leonarski_fandClaude Opus 5.5
ae7b68dd68
On stills a cell and a detector distance are degenerate: a spot's radius fixes only their ratio. The geometry refinement that -C switches on anchored the cell and refined the distance, so a deposited cell a percent off this crystal moved a correct distance by as much (MPCCD: 50.47 -> 50.14 mm, R-free 0.259 -> 0.318). Now the distance is held and the cell refined from the spots, starting from the given one. Only where the frames have rejected the file's distance (DecideStillsGeometry's grid, which is what -C recovers a bad header distance with) is the cell anchored and the distance refined from it. The grid itself asks the given cell, not one refined at the file's distance. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
64 lines
3.3 KiB
C++
64 lines
3.3 KiB
C++
// SPDX-FileCopyrightText: 2026 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 <vector>
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#include "../../common/CrystalLattice.h"
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#include "../../common/DiffractionGeometry.h"
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#include "../../common/UnitCell.h"
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#include "gemmi/symmetry.hpp"
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// Offline global (multi-frame) geometry refinement for serial stills. Pass 1 indexes many frames
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// independently; this joint bundle adjustment then determines the ONE shared detector geometry (beam
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// centre, distance, cell scale) that per-image refinement cannot reach from a single sparse still, so
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// re-indexing with it converts more frames. Mirrors the validated Python prototype: one Ceres problem
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// with shared beam/distance/cell blocks and a per-frame orientation block, robust loss, and a cell
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// regularizer that anchors the (known) cell to break the distance<->cell-scale degeneracy at low
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// resolution. Detector tilt (rot1/rot2) is NOT refined (gauge-coupled with the beam; zero indexing gain).
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struct GeomRefineSpot {
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float x = 0, y = 0; // observed (raw) spot position, pixels
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int32_t h = 0, k = 0, l = 0; // integer Miller index assigned in pass 1
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};
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struct GeomRefineFrame {
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CrystalLattice lattice; // per-frame indexed lattice (real space), for the orientation seed
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std::vector<GeomRefineSpot> spots; // indexed spots on this frame
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int32_t ordinal = 0; // image this came from; ties are broken on it, so the
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// selected bundle does not depend on collection order
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};
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struct GeometryRefinerSettings {
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gemmi::CrystalSystem crystal_system = gemmi::CrystalSystem::Triclinic;
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// Cell-scale regularizer strength (anchors the cell lengths to the input cell so the otherwise
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// degenerate distance is determined). Large => cell effectively fixed (the validated safe regime).
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double cell_reg_coeff = 30.0;
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// With the distance held, the cell is no longer degenerate with it and is refined from the spots.
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bool refine_distance = true;
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int rounds = 3; // hkl-reassignment / tolerance-tightening rounds
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double beam_range_px = 8.0; // beam bound around the nominal value
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double distance_range_mm = 8.0; // distance bound around the nominal value
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int min_spots_total = 100; // refuse to refine below this many indexed spots
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int num_threads = 1;
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};
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struct GeometryRefinerResult {
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bool ok = false;
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double beam_x_px = 0, beam_y_px = 0; // refined beam centre (== direct beam, tilt not refined)
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double distance_mm = 0;
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UnitCell cell{}; // refined cell
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int frames_used = 0;
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int spots_used = 0;
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double median_residual_px = 0; // final per-spot detector residual (fit quality)
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};
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// nominal_geom supplies the starting beam/distance/tilt/wavelength/pixel size; input_cell is anchored by
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// the regularizer. Returns ok=false (and leaves the caller's geometry untouched) on any failure.
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GeometryRefinerResult RefineGlobalGeometry(const DiffractionGeometry &nominal_geom,
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const UnitCell &input_cell,
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const std::vector<GeomRefineFrame> &frames,
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const GeometryRefinerSettings &settings);
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