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FRC_.java
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Sat, Jan 18, 06:44

FRC_.java
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import ch.epfl.biop.frc.FRC.ThresholdMethod;
import ch.epfl.biop.frc.FRC;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.measure.ResultsTable;
import ij.plugin.PlugIn;
public class FRC_ implements PlugIn {
private static ResultsTable rt;
@Override
public void run(String arg) {
// Find number of current images
int n_images = WindowManager.getImageCount();
String[] image_list = WindowManager.getImageTitles();
// Prefill smartness
if(n_images<2) {
IJ.error("Need at least 2 images open for FRC Computation");
}
// FRC Thresholds
ThresholdMethod[] thr_methods = ThresholdMethod.values();
String[] thr_names = new String[thr_methods.length];
int k=0;
for(ThresholdMethod tm : thr_methods) {
thr_names[k] = tm.toString();
k++;
}
GenericDialog gd = new GenericDialog("FRC Calculation");
gd.addChoice("Image_1", image_list, image_list[0]);
gd.addChoice("Image_2", image_list, image_list[1]);
gd.addChoice("Resolution Criteria",thr_names, thr_names[0]);
gd.showDialog();
if(gd.wasCanceled()) {
return;
}
// Everything is ready now
ImagePlus im1 = WindowManager.getImage(gd.getNextChoice());
ImagePlus im2 = WindowManager.getImage(gd.getNextChoice());
ThresholdMethod tm = thr_methods[gd.getNextChoiceIndex()];
FRC frc = new FRC();
double fire = frc.calculateFireNumber(im1.getProcessor(), im2.getProcessor(), tm);
// Show results
if (rt == null) {
rt = new ResultsTable();
}
rt.incrementCounter();
rt.addLabel(im1.getTitle()+":"+im2.getTitle());
rt.addValue("FRC ["+tm+"]", fire);
rt.addValue("FRC ["+tm+"] Calibrated ["+im1.getCalibration().getUnit()+"]", fire*im1.getCalibration().pixelHeight);
rt.show("FRC Results");
}
public static void main(String[] args) {
// set the plugins.dir property to make the plugin appear in the Plugins menu
Class<?> clazz = FRC_.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 image1 = IJ.openImage("http://imagej.net/images/blobs.gif");
ImagePlus image2 = image1.duplicate();
IJ.run(image2, "Add Noise", "");
IJ.run(image1, "Add Noise", "");
image1.show();
image2.show();
// run the plugin
IJ.runPlugIn(clazz.getName(), "");
}
}

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