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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
* The needed tiles will be loaded.
* No border checking will be done due to performance.
*
* @param x
* @param y
* @return
*/
public int getPixel(int x, int y) {
r = getImage().getTile(getImage().XToTileX(x), getImage().YToTileY(y));
// System.out.println("rgba: "+image.getSample(x, y, 0)+" "+image.getSample(x, y, 1)+" "+image.getSample(x, y, 2)+" "+image.getSample(x, y, 3));
return ((255 & 0xFF) << 24) |
((r.getSample(x, y, 0) & 0xFF) << 16) |
((r.getSample(x, y, 1) & 0xFF) << 8) |
((r.getSample(x, y, 2) & 0xFF) << 0);
/*
return new Color(image.getSample(x, y, 0), // red
image.getSample(x, y, 1), // green
image.getSample(x, y, 2)) // blue
.getRGB();
*/
//colorModel.getRGB(pixel);
}
/**
* Returns the RGB value as int in sRGB colorspace from the image at position x,y.
* The needed tile is given by parameter r.
* No border checking will be done due to performance.
*
* @param x
* @param y
* @return
*/
public int getPixel(int x, int y, Raster r) {
return ((255 & 0xFF) << 24) |
((r.getSample(x, y, 0) & 0xFF) << 16) |
((r.getSample(x, y, 1) & 0xFF) << 8) |
((r.getSample(x, y, 2) & 0xFF) << 0);
}
public double[] getPixels(int x, int y, int windowSize, double[] preInitArr) {
double[] feats = preInitArr;
if (feats == null) feats = new double[(windowSize * 2 + 1) * (windowSize * 2 + 1) * 3 + 1];
int idx = 0;
// window
for (int px = x - windowSize; px <= x + windowSize; px++)
for (int py = y - windowSize; py <= y + windowSize; py++) {
if (px < 0) px = 0;
if (px >= width - 1) px = width - 1;
if (py < 0) py = 0;
if (py >= height - 1) py = height - 1;
double[] col = getRaster(px, py).getPixel(px, py, new double[3]);
feats[idx] = col[0];
idx++;
feats[idx] = col[1];
idx++;
feats[idx] = col[2];
idx++;
}
return feats;
}
public int getType() {
if (colorModel == null) return BufferedImage.TYPE_INT_RGB;
if (colorModel.hasAlpha()) return BufferedImage.TYPE_INT_ARGB;
else return BufferedImage.TYPE_INT_RGB;
}
/*
protected RenderedOp makeTiledImage(TiledImage img) {
ImageLayout tileLayout = new ImageLayout(img);
tileLayout.setTileWidth(tileWidth);
tileLayout.setTileHeight(tileHeight);
tileLayout.setSampleModel(sampleModel);
tileLayout.setColorModel(colorModel);
RenderingHints tileHints = new RenderingHints(JAI.KEY_IMAGE_LAYOUT, tileLayout);
ParameterBlock pb = new ParameterBlock();
pb.addSource(img);
return JAI.create("format", pb, tileHints);
}
*/
@SuppressWarnings("unused")
private String getTileInfo(DiskMemImageOrbit img) {
StringBuilder sb = new StringBuilder();
sb.append("imageName = " + imageName + "\n");
sb.append("imageWidth = " + img.getWidth() + "\n");
sb.append("imageHeight = " + img.getHeight() + "\n");
sb.append("tileWidth = " + img.getTileWidth() + "\n");
sb.append("tileHeight = " + img.getTileHeight() + "\n");
sb.append("maxTileIndexX = " + (img.getMinTileX() + img.getNumXTiles() - 1) + "\n");
sb.append("maxTileIndexY = " + (img.getMinTileY() + img.getNumYTiles() - 1) + "\n");
sb.append("maxTileCordX = " + img.getMaxX() + "\n");
sb.append("maxTileCordY = " + img.getMaxY() + "\n");
sb.append("minTileIndexX = " + img.getMinTileX() + "\n");
sb.append("minTileIndexY = " + img.getMinTileY() + "\n");
sb.append("minTileCordX = " + img.getMinX() + "\n");
sb.append("minTileCordY = " + img.getMinY() + "\n");
sb.append("tileGridXOffset = " + img.getTileGridXOffset() + "\n");
sb.append("tileGridYOffset = " + img.getTileGridYOffset() + "\n");
sb.append("tileCache: " + DiskMemImageOrbit.getCommonTileCache().getMemoryCapacity() / (1024 * 1024) + " MB");
return sb.toString();
}
/**
* ROIBB defines the boundingbox of the ROI. Only tiles inside this bb will be rendered.
*
* @param graphics
* @param _vpOffsX
* @param _vpOffsY
* @param _vpWidth
* @param _vpHeight
* @param scale
*/
public void drawImage(final Graphics2D graphics, final int _vpOffsX, final int _vpOffsY, final int _vpWidth, final int _vpHeight, final double scale) {
drawImageSingleThread(graphics, _vpOffsX, _vpOffsY, _vpWidth, _vpHeight, scale);
//drawImageMultiThread(graphics,_vpOffsX,_vpOffsY,_vpWidth,_vpHeight,scale, opacity);
}
/**
* ROIBB defines the boundingbox of the ROI. Only tiles inside this bb will be rendered. Multi threaded version.
* @param graphics
* @param _vpOffsX
* @param _vpOffsY
* @param _vpWidth
* @param _vpHeight
* @param scale
*/
/*
public void drawImageMultiThread(final Graphics2D graphics, final int _vpOffsX, final int _vpOffsY, final int _vpWidth, final int _vpHeight, final double scale, final float opacity) {
if (getImage()==null) return;
double sc = scale/100d;
int vpWidth = (int)(_vpWidth / sc);
int vpHeight = (int)(_vpHeight / sc);
int vpOffsX = (int)(_vpOffsX / sc);
int vpOffsY = (int)(_vpOffsY / sc);
int topIndex = Math.max(TiledImage.YToTileY(vpOffsY, 0, tileHeight), getImage().getMinTileY());
int bottomIndex = Math.min(TiledImage.YToTileY(vpOffsY+vpHeight, 0, tileHeight), getImage().getMaxTileY());
int leftIndex = Math.max(TiledImage.XToTileX(vpOffsX, 0, tileWidth), getImage().getMinTileX());
int rightIndex = Math.min(TiledImage.XToTileX(vpOffsX+vpWidth, 0, tileWidth), getImage().getMaxTileX());
final long start = System.currentTimeMillis();
final List tileInd = new ArrayList<>((bottomIndex-topIndex)*(rightIndex-leftIndex));
for(int tj = topIndex; tj <= bottomIndex; tj++) {
for(int ti = leftIndex; ti <= rightIndex; ti++) {
tileInd.add(new Point(ti,tj));
}
}
Collections.sort(tileInd, new TileSorter(leftIndex,rightIndex,topIndex,bottomIndex)); // render from middle to outside
final List> taskList= new ArrayList>();
timeOut.set(System.currentTimeMillis());
for (Point tileP: tileInd) {
final int ti = tileP.x;
final int tj = tileP.y;
final long startTime = System.currentTimeMillis();
final Callable renderTile = new Callable() {
@Override
public Void call() throws Exception {
long usedTime = System.currentTimeMillis()-start;
if (usedTime>200L) return null;
// if (timeOut.get()>startTime) {
// System.out.println("canceled");
// return null;
// }
Raster tile = getImage().getTile(ti, tj);
DataBuffer dataBuffer = tile.getDataBuffer();
WritableRaster wr = Raster.createWritableRaster(sampleModel,
dataBuffer, new Point(0, 0));
BufferedImage bi;
GraphicsConfiguration graphicConfig = graphics.getDeviceConfiguration();
if (graphicConfig != null) {
bi = graphics.getDeviceConfiguration().createCompatibleImage(sampleModel.getWidth(), sampleModel.getHeight(), colorModel.getTransparency());
bi.setData(wr);
} else {
bi = new BufferedImage(colorModel, wr, colorModel.isAlphaPremultiplied(), null);
}
// if(bi == null) continue;
// bound check
if ((getImage().tileYToY(tj) + bi.getHeight() > getImage().getHeight())) {
bi = bi.getSubimage(0, 0, bi.getWidth(), bi.getHeight() - (getImage().tileYToY(tj) + bi.getHeight() - getImage().getHeight()));
}
if ((getImage().tileXToX(ti) + bi.getWidth() > getImage().getWidth())) {
bi = bi.getSubimage(0, 0, bi.getWidth() - (getImage().tileXToX(ti) + bi.getWidth() - getImage().getWidth()), bi.getHeight());
}
// float[] scales = {1f, 1f, 1f, opacity};
// float[] offsets = new float[4];
// RescaleOp rop = new RescaleOp(scales, offsets, null);
int xInTile = (getImage().tileXToX(ti));
int yInTile = (getImage().tileYToY(tj));
// ((Graphics2D) graphics).drawImage(bi, rop, xInTile, yInTile);
graphics.drawImage(bi, xInTile, yInTile, null);
return null;
}
};
taskList.add(renderTile);
}
try {
//TiledImageWriter.executorService.invokeAll (taskList, maxRenderingTime, TimeUnit.MILLISECONDS);
ExecutorService executorService = Executors.newCachedThreadPool();
executorService.invokeAll (taskList);
executorService.shutdownNow();
} catch (Exception e) {
logger.warn("error rendering classification tile", e);
}
}
*/
/**
* ROIBB defines the boundingbox of the ROI. Only tiles inside this bb will be rendered. Single threaded version.
*
* @param graphics
* @param _vpOffsX
* @param _vpOffsY
* @param _vpWidth
* @param _vpHeight
* @param scale
*/
public void drawImageSingleThread(Graphics2D graphics, int _vpOffsX, int _vpOffsY, int _vpWidth, int _vpHeight, double scale) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
if (painting.get()) return;
painting.set(true);
// RenderPos renderPos = new RenderPos(_vpOffsX, _vpOffsY, _vpWidth, _vpHeight, scale, opacity);
// if (renderPos.equals(lastRenderPos)) return;
// lastRenderPos = renderPos;
// if (System.currentTimeMillis()-lastRepaint < 100) return;
// lastRepaint = System.currentTimeMillis();
long start = System.currentTimeMillis();
if (getImage() == null) {
painting.set(false);
return;
}
double sc = scale / 100d;
int vpWidth = (int) (_vpWidth / sc);
int vpHeight = (int) (_vpHeight / sc);
int vpOffsX = (int) (_vpOffsX / sc);
int vpOffsY = (int) (_vpOffsY / sc);
int topIndex = Math.max(TiledImage.YToTileY(vpOffsY, 0, tileHeight), getImage().getMinTileY());
int bottomIndex = Math.min(TiledImage.YToTileY(vpOffsY + vpHeight, 0, tileHeight), getImage().getMaxTileY());
int leftIndex = Math.max(TiledImage.XToTileX(vpOffsX, 0, tileWidth), getImage().getMinTileX());
int rightIndex = Math.min(TiledImage.XToTileX(vpOffsX + vpWidth, 0, tileWidth), getImage().getMaxTileX());
int capacity = (bottomIndex - topIndex) * (rightIndex - leftIndex);
if (capacity < 0) return; // classImage(roi) out of viewport
List tileInd = new ArrayList<>(capacity);
for (int tj = topIndex; tj <= bottomIndex; tj++) {
for (int ti = leftIndex; ti <= rightIndex; ti++) {
tileInd.add(new Point(ti, tj));
}
}
Collections.sort(tileInd, new TileSorter(leftIndex, rightIndex, topIndex, bottomIndex)); // render from middle to outside
for (Point tileP : tileInd) {
/*
try {
AWTEvent event = java.awt.Toolkit.getDefaultToolkit().getSystemEventQueue().peekEvent();
if (event != null) {
//if (event.toString().contains("RepaintManager")) break;
if (event.toString().contains("org.pushingpixels.trident.Timeline") ||
event.toString().contains("java.awt.SentEvent") ) {
TiledImageWriter.timeOut.set(System.currentTimeMillis());
};
System.out.println(event);
}
} catch (Exception e) {
e.printStackTrace();
}
*/
final int ti = tileP.x;
final int tj = tileP.y;
long usedTime = System.currentTimeMillis() - start;
if (usedTime > maxRenderingTime) {
painting.set(false);
break;
}
if (TiledImageWriter.timeOut.get() > start) {
System.out.println("break");
painting.set(false);
break;
} else {
//System.out.println("paint: "+(TiledImageWriter.timeOut.get()-start));
}
Raster tile = getImage().getTile(ti, tj);
DataBuffer dataBuffer = tile.getDataBuffer();
WritableRaster wr = Raster.createWritableRaster(sampleModel,
dataBuffer, new Point(0, 0));
BufferedImage bi;
GraphicsConfiguration graphicConfig = getGraphicsConfig();
if (graphicConfig != null) {
bi = graphicConfig.createCompatibleImage(sampleModel.getWidth(), sampleModel.getHeight(), colorModel.getTransparency()); // or volatil image???
bi.setData(wr);
} else {
bi = new BufferedImage(colorModel, wr, colorModel.isAlphaPremultiplied(), null);
}
// if(bi == null) continue;
// bound check
if ((getImage().tileYToY(tj) + bi.getHeight() > getImage().getHeight())) {
bi = bi.getSubimage(0, 0, bi.getWidth(), bi.getHeight() - (getImage().tileYToY(tj) + bi.getHeight() - getImage().getHeight()));
}
if ((getImage().tileXToX(ti) + bi.getWidth() > getImage().getWidth())) {
bi = bi.getSubimage(0, 0, bi.getWidth() - (getImage().tileXToX(ti) + bi.getWidth() - getImage().getWidth()), bi.getHeight());
}
// float[] scales = {1f, 1f, 1f, opacity};
// float[] offsets = new float[4];
// RescaleOp rop = new RescaleOp(scales, offsets, null);
int xPos = getImage().tileXToX(ti);
int yPos = getImage().tileYToY(tj);
graphics.drawImage(bi, xPos, yPos, null);
// graphics.drawImage(bi, rop, xPos, yPos);
// AlphaComposite.getInstance(AlphaComposite.SRC_OVER, opacity);
// AffineTransform tx = AffineTransform.getTranslateInstance(xInTile,yInTile);
// graphics.drawRenderedImage( bi, tx);
bi.flush();
//System.out.println(graphics.getDeviceConfiguration().getDevice().getAvailableAcceleratedMemory());
painting.set(false);
}
}
private synchronized GraphicsConfiguration getGraphicsConfig() {
if (graphicsConfiguration==null) {
GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
if (!ge.isHeadlessInstance()) {
GraphicsDevice[] gs = ge.getScreenDevices();
if (gs != null && gs.length > 1) {
graphicsConfiguration = gs[0].getDefaultConfiguration();
}
}
}
return graphicsConfiguration;
}
public AtomicBoolean getPainting() {
return painting;
}
public int getTileWidth() {
return tileWidth;
}
public int getTileHeight() {
return tileHeight;
}
public void setTileWidth(int tileWidth) {
this.tileWidth = tileWidth;
}
public void setTileHeight(int tileHeight) {
this.tileHeight = tileHeight;
}
public int getWidth() {
return width;
}
public int getHeight() {
return height;
}
public void setImage(TiledImage image) {
this.image = image;
}
public TiledImage getImage() {
return image;
}
class RenderPos {
private int x;
private int y;
private int width;
private int height;
private double scale;
private float opacity;
public RenderPos(int x, int y, int width, int height, double scale, float opacity) {
this.x = x;
this.y = y;
this.width = width;
this.height = height;
this.scale = scale;
this.opacity = opacity;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
RenderPos renderPos = (RenderPos) o;
if (x != renderPos.x) return false;
if (y != renderPos.y) return false;
if (width != renderPos.width) return false;
if (height != renderPos.height) return false;
if (Double.compare(renderPos.scale, scale) != 0.0001d) return false;
return Float.compare(renderPos.opacity, opacity) == 0.001f;
}
@Override
public int hashCode() {
int result;
long temp;
result = x;
result = 31 * result + y;
result = 31 * result + width;
result = 31 * result + height;
temp = Double.doubleToLongBits(scale);
result = 31 * result + (int) (temp ^ (temp >>> 32));
result = 31 * result + (opacity != +0.0f ? Float.floatToIntBits(opacity) : 0);
return result;
}
}
}