Skip to content

Reader and Writer

napari_relax._reader

napari reader for LineageTree files and the formats LineageTree loads.

Opening a file shows the loader selection and Loading Parameters dialogs, then builds a Points layer (and a Surface layer when the dataset has meshes) that carries the LineageTree in its metadata. See https://napari.org/stable/plugins/guides.html#readers.

napari_get_reader(path)

Return the ReLAX reader if the file extension is supported.

Parameters:

Name Type Description Default
path str or list of str

Path to file, or list of paths.

 required

Returns:

Type Description
function or None

If the path is a recognized format, return a function that accepts the same path or list of paths, and returns a list of layer data tuples.

reader_function(path)

Load a dataset and return the napari layers to create.

Readers are expected to return data as a list of tuples, where each tuple is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are both optional.

Parameters:

Name Type Description Default
path str

Path to the file to open.

 required

Returns:

Type Description
list of tuple or None

A list of LayerData tuples (data, add_kwargs, layer_type), or None if the Loading Parameters dialog was cancelled.

initial_loading(lT, scaling=False)

Compute the minimal data needed to display a LineageTree.

Parameters:

Name Type Description Default
lT LineageTree

The LineageTree to load.

 required
scaling bool

If True, divide the positions by the largest distance between two cells, by default False.

 False

Returns:

Type Description
namedtuple

initial_spatial_data with the fields:

  • data: point positions as (track, time, z, y, x) rows;
  • lT_to_here and here_to_lT: mappings between LineageTree node IDs and napari point indices;
  • clone: index of the root lineage of each point;
  • default_colors: RGBA color of each point;
  • cmap: colormap used to color the lineages;
  • barycenter: center removed from the positions;
  • last_c_of_track and first_c_to_track: first and last node of each chain, used to build the graphs;
  • rescaling_factor: factor the positions were divided by.

graph_loading(lT, last_c_of_track, first_c_to_track, divisor)

Build the lineage graphs displayed in the Lineage Viewer.

Parameters:

Name Type Description Default
lT LineageTree

The LineageTree to draw.

 required
last_c_of_track dict

Last node of each chain, from initial_loading.

 required
first_c_to_track dict

Chain index of each first node, from initial_loading.

 required
divisor int

Filter value from the Loading Parameters dialog. Lineages with fewer than (number of timepoints / divisor) nodes are skipped; 0 keeps every lineage.

 required

Returns:

Type Description
tuple of dict

The graph of each lineage, the node positions of each graph, and the chain connectivity used to build a Tracks layer.

layer_preparation(lT, points_layer_name, no_graph=False, parameters=None)

Prepare the napari layers for a LineageTree.

Parameters:

Name Type Description Default
lT LineageTree

The LineageTree to display.

 required
points_layer_name str or Path

Name of the Points layer. If it is an existing file path, its stem is used.

 required
no_graph bool

If True, skip building the Lineage Viewer graphs, by default False.

 False
parameters dict

Loading parameters: rescale (bool) and divisor (int).

 None

Returns:

Type Description
list of tuple

LayerData tuples: one Points layer, plus one Surface layer if the LineageTree has meshes.

napari_relax._writer

napari writer saving a LineageTree as a .lT file.

write_single_image(path, data, meta)

Save the LineageTree of a layer as a .lT file.

Parameters:

Name Type Description Default
path str

Destination path. .lT is used if it has another extension.

 required
data Any

Layer data, unused.

 required
meta dict

Layer attributes; the LineageTree is read from its metadata or from the metadata of the linked layer.

 required

Returns:

Type Description
list of str

The path that was written.