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merge: mask ice rings whose CC1/2 collapses below their resolution neighbours

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An ice-contaminated ring decorrelates its reflections, so its merged half-set
CC1/2 falls well below the Bragg trend of its resolution shoulders (e.g.
EP_cs_01-17 2.25A ring CC1/2 0.12 vs shoulders 0.89). After the final merge,
compute per-hexagonal-ice-ring CC1/2 in the ring band (+/- ice width in q=2pi/d)
against the shoulders either side, mask any ring more than 0.05 below its
shoulders (reliable shoulder CC1/2 > 0.5, >=20 reflections each) and re-merge
without them. Weak/absent rings track their neighbours and stay, so clean
crystals are untouched.

Data-driven and robust on /data/rotation_test: 16/18 crystals mask nothing and
are unchanged (every clean crystal, plus icy-but-fine EP_cs_02-10); EP_cs_01-17
masks 6 rings, CC1/2 6.9% -> 28%; CQ066/pding4_003 mask one marginal ring each.
A well-scaled CC1/2 test, replacing the fragile per-image azimuthal cutoffs.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-02 16:06:39 +02:00
co-authored by Claude Fable 5
parent cdbd0bed5d
commit 6ffb16f142
4 changed files with 72 additions and 0 deletions
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process/JFJochProcess.cpp
+38
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@@ -35,6 +35,7 @@
#include "../image_analysis/scale_merge/HKLKey.h"
#include "../image_analysis/WriteReflections.h"
#include "../common/Definitions.h"
#include "../common/CorrelationCoefficient.h"
#include <array>
#include <map>
#include <Eigen/Dense>
@@ -566,6 +567,9 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
// Smoothing it more than once would compound the correction, so do it only on the first
// pass. The no-reference path recomputes G from scratch each pass and re-smooths correctly.
bool reference_g_smoothed = false;
// Ice rings masked from the merge by the CC1/2 test after the final merge; empty until then,
// at which point a re-merge applies them.
std::vector<char> masked_ice_rings;
auto scale_and_merge = [&](const std::string &label, bool for_search) -> ScaleMergeResult {
// ScaleOnTheFly self-scaling is only for the no-reference path; with a reference each
// image is already scaled against it during the per-image pass, so we merge directly.
@@ -620,6 +624,7 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
// intensities and the error model, so the space-group search sees clean data; the final
// in-symmetry merge keeps them so completeness is not lost.
merge_engine.ExcludeIceRings(for_search);
merge_engine.MaskIceRings(masked_ice_rings, config_.spot_finding.ice_ring_width_Q_recipA);
if (result.consensus_cell.has_value())
merge_engine.ReferenceCell(*result.consensus_cell);
merge_engine.RefineErrorModel(merge_input);
@@ -670,6 +675,39 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
}
}
// Ice-ring CC1/2 mask: a hexagonal-ice ring whose merged half-set CC1/2 collapses well below its
// resolution shoulders has been decorrelated by ice (its Bragg is unrecoverable) - drop it and
// re-merge. Weak/absent rings track their neighbours and stay, so completeness on clean crystals
// is untouched. Uses the ring band (+/- ice width in q=2pi/d) vs the shoulders either side.
if (experiment_.IsDetectIceRings() && !sm.merged.empty()) {
constexpr float two_pi = 6.283185307f;
const float w = config_.spot_finding.ice_ring_width_Q_recipA;
std::vector<char> mask(ICE_RING_RES_A.size(), 0);
for (size_t i = 0; i < ICE_RING_RES_A.size(); ++i) {
const float q_ring = two_pi / ICE_RING_RES_A[i];
CorrelationCoefficient ring, shoulder;
size_t n_ring = 0, n_shoulder = 0;
for (const auto &m : sm.merged) {
if (!(m.d > 0.0f) || !std::isfinite(m.I_half[0]) || !std::isfinite(m.I_half[1]))
continue;
const float dq = std::fabs(two_pi / m.d - q_ring);
if (dq < w) { ring.Add(m.I_half[0], m.I_half[1]); ++n_ring; }
else if (dq < 3.0f * w) { shoulder.Add(m.I_half[0], m.I_half[1]); ++n_shoulder; }
}
if (n_ring >= 20 && n_shoulder >= 20 && shoulder.GetCC() > 0.5
&& ring.GetCC() < shoulder.GetCC() - 0.05) {
mask[i] = 1;
logger.Info("Ice-ring mask: {:.2f} A ring CC1/2 {:.3f} << shoulders {:.3f}; masked from merge",
ICE_RING_RES_A[i], ring.GetCC(), shoulder.GetCC());
}
}
if (std::any_of(mask.begin(), mask.end(), [](char c) { return c != 0; })) {
masked_ice_rings = std::move(mask);
const auto final_sg = experiment_.GetGemmiSpaceGroup();
sm = scale_and_merge(final_sg ? final_sg->short_name() : "P1", false);
}
}
const auto twin_sg_number = experiment_.GetSpaceGroupNumber();
const gemmi::SpaceGroup *twin_sg = twin_sg_number
? gemmi::find_spacegroup_by_number(twin_sg_number.value()) : nullptr;