"""
Testing for Support Vector Machine module (sklearn.svm)

TODO: remove hard coded numerical results when possible
"""

import warnings
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
                           assert_almost_equal)
from scipy import sparse
from nose.tools import assert_raises, assert_true, assert_equal, assert_false

from sklearn import svm, linear_model, datasets, metrics, base
from sklearn.datasets.samples_generator import make_classification
from sklearn.metrics import f1_score
from sklearn.utils import check_random_state
from sklearn.utils import ConvergenceWarning
from sklearn.utils.testing import assert_greater, assert_less

# toy sample
X = [[-2, -1], [-1, -1], [-1, -2], [1, 1], [1, 2], [2, 1]]
Y = [1, 1, 1, 2, 2, 2]
T = [[-1, -1], [2, 2], [3, 2]]
true_result = [1, 2, 2]

# also load the iris dataset
iris = datasets.load_iris()
rng = check_random_state(42)
perm = rng.permutation(iris.target.size)
iris.data = iris.data[perm]
iris.target = iris.target[perm]


def test_libsvm_parameters():
    """
    Test parameters on classes that make use of libsvm.
    """
    clf = svm.SVC(kernel='linear').fit(X, Y)
    assert_array_equal(clf.dual_coef_, [[0.25, -.25]])
    assert_array_equal(clf.support_, [1, 3])
    assert_array_equal(clf.support_vectors_, (X[1], X[3]))
    assert_array_equal(clf.intercept_, [0.])
    assert_array_equal(clf.predict(X), Y)


def test_libsvm_iris():
    """
    Check consistency on dataset iris.
    """

    # shuffle the dataset so that labels are not ordered
    for k in ('linear', 'rbf'):
        clf = svm.SVC(kernel=k).fit(iris.data, iris.target)
        assert_greater(np.mean(clf.predict(iris.data) == iris.target), 0.9)

    # check deprecated ``label_`` attribute:
    with warnings.catch_warnings(record=True):
        # catch deprecation warning
        assert_array_equal(clf.label_, np.sort(clf.label_))

    assert_array_equal(clf.classes_, np.sort(clf.classes_))

    # check also the low-level API
    model = svm.libsvm.fit(iris.data, iris.target.astype(np.float64))
    pred = svm.libsvm.predict(iris.data, *model)
    assert_greater(np.mean(pred == iris.target), .95)

    model = svm.libsvm.fit(iris.data, iris.target.astype(np.float64),
                           kernel='linear')
    pred = svm.libsvm.predict(iris.data, *model, kernel='linear')
    assert_greater(np.mean(pred == iris.target), .95)

    pred = svm.libsvm.cross_validation(iris.data,
                                       iris.target.astype(np.float64), 5,
                                       kernel='linear')
    assert_greater(np.mean(pred == iris.target), .95)


def test_single_sample_1d():
    """
    Test whether SVCs work on a single sample given as a 1-d array
    """

    clf = svm.SVC().fit(X, Y)
    clf.predict(X[0])

    clf = svm.LinearSVC(random_state=0).fit(X, Y)
    clf.predict(X[0])


def test_precomputed():
    """
    SVC with a precomputed kernel.

    We test it with a toy dataset and with iris.
    """
    clf = svm.SVC(kernel='precomputed')
    # Gram matrix for train data (square matrix)
    # (we use just a linear kernel)
    K = np.dot(X, np.array(X).T)
    clf.fit(K, Y)
    # Gram matrix for test data (rectangular matrix)
    KT = np.dot(T, np.array(X).T)
    pred = clf.predict(KT)
    assert_raises(ValueError, clf.predict, KT.T)

    assert_array_equal(clf.dual_coef_, [[0.25, -.25]])
    assert_array_equal(clf.support_, [1, 3])
    assert_array_equal(clf.intercept_, [0])
    assert_array_almost_equal(clf.support_, [1, 3])
    assert_array_equal(pred, true_result)

    # Gram matrix for test data but compute KT[i,j]
    # for support vectors j only.
    KT = np.zeros_like(KT)
    for i in range(len(T)):
        for j in clf.support_:
            KT[i, j] = np.dot(T[i], X[j])

    pred = clf.predict(KT)
    assert_array_equal(pred, true_result)

    # same as before, but using a callable function instead of the kernel
    # matrix. kernel is just a linear kernel

    kfunc = lambda x, y: np.dot(x, y.T)
    clf = svm.SVC(kernel=kfunc)
    clf.fit(X, Y)
    pred = clf.predict(T)

    assert_array_equal(clf.dual_coef_, [[0.25, -.25]])
    assert_array_equal(clf.intercept_, [0])
    assert_array_almost_equal(clf.support_, [1, 3])
    assert_array_equal(pred, true_result)

    # test a precomputed kernel with the iris dataset
    # and check parameters against a linear SVC
    clf = svm.SVC(kernel='precomputed')
    clf2 = svm.SVC(kernel='linear')
    K = np.dot(iris.data, iris.data.T)
    clf.fit(K, iris.target)
    clf2.fit(iris.data, iris.target)
    pred = clf.predict(K)
    assert_array_almost_equal(clf.support_, clf2.support_)
    assert_array_almost_equal(clf.dual_coef_, clf2.dual_coef_)
    assert_array_almost_equal(clf.intercept_, clf2.intercept_)
    assert_almost_equal(np.mean(pred == iris.target), .99, decimal=2)

    # Gram matrix for test data but compute KT[i,j]
    # for support vectors j only.
    K = np.zeros_like(K)
    for i in range(len(iris.data)):
        for j in clf.support_:
            K[i, j] = np.dot(iris.data[i], iris.data[j])

    pred = clf.predict(K)
    assert_almost_equal(np.mean(pred == iris.target), .99, decimal=2)

    clf = svm.SVC(kernel=kfunc)
    clf.fit(iris.data, iris.target)
    assert_almost_equal(np.mean(pred == iris.target), .99, decimal=2)


def test_svr():
    """
    Test Support Vector Regression
    """

    diabetes = datasets.load_diabetes()
    for clf in (svm.NuSVR(kernel='linear', nu=.4, C=1.0),
                svm.NuSVR(kernel='linear', nu=.4, C=10.),
                svm.SVR(kernel='linear', C=10.)):
        clf.fit(diabetes.data, diabetes.target)
        assert_greater(clf.score(diabetes.data, diabetes.target), 0.02)


def test_svr_errors():
    X = [[0.0], [1.0]]
    y = [0.0, 0.5]

    # Bad kernel
    clf = svm.SVR(kernel=lambda x, y: np.array([[1.0]]))
    clf.fit(X, y)
    assert_raises(ValueError, clf.predict, X)


def test_oneclass():
    """
    Test OneClassSVM
    """
    clf = svm.OneClassSVM()
    clf.fit(X)
    pred = clf.predict(T)

    assert_array_almost_equal(pred, [-1, -1, -1])
    assert_array_almost_equal(clf.intercept_, [-1.008], decimal=3)
    assert_array_almost_equal(clf.dual_coef_,
                              [[0.632, 0.233, 0.633, 0.234, 0.632, 0.633]],
                              decimal=3)
    assert_raises(ValueError, lambda: clf.coef_)


def test_oneclass_decision_function():
    """
    Test OneClassSVM decision function
    """
    clf = svm.OneClassSVM()
    rnd = check_random_state(2)

    # Generate train data
    X = 0.3 * rnd.randn(100, 2)
    X_train = np.r_[X + 2, X - 2]

    # Generate some regular novel observations
    X = 0.3 * rnd.randn(20, 2)
    X_test = np.r_[X + 2, X - 2]
    # Generate some abnormal novel observations
    X_outliers = rnd.uniform(low=-4, high=4, size=(20, 2))

    # fit the model
    clf = svm.OneClassSVM(nu=0.1, kernel="rbf", gamma=0.1)
    clf.fit(X_train)

    # predict things
    y_pred_test = clf.predict(X_test)
    assert_greater(np.mean(y_pred_test == 1), .9)
    y_pred_outliers = clf.predict(X_outliers)
    assert_greater(np.mean(y_pred_outliers == -1), .9)
    dec_func_test = clf.decision_function(X_test)
    assert_array_equal((dec_func_test > 0).ravel(), y_pred_test == 1)
    dec_func_outliers = clf.decision_function(X_outliers)
    assert_array_equal((dec_func_outliers > 0).ravel(),  y_pred_outliers == 1)


def test_tweak_params():
    """
    Make sure some tweaking of parameters works.

    We change clf.dual_coef_ at run time and expect .predict() to change
    accordingly. Notice that this is not trivial since it involves a lot
    of C/Python copying in the libsvm bindings.

    The success of this test ensures that the mapping between libsvm and
    the python classifier is complete.
    """
    clf = svm.SVC(kernel='linear', C=1.0)
    clf.fit(X, Y)
    assert_array_equal(clf.dual_coef_, [[.25, -.25]])
    assert_array_equal(clf.predict([[-.1, -.1]]), [1])
    clf.dual_coef_ = np.array([[.0, 1.]])
    assert_array_equal(clf.predict([[-.1, -.1]]), [2])


def test_probability():
    """
    Predict probabilities using SVC

    This uses cross validation, so we use a slightly bigger testing set.
    """

    for clf in (svm.SVC(probability=True, C=1.0),
                svm.NuSVC(probability=True)):

        clf.fit(iris.data, iris.target)

        prob_predict = clf.predict_proba(iris.data)
        assert_array_almost_equal(
            np.sum(prob_predict, 1), np.ones(iris.data.shape[0]))
        assert_true(np.mean(np.argmax(prob_predict, 1)
                    == clf.predict(iris.data)) > 0.9)

        assert_almost_equal(clf.predict_proba(iris.data),
                            np.exp(clf.predict_log_proba(iris.data)), 8)


def test_decision_function():
    """
    Test decision_function

    Sanity check, test that decision_function implemented in python
    returns the same as the one in libsvm

    """
    # multi class:
    clf = svm.SVC(kernel='linear', C=0.1).fit(iris.data, iris.target)

    dec = np.dot(iris.data, clf.coef_.T) + clf.intercept_

    assert_array_almost_equal(dec, clf.decision_function(iris.data))

    # binary:
    clf.fit(X, Y)
    dec = np.dot(X, clf.coef_.T) + clf.intercept_
    prediction = clf.predict(X)
    assert_array_almost_equal(dec, clf.decision_function(X))
    assert_array_almost_equal(
        prediction,
        clf.classes_[(clf.decision_function(X) > 0).astype(np.int).ravel()])
    expected = np.array([[-1.], [-0.66], [-1.], [0.66], [1.], [1.]])
    assert_array_almost_equal(clf.decision_function(X), expected, 2)


def test_weight():
    """
    Test class weights
    """
    clf = svm.SVC(class_weight={1: 0.1})
    # we give a small weights to class 1
    clf.fit(X, Y)
    # so all predicted values belong to class 2
    assert_array_almost_equal(clf.predict(X), [2] * 6)

    X_, y_ = make_classification(n_samples=200, n_features=10,
                                 weights=[0.833, 0.167], random_state=2)

    for clf in (linear_model.LogisticRegression(),
                svm.LinearSVC(random_state=0), svm.SVC()):
        clf.set_params(class_weight={0: .1, 1: 10})
        clf.fit(X_[:100], y_[:100])
        y_pred = clf.predict(X_[100:])
        assert_true(f1_score(y_[100:], y_pred) > .3)


def test_sample_weights():
    """
    Test weights on individual samples
    """
    # TODO: check on NuSVR, OneClass, etc.
    clf = svm.SVC()
    clf.fit(X, Y)
    assert_array_equal(clf.predict(X[2]), [1.])

    sample_weight = [.1] * 3 + [10] * 3
    clf.fit(X, Y, sample_weight=sample_weight)
    assert_array_equal(clf.predict(X[2]), [2.])


def test_auto_weight():
    """Test class weights for imbalanced data"""
    from sklearn.linear_model import LogisticRegression
    # we take as dataset a the two-dimensional projection of iris so
    # that it is not separable and remove half of predictors from
    # class 1
    from sklearn.utils import compute_class_weight
    X, y = iris.data[:, :2], iris.target
    unbalanced = np.delete(np.arange(y.size), np.where(y > 1)[0][::2])

    classes = np.unique(y[unbalanced])
    class_weights = compute_class_weight('auto', classes, y[unbalanced])
    assert_true(np.argmax(class_weights) == 2)

    for clf in (svm.SVC(kernel='linear'), svm.LinearSVC(random_state=0),
                LogisticRegression()):
        # check that score is better when class='auto' is set.
        y_pred = clf.fit(X[unbalanced], y[unbalanced]).predict(X)
        clf.set_params(class_weight='auto')
        y_pred_balanced = clf.fit(X[unbalanced], y[unbalanced],).predict(X)
        assert_true(metrics.f1_score(y, y_pred)
                    <= metrics.f1_score(y, y_pred_balanced))


def test_bad_input():
    """
    Test that it gives proper exception on deficient input
    """
    # impossible value of C
    assert_raises(ValueError, svm.SVC(C=-1).fit, X, Y)

    # impossible value of nu
    clf = svm.NuSVC(nu=0.0)
    assert_raises(ValueError, clf.fit, X, Y)

    Y2 = Y[:-1]  # wrong dimensions for labels
    assert_raises(ValueError, clf.fit, X, Y2)

    # Test with arrays that are non-contiguous.
    for clf in (svm.SVC(), svm.LinearSVC(random_state=0)):
        Xf = np.asfortranarray(X)
        assert_false(Xf.flags['C_CONTIGUOUS'])
        yf = np.ascontiguousarray(np.tile(Y, (2, 1)).T)
        yf = yf[:, -1]
        assert_false(yf.flags['F_CONTIGUOUS'])
        assert_false(yf.flags['C_CONTIGUOUS'])
        clf.fit(Xf, yf)
        assert_array_equal(clf.predict(T), true_result)

    # error for precomputed kernelsx
    clf = svm.SVC(kernel='precomputed')
    assert_raises(ValueError, clf.fit, X, Y)

    # sample_weight bad dimensions
    clf = svm.SVC()
    assert_raises(ValueError, clf.fit, X, Y, sample_weight=range(len(X) - 1))

    # predict with sparse input when trained with dense
    clf = svm.SVC().fit(X, Y)
    assert_raises(ValueError, clf.predict, sparse.lil_matrix(X))

    Xt = np.array(X).T
    clf.fit(np.dot(X, Xt), Y)
    assert_raises(ValueError, clf.predict, X)

    clf = svm.SVC()
    clf.fit(X, Y)
    assert_raises(ValueError, clf.predict, Xt)


def test_linearsvc_parameters():
    """
    Test possible parameter combinations in LinearSVC
    """
    # generate list of possible parameter combinations
    params = [(dual, loss, penalty) for dual in [True, False]
              for loss in ['l1', 'l2', 'lr'] for penalty in ['l1', 'l2']]

    for dual, loss, penalty in params:
            if loss == 'l1' and penalty == 'l1':
                assert_raises(ValueError, svm.LinearSVC, penalty=penalty,
                              loss=loss, dual=dual)
            elif loss == 'l1' and penalty == 'l2' and not dual:
                assert_raises(ValueError, svm.LinearSVC, penalty=penalty,
                              loss=loss, dual=dual)
            elif penalty == 'l1' and dual:
                assert_raises(ValueError, svm.LinearSVC, penalty=penalty,
                              loss=loss, dual=dual)
            else:
                svm.LinearSVC(penalty=penalty, loss=loss, dual=dual)


def test_linearsvc():
    """
    Test basic routines using LinearSVC
    """
    clf = svm.LinearSVC(random_state=0).fit(X, Y)

    # by default should have intercept
    assert_true(clf.fit_intercept)

    assert_array_equal(clf.predict(T), true_result)
    assert_array_almost_equal(clf.intercept_, [0], decimal=3)

    # the same with l1 penalty
    clf = svm.LinearSVC(penalty='l1', dual=False, random_state=0).fit(X, Y)
    assert_array_equal(clf.predict(T), true_result)

    # l2 penalty with dual formulation
    clf = svm.LinearSVC(penalty='l2', dual=True, random_state=0).fit(X, Y)
    assert_array_equal(clf.predict(T), true_result)

    # l2 penalty, l1 loss
    clf = svm.LinearSVC(penalty='l2', loss='l1', dual=True, random_state=0)
    clf.fit(X, Y)
    assert_array_equal(clf.predict(T), true_result)

    # test also decision function
    dec = clf.decision_function(T)
    res = (dec > 0).astype(np.int) + 1
    assert_array_equal(res, true_result)


def test_linearsvc_crammer_singer():
    """Test LinearSVC with crammer_singer multi-class svm"""
    ovr_clf = svm.LinearSVC(random_state=0).fit(iris.data, iris.target)
    cs_clf = svm.LinearSVC(multi_class='crammer_singer', random_state=0)
    cs_clf.fit(iris.data, iris.target)

    # similar prediction for ovr and crammer-singer:
    assert_true((ovr_clf.predict(iris.data) ==
                 cs_clf.predict(iris.data)).mean() > .9)

    # classifiers shouldn't be the same
    assert_true((ovr_clf.coef_ != cs_clf.coef_).all())

    # test decision function
    assert_array_equal(cs_clf.predict(iris.data),
                       np.argmax(cs_clf.decision_function(iris.data), axis=1))
    dec_func = np.dot(iris.data, cs_clf.coef_.T) + cs_clf.intercept_
    assert_array_almost_equal(dec_func, cs_clf.decision_function(iris.data))


def test_linearsvc_iris():
    """
    Test that LinearSVC gives plausible predictions on the iris dataset

    Also, test symbolic class names (classes_).
    """
    target = iris.target_names[iris.target]
    clf = svm.LinearSVC(random_state=0).fit(iris.data, target)
    assert_equal(set(clf.classes_), set(iris.target_names))
    assert_greater(np.mean(clf.predict(iris.data) == target), 0.8)

    dec = clf.decision_function(iris.data)
    pred = iris.target_names[np.argmax(dec, 1)]
    assert_array_equal(pred, clf.predict(iris.data))


def test_dense_liblinear_intercept_handling(classifier=svm.LinearSVC):
    """
    Test that dense liblinear honours intercept_scaling param
    """
    X = [[2, 1],
         [3, 1],
         [1, 3],
         [2, 3]]
    y = [0, 0, 1, 1]
    clf = classifier(fit_intercept=True, penalty='l1', loss='l2',
                     dual=False, C=4, tol=1e-7, random_state=0)
    assert_true(clf.intercept_scaling == 1, clf.intercept_scaling)
    assert_true(clf.fit_intercept)

    # when intercept_scaling is low the intercept value is highly "penalized"
    # by regularization
    clf.intercept_scaling = 1
    clf.fit(X, y)
    assert_almost_equal(clf.intercept_, 0, decimal=5)

    # when intercept_scaling is sufficiently high, the intercept value
    # is not affected by regularization
    clf.intercept_scaling = 100
    clf.fit(X, y)
    intercept1 = clf.intercept_
    assert_less(intercept1, -1)

    # when intercept_scaling is sufficiently high, the intercept value
    # doesn't depend on intercept_scaling value
    clf.intercept_scaling = 1000
    clf.fit(X, y)
    intercept2 = clf.intercept_
    assert_array_almost_equal(intercept1, intercept2, decimal=2)


def test_liblinear_set_coef():
    # multi-class case
    clf = svm.LinearSVC().fit(iris.data, iris.target)
    values = clf.decision_function(iris.data)
    clf.coef_ = clf.coef_.copy()
    clf.intercept_ = clf.intercept_.copy()
    values2 = clf.decision_function(iris.data)
    assert_array_almost_equal(values, values2)

    # binary-class case
    X = [[2, 1],
         [3, 1],
         [1, 3],
         [2, 3]]
    y = [0, 0, 1, 1]

    clf = svm.LinearSVC().fit(X, y)
    values = clf.decision_function(X)
    clf.coef_ = clf.coef_.copy()
    clf.intercept_ = clf.intercept_.copy()
    values2 = clf.decision_function(X)
    assert_array_equal(values, values2)


def test_immutable_coef_property():
    """Check that primal coef modification are not silently ignored"""
    svms = [
        svm.SVC(kernel='linear').fit(iris.data, iris.target),
        svm.NuSVC(kernel='linear').fit(iris.data, iris.target),
        svm.SVR(kernel='linear').fit(iris.data, iris.target),
        svm.NuSVR(kernel='linear').fit(iris.data, iris.target),
        svm.OneClassSVM(kernel='linear').fit(iris.data),
    ]
    for clf in svms:
        assert_raises(AttributeError, clf.__setattr__, 'coef_', np.arange(3))
        assert_raises((RuntimeError, ValueError),
                      clf.coef_.__setitem__, (0, 0), 0)


def test_inheritance():
    # check that SVC classes can do inheritance
    class ChildSVC(svm.SVC):
        def __init__(self, foo=0):
            self.foo = foo
            svm.SVC.__init__(self)

    clf = ChildSVC()
    clf.fit(iris.data, iris.target)
    clf.predict(iris.data[-1])
    clf.decision_function(iris.data[-1])


def test_linearsvc_verbose():
    # stdout: redirect
    import os
    stdout = os.dup(1)  # save original stdout
    os.dup2(os.pipe()[1], 1)  # replace it

    # actual call
    clf = svm.LinearSVC(verbose=1)
    clf.fit(X, Y)

    # stdout: restore
    os.dup2(stdout, 1)  # restore original stdout


def test_svc_clone_with_callable_kernel():
    a = svm.SVC(kernel=lambda x, y: np.dot(x, y.T), probability=True)
    b = base.clone(a)

    b.fit(X, Y)
    b.predict(X)
    b.predict_proba(X)
    b.decision_function(X)


def test_svc_bad_kernel():
    svc = svm.SVC(kernel=lambda x, y: x)
    assert_raises(ValueError, svc.fit, X, Y)


def test_timeout():
    a = svm.SVC(kernel=lambda x, y: np.dot(x, y.T), probability=True,
                max_iter=1)
    with warnings.catch_warnings(record=True) as foo:
        # Hackish way to reset the  warning counter
        from sklearn.svm import base
        base.__warningregistry__ = {}
        warnings.simplefilter("always")
        a.fit(X, Y)
        assert_equal(len(foo), 1, msg=foo)
        assert_equal(foo[0].category, ConvergenceWarning, msg=foo[0].category)


if __name__ == '__main__':
    import nose
    nose.runmodule()