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ColocImgLibGadgets.java
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Mon, Aug 26, 23:59

ColocImgLibGadgets.java
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import ij.IJ;
import ij.ImagePlus;
import ij.plugin.PlugIn;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Random;
import net.imglib2.Cursor;
import net.imglib2.algorithm.math.ImageStatistics;
import net.imglib2.img.ImagePlusAdapter;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
public class ColocImgLibGadgets<T extends RealType<T> & NativeType<T>> implements PlugIn {
protected Img<T> img1, img2;
@Override
public void run(String arg) {
ImagePlus imp1 = IJ.openImage("/Users/dan/Documents/Dresden/ipf/colocPluginDesign/red.tif");
img1 = ImagePlusAdapter.wrap(imp1);
ImagePlus imp2 = IJ.openImage("/Users/dan/Documents/Dresden/ipf/colocPluginDesign/green.tif");
img2 = ImagePlusAdapter.wrap(imp2);
double pearson = calculatePearson();
Img<T> ranImg = generateRandomImageStack(img1, new int[] {2,2,1});
}
/**
* To randomize blockwise we enumerate the blocks, shuffle that list and
* write the data to their new position based on the shuffled list.
*/
protected Img<T> generateRandomImageStack(Img<T> img, int[] blockDimensions) {
int numberOfDimensions = Math.min(img.numDimensions(), blockDimensions.length);
int numberOfBlocks = 0;
long[] numberOfBlocksPerDimension = new long[numberOfDimensions];
for (int i = 0 ; i<numberOfDimensions; i++){
if (img.dimension(i) % blockDimensions[i] != 0){
System.out.println("sorry, for now image dims must be divisable by block size");
return null;
}
numberOfBlocksPerDimension[i] = img.dimension(i) / blockDimensions[i];
numberOfBlocks *= numberOfBlocksPerDimension[i];
}
List<Integer> allTheBlocks = new ArrayList<Integer>(numberOfBlocks);
for (int i = 0; i<numberOfBlocks; i++){
allTheBlocks.add(new Integer(i));
}
Collections.shuffle(allTheBlocks, new Random());
Cursor<T> cursor = img.cursor();
// create factories for new image stack
//ContainerFactory containerFactory = new ImagePlusContainerFactory();
ImgFactory<T> imgFactory = new ArrayImgFactory<T>();
//new ImageFactory<T>(cursor.getType(), containerFactory);
// create a new stack for the random images
final long[] dim = new long[ img.numDimensions() ];
img.dimensions(dim);
Img<T> randomStack = imgFactory.create(dim, img.firstElement().createVariable());
// iterate over image data
while (cursor.hasNext()) {
cursor.fwd();
T type = cursor.get();
// type.getRealDouble();
}
return randomStack;
}
protected double calculatePearson() {
Cursor<T> cursor1 = img1.cursor();
Cursor<T> cursor2 = img2.cursor();
double mean1 = getImageMean(img1);
double mean2 = getImageMean(img2);
// Do some rather simple performance testing
long startTime = System.currentTimeMillis();
double pearson = calculatePearson(cursor1, mean1, cursor2, mean2);
// End performance testing
long finishTime = System.currentTimeMillis();
long elapsed = finishTime - startTime;
// print some output to IJ log
IJ.log("mean of ch1: " + mean1 + " " + "mean of ch2: " + mean2);
IJ.log("Pearson's Coefficient " + pearson);
IJ.log("That took: " + elapsed + " ms");
return pearson;
}
protected double calculatePearson(Cursor<T> cursor1, double mean1, Cursor<T> cursor2, double mean2) {
double pearsonDenominator = 0;
double ch1diffSquaredSum = 0;
double ch2diffSquaredSum = 0;
while (cursor1.hasNext() && cursor2.hasNext()) {
cursor1.fwd();
cursor2.fwd();
T type1 = cursor1.get();
double ch1diff = type1.getRealDouble() - mean1;
T type2 = cursor2.get();
double ch2diff = type2.getRealDouble() - mean2;
pearsonDenominator += ch1diff*ch2diff;
ch1diffSquaredSum += (ch1diff*ch1diff);
ch2diffSquaredSum += (ch2diff*ch2diff);
}
double pearsonNumerator = Math.sqrt(ch1diffSquaredSum * ch2diffSquaredSum);
return pearsonDenominator / pearsonNumerator;
}
protected double getImageMean(Img<T> img) {
double sum = 0;
Cursor<T> cursor = img.cursor();
while (cursor.hasNext()) {
cursor.fwd();
T type = cursor.get();
sum += type.getRealDouble();
}
return sum / ImageStatistics.getNumPixels(img);
}
}

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