Radial background: one mechanism for stills and rotation, decided per run on empty apertures (D5)
Wherever the correction is set for the whole run its curve is the frame's peak-excluded ring background (the adaptive spot finder's, whole frame) and the ring's clip follows it - as stills have done since integ-pal - now rotation too. One empty-aperture measurement (BackgroundAperture) decides it for both workflows: - The apertures' corrected difference is now taken as the integrator applies the correction: the clip follows the curve (each ring pixel's threshold raised by the curve's rise from the centre, in whole counts) as well as the kernel correction. Before, the tally clipped flat, so it measured a correction the engine never applies. - Rotation measures the stencils the spot width can give it (r1 = 4, 5, 6 with the ring-area rule, RotationStencil) and decides on the one it gets, and separately on the pre-adaptive stencil the geometry pre-pass and the starvation guard return to. - Stills: on wherever the corrected ring predicts the empty disk better (unchanged rule). Rotation: the frame's curve on every image only where it takes >= 10% of the apertures' mean square error away (ROTATION_RADIAL_MIN_GAIN); otherwise the existing per-image ice gate with the reflections' curve is left exactly as it was. Why a margin on rotation only: a still has no other correction, a sweep has one. Measured over 18 rotation sets (forced on every image): photon-counting sweeps gain 0.1-5% on the apertures (z 3-4) and lose ISa/anomalous signal when corrected (insulin, lysozyme, cytochrome c; 9yzk R-free +0.009 at 1.2%), as the earlier stills-rule trial found; the home-source CCD and smooth-ice runs gain 13-31%. Result (CPU A/B vs 87684012f, 18 rotation sets): 12 .hkl byte-identical (every photon-counting control without ice), 5uth R-free 0.210 -> 0.201 / ISa 10.4 -> 10.8, the ice set neutral; stills: lcls242_s turns the correction on (the clip-following tally), R-free 0.2399 -> 0.2406. No integration kernel changed; the tally is host code. Tests: BackgroundAperture_CorrectedClipFollowsTheCurve, RadialHelps margins. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit dd3f3f2da39f5338e7dda1874bbdd535229bce98)
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@@ -237,9 +237,11 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
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// Where no such background exists (no adaptive finder), auto leaves the correction off: the
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// plain profile carries the Bragg peaks and cannot support an absolute threshold.
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//
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// On stills the correction also takes its CURVE from that background, and auto applies it to
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// every image that has one (rugnux's pre-scan turns it off for a run whose empty apertures say
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// the radial model does not hold there). A serial frame has a few dozen predicted reflections, so their own
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// On stills - and wherever the correction is set for the whole run rather than left to auto, as
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// rugnux's pre-scan sets it on a rotation run whose empty apertures ask for it - the correction
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// takes its CURVE from that background, and on stills auto applies it to every image that has one
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// (the pre-scan turns it off for a run whose empty apertures say the radial model does not hold
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// there). A serial frame has a few dozen predicted reflections, so their own
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// ring pixels - where the curve comes from otherwise - sample the radial background sparsely,
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// while the finder's rings hold every pixel of the frame. And the correction is the measured
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// curvature itself: where the background has none it is zero, so there is nothing for a gate
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@@ -254,7 +256,7 @@ void MXAnalysisWithoutFPGA::Analyze(DataMessage &output,
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const std::vector<float> &ring_bkg = spot_finding_settings.adaptive_threshold
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? adaptiveSpotFinder->GetRingBackground() : no_rings;
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const bool stills = !experiment.IsRotationIndexing();
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if (stills)
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if (stills || !bragg_engine->IsBackgroundRadialAuto())
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bragg_engine->RadialBackgroundFromRings(ring_bkg, integration.GetQBinCount(),
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integration.Settings().GetLowQ_recipA(),
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integration.Settings().GetQSpacing_recipA());
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