:orphan:

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

.. py:module:: traccuracy.loaders._ctc


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


Functions
~~~~~~~~~

.. autoapisummary::

   traccuracy.loaders._ctc.ctc_to_graph
   traccuracy.loaders._ctc.load_tiffs
   traccuracy.loaders._ctc.load_ctc_data



Attributes
~~~~~~~~~~

.. autoapisummary::

   traccuracy.loaders._ctc.logger


.. py:data:: logger

   

.. py:function:: ctc_to_graph(df: pandas.DataFrame, detections: pandas.DataFrame) -> networkx.DiGraph

   Create a Graph from DataFrame of CTC info with node attributes.

   :param df: CTC-style dataframe with columns
              [segmentation_id, start_frame, end_frame, parent_id]
   :type df: pd.DataFrame
   :param detections: Dataframe from _get_node_attributes with position
                      and segmentation label for each cell detection
   :type detections: pd.DataFrame

   :returns: Graph representation of the CTC data.
   :rtype: networkx.DiGraph


.. py:function:: load_tiffs(data_dir: str) -> numpy.ndarray

   Load a directory of individual frames into a stack.

   :param data_dir: Path to directory of tiff files
   :type data_dir: str

   :raises FileNotFoundError: No tif files found in data_dir

   :returns: 4D array with dims TYXC
   :rtype: np.array


.. py:function:: load_ctc_data(data_dir: str, track_path: str | None = None, name: str | None = None, run_checks: bool = True, border_margin: float | None = None) -> traccuracy._tracking_graph.TrackingGraph

   Read the CTC segmentations and track file and create a TrackingGraph.

   :param data_dir: Path to directory containing CTC tiffs.
   :type data_dir: str
   :param track_path: Path to CTC track file. If not passed,
                      finds `*_track.txt` in data_dir.
   :type track_path: optional, str
   :param name: Name of data to store in TrackingGraph
   :type name: optional, str
   :param run_checks: If set to `True` (default), runs checks on the data
                      to ensure valid CTC format.
   :type run_checks: optional, bool
   :param border_margin: If set, nodes whose centroid is within this
                         distance (in pixels) of the spatial border will be excluded from the graph.
                         Defaults to None (no filtering).
   :type border_margin: float, optional

   :returns: TrackingGraph object containing segmentations and graph.
   :rtype: traccuracy.TrackingGraph

   :raises ValueError: If the tracks file is not found.
       If `run_checks` is True, whenever any of the CTC format checks are violated.
       If `run_checks` is False, whenever any other Exception occurs while creating the graph.