Keeping not_indexed dummy phase after orientation refinement

[Erlendos12]

Hough indexing may assign the dummy phase "not_indexed". How would I keep (or deal with it) when refining orientations? I have explored 3 alternatives where neither works.

1. Keeping it while refining orientations is not possible, as it is not allowed to have multiple phases present.
2. Adding the not_indexed points in the crystal map when merging with the refined ones is not possible, because they contain no "scores" attribute.
3. I then tried adding the not_indexed phase to the refined crystal map, which would be present when doing refined_xmap.phases, but not when doing refined_xmap or refined_xmap.phases_in_data. I also tried manually setting the phase id of the points which were not indexed, however it did still not update. Here is the code:

ref_xmap.phases.add_not_indexed()
if not xmap.all_indexed:
    for x in range(xmap.shape[0]):
        for y in range(xmap.shape[1]):
            if not xmap[x,y].is_indexed.any():
                print("Adding not indexed")
                ref_xmap[x,y].phase_id = -1

I know this is more related to orix than kikuchipy, but any ideas on how to keep not_indexed phase in the refined crystal map?

[hakonanes]

Good question. I'd consider this a bug in kikuchipy, and we need to somehow bring along the "not indexed" points when merging multiple refined crystal maps. Let's continue the discussion in an issue.

[hakonanes]

This should not be an issue anymore with kikuchipy 0.8.4, just released. Thank you reporting this problem!