// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X 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
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
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  // module which is not derived from or based on this library. If you modify this
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  // ******************************************************************************
  package ffx.xray;
  
  import static java.lang.Double.isNaN;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.PI;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  import ffx.crystal.ReflectionList;
  import ffx.numerics.math.ComplexNumber;
  import java.util.Random;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  /**
   * DiffractionRefinementData class.
   *
   * @author Timothy D. Fenn
   * @since 1.0
   */
  public class DiffractionRefinementData {
  
    private static final Logger logger = Logger.getLogger(DiffractionRefinementData.class.getName());
    /** Number of reflections in the data set. */
    public final int n;
    /** Array of R free flags; */
    public final int[] freeR;
    /** Calculated atomic structure factors. */
    public final double[][] fc;
    /** Calculated bulk solvent structure factors. */
    public final double[][] fs;
    /** Figure of merit and phase. */
    public final double[][] fomPhi;
    /** mFo - DFc coefficients. */
    public final double[][] foFc1;
  
    public final double fSigFCutoff;
    /** Number of scale parameters. */
    final int nScale;
    /** 2D array of F/sigF data. */
    final double[][] fSigF;
    /** Scaled sum of Fc and Fs */
    final double[][] fcTot;
    /** 2mFo - DFc coefficients. */
    final double[][] foFc2;
    /** Derivatives with respect to Fc. */
    final double[][] dFc;
    /** Derivatives with respect to Fs. */
    final double[][] dFs;
    /** Number of resolution bins. */
    final int nBins;
    /** Spine scaling coefficients. */
    public double[] spline;
    /** SigmaA coefficient - s. */
    public double[] sigmaA;
    /** SigmaA coefficient - w. */
    public double[] sigmaW;
    /**
     * Duplicated settings - these are also in DiffractionData, but duplicated here until settings are
     * put in their own class.
     */
    public int rFreeFlag;
   /** Log Likelihoods. */
   double llkR, llkF;
   /** Reciprocal space reference for structure factor calculations and computing derivatives. */
   CrystalReciprocalSpace crystalReciprocalSpaceFc;
   /**
    * Reciprocal space reference for bulk solvent structure factor calculations and computing
    * derivatives.
    */
   CrystalReciprocalSpace crystalReciprocalSpaceFs;
   /** Scaled, E-like Fc. */
   double[] esqFc;
   /** Scaled, E-like Fo. */
   double[] esqFo;
   /** Bulk solvent parameters. */
   double solventA, solventB;
   /** bulk solvent scale and Ueq */
   double bulkSolventK, bulkSolventUeq;
   /** Overall model scale. */
   double modelScaleK;
   /** model anisotropic B */
   double[] modelAnisoB = new double[6];
 
   /**
    * allocate data given a {@link ffx.crystal.ReflectionList}
    *
    * @param properties configuration properties
    * @param reflectionList {@link ffx.crystal.ReflectionList} to use to allocate data
    */
   public DiffractionRefinementData(
       CompositeConfiguration properties, ReflectionList reflectionList) {
 
     int rflag = -1;
     if (properties != null) {
       rflag = properties.getInt("rfree-flag", -1);
       fSigFCutoff = properties.getDouble("f-sigf-cutoff", -1.0);
     } else {
       fSigFCutoff = -1.0;
     }
 
     this.n = reflectionList.hklList.size();
     this.nScale = reflectionList.crystal.scaleN;
     this.rFreeFlag = rflag;
     this.nBins = reflectionList.nBins;
     fSigF = new double[n][2];
     freeR = new int[n];
     fc = new double[n][2];
     fs = new double[n][2];
     fcTot = new double[n][2];
     fomPhi = new double[n][2];
     foFc2 = new double[n][2];
     foFc1 = new double[n][2];
     dFc = new double[n][2];
     dFs = new double[n][2];
 
     for (int i = 0; i < n; i++) {
       fSigF[i][0] = fSigF[i][1] = Double.NaN;
       fcTot[i][0] = fcTot[i][1] = Double.NaN;
     }
 
     spline = new double[nBins * 2];
     sigmaA = new double[nBins];
     sigmaW = new double[nBins];
     esqFc = new double[nBins];
     esqFo = new double[nBins];
     for (int i = 0; i < nBins; i++) {
       spline[i] = spline[i + nBins] = sigmaA[i] = esqFc[i] = esqFo[i] = 1.0;
       sigmaW[i] = 0.05;
     }
 
     // Initial guess for scaling/bulk solvent correction.
     bulkSolventK = 0.33;
     bulkSolventUeq = 50.0 / (8.0 * PI * PI);
     modelScaleK = 0.0;
   }
 
   /**
    * FoFc2F
    *
    * @param i a int.
    * @return a double.
    */
   public double FoFc2F(int i) {
     ComplexNumber c = new ComplexNumber(foFc2[i][0], foFc2[i][1]);
     return c.abs();
   }
 
   /**
    * FoFc2Phi
    *
    * @param i a int.
    * @return a double.
    */
   public double FoFc2Phi(int i) {
     ComplexNumber c = new ComplexNumber(foFc2[i][0], foFc2[i][1]);
     return c.phase();
   }
 
   /**
    * get the amplitude of a complex Fc
    *
    * @param i reflection to get
    * @return amplitude of Fc
    */
   public double fcF(int i) {
     ComplexNumber c = new ComplexNumber(fc[i][0], fc[i][1]);
     return c.abs();
   }
 
   /**
    * get the phase of a complex Fc
    *
    * @param i reflection to get
    * @return phase of Fc
    */
   public double fcPhi(int i) {
     ComplexNumber c = new ComplexNumber(fc[i][0], fc[i][1]);
     return c.phase();
   }
 
   /**
    * fcTotF
    *
    * @param i a int.
    * @return a double.
    */
   public double fcTotF(int i) {
     ComplexNumber c = new ComplexNumber(fcTot[i][0], fcTot[i][1]);
     return c.abs();
   }
 
   /**
    * fcTotPhi
    *
    * @param i a int.
    * @return a double.
    */
   public double fcTotPhi(int i) {
     ComplexNumber c = new ComplexNumber(fcTot[i][0], fcTot[i][1]);
     return c.phase();
   }
 
   /**
    * foFc1F
    *
    * @param i a int.
    * @return a double.
    */
   public double foFc1F(int i) {
     ComplexNumber c = new ComplexNumber(foFc1[i][0], foFc1[i][1]);
     return c.abs();
   }
 
   /**
    * foFc1Phi
    *
    * @param i a int.
    * @return a double.
    */
   public double foFc1Phi(int i) {
     ComplexNumber c = new ComplexNumber(foFc1[i][0], foFc1[i][1]);
     return c.phase();
   }
 
   /**
    * fsF
    *
    * @param i a int.
    * @return a double.
    */
   public double fsF(int i) {
     ComplexNumber c = new ComplexNumber(fs[i][0], fs[i][1]);
     return c.abs();
   }
 
   /**
    * fsPhi
    *
    * @param i a int.
    * @return a double.
    */
   public double fsPhi(int i) {
     ComplexNumber c = new ComplexNumber(fs[i][0], fs[i][1]);
     return c.phase();
   }
 
   /**
    * Generate average F/sigF from anomalous F/sigF.
    *
    * @param anomalousFsigF an array of double.
    */
   public void generateFsigFfromAnomalousFsigF(double[][] anomalousFsigF) {
     for (int i = 0; i < n; i++) {
       if (isNaN(anomalousFsigF[i][0]) && isNaN(anomalousFsigF[i][2])) {
         // Do Nothing.
       } else if (isNaN(anomalousFsigF[i][0])) {
         fSigF[i][0] = anomalousFsigF[i][2];
         fSigF[i][1] = anomalousFsigF[i][3];
       } else if (isNaN(anomalousFsigF[i][2])) {
         fSigF[i][0] = anomalousFsigF[i][0];
         fSigF[i][1] = anomalousFsigF[i][1];
       } else {
         fSigF[i][0] = (anomalousFsigF[i][0] + anomalousFsigF[i][2]) / 2.0;
         fSigF[i][1] =
             sqrt(
                 anomalousFsigF[i][1] * anomalousFsigF[i][1]
                     + anomalousFsigF[i][3] * anomalousFsigF[i][3]);
       }
     }
   }
 
   /** Mark 5% of reflections for cross validation (R free flags). */
   public void generateRFree() {
     Random generator = new Random();
     int free;
     int nonfree;
     int nfree = 0;
 
     if (rFreeFlag == 0) {
       free = 0;
       nonfree = 1;
     } else {
       free = 1;
       nonfree = 0;
     }
 
     for (int i = 0; i < n; i++) {
       if (isNaN(fSigF[i][0])) {
         freeR[i] = nonfree;
         continue;
       }
 
       int randomi = generator.nextInt(100);
       if (randomi < 5) {
         freeR[i] = free;
         nfree++;
       } else {
         freeR[i] = nonfree;
       }
     }
 
     if (logger.isLoggable(Level.INFO)) {
       logger.info(format(" Assigned %d of %d reflections to the R free set (5%%).\n", nfree, n));
     }
   }
 
   /**
    * getF
    *
    * @param i a int.
    * @return a double.
    */
   public double getF(int i) {
     return fSigF[i][0];
   }
 
   /**
    * getFSigF
    *
    * @param i a int.
    * @return an array of double.
    */
   public double[] getFSigF(int i) {
     return fSigF[i];
   }
 
   /**
    * getFcTot
    *
    * @param i a int.
    * @return a {@link ComplexNumber} object.
    */
   public ComplexNumber getFcTot(int i) {
     return new ComplexNumber(fcTot[i][0], fcTot[i][1]);
   }
 
   /**
    * getFoFc1
    *
    * @param i a int.
    * @return a {@link ComplexNumber} object.
    */
   public ComplexNumber getFoFc1(int i) {
     return new ComplexNumber(foFc1[i][0], foFc1[i][1]);
   }
 
   /**
    * getFoFc1IP
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   public void getFoFc1IP(int i, ComplexNumber c) {
     c.re(foFc1[i][0]);
     c.im(foFc1[i][1]);
   }
 
   /**
    * getFoFc2
    *
    * @param i a int.
    * @return a {@link ComplexNumber} object.
    */
   public ComplexNumber getFoFc2(int i) {
     return new ComplexNumber(foFc2[i][0], foFc2[i][1]);
   }
 
   /**
    * getFoFc2IP
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   public void getFoFc2IP(int i, ComplexNumber c) {
     c.re(foFc2[i][0]);
     c.im(foFc2[i][1]);
   }
 
   /**
    * getFreeR
    *
    * @param i a int.
    * @return a int.
    */
   public int getFreeR(int i) {
     return freeR[i];
   }
 
   /**
    * getFs
    *
    * @param i a int.
    * @return a {@link ComplexNumber} object.
    */
   public ComplexNumber getFs(int i) {
     return new ComplexNumber(fs[i][0], fs[i][1]);
   }
 
   /**
    * getSigF
    *
    * @param i a int.
    * @return a double.
    */
   public double getSigF(int i) {
     return fSigF[i][1];
   }
 
   /**
    * Generate amplitudes from intensities.
    *
    * <p>This does NOT use French and Wilson caling, but just a simple square root.
    */
   public void intensitiesToAmplitudes() {
     double tmp;
 
     for (int i = 0; i < n; i++) {
       if (fSigF[i][0] > 0.0) {
         tmp = fSigF[i][0];
         fSigF[i][0] = sqrt(tmp);
         if (fSigF[i][1] < tmp) {
           fSigF[i][1] = fSigF[i][0] - sqrt(tmp - fSigF[i][1]);
         } else {
           fSigF[i][1] = fSigF[i][0];
         }
       } else if (!isNaN(fSigF[i][0])) {
         fSigF[i][0] = 0.0;
         fSigF[i][1] = 0.0;
       }
     }
 
     if (logger.isLoggable(Level.WARNING)) {
       StringBuilder sb = new StringBuilder();
       sb.append("\n Internally converting intensities to amplitudes.\n");
       sb.append(" This does not use French & Wilson scaling.\n");
       logger.info(sb.toString());
     }
   }
 
   /**
    * isFreeR
    *
    * @param i a int.
    * @param f a int.
    * @return a boolean.
    */
   public boolean isFreeR(int i, int f) {
     return (freeR[i] == f);
   }
 
   /**
    * return the current likelihood
    *
    * @return the free likelihood (Rfree based)
    */
   public double likelihoodFree() {
     return llkF;
   }
 
   /**
    * return the current likelihood
    *
    * @return the work likelihood (non-Rfree based)
    */
   public double likelihoodWork() {
     return llkR;
   }
 
   /**
    * Set amplitude (F).
    *
    * @param i reflection to set
    * @param f value of F desired
    */
   public void setF(int i, double f) {
     fSigF[i][0] = f;
   }
 
   /**
    * Set amplitude and sigF.
    *
    * @param i reflection to set
    * @param f value of F desired
    * @param sigf value of sigF desired
    */
   public void setFSigF(int i, double f, double sigf) {
     fSigF[i][0] = f;
     fSigF[i][1] = sigf;
   }
 
   /**
    * set complex Fc
    *
    * @param i reflection to set
    * @param c {@link ComplexNumber} to set reflection to
    */
   public void setFc(int i, ComplexNumber c) {
     fc[i][0] = c.re();
     fc[i][1] = c.im();
   }
 
   /**
    * setFcTot
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   public void setFcTot(int i, ComplexNumber c) {
     fcTot[i][0] = c.re();
     fcTot[i][1] = c.im();
   }
 
   /**
    * setFoFc1
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   public void setFoFc1(int i, ComplexNumber c) {
     foFc1[i][0] = c.re();
     foFc1[i][1] = c.im();
   }
 
   /**
    * setFoFc2
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   public void setFoFc2(int i, ComplexNumber c) {
     foFc2[i][0] = c.re();
     foFc2[i][1] = c.im();
   }
 
   /**
    * Set FreeR value flag of a reflection.
    *
    * @param i reflection to set
    * @param f FreeR value to set reflection to
    */
   public void setFreeR(int i, int f) {
     freeR[i] = f;
   }
 
   /**
    * Set FreeR value flag.
    *
    * @param i If FreeR value is i, it is marked for cross validation.
    */
   public void setFreeRFlag(int i) {
     rFreeFlag = i;
   }
 
   /**
    * setFs
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   public void setFs(int i, ComplexNumber c) {
     fs[i][0] = c.re();
     fs[i][1] = c.im();
   }
 
   /**
    * Set amplitude sigma (sigF).
    *
    * @param i reflection to set
    * @param sigF value of sigF desired
    */
   public void setSigF(int i, double sigF) {
     fSigF[i][1] = sigF;
   }
 
   /**
    * setCrystalReciprocalSpace_fc
    *
    * @param crystalReciprocalSpace a {@link ffx.xray.CrystalReciprocalSpace} object.
    */
   void setCrystalReciprocalSpaceFc(CrystalReciprocalSpace crystalReciprocalSpace) {
     this.crystalReciprocalSpaceFc = crystalReciprocalSpace;
   }
 
   /**
    * setCrystalReciprocalSpace_fs
    *
    * @param crystalReciprocalSpace a {@link ffx.xray.CrystalReciprocalSpace} object.
    */
   void setCrystalReciprocalSpaceFs(CrystalReciprocalSpace crystalReciprocalSpace) {
     this.crystalReciprocalSpaceFs = crystalReciprocalSpace;
   }
 
   /**
    * isFreeR
    *
    * @param i a int.
    * @return a boolean.
    */
   boolean isFreeR(int i) {
     return (freeR[i] == rFreeFlag);
   }
 
   /**
    * get the complex number for a Fc reflection
    *
    * @param i reflection to get
    * @return newly allocated {@link ComplexNumber}
    */
   ComplexNumber getFc(int i) {
     return new ComplexNumber(fc[i][0], fc[i][1]);
   }
 
   /**
    * get the complex number for a Fc reflection
    *
    * @param i reflection to get
    * @param c {@link ComplexNumber} to fill
    */
   void getFcIP(int i, ComplexNumber c) {
     c.re(fc[i][0]);
     c.im(fc[i][1]);
   }
 
   /**
    * getFsIP
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   void getFsIP(int i, ComplexNumber c) {
     c.re(fs[i][0]);
     c.im(fs[i][1]);
   }
 
   /**
    * getFcTotIP
    *
    * @param i a int.
    * @param c a {@link ComplexNumber} object.
    */
   void getFcTotIP(int i, ComplexNumber c) {
     c.re(fcTot[i][0]);
     c.im(fcTot[i][1]);
   }
 }