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ijp-pts/src/Max_Inscribed_Circles.java
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Max_Inscribed_Circles.java
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import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.gui.GenericDialog;
import ij.gui.Roi;
import ij.plugin.PlugIn;
import ij.plugin.frame.RoiManager;
import java.util.ArrayList;
import ch.epfl.biop.MaxInscribedCircles;
/**
* PlugIn to find the largest circle or circles inside a mask.
* Macro recordable
* @author Olivier Burri
* @version 1.0
*/
public class Max_Inscribed_Circles implements PlugIn {
private RoiManager rm;
private double minD;
private boolean isSelectionOnly;
@Override
public void run(String arg0) {
ImagePlus imp = IJ.getImage();
if (!imp.getProcessor().isBinary() && imp.getRoi() == null) {
IJ.error("Need selection or a binary image!");
}
this.minD = Prefs.get("largest.circ.minD", 4);
this.isSelectionOnly = Prefs.get("largest.circ.isSelOnly", false);
GenericDialog gd = new GenericDialog("Find Largest Circles");
gd.addNumericField("Minimum Disk Diameter (px)", this.minD, 1);
gd.addMessage("Set to 0 to get only the largest inscribed circle");
gd.addCheckbox("Use selection instead of mask", this.isSelectionOnly);
gd.showDialog();
if(gd.wasCanceled()) {
return;
}
this.minD = gd.getNextNumber();
this.isSelectionOnly = gd.getNextBoolean();
Prefs.set("largest.circ.minD", this.minD);
Prefs.set("largest.circ.isSelOnly", this.isSelectionOnly);
//Run the function
ArrayList<Roi> circles = MaxInscribedCircles.findCircles(imp, this.minD, this.isSelectionOnly);
//Add ROIS
rm = RoiManager.getInstance();
if (rm == null) {
rm = new RoiManager();
}
rm.setVisible(true);
for(Roi r : circles) {
rm.addRoi(r);
}
}
/**
* Main method for debugging.
* @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 = Max_Inscribed_Circles.class;
String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
System.setProperty("plugins.dir", pluginsDir);
// start ImageJ
new ImageJ();
ImagePlus imp1 = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif");
IJ.setAutoThreshold(imp1, "Default");
Prefs.blackBackground = false;
IJ.run(imp1, "Convert to Mask", "");
imp1.show();
}
}
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