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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 spotMap = new HashMap();
protected double radius = 0;
public PlanarImage process(final PlanarImage image) {
if (image == null || (image.getWidth() * image.getHeight() > 6000 * 6000L))
throw new IllegalArgumentException("this implementation can only handle images where width*height<=6000*6000. (And image cannot be null)");
TMAPointsResult res = findCircles(image);
this.radius = res.getRadius();
List pList = res.getSpotList();
HashMap pMap = clusterLines(pList);
pMap = discardDuplicatePoints(pMap);
BufferedImage buffImg = res.getSpotImage();
Graphics g = buffImg.createGraphics();
g.setColor(Color.blue);
g.setFont(new Font("System", Font.PLAIN, 9));
for (Point p : pMap.keySet()) {
Point pos = pMap.get(p);
g.drawString(pos.x + "/" + pos.y, p.x, p.y);
}
spotMap = pMap;
return PlanarImage.wrapRenderedImage(buffImg);
}
private TMAPointsResult findCircles(PlanarImage img) {
double r = 6d;
double d;
Color classCol = OrbitImageAnalysis.getInstance().getModel().getClassShapes().get(1).getColor();
int red = classCol.getRed();
int green = classCol.getGreen();
int blue = classCol.getBlue();
int[] c = new int[4];
logger.trace("class color: " + classCol.toString());
final Raster raster = img.getData();
short[][] buf = new short[img.getWidth()][img.getHeight()]; // num tissue pixels buffer
for (int x = 0; x < img.getWidth(); x++)
for (int y = 0; y < img.getHeight(); y++) {
// x,y is center. Now count #tissue pixel in radius around center
for (int bx = x - (int) r; bx <= x + r; bx++) {
if (bx < 0 || bx >= img.getWidth()) continue;
for (int by = y - (int) r; by <= y + r; by++) {
if (by < 0 || by >= img.getHeight()) continue;
d = Point.distance(bx, by, x, y);
if (d <= r) {
c = raster.getPixel(bx, by, c);
if (c[0] == red && c[1] == green && c[2] == blue) {
buf[x][y]++;
}
}
}
}
}
BufferedImage resImg = new BufferedImage(img.getWidth(), img.getHeight(), BufferedImage.TYPE_INT_RGB);
WritableRaster raster2 = resImg.getRaster();
for (int x = 0; x < resImg.getWidth(); x++)
for (int y = 0; y < resImg.getHeight(); y++) {
raster2.setPixel(x, y, new int[]{buf[x][y], buf[x][y], buf[x][y]});
//System.out.println(buf[x][y]);
}
// TODO: instead of UEP create TMPSpot lost, order (by score) and take highest scored spots
// and check for intersection (maybe with min threshold)
ImagePlus ip = new ImagePlus("TMAPoints", resImg);
thresholder.applyThreshold(ip);
edm.setup("points", null); // "points" for Ultimate points
edm.run(ip.getProcessor());
PlanarImage img1 = PlanarImage.wrapRenderedImage(ip.getBufferedImage());
List pList = reportPoints(img1, 1);
double radius = guessRadius(pList);
return new TMAPointsResult(pList, radius, resImg);
}
private TMAPointsResult findCirclesUEP(PlanarImage image) {
ImagePlus ip = new ImagePlus("TMAPoints", image.getAsBufferedImage());
// blur: this fills small 'holes'
GaussianBlur blur = new GaussianBlur();
blur.blur(ip.getProcessor(), 2d);
// Make Binary
thresholder.applyThreshold(ip);
// fill holes
binary.setup("fill", null);
binary.run(ip.getProcessor());
// open
binary.setup("open", null);
binary.run(ip.getProcessor());
// UEP
edm.setup("points", null); // "points" for Ultimate points
edm.run(ip.getProcessor());
PlanarImage img = PlanarImage.wrapRenderedImage(ip.getBufferedImage());
List pList = reportPoints(img, 1);
double radius = guessRadius(pList);
return new TMAPointsResult(pList, radius, ip.getBufferedImage());
}
public double guessRadius(List pList) {
int cnt = 0;
double dist = 0;
for (Point p : pList) {
Point c = getClosestPoint(p, pList);
if (c != null) {
dist += p.distance(c);
cnt++;
}
}
dist /= (double) cnt;
dist /= 2.0d; // diameter->radius
dist /= 1.5d; // assume space between points. Better: detect background between spots and estimate spot/space ratio with pattern recognition!
logger.trace("mean distance: " + dist);
return dist;
}
protected Point getClosestPoint(Point point, List pList) {
Point c = null;
double d = Double.MAX_VALUE;
double t;
for (Point p : pList) {
if (!p.equals(point)) {
t = p.distance(point);
if (t < d) {
c = p;
d = t;
}
}
}
return c;
}
/**
* returns all UEP with a threshold > min in a pointlist.
* The UEP process has to be applied before!
*
* @param img
* @param min
* @return
*/
private List reportPoints(PlanarImage img, int min) {
Raster r = img.getData();
int[] rgb = new int[3];
double d;
List pList = new ArrayList();
for (int x = 0; x < img.getWidth(); x++)
for (int y = 0; y < img.getHeight(); y++) {
rgb = r.getPixel(x, y, rgb);
d = (rgb[0]);
if (d > min) {
Point p = new Point(x, y);
pList.add(p);
if (logger.isTraceEnabled()) {
logger.trace(x + "," + y + ": " + d);
}
}
}
return pList;
}
/**
* returns x/y pairs for each input point
*
* @param pList
* @return
*/
private HashMap clusterLines(List pList) {
ArrayList attrListX = new ArrayList(2);
attrListX.add(new Attribute("xvalue"));
ArrayList attrListY = new ArrayList(2);
attrListY.add(new Attribute("yvalue"));
//attrList.add(new Attribute("class"));
Instances xInst = new Instances("xlines", attrListX, pList.size());
Instances yInst = new Instances("ylines", attrListY, pList.size());
//instances.setClassIndex(1);
for (Point p : pList) {
//Instance inst = new DenseInstance(1d, new double[]{p.x,Double.NaN});
Instance instX = new DenseInstance(1d, new double[]{p.x});
instX.setDataset(xInst);
//inst.setClassMissing();
xInst.add(instX);
Instance instY = new DenseInstance(1d, new double[]{p.y});
instY.setDataset(yInst);
yInst.add(instY);
}
try {
EM colClusterer = new EM();
int numCols = guessNumClusters(colClusterer, xInst, 1, 20);
colClusterer.setNumClusters(numCols);
colClusterer.buildClusterer(xInst);
logger.debug("NumCols: " + colClusterer.getNumClusters());
EM rowClusterer = new EM();
int numRows = guessNumClusters(rowClusterer, yInst, 1, 20);
rowClusterer.setNumClusters(numRows);
rowClusterer.buildClusterer(yInst);
logger.debug("NumRows: " + rowClusterer.getNumClusters());
logger.trace("ColClusterer:");
HashMap colHash = sortAndpPrintCluster(colClusterer);
logger.trace("RowClusterer:");
HashMap rowHash = sortAndpPrintCluster(rowClusterer);
if (logger.isTraceEnabled()) {
logger.trace("ColHash:");
for (Integer i : colHash.keySet()) {
logger.trace("cluster " + i + ": " + colHash.get(i));
}
logger.trace("RowHash:");
for (Integer i : rowHash.keySet()) {
logger.trace("cluster " + i + ": " + rowHash.get(i));
}
}
// classify points
HashMap pMap = new HashMap();
for (Point p : pList) {
Instance instX = new DenseInstance(1d, new double[]{p.x});
instX.setDataset(xInst);
Instance instY = new DenseInstance(1d, new double[]{p.y});
instY.setDataset(yInst);
int x = colClusterer.clusterInstance(instX);
int y = rowClusterer.clusterInstance(instY);
x = colHash.get(x);
y = rowHash.get(y);
logger.trace(p + ": " + x + "/" + y);
pMap.put(p, new Point(x, y));
}
return pMap;
} catch (Exception e) {
e.printStackTrace();
logger.error("error while clustering points", e);
return null;
}
}
/**
* Returns a Point->Spotposition mapping based on a Point->Spotposition but without duplicate target Spotpositions.
* (So that each TMA spot has one and only one position.)
*
* @param pMap
* @return
*/
private HashMap discardDuplicatePoints(HashMap pMap) {
HashMap res = new HashMap(pMap.size());
HashSet availablePos = new HashSet(pMap.size());
for (Point p : pMap.keySet()) {
Point pos = pMap.get(p);
if (!availablePos.contains(pos)) {
res.put(p, pos);
availablePos.add(pos);
} else {
// adjust old point (position in the middle of old and new point)
for (Point old : res.keySet().toArray(new Point[0])) {
if (res.get(old).equals(pos)) {
res.remove(old);
old.setLocation((old.x + p.x) / 2, (old.y + p.y) / 2);
res.put(old, pos);
}
}
logger.trace("discarded mapping: " + p + " -> " + pos);
}
}
return res;
}
@SuppressWarnings("unchecked")
private HashMap sortAndpPrintCluster(EM clusterer) {
List vals = new ArrayList(clusterer.getNumClusters());
for (int c = 0; c < clusterer.getNumClusters(); c++) {
vals.add(new double[]{clusterer.getClusterModelsNumericAtts()[c][0][0], // mean
clusterer.getClusterModelsNumericAtts()[c][0][1], // var
clusterer.getClusterModelsNumericAtts()[c][0][2], // prior
clusterer.getClusterPriors()[c], // priors normalized
c // cluster number
});
}
Collections.sort(vals, new Comparator() {
public int compare(Object o1, Object o2) {
double[] d1 = (double[]) o1;
double[] d2 = (double[]) o2;
return (int) Math.signum(d1[0] - d2[0]);
}
});
for (int c = 0; c < vals.size(); c++) {
logger.trace("Cluster " + c + ":" + vals.get(c)[0] + " Var:" + vals.get(c)[1] + " Z:" + vals.get(c)[2] + " Prior:" + vals.get(c)[3] + " Cluster:" + vals.get(c)[4]);
}
return mergeClusters(vals);
}
private int guessNumClusters(EM clusterer, Instances instances, int start, int end) throws Exception {
ClusterEvaluation eval = new ClusterEvaluation();
int bestNum = start;
double best = Double.POSITIVE_INFINITY;
double bic;
for (int c = start; c <= end; c++) {
clusterer.setNumClusters(c);
clusterer.buildClusterer(instances);
eval.setClusterer(clusterer);
eval.evaluateClusterer(instances);
bic = bic(eval.getLogLikelihood(), c, instances.numInstances());
logger.trace("numCluster " + c + " -> BIC: " + bic);
if (bic < best) {
best = bic;
bestNum = c;
logger.trace("bestNum: " + bestNum);
}
}
return bestNum;
}
private double bic(double llh, int numClust, int sampleSize) {
final int k = numClust * 2;
//System.out.println("llh:"+llh+" k:"+k+" llhsamp: "+Math.log(sampleSize)+" 2llh:"+2*llh+" klogn:"+k*Math.log(sampleSize));
return -2d * llh * sampleSize + k * Math.log(sampleSize);
}
/**
* If two row or column line-clusters have a difference of less than half of the mean difference all clusters have,
* then these clusters are merged. Merging here means that the mean of the cluster with the higher prior is taken the the other
* cluster discarded, so in the mapping the discarded cluster is mapped to the other one.
*
* @param vals
* @return
*/
private HashMap mergeClusters(List vals) {
double[] means = new double[vals.size() - 1];
double mean = 0;
for (int i = 0; i < vals.size() - 1; i++) {
means[i] = vals.get(i + 1)[0] - vals.get(i)[0];
mean += means[i];
}
mean /= ((double) vals.size() - 1);
logger.trace("mean: " + mean);
HashMap map = new HashMap();
List res = new ArrayList();
int j = 0;
for (int i = 0; i < vals.size(); i++) {
if ((i < vals.size() - 1) && (vals.get(i + 1)[0] - vals.get(i)[0] < mean / 2d)) { // merge clusters
double[] d = vals.get(i);
if (vals.get(i + 1)[3] > vals.get(i)[3]) d = vals.get(i + 1); // higher prior, so take this cluster
res.add(d);
map.put((int) vals.get(i)[4], j);
map.put((int) vals.get(i + 1)[4], j);
i++;
} else {
res.add(vals.get(i));
map.put((int) vals.get(i)[4], j);
}
j++;
}
logger.trace("merged Clusters: ");
for (int c = 0; c < res.size(); c++) {
logger.trace("Cluster " + c + ":" + res.get(c)[0] + " Var:" + res.get(c)[1] + " Z:" + res.get(c)[2] + " Prior:" + res.get(c)[3] + " Cluster:" + res.get(c)[4]);
}
return map;
}
public HashMap getSpotMap() {
return spotMap;
}
public void setSpotMap(HashMap spotMap) {
this.spotMap = spotMap;
}
public double getRadius() {
return radius;
}
public void setRadius(double radius) {
this.radius = radius;
}
public class TMASpot implements Comparable {
private Point spot = null;
private int score = 0;
public TMASpot(Point spot, int score) {
this.spot = spot;
this.score = score;
}
public Point getSpot() {
return spot;
}
public void setSpot(Point spot) {
this.spot = spot;
}
public int getScore() {
return score;
}
public void setScore(int score) {
this.score = score;
}
public int compareTo(TMASpot o) {
return score - o.getScore();
}
}
public class TMAPointsResult {
private List spotList = new ArrayList();
private BufferedImage spotImage = null;
private double radius = 0;
public TMAPointsResult() {
}
public TMAPointsResult(List spotList, double radius, BufferedImage spotImage) {
this.spotList = spotList;
this.spotImage = spotImage;
this.radius = radius;
}
public List getSpotList() {
return spotList;
}
public void setSpotList(List spotList) {
this.spotList = spotList;
}
public BufferedImage getSpotImage() {
return spotImage;
}
public void setSpotImage(BufferedImage spotImage) {
this.spotImage = spotImage;
}
public double getRadius() {
return radius;
}
public void setRadius(double radius) {
this.radius = radius;
}
}
}