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rugnux: name the beam centre when two candidate cells are axis harmonics

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The first pass already has the evidence and says nothing about what it means. When two schemes come
back with primitive volumes related by a small integer - or by sqrt(3), which is the hexagonal
harmonic and is not a whole number - one of them is the other's axis harmonic, and what decides
between them is the beam centre to a fraction of a pixel.

The mechanism is that the J0 law is about the FFT AMPLITUDE, which is translation-invariant. A
centre error along the spindle translates the derotated cloud rigidly, so the transform cannot see
it, the peaks stay sharp, and the lattice fit that follows - whose origin is the beam, and which is
not translation-invariant - commits with confidence to a sub-multiple. Measured on a deposited
dataset: 0.12 px of centre, 0.09 px of it across the spindle against a 2.78 px need, is the whole
difference between the deposited cell and a halved axis, and the halved one is the answer that
indexed MORE frames - 100.00 % against 99.23 %.

So the message is deliberately not conditioned on any indexing-quality signal, and it is taken over
the whole pair rather than only over the tie: on this failure the frame count points the wrong way,
which is exactly why it cannot arbitrate. Nothing is decided differently; the integer-subcell
tie-break below is unchanged.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01T3yNBXk4wKdMZy1ak2NY7f
This commit is contained in:
leonarski_f
2026-08-30 08:37:55 +02:00
co-authored by Claude Opus 5
parent 52e9e9da2b
commit 4d2bb98a13
1 changed files with 27 additions and 2 deletions
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rugnux/Rugnux.cpp
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@@ -2017,14 +2017,39 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
// ratio separates a real axis multiplication from a centering coincidence. Volumes are
// primitive (see above), so a pure setting difference is a ratio of 1 and never fires.
bool integer_subcell = false;
if (bp.result.has_value() && !clearly_more && vol > 1.0 && bp.vol > 1.0) {
double harmonic_ratio = 0.0;
if (bp.result.has_value() && vol > 1.0 && bp.vol > 1.0) {
const bool tied = static_cast<float>(score) >= bp.score * 0.9f - 0.5f;
const double ratio = (vol < bp.vol) ? bp.vol / vol : vol / bp.vol;
const double nearest = std::round(ratio);
const bool integer_multiple = nearest >= 2.0 && std::abs(ratio - nearest) < 0.15;
integer_subcell = tied && integer_multiple && vol < bp.vol;
integer_subcell = tied && !clearly_more && integer_multiple && vol < bp.vol;
// sqrt(3) as well as an integer: a hexagonal supercell that lengthens one axis by
// sqrt(3) is the other harmonic seen on real data and its volume ratio is not a
// whole number. This is a REPORT and not a decision - it is deliberately taken
// over the whole pair, `clearly_more` included, because the harmonic is often the
// one that indexes more frames (see below).
if (integer_multiple || std::abs(ratio - std::sqrt(3.0)) < 0.15)
harmonic_ratio = ratio;
}
// Two candidates whose primitive volumes differ by a small integer or by sqrt(3) are
// one lattice and its axis harmonic, and what decides between them is the BEAM CENTRE.
// A centre error along the spindle translates the derotated cloud rigidly, which the
// FFT amplitude cannot see at all, so the peaks stay sharp and the indexer commits -
// with confidence - to a sub-multiple. Measured on real data: a 0.12 px change of
// centre, 0.03x of what the J0 law asks across the spindle, is the whole difference
// between the deposited cell and a halved axis, and the halved one is the answer that
// indexed MORE frames (100.00 % against 99.23 %). So the frame count cannot arbitrate
// this pair, and until this line nothing in the run said what the pair meant.
if (harmonic_ratio > 0.0)
logger.Warning("Scheme '{}' (primitive cell volume {:.0f} A^3) and '{}' ({:.0f} A^3) "
"differ by {:.2f}x - one is an axis harmonic of the other. Which of "
"the two is right is settled by the beam centre to a fraction of a "
"pixel, and the harmonic is often the one that indexes MORE frames, "
"so the frame counts above cannot decide it. Check the beam centre "
"(--estimate-beam-center)", name, vol, bp.name, bp.vol, harmonic_ratio);
if (!bp.result.has_value() || clearly_more || integer_subcell) {
if (integer_subcell)
logger.Info("Scheme '{}' cell (vol {:.0f}) is a {:.0f}x sub-cell of '{}' (vol {:.0f}) at "