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rugnux: per-batch relative-B correction + radiation-damage B monitor

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Rotation scaling modelled dose-dependent scattering power with a single
global relative-B decay slope only (RefineDecay); per-frame refinement was
scale-only. Add a per-batch relative Debye-Waller B, both as an opt-in
correction and as an always-on measurement.

- FitRelativeBCurve / SolveCurvatureSmoothedB: per rotation-range batch, fit
  the s^2 slope of ln(Iref/Iobs) that the resolution-flat per-frame G leaves,
  regularised by a second-difference (curvature) penalty so a genuine smooth
  relative-B is kept while resolution-correlated noise (which an unconstrained
  per-batch fit would chase into an oscillating curve) is suppressed.

- Correction (--relative-b[=deg], default off): applied after RefineDecay,
  gated by a physical peak-to-peak floor and cross-validated by ASU-group
  parity (a per-batch parameter owns whole frames, so it is scored on held-out
  equivalents, not held-out frames). On a battery re-scaling identical stored
  reflections it is a no-op on well-behaved data and a small gain on
  radiation-damaged rotation data; never a regression.

- Radiation-damage monitor (always on for rotation, report-only): measure the
  relative-B change from the pristine low-dose start of the run to its end
  (a whole-run-mean reference inverts on damaged data) plus the per-batch
  curve, and report them on the command line (in the radiation-damage report
  and the merge statistics) and in the mmCIF (_reflns.jfjoch_radiation_damage_
  relative_B and a per-batch loop). A large magnitude flags radiation damage,
  complementing the existing per-image CC / mosaicity read.

- --scale now reproduces the de-novo rotation merge (it previously omitted
  scale-fulls and smooth-G, silently using a weaker model), and honours
  --relative-b, so an offline re-scale matches the full pipeline.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-18 22:08:09 +02:00
co-authored by Claude Opus 4.8
parent e97a610091
commit c5cfdcef7e
9 changed files with 361 additions and 1 deletions
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image_analysis/WriteReflections.cpp
+20
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@@ -170,8 +170,28 @@ void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
if (twinning.moment_reflections > 0)
out << "_reflns.jfjoch_second_moment_I " << Fmt(twinning.second_moment, 3)
<< " # <I^2>/<I>^2 (untwinned 2.00, perfect twin 1.50)\n";
// Radiation-damage monitor (rotation): the relative Debye-Waller B change from the first to the last
// frame (A^2). A large magnitude flags a dose-dependent resolution-scale change = radiation damage;
// positive is the typical direction (high-resolution intensity fades with dose). No standard mmCIF item.
if (std::isfinite(statistics.radiation_damage_delta_b))
out << "_reflns.jfjoch_radiation_damage_relative_B " << Fmt(statistics.radiation_damage_delta_b, 2)
<< " # relative-B first->last over the run (A^2); + = high-res fades with dose\n";
out << "#\n";
// Per-batch relative-B curve (the radiation-damage monitor, rotation): one relative Debye-Waller B
// per rotation-range batch, measured before any correction. rotation_start_deg = id * batch_deg.
if (!statistics.radiation_damage_b_batch.empty()) {
out << "loop_\n";
out << "_jfjoch_radiation_damage_batch.id\n";
out << "_jfjoch_radiation_damage_batch.rotation_start_deg\n";
out << "_jfjoch_radiation_damage_batch.relative_B\n";
for (size_t i = 0; i < statistics.radiation_damage_b_batch.size(); ++i)
out << " " << (i + 1) << " "
<< Fmt(static_cast<double>(i) * statistics.radiation_damage_batch_deg, 1) << " "
<< Fmt(statistics.radiation_damage_b_batch[i], 2) << "\n";
out << "#\n";
}
out << "loop_\n";
out << "_reflns_shell.d_res_high\n";
out << "_reflns_shell.d_res_low\n";