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Parallel_Roi_Creator.java
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Mon, Nov 11, 13:44

Parallel_Roi_Creator.java
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/*
* To the extent possible under law, the Fiji developers have waived
* all copyright and related or neighboring rights to this tutorial code.
*
* See the CC0 1.0 Universal license for details:
* http://creativecommons.org/publicdomain/zero/1.0/
*/
import java.util.concurrent.atomic.AtomicInteger;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.gui.OvalRoi;
import ij.gui.Roi;
import ij.plugin.PlugIn;
import ij.plugin.filter.PlugInFilter;
import ij.plugin.frame.RoiManager;
import ij.process.ImageProcessor;
/**
* Parallel_Roi_Creator
*
* A plugin to create ROIs in a parallel way.
*
* @author Romain Guiet (from minimal plugin fiji crew! )
*/
public class Parallel_Roi_Creator implements PlugIn {
public void run(String arg) {
final RoiManager rm = RoiManager.getInstance();
final ImagePlus imp_ori = WindowManager.getImage(1);
final ImagePlus imp_input = WindowManager.getImage(2);
IJ.log("ori:" +imp_ori );
IJ.log("input:" +imp_input );
final int rows = imp_input.getHeight();
IJ.log("rows:" +rows );
final AtomicInteger ai = new AtomicInteger(0);
long start=System.currentTimeMillis();
final Thread[] threads = newThreadArray();
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] = new Thread() {
{ setPriority(Thread.NORM_PRIORITY); }
public void run() {
// Each thread processes a few items in the total list
// Each loop iteration within the run method
// has a unique 'i' number to work with
// and to use as index in the results array:
for (int i = ai.getAndIncrement(); i < rows; i = ai.getAndIncrement()) {
int x_center = (int) Float.intBitsToFloat(imp_input.getProcessor().getPixel( 0, i)) ;
int y_center = (int) Float.intBitsToFloat(imp_input.getProcessor().getPixel( 1, i)) ;
float diameter = Float.intBitsToFloat(imp_input.getProcessor().getPixel( 2, i)) ; // keep it as a float
float radius = diameter /2 ;
//int cat_nbr = (int) Float.intBitsToFloat(imp_input.getProcessor().getPixel( 4, i)) ;
IJ.log("Roi "+i+"="+ x_center +", "+ y_center +", radius = " + radius);
Roi roi = new OvalRoi( (x_center - radius) , (y_center - radius), diameter, diameter) ;
roi.setName("ROI-"+IJ.pad(i,6) );
rm.addRoi(roi);
}
}};
}
startAndJoin(threads);
long end=System.currentTimeMillis();
IJ.log("Processing time convolution in msec: "+(end-start) );
rm.runCommand("Sort");
}
/** Create a Thread[] array as large as the number of processors available.
* From Stephan Preibisch's Multithreading.java class. See:
* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
*/
private Thread[] newThreadArray() {
int n_cpus = Runtime.getRuntime().availableProcessors();
return new Thread[n_cpus];
}
/** Start all given threads and wait on each of them until all are done.
* From Stephan Preibisch's Multithreading.java class. See:
* http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
*/
public static void startAndJoin(Thread[] threads)
{
for (int ithread = 0; ithread < threads.length; ++ithread)
{
threads[ithread].setPriority(Thread.NORM_PRIORITY);
threads[ithread].start();
}
try
{
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread].join();
} catch (InterruptedException ie)
{
throw new RuntimeException(ie);
}
}
/**
* Main method for debugging.
*
* For debugging, it is convenient to have a method that starts ImageJ, loads an
* image and calls the plugin, e.g. after setting breakpoints.
*
* @param args unused
*/
public static void main(String[] args) {
// set the plugins.dir property to make the plugin appear in the Plugins menu
Class<?> clazz = Parallel_Roi_Creator.class;
String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
String pluginsDir = url.substring("file:".length(), url.length() - clazz.getName().length() - ".class".length());
System.setProperty("plugins.dir", pluginsDir);
// start ImageJ
new ImageJ();
RoiManager rm = new RoiManager();
rm.setVisible(true);
// open the Clown sample
ImagePlus image = IJ.openImage("http://imagej.net/images/blobs.gif");
image.show();
ImagePlus imageParam = IJ.openImage("I:/UsersProjects/Sophie_Wurth/Myelin_Axon_hug_Quantifier/ParalleleFit/TestRois/test.tif");
imageParam.show();
// run the plugin
IJ.runPlugIn(clazz.getName(), "");
}
}

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