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AxialDiffractionSimulation.java
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Sun, Feb 16, 23:23

AxialDiffractionSimulation.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 deconvolutionlab.monitor.Monitors;
import fft.AbstractFFT;
import fft.FFT;
import signal.ComplexSignal;
import signal.RealSignal;
import signal.factory.complex.ComplexSignalFactory;
public class AxialDiffractionSimulation extends SignalFactory {
private double pupil = 10;
private double defocusFactor = 10;
private double waveNumberAxial = 2;
public AxialDiffractionSimulation(double pupil, double defocusFactor, double waveNumberAxial) {
super(new double[] {pupil, defocusFactor, waveNumberAxial});
setParameters(new double[] {pupil, defocusFactor, waveNumberAxial});
}
@Override
public String getName() {
return "AxialDiffractionSimulation";
}
@Override
public String[] getParametersName() {
return new String[] { "Pupil Size", "Defocus Factor", "Wave Number (Axial)" };
}
@Override
public void setParameters(double[] parameters) {
if (parameters.length >= 1)
this.pupil = parameters[0];
if (parameters.length >= 2)
this.defocusFactor = parameters[1];
if (parameters.length >= 3)
this.waveNumberAxial = parameters[2];
}
@Override
public double[] getParameters() {
return new double[] {pupil, defocusFactor, waveNumberAxial};
}
@Override
public void fill(RealSignal signal) {
AbstractFFT fft = FFT.getFastestFFT().getDefaultFFT();
fft.init(Monitors.createDefaultMonitor(), nx, ny, 1);
double defocusTop = 2.0*Math.PI / (defocusFactor*pupil);
double defocusCen = 2.0*Math.PI / pupil;
int xsize = nx / 2;
int ysize = ny / 2;
int zsize = nz / 2;
double diag = Math.sqrt(xsize*xsize + ysize*ysize);
double wx, wy, wz;
for (int z = 0; z <= zsize; z++) {
float[][][] real = new float[xsize + 1][ysize + 1][1];
float[][][] imag = new float[xsize + 1][ysize + 1][1];
wz = waveNumberAxial*(zsize-z)*2.0*Math.PI / zsize;
double cosz = Math.cos(wz);
double sinz = Math.sin(wz);
double fcz = z * Math.abs(defocusTop-defocusCen) / zsize + defocusCen;
double fcz2 = fcz*fcz;
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
wx = x * x;
wy = y * y;
double g = (wy + wx) / diag;
if (g < fcz2) {
real[x][y][0] = (float) (g * cosz);
imag[x][y][0] = (float) (g * sinz);
}
}
ComplexSignal c = ComplexSignalFactory.createHermitian(""+z, nx, ny, 1, real, imag);
RealSignal pz = fft.inverse(c).circular();
signal.setXY(z, pz.getXY(0));
signal.setXY(nz-1-z, pz.duplicate().getXY(0));
}
signal.rescale(0, amplitude);
}
}

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