Page MenuHomec4science
Files F90655309

DeconvolutionLab2_Course_Bigradient.java
No OneTemporary
Actions

File Metadata

Created
Sun, Nov 3, 15:10

DeconvolutionLab2_Course_Bigradient.java
View Options

/*
* 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 java.io.File;
import javax.swing.filechooser.FileSystemView;
import deconvolution.Deconvolution;
import ij.plugin.PlugIn;
public class DeconvolutionLab2_Course_Bigradient implements PlugIn {
private String desktop = FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator + "Desktop";
private String root = desktop + File.separator + "Deconvolution" + File.separator;
private String res = root + "results" + File.separator + "bigradient" + File.separator;
private String data = root + "data" + File.separator + "bigradient" + File.separator;
public DeconvolutionLab2_Course_Bigradient() {
new File(res).mkdir();
System.setProperty("user.dir", res);
new File(res + "TRIF").mkdir();
new File(res + "RIF").mkdir();
new File(res + "LW").mkdir();
new File(res + "LW-ITER").mkdir();
new File(res + "LW+").mkdir();
new File(res + "LW+-ITER").mkdir();
new File(res + "RL").mkdir();
new File(res + "RL-ITER").mkdir();
new File(res + "RLTV").mkdir();
new File(res + "RLTV-ITER").mkdir();
new File(res + "FISTA").mkdir();
new File(res + "FISTA-ITER").mkdir();
String psf = " -psf file " + data + "psf.tif -reference " + data + "ref.tif ";
String noisy = " -image file convnoise.tif";
new Deconvolution("run", "-image file " + data + "ref.tif" + psf + " -algorithm SIM 0 1 1 -out stack convnoise -out stack conbnoise_8 rescaled byte noshow").deconvolve();
new Deconvolution("run", noisy + psf + " -algorithm NIF -out stack NIF").deconvolve();
new Deconvolution("run", noisy + psf + " -algorithm DIV -out stack DIV").deconvolve();
for(int i=0; i<=3; i++) {
double p = Math.pow(5, i-10);
String name = "RIF" + String.format("%02d", i);
new Deconvolution("run", noisy + psf + " -algorithm RIF " + p + out("RIF" + File.separator, name)).deconvolve();
}
for(int i=0; i<=3; i++) {
double p = Math.pow(5, i-10);
String name = "TRIF" + String.format("%02d", i);
new Deconvolution("run", noisy + psf + " -algorithm TRIF " + p + out("TRIF" + File.separator, name)).deconvolve();
}
String lw = " -algorithm LW 20 1 -out mip @2 LW-ITER/I -out stats @1 LW nosave";
new Deconvolution("run", noisy + psf + lw).deconvolve();
new File(res + "LW-ITER/I.tif").delete();
String lwp = " -algorithm LW+ 20 1 -out mip @2 LW+-ITER/I -out stats @1 LW+ nosave";
new Deconvolution("run", noisy + psf + lwp).deconvolve();
new File(res + "LW+-ITER/I.tif").delete();
String rl = " -algorithm RL 20 -out mip @2 RL-ITER/I -out stats @1 RL nosave";
new Deconvolution("run", noisy + psf + rl).deconvolve();
new File(res + "RL-ITER/I.tif").delete();
String rltv = " -algorithm RLTV 20 10 -out mip @2 RLTV-ITER/I -out stats @1 RLTV nosave";
new Deconvolution("run", noisy + psf + rltv).deconvolve();
new File(res + "RLTV-ITER/I.tif").delete();
String fista = " -algorithm FISTA 20 1 1 Spline3 3 -mip @2 FISTA-ITER/I -out stats @1 FISTA nosave";
new Deconvolution("run", noisy + psf + fista).deconvolve();
new File(res + "FISTA-ITER/I.tif").delete();
}
private static String out(String root, String name) {
return "out stats " + root + name +
" -out stack " + root + name + "_32 -out stack " + root + name + "_8 rescaled byte noshow";
}
public static void main(String arg[]) {
new DeconvolutionLab2_Course_Bigradient();
}
@Override
public void run(String arg) {
new DeconvolutionLab2_Course_Bigradient();
}
}

Event Timeline

c4science · Help