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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;

/**
 * Wrap a function and store the values from the procedure.
 */
public class Gradient2FunctionStore extends Gradient1FunctionStore
    implements Gradient2Function, Gradient2Procedure {
  private final Gradient2Function function2;
  private Gradient2Procedure procedure;

  /**
   * The gradients from the last call to {@link #forEach(Gradient2Procedure)}.
   */
  public double[][] d2yda2;

  /**
   * Instantiates a new gradient 2 function store.
   *
   * @param function the function
   */
  public Gradient2FunctionStore(Gradient2Function function) {
    this(function, null, null, null);
  }

  /**
   * Instantiates a new gradient 2 function store with storage.
   *
   * @param function the function
   * @param values the values
   * @param dyda the dyda
   * @param d2yda2 the d2yda2
   */
  public Gradient2FunctionStore(Gradient2Function function, double[] values, double[][] dyda,
      double[][] d2yda2) {
    super(function, values, dyda);
    this.function2 = function;
    this.d2yda2 = d2yda2;
  }

  @Override
  public void initialise2(double[] a) {
    function2.initialise2(a);
  }

  @Override
  public void forEach(Gradient2Procedure procedure) {
    index = 0;
    createValues();
    createDyDa();
    createD2yDa2();
    this.procedure = procedure;
    function2.forEach((Gradient2Procedure) this);
  }

  /**
   * Creates the {@link #d2yda2} matrix.
   */
  protected void createD2yDa2() {
    if (d2yda2 == null || d2yda2.length != function2.size()) {
      d2yda2 = new double[values.length][length];
    }
  }

  @Override
  public void execute(double value, double[] dyDa, double[] d2yDa2) {
    values[index] = value;
    System.arraycopy(dyDa[index], 0, dyda[index], 0, length);
    System.arraycopy(d2yDa2[index], 0, d2yda2[index], 0, length);
    index++;
    procedure.execute(value, dyDa, d2yDa2);
  }
}