to rdfID. Annotation with name ROI are used as ROI, if useAnnotationsAsInverseROI is true, all other annotations
* (description<>ROI are used as inverse ROI). ROI and inverse ROIs can be combined.
*/
@Deprecated
public void loadAnnotationROIOld(int rdfID, boolean useAnnotationsAsInverseROI) {
try {
List annotations = DALConfig.getImageProvider().LoadRawAnnotationsByRawDataFile(rdfID, RawAnnotation.ANNOTATION_TYPE_IMAGE);
List pList = new ArrayList(annotations.size());
Shape annotationROI = null;
for (RawAnnotation anno : annotations) {
if (anno.getRawAnnotationType() == RawAnnotation.ANNOTATION_TYPE_IMAGE) {
ImageAnnotation ia = new ImageAnnotation(anno);
if (ia.getShape().getShapeList().size() > 0) {
IScaleableShape poly = (IScaleableShape) ia.getShape().getShapeList().get(0);
IScaleableShape pScaled = (IScaleableShape) poly.getScaledInstance(100d, new Point(0, 0));
if (anno.getDescription().trim().equalsIgnoreCase("ROI")) {
annotationROI = pScaled;
} else {
if (useAnnotationsAsInverseROI)
pList.add(pScaled);
}
}
}
}
ShapeExtListInvers roi = new ShapeExtListInvers(annotationROI, pList, new Rectangle(Integer.MAX_VALUE, Integer.MAX_VALUE));
setROI(roi);
logger.trace("invers annotation ROI successfully set: " + pList.size());
} catch (Exception e) {
logger.error("cannot load raw annotations", e);
}
}
/**
* Creates a BufferedImage of the raster with 0,0 as origin and ColorModel from the current image (bimg.getImage()).
*/
public BufferedImage createBufferedImage(final Raster r) {
WritableRaster writableRaster = r.createCompatibleWritableRaster(r.getWidth(),r.getHeight());
writableRaster.setDataElements(0, 0, r.createTranslatedChild(0,0));
DataBuffer dataBuffer = writableRaster.getDataBuffer();
WritableRaster wr = Raster.createWritableRaster(bimg.getImage().getColorModel().createCompatibleSampleModel(writableRaster.getWidth(),writableRaster.getHeight()),
dataBuffer, new Point(0, 0));
BufferedImage bi = new BufferedImage(bimg.getImage().getColorModel(),
wr,
bimg.getImage().getColorModel().isAlphaPremultiplied(),
null);
return bi;
}
public BufferedImage getViewportImage(Point2D center, int vpWidth, int vpHeight) throws Exception {
if (bimg==null) throw new Exception("no image tiledImagePainter available (bimg=null)");
double vpX = -(vpWidth/2d);
double vpY = -(vpHeight/2d);
BufferedImage bi = new BufferedImage(vpWidth,vpHeight,BufferedImage.TYPE_INT_RGB);
Graphics2D g2d = (Graphics2D) bi.getGraphics();
g2d.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g2d.setRenderingHint(RenderingHints.KEY_ALPHA_INTERPOLATION, RenderingHints.VALUE_ALPHA_INTERPOLATION_QUALITY);
g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BICUBIC);
g2d.setRenderingHint(RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY);
double sc = scale / 100d;
double vpOffsX = center.getX()*sc +vpX;
double vpOffsY = center.getY()*sc +vpY;
g2d.translate(-vpOffsX,-vpOffsY);
g2d.scale(sc, sc);
bimg.drawImage(g2d,vpOffsX,vpOffsY,vpWidth,vpHeight,scale,0);
bi.flush();
return bi;
}
/**
* loads the mu meter per pixel meta data from raw meta database
*/
public void loadImageScale(int rdfId) {
setMuMeterPerPixel(OrbitUtils.loadImageScale(rdfId));
}
@Override
public String toString() {
return "RecognitionFrame [picName=" + picName + ", ROI=" + ROI + ", scale=" + scale + ", muMeterPerPixel=" + muMeterPerPixel + ", bimg=" + bimg + "]";
}
public String getPicName() {
return picName;
}
public void setPicName(String picName) {
this.picName = picName;
}
public float getOpacity() {
return opacity;
}
public void setOpacity(float opacity) {
forceRepaint.set(true);
this.opacity = opacity;
}
public double[] getRatio() {
return ratio;
}
public void setRatio(double[] ratio) {
this.ratio = ratio;
}
public TiledImageWriter getClassImage() {
return classImage;
}
public void setClassImage(TiledImageWriter classImage) {
this.classImage = classImage;
}
public boolean isDrawMarkup() {
return drawMarkup;
}
public void setDrawMarkup(boolean drawMarkup) {
this.drawMarkup = drawMarkup;
}
public double getTargetRadius() {
return targetRadius;
}
public void setTargetRadius(double targetRadius) {
this.targetRadius = targetRadius;
}
public int getWindowSize() {
return windowSize;
}
public void setWindowSize(int windowSize) {
this.windowSize = windowSize;
}
public double getSegmentationClassSize() {
return segmentationClassSize;
}
public void setSegmentationClassSize(double segmentationClassSize) {
this.segmentationClassSize = segmentationClassSize;
}
public List getClassList() {
return classList;
}
public void clearClassList() {
classListLock.writeLock().lock();
try {
this.classList.clear();
} finally {
classListLock.writeLock().unlock();
}
}
public List getObjectSegmentationList() {
return objectSegmentationList;
}
public void setObjectSegmentationList(List objectSegmentationList) {
this.objectSegmentationList = objectSegmentationList;
}
public List getObjectSegmentationColors() {
return objectSegmentationColors;
}
public void setObjectSegmentationColors(List objectSegmentationColors) {
this.objectSegmentationColors = objectSegmentationColors;
}
public List getCenterList() {
return centerList;
}
public void setCenterList(List centerList) {
this.centerList = centerList;
}
public List getCentroidList() {
return centroidList;
}
public void setCentroidList(List centroidList) {
this.centroidList = centroidList;
}
public void setScale(double scale) {
this.scale = scale;
prepareBuffer();
}
/**
* scale 0..100
*
* @return
*/
public double getScale() {
//return ((double)bimg.getWidth() / originalWidth)*(double)100;
return scale;
}
public Point2D getViewPortOffset() {
return viewPortOffset;
}
public void setViewPortOffset(Point2D viewPortOffset) {
this.viewPortOffset = viewPortOffset;
prepareBuffer();
}
public void addViewPortOffset(Point2D addOffset) {
this.viewPortOffset.setLocation(viewPortOffset.getX() + addOffset.getX(), viewPortOffset.getY() + addOffset.getY());
prepareBuffer();
}
public Tools getSelectedTool() {
return selectedTool;
}
public void setSelectedTool(Tools selectedTool) {
this.selectedTool = selectedTool;
}
public ShapePainterListener getMyListener() {
return myListener;
}
public void setMyListener(ShapePainterListener myListener) {
this.myListener = myListener;
}
@Deprecated
public boolean isContextClassificationEnabled() {
return contextClassificationEnabled;
}
@Deprecated
public void setContextClassificationEnabled(boolean contextClassificationEnabled) {
this.contextClassificationEnabled = contextClassificationEnabled;
}
@Deprecated
public int getBoundaryClass() {
return boundaryClass;
}
@Deprecated
public void setBoundaryClass(int boundaryClass) {
this.boundaryClass = boundaryClass;
if (boundaryClass == -1) classBounds = null;
}
public String getToolTip() {
return toolTip;
}
public void setToolTip(String toolTip) {
this.toolTip = toolTip;
}
public Point getToolTipPosition() {
return toolTipPosition;
}
public void setToolTipPosition(Point toolTipPosition) {
this.toolTipPosition = toolTipPosition;
}
public boolean isShowObjectToolTip() {
return showObjectToolTip;
}
public void setShowObjectToolTip(boolean showObjectToolTip) {
this.showObjectToolTip = showObjectToolTip;
}
public MixtureStatistics getMixStats() {
return mixStats;
}
public void setMixStats(MixtureStatistics mixStats) {
this.mixStats = mixStats;
}
public double getToolTipCurrentScale() {
return toolTipCurrentScale;
}
public void setToolTipCurrentScale(double toolTipCurrentScale) {
this.toolTipCurrentScale = toolTipCurrentScale;
}
public double getOldScale() {
return oldScale;
}
public void setOldScale(double oldScale) {
this.oldScale = oldScale;
}
public int[] getObjectClassificationList() {
return objectClassificationList;
}
public synchronized void setObjectClassificationList(int[] objectClassificationList) {
this.objectClassificationList = objectClassificationList;
}
public FeatureDescription getFeatureDescription() {
return featureDescription;
}
public IScaleableShape getROI() {
return ROI;
}
public void setROI(IScaleableShape rOI) {
ROI = rOI;
}
public List getAnnotations() {
return annotations;
}
public float getClassImageScale() {
return classImageScale;
}
public void setClassImageScale(float classImageScale) {
this.classImageScale = classImageScale;
}
public double getMuMeterPerPixel() {
return muMeterPerPixel;
}
public void setMuMeterPerPixel(double muMeterPerPixel) {
this.muMeterPerPixel = muMeterPerPixel;
}
public Color getGaugeColor() {
return gaugeColor;
}
public void setGaugeColor(Color gaugeColor) {
this.gaugeColor = gaugeColor;
}
public Dimension2D getViewPortSize() {
return viewPortSize;
}
public void setViewPortSize(Dimension2D viewPortSize) {
this.viewPortSize = viewPortSize;
prepareBuffer();
}
@Deprecated
public RecognitionFrame getNegativeChannel() {
return negativeChannel;
}
@Deprecated
public void setNegativeChannel(RecognitionFrame negativeChannel) {
this.negativeChannel = negativeChannel;
}
// public ExclusionMapGen getExMapGen() {
// return exMapGen;
// }
//
// public void setExMapGen(ExclusionMapGen exMapGen) {
// this.exMapGen = exMapGen;
// }
/**
* sets windowSize and contextClassification based on the featureDescription
*
* @param featureDescription
*/
public void setFeatureDescription(FeatureDescription featureDescription) {
this.setWindowSize(featureDescription.getWindowSize());
this.setContextClassificationEnabled(featureDescription.isContextClassificationEnabled());
this.featureDescription = featureDescription;
}
public String getOriginalName() {
return originalName;
}
public void setOriginalName(String originalName) {
this.originalName = originalName;
}
public boolean isDisplayAnnotationLabels() {
return displayAnnotationLabels;
}
public void setDisplayAnnotationLabels(boolean displayAnnotationLabels) {
this.displayAnnotationLabels = displayAnnotationLabels;
}
public double getMipScale() {
return mipScale;
}
public void setMipScale(double mipScale) {
this.mipScale = mipScale;
}
public List getSecondaryObjectSegmentationList() {
return secondaryObjectSegmentationList;
}
public void setSecondaryObjectSegmentationList(List secondaryObjectSegmentationList) {
this.secondaryObjectSegmentationList = secondaryObjectSegmentationList;
}
public static AtomicInteger getActiveAnnotationGroup() {
return activeAnnotationGroup;
}
public void propertyChange(PropertyChangeEvent evt) {
if (evt.getPropertyName().equals(ClassificationTaskTiled.CLASSIFICATION_PROGRESS)) {
threadProgress.put(evt.getSource(), (Double) evt.getNewValue());
double progress = 0d;
for (Object obj : threadProgress.keySet()) {
progress += threadProgress.get(obj);
}
if ((taskList != null) && (taskList.size() > 0))
progress /= taskList.size();
long elapsed = (System.currentTimeMillis() - startTime) / 1000L;
double et = (elapsed / (progress / 100d)) * (1d - (progress / 100d));
logger.debug("Classification progress: " + String.format("%1$.2f", progress) + "% est. time: " + OrbitUtils.formatTime(et));
} else {
if (evt.getPropertyName().equals(RenderThread.RENDERBUFFER_READY)) {
forceRepaint.set(true);
repaint();
}
}
}
public AtomicBoolean getForceRepaint() {
return forceRepaint;
}
public void setForceRepaint(AtomicBoolean forceRepaint) {
this.forceRepaint = forceRepaint;
}
class ScreenProps {
double vpOffsX;
double vpOffsY;
double vpWidthM;
double vpHeight;
double scale;
public ScreenProps(double vpOffsX, double vpOffsY, double vpWidthM, double vpHeight, double scale) {
this.vpOffsX = vpOffsX;
this.vpOffsY = vpOffsY;
this.vpWidthM = vpWidthM;
this.vpHeight = vpHeight;
this.scale = scale;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
ScreenProps that = (ScreenProps) o;
return Double.compare(that.vpOffsX, vpOffsX) == 0 &&
Double.compare(that.vpOffsY, vpOffsY) == 0 &&
Double.compare(that.vpWidthM, vpWidthM) == 0 &&
Double.compare(that.vpHeight, vpHeight) == 0 &&
Double.compare(that.scale, scale) == 0;
}
@Override
public int hashCode() {
return Objects.hash(vpOffsX, vpOffsY, vpWidthM, vpHeight, scale);
}
}
}