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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 - 2017 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, 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
* Channel usage (useRed,useGreen,useBlue) is treated in feats[] assignment loop - all samples are calculated!
*/
public class TissueFeatures {
private final static Logger logger = LoggerFactory.getLogger(TissueFeatures.class);
private static double EPSILON = 0.00000001d;
private int featuresPerSample = 6;
private int samples = 3;
private int windowSize = 4;
private int[] buf = null;
private double[] pix = null;
private double[] mean = null;
private double[] min = null;
private double[] max = null;
private double[] sd = null;
private double[] edge = null; // edge intensity per sample
private TiledImagePainter bimg = null;
private int[] p = new int[4]; // buffer of one pixel up to 4 samples
private int featureSet = FeatureDescription.FEATURE_SET_PIX_MEAN_MIN_MAX_SD_EDGE;
private FeatureDescription featureDescription = null;
private TissueFeaturesOld oldFeatures = null; // for backward compatibility
public TissueFeatures() {
}
/**
* bimg can be null (then raster r in buildFeatures cannot be null)
*/
public TissueFeatures(final FeatureDescription featureDescription, final TiledImagePainter bimg) {
// for old featureDescription version use old features for backward compatibility
if (featureDescription.getFeatureVersion() < 1) {
oldFeatures = new TissueFeaturesOld(featureDescription, bimg);
logger.debug("using old tissue features for backward compatibility");
}
this.samples = featureDescription.getSampleSize();
this.windowSize = featureDescription.getWindowSize();
this.featureSet = featureDescription.getFeatureSet();
this.featureDescription = featureDescription;
this.bimg = bimg;
buf = new int[(windowSize * 2 + 1) * (windowSize * 2 + 1) * samples];
pix = new double[samples];
mean = new double[samples];
min = new double[samples];
max = new double[samples];
sd = new double[samples];
edge = new double[samples];
if (featureSet == FeatureDescription.FEATURE_SET_INTENS) featuresPerSample = 1;
else if (featureSet == FeatureDescription.FEATURE_SET_PIX_MEAN_MIN_MAX_SD) featuresPerSample = 5;
else featuresPerSample = 6; // with edge
}
/**
* Initializes a double array of a sufficient size given the feature description.
*
* @return
*/
public double[] prepareDoubleArray() {
return new double[(windowSize * 2 + 1) * (windowSize * 2 + 1) * samples + 1]; // +1 for contextclassification???
}
/**
* computes tissue features (mean,min,max,sd of each sample (r,g,b or grey)).
* Not thread-safe!!!
*
* @param r can be null (then bimg cannot be null in the constructor)
* @param x
* @param y
* @param classVal (set to Double.NaN for classification)
* @return
* @throws OrbitImageServletException
*/
public double[] buildFeatures(final Raster r, final int x, final int y, final double classVal) throws OrbitImageServletException {
// check backward compatibility
if (oldFeatures != null) return oldFeatures.buildFeatures(r, x, y, classVal);
if (featureSet == FeatureDescription.FEATURE_SET_INTENS) return buildIntensFeatures(r, x, y, classVal);
// init
for (int i = 0; i < samples; i++) {
mean[i] = 0d;
min[i] = Double.NaN;
max[i] = Double.NaN;
sd[i] = 0d;
edge[i] = 0d;
}
if (r != null) // faster if raster is pre-assigned (e.g. the shape fits into memory)
{
buf = r.getPixels(x - windowSize, y - windowSize, (windowSize * 2) + 1, (windowSize * 2) + 1, buf);
p = r.getPixel(x, y, p); // mid-pixel
} else { // slower, but works for very large shapes
Raster r2 = bimg.getData(new Rectangle(x - windowSize, y - windowSize, (windowSize * 2) + 1, (windowSize * 2) + 1), featureDescription);
// The modifyRaster works very slow. As optimization the getData() method in OrbitTiledImage2 could be overwritten (copy code from PlanarImage) with featureDescription as argument, then this new method
// would use the getTile() method with featureDescription as argument and not the standard getTile method. This would make use of the tile caching mechanism in OrbitTiledImage2.
// However, normally such large shapes are not used at all.
r2 = OrbitUtils.getModifiedRaster(r2, featureDescription, bimg.getImage().getColorModel(), bimg.getImage().getLevel());
if (r2 == null) System.out.println("r2 is null!!");
buf = r2.getPixels(x - windowSize, y - windowSize, (windowSize * 2) + 1, (windowSize * 2) + 1, buf);
p = r2.getPixel(x, y, p);
}
// System.out.println("pixel: "+Arrays.toString(p));
// System.out.println("buf: "+Arrays.toString(buf));
// System.out.println("samples: "+samples+" windowSize: "+windowSize);
// middle pixel
for (int i = 0; i < samples; i++) pix[i] = p[i];
// Remark: System.arraycopy() does not work here because pix is double[] and p is int[]!
//int[] p = new int[4]; // r,g,b,alpha (if available)
int cnt = 1; // bugfix due to +samples
int bufPos = 0;
//for (int px=x-windowSize; px<=x+windowSize; px++)
// for (int py=y-windowSize; py<=y+windowSize; py++)
while (bufPos < buf.length - samples) {
//if (r!=null)
//p = r.getPixel(px, py, p); // better use getPixels()...
//else p = bimg.getPixels(px, py, windowSize, p);
//int d = Math.max(Math.abs(px-x), Math.abs(py-y)); // use it as weights
for (int i = 0; i < samples; i++) {
/*
mean[i] +=p[i];
if (Double.isNaN(min[i]) || (min[i] > p[i])) min[i] = p[i];
if (Double.isNaN(max[i]) || (max[i] < p[i])) max[i] = p[i];
*/
mean[i] += buf[bufPos];
if (Double.isNaN(min[i]) || (min[i] > buf[bufPos])) min[i] = buf[bufPos]; //bufPos++; // bugfix
if (Double.isNaN(max[i]) || (max[i] < buf[bufPos])) max[i] = buf[bufPos]; //bufPos++; // bugfix
bufPos++;
}
cnt++;
}
if (cnt > 0)
for (int i = 0; i < samples; i++) {
if (mean[i] > 0)
mean[i] /= (double) cnt;
}
// sd and edge
cnt = 0;
bufPos = 0;
//for (int px=x-windowSize; px<=x+windowSize; px++)
// for (int py=y-windowSize; py<=y+windowSize; py++)
while (bufPos < buf.length) {
//p = r.getPixel(px, py, p); // better use getPixels()...
//int d = Math.max(Math.abs(px-x), Math.abs(py-y)); // use it as weights
for (int i = 0; i < samples; i++) {
//sd[i] += (mean[i]-p[i]) * (mean[i]-p[i]);
sd[i] += (mean[i] - buf[bufPos]) * (mean[i] - buf[bufPos]); //bufPos++;
edge[i] += (pix[i] - buf[bufPos]) * (pix[i] - buf[bufPos]);
bufPos++;
}
cnt++;
}
for (int i = 0; i < samples; i++) {
if (cnt > 1) {
sd[i] /= (double) (cnt - 1);
if (sd[i] > EPSILON) {
sd[i] = Math.sqrt(sd[i]);
} else sd[i] = Double.NaN;
edge[i] /= (double) (cnt - 1);
if (edge[i] > EPSILON) {
edge[i] = Math.sqrt(edge[i]);
} else edge[i] = Double.NaN;
} else {
sd[i] = Double.NaN;
edge[i] = Double.NaN;
}
}
// System.out.println("pix: "+Arrays.toString(pix));
// System.out.println("mean: "+Arrays.toString(mean));
// System.out.println("min: "+Arrays.toString(min));
// System.out.println("max: "+Arrays.toString(max));
// System.out.println("sd: "+Arrays.toString(sd));
// store features
double[] feats = new double[featuresPerSample * samples + 1];
for (int i = 0; i < samples; i++) {
if ((i == 0) && (featureDescription.isSkipRed())) continue;
if ((i == 1) && (featureDescription.isSkipGreen())) continue;
if ((i == 2) && (featureDescription.isSkipBlue())) continue;
feats[(samples * 0) + i] = pix[i];
feats[(samples * 1) + i] = mean[i];
feats[(samples * 2) + i] = min[i];
feats[(samples * 3) + i] = max[i];
feats[(samples * 4) + i] = sd[i];
if (featureSet >= FeatureDescription.FEATURE_SET_PIX_MEAN_MIN_MAX_SD_EDGE)
feats[(samples * 5) + i] = edge[i];
}
feats[feats.length - 1] = classVal;
//logger.trace(feats.toString());
return feats;
}
private double[] buildIntensFeatures(final Raster r, final int x, final int y, final double classVal) throws OrbitImageServletException {
// init
for (int i = 0; i < samples; i++) {
mean[i] = 0d;
}
if (r != null) // faster if raster is pre-assigned (e.g. the shape fits into memory)
{
buf = r.getPixels(x - windowSize, y - windowSize, (windowSize * 2) + 1, (windowSize * 2) + 1, buf);
p = r.getPixel(x, y, p); // mid-pixel
} else { // slower, but works for very large shapes
Raster r2 = bimg.getData(new Rectangle(x - windowSize, y - windowSize, (windowSize * 2) + 1, (windowSize * 2) + 1), featureDescription);
if (r2 == null) System.out.println("r2 is null!!");
buf = r2.getPixels(x - windowSize, y - windowSize, (windowSize * 2) + 1, (windowSize * 2) + 1, buf);
p = r2.getPixel(x, y, p);
}
for (int i = 0; i < samples; i++) {
mean[0] += p[i];
}
mean[0] /= (double) samples;
double[] feats = new double[featuresPerSample * samples + 1];
for (int i = 0; i < samples; i++) {
if ((i == 0) && (featureDescription.isSkipRed())) continue;
if ((i == 1) && (featureDescription.isSkipGreen())) continue;
if ((i == 2) && (featureDescription.isSkipBlue())) continue;
feats[(samples * 0) + i] = mean[i];
}
feats[feats.length - 1] = classVal;
//logger.trace(Arrays.toString(feats));
return feats;
}
public int getFeaturesPerSample() {
return featuresPerSample;
}
public static double extractSD(double[] feats) {
return sumOrNan(feats[12],feats[13],feats[14]);
}
public static double extractEdge(double[] feats) {
return sumOrNan(feats[15],feats[16],feats[17]);
}
public static double extractMin(double[] feats) {
return sumOrNan(feats[6],feats[7],feats[8]);
}
public static double extractMax(double[] feats) {
return sumOrNan(feats[9],feats[10],feats[11]);
}
public static double extractMean(double[] feats) {
return sumOrNan(feats[3],feats[4],feats[5]);
}
public static double extractPix(double[] feats) {
return sumOrNan(feats[0],feats[1],feats[2]);
}
/**
* returns 0 if the value is Double.NaN, otherwise the value
* @param d
* @return
*/
private static double v0(double d) {
return Double.isNaN(d)?0d:d;
}
private static double sumOrNan(double d1, double d2, double d3) {
if (Double.isNaN(d1)&&Double.isNaN(d2)&&Double.isNaN(d3)) {
return Double.NaN;
} else {
return v0(d1)+v0(d2)+v0(d3);
}
}
}