Overlap Tables

[donald-e-boyce]

This is an undocumented (until now) feature of hexrd. The fit-grains command will check for the existence of an overlap table, and if it exists, it will load it and use it to mark certain reflections as invalid. See the code section below.

Overlap Table Format

Unfortunately, there is no writer for the overlap table, but you can see the form of the table.

• The table(s) is saved in npz format inside the detector directory, named "overlap_table.npz". So there can be one for each detector.
• There can be multiple arrays in the file, although one should be sufficient. Each array has two columns, a grain ID column followed by a reflection ID column.

Discussion

We need to develop a writer for the overlap tables.
I think we can generate the spots using instrument.pull_spots().
The main question is how to determine whether a spot is an overlap.
More work needs to be done here.

Code

Here is the section of code inside hexrd/fitgrains.py,

            # if an overlap table has been written, load it and use it
            overlaps = np.zeros_like(idx, dtype=bool)
            try:
                ot = np.load(
                    os.path.join(
                        analysis_dirname, os.path.join(
                            det_key, 'overlap_table.npz'
                        )
                    )
                )
                for key in ot.keys():
                    for this_table in ot[key]:
                        these_overlaps = np.where(
                            this_table[:, 0] == grain_id)[0]
                        if len(these_overlaps) > 0:
                            mark_these = np.array(
                                this_table[these_overlaps, 1], dtype=int
                            )
                            otidx = [
                                np.where(refl_ids == mt)[0]
                                for mt in mark_these
                            ]
                            overlaps[otidx] = True
                idx = np.logical_and(idx, ~overlaps)
                # logger.info("found overlap table for '%s'", det_key)
            except(IOError, IndexError):
                # logger.info("no overlap table found for '%s'", det_key)
                pass