affinity_to_boundary#
- omnipose.core.affinity_to_boundary(masks, affinity_graph, coords)[source]#
Convert affinity graph to boundary map.
Internal hypervoxels are those that are fully connected to all their 3^D-1 neighbors, where D is the dimension. Boundary hypervoxels are those that are connected to fewer than this number and at least 1 other hypervoxel. Correct boundaries should have >=D connections, but the lower bound here is set to 1.
- masks: ND array, int or binary
label matrix or binary foreground mask
- affinity_graph: ND array, bool
hypervoxel affinity array, <3^D> by <number of foreground hypervoxels>
- coords: tuple or ND array
coordinates of foreground hypervoxels, <dim>x<npix>
boundary