:orphan:

:py:mod:`traccuracy.loaders._geff`
==================================

.. py:module:: traccuracy.loaders._geff


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   traccuracy.loaders._geff.load_geff_data



.. py:function:: load_geff_data(geff_path: str, load_geff_seg: bool = False, seg_path: str | None = None, seg_property: str | None = None, name: str | None = None, load_all_props: bool = False, border_margin: float | None = None) -> traccuracy._tracking_graph.TrackingGraph

   Load a graph into memory from a geff file

   Segmentations can be optionally loaded either from a related object specified in
   the geff (`load_geff_seg=True`) or with a path to a zarr array `seg_path` and `seg_property`.
   If loading graphs with flags, e.g. for visualization, pass `load_all_props=True`.

   :param geff_path: Path to a geff group inside of a zarr,
   :type geff_path: str
   :param load_geff_seg: Load segmentation based on a geff metadata of
                         related segmentation. Defaults to False.
   :type load_geff_seg: bool, optional
   :param seg_path: Path to a zarr array containing segmentation data.
                    We assume that the axes order in your segmentation array matches the axes in your geff.
                    If this is not true please load the segmentation yourself and add it to
                    TrackingGraph.segmentation. Defaults to None.
   :type seg_path: str | None, optional
   :param seg_property: If seg_path provided, this is the corresponding
                        property on the geff graph that contains the segmentation key. Defaults to None.
   :type seg_property: str | None, optional
   :param name: Optional name to store on TrackingGraph for identification.
                Defaults to None.
   :type name: str | None, optional
   :param load_all_props: If True, load all node and edge properties on the graph.
                          Defaults to False and only spatiotemporal and segmentation node properties are loaded.
                          Set to True to get already annotated error flags, e.g. for visualization.
   :type load_all_props: bool, optional
   :param border_margin: If set, nodes whose centroid is within this
                         distance (in pixels) of the spatial border will be excluded from the graph.
                         Requires segmentation to be loaded. Defaults to None (no filtering).
   :type border_margin: float, optional