leonarski_fandClaude Opus 5
f60768d49c
Two changes to the same variance chain; they are in one commit because the second exists to remove an assumption the first was breaking, and separating them leaves a tree that is correct only by luck. The reported sigma was floored at 2% of the intensity, a per-partial I/sigma cap of 50. It applied only to the box-sum seed, never to the profile fit, so the shipped default was unaffected - but the combine back-derives each partial's non-signal variance as sigma^2 - I, and a floored sigma makes that quantity mean nothing. It then read corr^2 * (0.0004 I^2 - I), which is not a background variance. Measured on --integrator boxsum: the reported sigma understated the true scatter by up to 16x at I ~ 21000 counts per partial, and pooled_I amplified a 1 ct/px background drift into an 11.5% intensity error on the strongest reflections. What the floor stood in for - that at high intensity the error is systematic rather than counting - is already carried downstream, twice: the fitted b in v = a*sigma^2 + (b*I)^2, measured from the data rather than assumed, and SigmaWithSystematicFloor on the merged sigma. The floor was that idea applied one level too early with a hardcoded b of 0.02. It arrived without a test or a setter and was unreachable from the CLI, the API and the config. The merge now takes the non-signal variance the integrator actually measured instead of inverting sigma^2 = I + N. That identity is exact for a box sum once the floor is gone and was never exact for a profile fit, whose sigma^2 = 1/den + (wsum/den)^2 * bkg_var is formed against a fitted intensity. The value is carried through BraggFitResult, Reflection and Obs, both engines, both merges, and the process-file round trip; files written before this change are read with the term absent, which is what they had. Battery, 37 crystals, paired: space groups unchanged, reflection sets unchanged, median delta zero on R_meas and CC1/2. --integrator boxsum on the reference crystal goes ISa 8.9 -> 20.2 with a 0.947 -> 1.032. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
63 lines
2.1 KiB
C++
63 lines
2.1 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <cstdint>
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#include <optional>
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#include <cmath>
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#include "SpotToSave.h"
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struct Reflection {
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int32_t h;
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int32_t k;
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int32_t l;
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float image_number; // Can be in-between for 3D integration
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float delta_phi_deg; // phi angle from XDS - difference from middle of current frame (NOT an absolute angle)
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float predicted_x;
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float predicted_y;
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float observed_x;
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float observed_y;
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float d;
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float I;
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float bkg;
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float var_bkg; // non-signal (background) part of sigma^2, carried to the merge
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float sigma;
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float dist_ewald;
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float rlp;
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float partiality; // fraction of the reflection recorded in the sampled (rocking) slice
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float zeta;
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float image_scale_corr; // I_true = scaling_correction * I; scaling_correction = rlp / (partiality * image_scale)
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bool observed = false;
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bool on_ice_ring = false; // sits on a hexagonal-ice powder ring: excluded from scaling, kept for merging
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};
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struct MergedReflection {
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int32_t h = 0;
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int32_t k = 0;
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int32_t l = 0;
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float I = NAN;
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float sigma = NAN;
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float I_half[2] = {NAN, NAN};
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float sigma_half[2] = {NAN, NAN};
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float d = 0.0;
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bool rfree_flag = false;
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float F = NAN; // French-Wilson amplitude |F| (filled by ApplyFrenchWilson at end of merge)
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float sigmaF = NAN; // its sigma
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// Anomalous (Bijvoet) split of this reflection's own observations, kept even when the merge is
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// Friedel-averaged (I above is the Friedel mean). Lets I(+)/I(-) be written and CCano reported by
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// default without scaling anomalously; NaN when a hand was not measured or for centrics.
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float I_plus = NAN;
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float sigma_plus = NAN;
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float I_minus = NAN;
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float sigma_minus = NAN;
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// French-Wilson amplitudes of the two hands (filled by ApplyFrenchWilson from I_plus/I_minus).
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float F_plus = NAN;
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float sigmaF_plus = NAN;
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float F_minus = NAN;
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float sigmaF_minus = NAN;
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};
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