Support for distributed skeleton analysis

[GenevieveBuckley]

Notes from the hack day:

• Separate sparse graph values from construction of sparse array
• Add dask delayed list comprehension somewhere?
• Summarize -> move to function instead of class method
  • skel.coordinates
  • skel.graph
  • skel.paths (relies on skel.nbgraph in _build_skeleton_path_graph)
  • skel.degrees

@delayed
def skeleton_graph_func(skelint, spacing=1):
    ndim = skelint.ndim
    spacing = np.ones(ndim, dtype=float) * spacing
    num_edges = _num_edges(skelint.astype(bool))
    padded_skelint = np.pad(skelint, 1)  # pad image to prevent looparound errors
    steps, distances = raveled_steps_to_neighbors(padded_skelint.shape, ndim,
                                                  spacing=spacing)

    # from function skan.csr._pixel_graph
    row = np.empty(num_edges, dtype=int)
    col = np.empty(num_edges, dtype=int)
    data = np.empty(num_edges, dtype=float)
    k = _write_pixel_graph(padded_skelint, steps, distances, row, col, data)

    return pd.DataFrame({"row": row, "col": col, "data": data})


# skeleton to csgraph
return graph, pixel_indices

@delayed
def skeleton_graph_func(skelint, spacing, block_id):
    csgraph, coords = skeleton_to_csgraph(skelint, spacing)
    coo = csgraph.tocoo()
    coords += block_coordinates
    return pd.DataFrame(coo.row, coo.col, coo.data)

[GenevieveBuckley]

@jni the big question still to decide was: where are we going to put the dask delayed list comprehension? You suggested a dask_compat.py file, but does that mean anybody with a dask array input is going to use a different API than other users?

[GenevieveBuckley]

Link to experimental notebook: https://github.com/GenevieveBuckley/distributed-skeleton-analysis/blob/main/distributed-skeleton-analysis-with-dask.ipynb

[GenevieveBuckley]

PR from pair programming today: #131

TODO

• Test case to check input/output is the same between numpy and dask
• Try uniquify_junctions with Marvin's map_coordinates PR Implement support for ndimage.map_coordinates dask/dask-image#237 (relates to issue Add support for ndimage.map_coordinates dask/dask-image#235)