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DeconvolutionLab2_Course_Celegans.java
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Sun, Nov 3, 14:31

DeconvolutionLab2_Course_Celegans.java
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/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 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.
*
* DL2 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
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package course;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.plugin.PlugIn;
import ij.process.ColorProcessor;
import java.io.File;
import javax.swing.filechooser.FileSystemView;
import deconvolution.Deconvolution;
public class DeconvolutionLab2_Course_Celegans implements PlugIn {
private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
private String root = desktop + File.separator + "DeconvolutionLab2-Course" + File.separator;
private String res = root + "Results" + File.separator + "c-elegans" + File.separator;
private String data = root + "Data" + File.separator + "c-elegans" + File.separator;
public DeconvolutionLab2_Course_Celegans() {
new File(res).mkdir();
System.setProperty("user.dir", res);
run(" -algorithm RIF 0.000001 ", "RIF6_");
run(" -algorithm RIF 0.0000001 ", "RIF7_");
//run(" -algorithm RL 100 ", "RL_");
run(" -algorithm LW+ 200 1 ", "LW+_");
//run(" -algorithm I ", "IN_");
//run(" -algorithm RIF 0.001 ", "RIF3_");
//run(" -algorithm RIF 0.0001 ", "RIF4_");
//run(" -algorithm RIF 0.00001 ", "RIF5_");
//run(" -algorithm VC 100 ", "VC");
//run(" -algorithm RLTV 10 0.1 ", "RLTV");
//run(" -algorithm FISTA 50 1 0.1 ", "FISTA");
//run(" -algorithm ISTA 50 1 0.1 ", "ISTA");
}
private void run(String a, String name) {
String channels[] = new String[] { "CY3", "FITC", "DAPI"};
ImagePlus[] ort = new ImagePlus[3];
ImagePlus[] fig = new ImagePlus[3];
for (int i=0; i<3; i++) {
String channel = channels[i];
String psf = " -psf file " + data + "psf-CElegans-" + channel + ".tif";
String img = " -image file " + data + "CElegans-" + channel +".tif";
String param = " -fft JTransforms -disable display multithreading";
String algo = a + out(name + channel);
new Deconvolution("deconvolve", img + psf + algo + param).deconvolve();
ort[i] = new Opener().openImage( res + name + channel + "_ortho_8.tif");
fig[i] = new Opener().openImage( res + name + channel + "_figure_8.tif");
}
new FileSaver(color(ort)).saveAsTiff(res + name + "-ortho-rgb.tif");
new FileSaver(color(fig)).saveAsTiff(res + name + "-figure-rgb.tif");
}
private static String out(String name) {
return
" -out ortho " + name + "_ortho_8 rescaled byte (160,180,50) noshow" +
" -out mip " + name + "_mip_8 rescaled byte noshow" +
" -out figure " + name + "_figure_8 rescaled byte (160,180,50) ";
}
private static ImagePlus color(ImagePlus imp[]) {
int nx = imp[0].getWidth();
int ny = imp[0].getHeight();
ColorProcessor cp = new ColorProcessor(nx, ny);
byte r[] = (byte[])imp[0].getProcessor().getPixels();
byte g[] = (byte[])imp[1].getProcessor().getPixels();
byte b[] = (byte[])imp[2].getProcessor().getPixels();
cp.setRGB(r, g, b);
ImagePlus out = new ImagePlus( "rgb", cp);
out.show();
return out;
}
public static void main(String arg[]) {
new DeconvolutionLab2_Course_Celegans();
}
@Override
public void run(String arg) {
new DeconvolutionLab2_Course_Celegans();
}
}

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