/*
    * 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;
  
  import java.io.ByteArrayInputStream;
  import java.io.ByteArrayOutputStream;
  import java.io.ObjectInputStream;
  import java.io.ObjectOutputStream;
  import java.text.DecimalFormat;
  
  import org.junit.Assert;
  
  import org.apache.commons.numbers.complex.Complex;
  import org.apache.commons.numbers.core.Precision;
  import org.apache.commons.statistics.distribution.ContinuousDistribution;
  import org.apache.commons.math4.legacy.core.FieldElement;
  import org.apache.commons.math4.core.jdkmath.JdkMath;
  import org.apache.commons.math4.legacy.util.ComplexFormat;
  import org.apache.commons.math4.legacy.linear.FieldMatrix;
  import org.apache.commons.math4.legacy.linear.RealMatrix;
  import org.apache.commons.math4.legacy.linear.RealVector;
  import org.apache.commons.math4.legacy.stat.inference.ChiSquareTest;
  
  /**
   */
  public final class TestUtils {
      /**
       * Collection of static methods used in math unit tests.
       */
      private TestUtils() {
          super();
      }
  
      /**
       * Verifies that expected and actual are within delta, or are both NaN or
       * infinities of the same sign.
       */
      public static void assertEquals(double expected, double actual, double delta) {
          Assert.assertEquals(null, expected, actual, delta);
      }
  
      /**
       * Verifies that expected and actual are within delta, or are both NaN or
       * infinities of the same sign.
       */
      public static void assertEquals(String msg, double expected, double actual, double delta) {
          // check for NaN
          if(Double.isNaN(expected)){
              Assert.assertTrue("" + actual + " is not NaN.",
                  Double.isNaN(actual));
          } else {
              Assert.assertEquals(msg, expected, actual, delta);
          }
      }
  
      /**
       * Verifies that the two arguments are exactly the same, either
       * both NaN or infinities of same sign, or identical floating point values.
       */
      public static void assertSame(double expected, double actual) {
       Assert.assertEquals(expected, actual, 0);
      }
  
      /**
       * Verifies that real and imaginary parts of the two complex arguments
       * are exactly the same.  Also ensures that NaN / infinite components match.
       */
      public static void assertSame(Complex expected, Complex actual) {
          assertSame(expected.getReal(), actual.getReal());
          assertSame(expected.getImaginary(), actual.getImaginary());
      }
  
      /**
       * Verifies that real and imaginary parts of the two complex arguments
       * differ by at most delta.  Also ensures that NaN / infinite components match.
       */
      public static void assertEquals(Complex expected, Complex actual, double delta) {
          Assert.assertEquals(expected.getReal(), actual.getReal(), delta);
          Assert.assertEquals(expected.getImaginary(), actual.getImaginary(), delta);
      }
  
      /**
       * Verifies that two double arrays have equal entries, up to tolerance
       */
     public static void assertEquals(double expected[], double observed[], double tolerance) {
         assertEquals("Array comparison failure", expected, observed, tolerance);
     }
 
     /**
      * Serializes an object to a bytes array and then recovers the object from the bytes array.
      * Returns the deserialized object.
      *
      * @param o  object to serialize and recover
      * @return  the recovered, deserialized object
      */
     public static Object serializeAndRecover(Object o) {
         try {
             // serialize the Object
             ByteArrayOutputStream bos = new ByteArrayOutputStream();
             ObjectOutputStream so = new ObjectOutputStream(bos);
             so.writeObject(o);
 
             // deserialize the Object
             ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());
             ObjectInputStream si = new ObjectInputStream(bis);
             return si.readObject();
         } catch (Exception e) {
             throw new RuntimeException(e);
         }
     }
 
     /**
      * Verifies that serialization preserves equals and hashCode.
      * Serializes the object, then recovers it and checks equals and hash code.
      *
      * @param object  the object to serialize and recover
      */
     public static void checkSerializedEquality(Object object) {
         Object object2 = serializeAndRecover(object);
         Assert.assertEquals("Equals check", object, object2);
         Assert.assertEquals("HashCode check", object.hashCode(), object2.hashCode());
     }
 
     /**
      * Verifies that the relative error in actual vs. expected is less than or
      * equal to relativeError.  If expected is infinite or NaN, actual must be
      * the same (NaN or infinity of the same sign).
      *
      * @param expected expected value
      * @param actual  observed value
      * @param relativeError  maximum allowable relative error
      */
     public static void assertRelativelyEquals(double expected, double actual,
             double relativeError) {
         assertRelativelyEquals(null, expected, actual, relativeError);
     }
 
     /**
      * Verifies that the relative error in actual vs. expected is less than or
      * equal to relativeError.  If expected is infinite or NaN, actual must be
      * the same (NaN or infinity of the same sign).
      *
      * @param msg  message to return with failure
      * @param expected expected value
      * @param actual  observed value
      * @param relativeError  maximum allowable relative error
      */
     public static void assertRelativelyEquals(String msg, double expected,
             double actual, double relativeError) {
         if (Double.isNaN(expected)) {
             Assert.assertTrue(msg, Double.isNaN(actual));
         } else if (Double.isNaN(actual)) {
             Assert.assertTrue(msg, Double.isNaN(expected));
         } else if (Double.isInfinite(actual) || Double.isInfinite(expected)) {
             Assert.assertEquals(expected, actual, relativeError);
         } else if (expected == 0.0) {
             Assert.assertEquals(msg, actual, expected, relativeError);
         } else {
             double absError = JdkMath.abs(expected) * relativeError;
             Assert.assertEquals(msg, expected, actual, absError);
         }
     }
 
     /**
      * Fails iff values does not contain a number within epsilon of z.
      *
      * @param msg  message to return with failure
      * @param values complex array to search
      * @param z  value sought
      * @param epsilon  tolerance
      */
     public static void assertContains(String msg, Complex[] values,
                                       Complex z, double epsilon) {
         for (Complex value : values) {
             if (Precision.equals(value.getReal(), z.getReal(), epsilon) &&
                 Precision.equals(value.getImaginary(), z.getImaginary(), epsilon)) {
                 return;
             }
         }
         Assert.fail(msg + " Unable to find " + (new ComplexFormat()).format(z));
     }
 
     /**
      * Fails iff values does not contain a number within epsilon of z.
      *
      * @param values complex array to search
      * @param z  value sought
      * @param epsilon  tolerance
      */
     public static void assertContains(Complex[] values,
             Complex z, double epsilon) {
         assertContains(null, values, z, epsilon);
     }
 
     /**
      * Fails iff values does not contain a number within epsilon of x.
      *
      * @param msg  message to return with failure
      * @param values double array to search
      * @param x value sought
      * @param epsilon  tolerance
      */
     public static void assertContains(String msg, double[] values,
             double x, double epsilon) {
         for (double value : values) {
             if (Precision.equals(value, x, epsilon)) {
                 return;
             }
         }
         Assert.fail(msg + " Unable to find " + x);
     }
 
     /**
      * Fails iff values does not contain a number within epsilon of x.
      *
      * @param values double array to search
      * @param x value sought
      * @param epsilon  tolerance
      */
     public static void assertContains(double[] values, double x,
             double epsilon) {
        assertContains(null, values, x, epsilon);
     }
 
     /**
      * Asserts that all entries of the specified vectors are equal to within a
      * positive {@code delta}.
      *
      * @param message the identifying message for the assertion error (can be
      * {@code null})
      * @param expected expected value
      * @param actual actual value
      * @param delta the maximum difference between the entries of the expected
      * and actual vectors for which both entries are still considered equal
      */
     public static void assertEquals(final String message,
         final double[] expected, final RealVector actual, final double delta) {
         final String msgAndSep = message.isEmpty() ? "" : message + ", ";
         Assert.assertEquals(msgAndSep + "dimension", expected.length,
             actual.getDimension());
         for (int i = 0; i < expected.length; i++) {
             Assert.assertEquals(msgAndSep + "entry #" + i, expected[i],
                 actual.getEntry(i), delta);
         }
     }
 
     /**
      * Asserts that all entries of the specified vectors are equal to within a
      * positive {@code delta}.
      *
      * @param message the identifying message for the assertion error (can be
      * {@code null})
      * @param expected expected value
      * @param actual actual value
      * @param delta the maximum difference between the entries of the expected
      * and actual vectors for which both entries are still considered equal
      */
     public static void assertEquals(final String message,
         final RealVector expected, final RealVector actual, final double delta) {
         final String msgAndSep = message.isEmpty() ? "" : message + ", ";
         Assert.assertEquals(msgAndSep + "dimension", expected.getDimension(),
             actual.getDimension());
         final int dim = expected.getDimension();
         for (int i = 0; i < dim; i++) {
             Assert.assertEquals(msgAndSep + "entry #" + i,
                 expected.getEntry(i), actual.getEntry(i), delta);
         }
     }
 
     /** verifies that two matrices are close (1-norm) */
     public static void assertEquals(String msg, RealMatrix expected, RealMatrix observed, double tolerance) {
 
         Assert.assertNotNull(msg + "\nObserved should not be null",observed);
 
         if (expected.getColumnDimension() != observed.getColumnDimension() ||
                 expected.getRowDimension() != observed.getRowDimension()) {
             StringBuilder messageBuffer = new StringBuilder(msg);
             messageBuffer.append("\nObserved has incorrect dimensions.");
             messageBuffer.append("\nobserved is " + observed.getRowDimension() +
                     " x " + observed.getColumnDimension());
             messageBuffer.append("\nexpected " + expected.getRowDimension() +
                     " x " + expected.getColumnDimension());
             Assert.fail(messageBuffer.toString());
         }
 
         RealMatrix delta = expected.subtract(observed);
         if (delta.getNorm() >= tolerance) {
             StringBuilder messageBuffer = new StringBuilder(msg);
             messageBuffer.append("\nExpected: " + expected);
             messageBuffer.append("\nObserved: " + observed);
             messageBuffer.append("\nexpected - observed: " + delta);
             Assert.fail(messageBuffer.toString());
         }
     }
 
     /** verifies that two matrices are equal */
     public static void assertEquals(FieldMatrix<? extends FieldElement<?>> expected,
                                     FieldMatrix<? extends FieldElement<?>> observed) {
 
         Assert.assertNotNull("Observed should not be null",observed);
 
         if (expected.getColumnDimension() != observed.getColumnDimension() ||
                 expected.getRowDimension() != observed.getRowDimension()) {
             StringBuilder messageBuffer = new StringBuilder();
             messageBuffer.append("Observed has incorrect dimensions.");
             messageBuffer.append("\nobserved is " + observed.getRowDimension() +
                     " x " + observed.getColumnDimension());
             messageBuffer.append("\nexpected " + expected.getRowDimension() +
                     " x " + expected.getColumnDimension());
             Assert.fail(messageBuffer.toString());
         }
 
         for (int i = 0; i < expected.getRowDimension(); ++i) {
             for (int j = 0; j < expected.getColumnDimension(); ++j) {
                 FieldElement<?> eij = expected.getEntry(i, j);
                 FieldElement<?> oij = observed.getEntry(i, j);
                 Assert.assertEquals(eij, oij);
             }
         }
     }
 
     /** verifies that two arrays are close (sup norm) */
     public static void assertEquals(String msg, double[] expected, double[] observed, double tolerance) {
         StringBuilder out = new StringBuilder(msg);
         if (expected.length != observed.length) {
             out.append("\n Arrays not same length. \n");
             out.append("expected has length ");
             out.append(expected.length);
             out.append(" observed length = ");
             out.append(observed.length);
             Assert.fail(out.toString());
         }
         boolean failure = false;
         for (int i=0; i < expected.length; i++) {
             if (!Precision.equalsIncludingNaN(expected[i], observed[i], tolerance)) {
                 failure = true;
                 out.append("\n Elements at index ");
                 out.append(i);
                 out.append(" differ. ");
                 out.append(" expected = ");
                 out.append(expected[i]);
                 out.append(" observed = ");
                 out.append(observed[i]);
             }
         }
         if (failure) {
             Assert.fail(out.toString());
         }
     }
 
     /** verifies that two arrays are close (sup norm) */
     public static void assertEquals(String msg, float[] expected, float[] observed, float tolerance) {
         StringBuilder out = new StringBuilder(msg);
         if (expected.length != observed.length) {
             out.append("\n Arrays not same length. \n");
             out.append("expected has length ");
             out.append(expected.length);
             out.append(" observed length = ");
             out.append(observed.length);
             Assert.fail(out.toString());
         }
         boolean failure = false;
         for (int i=0; i < expected.length; i++) {
             if (!Precision.equalsIncludingNaN(expected[i], observed[i], tolerance)) {
                 failure = true;
                 out.append("\n Elements at index ");
                 out.append(i);
                 out.append(" differ. ");
                 out.append(" expected = ");
                 out.append(expected[i]);
                 out.append(" observed = ");
                 out.append(observed[i]);
             }
         }
         if (failure) {
             Assert.fail(out.toString());
         }
     }
 
     /** verifies that two arrays are close (sup norm) */
     public static void assertEquals(String msg, Complex[] expected, Complex[] observed, double tolerance) {
         StringBuilder out = new StringBuilder(msg);
         if (expected.length != observed.length) {
             out.append("\n Arrays not same length. \n");
             out.append("expected has length ");
             out.append(expected.length);
             out.append(" observed length = ");
             out.append(observed.length);
             Assert.fail(out.toString());
         }
         boolean failure = false;
         for (int i=0; i < expected.length; i++) {
             if (!Precision.equalsIncludingNaN(expected[i].getReal(), observed[i].getReal(), tolerance)) {
                 failure = true;
                 out.append("\n Real elements at index ");
                 out.append(i);
                 out.append(" differ. ");
                 out.append(" expected = ");
                 out.append(expected[i].getReal());
                 out.append(" observed = ");
                 out.append(observed[i].getReal());
             }
             if (!Precision.equalsIncludingNaN(expected[i].getImaginary(), observed[i].getImaginary(), tolerance)) {
                 failure = true;
                 out.append("\n Imaginary elements at index ");
                 out.append(i);
                 out.append(" differ. ");
                 out.append(" expected = ");
                 out.append(expected[i].getImaginary());
                 out.append(" observed = ");
                 out.append(observed[i].getImaginary());
             }
         }
         if (failure) {
             Assert.fail(out.toString());
         }
     }
 
     /** verifies that two arrays are equal */
     public static <T extends FieldElement<T>> void assertEquals(T[] m, T[] n) {
         if (m.length != n.length) {
             Assert.fail("vectors not same length");
         }
         for (int i = 0; i < m.length; i++) {
             Assert.assertEquals(m[i],n[i]);
         }
     }
 
     /**
      * Computes the sum of squared deviations of <values> from <target>
      * @param values array of deviates
      * @param target value to compute deviations from
      *
      * @return sum of squared deviations
      */
     public static double sumSquareDev(double[] values, double target) {
         double sumsq = 0d;
         for (int i = 0; i < values.length; i++) {
             final double dev = values[i] - target;
             sumsq += dev * dev;
         }
         return sumsq;
     }
 
     /**
      * Asserts the null hypothesis for a ChiSquare test.  Fails and dumps arguments and test
      * statistics if the null hypothesis can be rejected with confidence 100 * (1 - alpha)%
      *
      * @param valueLabels labels for the values of the discrete distribution under test
      * @param expected expected counts
      * @param observed observed counts
      * @param alpha significance level of the test
      */
     public static void assertChiSquareAccept(String[] valueLabels, double[] expected, long[] observed, double alpha) {
         ChiSquareTest chiSquareTest = new ChiSquareTest();
 
         // Fail if we can reject null hypothesis that distributions are the same
         if (chiSquareTest.chiSquareTest(expected, observed, alpha)) {
             StringBuilder msgBuffer = new StringBuilder();
             DecimalFormat df = new DecimalFormat("#.##");
             msgBuffer.append("Chisquare test failed");
             msgBuffer.append(" p-value = ");
             msgBuffer.append(chiSquareTest.chiSquareTest(expected, observed));
             msgBuffer.append(" chisquare statistic = ");
             msgBuffer.append(chiSquareTest.chiSquare(expected, observed));
             msgBuffer.append(". \n");
             msgBuffer.append("value\texpected\tobserved\n");
             for (int i = 0; i < expected.length; i++) {
                 msgBuffer.append(valueLabels[i]);
                 msgBuffer.append("\t");
                 msgBuffer.append(df.format(expected[i]));
                 msgBuffer.append("\t\t");
                 msgBuffer.append(observed[i]);
                 msgBuffer.append("\n");
             }
             msgBuffer.append("This test can fail randomly due to sampling error with probability ");
             msgBuffer.append(alpha);
             msgBuffer.append(".");
             Assert.fail(msgBuffer.toString());
         }
     }
 
     /**
      * Asserts the null hypothesis for a ChiSquare test.  Fails and dumps arguments and test
      * statistics if the null hypothesis can be rejected with confidence 100 * (1 - alpha)%
      *
      * @param values integer values whose observed and expected counts are being compared
      * @param expected expected counts
      * @param observed observed counts
      * @param alpha significance level of the test
      */
     public static void assertChiSquareAccept(int[] values, double[] expected, long[] observed, double alpha) {
         String[] labels = new String[values.length];
         for (int i = 0; i < values.length; i++) {
             labels[i] = Integer.toString(values[i]);
         }
         assertChiSquareAccept(labels, expected, observed, alpha);
     }
 
     /**
      * Asserts the null hypothesis for a ChiSquare test.  Fails and dumps arguments and test
      * statistics if the null hypothesis can be rejected with confidence 100 * (1 - alpha)%
      *
      * @param expected expected counts
      * @param observed observed counts
      * @param alpha significance level of the test
      */
     public static void assertChiSquareAccept(double[] expected, long[] observed, double alpha) {
         String[] labels = new String[expected.length];
         for (int i = 0; i < labels.length; i++) {
             labels[i] = Integer.toString(i + 1);
         }
         assertChiSquareAccept(labels, expected, observed, alpha);
     }
 
     /**
      * Computes the 25th, 50th and 75th percentiles of the given distribution and returns
      * these values in an array.
      */
     public static double[] getDistributionQuartiles(ContinuousDistribution distribution) {
         double[] quantiles = new double[3];
         quantiles[0] = distribution.inverseCumulativeProbability(0.25d);
         quantiles[1] = distribution.inverseCumulativeProbability(0.5d);
         quantiles[2] = distribution.inverseCumulativeProbability(0.75d);
         return quantiles;
     }
 
     /**
      * Updates observed counts of values in quartiles.
      * counts[0] <-> 1st quartile ... counts[3] <-> top quartile
      */
     public static void updateCounts(double value, long[] counts, double[] quartiles) {
         if (value < quartiles[0]) {
             counts[0]++;
         } else if (value > quartiles[2]) {
             counts[3]++;
         } else if (value > quartiles[1]) {
             counts[2]++;
         } else {
             counts[1]++;
         }
     }
 
     /**
      * Eliminates points with zero mass from densityPoints and densityValues parallel
      * arrays.  Returns the number of positive mass points and collapses the arrays so
      * that the first <returned value> elements of the input arrays represent the positive
      * mass points.
      */
     public static int eliminateZeroMassPoints(int[] densityPoints, double[] densityValues) {
         int positiveMassCount = 0;
         for (int i = 0; i < densityValues.length; i++) {
             if (densityValues[i] > 0) {
                 positiveMassCount++;
             }
         }
         if (positiveMassCount < densityValues.length) {
             int[] newPoints = new int[positiveMassCount];
             double[] newValues = new double[positiveMassCount];
             int j = 0;
             for (int i = 0; i < densityValues.length; i++) {
                 if (densityValues[i] > 0) {
                     newPoints[j] = densityPoints[i];
                     newValues[j] = densityValues[i];
                     j++;
                 }
             }
             System.arraycopy(newPoints,0,densityPoints,0,positiveMassCount);
             System.arraycopy(newValues,0,densityValues,0,positiveMassCount);
         }
         return positiveMassCount;
     }
 }