//  [python]
def calculate_all_metafeatures(X, y, categorical, dataset_name,
        calculate=None, dont_calculate=None, densify_threshold=1000):
    logger = get_logger(__name__)

    """Calculate all metafeatures."""
    helper_functions.clear()
    metafeatures.clear()
    mf_ = dict()

    visited = set()
    to_visit = deque()
    to_visit.extend(metafeatures)
    print("X")
    print(X)
    print("y")
    print(y)
    print("categoricals")
    print(categorical)
    X_transformed = None
    y_transformed = None

    # TODO calculate the numpy metafeatures after all others to consume less
    # memory
    while len(to_visit) > 0:
        name = to_visit.pop()
        if calculate is not None and name not in calculate:
            continue
        if dont_calculate is not None and name in dont_calculate:
            continue

        if name in npy_metafeatures:
            if X_transformed is None:
                # TODO make sure this is done as efficient as possible (no copy for
                # sparse matrices because of wrong sparse format)
                sparse = scipy.sparse.issparse(X)
                if any(categorical):
                    ohe = OneHotEncoder(categorical_features=categorical, sparse=True)
                    X_transformed = ohe.fit_transform(X)
                else:
                    X_transformed = X
                imputer = Imputer(strategy='mean', copy=False)
                X_transformed = imputer.fit_transform(X_transformed)
                center = not scipy.sparse.isspmatrix(X_transformed)
                standard_scaler = StandardScaler(copy=False, with_mean=center)
                X_transformed = standard_scaler.fit_transform(X_transformed)
                categorical_transformed = [False] * X_transformed.shape[1]

                # Densify the transformed matrix
                if not sparse and scipy.sparse.issparse(X_transformed):
                    bytes_per_float = X_transformed.dtype.itemsize
                    num_elements = X_transformed.shape[0] * X_transformed.shape[1]
                    megabytes_required = num_elements * bytes_per_float / 1000 / 1000
                    if megabytes_required < densify_threshold:
                        X_transformed = X_transformed.todense()

                # This is not only important for datasets which are somehow
                # sorted in a strange way, but also prevents lda from failing in
                # some cases.
                # Because this is advanced indexing, a copy of the data is returned!!!
                X_transformed = check_array(X_transformed,
                                            force_all_finite=True,
                                            accept_sparse='csr')
                rs = np.random.RandomState(42)
                indices = np.arange(X_transformed.shape[0])
                rs.shuffle(indices)
                # TODO Shuffle inplace
                X_transformed = X_transformed[indices]
                y_transformed = y[indices]

            X_ = X_transformed
            y_ = y_transformed
            categorical_ = categorical_transformed
        else:
            X_ = X
            y_ = y
            categorical_ = categorical

        dependency = metafeatures.get_dependency(name)
        if dependency is not None:
            is_metafeature = dependency in metafeatures
            is_helper_function = dependency in helper_functions

            if is_metafeature and is_helper_function:
                raise ValueError(dependency)
            elif not is_metafeature and not is_helper_function:
                raise NotImplementedError()
            elif is_metafeature and not metafeatures.is_calculated(dependency):
                to_visit.appendleft(name)
                continue
            elif is_helper_function and not helper_functions.is_calculated(
                    dependency):
                logger.info("%s: Going to calculate: %s", dataset_name,
                            dependency)
                value = helper_functions[dependency](X_, y_, categorical_)
                helper_functions.set_value(dependency, value)
                mf_[dependency] = value

        logger.info("%s: Going to calculate: %s", dataset_name,
                    name)

        value = metafeatures[name](X_, y_, categorical_)
        metafeatures.set_value(name, value)
        mf_[name] = value
        visited.add(name)

    mf_ = DatasetMetafeatures(dataset_name, mf_)
    return mf_