Page MenuHomec4science
Files F85830384

ComplexSignalFactory.java
No OneTemporary
Actions

File Metadata

Created
Wed, Oct 2, 09:50

ComplexSignalFactory.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 signal.factory.complex;
import signal.ComplexSignal;
public class ComplexSignalFactory {
public static ComplexSignal gaussian(int nx, int ny, int nz, double sigma) {
double K = sigma * sigma / 2.0;
int xsize = nx / 2;
int ysize = ny / 2;
int zsize = nz / 2;
float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
double wx, wy, wz, wr;
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
wx = (xsize > 0 ? Math.PI * x / xsize : 0);
wy = (ysize > 0 ? Math.PI * y / ysize : 0);
wz = (zsize > 0 ? Math.PI * z / zsize : 0);
wr = Math.sqrt(wx * wx + wy * wy + wz * wz);
function[x][y][z] = (float) Math.exp(-wr * wr * K);
}
return createHermitian("Gaussian", nx, ny, nz, function);
}
public static ComplexSignal identity(int nx, int ny, int nz) {
int xsize = nx / 2;
int ysize = ny / 2;
int zsize = nz / 2;
float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++)
function[x][y][z] = 1.0f;
return createHermitian("Identity", nx, ny, nz, function);
}
public static ComplexSignal laplacian(int nx, int ny, int nz) {
int xsize = nx / 2;
int ysize = ny / 2;
int zsize = nz / 2;
float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
double wx, wy, wz;
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
wx = (xsize > 0 ? Math.PI * x / xsize : 0);
wy = (ysize > 0 ? Math.PI * y / ysize : 0);
wz = (zsize > 0 ? Math.PI * z / zsize : 0);
function[x][y][z] = (float) ((wx * wx + wy * wy + wz * wz));
}
return createHermitian("Laplacian", nx, ny, nz, function);
}
public static ComplexSignal directionalDerivative(int nx, int ny, int nz, double vx, double vy, double vz) {
int xsize = nx / 2;
int ysize = ny / 2;
int zsize = nz / 2;
float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
double wx, wy, wz;
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
wx = (xsize > 0 ? Math.PI * x / xsize : 0);
wy = (ysize > 0 ? Math.PI * y / ysize : 0);
wz = (zsize > 0 ? Math.PI * z / zsize : 0);
function[x][y][z] = (float) ((wx * vx + vy * wy + vz * wz));
}
return createHermitian("Directional Derivative", nx, ny, nz, function);
}
public static ComplexSignal rings(int nx, int ny, int nz, double mu) {
int xsize = nx / 2;
int ysize = ny / 2;
int zsize = nz / 2;
double K = ysize/2;
float[][][] function = new float[xsize + 1][ysize + 1][zsize + 1];
double wx, wy, wz, wr;
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
wx = (xsize > 0 ? Math.PI * x / xsize : 0);
wy = (ysize > 0 ? Math.PI * y / ysize : 0);
wz = (zsize > 0 ? Math.PI * z / zsize : 0);
wr = Math.sqrt(wx * wx + wy * wy + wz*wz);
function[x][y][z] =
(float) (1.0 - 1.0 / (1.0 + Math.exp(-K * (wr - mu)))
+ 1.0 / (1.0 + Math.exp(-K * (wr - 0.6 * mu)))
- 1.0 / (1.0 + Math.exp(-K * (wr - 0.4 * mu))));
}
return createHermitian("Airy", nx, ny, nz, function);
}
public static ComplexSignal createHermitian(String name, int nx, int ny, int nz, float[][][] firstQuadrantReal, float[][][] firstQuadrantImag) {
ComplexSignal signal = new ComplexSignal(name, nx, ny, nz);
int xsize = firstQuadrantReal.length - 1;
int ysize = firstQuadrantReal[0].length - 1;
int zsize = firstQuadrantReal[0][0].length - 1;
if (xsize >= 1 && ysize >= 1 && zsize >= 1) {
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
signal.data[z][2 * (x + nx * y)] = firstQuadrantReal[x][y][z];
signal.data[z][2 * (x + nx * y)+1] = firstQuadrantImag[x][y][z];
}
for (int z = 0; z < zsize; z++)
for (int y = 0; y < ysize; y++)
for (int x = 0; x < xsize; x++) {
int a = nx - 1 - x;
int b = nx * (ny - 1 - y);
signal.data[z][2 * (a + nx * y)] = firstQuadrantReal[x + 1][y][z];
signal.data[z][2 * (a + b)] = firstQuadrantReal[x + 1][y + 1][z];
signal.data[z][2 * (x + b)] = firstQuadrantReal[x][y + 1][z];
signal.data[z][1 + 2 * (a + nx * y)] = firstQuadrantImag[x + 1][y][z];
signal.data[z][1 + 2 * (a + b)] = firstQuadrantImag[x + 1][y + 1][z];
signal.data[z][1 + 2 * (x + b)] = firstQuadrantImag[x][y + 1][z];
int c = nz - 1 - z;
signal.data[c][2 * (x + nx * y)] = firstQuadrantReal[x][y][z + 1];
signal.data[c][2 * (a + nx * y)] = firstQuadrantReal[x + 1][y][z + 1];
signal.data[c][2 * (a + b)] = firstQuadrantReal[x + 1][y + 1][z + 1];
signal.data[c][2 * (x + b)] = firstQuadrantReal[x][y + 1][z + 1];
signal.data[c][1 + 2 * (x + nx * y)] = firstQuadrantImag[x][y][z + 1];
signal.data[c][1 + 2 * (a + nx * y)] = firstQuadrantImag[x + 1][y][z + 1];
signal.data[c][1 + 2 * (a + b)] = firstQuadrantImag[x + 1][y + 1][z + 1];
signal.data[c][1 + 2 * (x + b)] = firstQuadrantImag[x][y + 1][z + 1];
}
}
if (zsize == 0) {
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
signal.data[0][2 * (x + nx * y)] = firstQuadrantReal[x][y][0];
signal.data[0][1 + 2 * (x + nx * y)] = firstQuadrantImag[x][y][0];
}
for (int y = 0; y < ysize; y++)
for (int x = 0; x < xsize; x++) {
int a = nx - 1 - x;
int b = nx * (ny - 1 - y);
signal.data[0][2 * (a + nx * y)] = firstQuadrantReal[x + 1][y][0];
signal.data[0][2 * (a + b)] = firstQuadrantReal[x + 1][y + 1][0];
signal.data[0][2 * (x + b)] = firstQuadrantReal[x][y + 1][0];
signal.data[0][1 + 2 * (a + nx * y)] = firstQuadrantImag[x + 1][y][0];
signal.data[0][1 + 2 * (a + b)] = firstQuadrantImag[x + 1][y + 1][0];
signal.data[0][1 + 2 * (x + b)] = firstQuadrantImag[x][y + 1][0];
}
}
return signal;
}
public static ComplexSignal createHermitian(String name, int nx, int ny, int nz, float[][][] firstQuadrant) {
ComplexSignal signal = new ComplexSignal(name, nx, ny, nz);
int xsize = firstQuadrant.length - 1;
int ysize = firstQuadrant[0].length - 1;
int zsize = firstQuadrant[0][0].length - 1;
if (xsize >= 1 && ysize >= 1 && zsize >= 1) {
for (int z = 0; z <= zsize; z++)
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
signal.data[z][2 * (x + nx * y)] = firstQuadrant[x][y][z];
}
for (int z = 0; z < zsize; z++)
for (int y = 0; y < ysize; y++)
for (int x = 0; x < xsize; x++) {
int a = nx - 1 - x;
int b = nx * (ny - 1 - y);
signal.data[z][2 * (a + nx * y)] = firstQuadrant[x + 1][y][z];
signal.data[z][2 * (a + b)] = firstQuadrant[x + 1][y + 1][z];
signal.data[z][2 * (x + b)] = firstQuadrant[x][y + 1][z];
int c = nz - 1 - z;
signal.data[c][2 * (x + nx * y)] = firstQuadrant[x][y][z + 1];
signal.data[c][2 * (a + nx * y)] = firstQuadrant[x + 1][y][z + 1];
signal.data[c][2 * (a + b)] = firstQuadrant[x + 1][y + 1][z + 1];
signal.data[c][2 * (x + b)] = firstQuadrant[x][y + 1][z + 1];
}
}
if (zsize == 0) {
for (int y = 0; y <= ysize; y++)
for (int x = 0; x <= xsize; x++) {
signal.data[0][2 * (x + nx * y)] = firstQuadrant[x][y][0];
}
for (int y = 0; y < ysize; y++)
for (int x = 0; x < xsize; x++) {
int a = nx - 1 - x;
int b = nx * (ny - 1 - y);
signal.data[0][2 * (a + nx * y)] = firstQuadrant[x + 1][y][0];
signal.data[0][2 * (a + b)] = firstQuadrant[x + 1][y + 1][0];
signal.data[0][2 * (x + b)] = firstQuadrant[x][y + 1][0];
}
}
return signal;
}
}

Event Timeline

c4science · Help