EventStream.data.dataset_polars module¶

The polars implementation of the Dataset class.

EventStream.data.dataset_polars.INPUT_DF_T¶: The types of supported input dataframes, which includes paths, pandas dataframes, polars dataframes, or queries.

EventStream.data.dataset_polars.DF_T¶: The types of supported dataframes, which include polars lazyframes, dataframes, expressions, or series.

class EventStream.data.dataset_polars.Dataset(config: DatasetConfig, subjects_df: DF_T | None = None, events_df: DF_T | None = None, dynamic_measurements_df: DF_T | None = None, input_schema: DatasetSchema | None = None, **kwargs)[source]¶

The polars specific implementation of the dataset.

Parameters:¶

config: DatasetConfig¶: Configuration object for this dataset.
subjects_df: DF_T | None = None¶: The dataframe containing all static, subject-level data. If this is specified, events_df and dynamic_measurements_df should also be specified. Otherwise, this will be built from source via the extraction pipeline defined in input_schema.
events_df: DF_T | None = None¶: The dataframe containing all event timestamps, types, and subject IDs. If this is specified, subjects_df and dynamic_measurements_df should also be specified. Otherwise, this will be built from source via the extraction pipeline defined in input_schema.
dynamic_measurements_df: DF_T | None = None¶: The dataframe containing all time-varying measurement observations. If this is specified, subjects_df and events_df should also be specified. Otherwise, this will be built from source via the extraction pipeline defined in input_schema.
input_schema: DatasetSchema | None = None¶: The schema configuration object to define the extraction pipeline for pulling raw data from source and produce the subjects_df, events_df, dynamic_measurements_df input view.

property ESDS_schema : schema¶

METADATA_SCHEMA = {'censor_lower_bound': Float64, 'censor_upper_bound': Float64, 'drop_lower_bound': Float64, 'drop_lower_bound_inclusive': Boolean, 'drop_upper_bound': Float64, 'drop_upper_bound_inclusive': Boolean, 'mean': Float64, 'std': Float64, 'thresh_high': Float64, 'thresh_low': Float64, 'value_type': Categorical}¶: The Polars schema of the numerical measurement metadata dataframes which track fit parameters.

STREAMING = True¶: Execute any lazy query in streaming mode.

WRITE_USE_PYARROW = False¶: Use C++ parquet implementation vs Rust parquet implementation for writing parquets.

build_DL_cached_representation(subject_ids: list[int] | None = None, do_sort_outputs: bool = False) → LazyFrame | DataFrame | Expr | Series[source]¶: Produces the deep learning format dataframe described previously for the passed subjects:

build_ESDS_representation(subject_ids: list[int] | None = None, do_sort_outputs: bool = False) → DataFrame[source]¶

static drop_or_censor(col: Expr, drop_lower_bound: Expr | None = None, drop_lower_bound_inclusive: Expr | None = None, drop_upper_bound: Expr | None = None, drop_upper_bound_inclusive: Expr | None = None, censor_lower_bound: Expr | None = None, censor_upper_bound: Expr | None = None, **ignored_kwargs) → Expr[source]¶

Appropriately either drops (returns float(‘nan’)) or censors (returns the censor value) the value val based on the bounds in row.

TODO(mmd): could move this code to an outlier model in Preprocessing and have it be one that is pre-set in metadata.

Parameters:¶

val: The value to drop, censor, or return unchanged.
drop_lower_bound: Expr | None = None¶: A lower bound such that if val is either below or at or below this level, float('nan') will be returned. If None or float('nan'), no bound will be applied.
drop_lower_bound_inclusive: Expr | None = None¶: If True, returns float('nan') if val <= row['drop_lower_bound']. Else, returns float('nan') if val < row['drop_lower_bound'].
drop_upper_bound: Expr | None = None¶: An upper bound such that if val is either above or at or above this level, float('nan') will be returned. If None or float('nan'), no bound will be applied.
drop_upper_bound_inclusive: Expr | None = None¶: If True, returns float('nan') if val >= row['drop_upper_bound']. Else, returns float('nan') if val > row['drop_upper_bound'].
censor_lower_bound: Expr | None = None¶: A lower bound such that if val is below this level but above drop_lower_bound, censor_lower_bound will be returned. If None or float('nan'), no bound will be applied.
censor_upper_bound: Expr | None = None¶: An upper bound such that if val is above this level but below drop_upper_bound, censor_upper_bound will be returned. If None or float('nan'), no bound will be applied.

get_metadata_schema(config: MeasurementConfig) → dict[str, DataType][source]¶

static get_smallest_valid_uint_type(num: int | float | Expr) → DataType[source]¶

Returns the smallest valid unsigned integral type for an ID variable with num unique options.

Parameters:¶

num: int | float | Expr¶: The number of IDs that must be uniquely expressed.

Raises:¶

ValueError – If there is no unsigned int type big enough to express the passed number of ID variables.

Examples

>>> import polars as pl
>>> Dataset.get_smallest_valid_uint_type(num=1)
UInt8
>>> Dataset.get_smallest_valid_uint_type(num=2**8-1)
UInt16
>>> Dataset.get_smallest_valid_uint_type(num=2**16-1)
UInt32
>>> Dataset.get_smallest_valid_uint_type(num=2**32-1)
UInt64
>>> Dataset.get_smallest_valid_uint_type(num=2**64-1)
Traceback (most recent call last):
    ...
ValueError: Value is too large to be expressed as an int!

Bases: object

A structure for database query based input dataframes.

Parameters:¶

connection_uri: str¶: The connection URI for the database. This is in the `connectorx`_ format.
query: str | Path | list[str | Path]¶: The query to be run over the database. It can be specified either as a direct string, a path to a file on disk containing the query in txt format, or a list of said options.
partition_on: str | None = None¶: If the query should be partitioned, on what column should it be partitioned? See the `polars documentation`_ for more details.
partition_num: int | None = None¶: If the query should be partitioned, into how many partitions should it be divided? See the `polars documentation`_ for more details.
protocol: str = 'binary'¶: The `connectorx`_ backend protocol.

connection_uri : str¶

partition_num : int | None = None¶

partition_on : str | None = None¶

protocol : str = 'binary'¶

query : str | Path | list[str | Path]¶