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jungfrauandClaude Opus 5 50941f8df0 Make the beam-stop mask O(pixels) and parallel

GetMask() was 3.28 s of the 4.78 s pre-scan on a 16M-pixel detector, all on
one thread. Four changes, none of which alters the mask:

dilate() was a multi-source BFS. On a full rectangle with no obstacles the
8-connected graph distance IS the Chebyshev distance - a path stepping towards
the target never has to leave the frame - so the result is a dilation by the
(2r+1) square clipped to the frame, which separates into a pass along x and a
pass along y. That is O(1) per pixel whatever r is, with no queue and no
4-bytes-per-pixel distance array (72 MB, allocated and filled five times per
call). The erode() case is the one that hurt: it dilates the COMPLEMENT, so on
a detector whose shadow is under 1% of the pixels it seeded the BFS from
essentially every pixel.

fill_holes() floods the background from the border. It now floods the bounding
box of the region grown by one: everything outside that box is background and
the box's own ring is background, so the whole outside is one border-connected
component and a background pixel inside the box is border-connected exactly
when it reaches the ring.

The three baseline iterations re-binned every pixel by radius and re-took a
median each time. The iteration only ever excludes pixels whose background is
below a cut, and dividing by a positive baseline is monotone, so a ring's
excluded pixels are exactly its lowest ones and the next median is an order
statistic of the same, unchanging ring. The rings are binned and sorted once;
each iteration then picks a rank and counts a prefix. Nine full-image passes
become one.

box_sum's vertical pass walked one column at a time, striding a whole row per
step and missing on every access; it now carries a strip of columns together.
Each row's and each column's running sum keeps its terms in its order, so the
floating-point rounding is unchanged - only the traversal differs. The pooled
COUNT is a count of at most 25 pixels, so it is an exact integer box sum now
rather than a floating-point one; the background itself stays in double,
because its running sum adds and subtracts across a whole row and in float the
two roundings would not cancel.

The per-pixel passes then run on all threads, and GetMask takes a thread count.

Measured on a 16M-pixel rotation dataset: GetMask 3.28 s -> 0.99 s, whole
pre-scan 4.78 s -> 2.37 s, whole run 1m10s -> 1m03s. The mask is unchanged on
both a 16M and a 2M-pixel dataset (139126 and 22143 shadow pixels), as are the
space group, the merged reflection count and the merging statistics.

Also corrected the comment on erode(): the dilation cannot seed outside the
frame, so outside behaves as foreground, not as complement.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

2026-08-15 17:50:06 -04:00