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Astigmatism.java
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Tue, Nov 26, 02:08

Astigmatism.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 signal.factory;
import signal.RealSignal;
public class Astigmatism extends SignalFactory {
private double fwhm = 5.0;
private double factor = 1;
public Astigmatism(double fwhm, double factor) {
super(new double[] {fwhm, factor});
setParameters(new double[] {fwhm, factor});
}
@Override
public String getName() {
return "Astigmatism";
}
@Override
public String[] getParametersName() {
return new String[] {"FWHM at focus plane", "Astigmatism factor"};
}
@Override
public void setParameters(double[] parameters) {
if (parameters.length >= 1)
this.fwhm = parameters[0];
if (parameters.length >= 2)
this.factor = parameters[1];
}
@Override
public double[] getParameters() {
return new double[] {fwhm, factor};
}
@Override
public void fill(RealSignal signal) {
double sigma = 0.8493218 * fwhm; // 1/sqrt(-2*log(0.5))
factor = 1;
for(int z=0; z<nz; z++) {
double dx = 1.0;
double dy = 1.0;
if (z>zc) {
dy = (1.0-factor*(z-zc)/(double)nz);
dx = 1.0 / dy;
}
if (z<zc) {
dx = (1.0-factor*(zc-z)/(double)nz);
dy = 1.0 / dx;
}
double kx = 1.0 / (dx * dx * sigma * sigma * 2.0);
double ky = 1.0 / (dy * dy * sigma * sigma * 2.0);
for(int x=0; x<nx; x++)
for(int y=0; y<ny; y++) {
double r2 = kx*(x-xc)*(x-xc) + ky*(y-yc)*(y-yc);
signal.data[z][x+nx*y] = (float)(amplitude * Math.exp(-r2));
}
}
}
}

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