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ijp-localizej/src/main/java/Parallel_Roi_Creator.java
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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.PointRoi;
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 pluggin that use and image to create at a define position, a circular ROIs with specified diameter and names, in a parallel way!
*
* @author Romain Guiet (from minimal plugin fiji crew! AND A LOT of help from Olivier Burri)
*/
public class Parallel_Roi_Creator implements PlugIn {
public void run(String arg) {
// we want that pluggin to retrieve informations from the current image to create circular ROIs
// each row corresponds to a ROI
// each column contains informations
// column 0 : x
// column 1 : y
// column 2 : diameter
// column 3 : an index that defines the name (from a list)
final ImagePlus roi_coord_imp = IJ.getImage(); // get the active image
final int rows = roi_coord_imp.getHeight(); // the number of ROI to create corresponds to the number of row
boolean is_cat = false ; // because of parallel processing we have to declare a the temporary variables
String[] temp_suffix_array = new String[1] ; // is_cat and temp_cat_names_array.
String temp_prefix = "" ;
if (roi_coord_imp.getWidth() > 3 ){ // if the image contains more than 3 columns
GenericDialog gd = new GenericDialog("Parameters"); // Create a generic dialog
gd.addStringField("ROIs prefix (limited to 1)", "");
gd.addStringField("ROIs suffix(es) (list separated by comma) ", "");// to get the index of the names of the ROIs
gd.addMessage("NB : prefix and suffix should be more than 4 characters long");
gd.showDialog(); // (the pixel value should correspond to the position in the comma separated list above.)
if (gd.wasCanceled()) return ; // to handle cancellation
temp_prefix = gd.getNextString();
String temp_suffix = gd.getNextString(); // get the entered String.
if ( !temp_suffix.isEmpty() ) { // if it's not empty and the image contains more than 3 columns
temp_suffix_array = temp_suffix.split(","); // we split the string into an array
is_cat = true ; // and defines is_cat as true
}
}
final boolean use_cat = is_cat; // make the final variables from the temporary ones
final String[] suffix_array = temp_suffix_array; //
final String prefix = temp_prefix;
if ( RoiManager.getInstance() == null ) new RoiManager(); // if the ROI Manager is not open, open it!
final RoiManager rm = RoiManager.getInstance(); // and get it as rm
final AtomicInteger ai = new AtomicInteger(0); // for parallel processing, we need the ai
long start = System.currentTimeMillis(); // to measure the time required
final Thread[] threads = newThreadArray(); // create the thread array
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(roi_coord_imp.getProcessor().getPixel( 0, i)) ; // get x (pixel are float , convert it to int )
int y_center = (int) Float.intBitsToFloat(roi_coord_imp.getProcessor().getPixel( 1, i)) ; // and y
float diameter = Float.intBitsToFloat(roi_coord_imp.getProcessor().getPixel( 2, i)) ; // diameter is a float keep it as a float
float radius = diameter /2 ; // define radius
String roi_name ;
if (use_cat){ // but if we use cat_name from column
int cat_nbr = (int) Float.intBitsToFloat(roi_coord_imp.getProcessor().getPixel( 3, i)) ; // from the image get the index in the list of name
roi_name = prefix+"-"+IJ.pad((i+1),6)+"-"+suffix_array[cat_nbr]; // here, we use 1st the number of the ROI, then its name beacauzse of sorting at the end
}else{
roi_name = "ROI-"+IJ.pad(i,6); // otherwise by default the name will be ROI-nbr
}
//IJ.log("Roi "+i+"="+ x_center +", "+ y_center +", radius = " + radius+ ", name "+roi_name);
Roi roi;
if (Float.isNaN(diameter)){
roi = new PointRoi( x_center , y_center) ; // define the roi as a point
}else{
roi = new OvalRoi( (x_center - radius) , (y_center - radius), diameter, diameter) ; // define the roi
}
roi.setName(roi_name); // and set its name
rm.addRoi(roi); // before creating it
}
}};
}
startAndJoin(threads); // DO THE MAGIC !
long end=System.currentTimeMillis();
IJ.log("ROI creation time in msec: "+(end-start) );
rm.runCommand("Sort"); // the parallel processing scrambles the order of the ROIs, so we sort them here.
}
/** 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();
// open the blobs 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_cat.tif");
imageParam.show();
// run the plugin
IJ.runPlugIn(clazz.getName(), "");
//IJ.runPlugIn(clazz.getName(), "rois=categ1,categ2,categ3");
}
}
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