/*
    * Licensed to the Apache Software Foundation (ASF) under one or more
    * contributor license agreements.  See the NOTICE file distributed with
    * this work for additional information regarding copyright ownership.
    * The ASF licenses this file to You under the Apache License, Version 2.0
    * (the "License"); you may not use this file except in compliance with
    * the License.  You may obtain a copy of the License at
    *
    *      http://www.apache.org/licenses/LICENSE-2.0
   *
   * Unless required by applicable law or agreed to in writing, software
   * distributed under the License is distributed on an "AS IS" BASIS,
   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   * See the License for the specific language governing permissions and
   * limitations under the License.
   */
  package org.apache.commons.math4.legacy.fitting.leastsquares;
  
  import java.io.BufferedReader;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.Arrays;
  
  import org.apache.commons.math4.legacy.analysis.MultivariateMatrixFunction;
  import org.apache.commons.math4.legacy.analysis.MultivariateVectorFunction;
  
  /**
   * This class gives access to the statistical reference datasets provided by the
   * NIST (available
   * <a href="http://www.itl.nist.gov/div898/strd/general/dataarchive.html">here</a>).
   * Instances of this class can be created by invocation of the
   * {@link StatisticalReferenceDatasetFactory}.
   */
  public abstract class StatisticalReferenceDataset {
      /** The name of this dataset. */
      private final String name;
      /** The total number of observations (data points). */
      private final int numObservations;
      /** The total number of parameters. */
      private final int numParameters;
      /** The total number of starting points for the optimizations. */
      private final int numStartingPoints;
      /** The values of the predictor. */
      private final double[] x;
      /** The values of the response. */
      private final double[] y;
      /**
       * The starting values. {@code startingValues[j][i]} is the value of the
       * {@code i}-th parameter in the {@code j}-th set of starting values.
       */
      private final double[][] startingValues;
      /** The certified values of the parameters. */
      private final double[] a;
      /** The certified values of the standard deviation of the parameters. */
      private final double[] sigA;
      /** The certified value of the residual sum of squares. */
      private double residualSumOfSquares;
      /** The least-squares problem. */
      private final LeastSquaresProblem problem;
  
      /**
       * Creates a new instance of this class from the specified data file. The
       * file must follow the StRD format.
       *
       * @param in the data file
       * @throws IOException if an I/O error occurs
       */
      public StatisticalReferenceDataset(final BufferedReader in)
          throws IOException {
  
          final ArrayList<String> lines = new ArrayList<>();
          for (String line = in.readLine(); line != null; line = in.readLine()) {
              lines.add(line);
          }
          int[] index = findLineNumbers("Data", lines);
          if (index == null) {
              throw new AssertionError("could not find line indices for data");
          }
          this.numObservations = index[1] - index[0] + 1;
          this.x = new double[this.numObservations];
          this.y = new double[this.numObservations];
          for (int i = 0; i < this.numObservations; i++) {
              final String line = lines.get(index[0] + i - 1);
              final String[] tokens = line.trim().split(" ++");
              // Data columns are in reverse order!!!
              this.y[i] = Double.parseDouble(tokens[0]);
              this.x[i] = Double.parseDouble(tokens[1]);
          }
  
          index = findLineNumbers("Starting Values", lines);
          if (index == null) {
              throw new AssertionError(
                                       "could not find line indices for starting values");
          }
          this.numParameters = index[1] - index[0] + 1;
  
          double[][] start = null;
          this.a = new double[numParameters];
          this.sigA = new double[numParameters];
         for (int i = 0; i < numParameters; i++) {
             final String line = lines.get(index[0] + i - 1);
             final String[] tokens = line.trim().split(" ++");
             if (start == null) {
                 start = new double[tokens.length - 4][numParameters];
             }
             for (int j = 2; j < tokens.length - 2; j++) {
                 start[j - 2][i] = Double.parseDouble(tokens[j]);
             }
             this.a[i] = Double.parseDouble(tokens[tokens.length - 2]);
             this.sigA[i] = Double.parseDouble(tokens[tokens.length - 1]);
         }
         if (start == null) {
             throw new IOException("could not find starting values");
         }
         this.numStartingPoints = start.length;
         this.startingValues = start;
 
         double dummyDouble = Double.NaN;
         String dummyString = null;
         for (String line : lines) {
             if (line.contains("Dataset Name:")) {
                 dummyString = line
                     .substring(line.indexOf("Dataset Name:") + 13,
                                line.indexOf("(")).trim();
             }
             if (line.contains("Residual Sum of Squares")) {
                 final String[] tokens = line.split(" ++");
                 dummyDouble = Double.parseDouble(tokens[4].trim());
             }
         }
         if (Double.isNaN(dummyDouble)) {
             throw new IOException(
                                   "could not find certified value of residual sum of squares");
         }
         this.residualSumOfSquares = dummyDouble;
 
         if (dummyString == null) {
             throw new IOException("could not find dataset name");
         }
         this.name = dummyString;
 
         this.problem = new LeastSquaresProblem();
     }
 
     class LeastSquaresProblem {
         public MultivariateVectorFunction getModelFunction() {
             return new MultivariateVectorFunction() {
                 @Override
                 public double[] value(final double[] a) {
                     final int n = getNumObservations();
                     final double[] yhat = new double[n];
                     for (int i = 0; i < n; i++) {
                         yhat[i] = getModelValue(getX(i), a);
                     }
                     return yhat;
                 }
             };
         }
 
         public MultivariateMatrixFunction getModelFunctionJacobian() {
             return new MultivariateMatrixFunction() {
                 @Override
                 public double[][] value(final double[] a)
                     throws IllegalArgumentException {
                     final int n = getNumObservations();
                     final double[][] j = new double[n][];
                     for (int i = 0; i < n; i++) {
                         j[i] = getModelDerivatives(getX(i), a);
                     }
                     return j;
                 }
             };
         }
     }
 
     /**
      * Returns the name of this dataset.
      *
      * @return the name of the dataset
      */
     public String getName() {
         return name;
     }
 
     /**
      * Returns the total number of observations (data points).
      *
      * @return the number of observations
      */
     public int getNumObservations() {
         return numObservations;
     }
 
     /**
      * Returns a copy of the data arrays. The data is laid out as follows <li>
      * {@code data[0][i] = x[i]},</li> <li>{@code data[1][i] = y[i]},</li>
      *
      * @return the array of data points.
      */
     public double[][] getData() {
         return new double[][] {
             Arrays.copyOf(x, x.length), Arrays.copyOf(y, y.length)
         };
     }
 
     /**
      * Returns the x-value of the {@code i}-th data point.
      *
      * @param i the index of the data point
      * @return the x-value
      */
     public double getX(final int i) {
         return x[i];
     }
 
     /**
      * Returns the y-value of the {@code i}-th data point.
      *
      * @param i the index of the data point
      * @return the y-value
      */
     public double getY(final int i) {
         return y[i];
     }
 
     /**
      * Returns the total number of parameters.
      *
      * @return the number of parameters
      */
     public int getNumParameters() {
         return numParameters;
     }
 
     /**
      * Returns the certified values of the paramters.
      *
      * @return the values of the parameters
      */
     public double[] getParameters() {
         return Arrays.copyOf(a, a.length);
     }
 
     /**
      * Returns the certified value of the {@code i}-th parameter.
      *
      * @param i the index of the parameter
      * @return the value of the parameter
      */
     public double getParameter(final int i) {
         return a[i];
     }
 
     /**
      * Reurns the certified values of the standard deviations of the parameters.
      *
      * @return the standard deviations of the parameters
      */
     public double[] getParametersStandardDeviations() {
         return Arrays.copyOf(sigA, sigA.length);
     }
 
     /**
      * Returns the certified value of the standard deviation of the {@code i}-th
      * parameter.
      *
      * @param i the index of the parameter
      * @return the standard deviation of the parameter
      */
     public double getParameterStandardDeviation(final int i) {
         return sigA[i];
     }
 
     /**
      * Returns the certified value of the residual sum of squares.
      *
      * @return the residual sum of squares
      */
     public double getResidualSumOfSquares() {
         return residualSumOfSquares;
     }
 
     /**
      * Returns the total number of starting points (initial guesses for the
      * optimization process).
      *
      * @return the number of starting points
      */
     public int getNumStartingPoints() {
         return numStartingPoints;
     }
 
     /**
      * Returns the {@code i}-th set of initial values of the parameters.
      *
      * @param i the index of the starting point
      * @return the starting point
      */
     public double[] getStartingPoint(final int i) {
         return Arrays.copyOf(startingValues[i], startingValues[i].length);
     }
 
     /**
      * Returns the least-squares problem corresponding to fitting the model to
      * the specified data.
      *
      * @return the least-squares problem
      */
     public LeastSquaresProblem getLeastSquaresProblem() {
         return problem;
     }
 
     /**
      * Returns the value of the model for the specified values of the predictor
      * variable and the parameters.
      *
      * @param x the predictor variable
      * @param a the parameters
      * @return the value of the model
      */
     public abstract double getModelValue(double x, double[] a);
 
     /**
      * Returns the values of the partial derivatives of the model with respect
      * to the parameters.
      *
      * @param x the predictor variable
      * @param a the parameters
      * @return the partial derivatives
      */
     public abstract double[] getModelDerivatives(double x,
                                                  double[] a);
 
     /**
      * <p>
      * Parses the specified text lines, and extracts the indices of the first
      * and last lines of the data defined by the specified {@code key}. This key
      * must be one of
      * </p>
      * <ul>
      * <li>{@code "Starting Values"},</li>
      * <li>{@code "Certified Values"},</li>
      * <li>{@code "Data"}.</li>
      * </ul>
      * <p>
      * In the NIST data files, the line indices are separated by the keywords
      * {@code "lines"} and {@code "to"}.
      * </p>
      *
      * @param lines the line of text to be parsed
      * @return an array of two {@code int}s. First value is the index of the
      *         first line, second value is the index of the last line.
      *         {@code null} if the line could not be parsed.
      */
     private static int[] findLineNumbers(final String key,
                                          final Iterable<String> lines) {
         for (String text : lines) {
             boolean flag = text.contains(key) && text.contains("lines") &&
                            text.contains("to") && text.contains(")");
             if (flag) {
                 final int[] numbers = new int[2];
                 final String from = text.substring(text.indexOf("lines") + 5,
                                                    text.indexOf("to"));
                 numbers[0] = Integer.parseInt(from.trim());
                 final String to = text.substring(text.indexOf("to") + 2,
                                                  text.indexOf(")"));
                 numbers[1] = Integer.parseInt(to.trim());
                 return numbers;
             }
         }
         return null;
     }
 }