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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.engine;

import uk.ac.sussex.gdsc.smlm.filters.Spot;

/**
 * Extends the Spot class with fields used during fitting.
 */
class Candidate extends Spot {

  /** The index. */
  public final int index;

  /** Flag to indicate if the candidate has been fit. */
  public boolean fit;

  // Results of fitting

  /** The params. */
  public float[] params;

  /** The param deviations. */
  public float[] paramDevs;

  /** The error. */
  public double error;

  /** The noise. */
  public float noise;

  /** The mean intensity. */
  public float meanIntensity;

  /** The precision. */
  public double precision;

  /**
   * Instantiates a new candidate.
   *
   * @param x the x
   * @param y the y
   * @param intensity the intensity
   * @param score the score
   * @param index the index
   */
  public Candidate(int x, int y, float intensity, float score, int index) {
    super(x, y, intensity, score);
    this.index = index;
  }

  /**
   * Instantiates a new candidate.
   *
   * @param x the x
   * @param y the y
   * @param index the index
   * @param params the params
   * @param paramDevs the param deviations
   * @param error the error
   * @param noise the noise
   * @param meanIntensity the mean intensity
   * @param valid the valid
   */
  public Candidate(int x, int y, int index, float[] params, float[] paramDevs, double error,
      float noise, float meanIntensity, boolean valid) {
    super(x, y, 0, 0);
    this.index = index;
    this.params = params;
    this.paramDevs = paramDevs;
    this.error = error;
    this.noise = noise;
    this.meanIntensity = meanIntensity;
    this.fit = valid;
  }

  /**
   * Instantiates a new candidate.
   *
   * @param spot the spot
   * @param index the index
   */
  public Candidate(Spot spot, int index) {
    super(spot.x, spot.y, spot.intensity, spot.getScore());
    this.index = index;
  }

  /**
   * Creates a fitted candidate with fitted parameters.
   *
   * @param x the x
   * @param y the y
   * @param index the index
   * @param params the params
   * @param paramDevs the param deviations
   * @param error the error
   * @param noise the noise
   * @param meanIntensity the mean intensity
   * @param valid the valid
   * @return the candidate
   */
  public Candidate createFitted(int x, int y, int index, float[] params, float[] paramDevs,
      double error, float noise, float meanIntensity, boolean valid) {
    final Candidate c = new Candidate(x, y, intensity, getScore(), index);
    c.params = params;
    c.paramDevs = paramDevs;
    c.error = error;
    c.noise = noise;
    c.meanIntensity = meanIntensity;
    c.fit = valid;
    return c;
  }
}