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Genome Damage and Stability Centre SMLM Package Software for single molecule localisation microscopy (SMLM)

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/*-
 * #%L
 * Genome Damage and Stability Centre SMLM Package
 *
 * Software for single molecule localisation microscopy (SMLM)
 * %%
 * Copyright (C) 2011 - 2023 Alex Herbert
 * %%
 * This program 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.
 *
 * This program 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 this program.  If not, see
 * .
 * #L%
 */

package uk.ac.sussex.gdsc.smlm.function.gaussian;

import uk.ac.sussex.gdsc.smlm.utils.StdMath;

/**
 * Evaluates a 2-dimensional Gaussian function for a single peak.
 *
 * 

The single parameter x in the {@link #eval(int, double[])} function is assumed to be a linear * index into 2-dimensional data. The dimensions of the data must be specified to allow unpacking to * coordinates. * *

Data should be packed in descending dimension order, e.g. Y,X : Index for [x,y] = MaxX*y + x. */ public class SingleNbFreeCircularGaussian2DFunction extends SingleFreeCircularGaussian2DFunction { private static final int[] gradientIndices; static { gradientIndices = createGradientIndices(1, new SingleNbFreeCircularGaussian2DFunction(1, 1)); } /** * Constructor. * * @param maxx The maximum x value of the 2-dimensional data (used to unpack a linear index into * coordinates) * @param maxy The maximum y value of the 2-dimensional data (used to unpack a linear index into * coordinates) */ public SingleNbFreeCircularGaussian2DFunction(int maxx, int maxy) { super(maxx, maxy); } @Override public Gaussian2DFunction copy() { return new SingleNbFreeCircularGaussian2DFunction(maxx, maxy); } /** * Evaluates a 2-dimensional elliptical Gaussian function for a single peak. * *

{@inheritDoc} */ @Override public double eval(final int x, final double[] dyda) { // Unpack the predictor into the dimensions final int x1 = x / maxx; final int x0 = x % maxx; return background + gaussian(x0, x1, dyda); } private double gaussian(final int x0, final int x1, final double[] dyDa) { final double dx = x0 - x0pos; final double dy = x1 - x1pos; final double dx2 = dx * dx; final double dy2 = dy * dy; // Calculate gradients if (zeroAngle) { final double exp = StdMath.exp(aa * dx2 + cc * dy2); dyDa[0] = norm * exp; final double y = height * exp; dyDa[1] = y * (-2.0 * aa * dx); dyDa[2] = y * (-2.0 * cc * dy); dyDa[3] = y * (nx + ax * dx2); dyDa[4] = y * (ny + cy * dy2); return y; } final double dxy = dx * dy; final double exp = StdMath.exp(aa * dx2 + bb * dxy + cc * dy2); dyDa[0] = norm * exp; final double y = height * exp; dyDa[1] = y * (-2.0 * aa * dx - bb * dy); dyDa[2] = y * (-2.0 * cc * dy - bb * dx); dyDa[3] = y * (nx + ax * dx2 + bx * dxy + cx * dy2); dyDa[4] = y * (ny + ay * dx2 + by * dxy + cy * dy2); return y; } @Override public boolean evaluatesBackground() { return false; } @Override public int[] gradientIndices() { return gradientIndices; } }





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