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R2075/DeconvolutionLab2/src/course/DeconvolutionLab2_Course_Border.java
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DeconvolutionLab2_Course_Border.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.plugin.PlugIn;
import java.io.File;
import javax.swing.filechooser.FileSystemView;
import signal.RealSignal;
import signal.factory.Cube;
import signal.factory.Gaussian;
import deconvolution.Deconvolution;
import deconvolutionlab.Lab;
import deconvolutionlab.monitor.Monitors;
public class DeconvolutionLab2_Course_Border 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 + "border" + File.separator;
public DeconvolutionLab2_Course_Border() {
Monitors monitors = Monitors.createDefaultMonitor();
new File(res).mkdir();
System.setProperty("user.dir", res);
int nx = 200;
int ny = 200;
int nz = 40;
RealSignal im = new Cube(22, .1).intensity(0, 100).center(0.25, 0.00, 0.05).generate(nx, ny, nz);
RealSignal i0 = new Cube(22, .1).intensity(0, 100).center(0.25, 0.05, 0.05).generate(nx, ny, nz);
RealSignal i1 = new Cube(22, .1).intensity(0, 100).center(0.25, 0.10, 0.05).generate(nx, ny, nz);
RealSignal i2 = new Cube(22, .1).intensity(0, 100).center(0.25, 0.15, 0.05).generate(nx, ny, nz);
im.max(i1.max(i2).max(i0));
RealSignal g = new Gaussian(10, 10, 10).intensity(0, 101).generate(nx, ny, nz);
Lab.save(monitors, im, res + "ref.tif");
Lab.save(monitors, g, res + "psf.tif");
String psf = " -psf file " + "psf.tif";
String ref = " -image file " + "ref.tif";
String cst = " -image synthetic constant 250 0 size 200 200 40";
String algo = " -algorithm CONV -out ortho REFo (64,32,16)";
new Deconvolution("run", ref + " -psf synthetic impulse " + algo).deconvolve();
algo = " -algorithm CONV -stack CONV -out ortho CONVo rescaled byte (64,32,16) -out mip CONVp rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -pad NO NO 200 200 -out ortho PADo200 rescaled byte (64,32,16) -out mip PADp200 rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -pad NO NO 100 100 -out ortho PADo100 rescaled byte (64,32,16) -out mip PADp100 rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -pad NO NO 40 40 -out ortho PADo40 rescaled byte (64,32,16) -out mip PADp40 rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -pad NO NO 20 20 -out ortho PADo20 rescaled byte (64,32,16) -out mip PADp20 rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -pad NO NO 10 10 -out ortho PADo10 rescaled byte (64,32,16) -out mip PADp10 rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -pad NO NO 5 5 -out ortho PADo2 rescaled byte (64,32,16) -out mip PADp2 rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -apo HANN HANN -out ortho HANNo rescaled byte (64,32,16) -out mip HANNp rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -apo TUKEY TUKEY -out ortho TUKEYo rescaled byte (64,32,16) -out mip TUKEYp rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV --pad NO NO 8 8 apo HANN HANN -out ortho PAD8_HANNo rescaled byte (64,32,16) -out mip PAD8_HANNp rescaled byte";
new Deconvolution("run", ref + psf + algo).deconvolve();
algo = " -algorithm CONV -apo HANN HANN -out ortho HANN_CSTo rescaled byte -out mip HANN_CSTp rescaled byte";
new Deconvolution("run", cst + psf + algo).deconvolve();
algo = " -algorithm CONV -apo TUKEY TUKEY -out ortho TUKEY_CSTo rescaled byte -out mip TUKEY_CSTp rescaled byte";
new Deconvolution("run", cst + psf + algo).deconvolve();
algo = " -algorithm CONV -pad E2 E2 -out ortho PADpPower2FFTW rescaled byte (64,32,16) -out mip PADpPower2FFTW rescaled byte";
new Deconvolution("run", cst + psf + algo + " -fft FFTW2 ").deconvolve();
new Deconvolution("run", cst + psf + algo + " -fft Academic ").deconvolve();
new Deconvolution("run", cst + psf + algo + " -fft JTransforms ").deconvolve();
}
public static void main(String arg[]) {
new DeconvolutionLab2_Course_Border();
}
@Override
public void run(String arg) {
new DeconvolutionLab2_Course_Border();
}
}
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