def runPrintResults(X, y, alpha, name):

    print(name+":\n=========")

    if (alpha is not None):
        X_new = np.divide(X, alpha)
    else:
        X_new = X

    enetCV = ElasticNetCV(l1_ratio=0.8, fit_intercept=False) # cv=nCV, max_iter=5000
    # enetCV = LassoCV(fit_intercept=False) # cv=nCV, max_iter=5000

    enetCV.fit(X_new, y)
    y_pred_enet = enetCV.predict(X_new)
    r2_score_enet = r2_score(y, y_pred_enet)
    print("R2= ", r2_score_enet)


    if (alpha is not None):
        enetCV_coef = np.divide(enetCV.coef_, alpha)
    else:
        enetCV_coef = enetCV.coef_

    print("Best Alpha: {}".format(enetCV.alpha_))
    # print("coefs_: {}".format(enetCV.coef_))
    print("coefs_/alpha: {}".format(enetCV_coef))

    return enetCV.alpha_, enetCV_coef

def test_enet_path():
    # We use a large number of samples and of informative features so that
    # the l1_ratio selected is more toward ridge than lasso
    X, y, X_test, y_test = build_dataset(n_samples=200, n_features=100,
                                         n_informative_features=100)
    max_iter = 150

    # Here we have a small number of iterations, and thus the
    # ElasticNet might not converge. This is to speed up tests
    clf = ElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7], cv=3,
                       max_iter=max_iter)
    ignore_warnings(clf.fit)(X, y)
    # Well-conditioned settings, we should have selected our
    # smallest penalty
    assert_almost_equal(clf.alpha_, min(clf.alphas_))
    # Non-sparse ground truth: we should have seleted an elastic-net
    # that is closer to ridge than to lasso
    assert_equal(clf.l1_ratio_, min(clf.l1_ratio))

    clf = ElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7], cv=3,
                       max_iter=max_iter, precompute=True)
    ignore_warnings(clf.fit)(X, y)


    # Well-conditioned settings, we should have selected our
    # smallest penalty
    assert_almost_equal(clf.alpha_, min(clf.alphas_))
    # Non-sparse ground truth: we should have seleted an elastic-net
    # that is closer to ridge than to lasso
    assert_equal(clf.l1_ratio_, min(clf.l1_ratio))

    # We are in well-conditioned settings with low noise: we should
    # have a good test-set performance
    assert_greater(clf.score(X_test, y_test), 0.99)

def test_path_parameters():
    X, y, _, _ = build_dataset()
    max_iter = 50

    clf = ElasticNetCV(n_alphas=50, eps=1e-3, max_iter=max_iter, l1_ratio=0.5)
    clf.fit(X, y)  # new params
    assert_almost_equal(0.5, clf.l1_ratio)
    assert_equal(50, clf.n_alphas)
    assert_equal(50, len(clf.alphas_))

def test_path_parameters():
    X, y = make_sparse_data()
    max_iter = 50
    n_alphas = 10
    clf = ElasticNetCV(n_alphas=n_alphas, eps=1e-3, max_iter=max_iter,
                       l1_ratio=0.5, fit_intercept=False)
    clf.fit(X, y)  # new params
    assert_almost_equal(0.5, clf.l1_ratio)
    assert_equal(n_alphas, clf.n_alphas)
    assert_equal(n_alphas, len(clf.alphas_))

def test_1d_multioutput_enet_and_multitask_enet_cv():
    X, y, _, _ = build_dataset(n_features=10)
    y = y[:, np.newaxis]
    clf = ElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7])
    clf.fit(X, y[:, 0])
    clf1 = MultiTaskElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7])
    clf1.fit(X, y)
    assert_almost_equal(clf.l1_ratio_, clf1.l1_ratio_)
    assert_almost_equal(clf.alpha_, clf1.alpha_)
    assert_almost_equal(clf.coef_, clf1.coef_[0])
    assert_almost_equal(clf.intercept_, clf1.intercept_[0])

def test_path_parameters():
    X, y = make_sparse_data()
    max_iter = 50
    n_alphas = 10
    clf = ElasticNetCV(n_alphas=n_alphas, eps=1e-3, max_iter=max_iter,
                       l1_ratio=0.5, fit_intercept=False)
    clf.fit(X, y)  # new params
    assert_almost_equal(0.5, clf.l1_ratio)
    assert_equal(n_alphas, clf.n_alphas)
    assert_equal(n_alphas, len(clf.alphas_))
    sparse_mse_path = clf.mse_path_
    clf.fit(X.toarray(), y)  # compare with dense data
    assert_almost_equal(clf.mse_path_, sparse_mse_path)

def test_path_parameters():

    # build an ill-posed linear regression problem with many noisy features and
    # comparatively few samples
    n_samples, n_features, max_iter = 50, 200, 50
    random_state = np.random.RandomState(0)
    w = random_state.randn(n_features)
    w[10:] = 0.0  # only the top 10 features are impacting the model
    X = random_state.randn(n_samples, n_features)
    y = np.dot(X, w)

    clf = ElasticNetCV(n_alphas=50, eps=1e-3, max_iter=max_iter,
                       rho=0.5)
    clf.fit(X, y)  # new params
    assert_almost_equal(0.5, clf.rho)
    assert_equal(50, clf.n_alphas)
    assert_equal(50, len(clf.alphas))

def test_enet_path():
    # We use a large number of samples and of informative features so that
    # the l1_ratio selected is more toward ridge than lasso
    X, y, X_test, y_test = build_dataset(n_samples=200, n_features=100,
                                         n_informative_features=100)
    max_iter = 150

    # Here we have a small number of iterations, and thus the
    # ElasticNet might not converge. This is to speed up tests
    clf = ElasticNetCV(alphas=[0.01, 0.05, 0.1], eps=2e-3,
                       l1_ratio=[0.5, 0.7], cv=3,
                       max_iter=max_iter)
    ignore_warnings(clf.fit)(X, y)
    # Well-conditioned settings, we should have selected our
    # smallest penalty
    assert_almost_equal(clf.alpha_, min(clf.alphas_))
    # Non-sparse ground truth: we should have selected an elastic-net
    # that is closer to ridge than to lasso
    assert_equal(clf.l1_ratio_, min(clf.l1_ratio))

    clf = ElasticNetCV(alphas=[0.01, 0.05, 0.1], eps=2e-3,
                       l1_ratio=[0.5, 0.7], cv=3,
                       max_iter=max_iter, precompute=True)
    ignore_warnings(clf.fit)(X, y)

    # Well-conditioned settings, we should have selected our
    # smallest penalty
    assert_almost_equal(clf.alpha_, min(clf.alphas_))
    # Non-sparse ground truth: we should have selected an elastic-net
    # that is closer to ridge than to lasso
    assert_equal(clf.l1_ratio_, min(clf.l1_ratio))

    # We are in well-conditioned settings with low noise: we should
    # have a good test-set performance
    assert_greater(clf.score(X_test, y_test), 0.99)

    # Multi-output/target case
    X, y, X_test, y_test = build_dataset(n_features=10, n_targets=3)
    clf = MultiTaskElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7],
                                cv=3, max_iter=max_iter)
    ignore_warnings(clf.fit)(X, y)
    # We are in well-conditioned settings with low noise: we should
    # have a good test-set performance
    assert_greater(clf.score(X_test, y_test), 0.99)
    assert_equal(clf.coef_.shape, (3, 10))

    # Mono-output should have same cross-validated alpha_ and l1_ratio_
    # in both cases.
    X, y, _, _ = build_dataset(n_features=10)
    clf1 = ElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7])
    clf1.fit(X, y)
    clf2 = MultiTaskElasticNetCV(n_alphas=5, eps=2e-3, l1_ratio=[0.5, 0.7])
    clf2.fit(X, y[:, np.newaxis])
    assert_almost_equal(clf1.l1_ratio_, clf2.l1_ratio_)
    assert_almost_equal(clf1.alpha_, clf2.alpha_)

def test_enet_path():

    # build an ill-posed linear regression problem with many noisy features and
    # comparatively few samples
    n_samples, n_features, max_iter = 50, 200, 50
    random_state = np.random.RandomState(0)
    w = random_state.randn(n_features)
    w[10:] = 0.0  # only the top 10 features are impacting the model
    X = random_state.randn(n_samples, n_features)
    y = np.dot(X, w)

    clf = ElasticNetCV(n_alphas=10, eps=1e-3, rho=0.95, cv=5,
            max_iter=max_iter)
    clf.fit(X, y)
    assert_almost_equal(clf.alpha, 0.002, 2)

    clf = ElasticNetCV(n_alphas=10, eps=1e-3, rho=0.95, cv=5,
                       max_iter=max_iter, precompute=True)
    clf.fit(X, y)
    assert_almost_equal(clf.alpha, 0.002, 2)

    # test set
    X_test = random_state.randn(n_samples, n_features)
    y_test = np.dot(X_test, w)
    assert clf.score(X_test, y_test) > 0.99

    def train_all(self):
        positions = ['PG.csv', 'SG.csv', 'SF.csv', 'PF.csv', 'C.csv']
        with open(self.models_file_path, 'w') as model_file:
            model_file_writer = csv.writer(model_file)
            for (first, filename) in izip(chain((True,), repeat(False)), positions):
                with open(os.path.join(self.cleaned_data_directory_path, filename),
                          'r') as cleaned_data:
                    cleaned_data_reader = csv.reader(cleaned_data)
                    cleaned_data_headers = cleaned_data_reader.next()
                    lines = [map(float, line[:-1]) + line[-1:] for line in cleaned_data_reader
                             if len(line) >= 2]

                # conver lines to numpy array
                num_data = len(lines)
                num_features = len(lines[0]) - 2

                X = np.zeros((num_data, num_features))
                Y = np.zeros((num_data))

                for (i, data) in enumerate(lines):
                    for (ii, feature) in enumerate(data[:-2]):
                        X[i][ii] = feature
                    Y[i] = lines[i][-2]  # last one is name

                # create an instance of elasticnet
                net = ElasticNetCV(alphas=[0.01, 0.05, 0.1], eps=2e-3,
                                   l1_ratio=[0.5, 0.7, 1], cv=3, normalize=True)

                # create a model based on our data
                net.fit(X, Y)
                if first:
                    model_file_writer.writerow(cleaned_data_headers[:-2])
                model_file_writer.writerow(net.coef_)

                with open(os.path.join(
                        self.residual_data_path,
                        '_'.join(('resid', filename))), 'w') as resid_file:
                    resid_file_writer = csv.writer(resid_file)
                    # get the residuals
                    resid = X.dot(net.coef_) - Y
                    for (name, row) in izip(imap(lambda l: l[-1], lines), resid):
                        resid_file_writer.writerow((name, row))
                    print sum(resid)

def test_enet_path():
    X, y, X_test, y_test = build_dataset()
    max_iter = 50

    clf = ElasticNetCV(n_alphas=10, eps=1e-3, rho=0.95, cv=5,
            max_iter=max_iter)
    clf.fit(X, y)
    assert_almost_equal(clf.alpha, 0.002, 2)

    clf = ElasticNetCV(n_alphas=10, eps=1e-3, rho=0.95, cv=5,
                       max_iter=max_iter, precompute=True)
    clf.fit(X, y)
    assert_almost_equal(clf.alpha, 0.002, 2)

    # test set
    assert clf.score(X_test, y_test) > 0.99

def test_enet_cv_positive_constraint():
    X, y, X_test, y_test = build_dataset()
    max_iter = 500

    # Ensure the unconstrained fit has a negative coefficient
    enetcv_unconstrained = ElasticNetCV(n_alphas=3, eps=1e-1, max_iter=max_iter, cv=2, n_jobs=1)
    enetcv_unconstrained.fit(X, y)
    assert_true(min(enetcv_unconstrained.coef_) < 0)

    # On same data, constrained fit has non-negative coefficients
    enetcv_constrained = ElasticNetCV(n_alphas=3, eps=1e-1, max_iter=max_iter, cv=2, positive=True, n_jobs=1)
    enetcv_constrained.fit(X, y)
    assert_true(min(enetcv_constrained.coef_) >= 0)

def test_enet_path():
    X, y, X_test, y_test = build_dataset()
    max_iter = 150

    with warnings.catch_warnings():
        # Here we have a small number of iterations, and thus the
        # ElasticNet might not converge. This is to speed up tests
        warnings.simplefilter("ignore", UserWarning)
        clf = ElasticNetCV(n_alphas=5, eps=2e-3, rho=[0.9, 0.95], cv=3, max_iter=max_iter)
        clf.fit(X, y)
        assert_almost_equal(clf.alpha, 0.002, 2)
        assert_equal(clf.rho_, 0.95)

        clf = ElasticNetCV(n_alphas=5, eps=2e-3, rho=[0.9, 0.95], cv=3, max_iter=max_iter, precompute=True)
        clf.fit(X, y)
    assert_almost_equal(clf.alpha, 0.002, 2)
    assert_equal(clf.rho_, 0.95)

    # test set
    assert_greater(clf.score(X_test, y_test), 0.99)

def test_enet_l1_ratio():
    # Test that an error message is raised if an estimator that
    # uses _alpha_grid is called with l1_ratio=0
    msg = ("Automatic alpha grid generation is not supported for l1_ratio=0. "
           "Please supply a grid by providing your estimator with the "
           "appropriate `alphas=` argument.")
    X = np.array([[1, 2, 4, 5, 8], [3, 5, 7, 7, 8]]).T
    y = np.array([12, 10, 11, 21, 5])

    assert_raise_message(ValueError, msg, ElasticNetCV(
        l1_ratio=0, random_state=42).fit, X, y)
    assert_raise_message(ValueError, msg, MultiTaskElasticNetCV(
        l1_ratio=0, random_state=42).fit, X, y[:, None])

    # Test that l1_ratio=0 is allowed if we supply a grid manually
    alphas = [0.1, 10]
    estkwds = {'alphas': alphas, 'random_state': 42}
    est_desired = ElasticNetCV(l1_ratio=0.00001, **estkwds)
    est = ElasticNetCV(l1_ratio=0, **estkwds)
    with ignore_warnings():
        est_desired.fit(X, y)
        est.fit(X, y)
    assert_array_almost_equal(est.coef_, est_desired.coef_, decimal=5)

    est_desired = MultiTaskElasticNetCV(l1_ratio=0.00001, **estkwds)
    est = MultiTaskElasticNetCV(l1_ratio=0, **estkwds)
    with ignore_warnings():
        est.fit(X, y[:, None])
        est_desired.fit(X, y[:, None])
    assert_array_almost_equal(est.coef_, est_desired.coef_, decimal=5)

def test_sparse_input_dtype_enet_and_lassocv():
    X, y, _, _ = build_dataset(n_features=10)
    clf = ElasticNetCV(n_alphas=5)
    clf.fit(sparse.csr_matrix(X), y)
    clf1 = ElasticNetCV(n_alphas=5)
    clf1.fit(sparse.csr_matrix(X, dtype=np.float32), y)
    assert_almost_equal(clf.alpha_, clf1.alpha_, decimal=6)
    assert_almost_equal(clf.coef_, clf1.coef_, decimal=6)

    clf = LassoCV(n_alphas=5)
    clf.fit(sparse.csr_matrix(X), y)
    clf1 = LassoCV(n_alphas=5)
    clf1.fit(sparse.csr_matrix(X, dtype=np.float32), y)
    assert_almost_equal(clf.alpha_, clf1.alpha_, decimal=6)
    assert_almost_equal(clf.coef_, clf1.coef_, decimal=6)

labels_group = ['elderly', 'mci', 'young']
j = 0
for _, x in enumerate(X.T):
    if (j%n_rows) == 0:
        f = pl.figure()
    
    for i in range(n_rows):
        a = f.add_subplot(n_rows, n_rows,(n_rows)*(j%n_rows)+(i+1))
        title = node_names[indexes[j][0]]+' -- '+node_names[indexes[j][1]]
        pl.scatter(x[groups==i], y[groups==i], c=color[i], s=40, label=labels_group[i])
        a.set_title(title)
        pl.legend()
    
    j+=1
######################################################
enetcv = ElasticNetCV(alphas=np.linspace(1, 0.05, 50), 
                          cv=ShuffleSplit(len(y), n_iter=50, test_size=0.25))

lassocv = LassoCV(alphas=np.linspace(1, 0.05, 50), 
                          cv=ShuffleSplit(len(y), n_iter=50, test_size=0.25))
for i in range(n_rows):
    
    X_ = conn_data[groups==i,:]
    y_ = y[groups==i]
    
    enetcv = ElasticNetCV(alphas=np.linspace(1, 0.05, 50), 
                          cv=ShuffleSplit(len(y_), n_iter=50, test_size=0.25))

    lassocv = LassoCV(alphas=np.linspace(1, 0.05, 50), 
                          cv=ShuffleSplit(len(y_), n_iter=50, test_size=0.25))