python类f_classif()的实例源码

def test_SelectKBest():
    '''
    test the method of SelectKBert
    :return:  None
    '''
    X=[   [1,2,3,4,5],
          [5,4,3,2,1],
          [3,3,3,3,3,],
          [1,1,1,1,1] ]
    y=[0,1,0,1]
    print("before transform:",X)
    selector=SelectKBest(score_func=f_classif,k=3)
    selector.fit(X,y)
    print("scores_:",selector.scores_)
    print("pvalues_:",selector.pvalues_)
    print("selected index:",selector.get_support(True))
    print("after transform:",selector.transform(X))

def select_feat(X,y,percentile=20):
    "Select best 20 % of features using Anova F-value - *f_classif* from scikit.learn"
    selector = SelectPercentile(f_classif, percentile=percentile)
    selector.fit(X, y)
    return  selector.transform(X)

def select_kbest_clf(data_frame, target, k=4):
    """
    Selecting K-Best features for classification
    :param data_frame: A pandas dataFrame with the training data
    :param target: target variable name in DataFrame
    :param k: desired number of features from the data
    :returns feature_scores: scores for each feature in the data as 
    pandas DataFrame
    """
    feat_selector = SelectKBest(f_classif, k=k)
    _ = feat_selector.fit(data_frame.drop(target, axis=1), data_frame[target])

    feat_scores = pd.DataFrame()
    feat_scores["F Score"] = feat_selector.scores_
    feat_scores["P Value"] = feat_selector.pvalues_
    feat_scores["Support"] = feat_selector.get_support()
    feat_scores["Attribute"] = data_frame.drop(target, axis=1).columns

    return feat_scores

def get_classification_data(self, division_dummies=True, samples=None, percentile=100):
        raw = PlayerCollection.filter_by_class(self.raw)
        df = PlayerCollection.raw_to_df(raw)
        players, divisions = PlayerCollection.aggregate_df(df)
        players, divisions = PlayerCollection.to_matrix(players, divisions)
        players, divisions = PlayerCollection.subsample(players, divisions, samples)
        X_train, X_test, y_train, y_test = train_test_split(
            players, divisions, random_state=42, stratify=divisions)

        selector = SelectPercentile(f_classif, percentile=percentile)
        selector.fit(X_train, y_train)
        X_train = selector.transform(X_train)
        X_test = selector.transform(X_test)

        if division_dummies:
            y_train = pd.get_dummies(y_train).as_matrix()
            y_test = pd.get_dummies(y_test).as_matrix()
        scaler = StandardScaler()
        X_train = scaler.fit_transform(X_train)
        X_test = scaler.transform(X_test)
        return X_train, X_test, y_train, y_test

def test_clone():
    # Tests that clone creates a correct deep copy.
    # We create an estimator, make a copy of its original state
    # (which, in this case, is the current state of the estimator),
    # and check that the obtained copy is a correct deep copy.

    from sklearn.feature_selection import SelectFpr, f_classif

    selector = SelectFpr(f_classif, alpha=0.1)
    new_selector = clone(selector)
    assert_true(selector is not new_selector)
    assert_equal(selector.get_params(), new_selector.get_params())

    selector = SelectFpr(f_classif, alpha=np.zeros((10, 2)))
    new_selector = clone(selector)
    assert_true(selector is not new_selector)

def test_randomized_logistic():
    # Check randomized sparse logistic regression
    iris = load_iris()
    X = iris.data[:, [0, 2]]
    y = iris.target
    X = X[y != 2]
    y = y[y != 2]

    F, _ = f_classif(X, y)

    scaling = 0.3
    clf = RandomizedLogisticRegression(verbose=False, C=1., random_state=42,
                                       scaling=scaling, n_resampling=50,
                                       tol=1e-3)
    X_orig = X.copy()
    feature_scores = clf.fit(X, y).scores_
    assert_array_equal(X, X_orig)   # fit does not modify X
    assert_array_equal(np.argsort(F), np.argsort(feature_scores))

    clf = RandomizedLogisticRegression(verbose=False, C=[1., 0.5],
                                       random_state=42, scaling=scaling,
                                       n_resampling=50, tol=1e-3)
    feature_scores = clf.fit(X, y).scores_
    assert_array_equal(np.argsort(F), np.argsort(feature_scores))

def thresholds():
  for name in ['ant', 'ivy', 'jedit', 'lucene', 'poi']:
    print("##", name)
    train, test = explore(dir='../Data/Jureczko/', name=name)
    data_DF=csv2DF(train, toBin=True)
    metrics=[str[1:] for str in data_DF[data_DF.columns[:-1]]]
    ubr = LogisticRegression()
    X = data_DF[data_DF.columns[:-1]].values
    y = data_DF[data_DF.columns[-1]].values
    ubr.fit(X,y)
    inter, coef, pVal = ubr.intercept_[0], ubr.coef_[0], f_classif(X,y)[1]

    table= texttable.Texttable()
    table.set_cols_align(["l","l","l"])
    table.set_cols_valign(["m","m","m"])
    table.set_cols_dtype(['t', 't', 't'])
    table_rows=[["Metric", "Threshold", "P-Value"]]

    for i in xrange(len(metrics)):
      if VARL(coef[i], inter, p0=0.05)>0 and pVal[i]<0.05:
        thresh="%0.2f"%VARL(coef[i], inter, p0=0.1)
        table_rows.append([metrics[i], thresh, "%0.3f"%pVal[i]])

    table.add_rows(table_rows)
    print(table.draw())

  # === DEBUG ===
  set_trace()
  return None

def transform_select_K_best(X_train,Y_train, X_all, K=100):
    """Selects the best K features given the training data.

    Args:
        X_train: A matrix containing training data
        Y_train: Classification labels for the training data
        X_all: A matrix containing all the data
        K: The number of features to select
    """
    skb = SelectKBest(f_classif,K)
    skb.fit(X_train,Y_train)

    return skb.transform(X_all)

def __init__(self, filename=None):
        super().__init__(filename)

        if not filename:
            self.clf = Pipeline([
                ('tfidf', TfidfVectorizer(stop_words=sw.words('dutch'))),
                ('anova', SelectPercentile(f_classif)),
                ('clf', MultinomialNB())
            ])

def __init__(self, conf):
        SemiSupervisedFeatureSelection.__init__(self, conf)
        self.projection = SelectKBest(f_classif, k = conf.num_components)

def buildEstimators(mode):
    if mode == 'train' or mode == 'cv':
        # best parameters got by gridsearchCV, best score: 1
        estimators = [('anova_filter', SelectKBest(f_classif, k='all')),
                      ('xgb', xgb.XGBClassifier(learning_rate=0.1,n_estimators=300,max_depth=3))]
        clf = Pipeline(estimators)
    elif mode == 'test':
        clf = pickle.load(open(join(classifier_path,"xgb_classifier.plk"), "r"))
    return clf

def de_f_and_p_value(X,y):
    dim = X.shape[1]
    de  = min(2000,dim)
    clf = SelectKBest(f_classif,k=de)
    clf.fit(X, y)
    def _func(X1,X2):
        return clf.transform(X1),clf.transform(X2)
    return _func

def de_f_and_p_value(X,y):
    """ f&p value """
    dim = X.shape[1]
    de  = min(2000,dim)
    clf = SelectKBest(f_classif,k=de)
    clf.fit(X, y)
    def _func(X1,X2):
        return clf.transform(X1),clf.transform(X2)
    return _func

def new(method='centroid',n_features=8):

  # Clustering method
  nc = METHODS[method]

  # Orthogonal feature selector
  if n_features is None: n_features = 'all'
  selector = SelectKBest(f_classif, k=n_features)

  # NOTE: The only last operation of the list
  # must be a classifier or clustering model
  print(colored('Cluster model created','yellow'))
  return [selector, nc]

def feature_importance_classification(features, target, n_neighbors=3, random_state=None):

    cont = features.select_dtypes(include=[np.floating])
    disc = features.select_dtypes(include=[np.integer, np.bool])

    cont_imp = pd.DataFrame(index=cont.columns)
    disc_imp = pd.DataFrame(index=disc.columns)

    # Continuous features
    if cont_imp.index.size > 0:

        # F-test
        f_test = feature_selection.f_classif(cont, target)
        cont_imp['f_statistic'] = f_test[0]
        cont_imp['f_p_value'] = f_test[1]

        # Mutual information
        mut_inf = feature_selection.mutual_info_classif(cont, target, discrete_features=False,
                                                        n_neighbors=n_neighbors,
                                                        random_state=random_state)
        cont_imp['mutual_information'] = mut_inf

    # Discrete features
    if disc_imp.index.size > 0:

        # Chi²-test
        chi2_tests = defaultdict(dict)

        for feature in disc.columns:
            cont = pd.crosstab(disc[feature], target)
            statistic, p_value, _, _ = stats.chi2_contingency(cont)
            chi2_tests[feature]['chi2_statistic'] = statistic
            chi2_tests[feature]['chi2_p_value'] = p_value

        chi2_tests_df = pd.DataFrame.from_dict(chi2_tests, orient='index')
        disc_imp['chi2_statistic'] = chi2_tests_df['chi2_statistic']
        disc_imp['chi2_p_value'] = chi2_tests_df['chi2_p_value']

        # Cramér's V (corrected)
        disc_imp['cramers_v'] = [
            cramers_v_corrected_stat(pd.crosstab(feature, target).values)
            for _, feature in disc.iteritems()
        ]

        # Mutual information
        mut_inf = feature_selection.mutual_info_classif(disc, target, discrete_features=True,
                                                        n_neighbors=n_neighbors,
                                                        random_state=random_state)
        disc_imp['mutual_information'] = mut_inf

    return cont_imp, disc_imp

def main():
     data_table = pd.read_csv("total_set.csv",index_col=0)
     film_titles = data_table.index  # list of all of our movie titles in the dataset.
     #print film_titles
     lst = [   'Sequel',
               'Budget',
               'YouTube Trailer Views',
               'YouTube Like',
               'YouTube Dislike',
               'YouTube Like:Dislike',
               'Reddit UpVotes',
               'Distributor',
               'Reddit Ratio',
               'Reddit Comments',
               'Date',
               'Runtime',
               'MPAA',
               'Comedy',
               'Action/Adventure',
               'Animated',
               'Drama'
               ]

     data = data_table[lst]
     target = data_table['Profitable']

     print data.shape
     data_new = SelectKBest(f_classif, k=10).fit_transform(data, target)
     print data_new.shape

     no_select=compute_cross_fold(data, target)
     with_select=compute_cross_fold(data_new, target)

     print no_select
     print with_select

def test_clone_2():
    # Tests that clone doesn't copy everything.
    # We first create an estimator, give it an own attribute, and
    # make a copy of its original state. Then we check that the copy doesn't
    # have the specific attribute we manually added to the initial estimator.

    from sklearn.feature_selection import SelectFpr, f_classif

    selector = SelectFpr(f_classif, alpha=0.1)
    selector.own_attribute = "test"
    new_selector = clone(selector)
    assert_false(hasattr(new_selector, "own_attribute"))

def test_pipeline_methods_anova():
    # Test the various methods of the pipeline (anova).
    iris = load_iris()
    X = iris.data
    y = iris.target
    # Test with Anova + LogisticRegression
    clf = LogisticRegression()
    filter1 = SelectKBest(f_classif, k=2)
    pipe = Pipeline([('anova', filter1), ('logistic', clf)])
    pipe.fit(X, y)
    pipe.predict(X)
    pipe.predict_proba(X)
    pipe.predict_log_proba(X)
    pipe.score(X, y)

def preprocess(X,y):
    ### test_size is the percentage of events assigned to the test set
    ### (remainder go into training)
    features_train, features_test, labels_train, labels_test = model_selection.train_test_split(X, y, test_size=0.2, random_state=42)


   ### text vectorization--go from strings to lists of numbers
    vectorizer = TfidfVectorizer(sublinear_tf=True, max_df=0.5, stop_words='english')
    features_train_transformed = vectorizer.fit_transform(features_train)
    features_test_transformed  = vectorizer.transform(features_test)
    joblib.dump(vectorizer, 'vectorizer_intent.pkl')

   ### feature selection, because text is super high dimensional and
    ### can be really computationally chewy as a result
    selector = SelectPercentile(f_classif, percentile=10)
    selector.fit(features_train_transformed, labels_train)
    joblib.dump(selector, 'selector_intent.pkl')
    features_train_transformed = selector.transform(features_train_transformed).toarray()
    features_test_transformed  = selector.transform(features_test_transformed).toarray()
    return features_train_transformed, features_test_transformed, labels_train, labels_test

def build(self, dataset, max_feature=10, score_threshold=0.6):
        variation = []
        for f in self.field_manager.features:
            if f.is_categorizable() and not f.category_feature:
                variation.append([(f.field_code, False), (f.field_code, True)])

        judge_scenarios = itertools.product(*variation)
        criteria = f_classif if self.field_manager.target.is_categorizable() else f_regression
        self._best_scenario = []
        self._best_features = {}
        top_score = 0
        for s in judge_scenarios:
            # prepare the feature
            for code, is_category in s:
                self.field_manager.get_feature(code).category_feature = is_category

            # adjust the dataset
            adjusted = self.field_manager.adjust(dataset)

            # evaluate the feature
            selector = SelectKBest(criteria, k=min(max_feature, len(adjusted.feature_names)))
            selector.fit(adjusted.data, adjusted.target)
            threshold = max(selector.scores_) * score_threshold
            candidates = {}
            for i, selected in enumerate(selector.get_support()):
                if selected and selector.scores_[i] > threshold:
                    candidates[adjusted.feature_names[i]] = selector.scores_[i]

            if sum(selector.scores_) > top_score:
                self._best_scenario = s
                self._best_features = candidates
                top_score = sum(selector.scores_)

        # reflect the setting to field_manager
        for code, is_category in self._best_scenario:
            self.field_manager.get_feature(code).category_feature = is_category
            self.field_manager.selected = list(self._best_features.keys())

def get_params_for_est(estimator, name):
    '''Choose initialization parameters for an estimator for auto-testing'''
    is_classifier = ClassifierMixin in estimator.__mro__
    is_cluster = ClusterMixin in estimator.__mro__
    is_ensemble = BaseEnsemble in estimator.__mro__
    uses_counts = any(c in name for c in USES_COUNTS)
    as_1d = name in REQUIRES_1D
    args, params, _ = get_args_kwargs_defaults(estimator.__init__)
    est_keys = set(('estimator', 'base_estimator', 'estimators'))
    est_keys = (set(params) | set(args)) & est_keys
    if is_classifier:
        score_func = feat.f_classif
    else:
        score_func = feat.f_regression
    for key in est_keys:
        if name == 'SelectFromModel':
            params[key] = sklearn.linear_model.LassoCV()
        elif is_classifier:
            params[key] = sklearn.tree.DecisionTreeClassifier()
        else:
            params[key] = sklearn.tree.DecisionTreeRegressor()
        if key == 'estimators':
            params[key] = [(str(_), clone(params[key])) for _ in range(10)]
    kw = dict(is_classifier=is_classifier, is_cluster=is_cluster,
              is_ensemble=is_ensemble, uses_counts=uses_counts)
    if 'score_func' in params:
        params['score_func'] = score_func
    X, y = make_X_y(**kw)
    return X, y, params, kw

def preprocess(words_file = "../tools/word_data.pkl", authors_file="../tools/email_authors.pkl"):
    """
        this function takes a pre-made list of email texts (by default word_data.pkl)
        and the corresponding authors (by default email_authors.pkl) and performs
        a number of preprocessing steps:
            -- splits into training/testing sets (10% testing)
            -- vectorizes into tfidf matrix
            -- selects/keeps most helpful features

        after this, the feaures and labels are put into numpy arrays, which play nice with sklearn functions

        4 objects are returned:
            -- training/testing features
            -- training/testing labels

    """

    ### the words (features) and authors (labels), already largely preprocessed
    ### this preprocessing will be repeated in the text learning mini-project
    authors_file_handler = open(authors_file, "r")
    authors = pickle.load(authors_file_handler)
    authors_file_handler.close()

    words_file_handler = open(words_file, "r")
    word_data = cPickle.load(words_file_handler)
    words_file_handler.close()

    ### test_size is the percentage of events assigned to the test set
    ### (remainder go into training)
    features_train, features_test, labels_train, labels_test = cross_validation.train_test_split(word_data, authors, test_size=0.1, random_state=42)



    ### text vectorization--go from strings to lists of numbers
    vectorizer = TfidfVectorizer(sublinear_tf=True, max_df=0.5,
                                 stop_words='english')
    features_train_transformed = vectorizer.fit_transform(features_train)
    features_test_transformed  = vectorizer.transform(features_test)



    ### feature selection, because text is super high dimensional and
    ### can be really computationally chewy as a result
    selector = SelectPercentile(f_classif, percentile=1)
    selector.fit(features_train_transformed, labels_train)
    features_train_transformed = selector.transform(features_train_transformed).toarray()
    features_test_transformed  = selector.transform(features_test_transformed).toarray()

    ### info on the data
    print "no. of Chris training emails:", sum(labels_train)
    print "no. of Sara training emails:", len(labels_train)-sum(labels_train)

    return features_train_transformed, features_test_transformed, labels_train, labels_test

def test_pipeline_init():
    # Test the various init parameters of the pipeline.
    assert_raises(TypeError, Pipeline)
    # Check that we can't instantiate pipelines with objects without fit
    # method
    pipe = assert_raises(TypeError, Pipeline, [('svc', IncorrectT)])
    # Smoke test with only an estimator
    clf = T()
    pipe = Pipeline([('svc', clf)])
    assert_equal(pipe.get_params(deep=True),
                 dict(svc__a=None, svc__b=None, svc=clf,
                      **pipe.get_params(deep=False)))

    # Check that params are set
    pipe.set_params(svc__a=0.1)
    assert_equal(clf.a, 0.1)
    assert_equal(clf.b, None)
    # Smoke test the repr:
    repr(pipe)

    # Test with two objects
    clf = SVC()
    filter1 = SelectKBest(f_classif)
    pipe = Pipeline([('anova', filter1), ('svc', clf)])

    # Check that we can't use the same stage name twice
    assert_raises(ValueError, Pipeline, [('svc', SVC()), ('svc', SVC())])

    # Check that params are set
    pipe.set_params(svc__C=0.1)
    assert_equal(clf.C, 0.1)
    # Smoke test the repr:
    repr(pipe)

    # Check that params are not set when naming them wrong
    assert_raises(ValueError, pipe.set_params, anova__C=0.1)

    # Test clone
    pipe2 = clone(pipe)
    assert_false(pipe.named_steps['svc'] is pipe2.named_steps['svc'])

    # Check that apart from estimators, the parameters are the same
    params = pipe.get_params(deep=True)
    params2 = pipe2.get_params(deep=True)

    for x in pipe.get_params(deep=False):
        params.pop(x)

    for x in pipe2.get_params(deep=False):
        params2.pop(x)

    # Remove estimators that where copied
    params.pop('svc')
    params.pop('anova')
    params2.pop('svc')
    params2.pop('anova')
    assert_equal(params, params2)

def describe_data(data, info=False, describe=False, value_counts=None, unique=None,
                  univariate_feature_selection=None, description=None):
    # Data diagnostics
    if description is not None:
        print("\n" + description)

    # Info
    if info:
        print("\nInfo:")
        print(data.info())

    # Description
    if describe:
        print("\nDescribe:")
        print(data.describe())

    # Value counts
    if value_counts is not None:
        for feature in value_counts:
            print("\nValue Counts [" + feature + "]")
            print(pd.value_counts(data[feature]))

    # Unique values
    if unique is not None:
        for feature in unique:
            print("\nUnique [" + feature + "]")
            print(data[feature].unique())

    # Univariate feature selection
    if univariate_feature_selection is not None:
        # Extract predictors and target
        predictors = univariate_feature_selection[0]
        target = univariate_feature_selection[1]

        # Perform feature selection
        selector = SelectKBest(f_classif, k="all")
        selector.fit(data[predictors], data[target])

        # Get the raw p-values for each feature, and transform from p-values into scores
        scores = -np.log10(selector.pvalues_)
        print("\nUnivariate Feature Selection:")
        for feature, imp in sorted(zip(predictors, scores), key=lambda x: x[1] if pd.notnull(x[1]) else 0):
            print(feature, imp)