bacteria_density.graph module

bacteria_density.graph.find_next_bbox(hint, leaves, used_bboxes)

bacteria_density.graph.find_root(leaves, hint)

Among all leaf nodes, finds the one closest to the provided hint point. It will define the root of the graph traversal to find the longest path.

Parameters:

• leaves (-) – A list of leaf nodes, where each node is a tuple (z, y, x).

• hint (-) – A 2D point (y, x) to guide the root selection.

Returns:

The leaf node closest to the hint point.

Return type:

(tuple)

bacteria_density.graph.get_leaves(bbox, graph)

Identifies leaf nodes in the graph, which are nodes with only one connection.

bacteria_density.graph.longest_path_from(root, graph, bbox)

bacteria_density.graph.path_as_img(path)

bacteria_density.graph.run1()

bacteria_density.graph.skeleton_to_undirected_graph(skel)

Converts a 3D skeleton into an undirected graph representation. First pass: create edges for direct (6-face) neighbors only. Second pass: add diagonal edges (edge and corner) only when the two voxels are not already connected via a path of direct neighbors.

Parameters:

skel (-) – A binary 3D numpy array representing the skeleton.

Returns:

A dictionary where keys are voxel coordinates (z, y, x) and

values are sets of neighboring voxel coordinates.

Return type:

(dict)