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ijp-frc/src/main/java/ch/epfl/biop/frc/FRC_.java
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FRC_.java
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package ch.epfl.biop.frc;
import java.io.File;
import ch.epfl.biop.frc.FRC.ThresholdMethod;
import fiji.util.gui.GenericDialogPlus;
import ij.IJ;
import ij.ImageJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.gui.Plot;
import ij.measure.ResultsTable;
import ij.plugin.PlugIn;
/**
* @author Olivier Burri
* BioImaging And Optics Platform (BIOP)
* EPFL Lausanne, Switzerland
*
* The FRC_ Plugin exposes the functionality of the FRC class originally written
* by Alex Herbert at The Genome Damage and Stability Centre, University of Sussex
*
* Copyright (C) 2016 Olivier Burri
*
* 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/>.
*/
public class FRC_ implements PlugIn {
private static ResultsTable rt;
private static final String pref = "biop.frc.";
@Override
public void run(String arg) {
// 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++;
}
// Initialize Results Table
if (rt == null || WindowManager.getWindow("FRC Results") == null)
rt = new ResultsTable();
// Call FRC Class
FRC frc = new FRC();
// Default Threshold Method
int thr_i = (int) Prefs.get(pref+"thrm.index", 0);
// Default plot choice
boolean is_plot = Prefs.get(pref+"is.plot", false);
if(arg.compareTo("batch") == 0) {
// Grab previous directories
String dir1 = Prefs.get(pref+"dir1", "");
String dir2 = Prefs.get(pref+"dir2", "");
// Different Dialog
GenericDialogPlus gdp = new GenericDialogPlus("Batch FRC Calculation");
gdp.addMessage("Two folders must be provided.\nEach folder has a matching file in the other.");
gdp.addDirectoryField("First Folder", dir1);
gdp.addDirectoryField("Second Folder", dir2);
gdp.addChoice("Resolution Criteria",thr_names, thr_names[thr_i]);
gdp.addCheckbox("Save Plot", is_plot);
gdp.showDialog();
if(gdp.wasCanceled()) return;
// Get choices
dir1 = gdp.getNextString();
dir2 = gdp.getNextString();
thr_i = gdp.getNextChoiceIndex();
is_plot = gdp.getNextBoolean();
// Save preferences
Prefs.set(pref+"dir1", dir1);
Prefs.set(pref+"dir2", dir2);
Prefs.set(pref+"thrm.index", thr_i);
Prefs.set(pref+"is.plot", is_plot);
// Call the bath FIRE calculator method
File d1 = new File(dir1);
File d2 = new File(dir2);
ThresholdMethod tm = thr_methods[thr_i];
frc.batchCalculateFireNumber(d1, d2, tm, rt, is_plot);
} else {
// Run plugin that will work on two open images
// Get Current Images
String[] image_list = WindowManager.getImageTitles();
if(image_list.length<2) {
IJ.error("Need at least 2 images open for FRC Computation");
}
// Make Dialog choices
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[thr_i]);
gd.addCheckbox("Display Plot", is_plot);
gd.showDialog();
if(gd.wasCanceled()) {
return;
}
// Everything is ready now
ImagePlus im1 = WindowManager.getImage(gd.getNextChoice());
ImagePlus im2 = WindowManager.getImage(gd.getNextChoice());
thr_i = gd.getNextChoiceIndex();
is_plot = gd.getNextBoolean();
ThresholdMethod tm = thr_methods[thr_i];
// Set Preferences again
Prefs.set(pref+"thrm.index", thr_i);
Prefs.set(pref+"is.plot", is_plot);
// Finally calculate FRC
double[][] frc_curve = frc.calculateFrcCurve(im1.getProcessor(), im2.getProcessor());
// Smooth Curve using LOESS
double[][] smooth_frc = frc.getSmoothedCurve(frc_curve);
// Fourier Image REsolution number ("FIRE")
double fire = frc.calculateFireNumber(smooth_frc, tm);
// Append results
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");
// Plot if requested
if(is_plot) {
Plot p = frc.doPlot(frc_curve, smooth_frc, tm, fire, im1.getTitle());
p.show();
}
}
}
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(),"");
//IJ.runPlugIn(clazz.getName(),"batch"); // Running the plugin to test batch processing.
}
}
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