Page MenuHomec4science
Files F61071768

LiICQ.java
No OneTemporary
Actions

File Metadata

Created
Sat, May 4, 08:48

LiICQ.java
View Options

/*-
* #%L
* Fiji's plugin for colocalization analysis.
* %%
* Copyright (C) 2009 - 2017 Fiji developers.
* %%
* 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
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package sc.fiji.coloc.algorithms;
import net.imglib2.RandomAccessible;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.TwinCursor;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
import sc.fiji.coloc.gadgets.DataContainer;
import sc.fiji.coloc.results.ResultHandler;
/**
* This algorithm calculates Li et al.'s ICQ (intensity
* correlation quotient).
*
* @param <T>
*/
public class LiICQ<T extends RealType< T >> extends Algorithm<T> {
// the resulting ICQ value
double icqValue;
public LiICQ() {
super("Li ICQ calculation");
}
@Override
public void execute(DataContainer<T> container)
throws MissingPreconditionException {
double mean1 = container.getMeanCh1();
double mean2 = container.getMeanCh2();
// get the 2 images for the calculation of Li's ICQ
RandomAccessible<T> img1 = container.getSourceImage1();
RandomAccessible<T> img2 = container.getSourceImage2();
RandomAccessibleInterval<BitType> mask = container.getMask();
TwinCursor<T> cursor = new TwinCursor<T>(img1.randomAccess(),
img2.randomAccess(), Views.iterable(mask).localizingCursor());
// calculate ICQ value
icqValue = calculateLisICQ(cursor, mean1, mean2);
}
/**
* Calculates Li et al.'s intensity correlation quotient (ICQ) for
* two images.
*
* @param cursor A TwinCursor that iterates over two images
* @param mean1 The first images mean
* @param mean2 The second images mean
* @return Li et al.'s ICQ value
*/
public static <T extends RealType<T>> double calculateLisICQ(TwinCursor<T> cursor, double mean1, double mean2) {
/* variables to count the positive and negative results
* of Li's product of the difference of means.
*/
long numPositiveProducts = 0;
long numNegativeProducts = 0;
// iterate over image
while (cursor.hasNext()) {
cursor.fwd();
T type1 = cursor.getFirst();
T type2 = cursor.getSecond();
double ch1 = type1.getRealDouble();
double ch2 = type2.getRealDouble();
double productOfDifferenceOfMeans = (mean1 - ch1) * (mean2 - ch2);
// check for positive and negative values
if (productOfDifferenceOfMeans < 0.0 )
++numNegativeProducts;
else
++numPositiveProducts;
}
/* calculate Li's ICQ value by dividing the amount of "positive pixels" to the
* total number of pixels. Then shift it in the -0.5,0.5 range.
*/
return ( (double) numPositiveProducts / (double) (numNegativeProducts + numPositiveProducts) ) - 0.5;
}
@Override
public void processResults(ResultHandler<T> handler) {
super.processResults(handler);
handler.handleValue("Li's ICQ value", icqValue);
}
}

Event Timeline

c4science · Help