A simple example
****************

A simple pipeline is shown below. Others can be found in the `examples folder of the repository <https://github.com/quantumjot/btrack/tree/master/examples>`_.

This example shows ....


.. code:: python


  import btrack
  from skimage.io import imread

  # load your segmentation data
  segmentation = imread('/path/to/segmentation.tif')

  # create btrack objects (with properties) from the segmentation data
  # (you can also calculate properties, based on scikit-image regionprops)
  objects = btrack.utils.segmentation_to_objects(
    segmentation, properties=('area', )
  )

  # initialise a tracker session using a context manager
  with btrack.BayesianTracker() as tracker:

    # configure the tracker using a config file
    tracker.configure('/path/to/your/models/cell_config.json')

    # append the objects to be tracked
    tracker.append(objects)

    # set the volume (Z axis volume limits default to [-1e5, 1e5] for 2D data)
    tracker.volume = ((0, 1200), (0, 1600))

    # track them (in interactive mode)
    tracker.track_interactive(step_size=100)

    # generate hypotheses and run the global optimizer
    tracker.optimize()

    # store the data in an HDF5 file
    tracker.export('/path/to/tracks.h5', obj_type='obj_type_1')

    # get the tracks as a python list
    tracks = tracker.tracks

    # optional: get the data in a format for napari
    data, properties, graph = tracker.to_napari()



Tracks themselves are python objects with properties

.. code:: python


    # get the first track
    track_zero = tracks[0]

    # print the length of the track
    print(len(track_zero))

    # print all of the xyzt positions in the track
    print(track_zero.x)
    print(track_zero.y)
    print(track_zero.z)
    print(track_zero.t)

    # print the fate of the track
    print(track_zero.fate)

    # print the track ID, root node, parent node, children and generational depth
    print(track_zero.ID)
    print(track_zero.root)
    print(track_zero.parent)
    print(track_zero.children)
    print(track_zero.generation)