Source code for apache_beam.ml.inference.sklearn_inference

#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements.  See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License.  You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

import enum
import pickle
import sys
from typing import Any
from typing import Callable
from typing import Dict
from typing import Iterable
from typing import Optional
from typing import Sequence

import numpy
import pandas
from sklearn.base import BaseEstimator

from apache_beam.io.filesystems import FileSystems
from apache_beam.ml.inference import utils
from apache_beam.ml.inference.base import ModelHandler
from apache_beam.ml.inference.base import PredictionResult

try:
  import joblib
except ImportError:
  # joblib is an optional dependency.
  pass

__all__ = [
    'SklearnModelHandlerNumpy',
    'SklearnModelHandlerPandas',
]

NumpyInferenceFn = Callable[
    [BaseEstimator, Sequence[numpy.ndarray], Optional[Dict[str, Any]]], Any]


class ModelFileType(enum.Enum):
  """Defines how a model file is serialized. Options are pickle or joblib."""
  PICKLE = 1
  JOBLIB = 2


def _load_model(model_uri, file_type):
  file = FileSystems.open(model_uri, 'rb')
  if file_type == ModelFileType.PICKLE:
    return pickle.load(file)
  elif file_type == ModelFileType.JOBLIB:
    if not joblib:
      raise ImportError(
          'Could not import joblib in this execution environment. '
          'For help with managing dependencies on Python workers.'
          'see https://beam.apache.org/documentation/sdks/python-pipeline-dependencies/'  # pylint: disable=line-too-long
      )
    return joblib.load(file)
  raise AssertionError('Unsupported serialization type.')


def _default_numpy_inference_fn(
    model: BaseEstimator,
    batch: Sequence[numpy.ndarray],
    inference_args: Optional[Dict[str, Any]] = None) -> Any:
  # vectorize data for better performance
  vectorized_batch = numpy.stack(batch, axis=0)
  return model.predict(vectorized_batch)


[docs]class SklearnModelHandlerNumpy(ModelHandler[numpy.ndarray, PredictionResult, BaseEstimator]): def __init__( self, model_uri: str, model_file_type: ModelFileType = ModelFileType.PICKLE, *, inference_fn: NumpyInferenceFn = _default_numpy_inference_fn, min_batch_size: Optional[int] = None, max_batch_size: Optional[int] = None, large_model: bool = False, **kwargs): """ Implementation of the ModelHandler interface for scikit-learn using numpy arrays as input. Example Usage:: pcoll | RunInference(SklearnModelHandlerNumpy(model_uri="my_uri")) Args: model_uri: The URI to where the model is saved. model_file_type: The method of serialization of the argument. default=pickle inference_fn: The inference function to use. default=_default_numpy_inference_fn min_batch_size: the minimum batch size to use when batching inputs. This batch will be fed into the inference_fn as a Sequence of Numpy ndarrays. max_batch_size: the maximum batch size to use when batching inputs. This batch will be fed into the inference_fn as a Sequence of Numpy ndarrays. large_model: set to true if your model is large enough to run into memory pressure if you load multiple copies. Given a model that consumes N memory and a machine with W cores and M memory, you should set this to True if N*W > M. kwargs: 'env_vars' can be used to set environment variables before loading the model. """ self._model_uri = model_uri self._model_file_type = model_file_type self._model_inference_fn = inference_fn self._batching_kwargs = {} if min_batch_size is not None: self._batching_kwargs['min_batch_size'] = min_batch_size if max_batch_size is not None: self._batching_kwargs['max_batch_size'] = max_batch_size self._env_vars = kwargs.get('env_vars', {}) self._large_model = large_model
[docs] def load_model(self) -> BaseEstimator: """Loads and initializes a model for processing.""" return _load_model(self._model_uri, self._model_file_type)
[docs] def update_model_path(self, model_path: Optional[str] = None): self._model_uri = model_path if model_path else self._model_uri
[docs] def run_inference( self, batch: Sequence[numpy.ndarray], model: BaseEstimator, inference_args: Optional[Dict[str, Any]] = None ) -> Iterable[PredictionResult]: """Runs inferences on a batch of numpy arrays. Args: batch: A sequence of examples as numpy arrays. They should be single examples. model: A numpy model or pipeline. Must implement predict(X). Where the parameter X is a numpy array. inference_args: Any additional arguments for an inference. Returns: An Iterable of type PredictionResult. """ predictions = self._model_inference_fn( model, batch, inference_args, ) return utils._convert_to_result( batch, predictions, model_id=self._model_uri)
[docs] def get_num_bytes(self, batch: Sequence[numpy.ndarray]) -> int: """ Returns: The number of bytes of data for a batch. """ return sum(sys.getsizeof(element) for element in batch)
[docs] def get_metrics_namespace(self) -> str: """ Returns: A namespace for metrics collected by the RunInference transform. """ return 'BeamML_Sklearn'
[docs] def batch_elements_kwargs(self): return self._batching_kwargs
[docs] def share_model_across_processes(self) -> bool: return self._large_model
PandasInferenceFn = Callable[ [BaseEstimator, Sequence[pandas.DataFrame], Optional[Dict[str, Any]]], Any] def _default_pandas_inference_fn( model: BaseEstimator, batch: Sequence[pandas.DataFrame], inference_args: Optional[Dict[str, Any]] = None) -> Any: # vectorize data for better performance vectorized_batch = pandas.concat(batch, axis=0) predictions = model.predict(vectorized_batch) splits = [ vectorized_batch.iloc[[i]] for i in range(vectorized_batch.shape[0]) ] return predictions, splits
[docs]class SklearnModelHandlerPandas(ModelHandler[pandas.DataFrame, PredictionResult, BaseEstimator]): def __init__( self, model_uri: str, model_file_type: ModelFileType = ModelFileType.PICKLE, *, inference_fn: PandasInferenceFn = _default_pandas_inference_fn, min_batch_size: Optional[int] = None, max_batch_size: Optional[int] = None, large_model: bool = False, **kwargs): """Implementation of the ModelHandler interface for scikit-learn that supports pandas dataframes. Example Usage:: pcoll | RunInference(SklearnModelHandlerPandas(model_uri="my_uri")) **NOTE:** This API and its implementation are under development and do not provide backward compatibility guarantees. Args: model_uri: The URI to where the model is saved. model_file_type: The method of serialization of the argument. default=pickle inference_fn: The inference function to use. default=_default_pandas_inference_fn min_batch_size: the minimum batch size to use when batching inputs. This batch will be fed into the inference_fn as a Sequence of Pandas Dataframes. max_batch_size: the maximum batch size to use when batching inputs. This batch will be fed into the inference_fn as a Sequence of Pandas Dataframes. large_model: set to true if your model is large enough to run into memory pressure if you load multiple copies. Given a model that consumes N memory and a machine with W cores and M memory, you should set this to True if N*W > M. kwargs: 'env_vars' can be used to set environment variables before loading the model. """ self._model_uri = model_uri self._model_file_type = model_file_type self._model_inference_fn = inference_fn self._batching_kwargs = {} if min_batch_size is not None: self._batching_kwargs['min_batch_size'] = min_batch_size if max_batch_size is not None: self._batching_kwargs['max_batch_size'] = max_batch_size self._env_vars = kwargs.get('env_vars', {}) self._large_model = large_model
[docs] def load_model(self) -> BaseEstimator: """Loads and initializes a model for processing.""" return _load_model(self._model_uri, self._model_file_type)
[docs] def update_model_path(self, model_path: Optional[str] = None): self._model_uri = model_path if model_path else self._model_uri
[docs] def run_inference( self, batch: Sequence[pandas.DataFrame], model: BaseEstimator, inference_args: Optional[Dict[str, Any]] = None ) -> Iterable[PredictionResult]: """ Runs inferences on a batch of pandas dataframes. Args: batch: A sequence of examples as numpy arrays. They should be single examples. model: A dataframe model or pipeline. Must implement predict(X). Where the parameter X is a pandas dataframe. inference_args: Any additional arguments for an inference. Returns: An Iterable of type PredictionResult. """ # sklearn_inference currently only supports single rowed dataframes. for dataframe in iter(batch): if dataframe.shape[0] != 1: raise ValueError('Only dataframes with single rows are supported.') predictions, splits = self._model_inference_fn(model, batch, inference_args) return utils._convert_to_result( splits, predictions, model_id=self._model_uri)
[docs] def get_num_bytes(self, batch: Sequence[pandas.DataFrame]) -> int: """ Returns: The number of bytes of data for a batch. """ return sum(df.memory_usage(deep=True).sum() for df in batch)
[docs] def get_metrics_namespace(self) -> str: """ Returns: A namespace for metrics collected by the RunInference transform. """ return 'BeamML_Sklearn'
[docs] def batch_elements_kwargs(self): return self._batching_kwargs
[docs] def share_model_across_processes(self) -> bool: return self._large_model