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"""Unit tests for PyMVPA stats helpers -- those requiring scipy"""

from mvpa2.testing import *
skip_if_no_external('scipy')

from scipy.stats import f_oneway
from mvpa2.tests.test_stats import *

from mvpa2.clfs.stats import match_distribution, rv_semifrozen
from mvpa2.misc.stats import chisquare, binomial_proportion_ci
from mvpa2.misc.attrmap import AttributeMap
from mvpa2.generators.permutation import AttributePermutator
from mvpa2.misc.data_generators import simple_hrf_dataset

class StatsTestsScipy(unittest.TestCase):
    """Unittests for various statistics which use scipy"""

    @sweepargs(exp=('uniform', 'indep_rows', 'indep_cols'))
    def test_chi_square(self, exp):
        """Test chi-square distribution"""
        # test equal distribution
        tbl = np.array([[5, 5], [5, 5]])
        chi, p = chisquare(tbl, exp=exp)
        self.assertTrue(chi == 0.0)
        self.assertTrue(p == 1.0)

        # test perfect "generalization"
        tbl = np.array([[4, 0], [0, 4]])
        chi, p = chisquare(tbl, exp=exp)
        self.assertTrue(chi == 8.0)
        self.assertTrue(p < 0.05)

    def test_chi_square_disbalanced(self):
        # test perfect "generalization"
        tbl = np.array([[1, 100], [1, 100]])
        chi, p = chisquare(tbl, exp='indep_rows')
        self.assertTrue(chi == 0)
        self.assertTrue(p == 1)

        chi, p = chisquare(tbl, exp='uniform')
        self.assertTrue(chi > 194)
        self.assertTrue(p < 1e-10)

        # by default lets do uniform
        chi_, p_ = chisquare(tbl)
        self.assertTrue(chi == chi_)
        self.assertTrue(p == p_)


    def test_null_dist_prob_any(self):
        """Test 'any' tail statistics estimation"""
        skip_if_no_external('scipy')

        # test 'any' mode
        from mvpa2.measures.corrcoef import CorrCoef
        # we will reassign targets later on, so let's operate on a
        # copy
        ds = datasets['uni2medium'].copy()

        permutator = AttributePermutator('targets', count=20)
        null = MCNullDist(permutator, tail='any')

        assert_raises(ValueError, null.fit, CorrCoef(), ds)
        # cheat and map to numeric for this test
        ds.sa.targets = AttributeMap().to_numeric(ds.targets)
        null.fit(CorrCoef(), ds)

        # 100 and -100 should both have zero probability on their respective
        # tails
        pm100 = null.p([-100] + [0] * (ds.nfeatures - 1))
        p100 = null.p([100] + [0] * (ds.nfeatures - 1))
        assert_array_almost_equal(pm100, p100)

        # With 20 samples it isn't that easy to get a reliable sampling for
        # non-parametric, so we can allow somewhat low significance
        self.assertTrue(pm100[0] <= 0.1)
        self.assertTrue(p100[0] <= 0.1)

        self.assertTrue(np.all(pm100[1:] > 0.05))
        self.assertTrue(np.all(p100[1:] > 0.05))
        # same test with just scalar measure/feature
        null.fit(CorrCoef(), ds[:, 0])
        p_100 = null.p(100)
        self.assertAlmostEqual(null.p(-100), p_100)
        self.assertAlmostEqual(p100[0], p_100)


    @sweepargs(nd=nulldist_sweep)
    def test_dataset_measure_prob(self, nd):
        """Test estimation of measures statistics"""
        skip_if_no_external('scipy')

        ds = datasets['uni2medium']

        m = OneWayAnova(null_dist=nd, enable_ca=['null_t'])
        score = m(ds)

        score_nonbogus = np.mean(score.samples[:, ds.a.nonbogus_features])
        score_bogus = np.mean(score.samples[:, ds.a.bogus_features])
        # plausability check
        self.assertTrue(score_bogus < score_nonbogus)

        # [0] because the first axis is len == 0
        null_prob_nonbogus = m.ca.null_prob[0, ds.a.nonbogus_features]
        null_prob_bogus = m.ca.null_prob[0, ds.a.bogus_features]

        self.assertTrue((null_prob_nonbogus.samples < 0.05).all(),
            msg="Nonbogus features should have a very unlikely value. Got %s"
                % null_prob_nonbogus)

        # the others should be a lot larger
        self.assertTrue(np.mean(np.abs(null_prob_bogus)) >
                        np.mean(np.abs(null_prob_nonbogus)))

        if isinstance(nd, MCNullDist):
            # MCs are not stable with just 10 samples... so lets skip them
            return

        if cfg.getboolean('tests', 'labile', default='yes'):
            # Failed on c94ec26eb593687f25d8c27e5cfdc5917e352a69
            # with MVPA_SEED=833393575
            self.assertTrue(
                (np.abs(m.ca.null_t[0, ds.a.nonbogus_features]) >= 5).all(),
                msg="Nonbogus features should have high t-score. Got %s"
                % (m.ca.null_t[0, ds.a.nonbogus_features]))

            bogus_min = min(np.abs(m.ca.null_t.samples[0][ds.a.bogus_features]))
            self.assertTrue(bogus_min < 4,
                msg="Some bogus features should have low t-score of %g."
                    "Got (t,p,sens):%s"
                    % (bogus_min,
                        list(zip(m.ca.null_t[0, ds.a.bogus_features],
                            m.ca.null_prob[0, ds.a.bogus_features],
                            score.samples[0][ds.a.bogus_features]))))

    @reseed_rng()
    def test_negative_t(self):
        """Basic testing of the sign in p and t scores
        """
        from mvpa2.measures.base import FeaturewiseMeasure

        class BogusMeasure(FeaturewiseMeasure):
            """Just put high positive into first 2 features, and high
            negative into 2nd two
            """
            is_trained = True
            def _call(self, dataset):
                """just a little helper... pylint shut up!"""
                res = np.random.normal(size=(dataset.nfeatures,))
                res[0] = res[1] = 100
                res[2] = res[3] = -100
                return Dataset([res])

        nd = FixedNullDist(scipy.stats.norm(0, 0.1), tail='any')
        m = BogusMeasure(null_dist=nd, enable_ca=['null_t'])
        ds = datasets['uni2small']
        _ = m(ds)
        t, p = m.ca.null_t, m.ca.null_prob
        assert_array_less(-1e-30, p.samples) # just that all >= 0
        assert_array_less(0, t.samples[0, :2])
        assert_array_less(t.samples[0, 2:4], 0)


    def test_match_distribution(self):
        """Some really basic testing for match_distribution
        """
        ds = datasets['uni2medium']      # large to get stable stats
        data = ds.samples[:, ds.a.bogus_features[0]]
        # choose bogus feature, which
        # should have close to normal distribution

        # Lets test ad-hoc rv_semifrozen
        floc = rv_semifrozen(scipy.stats.norm, loc=0).fit(data)
        self.assertTrue(floc[0] == 0)

        fscale = rv_semifrozen(scipy.stats.norm, scale=1.0).fit(data)
        self.assertTrue(fscale[1] == 1)

        flocscale = rv_semifrozen(scipy.stats.norm, loc=0, scale=1.0).fit(data)
        self.assertTrue(flocscale[1] == 1 and flocscale[0] == 0)

        full = scipy.stats.norm.fit(data)
        for res in [floc, fscale, flocscale, full]:
            self.assertTrue(len(res) == 2)

        data_mean = np.mean(data)
        for loc in [None, data_mean]:
            for test in ['p-roc', 'kstest']:
                # some really basic testing
                matched = match_distribution(
                    data=data,
                    distributions=['scipy',
                                     ('norm',
                                      {'name': 'norm_fixed',
                                       'loc': 0.2,
                                       'scale': 0.3})],
                    test=test, loc=loc, p=0.05)
                # at least norm should be in there
                names = [m[2] for m in matched]
                if test == 'p-roc':
                    if cfg.getboolean('tests', 'labile', default='yes'):
                        # we can guarantee that only for norm_fixed
                        self.assertTrue('norm' in names)
                        self.assertTrue('norm_fixed' in names)
                        inorm = names.index('norm_fixed')
                        # and it should be at least in the first
                        # 30 best matching ;-)
                        self.assertTrue(inorm <= 30)
                    # Test plotting only once
                    if loc is None and externals.exists("pylab plottable"):
                        import pylab as pl
                        from mvpa2.clfs.stats import plot_distribution_matches
                        fig = pl.figure()
                        plot_distribution_matches(data, matched, legend=1, nbest=5)
                        #pl.show()
                        pl.close(fig)

    def test_match_distribution_semifrozen(self):
        """Handle frozen params in match_distribution
        """
        matches = match_distribution(np.arange(10),
                                     distributions=[
                                         'uniform',
                                         ('uniform', {'loc': 0})
                                         ],
                                     p= -1 # so we get all matches
                                     )
        self.assertEqual(len(matches), 2) # we must get some match

        self.assertTrue(abs(matches[0][-1][0]) < 4e-1) # full fit should get close to true loc
        self.assertEqual(matches[1][-1][0], 0) # frozen should maintain the loc

        if externals.versions['scipy'] >= '0.10':
            # known to work on 0.10 and fail on 0.7.3
            self.assertTrue(abs(matches[0][-1][1] - 9) < 1e-1) # full fit should get close to true scale
        else:
            raise SkipTest("KnownFailure to fit uniform on older scipy")

        # actually it fails ATM to fit uniform with frozen loc=0
        # nicely -- sets scale = 1 :-/   TODO
        raise SkipTest("TODO: Known failure to fit uniform with frozen loc")
        self.assertTrue(abs(matches[1][-1][1] - 9) < 1e-1) # frozen fit of scale

    def test_r_dist_stability(self):
        """Test either rdist distribution performs nicely
        """
        try:
            # actually I haven't managed to cause this error
            scipy.stats.rdist(1.32, 0, 1).pdf(-1.0 + np.finfo(float).eps)
        except Exception as e:
            self.fail('Failed to compute rdist.pdf due to numeric'
                      ' loss of precision. Exception was %s' % e)

        try:
            # this one should fail with recent scipy with error
            # ZeroDivisionError: 0.0 cannot be raised to a negative power

            # XXX: There is 1 more bug in etch's scipy.stats or numpy
            #      (vectorize), so I have to put 2 elements in the
            #      queried x's, otherwise it
            #      would puke. But for now that fix is not here
            #
            # value = scipy.stats.rdist(1.32, 0, 1).cdf(
            #      [-1.0+np.finfo(float).eps, 0])
            #
            # to cause it now just run this unittest only with
            #  nosetests -s test_stats:StatsTests.testRDistStability

            # NB: very cool way to store the trace of the execution
            #import pydb
            #pydb.debugger(dbg_cmds=['bt', 'l', 's']*300 + ['c'])
            scipy.stats.rdist(1.32, 0, 1).cdf(-1.0 + np.finfo(float).eps)
        except IndexError as e:
            self.fail('Failed due to bug which leads to InvalidIndex if only'
                      ' scalar is provided to cdf')
        except Exception as e:
            self.fail('Failed to compute rdist.cdf due to numeric'
                      ' loss of precision. Exception was %s' % e)

        v = scipy.stats.rdist(10000, 0, 1).cdf([-0.1])
        self.assertTrue(v >= 0, v <= 1)

    @reseed_rng()
    def test_scipy_fit_2fparams(self):
        # fixing parameters was not before this version
        skip_if_no_external('scipy', min_version='0.8.1')
        t = scipy.stats.t
        d = t(10, 1, 10).rvs(10)
        params = t.fit(d, floc=1, fscale=10.)
        # assured result to be a tuple due to failure on
        # travis-ci (ubuntu precise)
        # http://travis-ci.org/#!/PyMVPA/PyMVPA/builds/2459017
        self.assertEqual(tuple(params[1:]), (1, 10.))
        # df's are apparently quite difficult to assess unless plenty
        # of samples
        #self.assertTrue(abs(params[0] - 10) < 7) # estimate df at least in the right ball park

    def test_anova_compliance(self):
        ds = datasets['uni2large']

        fwm = OneWayAnova()
        f = fwm(ds)
        f_sp = f_oneway(ds[ds.targets == 'L1'].samples,
                        ds[ds.targets == 'L0'].samples)

        # SciPy needs to compute the same F-scores
        assert_array_almost_equal(f, f_sp[0:1])


    @reseed_rng()
    def test_statsmodels(self):
        """Test GLM
        """
        skip_if_no_external('statsmodels')
        from mvpa2.measures.statsmodels_adaptor import GLM
        # high SNR dataset for such a short timeseries
        data = simple_hrf_dataset(signal_level=2, noise_level=0.5)
        X = data.sa.design

        # check GLM betas
        glm = GLM(X)
        betas = glm(data)

        # betas for each feature and each regressor
        self.assertTrue(betas.shape == (X.shape[1], data.nfeatures))

        self.assertTrue(np.absolute(betas.samples[1] - data.a.baseline < 10).all(),
            msg="baseline betas should be huge and around 800")

        self.assertTrue(betas.samples[0, 0] > betas[0, 1],
            msg="feature (with signal) beta should be larger than for noise")

        if cfg.getboolean('tests', 'labile', default='yes'):
            self.assertTrue(np.absolute(betas[0, 1]) < 0.5)
            self.assertTrue(np.absolute(betas[0, 0]) > 1.0)

        # check GLM t values
        glm = GLM(X, voi='tvalues')
        tstats = glm(data)

        self.assertTrue(tstats.shape == betas.shape)

        self.assertTrue((tstats.samples[1] > 1000).all(),
                msg='constant tvalues should be huge')

        if cfg.getboolean('tests', 'labile', default='yes'):
            self.assertTrue(np.absolute(betas[0, 0]) > betas[0, 1],
                msg='with signal should have higher tvalues')

        # check t-contrast -- should do the same as tvalues for the first
        # parameter
        glm = GLM(X, voi=[1, 0])
        contrast = glm(data)
        assert_array_almost_equal(contrast.samples[0], tstats.samples[0])
        assert_equals(len(contrast), 6)
        # we should be able to recover the approximate effect size of the signal
        # which is constructed with a baseline offset of 2 (see above)
        if cfg.getboolean('tests', 'labile', default='yes'):
            assert_true(1.5 < contrast.samples[2, 0] < 2.5)

        # check F-test
        glm = GLM(X, voi=[[1, 0]])
        ftest = glm(data)
        assert_equals(len(ftest), 4)
        assert_true(ftest.samples[0, 0] > ftest.samples[0, 1])


    def test_binomdist_ppf(self):
        """Test if binomial distribution works ok

        after possibly a monkey patch
        """
        bdist = scipy.stats.binom(100, 0.5)
        self.assertTrue(bdist.ppf(1.0) == 100)
        self.assertTrue(bdist.ppf(0.9) <= 60)
        self.assertTrue(bdist.ppf(0.5) == 50)
        self.assertTrue(bdist.ppf(0) == -1)

    def test_right_tail(self):
        # Test if we are getting "correct" p-value for right tail in
        # "interesting" cases
        # TODO:  some of it is done in
        #   test_transerror.py:ErrorsTests.test_confusionmatrix_nulldist
        pass

def test_binomial_proportion_ci():
    # compare to gold-standard values from the matlab implementation
    from numpy import testing as npt
    n = 100
    X = 50
    p = .05
    matlab_truth = {
        'wald': (.4020, .5980),
        'wilson': (.4038, .5962),
        'agresti-coull': (.4038, .5962),
        'jeffreys': (.4032, .5968),
        'clopper-pearson': (.3983, .6017),
        'arc-sine': (.4026, .5974),
        'logit': (.4032, .5968),
        'anscombe': (.4037, .5963)
    }
    for m in list(matlab_truth.keys()):
        npt.assert_array_almost_equal(matlab_truth[m],
                                      binomial_proportion_ci(n, X, p, m),
                                      decimal=4,
                                      err_msg=m)
        # can deal with the extremes
        # those two have numerical limits
        if not m in ('clopper-pearson', 'logit'):
            npt.assert_array_almost_equal(
                    binomial_proportion_ci(1000, 1000, .05, m),
                    [1, 1],
                    decimal=2)
            npt.assert_array_almost_equal(
                    binomial_proportion_ci(1000, 0, .05, m),
                    [0, 0],
                    decimal=2)
    vec = binomial_proportion_ci(1000, [600,100,900])
    assert_equal(vec.shape, (2, 3))

def suite():  # pragma: no cover
    """Create the suite"""
    return unittest.makeSuite(StatsTestsScipy)


if __name__ == '__main__':  # pragma: no cover
    import runner
    runner.run()

