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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.results;

/**
 * Contains helper functions for working with peak results.
 */
public final class PeakResultHelper {
  /**
   * No public constructor.
   */
  private PeakResultHelper() {}

  /**
   * Convert the local background to an estimate of noise. Local background and noise are in ADU
   * count units.
   *
   * This assumes the local background is photon shot noise. The background is first converted to
   * photons using the gain. The shot noise is taken assuming a Poisson distribution (thus the
   * variance equals the number of photons). This is amplified by 2 if the data was taken on an
   * EM-CCD camera. The square root is the noise in photons. This is converted back to ADUs using
   * the gain. E.G.
   *
   * 
   * return Math.sqrt((background / gain) * ((emCcd) ? 2 : 1)) * gain;
   * 
   *
   * @param background the background
   * @param gain the gain
   * @param emCcd True if an emCcd camera
   * @return the noise estimate
   */
  public static double localBackgroundToNoise(double background, double gain, boolean emCcd) {
    if (background <= 0) {
      return 0;
    }
    return Math.sqrt((background / gain) * ((emCcd) ? 2 : 1)) * gain;
  }

  /**
   * Convert the local background to an estimate of noise. Local background and noise are in photons
   * units.
   *
   * This assumes the local background is photon shot noise. The shot noise is taken assuming a
   * Poisson distribution (thus the variance equals the number of photons). This is amplified by 2
   * if the data was taken on an EM-CCD camera. The square root is the noise in photons.
   *
   * 
   * return Math.sqrt((background) * ((emCcd) ? 2 : 1));
   * 
   *
   * @param background the background
   * @param emCcd True if an emCcd camera
   * @return the noise estimate
   */
  public static double localBackgroundToNoise(double background, boolean emCcd) {
    if (background <= 0) {
      return 0;
    }
    return Math.sqrt((background) * ((emCcd) ? 2 : 1));
  }

  /**
   * Convert the noise to local background. Local background and noise are in ADU count units.
   *
   * This assumes the local background is photon shot noise. This is the opposite conversion to
   * {@link #localBackgroundToNoise(double, double, boolean)}.
   *
   * @param noise the noise
   * @param gain the gain
   * @param emCcd True if an emCcd camera
   * @return the local background estimate
   */
  public static double noiseToLocalBackground(double noise, double gain, boolean emCcd) {
    if (noise <= 0) {
      return 0;
    }
    noise /= gain;
    noise *= noise;
    if (emCcd) {
      noise /= 2;
    }
    return noise * gain;
  }

  /**
   * Convert the noise to local background. Local background and noise are in ADU count units.
   *
   * This assumes the local background is photon shot noise. This is the opposite conversion to
   * {@link #localBackgroundToNoise(double, boolean)}.
   *
   * @param noise the noise
   * @param emCcd True if an emCcd camera
   * @return the local background estimate
   */
  public static double noiseToLocalBackground(double noise, boolean emCcd) {
    if (noise <= 0) {
      return 0;
    }
    noise *= noise;
    if (emCcd) {
      noise /= 2;
    }
    return noise;
  }
}