funtracks.import_export.import_from_geff

Deprecated: Import from funtracks.import_export instead.

This module is deprecated and will be removed in funtracks v2.0. Use: from funtracks.import_export import import_from_geff

.. deprecated:: 1.0 This module location is deprecated. Import from the main package instead: from funtracks.import_export import import_from_geff

import_from_geff

import_from_geff(
    directory: Path,
    node_name_map: dict[str, str | list[str]] | None = None,
    segmentation_path: Path | None = None,
    scale: list[float] | None = None,
    node_features: dict[str, bool] | None = None,
    edge_features: dict[str, bool] | None = None,
    extra_features: dict[str, bool] | None = None,
    edge_name_map: dict[str, str | list[str]] | None = None,
    edge_prop_filter: list[str] | None = None,
    name_map: dict[str, str | list[str]] | None = None,
) -> SolutionTracks

Import tracks from GEFF format.

Parameters:

Name	Type	Description	Default
directory	Path	Path to GEFF zarr store	required
node_name_map	dict[str, str | list[str]] | None	Optional mapping from standard funtracks keys to GEFF property names: {standard_key: geff_property_name}. For example: {"time": "t", "pos": ["y", "x"], "seg_id": "label"} - Keys are standard funtracks attribute names (e.g., "time", "pos") - Values are property names from the GEFF store (e.g., "t", "label") - For multi-value features like position, use a list: {"pos": ["y", "x"]} If None, property names are auto-inferred using fuzzy matching.	None
segmentation_path	Path | None	Optional path to segmentation data	None
scale	list[float] | None	Optional spatial scale	None
node_features	dict[str, bool] | None	Optional node features to enable/load	None
edge_features	dict[str, bool] | None	Optional edge features to enable/load	None
extra_features	dict[str, bool] | None	(Deprecated) Use node_features instead. Kept for backward compatibility.	None
edge_name_map	dict[str, str | list[str]] | None	Optional mapping from standard funtracks keys to GEFF edge property names. Example: {"iou": "overlap"}	None
edge_prop_filter	list[str] | None	(Deprecated) Use edge_name_map instead. Kept for backward compatibility.	None
name_map	dict[str, str | list[str]] | None	Deprecated. Use node_name_map instead.	None

Returns:

Type	Description
SolutionTracks	SolutionTracks object

Raises:

Type	Description
ValueError	If both node_features and extra_features are provided

import_graph_from_geff

import_graph_from_geff(
    directory: Path,
    node_name_map: dict[str, str | list[str]],
    edge_name_map: dict[str, str | list[str]] | None = None,
) -> tuple[InMemoryGeff, list[str], int]

Load GEFF data and rename property keys to standard names.

All property keys are renamed before NetworkX graph construction.

Parameters:

Name	Type	Description	Default
directory	Path	Path to GEFF data directory or zarr store	required
node_name_map	dict[str, str | list[str]]	Mapping from standard funtracks keys to GEFF property names: {standard_key: geff_property_name}. For example: {"time": "t", "pos": ["y", "x"], "seg_id": "label"} - Keys are standard funtracks attribute names (e.g., "time", "pos") - Values are property names from the GEFF store (e.g., "t", "label") - For multi-value features like position, use a list: {"pos": ["y", "x"]} Required keys: "time", "pos" (with spatial coordinates) Optional: "seg_id", "tracklet_id", "lineage_id", custom features Only properties included here will be loaded.	required
edge_name_map	dict[str, str | list[str]] | None	Mapping from standard funtracks keys to GEFF edge property names. If None, all edge properties loaded with original names. If provided, only specified properties loaded and renamed. Example: {"iou": "overlap"}	None

Returns:

Type	Description
InMemoryGeff	(in_memory_geff, position_attr, ndims) where in_memory_geff has
list[str]	all properties renamed to standard keys

Raises:

Type	Description
ValueError	If node_name_map contains None or duplicate values