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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 rmList = DALConfig.getImageProvider().LoadRawMetasByRawDataFile(rdfId);
List rmDataList = DALConfig.getImageProvider().LoadRawMetasByRawData(rd.getRawDataId());
rmList.addAll(rmDataList);
HashMap rmHash = RawUtilsCommon.getHashFromMetaList(rmList);
if (!rmHash.containsKey(RawUtilsCommon.STR_META_CHANNEL))
throw new Exception("Error: Meta data 'Channel' not available for RawDataFile " + rdfId);
//int channel = Integer.parseInt(rmHash.get(RawUtils.STR_META_CHANNEL).getValue()) - 1;
int channel = Integer.parseInt(rmHash.get(RawUtilsCommon.STR_META_CHANNEL).getValue());
String metaKey = "Percentiles_wvlength_" + channel + "_channel_0";
if (!rmHash.containsKey(metaKey))
throw new Exception("Error: Meta data '" + metaKey + "' not available for RawDataFile " + rdfId);
String val = rmHash.get(metaKey).getValue();
int[] minmax = parseMinMax(val, plateScalingMin, plateScalingMax);
BufferedImage bi = null;
if (bi16.getSampleModel().getNumBands() == 1) {
bi16 = ImageUtils.scaleIntensities(bi16, new int[]{minmax[0]}, new int[]{minmax[1]});
bi = new BufferedImage(bi16.getWidth(), bi16.getHeight(), BufferedImage.TYPE_BYTE_GRAY);
} else {
throw new IllegalArgumentException("Only images with 1 band (gray-color) supported. This image has " + bi16.getSampleModel().getNumBands() + " bands.");
}
Graphics2D g2d = bi.createGraphics();
g2d.drawImage(bi16, 0, 0, null);
g2d.dispose();
return bi;
}
/**
* input format is e.g. "MIN=82;0.1%=176;0.5%=186;1%=191;5%=204;95%=1726;99%=4239;99.5%=4832;99.9%=6079;MAX=65535";
* returns int[2] with int[0]=minValue and int[1]=maxValue
*
* @param percentiles
* @return
*/
public static int[] parseMinMax(String percentiles, PlateScalingMin min, PlateScalingMax max) {
//String percentiles = "MIN=82;0.1%=176;0.5%=186;1%=191;5%=204;95%=1726;99%=4239;99.5%=4832;99.9%=6079;MAX=65535";
int[] minmax = new int[2];
String[] split = percentiles.split(";", -1);
for (String s : split) {
String[] keyval = s.split("=", -1);
//System.out.println("test: "+keyval[0]+" min: "+min.toString()+" max: "+max.toString());
if (keyval[0].equalsIgnoreCase(getMinIntensityName(min))) minmax[0] = Integer.parseInt(keyval[1]);
if (keyval[0].equalsIgnoreCase(getMaxIntensityName(max))) minmax[1] = Integer.parseInt(keyval[1]);
}
return minmax;
}
/**
* Rescales using predefined min,max intensities and converts to 8bit. Works for gray- and rgb color images.
*
* @param bi16
* @return
*/
public static BufferedImage convertTo8bit(BufferedImage bi16, int min, int max) {
BufferedImage bi = null;
if (bi16.getSampleModel().getNumBands() == 1) {
bi16 = ImageUtils.scaleIntensities(bi16, new int[]{min}, new int[]{max});
bi = new BufferedImage(bi16.getWidth(), bi16.getHeight(), BufferedImage.TYPE_BYTE_GRAY);
} else if (bi16.getSampleModel().getNumBands() == 3) {
throw new IllegalArgumentException("only grayscale images supported");
} else {
throw new IllegalArgumentException("Only images with 1 band (gray-color) or 3 bands (rgb) supported. This image has " + bi16.getSampleModel().getNumBands() + " bands.");
}
Graphics2D g2d = bi.createGraphics();
g2d.drawImage(bi16, 0, 0, null);
g2d.dispose();
return bi;
}
private static String getMinIntensityName(PlateScalingMin plateScalingMin) {
switch (plateScalingMin) {
case min:
return "MIN";
case p01:
return "0.1%";
case p05:
return "0.5%";
case p1:
return "1%";
case p5:
return "5%";
default:
return "MIN";
}
}
private static String getMaxIntensityName(PlateScalingMax plateScalingMax) {
switch (plateScalingMax) {
case max:
return "MAX";
case p95:
return "95%";
case p99:
return "99%";
case p995:
return "99.5%";
case p999:
return "99.9%";
default:
return "MAX";
}
}
/**
* scales bands to min = 0 & max = 2^8 or 2^16
*
* @param image
* @param min int[] containing minima per band
* @param max
* @return
*/
public static BufferedImage scaleIntensities(BufferedImage image, int[] min, int[] max) throws IllegalArgumentException {
WritableRaster raster = image.getRaster();
if ((min.length != max.length) || min.length != raster.getNumBands())
throw new IllegalArgumentException("Please ensure consistency of min and max arrays and number of bands in image");
int width = image.getWidth();
int height = image.getHeight();
for (int row = 0; row < height; row++) {
for (int col = 0; col < width; col++) {
for (int band = 0; band < raster.getNumBands(); band++) {
int pixel = raster.getSample(col, row, band);
if (pixel < min[band]) pixel = min[band];
if (pixel > max[band]) pixel = max[band];
pixel = ((int) (((((double) pixel - min[band]) / (max[band] - min[band])) * ((int) Math.pow(2, image.getColorModel().getPixelSize()) - 1)) + 0.5));
raster.setSample(col, row, band, pixel);
}
}
}
return image;
}
/**
* Can be used to verify impact of different encoding algorithms. Compares two BufferedImages and outputs differences between those.
*
* @param image
* @param image2
* @return
*/
public static int[] calculateBufferedImageDifferencesPxByPx(BufferedImage image, BufferedImage image2) {
int width = image.getWidth();
int height = image.getHeight();
int width2 = image2.getWidth();
int height2 = image2.getHeight();
WritableRaster raster1 = image.getRaster();
WritableRaster raster2 = image2.getRaster();
if (width != width2 || height != height2)
throw new IllegalArgumentException("Please insert two identical images that were treated with different image algorithms");
int[] diff = new int[width * height];
for (int row = 0; row < height; row++) {
for (int col = 0; col < width; col++) {
for (int band = 0; band < raster1.getNumBands(); band++) {
int p1 = raster1.getSample(col, row, band);
int p2 = raster2.getSample(col, row, band);
diff[((row * width) + col)] = p2 - p1;
}
}
}
return diff;
}
/**
* Returns min and max intensities and percentiles 0.01, 0.05, 0.1, 0.9, 0.95, 0.99 of a BufferedImage.
*
* @param image
* @return
*/
public static int[][] getMinMaxIntensitiesOfBI(BufferedImage image) {
WritableRaster raster = image.getRaster();
// per band: { min, 1%, 5%, 10%, 90%, 95%, 99%, max }
int[][] intensities = new int[raster.getNumBands()][8];
DescriptiveStatistics[] ds = new DescriptiveStatistics[raster.getNumBands()];
for (int i = 0; i < raster.getNumBands(); i++)
ds[i] = new DescriptiveStatistics();
int width = image.getWidth();
int height = image.getHeight();
for (int row = 0; row < height; row++) {
for (int col = 0; col < width; col++) {
for (int band = 0; band < raster.getNumBands(); band++) {
ds[band].addValue(raster.getSample(col, row, band));
}
}
}
for (int i = 0; i < ds.length; i++) {
intensities[i][0] = (int) ds[i].getMin();
intensities[i][1] = (int) ds[i].getPercentile(1);
intensities[i][2] = (int) ds[i].getPercentile(5);
intensities[i][3] = (int) ds[i].getPercentile(10);
intensities[i][4] = (int) ds[i].getPercentile(90);
intensities[i][5] = (int) ds[i].getPercentile(95);
intensities[i][6] = (int) ds[i].getPercentile(99);
intensities[i][7] = (int) ds[i].getMax();
}
return intensities;
}
public static int[] getPercentileIntensity(BufferedImage image, double percentile) {
WritableRaster raster = image.getRaster();
int[] intensities = new int[raster.getNumBands()];
DescriptiveStatistics[] ds = new DescriptiveStatistics[raster.getNumBands()];
for (int i = 0; i < raster.getNumBands(); i++)
ds[i] = new DescriptiveStatistics();
int width = image.getWidth();
int height = image.getHeight();
for (int row = 0; row < height; row++) {
for (int col = 0; col < width; col++) {
for (int band = 0; band < raster.getNumBands(); band++) {
ds[band].addValue(raster.getSample(col, row, band));
}
}
}
for (int i = 0; i < ds.length; i++) {
if (percentile == 0d) intensities[i] = (int) ds[i].getMin();
else if (percentile == 100d) intensities[i] = (int) ds[i].getMax();
else
intensities[i] = (int) ds[i].getPercentile(percentile);
}
return intensities;
}
/**
* Calculates and returns band histograms of a BufferedImage
*
* @param image
* @return
*/
public static int[][] getChannelHistograms(BufferedImage image) {
WritableRaster raster = image.getRaster();
int[][] histograms = new int[raster.getNumBands()][(int) (Math.pow(2, image.getColorModel().getPixelSize()) - 1)];
int width = image.getWidth();
int height = image.getHeight();
for (int row = 0; row < height; row++) {
for (int col = 0; col < width; col++) {
for (int band = 0; band < raster.getNumBands(); band++) {
histograms[band][raster.getSample(col, row, band)]++;
}
}
}
return histograms;
}
/**
* Calculates and returns band histograms of a BufferedImage w/o a need to extract the raster
*
* @param raster
* @param width
* @param height
* @param iNumBins
* @return
*/
public static int[][] getChannelHistograms(WritableRaster raster, int width, int height, int iNumBins) {
int[][] histograms = new int[raster.getNumBands()][iNumBins];
for (int row = 0; row < height; row++) {
for (int col = 0; col < width; col++) {
for (int band = 0; band < raster.getNumBands(); band++) {
histograms[band][raster.getSample(col, row, band)]++;
}
}
}
return histograms;
}
}