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rugnux: stop the space-group search starving on a low-ISa merge

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The correlation stage kept only reflections with I/sigma >= present_i_over_sigma
(3.0). That statistic is taken on the P1-MERGED intensities, whose sigma is
floored at b|I| (Merge.h, SigmaWithSystematicFloor) so that ISa = 1/b is the
asymptotic I/sigma ceiling - no reflection in a merge can read above it.
Verified over the rotation battery: max I/sigma equals 1/b on every merge.

So a fixed cut is not a per-reflection test at all. Every reflection sitting at
the floor reads 1/b exactly, however strong, and on a merge whose ISa falls
below the cut NOTHING passes: every operator is left with no pairs, its CC is
NaN, and the point group collapses to 1. The predicate "search-merge ISa < 3"
identifies the affected crystals exactly.

It is latent today - no crystal in the battery starves on the shipped
integration background - but it fires on four as soon as an additive intensity
bias is removed, and it is not a data-quality verdict: the crystals it silences
have final merges at ISa 19-22 while their low-multiplicity search merge sits
at 3.5-4.0, just above the cut.

Cap the cut at the merge's own I/sigma quantile so the correlation stage always
keeps at least its strongest quarter. A no-op wherever the fixed cut already
keeps that many - the cut stays exactly 3.000 on healthy merges. Battery
unchanged at 34 space groups matching XDS / 3 differing, with merged
observations identical to 0.000% on all 37 crystals.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-08-05 16:48:40 +02:00
co-authored by Claude Opus 5
parent fb55645b81
commit 8ecd126e93
2 changed files with 36 additions and 6 deletions
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image_analysis/scale_merge/SearchSpaceGroup.cpp
+33 -6
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@@ -219,14 +219,41 @@ SearchSpaceGroupResult SearchSpaceGroup(
const bool in_range = finite && (opt.d_min_limit_A <= 0 || r.d >= opt.d_min_limit_A);
IoverSigma[i] = finite ? r.I / r.sigma : 0.0;
pass_absence[i] = in_range;
// The correlation stage uses only genuinely-present reflections. Near-zero (systematically
// absent) reflections would otherwise form a second cluster at the origin and fake a high
// correlation for false operators - fatal on centered lattices, where half the reflections
// are extinct.
pass_cc[i] = in_range && IoverSigma[i] >= opt.present_i_over_sigma &&
(opt.min_i_over_sigma <= 0 || IoverSigma[i] >= opt.min_i_over_sigma);
}
// The merge floors the merged sigma at b|I| (Merge.h SigmaWithSystematicFloor) so that ISa = 1/b
// stays the asymptotic I/sigma ceiling: no reflection in the merge can read above it. A fixed
// I/sigma cut is therefore not a per-reflection test but a switch on the error model - every
// reflection at the floor reads 1/b exactly, however strong it is, and on a merge whose ISa falls
// below the cut NOTHING passes, so every operator is left with no pairs and the point group
// collapses to 1. Measured over the rotation battery: max I/sigma equals 1/b on every merge, and
// the four crystals that lose symmetry are exactly the four whose search merge sits at ISa 3.5-4.0
// - just above this cut - and drops below 3 when the integration background changes.
// So cap the cut at the merge's own I/sigma quantile: the correlation stage always keeps at least
// its strongest quarter. This is a no-op on any merge where the fixed cut already keeps that many.
constexpr double MIN_PRESENT_FRACTION = 0.25;
double present_cut = opt.present_i_over_sigma;
{
std::vector<double> v;
v.reserve(n);
for (size_t i = 0; i < n; ++i)
if (pass_absence[i])
v.push_back(IoverSigma[i]);
if (!v.empty()) {
const size_t k = static_cast<size_t>((1.0 - MIN_PRESENT_FRACTION) * (v.size() - 1));
std::nth_element(v.begin(), v.begin() + k, v.end());
present_cut = std::min(present_cut, v[k]);
}
}
// The correlation stage uses only genuinely-present reflections. Near-zero (systematically
// absent) reflections would otherwise form a second cluster at the origin and fake a high
// correlation for false operators - fatal on centered lattices, where half the reflections
// are extinct.
for (size_t i = 0; i < n; ++i)
pass_cc[i] = pass_absence[i] && IoverSigma[i] >= present_cut &&
(opt.min_i_over_sigma <= 0 || IoverSigma[i] >= opt.min_i_over_sigma);
// Resolution-normalised intensity E^2 = I / <I>(shell), from equal-count resolution shells over
// the reflections the absence test uses. Lets the absence test judge "present" by intensity
// magnitude, not by a possibly under-estimated sigma (see present_e_squared).