# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------

from __future__ import absolute_import, division, print_function
from unittest import TestCase, main

import numpy as np
import numpy.testing as npt
import pandas as pd

from skbio import DistanceMatrix
from skbio.stats.distance import (DissimilarityMatrixError,
                                  DistanceMatrixError, mantel, pwmantel)
from skbio.stats.distance._mantel import _order_dms
from skbio.util import get_data_path, assert_data_frame_almost_equal


class MantelTestData(TestCase):
    def setUp(self):
        # Small dataset of minimal size (3x3). Mix of floats and ints in a
        # native Python nested list structure.
        self.minx = [[0, 1, 2], [1, 0, 3], [2, 3, 0]]
        self.miny = [[0, 2, 7], [2, 0, 6], [7, 6, 0]]
        self.minz = [[0, 0.5, 0.25], [0.5, 0, 0.1], [0.25, 0.1, 0]]

        # Version of the above dataset stored as DistanceMatrix instances.
        self.minx_dm = DistanceMatrix(self.minx)
        self.miny_dm = DistanceMatrix(self.miny)
        self.minz_dm = DistanceMatrix(self.minz)

        # Versions of self.minx_dm and self.minz_dm that each have an extra ID
        # on the end.
        self.minx_dm_extra = DistanceMatrix([[0, 1, 2, 7],
                                             [1, 0, 3, 2],
                                             [2, 3, 0, 4],
                                             [7, 2, 4, 0]],
                                            ['0', '1', '2', 'foo'])
        self.minz_dm_extra = DistanceMatrix([[0, 0.5, 0.25, 3],
                                             [0.5, 0, 0.1, 24],
                                             [0.25, 0.1, 0, 5],
                                             [3, 24, 5, 0]],
                                            ['0', '1', '2', 'bar'])


class MantelTests(MantelTestData):
    """Results were verified with R 3.1.0 and vegan 2.0-10 (vegan::mantel).

    vegan::mantel performs a one-sided (greater) test and does not have the
    option to specify different alternative hypotheses. In order to test the
    other alternative hypotheses, I modified vegan::mantel to perform the
    appropriate test, source()'d the file and verified the output.

    """

    def setUp(self):
        super(MantelTests, self).setUp()

        self.methods = ('pearson', 'spearman')
        self.alternatives = ('two-sided', 'greater', 'less')

        # No variation in distances. Taken from Figure 10.20(b), pg. 603 in L&L
        # 3rd edition. Their example is 4x4 but using 3x3 here for easy
        # comparison to the minimal dataset above.
        self.no_variation = [[0, 0.667, 0.667],
                             [0.667, 0, 0.667],
                             [0.667, 0.667, 0]]

        # This second dataset is derived from vegan::mantel's example dataset.
        # The "veg" distance matrix contains Bray-Curtis distances derived from
        # the varespec data (named "veg.dist" in the example). The "env"
        # distance matrix contains Euclidean distances derived from scaled
        # varechem data (named "env.dist" in the example).
        self.veg_dm_vegan = np.loadtxt(
            get_data_path('mantel_veg_dm_vegan.txt'))
        self.env_dm_vegan = np.loadtxt(
            get_data_path('mantel_env_dm_vegan.txt'))

        # Expected test statistic when comparing x and y with method='pearson'.
        self.exp_x_vs_y = 0.7559289

        # Expected test statistic when comparing x and z with method='pearson'.
        self.exp_x_vs_z = -0.9897433

    def test_statistic_same_across_alternatives_and_permutations(self):
        # Varying permutations and alternative hypotheses shouldn't affect the
        # computed test statistics.
        for n in (0, 99, 999):
            for alt in self.alternatives:
                for method, exp in (('pearson', self.exp_x_vs_y),
                                    ('spearman', 0.5)):
                    obs = mantel(self.minx, self.miny, method=method,
                                 permutations=n, alternative=alt)[0]
                    self.assertAlmostEqual(obs, exp)

    def test_comparing_same_matrices(self):
        for method in self.methods:
            obs = mantel(self.minx, self.minx, method=method)[0]
            self.assertAlmostEqual(obs, 1)

            obs = mantel(self.miny, self.miny, method=method)[0]
            self.assertAlmostEqual(obs, 1)

    def test_negative_correlation(self):
        for method, exp in (('pearson', self.exp_x_vs_z), ('spearman', -1)):
            obs = mantel(self.minx, self.minz, method=method)[0]
            self.assertAlmostEqual(obs, exp)

    def test_zero_permutations(self):
        for alt in self.alternatives:
            for method, exp in (('pearson', self.exp_x_vs_y),
                                ('spearman', 0.5)):
                obs = mantel(self.minx, self.miny, permutations=0,
                             method=method, alternative=alt)
                self.assertAlmostEqual(obs[0], exp)
                npt.assert_equal(obs[1], np.nan)
                self.assertEqual(obs[2], 3)

                # swapping order of matrices should give same result
                obs = mantel(self.miny, self.minx, permutations=0,
                             method=method, alternative=alt)
                self.assertAlmostEqual(obs[0], exp)
                npt.assert_equal(obs[1], np.nan)
                self.assertEqual(obs[2], 3)

    def test_distance_matrix_instances_as_input(self):
        # Matrices with all matching IDs in the same order.
        np.random.seed(0)

        obs = mantel(self.minx_dm, self.miny_dm, alternative='less')

        self.assertAlmostEqual(obs[0], self.exp_x_vs_y)
        self.assertAlmostEqual(obs[1], 0.843)
        self.assertEqual(obs[2], 3)

    def test_distance_matrix_instances_with_reordering_and_nonmatching(self):
        x = self.minx_dm_extra.filter(['1', '0', 'foo', '2'])
        y = self.miny_dm.filter(['0', '2', '1'])

        # strict=True should disallow IDs that aren't found in both matrices
        with self.assertRaises(ValueError):
            mantel(x, y, alternative='less', strict=True)

        np.random.seed(0)

        # strict=False should ignore IDs that aren't found in both matrices
        obs = mantel(x, y, alternative='less', strict=False)

        self.assertAlmostEqual(obs[0], self.exp_x_vs_y)
        self.assertAlmostEqual(obs[1], 0.843)
        self.assertEqual(obs[2], 3)

    def test_distance_matrix_instances_with_lookup(self):
        self.minx_dm.ids = ('a', 'b', 'c')
        self.miny_dm.ids = ('d', 'e', 'f')
        lookup = {'a': 'A', 'b': 'B', 'c': 'C',
                  'd': 'A', 'e': 'B', 'f': 'C'}

        np.random.seed(0)

        obs = mantel(self.minx_dm, self.miny_dm, alternative='less',
                     lookup=lookup)
        self.assertAlmostEqual(obs[0], self.exp_x_vs_y)
        self.assertAlmostEqual(obs[1], 0.843)
        self.assertEqual(obs[2], 3)

    def test_one_sided_greater(self):
        np.random.seed(0)

        obs = mantel(self.minx, self.miny, alternative='greater')
        self.assertAlmostEqual(obs[0], self.exp_x_vs_y)
        self.assertAlmostEqual(obs[1], 0.324)
        self.assertEqual(obs[2], 3)

        obs = mantel(self.minx, self.minx, alternative='greater')
        self.assertAlmostEqual(obs[0], 1)
        self.assertAlmostEqual(obs[1], 0.172)
        self.assertEqual(obs[2], 3)

    def test_one_sided_less(self):
        # no need to seed here as permuted test statistics will all be less
        # than or equal to the observed test statistic (1.0)
        for method in self.methods:
            obs = mantel(self.minx, self.minx, method=method,
                         alternative='less')
            self.assertEqual(obs, (1, 1, 3))

        np.random.seed(0)

        obs = mantel(self.minx, self.miny, alternative='less')
        self.assertAlmostEqual(obs[0], self.exp_x_vs_y)
        self.assertAlmostEqual(obs[1], 0.843)
        self.assertEqual(obs[2], 3)

        obs = mantel(self.minx, self.minz, alternative='less')
        self.assertAlmostEqual(obs[0], self.exp_x_vs_z)
        self.assertAlmostEqual(obs[1], 0.172)
        self.assertEqual(obs[2], 3)

    def test_two_sided(self):
        np.random.seed(0)

        obs = mantel(self.minx, self.minx, method='spearman',
                     alternative='two-sided')
        self.assertEqual(obs[0], 1)
        self.assertAlmostEqual(obs[1], 0.328)
        self.assertEqual(obs[2], 3)

        obs = mantel(self.minx, self.miny, method='spearman',
                     alternative='two-sided')
        self.assertAlmostEqual(obs[0], 0.5)
        self.assertAlmostEqual(obs[1], 1.0)
        self.assertEqual(obs[2], 3)

        obs = mantel(self.minx, self.minz, method='spearman',
                     alternative='two-sided')
        self.assertAlmostEqual(obs[0], -1)
        self.assertAlmostEqual(obs[1], 0.322)
        self.assertEqual(obs[2], 3)

    def test_vegan_example(self):
        np.random.seed(0)

        # pearson
        obs = mantel(self.veg_dm_vegan, self.env_dm_vegan,
                     alternative='greater')
        self.assertAlmostEqual(obs[0], 0.3047454)
        self.assertAlmostEqual(obs[1], 0.002)
        self.assertEqual(obs[2], 24)

        # spearman
        obs = mantel(self.veg_dm_vegan, self.env_dm_vegan,
                     alternative='greater', method='spearman')
        self.assertAlmostEqual(obs[0], 0.283791)
        self.assertAlmostEqual(obs[1], 0.003)
        self.assertEqual(obs[2], 24)

    def test_no_variation_pearson(self):
        # Output doesn't match vegan::mantel with method='pearson'. Consider
        # revising output and this test depending on outcome of
        # https://github.com/scipy/scipy/issues/3728
        for alt in self.alternatives:
            # test one or both inputs having no variation in their
            # distances
            obs = mantel(self.miny, self.no_variation, method='pearson',
                         alternative=alt)
            npt.assert_equal(obs, (0.0, 1.0, 3))

            obs = mantel(self.no_variation, self.miny, method='pearson',
                         alternative=alt)
            npt.assert_equal(obs, (0.0, 1.0, 3))

            obs = mantel(self.no_variation, self.no_variation,
                         method='pearson', alternative=alt)
            npt.assert_equal(obs, (1.0, 1.0, 3))

    def test_no_variation_spearman(self):
        exp = (np.nan, np.nan, 3)
        for alt in self.alternatives:
            obs = mantel(self.miny, self.no_variation, method='spearman',
                         alternative=alt)
            npt.assert_equal(obs, exp)

            obs = mantel(self.no_variation, self.miny, method='spearman',
                         alternative=alt)
            npt.assert_equal(obs, exp)

            obs = mantel(self.no_variation, self.no_variation,
                         method='spearman', alternative=alt)
            npt.assert_equal(obs, exp)

    def test_no_side_effects(self):
        minx = np.asarray(self.minx, dtype='float')
        miny = np.asarray(self.miny, dtype='float')

        minx_copy = np.copy(minx)
        miny_copy = np.copy(miny)

        mantel(minx, miny)

        # Make sure we haven't modified the input.
        npt.assert_equal(minx, minx_copy)
        npt.assert_equal(miny, miny_copy)

    def test_invalid_distance_matrix(self):
        # Single asymmetric, non-hollow distance matrix.
        with self.assertRaises(DissimilarityMatrixError):
            mantel([[1, 2], [3, 4]], [[0, 0], [0, 0]])

        # Two asymmetric distance matrices.
        with self.assertRaises(DistanceMatrixError):
            mantel([[0, 2], [3, 0]], [[0, 1], [0, 0]])

    def test_invalid_input(self):
        # invalid correlation method
        with self.assertRaises(ValueError):
            mantel([[1]], [[1]], method='brofist')

        # invalid permutations
        with self.assertRaises(ValueError):
            mantel([[1]], [[1]], permutations=-1)

        # invalid alternative
        with self.assertRaises(ValueError):
            mantel([[1]], [[1]], alternative='no cog yay')

        # too small dms
        with self.assertRaises(ValueError):
            mantel([[0, 3], [3, 0]], [[0, 2], [2, 0]])


class PairwiseMantelTests(MantelTestData):
    def setUp(self):
        super(PairwiseMantelTests, self).setUp()

        self.min_dms = (self.minx_dm, self.miny_dm, self.minz_dm)

        self.exp_results_minimal = pd.read_csv(
            get_data_path('pwmantel_exp_results_minimal.txt'), sep='\t',
            index_col=(0, 1))

        self.exp_results_minimal_with_labels = pd.read_csv(
            get_data_path('pwmantel_exp_results_minimal_with_labels.txt'),
            sep='\t', index_col=(0, 1))

        self.exp_results_duplicate_dms = pd.read_csv(
            get_data_path('pwmantel_exp_results_duplicate_dms.txt'),
            sep='\t', index_col=(0, 1))

        self.exp_results_na_p_value = pd.read_csv(
            get_data_path('pwmantel_exp_results_na_p_value.txt'),
            sep='\t', index_col=(0, 1))

        self.exp_results_reordered_distance_matrices = pd.read_csv(
            get_data_path('pwmantel_exp_results_reordered_distance_matrices'
                          '.txt'),
            sep='\t', index_col=(0, 1))

        self.exp_results_dm_dm2 = pd.read_csv(
            get_data_path('pwmantel_exp_results_dm_dm2.txt'),
            sep='\t', index_col=(0, 1))

        self.exp_results_all_dms = pd.read_csv(
            get_data_path('pwmantel_exp_results_all_dms.txt'),
            sep='\t', index_col=(0, 1))

    def test_minimal_compatible_input(self):
        # Matrices are already in the correct order and have matching IDs.
        np.random.seed(0)

        # input as DistanceMatrix instances
        obs = pwmantel(self.min_dms, alternative='greater')
        assert_data_frame_almost_equal(obs, self.exp_results_minimal)

        np.random.seed(0)

        # input as array_like
        obs = pwmantel((self.minx, self.miny, self.minz),
                       alternative='greater')
        assert_data_frame_almost_equal(obs, self.exp_results_minimal)

    def test_minimal_compatible_input_with_labels(self):
        np.random.seed(0)

        obs = pwmantel(self.min_dms, alternative='greater',
                       labels=('minx', 'miny', 'minz'))
        assert_data_frame_almost_equal(
            obs,
            self.exp_results_minimal_with_labels)

    def test_duplicate_dms(self):
        obs = pwmantel((self.minx_dm, self.minx_dm, self.minx_dm),
                       alternative='less')
        assert_data_frame_almost_equal(obs, self.exp_results_duplicate_dms)

    def test_na_p_value(self):
        obs = pwmantel((self.miny_dm, self.minx_dm), method='spearman',
                       permutations=0)
        assert_data_frame_almost_equal(obs, self.exp_results_na_p_value)

    def test_reordered_distance_matrices(self):
        # Matrices have matching IDs but they all have different ordering.
        x = self.minx_dm.filter(['1', '0', '2'])
        y = self.miny_dm.filter(['0', '2', '1'])
        z = self.minz_dm.filter(['1', '2', '0'])

        np.random.seed(0)

        obs = pwmantel((x, y, z), alternative='greater')
        assert_data_frame_almost_equal(
            obs,
            self.exp_results_reordered_distance_matrices)

    def test_strict(self):
        # Matrices have some matching and nonmatching IDs, with different
        # ordering.
        x = self.minx_dm_extra.filter(['1', '0', 'foo', '2'])
        y = self.miny_dm.filter(['0', '2', '1'])
        z = self.minz_dm_extra.filter(['bar', '1', '2', '0'])

        np.random.seed(0)

        # strict=False should discard IDs that aren't found in both matrices
        obs = pwmantel((x, y, z), alternative='greater', strict=False)
        assert_data_frame_almost_equal(
            obs,
            self.exp_results_reordered_distance_matrices)

    def test_id_lookup(self):
        # Matrices have mismatched IDs but a lookup is provided.
        self.minx_dm_extra.ids = ['a', 'b', 'c', 'foo']
        self.minz_dm_extra.ids = ['d', 'e', 'f', 'bar']
        lookup = {'a': '0', 'b': '1', 'c': '2', 'foo': 'foo',
                  'd': '0', 'e': '1', 'f': '2', 'bar': 'bar',
                  '0': '0', '1': '1', '2': '2'}

        x = self.minx_dm_extra.filter(['b', 'a', 'foo', 'c'])
        y = self.miny_dm.filter(['0', '2', '1'])
        z = self.minz_dm_extra.filter(['bar', 'e', 'f', 'd'])

        x_copy = x.copy()
        y_copy = y.copy()
        z_copy = z.copy()

        np.random.seed(0)

        obs = pwmantel((x, y, z), alternative='greater', strict=False,
                       lookup=lookup)
        assert_data_frame_almost_equal(
            obs,
            self.exp_results_reordered_distance_matrices)

        # Make sure the inputs aren't modified.
        self.assertEqual(x, x_copy)
        self.assertEqual(y, y_copy)
        self.assertEqual(z, z_copy)

    def test_too_few_dms(self):
        with self.assertRaises(ValueError):
            pwmantel([self.miny_dm])

    def test_wrong_number_of_labels(self):
        with self.assertRaises(ValueError):
            pwmantel(self.min_dms, labels=['foo', 'bar'])

    def test_duplicate_labels(self):
        with self.assertRaises(ValueError):
            pwmantel(self.min_dms, labels=['foo', 'bar', 'foo'])

    def test_mixed_input_types(self):
        # DistanceMatrix, DistanceMatrix, array_like
        with self.assertRaises(TypeError):
            pwmantel((self.miny_dm, self.minx_dm, self.minz))

    def test_filepaths_as_input(self):
        dms = [
            get_data_path('dm.txt'),
            get_data_path('dm2.txt'),
        ]
        np.random.seed(0)

        obs = pwmantel(dms)
        assert_data_frame_almost_equal(obs, self.exp_results_dm_dm2)

    def test_many_filepaths_as_input(self):
        dms = [
            get_data_path('dm2.txt'),
            get_data_path('dm.txt'),
            get_data_path('dm4.txt'),
            get_data_path('dm3.txt')
        ]
        np.random.seed(0)

        obs = pwmantel(dms)
        assert_data_frame_almost_equal(obs, self.exp_results_all_dms)


class OrderDistanceMatricesTests(MantelTestData):
    def setUp(self):
        super(OrderDistanceMatricesTests, self).setUp()

    def test_array_like_input(self):
        obs = _order_dms(self.minx, self.miny)
        self.assertEqual(obs, (self.minx_dm, self.miny_dm))

    def test_reordered_distance_matrices(self):
        # All matching IDs but with different orderings.
        x = self.minx_dm.filter(['1', '0', '2'])
        y = self.miny_dm.filter(['0', '2', '1'])

        exp = (x, y.filter(['1', '0', '2']))
        obs = _order_dms(x, y)
        self.assertEqual(obs, exp)