Source code for evalml.utils.gen_utils

import importlib
import os
import warnings
from collections import namedtuple
from functools import reduce

import numpy as np
import pandas as pd
import woodwork as ww
from sklearn.utils import check_random_state

from evalml.exceptions import (
from evalml.utils import get_logger

logger = get_logger(__file__)

numeric_dtypes = ['int16', 'int32', 'int64', 'float16', 'float32', 'float64']
boolean = ['bool']
numeric_and_boolean_dtypes = numeric_dtypes + boolean
categorical_dtypes = ['object', 'category']
datetime_dtypes = [np.datetime64]

[docs]def import_or_raise(library, error_msg=None, warning=False): """Attempts to import the requested library by name. If the import fails, raises an ImportError or warning. Arguments: library (str): the name of the library error_msg (str): error message to return if the import fails warning (bool): if True, import_or_raise gives a warning instead of ImportError. Defaults to False. """ try: return importlib.import_module(library) except ImportError: if error_msg is None: error_msg = "" msg = (f"Missing optional dependency '{library}'. Please use pip to install {library}. {error_msg}") if warning: warnings.warn(msg) else: raise ImportError(msg) except Exception as ex: msg = (f"An exception occurred while trying to import `{library}`: {str(ex)}") if warning: warnings.warn(msg) else: raise Exception(msg)
[docs]def convert_to_seconds(input_str): """Converts a string describing a length of time to its length in seconds.""" hours = {'h', 'hr', 'hour', 'hours'} minutes = {'m', 'min', 'minute', 'minutes'} seconds = {'s', 'sec', 'second', 'seconds'} value, unit = input_str.split() if unit[-1] == 's' and len(unit) != 1: unit = unit[:-1] if unit in seconds: return float(value) elif unit in minutes: return float(value) * 60 elif unit in hours: return float(value) * 3600 else: msg = "Invalid unit. Units must be hours, mins, or seconds. Received '{}'".format(unit) raise AssertionError(msg)
# specifies the min and max values a seed to np.random.RandomState is allowed to take. # these limits were chosen to fit in the numpy.int32 datatype to avoid issues with 32-bit systems # see SEED_BOUNDS = namedtuple('SEED_BOUNDS', ('min_bound', 'max_bound'))(0, 2**31 - 1)
[docs]def get_random_state(seed): """Generates a numpy.random.RandomState instance using seed. Arguments: seed (None, int, np.random.RandomState object): seed to use to generate numpy.random.RandomState. Must be between SEED_BOUNDS.min_bound and SEED_BOUNDS.max_bound, inclusive. Otherwise, an exception will be thrown. """ if isinstance(seed, (int, np.integer)) and (seed < SEED_BOUNDS.min_bound or SEED_BOUNDS.max_bound < seed): raise ValueError('Seed "{}" is not in the range [{}, {}], inclusive'.format(seed, SEED_BOUNDS.min_bound, SEED_BOUNDS.max_bound)) return check_random_state(seed)
[docs]def get_random_seed(random_state, min_bound=SEED_BOUNDS.min_bound, max_bound=SEED_BOUNDS.max_bound): """Given a numpy.random.RandomState object, generate an int representing a seed value for another random number generator. Or, if given an int, return that int. To protect against invalid input to a particular library's random number generator, if an int value is provided, and it is outside the bounds "[min_bound, max_bound)", the value will be projected into the range between the min_bound (inclusive) and max_bound (exclusive) using modular arithmetic. Arguments: random_state (int, numpy.random.RandomState): random state min_bound (None, int): if not default of None, will be min bound when generating seed (inclusive). Must be less than max_bound. max_bound (None, int): if not default of None, will be max bound when generating seed (exclusive). Must be greater than min_bound. Returns: int: seed for random number generator """ if not min_bound < max_bound: raise ValueError("Provided min_bound {} is not less than max_bound {}".format(min_bound, max_bound)) if isinstance(random_state, np.random.RandomState): return random_state.randint(min_bound, max_bound) if random_state < min_bound or random_state >= max_bound: return ((random_state - min_bound) % (max_bound - min_bound)) + min_bound return random_state
def check_random_state_equality(random_state, other_random_state): """Method to check for equality of two numpy.random.RandomState objects""" for self_rs_attr, other_rs_attr in zip(random_state.get_state(), other_random_state.get_state()): if isinstance(self_rs_attr, np.ndarray) and isinstance(other_rs_attr, np.ndarray): if not (self_rs_attr == other_rs_attr).all(): return False else: if not (self_rs_attr == other_rs_attr): return False return True class classproperty: """Allows function to be accessed as a class level property. Example: class LogisticRegressionBinaryPipeline(PipelineBase): component_graph = ['Simple Imputer', 'Logistic Regression Classifier'] @classproperty def summary(cls): summary = "" for component in cls.component_graph: component = handle_component_class(component) summary += + " + " return summary assert LogisticRegressionBinaryPipeline.summary == "Simple Imputer + Logistic Regression Classifier + " assert LogisticRegressionBinaryPipeline().summary == "Simple Imputer + Logistic Regression Classifier + " """ def __init__(self, func): self.func = func def __get__(self, _, klass): return self.func(klass) def _get_subclasses(base_class): """Gets all of the leaf nodes in the hiearchy tree for a given base class. Arguments: base_class (abc.ABCMeta): Class to find all of the children for. Returns: subclasses (list): List of all children that are not base classes. """ classes_to_check = base_class.__subclasses__() subclasses = [] while classes_to_check: subclass = classes_to_check.pop() children = subclass.__subclasses__() if children: classes_to_check.extend(children) else: subclasses.append(subclass) return subclasses _not_used_in_automl = {'BaselineClassifier', 'BaselineRegressor', 'TimeSeriesBaselineRegressor', 'StackedEnsembleClassifier', 'StackedEnsembleRegressor', 'ModeBaselineBinaryPipeline', 'BaselineBinaryPipeline', 'MeanBaselineRegressionPipeline', 'BaselineRegressionPipeline', 'ModeBaselineMulticlassPipeline', 'BaselineMulticlassPipeline', 'TimeSeriesBaselineRegressionPipeline'} def get_importable_subclasses(base_class, used_in_automl=True): """Get importable subclasses of a base class. Used to list all of our estimators, transformers, components and pipelines dynamically. Arguments: base_class (abc.ABCMeta): Base class to find all of the subclasses for. args (list): Args used to instantiate the subclass. [{}] for a pipeline, and [] for all other classes. used_in_automl: Not all components/pipelines/estimators are used in automl search. If True, only include those subclasses that are used in the search. This would mean excluding classes related to ExtraTrees, ElasticNet, and Baseline estimators. Returns: List of subclasses. """ all_classes = _get_subclasses(base_class) classes = [] for cls in all_classes: if 'evalml.pipelines' not in cls.__module__: continue try: cls() classes.append(cls) except (ImportError, MissingComponentError, TypeError): logger.debug(f'Could not import class {cls.__name__} in get_importable_subclasses') except EnsembleMissingPipelinesError: classes.append(cls) if used_in_automl: classes = [cls for cls in classes if cls.__name__ not in _not_used_in_automl] return classes def _rename_column_names_to_numeric(X): """Used in LightGBM classifier class and XGBoost classifier and regressor classes to rename column names when the input is a pd.DataFrame in case it has column names that contain symbols ([, ], <) that XGBoost cannot natively handle. Arguments: X (pd.DataFrame): the input training data of shape [n_samples, n_features] Returns: Transformed X where column names are renamed to numerical values """ X_t = X if isinstance(X, np.ndarray): return pd.DataFrame(X) if isinstance(X, ww.DataTable): X_t = X.to_dataframe() logical_types = X.logical_types name_to_col_num = dict((col, col_num) for col_num, col in enumerate(list(X.columns))) X_renamed = X_t.rename(columns=name_to_col_num, inplace=False) if isinstance(X, ww.DataTable): renamed_logical_types = dict((name_to_col_num[col], logical_types[col]) for col in logical_types) return ww.DataTable(X_renamed, logical_types=renamed_logical_types) return X_renamed def jupyter_check(): """Get whether or not the code is being run in a Ipython environment (such as Jupyter Notebook or Jupyter Lab) Arguments: None Returns: Boolean: True if Ipython, False otherwise """ try: ipy = import_or_raise("IPython") return ipy.core.getipython.get_ipython() except Exception: return False def safe_repr(value): """Convert the given value into a string that can safely be used for repr Arguments: value: the item to convert Returns: String representation of the value """ if isinstance(value, float): if pd.isna(value): return 'np.nan' if np.isinf(value): return f"float('{repr(value)}')" return repr(value) def is_all_numeric(df): """Checks if the given DataFrame contains only numeric values Arguments: df (DataFrame): The DataFrame to check datatypes of Returns: True if all the DataFrame columns are numeric and are not missing any values, False otherwise """ if df.isnull().any().any(): return False for dtype in df.dtypes: if dtype not in numeric_and_boolean_dtypes: return False return True
[docs]def infer_feature_types(data, feature_types=None): """Create a Woodwork structure from the given pandas or numpy input, with specified types for columns. If a column's type is not specified, it will be inferred by Woodwork. Arguments: data (pd.DataFrame): Input data to convert to a Woodwork data structure. feature_types (string, ww.logical_type obj, dict, optional): If data is a 2D structure, feature_types must be a dictionary mapping column names to the type of data represented in the column. If data is a 1D structure, then feature_types must be a Woodwork logical type or a string representing a Woodwork logical type ("Double", "Integer", "Boolean", "Categorical", "Datetime", "NaturalLanguage") Returns: A Woodwork data structure where the data type of each column was either specified or inferred. """ ww_data = _convert_to_woodwork_structure(data) if feature_types is not None: if len(ww_data.shape) == 1: ww_data = ww_data.set_logical_type(feature_types) else: ww_data = ww_data.set_types(logical_types=feature_types) return ww_data
def _convert_to_woodwork_structure(data): """ Takes input data structure, and if it is not a Woodwork data structure already, will convert it to a Woodwork DataTable or DataColumn structure. """ ww_data = data if isinstance(data, ww.DataTable) or isinstance(data, ww.DataColumn): return ww_data if isinstance(data, list): ww_data = np.array(data) ww_data = ww_data.copy() if len(ww_data.shape) == 1: return ww.DataColumn(ww_data) return ww.DataTable(ww_data) def _convert_woodwork_types_wrapper(pd_data): """ Converts a pandas data structure that may have extension or nullable dtypes to dtypes that numpy can understand and handle. Arguments: pd_data (pd.Series, pd.DataFrame, pd.ExtensionArray): Pandas data structure Returns: Modified pandas data structure (pd.DataFrame or pd.Series) with original data and dtypes that can be handled by numpy """ nullable_to_numpy_mapping = {pd.Int64Dtype: 'int64', pd.BooleanDtype: 'bool', pd.StringDtype: 'object'} nullable_to_numpy_mapping_nan = {pd.Int64Dtype: 'float64', pd.BooleanDtype: 'object', pd.StringDtype: 'object'} if isinstance(pd_data, pd.api.extensions.ExtensionArray): if pd.isna(pd_data).any(): return pd.Series(pd_data.to_numpy(na_value=np.nan), dtype=nullable_to_numpy_mapping_nan[type(pd_data.dtype)]) return pd.Series(pd_data.to_numpy(na_value=np.nan), dtype=nullable_to_numpy_mapping[type(pd_data.dtype)]) if (isinstance(pd_data, pd.Series) and type(pd_data.dtype) in nullable_to_numpy_mapping): if pd.isna(pd_data).any(): return pd.Series(pd_data.to_numpy(na_value=np.nan), dtype=nullable_to_numpy_mapping_nan[type(pd_data.dtype)], index=pd_data.index) return pd.Series(pd_data.to_numpy(na_value=np.nan), dtype=nullable_to_numpy_mapping[type(pd_data.dtype)], index=pd_data.index) if isinstance(pd_data, pd.DataFrame): for col_name, col in pd_data.iteritems(): if type(col.dtype) in nullable_to_numpy_mapping: if pd.isna(pd_data[col_name]).any(): pd_data[col_name] = pd.Series(pd_data[col_name].to_numpy(na_value=np.nan), dtype=nullable_to_numpy_mapping_nan[type(pd_data[col_name].dtype)]) else: pd_data[col_name] = pd_data[col_name].astype(nullable_to_numpy_mapping[type(col.dtype)]) return pd_data
[docs]def pad_with_nans(pd_data, num_to_pad): """Pad the beginning num_to_pad rows with nans. Arguments: pd_data (pd.DataFrame or pd.Series): Data to pad. Returns: pd.DataFrame or pd.Series """ if isinstance(pd_data, pd.Series): padding = pd.Series([np.nan] * num_to_pad) else: padding = pd.DataFrame({col: [np.nan] * num_to_pad for col in pd_data.columns}) padded = pd.concat([padding, pd_data], ignore_index=True) # By default, pd.concat will convert all types to object if there are mixed numerics and objects # The call to convert_dtypes ensures numerics stay numerics in the new dataframe. return padded.convert_dtypes(infer_objects=True, convert_string=False, convert_integer=False, convert_boolean=False)
def _get_rows_without_nans(*data): """Compute a boolean array marking where all entries in the data are non-nan. Arguments: *data (sequence of pd.Series or pd.DataFrame) Returns: np.ndarray: mask where each entry is True if and only if all corresponding entries in that index in data are non-nan. """ def _not_nan(pd_data): if pd_data is None: return np.array([True]) if isinstance(pd_data, pd.Series): return ~pd_data.isna().values elif isinstance(pd_data, pd.DataFrame): return ~pd_data.isna().any(axis=1).values else: return pd_data mask = reduce(lambda a, b: np.logical_and(_not_nan(a), _not_nan(b)), data) return mask
[docs]def drop_rows_with_nans(pd_data_1, pd_data_2): """Drop rows that have any NaNs in both pd_data_1 and pd_data_2. Arguments: pd_data_1 (pd.DataFrame or pd.Series): Data to subset. pd_data_2 (pd.DataFrame or pd.Series): Data to subset. Returns: tuple of pd.DataFrame or pd.Series """ mask = _get_rows_without_nans(pd_data_1, pd_data_2) return pd_data_1.iloc[mask], pd_data_2.iloc[mask]
def _file_path_check(filepath=None, format='png', interactive=False, is_plotly=False): """ Helper function to check the filepath being passed. Arguments: filepath (str or Path, optional): Location to save file. format (str): Extension for figure to be saved as. Defaults to 'png'. interactive (bool, optional): If True and fig is of type plotly.Figure, sets the format to 'html'. is_plotly (bool, optional): Check to see if the fig being passed is of type plotly.Figure. Returns: String representing the final filepath the image will be saved to. """ if filepath: filepath = str(filepath) path_and_name, extension = os.path.splitext(filepath) extension = extension[1:].lower() if extension else None if is_plotly and interactive: format_ = 'html' elif not extension and not interactive: format_ = format else: format_ = extension filepath = f'{path_and_name}.{format_}' try: f = open(filepath, 'w') f.close() except (IOError, FileNotFoundError): raise ValueError(('Specified filepath is not writeable: {}'.format(filepath))) return filepath def save_plot(fig, filepath=None, format='png', interactive=False, return_filepath=False): """Saves fig to filepath if specified, or to a default location if not. Arguments: fig (Figure): Figure to be saved. filepath (str or Path, optional): Location to save file. Default is with filename "test_plot". format (str): Extension for figure to be saved as. Ignored if interactive is True and fig is of type plotly.Figure. Defaults to 'png'. interactive (bool, optional): If True and fig is of type plotly.Figure, saves the fig as interactive instead of static, and format will be set to 'html'. Defaults to False. return_filepath (bool, optional): Whether to return the final filepath the image is saved to. Defaults to False. Returns: String representing the final filepath the image was saved to if return_filepath is set to True. Defaults to None. """ plotly_ = import_or_raise("plotly", error_msg="Cannot find dependency plotly") graphviz_ = import_or_raise('graphviz', error_msg='Please install graphviz to visualize trees.') matplotlib = import_or_raise("matplotlib", error_msg="Cannot find dependency matplotlib") plt_ = matplotlib.pyplot axes_ = matplotlib.axes is_plotly = False is_graphviz = False is_plt = False is_seaborn = False format = format if format else 'png' if isinstance(fig, plotly_.graph_objects.Figure): is_plotly = True elif isinstance(fig, graphviz_.Source): is_graphviz = True elif isinstance(fig, plt_.Figure): is_plt = True elif isinstance(fig, axes_.SubplotBase): is_seaborn = True if not filepath: extension = 'html' if interactive and is_plotly else format filepath = os.path.join(os.getcwd(), f'test_plot.{extension}') filepath = _file_path_check(filepath, format=format, interactive=interactive, is_plotly=is_plotly) if is_plotly and interactive: fig.write_html(file=filepath) elif is_plotly and not interactive: fig.write_image(file=filepath, engine="kaleido") elif is_graphviz: filepath_, format_ = os.path.splitext(filepath) fig.format = 'png' filepath = f'{filepath_}.png' fig.render(filename=filepath_, view=False, cleanup=True) elif is_plt: fig.savefig(fname=filepath) elif is_seaborn: fig = fig.figure fig.savefig(fname=filepath) if return_filepath: return filepath