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DeconvolutionLab2_Course_Piecewise.java
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Wed, Oct 2, 05:23

DeconvolutionLab2_Course_Piecewise.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 java.io.File;
import java.util.Random;
import javax.swing.filechooser.FileSystemView;
import deconvolution.Deconvolution;
import deconvolutionlab.Lab;
import deconvolutionlab.monitor.Monitors;
import ij.plugin.PlugIn;
import signal.RealSignal;
import signal.factory.Constant;
import signal.factory.Cube;
public class DeconvolutionLab2_Course_Piecewise 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 + "piecewise" + File.separator;
public DeconvolutionLab2_Course_Piecewise() {
Monitors monitors = Monitors.createDefaultMonitor();
new File(res).mkdir();
System.setProperty("user.dir", res);
new File(res + "RIF").mkdir();
new File(res + "LW").mkdir();
new File(res + "LW+").mkdir();
new File(res + "RL").mkdir();
new File(res + "RLTV").mkdir();
new File(res + "ISTA").mkdir();
new File(res + "FISTA").mkdir();
int nx = 128;
int ny = 128;
int nz = 128;
int spacing = 16;
Random rand = new Random(1234);
RealSignal x = new Constant().intensity(0, 10).generate(nx, ny, nz);
for(int i = 0; i< 12; i++) {
double xc = (rand.nextDouble()*0.6 + 0.2);
double yc = (rand.nextDouble()*0.6 + 0.2);
double zc = (rand.nextDouble()*0.6 + 0.2);
double size = 15 + (rand.nextDouble()*30);
double ampl = (rand.nextDouble()+0.5)*10;
x.plus(new Cube(size, 0.1).intensity(0, ampl).center(xc, yc, zc).generate(nx, ny, nz));
}
Lab.show(monitors, x, "reference");
Lab.save(monitors, x, res + "ref.tif");
String algo = " ";
String ground = " -image file " + res + "ref.tif ";
//String psf = " -psf file ../../Data/resolution/psfgl.tif";
String psf = " -psf synthetic gaussian 100.0 0.0 1.2 1.2 3.6 size ";
// nx + " " + ny + " " + nz;
String signal = " -image file signal.tif -reference " + res + "ref.tif -disable monitor";
String paramout = " intact float (" + spacing + "," + spacing + "," + spacing + ")";
algo = " -algorithm CONV -out stats @3 PR nosave -out stack PR -out ortho PRo ";
new Deconvolution("run", ground + "-reference reference.tif -psf synthetic impulse 100 0 size 128 128 128 " + algo).deconvolve();
algo = " -algorithm SIM 0 1 1 -out stats @3 SIM nosave -out stack signal -out ortho SIGNALo ";
new Deconvolution("run", ground + psf + algo).deconvolve();
algo = " -algorithm NIF -out ortho NIF " + paramout;
new Deconvolution("run", signal + psf + algo).deconvolve();
algo = " -algorithm RLTV 15 0.01 -out stats @1 RLTV nosave -out ortho @1 RLTV/RLTV" + paramout;
new Deconvolution("run", signal + psf + algo).deconvolve();
}
public static void main(String arg[]) {
new DeconvolutionLab2_Course_Piecewise();
}
@Override
public void run(String arg) {
new DeconvolutionLab2_Course_Piecewise();
}
}

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