spark-instrumented-optimizer/python/pyspark/mllib/tests/test_stat.py

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import array as pyarray
import unittest

from numpy import array

from pyspark.mllib.linalg import Vectors, Matrices
from pyspark.mllib.random import RandomRDDs
from pyspark.mllib.regression import LabeledPoint
from pyspark.mllib.stat import Statistics
from pyspark.sql.utils import IllegalArgumentException
from pyspark.testing.mllibutils import MLlibTestCase


class StatTests(MLlibTestCase):
    # SPARK-4023
    def test_col_with_different_rdds(self):
        # numpy
        data = RandomRDDs.normalVectorRDD(self.sc, 1000, 10, 10)
        summary = Statistics.colStats(data)
        self.assertEqual(1000, summary.count())
        # array
        data = self.sc.parallelize([range(10)] * 10)
        summary = Statistics.colStats(data)
        self.assertEqual(10, summary.count())
        # array
        data = self.sc.parallelize([pyarray.array("d", range(10))] * 10)
        summary = Statistics.colStats(data)
        self.assertEqual(10, summary.count())

    def test_col_norms(self):
        data = RandomRDDs.normalVectorRDD(self.sc, 1000, 10, 10)
        summary = Statistics.colStats(data)
        self.assertEqual(10, len(summary.normL1()))
        self.assertEqual(10, len(summary.normL2()))

        data2 = self.sc.parallelize(range(10)).map(lambda x: Vectors.dense(x))
        summary2 = Statistics.colStats(data2)
        self.assertEqual(array([45.0]), summary2.normL1())
        import math
        expectedNormL2 = math.sqrt(sum(map(lambda x: x*x, range(10))))
        self.assertTrue(math.fabs(summary2.normL2()[0] - expectedNormL2) < 1e-14)


class ChiSqTestTests(MLlibTestCase):
    def test_goodness_of_fit(self):
        from numpy import inf

        observed = Vectors.dense([4, 6, 5])
        pearson = Statistics.chiSqTest(observed)

        # Validated against the R command `chisq.test(c(4, 6, 5), p=c(1/3, 1/3, 1/3))`
        self.assertEqual(pearson.statistic, 0.4)
        self.assertEqual(pearson.degreesOfFreedom, 2)
        self.assertAlmostEqual(pearson.pValue, 0.8187, 4)

        # Different expected and observed sum
        observed1 = Vectors.dense([21, 38, 43, 80])
        expected1 = Vectors.dense([3, 5, 7, 20])
        pearson1 = Statistics.chiSqTest(observed1, expected1)

        # Results validated against the R command
        # `chisq.test(c(21, 38, 43, 80), p=c(3/35, 1/7, 1/5, 4/7))`
        self.assertAlmostEqual(pearson1.statistic, 14.1429, 4)
        self.assertEqual(pearson1.degreesOfFreedom, 3)
        self.assertAlmostEqual(pearson1.pValue, 0.002717, 4)

        # Vectors with different sizes
        observed3 = Vectors.dense([1.0, 2.0, 3.0])
        expected3 = Vectors.dense([1.0, 2.0, 3.0, 4.0])
        self.assertRaises(ValueError, Statistics.chiSqTest, observed3, expected3)

        # Negative counts in observed
        neg_obs = Vectors.dense([1.0, 2.0, 3.0, -4.0])
        self.assertRaises(IllegalArgumentException, Statistics.chiSqTest, neg_obs, expected1)

        # Count = 0.0 in expected but not observed
        zero_expected = Vectors.dense([1.0, 0.0, 3.0])
        pearson_inf = Statistics.chiSqTest(observed, zero_expected)
        self.assertEqual(pearson_inf.statistic, inf)
        self.assertEqual(pearson_inf.degreesOfFreedom, 2)
        self.assertEqual(pearson_inf.pValue, 0.0)

        # 0.0 in expected and observed simultaneously
        zero_observed = Vectors.dense([2.0, 0.0, 1.0])
        self.assertRaises(
            IllegalArgumentException, Statistics.chiSqTest, zero_observed, zero_expected)

    def test_matrix_independence(self):
        data = [40.0, 24.0, 29.0, 56.0, 32.0, 42.0, 31.0, 10.0, 0.0, 30.0, 15.0, 12.0]
        chi = Statistics.chiSqTest(Matrices.dense(3, 4, data))

        # Results validated against R command
        # `chisq.test(rbind(c(40, 56, 31, 30),c(24, 32, 10, 15), c(29, 42, 0, 12)))`
        self.assertAlmostEqual(chi.statistic, 21.9958, 4)
        self.assertEqual(chi.degreesOfFreedom, 6)
        self.assertAlmostEqual(chi.pValue, 0.001213, 4)

        # Negative counts
        neg_counts = Matrices.dense(2, 2, [4.0, 5.0, 3.0, -3.0])
        self.assertRaises(IllegalArgumentException, Statistics.chiSqTest, neg_counts)

        # Row sum = 0.0
        row_zero = Matrices.dense(2, 2, [0.0, 1.0, 0.0, 2.0])
        self.assertRaises(IllegalArgumentException, Statistics.chiSqTest, row_zero)

        # Column sum = 0.0
        col_zero = Matrices.dense(2, 2, [0.0, 0.0, 2.0, 2.0])
        self.assertRaises(IllegalArgumentException, Statistics.chiSqTest, col_zero)

    def test_chi_sq_pearson(self):
        data = [
            LabeledPoint(0.0, Vectors.dense([0.5, 10.0])),
            LabeledPoint(0.0, Vectors.dense([1.5, 20.0])),
            LabeledPoint(1.0, Vectors.dense([1.5, 30.0])),
            LabeledPoint(0.0, Vectors.dense([3.5, 30.0])),
            LabeledPoint(0.0, Vectors.dense([3.5, 40.0])),
            LabeledPoint(1.0, Vectors.dense([3.5, 40.0]))
        ]

        for numParts in [2, 4, 6, 8]:
            chi = Statistics.chiSqTest(self.sc.parallelize(data, numParts))
            feature1 = chi[0]
            self.assertEqual(feature1.statistic, 0.75)
            self.assertEqual(feature1.degreesOfFreedom, 2)
            self.assertAlmostEqual(feature1.pValue, 0.6873, 4)

            feature2 = chi[1]
            self.assertEqual(feature2.statistic, 1.5)
            self.assertEqual(feature2.degreesOfFreedom, 3)
            self.assertAlmostEqual(feature2.pValue, 0.6823, 4)

    def test_right_number_of_results(self):
        num_cols = 1001
        sparse_data = [
            LabeledPoint(0.0, Vectors.sparse(num_cols, [(100, 2.0)])),
            LabeledPoint(0.1, Vectors.sparse(num_cols, [(200, 1.0)]))
        ]
        chi = Statistics.chiSqTest(self.sc.parallelize(sparse_data))
        self.assertEqual(len(chi), num_cols)
        self.assertIsNotNone(chi[1000])


class KolmogorovSmirnovTest(MLlibTestCase):

    def test_R_implementation_equivalence(self):
        data = self.sc.parallelize([
            1.1626852897838, -0.585924465893051, 1.78546500331661, -1.33259371048501,
            -0.446566766553219, 0.569606122374976, -2.88971761441412, -0.869018343326555,
            -0.461702683149641, -0.555540910137444, -0.0201353678515895, -0.150382224136063,
            -0.628126755843964, 1.32322085193283, -1.52135057001199, -0.437427868856691,
            0.970577579543399, 0.0282226444247749, -0.0857821886527593, 0.389214404984942
        ])
        model = Statistics.kolmogorovSmirnovTest(data, "norm")
        self.assertAlmostEqual(model.statistic, 0.189, 3)
        self.assertAlmostEqual(model.pValue, 0.422, 3)

        model = Statistics.kolmogorovSmirnovTest(data, "norm", 0, 1)
        self.assertAlmostEqual(model.statistic, 0.189, 3)
        self.assertAlmostEqual(model.pValue, 0.422, 3)


if __name__ == "__main__":
    from pyspark.mllib.tests.test_stat import *  # noqa: F401

    try:
        import xmlrunner
        testRunner = xmlrunner.XMLTestRunner(output='target/test-reports', verbosity=2)
    except ImportError:
        testRunner = None
    unittest.main(testRunner=testRunner, verbosity=2)