leonarski_fandClaude Opus 5
5b8ce26c83
A reflection arriving at an angle to the detector normal crosses D/cos(alpha) of whatever lies between the sample and the sensor, not D, so it is attenuated more than one arriving head-on and reads low. That is the same geometry as the sensor crossing already corrected here and the opposite sign, and it was missing. The factor is exp(D/L*(1/cos(alpha)-1)) from the NIST attenuation coefficient of the medium, the stated distance and the stated wavelength. Nothing in it is fitted, and it is not justified by any measured amplitude: the flight path and the sensor crossing are collinear to better than 0.998 over the angular range any single experiment samples, so no fit of one can be evidence for the other. It is the tabulated absorption of a known thickness of a known material over a known path. The medium cannot be detected. No field of the NXmx application definition describes it, none of the masters this program reads carries one, and it cannot be inferred from the implied transmission either - in this corpus a station confirmed to use helium sits at 51% implied air transmission and one confirmed to use air at 63%, so any rule separating them is a threshold fitted between two points. It is therefore assumed, stated, and overridable: --flight-path air|helium|vacuum, defaulting to air. Helium is its own material rather than an alias for vacuum, attenuating about a six hundredth of air rather than nothing. On an untilted detector the correction is a function of resolution alone, so its entire effect on merged data is a shift in the Wilson B - which is what the report now prints beside the assumption, accurate to better than a tenth of an angstrom squared against measurement from 0.05 up to 28. Where that shift is large the report warns, because a wrong medium is then the largest number in the run: applied to data from the confirmed helium station it returns a B of 14 A^2 at 3.0 A resolution, which is not a value a crystal can have. The corpus contains its own control. One crystal, one station, three collections a quarter of an hour apart at falling energy through the same air: corrected, the Wilson B rises monotonically with the dose, as it must. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
84 lines
3.9 KiB
C++
84 lines
3.9 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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// The reciprocal Lorentz factor (rotation only - a still's Lorentz factor is one) times the
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// reciprocal polarization factor, and nothing else. This is what LP means everywhere in the
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// field, and it is what the CBOR key "rlp" and the HDF5 dataset "lp" store the reciprocal of.
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// What it is not is a scale: the fitted per-image scale and the partiality stay out of it and
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// are divided in separately below. (Named after DIALS's prescaling_correction.)
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float prescaling_corr;
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// The sensor's angle-dependent efficiency, QE(0)/QE(alpha): always <= 1, and exactly 1 where the
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// sensor is opaque or its material and thickness are unknown. It is carried BESIDE
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// prescaling_corr rather than inside it, because LP and detector response are two different
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// things and every file the field reads keeps them apart. The total deterministic correction on
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// a reflection is therefore prescaling_corr * qe_corr, and every site that corrects an intensity
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// multiplies the two. Defaulted to 1 so a reflection read from a file written before this
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// existed is a no-op rather than a zero.
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float qe_corr = 1.0f;
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// The air in the sample-to-pixel flight path, exp(D/L * (1/cos(alpha) - 1)): always >= 1, and
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// exactly 1 when the air correction is switched off. Carried beside the two above for the same
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// reason they are carried apart - it is neither beam geometry nor detector response but the
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// medium in between, and unlike either of them it is set by the flight distance. The total
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// deterministic correction on a reflection is prescaling_corr * qe_corr * flight_corr, and every
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// site that corrects an intensity multiplies all three. Defaulted to 1 so a reflection read
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// from a file written before this existed is a no-op rather than a zero.
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float flight_corr = 1.0f;
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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 = image_scale_corr * I; = prescaling_corr * qe_corr * flight_corr / (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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