tods/feature_analysis/StatisticalAbsSum.py

import os
from typing import Any,Optional,List
import statsmodels.api as sm
import numpy as np
from d3m import container, utils as d3m_utils
from d3m import utils

from numpy import ndarray
from collections import OrderedDict
from scipy import sparse
import os

import numpy
import typing
import time

from d3m import container
from d3m.primitive_interfaces import base, transformer

from d3m.container import DataFrame as d3m_dataframe
from d3m.metadata import hyperparams, params, base as metadata_base

from d3m.base import utils as base_utils
from d3m.exceptions import PrimitiveNotFittedError

__all__ = ('StatisticalAbsSumPrimitive',)

Inputs = container.DataFrame
Outputs = container.DataFrame

class Params(params.Params):
       #to-do : how to make params dynamic
       use_column_names: Optional[Any]



class Hyperparams(hyperparams.Hyperparams):

       #Tuning Parameter
       #default -1 considers entire time series is considered
       window_size = hyperparams.Hyperparameter(default=-1, semantic_types=[
           'https://metadata.datadrivendiscovery.org/types/TuningParameter',
       ], description="Window Size for decomposition")
       #control parameter
       use_columns = hyperparams.Set(
           elements=hyperparams.Hyperparameter[int](-1),
           default=(),
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter'],
           description="A set of column indices to force primitive to operate on. If any specified column cannot be parsed, it is skipped.",
       )
       exclude_columns = hyperparams.Set(
           elements=hyperparams.Hyperparameter[int](-1),
           default=(),
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter'],
           description="A set of column indices to not operate on. Applicable only if \"use_columns\" is not provided.",
       )
       return_result = hyperparams.Enumeration(
           values=['append', 'replace', 'new'],
           default='append',
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter'],
           description="Should parsed columns be appended, should they replace original columns, or should only parsed columns be returned? This hyperparam is ignored if use_semantic_types is set to false.",
       )
       use_semantic_types = hyperparams.UniformBool(
           default=False,
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter'],
           description="Controls whether semantic_types metadata will be used for filtering columns in input dataframe. Setting this to false makes the code ignore return_result and will produce only the output dataframe"
       )
       add_index_columns = hyperparams.UniformBool(
           default=False,
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter'],
           description="Also include primary index columns if input data has them. Applicable only if \"return_result\" is set to \"new\".",
       )
       error_on_no_input = hyperparams.UniformBool(
           default=True,
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter'],
           description="Throw an exception if no input column is selected/provided. Defaults to true to behave like sklearn. To prevent pipelines from breaking set this to False.",
       )

       return_semantic_type = hyperparams.Enumeration[str](
           values=['https://metadata.datadrivendiscovery.org/types/Attribute',
                   'https://metadata.datadrivendiscovery.org/types/ConstructedAttribute'],
           default='https://metadata.datadrivendiscovery.org/types/Attribute',
           description='Decides what semantic type to attach to generated attributes',
           semantic_types=['https://metadata.datadrivendiscovery.org/types/ControlParameter']
       )



class StatisticalAbsSumPrimitive(transformer.TransformerPrimitiveBase[Inputs, Outputs, Hyperparams]):
    """
    Primitive to find abs_sum of time series
    """
    __author__ = "DATA Lab at Texas A&M University",
    metadata = metadata_base.PrimitiveMetadata(
        {
            'id': 'fbc10e6f-d75b-4815-b4c8-5ad4f2f577db',
            'version': '0.1.0',
            'name': 'Time Series Absolute Sum',
            'python_path': 'd3m.primitives.tods.feature_analysis.statistical_abs_sum',
            'keywords': ['Time Series','AbsSum'],
            "hyperparams_to_tune": ['window_size'],
            'source': {
                'name': 'DATA Lab at Texas A&M University',
                'uris': ['https://gitlab.com/lhenry15/tods.git','https://gitlab.com/lhenry15/tods/-/blob/devesh/tods/feature_analysis/StatisticalAbsSum.py'],
                'contact': 'mailto:khlai037@tamu.edu'

            },
            'installation': [
                {'type': metadata_base.PrimitiveInstallationType.PIP,
                 'package_uri': 'git+https://gitlab.com/lhenry15/tods.git@{git_commit}#egg=TODS'.format(
                     git_commit=d3m_utils.current_git_commit(os.path.dirname(__file__)),
                 ),
                 }

            ],
            'algorithm_types': [
                metadata_base.PrimitiveAlgorithmType.DATA_PROFILING,
            ],
            'primitive_family': metadata_base.PrimitiveFamily.FEATURE_CONSTRUCTION,

        }
    )

    def produce(self, *, inputs: Inputs, timeout: float = None, iterations: int = None) -> base.CallResult[Outputs]:
        """

        Args:
            inputs: Container DataFrame
            timeout: Default
            iterations: Default

        Returns:
            Container DataFrame containing abs_sum of  time series
        """
        self.logger.info('Statistical AbsSum  Primitive called')

        # Get cols to fit.
        self._fitted = False
        self._training_inputs, self._training_indices = self._get_columns_to_fit(inputs, self.hyperparams)
        self._input_column_names = self._training_inputs.columns

        if len(self._training_indices) > 0:
            # self._clf.fit(self._training_inputs)
            self._fitted = True
        else:
            if self.hyperparams['error_on_no_input']:
                raise RuntimeError("No input columns were selected")
            self.logger.warn("No input columns were selected")

        if not self._fitted:
            raise PrimitiveNotFittedError("Primitive not fitted.")
        statistical_abs_sum_input = inputs
        if self.hyperparams['use_semantic_types']:
            statistical_abs_sum_input = inputs.iloc[:, self._training_indices]
        output_columns = []
        if len(self._training_indices) > 0:
            statistical_abs_sum_output = self._abs_sum(statistical_abs_sum_input,self.hyperparams["window_size"])

            if sparse.issparse(statistical_abs_sum_output):
                statistical_abs_sum_output = statistical_abs_sum_output.toarray()
            outputs = self._wrap_predictions(inputs, statistical_abs_sum_output)

            #if len(outputs.columns) == len(self._input_column_names):
               # outputs.columns = self._input_column_names

            output_columns = [outputs]


        else:
            if self.hyperparams['error_on_no_input']:
                raise RuntimeError("No input columns were selected")
            self.logger.warn("No input columns were selected")
        outputs = base_utils.combine_columns(return_result=self.hyperparams['return_result'],
                                             add_index_columns=self.hyperparams['add_index_columns'],
                                             inputs=inputs, column_indices=self._training_indices,
                                             columns_list=output_columns)

        self.logger.info('Statistical AbsSum  Primitive returned')

        return base.CallResult(outputs)

    @classmethod
    def _get_columns_to_fit(cls, inputs: Inputs, hyperparams: Hyperparams):
        """
        Select columns to fit.
        Args:
            inputs: Container DataFrame
            hyperparams: d3m.metadata.hyperparams.Hyperparams

        Returns:
            list
        """
        if not hyperparams['use_semantic_types']:
            return inputs, list(range(len(inputs.columns)))

        inputs_metadata = inputs.metadata

        def can_produce_column(column_index: int) -> bool:
            return cls._can_produce_column(inputs_metadata, column_index, hyperparams)

        use_columns = hyperparams['use_columns']
        exclude_columns = hyperparams['exclude_columns']

        columns_to_produce, columns_not_to_produce = base_utils.get_columns_to_use(inputs_metadata,
                                                                                   use_columns=use_columns,
                                                                                   exclude_columns=exclude_columns,
                                                                                   can_use_column=can_produce_column)
        return inputs.iloc[:, columns_to_produce], columns_to_produce
        # return columns_to_produce

    @classmethod
    def _can_produce_column(cls, inputs_metadata: metadata_base.DataMetadata, column_index: int,
                            hyperparams: Hyperparams) -> bool:
        """
        Output whether a column can be processed.
        Args:
            inputs_metadata: d3m.metadata.base.DataMetadata
            column_index: int

        Returns:
            bool
        """
        column_metadata = inputs_metadata.query((metadata_base.ALL_ELEMENTS, column_index))

        accepted_structural_types = (int, float, numpy.integer, numpy.float64)
        accepted_semantic_types = set()
        accepted_semantic_types.add("https://metadata.datadrivendiscovery.org/types/Attribute")
        if not issubclass(column_metadata['structural_type'], accepted_structural_types):
            return False

        semantic_types = set(column_metadata.get('semantic_types', []))
        return True
        if len(semantic_types) == 0:
            cls.logger.warning("No semantic types found in column metadata")
            return False

        # Making sure all accepted_semantic_types are available in semantic_types
        if len(accepted_semantic_types - semantic_types) == 0:
            return True

        return False

    @classmethod
    def _update_predictions_metadata(cls, inputs_metadata: metadata_base.DataMetadata, outputs: Optional[Outputs],
                                     target_columns_metadata: List[OrderedDict]) -> metadata_base.DataMetadata:
        """
        Updata metadata for selected columns.
        Args:
            inputs_metadata: metadata_base.DataMetadata
            outputs: Container Dataframe
            target_columns_metadata: list

        Returns:
            d3m.metadata.base.DataMetadata
        """
        outputs_metadata = metadata_base.DataMetadata().generate(value=outputs)

        for column_index, column_metadata in enumerate(target_columns_metadata):
            column_metadata.pop("structural_type", None)
            outputs_metadata = outputs_metadata.update_column(column_index, column_metadata)

        return outputs_metadata

    def _wrap_predictions(self, inputs: Inputs, predictions: ndarray) -> Outputs:
        """
        Wrap predictions into dataframe
        Args:
            inputs: Container Dataframe
            predictions: array-like data (n_samples, n_features)

        Returns:
            Dataframe
        """
        outputs = d3m_dataframe(predictions, generate_metadata=True)
        target_columns_metadata = self._add_target_columns_metadata(outputs.metadata, self.hyperparams)
        outputs.metadata = self._update_predictions_metadata(inputs.metadata, outputs, target_columns_metadata)

        return outputs

    @classmethod
    def _add_target_columns_metadata(cls, outputs_metadata: metadata_base.DataMetadata, hyperparams):
        """
        Add target columns metadata
        Args:
            outputs_metadata: metadata.base.DataMetadata
            hyperparams: d3m.metadata.hyperparams.Hyperparams

        Returns:
            List[OrderedDict]
        """
        outputs_length = outputs_metadata.query((metadata_base.ALL_ELEMENTS,))['dimension']['length']
        target_columns_metadata: List[OrderedDict] = []
        for column_index in range(outputs_length):
            # column_name = "output_{}".format(column_index)
            column_metadata = OrderedDict()
            semantic_types = set()
            semantic_types.add(hyperparams["return_semantic_type"])
            column_metadata['semantic_types'] = list(semantic_types)

            # column_metadata["name"] = str(column_name)
            target_columns_metadata.append(column_metadata)

        return target_columns_metadata

    def _write(self, inputs: Inputs):
        inputs.to_csv(str(time.time()) + '.csv')


    def _abs_sum(self,X,window_size):
        """ statistical abs_sum of time series sequence
           Args:
            X : DataFrame
               Time series.
        Returns:
            DataFrame
            A object with abs_sum
        """
        if(window_size==-1):
            window_size = len(X)
        transformed_X = utils.pandas.DataFrame()
        for column in X.columns:
            column_value = X[column].values
            column_abs_sum = np.zeros(len(column_value))
            for iter in range(window_size-1,len(column_value)):
                sequence = column_value[iter-window_size+1:iter+1]
                column_abs_sum[iter] = np.sum(np.abs(sequence))
            column_abs_sum[:window_size-1] = column_abs_sum[window_size-1]
            transformed_X[column + "_abs_sum"] = column_abs_sum

        return transformed_X