HereditaryStratigraphicSpecimen

class HereditaryStratigraphicSpecimen

Postprocessing representation of the differentia retained by an extant HereditaryStratigraphicColumn, indexed by deposition rank.

All entries correspond to retained differentia (i.e., no entries are null).

See Also

HereditaryStratigraphicAssemblageSpecimen

Specimen representation that allows for easier alignment among members of a population without perfectly homogeneous retained ranks.

specimen_from_records

Deserialize a HereditaryStratigraphicSpecimen from a dict composed of builtin data types.

col_to_specimen

Create a HereditaryStratigraphicSpecimen from a HereditaryStratigraphicColumn.

__init__(stratum_differentia_series: Series[DataType(uint64)], stratum_differentia_bit_width: int) → None

Initialize a HereditaryStratigraphicSpecimen object with a sequence of rank-indexed differentia and a differentia bit width.

Methods

GetData() → Series[DataType(uint64)]

Get the underlying Pandas Series containing differentia values indexed by rank.

Notes

This function directly returns the specimen’s underlying Series data, so mutation of the returned object will alter or invalidate this specimen.

GetDifferentiaVals() → ndarray

Get the integer underlying values in the stored Pandas Series.

Returns

differentianp.ndarray

A 1-dimensional NumPy integer ndarray containing differentia values, including garbage values where the underlying Series is null.

Notes

This function returns a direct view into the Series data, so no copy is made. Changes to the returned array will propagate to the Series object’s underlying values, and vice versa.

GetNumDiscardedStrata() → int

How many deposited strata have been discarded?

Determined by number of generations elapsed and the configured column retention policy.

GetNumStrataDeposited() → int

How many strata have been depostited on the column?

Note that a first stratum is deposited on the column during initialization.

GetNumStrataRetained() → int

How many strata are currently stored within the column?

May be fewer than the number of strata deposited if strata have been discarded as part of the configured stratum retention policy.

GetRankAtColumnIndex(index: int) → int

Map array position to generation of deposition.

What is the deposition rank of the stratum positioned at index i among retained strata? Index order is from most ancient (index 0) to most recent.

GetRankIndex() → ndarray

Get the integer index in the stored Pandas Series, representing the ranks of stratum entries.

Returns

ranksnp.ndarray

A numpy array containing ranks of differentia entries, including null entries for differentia that are not retained.

GetStratumDifferentiaBitWidth() → int

How many bits wide are the differentia of strata?

HasDiscardedStrata() → bool

Have any deposited strata been discarded?

IterRankDifferentiaZip(copyable: bool = False) → Iterator[Tuple[int, int]]

Iterate over ranks of retained strata and their differentia.

If copyable, return an iterator that can be copied to produce a new fully-independent iterator at the same position.

Equivalent to zip(specimen.IterRetainedRanks(), specimen.IterRetainedDifferentia()), but may be more efficient.

IterRetainedDifferentia() → Iterator[int]

Iterate over differentia of strata retained in the specimen.

Differentia yielded from most ancient to most recent.

IterRetainedRanks() → Iterator[int]

Iterate over deposition ranks of strata retained in the specimen.

__init__(stratum_differentia_series: Series[DataType(uint64)], stratum_differentia_bit_width: int) → None

Initialize a HereditaryStratigraphicSpecimen object with a sequence of rank-indexed differentia and a differentia bit width.