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import contextlib
from datetime import datetime
import pandas as pd
import numpy as np
from scipy import sparse
from sklearn.base import BaseEstimator, TransformerMixin
from .cross_validation import DataWrapper
from .pipeline import make_transformer_pipeline, _call_fit, TransformerPipeline
from . import logger
string_types = text_type = str
def _handle_feature(fea):
"""
Convert 1-dimensional arrays to 2-dimensional column vectors.
"""
if len(fea.shape) == 1:
fea = np.array([fea]).T
return fea
def _build_transformer(transformers):
if isinstance(transformers, list):
transformers = make_transformer_pipeline(*transformers)
return transformers
def _build_feature(columns, transformers, options={}, X=None):
if X is None:
return (columns, _build_transformer(transformers), options)
return (
columns(X) if callable(columns) else columns,
_build_transformer(transformers),
options
)
def _elapsed_secs(t1):
return (datetime.now()-t1).total_seconds()
def _get_feature_names(estimator):
"""
Attempt to extract feature names based on a given estimator
"""
if hasattr(estimator, 'classes_'):
return estimator.classes_
elif hasattr(estimator, 'get_feature_names'):
return estimator.get_feature_names()
return None
@contextlib.contextmanager
def add_column_names_to_exception(column_names):
# Stolen from https://stackoverflow.com/a/17677938/356729
try:
yield
except Exception as ex:
if ex.args:
msg = u'{}: {}'.format(column_names, ex.args[0])
else:
msg = text_type(column_names)
ex.args = (msg,) + ex.args[1:]
raise
class DataFrameMapper(BaseEstimator, TransformerMixin):
"""
Map Pandas data frame column subsets to their own
sklearn transformation.
"""
def __init__(self, features, default=False, sparse=False, df_out=False,
input_df=False, drop_cols=None):
"""
Params:
features a list of tuples with features definitions.
The first element is the pandas column selector. This can
be a string (for one column) or a list of strings.
The second element is an object that supports
sklearn's transform interface, or a list of such objects
The third element is optional and, if present, must be
a dictionary with the options to apply to the
transformation. Example: {'alias': 'day_of_week'}
default default transformer to apply to the columns not
explicitly selected in the mapper. If False (default),
discard them. If None, pass them through untouched. Any
other transformer will be applied to all the unselected
columns as a whole, taken as a 2d-array.
sparse will return sparse matrix if set True and any of the
extracted features is sparse. Defaults to False.
df_out return a pandas data frame, with each column named using
the pandas column that created it (if there's only one
input and output) or the input columns joined with '_'
if there's multiple inputs, and the name concatenated with
'_1', '_2' etc if there's multiple outputs. NB: does not
work if *default* or *sparse* are true
input_df If ``True`` pass the selected columns to the transformers
as a pandas DataFrame or Series. Otherwise pass them as a
numpy array. Defaults to ``False``.
drop_cols List of columns to be dropped. Defaults to None.
"""
self.features = features
self.default = default
self.built_default = None
self.sparse = sparse
self.df_out = df_out
self.input_df = input_df
self.drop_cols = [] if drop_cols is None else drop_cols
self.transformed_names_ = []
if (df_out and (sparse or default)):
raise ValueError("Can not use df_out with sparse or default")
def _build(self, X=None):
"""
Build attributes built_features and built_default.
"""
if isinstance(self.features, list):
self.built_features = [
_build_feature(*f, X=X) for f in self.features
]
else:
self.built_features = _build_feature(*self.features, X=X)
self.built_default = _build_transformer(self.default)
@property
def _selected_columns(self):
"""
Return a set of selected columns in the feature list.
"""
selected_columns = set()
for feature in self.features:
columns = feature[0]
if isinstance(columns, list):
selected_columns = selected_columns.union(set(columns))
else:
selected_columns.add(columns)
return selected_columns
def _unselected_columns(self, X):
"""
Return list of columns present in X and not selected explicitly in the
mapper.
Unselected columns are returned in the order they appear in the
dataframe to avoid issues with different ordering during default fit
and transform steps.
"""
X_columns = list(X.columns)
return [column for column in X_columns if
column not in self._selected_columns
and column not in self.drop_cols]
def __setstate__(self, state):
# compatibility for older versions of sklearn-pandas
super().__setstate__(state)
self.features = [_build_feature(*feat) for feat in state['features']]
self.sparse = state.get('sparse', False)
self.default = state.get('default', False)
self.df_out = state.get('df_out', False)
self.input_df = state.get('input_df', False)
self.drop_cols = state.get('drop_cols', [])
self.built_features = state.get('built_features', self.features)
self.built_default = state.get('built_default', self.default)
self.transformed_names_ = state.get('transformed_names_', [])
def __getstate__(self):
state = super().__getstate__()
state['features'] = self.features
state['sparse'] = self.sparse
state['default'] = self.default
state['df_out'] = self.df_out
state['input_df'] = self.input_df
state['drop_cols'] = self.drop_cols
state['build_features'] = getattr(self, 'built_features', None)
state['built_default'] = self.built_default
state['transformed_names_'] = self.transformed_names_
return state
def _get_col_subset(self, X, cols, input_df=False):
"""
Get a subset of columns from the given table X.
X a Pandas dataframe; the table to select columns from
cols a string or list of strings representing the columns to select.
It can also be a callable that returns True or False, i.e.
compatible with the built-in filter function.
Returns a numpy array with the data from the selected columns
"""
if isinstance(cols, string_types):
return_vector = True
cols = [cols]
else:
return_vector = False
# Needed when using the cross-validation compatibility
# layer for sklearn<0.16.0.
# Will be dropped on sklearn-pandas 2.0.
if isinstance(X, list):
X = [x[cols] for x in X]
X = pd.DataFrame(X)
elif isinstance(X, DataWrapper):
X = X.df # fetch underlying data
if return_vector:
t = X[cols[0]]
else:
t = X[cols]
# return either a DataFrame/Series or a numpy array
if input_df:
return t
else:
return t.values
def fit(self, X, y=None):
"""
Fit a transformation from the pipeline
X the data to fit
y the target vector relative to X, optional
"""
self._build(X=X)
for columns, transformers, options in self.built_features:
t1 = datetime.now()
input_df = options.get('input_df', self.input_df)
if transformers is not None:
with add_column_names_to_exception(columns):
Xt = self._get_col_subset(X, columns, input_df)
_call_fit(transformers.fit, Xt, y)
logger.info(f"[FIT] {columns}: {_elapsed_secs(t1)} secs")
# handle features not explicitly selected
if self.built_default: # not False and not None
unsel_cols = self._unselected_columns(X)
with add_column_names_to_exception(unsel_cols):
Xt = self._get_col_subset(X, unsel_cols, self.input_df)
_call_fit(self.built_default.fit, Xt, y)
return self
def get_names(self, columns, transformer, x, alias=None, prefix='',
suffix=''):
"""
Return verbose names for the transformed columns.
columns name (or list of names) of the original column(s)
transformer transformer - can be a TransformerPipeline
x transformed columns (numpy.ndarray)
alias base name to use for the selected columns
"""
if alias is not None:
name = alias
elif isinstance(columns, list):
name = '_'.join(map(str, columns))
else:
name = columns
num_cols = x.shape[1] if len(x.shape) > 1 else 1
output = []
if num_cols > 1:
# If there are as many columns as classes in the transformer,
# infer column names from classes names.
# If we are dealing with multiple transformers for these columns
# attempt to extract the names from each of them, starting from the
# last one
if isinstance(transformer, TransformerPipeline):
inverse_steps = transformer.steps[::-1]
estimators = (estimator for name, estimator in inverse_steps)
names_steps = (_get_feature_names(e) for e in estimators)
names = next((n for n in names_steps if n is not None), None)
# Otherwise use the only estimator present
else:
names = _get_feature_names(transformer)
if names is not None and len(names) == num_cols:
output = [f"{name}_{o}" for o in names]
# otherwise, return name concatenated with '_1', '_2', etc.
else:
output = [name + '_' + str(o) for o in range(num_cols)]
else:
output = [name]
if prefix == suffix == "":
return output
return ['{}{}{}'.format(prefix, x, suffix) for x in output]
def get_dtypes(self, extracted):
dtypes_features = [self.get_dtype(ex) for ex in extracted]
return [dtype for dtype_feature in dtypes_features
for dtype in dtype_feature]
def get_dtype(self, ex):
if isinstance(ex, np.ndarray) or sparse.issparse(ex):
return [ex.dtype] * ex.shape[1]
elif isinstance(ex, pd.DataFrame):
return list(ex.dtypes)
else:
raise TypeError(type(ex))
def _transform(self, X, y=None, do_fit=False):
"""
Transform the given data with possibility to fit in advance.
Avoids code duplication for implementation of transform and
fit_transform.
"""
if do_fit:
self._build(X=X)
extracted = []
transformed_names_ = []
for columns, transformers, options in self.built_features:
input_df = options.get('input_df', self.input_df)
# columns could be a string or list of
# strings; we don't care because pandas
# will handle either.
Xt = self._get_col_subset(X, columns, input_df)
if transformers is not None:
with add_column_names_to_exception(columns):
if do_fit and hasattr(transformers, 'fit_transform'):
t1 = datetime.now()
Xt = _call_fit(transformers.fit_transform, Xt, y)
logger.info(f"[FIT_TRANSFORM] {columns}: {_elapsed_secs(t1)} secs") # NOQA
else:
if do_fit:
t1 = datetime.now()
_call_fit(transformers.fit, Xt, y)
logger.info(
f"[FIT] {columns}: {_elapsed_secs(t1)} secs")
t1 = datetime.now()
Xt = transformers.transform(Xt)
logger.info(f"[TRANSFORM] {columns}: {_elapsed_secs(t1)} secs") # NOQA
extracted.append(_handle_feature(Xt))
alias = options.get('alias')
prefix = options.get('prefix', '')
suffix = options.get('suffix', '')
transformed_names_ += self.get_names(
columns, transformers, Xt, alias, prefix, suffix)
# handle features not explicitly selected
if self.built_default is not False:
unsel_cols = self._unselected_columns(X)
Xt = self._get_col_subset(X, unsel_cols, self.input_df)
if self.built_default is not None:
with add_column_names_to_exception(unsel_cols):
if do_fit and hasattr(self.built_default, 'fit_transform'):
Xt = _call_fit(self.built_default.fit_transform, Xt, y)
else:
if do_fit:
_call_fit(self.built_default.fit, Xt, y)
Xt = self.built_default.transform(Xt)
transformed_names_ += self.get_names(
unsel_cols, self.built_default, Xt)
else:
# if not applying a default transformer,
# keep column names unmodified
transformed_names_ += unsel_cols
extracted.append(_handle_feature(Xt))
self.transformed_names_ = transformed_names_
# combine the feature outputs into one array.
# at this point we lose track of which features
# were created from which input columns, so it's
# assumed that that doesn't matter to the model.
# If any of the extracted features is sparse, combine sparsely.
# Otherwise, combine as normal arrays.
if any(sparse.issparse(fea) for fea in extracted):
stacked = sparse.hstack(extracted).tocsr()
# return a sparse matrix only if the mapper was initialized
# with sparse=True
if not self.sparse:
stacked = stacked.toarray()
else:
stacked = np.hstack(extracted)
if self.df_out:
# if no rows were dropped preserve the original index,
# otherwise use a new integer one
no_rows_dropped = len(X) == len(stacked)
if no_rows_dropped:
index = X.index
else:
index = None
# output different data types, if appropriate
dtypes = self.get_dtypes(extracted)
df_out = pd.DataFrame(
stacked,
columns=self.transformed_names_,
index=index)
# preserve types
for col, dtype in zip(self.transformed_names_, dtypes):
df_out[col] = df_out[col].astype(dtype)
return df_out
else:
return stacked
def transform(self, X):
"""
Transform the given data. Assumes that fit has already been called.
X the data to transform
"""
return self._transform(X)
def fit_transform(self, X, y=None):
"""
Fit a transformation from the pipeline and directly apply
it to the given data.
X the data to fit
y the target vector relative to X, optional
"""
return self._transform(X, y, True)
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