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    *   http://www.apache.org/licenses/LICENSE-2.0
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  package org.orekit.propagation.semianalytical.dsst;
  
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.IdentityHashMap;
  import java.util.List;
  import java.util.Map;
  
  import org.hipparchus.analysis.differentiation.Gradient;
  import org.hipparchus.linear.MatrixUtils;
  import org.hipparchus.linear.RealMatrix;
  import org.orekit.orbits.OrbitType;
  import org.orekit.orbits.PositionAngleType;
  import org.orekit.propagation.AbstractMatricesHarvester;
  import org.orekit.propagation.FieldSpacecraftState;
  import org.orekit.propagation.PropagationType;
  import org.orekit.propagation.SpacecraftState;
  import org.orekit.propagation.semianalytical.dsst.forces.DSSTForceModel;
  import org.orekit.propagation.semianalytical.dsst.forces.FieldShortPeriodTerms;
  import org.orekit.propagation.semianalytical.dsst.utilities.FieldAuxiliaryElements;
  import org.orekit.utils.DoubleArrayDictionary;
  import org.orekit.utils.ParameterDriver;
  import org.orekit.utils.TimeSpanMap;
  import org.orekit.utils.TimeSpanMap.Span;
  
  /** Harvester between two-dimensional Jacobian matrices and one-dimensional {@link
   * SpacecraftState#getAdditionalState(String) additional state arrays}.
   * @author Luc Maisonobe
   * @author Bryan Cazabonne
   * @since 11.1
   */
  public class DSSTHarvester extends AbstractMatricesHarvester {
  
      /** Retrograde factor I.
       *  <p>
       *  DSST model needs equinoctial orbit as internal representation.
       *  Classical equinoctial elements have discontinuities when inclination
       *  is close to zero. In this representation, I = +1. <br>
       *  To avoid this discontinuity, another representation exists and equinoctial
       *  elements can be expressed in a different way, called "retrograde" orbit.
       *  This implies I = -1. <br>
       *  As Orekit doesn't implement the retrograde orbit, I is always set to +1.
       *  But for the sake of consistency with the theory, the retrograde factor
       *  has been kept in the formulas.
       *  </p>
       */
      private static final int I = 1;
  
      /** Propagator bound to this harvester. */
      private final DSSTPropagator propagator;
  
      /** Derivatives of the short period terms that apply to State Transition Matrix.*/
      private final double[][] shortPeriodDerivativesStm;
  
      /** Derivatives of the short period terms that apply to Jacobians columns. */
      private final DoubleArrayDictionary shortPeriodDerivativesJacobianColumns;
  
      /** Columns names for parameters. */
      private List<String> columnsNames;
  
      /**
       * Field short periodic terms. Key is the force model to which they pertain. Value is
       * the terms. They need to be stored in a map because the DsstForceModel interface
       * does not have a getter for the terms.
       */
      private final Map<DSSTForceModel, List<FieldShortPeriodTerms<Gradient>>>
              fieldShortPeriodTerms;
  
      /** Simple constructor.
       * <p>
       * The arguments for initial matrices <em>must</em> be compatible with the
       * {@link org.orekit.orbits.OrbitType#EQUINOCTIAL equinoctial orbit type}
       * and {@link PositionAngleType position angle} that will be used by propagator
       * </p>
       * @param propagator propagator bound to this harvester
       * @param stmName State Transition Matrix state name
       * @param initialStm initial State Transition Matrix ∂Y/∂Y₀,
       * if null (which is the most frequent case), assumed to be 6x6 identity
       * @param initialJacobianColumns initial columns of the Jacobians matrix with respect to parameters,
       * if null or if some selected parameters are missing from the dictionary, the corresponding
       * initial column is assumed to be 0
       */
      DSSTHarvester(final DSSTPropagator propagator, final String stmName,
                   final RealMatrix initialStm, final DoubleArrayDictionary initialJacobianColumns) {
         super(stmName, initialStm, initialJacobianColumns);
         this.propagator                            = propagator;
         this.shortPeriodDerivativesStm             = new double[STATE_DIMENSION][STATE_DIMENSION];
         this.shortPeriodDerivativesJacobianColumns = new DoubleArrayDictionary();
         // Use identity hash map to have the same behavior as a getter on the force model
         this.fieldShortPeriodTerms                 = new IdentityHashMap<>();
     }
 
     /** {@inheritDoc} */
     @Override
     public RealMatrix getStateTransitionMatrix(final SpacecraftState state) {
 
         final RealMatrix stm = super.getStateTransitionMatrix(state);
 
         if (propagator.getPropagationType() == PropagationType.OSCULATING) {
             // add the short period terms
             for (int i = 0; i < STATE_DIMENSION; i++) {
                 for (int j = 0; j < STATE_DIMENSION; j++) {
                     stm.addToEntry(i, j, shortPeriodDerivativesStm[i][j]);
                 }
             }
         }
 
         return stm;
 
     }
 
     /** {@inheritDoc} */
     @Override
     public RealMatrix getParametersJacobian(final SpacecraftState state) {
 
         final RealMatrix jacobian = super.getParametersJacobian(state);
         if (jacobian != null && propagator.getPropagationType() == PropagationType.OSCULATING) {
 
             // add the short period terms
             final List<String> names = getJacobiansColumnsNames();
             for (int j = 0; j < names.size(); ++j) {
                 final double[] column = shortPeriodDerivativesJacobianColumns.get(names.get(j));
                 for (int i = 0; i < STATE_DIMENSION; i++) {
                     jacobian.addToEntry(i, j, column[i]);
                 }
             }
 
         }
 
         return jacobian;
 
     }
 
     /** Get the Jacobian matrix B1 (B1 = ∂εη/∂Y).
      * <p>
      * B1 represents the partial derivatives of the short period motion
      * with respect to the mean equinoctial elements.
      * </p>
      * @return the B1 jacobian matrix
      */
     public RealMatrix getB1() {
 
         // Initialize B1
         final RealMatrix B1 = MatrixUtils.createRealMatrix(STATE_DIMENSION, STATE_DIMENSION);
 
         // add the short period terms
         for (int i = 0; i < STATE_DIMENSION; i++) {
             for (int j = 0; j < STATE_DIMENSION; j++) {
                 B1.addToEntry(i, j, shortPeriodDerivativesStm[i][j]);
             }
         }
 
         // Return B1
         return B1;
 
     }
 
     /** Get the Jacobian matrix B2 (B2 = ∂Y/∂Y₀).
      * <p>
      * B2 represents the partial derivatives of the mean equinoctial elements
      * with respect to the initial ones.
      * </p>
      * @param state spacecraft state
      * @return the B2 jacobian matrix
      */
     public RealMatrix getB2(final SpacecraftState state) {
         return super.getStateTransitionMatrix(state);
     }
 
     /** Get the Jacobian matrix B3 (B3 = ∂Y/∂P).
      * <p>
      * B3 represents the partial derivatives of the mean equinoctial elements
      * with respect to the estimated propagation parameters.
      * </p>
      * @param state spacecraft state
      * @return the B3 jacobian matrix
      */
     public RealMatrix getB3(final SpacecraftState state) {
         return super.getParametersJacobian(state);
     }
 
     /** Get the Jacobian matrix B4 (B4 = ∂εη/∂c).
      * <p>
      * B4 represents the partial derivatives of the short period motion
      * with respect to the estimated propagation parameters.
      * </p>
      * @return the B4 jacobian matrix
      */
     public RealMatrix getB4() {
 
         // Initialize B4
         final List<String> names = getJacobiansColumnsNames();
         final RealMatrix B4 = MatrixUtils.createRealMatrix(STATE_DIMENSION, names.size());
 
         // add the short period terms
         for (int j = 0; j < names.size(); ++j) {
             final double[] column = shortPeriodDerivativesJacobianColumns.get(names.get(j));
             for (int i = 0; i < STATE_DIMENSION; i++) {
                 B4.addToEntry(i, j, column[i]);
             }
         }
 
         // Return B4
         return B4;
 
     }
 
     /** Freeze the names of the Jacobian columns.
      * <p>
      * This method is called when proagation starts, i.e. when configuration is completed
      * </p>
      */
     public void freezeColumnsNames() {
         columnsNames = getJacobiansColumnsNames();
     }
 
     /** {@inheritDoc} */
     @Override
     public List<String> getJacobiansColumnsNames() {
         return columnsNames == null ? propagator.getJacobiansColumnsNames() : columnsNames;
     }
 
     /** Initialize the short periodic terms for the "field" elements.
      * @param reference current mean spacecraft state
      */
     public void initializeFieldShortPeriodTerms(final SpacecraftState reference) {
         initializeFieldShortPeriodTerms(reference, propagator.getPropagationType());
     }
 
     /**
      * Initialize the short periodic terms for the "field" elements.
      *
      * @param reference current mean spacecraft state
      * @param type      MEAN or OSCULATING
      */
     public void initializeFieldShortPeriodTerms(final SpacecraftState reference,
                                                 final PropagationType type) {
 
         // Converter
         final DSSTGradientConverter converter = new DSSTGradientConverter(reference, propagator.getAttitudeProvider());
 
         // clear old values
         // prevents duplicates or stale values when reusing a DSSTPropagator
         fieldShortPeriodTerms.clear();
 
         // Loop on force models
         for (final DSSTForceModel forceModel : propagator.getAllForceModels()) {
 
             // Convert to Gradient
             final FieldSpacecraftState<Gradient> dsState = converter.getState(forceModel);
             final Gradient[] dsParameters = converter.getParametersAtStateDate(dsState, forceModel);
             final FieldAuxiliaryElements<Gradient> auxiliaryElements = new FieldAuxiliaryElements<>(dsState.getOrbit(), I);
 
             // Initialize the "Field" short periodic terms, same mode as the propagator
             final List<FieldShortPeriodTerms<Gradient>> terms =
                     forceModel.initializeShortPeriodTerms(
                             auxiliaryElements,
                             type,
                             dsParameters);
             // create a copy of the list to protect against inadvertent modification
             final List<FieldShortPeriodTerms<Gradient>> list;
             synchronized (fieldShortPeriodTerms) {
                 list = fieldShortPeriodTerms.computeIfAbsent(forceModel, x -> new ArrayList<>());
             }
             list.addAll(terms);
 
         }
 
     }
 
     /** Update the short periodic terms for the "field" elements.
      * @param reference current mean spacecraft state
      */
     @SuppressWarnings("unchecked")
     public void updateFieldShortPeriodTerms(final SpacecraftState reference) {
 
         // Converter
         final DSSTGradientConverter converter = new DSSTGradientConverter(reference, propagator.getAttitudeProvider());
 
         // Loop on force models
         for (final DSSTForceModel forceModel : propagator.getAllForceModels()) {
 
             // Convert to Gradient
             final FieldSpacecraftState<Gradient> dsState = converter.getState(forceModel);
             final Gradient[] dsParameters = converter.getParameters(dsState, forceModel);
 
             // Update the short periodic terms for the current force model
             forceModel.updateShortPeriodTerms(dsParameters, dsState);
 
         }
 
     }
 
     /** {@inheritDoc} */
     @Override
     public void setReferenceState(final SpacecraftState reference) {
 
         // reset derivatives to zero
         for (final double[] row : shortPeriodDerivativesStm) {
             Arrays.fill(row, 0.0);
         }
 
         shortPeriodDerivativesJacobianColumns.clear();
 
         final DSSTGradientConverter converter = new DSSTGradientConverter(reference, propagator.getAttitudeProvider());
 
         // Compute Jacobian
         for (final DSSTForceModel forceModel : propagator.getAllForceModels()) {
 
             final FieldSpacecraftState<Gradient> dsState = converter.getState(forceModel);
             final Gradient zero = dsState.getDate().getField().getZero();
             final Gradient[] shortPeriod = new Gradient[6];
             Arrays.fill(shortPeriod, zero);
             final List<FieldShortPeriodTerms<Gradient>> terms;
             synchronized (fieldShortPeriodTerms) {
                 terms = fieldShortPeriodTerms.computeIfAbsent(forceModel, x -> new ArrayList<>(0));
             }
             for (final FieldShortPeriodTerms<Gradient> spt : terms) {
                 final Gradient[] spVariation = spt.value(dsState.getOrbit());
                 for (int i = 0; i < spVariation .length; i++) {
                     shortPeriod[i] = shortPeriod[i].add(spVariation[i]);
                 }
             }
 
             final double[] derivativesASP  = shortPeriod[0].getGradient();
             final double[] derivativesExSP = shortPeriod[1].getGradient();
             final double[] derivativesEySP = shortPeriod[2].getGradient();
             final double[] derivativesHxSP = shortPeriod[3].getGradient();
             final double[] derivativesHySP = shortPeriod[4].getGradient();
             final double[] derivativesLSP  = shortPeriod[5].getGradient();
 
             // update Jacobian with respect to state
             addToRow(derivativesASP,  0);
             addToRow(derivativesExSP, 1);
             addToRow(derivativesEySP, 2);
             addToRow(derivativesHxSP, 3);
             addToRow(derivativesHySP, 4);
             addToRow(derivativesLSP,  5);
 
             int paramsIndex = converter.getFreeStateParameters();
             for (ParameterDriver driver : forceModel.getParametersDrivers()) {
                 if (driver.isSelected()) {
 
                     final TimeSpanMap<String> driverNameSpanMap = driver.getNamesSpanMap();
                     // for each span (for each estimated value) corresponding name is added
 
                     for (Span<String> span = driverNameSpanMap.getFirstSpan(); span != null; span = span.next()) {
                         // get the partials derivatives for this driver
                         DoubleArrayDictionary.Entry entry = shortPeriodDerivativesJacobianColumns.getEntry(span.getData());
                         if (entry == null) {
                             // create an entry filled with zeroes
                             shortPeriodDerivativesJacobianColumns.put(span.getData(), new double[STATE_DIMENSION]);
                             entry = shortPeriodDerivativesJacobianColumns.getEntry(span.getData());
                         }
 
                         // add the contribution of the current force model
                         entry.increment(new double[] {
                             derivativesASP[paramsIndex], derivativesExSP[paramsIndex], derivativesEySP[paramsIndex],
                             derivativesHxSP[paramsIndex], derivativesHySP[paramsIndex], derivativesLSP[paramsIndex]
                         });
                         ++paramsIndex;
                     }
                 }
             }
         }
 
     }
 
     /** Fill State Transition Matrix rows.
      * @param derivatives derivatives of a component
      * @param index component index (0 for a, 1 for ex, 2 for ey, 3 for hx, 4 for hy, 5 for l)
      */
     private void addToRow(final double[] derivatives, final int index) {
         for (int i = 0; i < 6; i++) {
             shortPeriodDerivativesStm[index][i] += derivatives[i];
         }
     }
 
     /** {@inheritDoc} */
     @Override
     public OrbitType getOrbitType() {
         return propagator.getOrbitType();
     }
 
     /** {@inheritDoc} */
     @Override
     public PositionAngleType getPositionAngleType() {
         return propagator.getPositionAngleType();
     }
 
 }