ionique.datatypes

The datatypes module provides high-level data containers that build on the segment tree from core.

TraceFile — wraps a loaded nanopore recording (current, voltage, metadata) as a tree node at rank "file". Automatically creates voltage- step children when voltage boundaries are provided.
SessionFileManager — singleton root node that manages all loaded files in a session.

See Data Input for usage examples.

Data structure definitions and session file management for analysis.

class ionique.datatypes.SessionFileManager(*args, **kwargs)

Bases: MetaSegment

Singleton-based session manager for hierarchical data.

This class inherits from MetaSegment and uses the Singleton metaclass to ensure only one instance exists during a given session. It serves as the root segment for a data analysis session and is responsible for managing metadata and registered “affectors” (i.e., objects that modify or interact with the session).

rank

Fixed rank label "root" identifying this as the top of the hierarchy.

Type:: str

affector_table

Registry mapping UUID strings to metadata entries for each registered affector (class name, string representation, and timestamp).

Type:: dict

__init__() → None

Initialize the session manager.

Sets the session start time and prepares the affector log structure.

add_child(child: AnySegment) → None

Add a single child segment to the session’s hierarchy.

Parameters:: child (AnySegment) – The segment to be added as a child.

add_children(children: list[AnySegment]) → None

Add multiple child segments to the session.

Parameters:: children (list of AnySegment) – A list of segments to be added as children.

rank: str = 'root'

register_affector(affector)

Register an affector object that influences the session data.

Records metadata including class name, string representation, and timestamp, and logs the event with a unique identifier.

Parameters:: affector (object) – An object that modifies or interacts with the session.
Returns:: A UUID string uniquely identifying the registered affector.
Return type:: str

unique_features

class ionique.datatypes.TraceFile(current: ndarray, voltage=None, rank='file', parent=None, unique_features: dict = {}, metadata: dict = {})

Bases: Segment

Data structure for representing a single trace file with current and optional voltage information.

This class inherits from Segment and encapsulates current and voltage data. It sets up segment metadata, defines parent-child hierarchy, and optionally initializes child segments based on voltage steps. If voltage steps are provided, corresponding child segments of rank "vstep" are created automatically.

Parameters:

current (numpy.ndarray) – Array of ionic current values.
voltage (list of tuple or None, optional) – List of ((start, end), voltage_value) tuples used to create child segments for each voltage step. Defaults to None.
rank (str, optional) – Segment rank label. Defaults to "file".
parent (Segment or None, optional) – Parent segment to which this trace belongs. Defaults to None.
unique_features (dict, optional) – Dictionary of metadata such as sampling frequency. Defaults to an empty dict.
metadata (dict, optional) – Additional metadata. Defaults to an empty dict.

__init__(current: ndarray, voltage=None, rank='file', parent=None, unique_features: dict = {}, metadata: dict = {}): Initialize the TraceFile and optionally create voltage-step child segments.

children: list[AnySegment]

delete(): Delete the current object, removing it from its parent

end: int | None

parent: AnySegment | None

plot(rank, axes, downsample_per_rank, color_per_rank)

Plot the trace data at a specified rank with per-rank styling options.

Parameters:

rank (str) – The segment rank at which to render the plot.
axes (object) – The axes or figure object to draw on.
downsample_per_rank (dict) – Mapping of rank label to downsampling factor for rendering.
color_per_rank (dict) – Mapping of rank label to color specification for rendering.

Notes

Not yet implemented.

rank: str

start: int | None