leonarski_fandClaude Opus 4.8
e4b3064254
Reference dataset (a): LoadReferenceMtz adds column selection + cell/SG/resolution + a data-vs-reference consistency check; jfjoch_process/jfjoch_scale gain --reference-column; the viewer gets a Reference section in the MX settings dock (worker-owned, independent of the loaded dataset) that flows into reprocessing jobs. 3D combine (-P rot3d): Combine3D weight-sums a reflection's per-frame partials into one counting-limited full before merging (orthogonal ScalingSettings::combine_3d flag, not a partiality model), with a de-biased Poisson variance. Crystal 2: ISa 1.7->8.4, R-meas ~67%->18.9%, intensities unchanged (CCref held). Quality metrics (b): R-meas (Diederichs-Karplus) + redundancy columns in MergeStats; ISa logged. jfjoch fulls 18.9% vs XDS 4.5% (same ASU/run). Profile-fit integrator (experimental): ProfileIntegrate2D (--integrator gaussian|empirical) is a reference-free, rot3d-compatible profile-fit extraction (the decomposed PixelRefine intensity step). Gaussian: R-meas 18.9->14.6%, ISa ->9.5. Anisotropy/per-region add nothing (the discriminating info is in the discarded rocking direction). See NEXTGEN_INTEGRATOR.md. --dump-observations exports the unmerged fulls for XDS comparison. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
56 lines
3.0 KiB
C++
56 lines
3.0 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 <optional>
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#include <string>
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#include <vector>
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#include "../common/Reflection.h"
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#include "../common/UnitCell.h"
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// A column an MTZ offers as reference intensities/structure factors (type 'J' mean intensity or
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// 'F' amplitude). Surfaced so the caller (CLI flag / viewer combo) can pick which one to scale
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// against and report the choice, rather than the loader silently guessing.
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struct ReferenceMtzColumn {
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std::string label;
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char type = '\0'; // 'J' = mean intensity, 'F' = structure-factor amplitude
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};
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// Reference reflections loaded from an MTZ, plus the metadata a user needs to judge whether the
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// reference matches the data being scaled: which column was used, the cell / space group it was
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// recorded in, its resolution range and reflection count.
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struct ReferenceMtzData {
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std::vector<MergedReflection> reflections; // h,k,l,I,d set (sigma stays NaN)
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std::optional<UnitCell> cell;
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std::optional<int> space_group_number;
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std::string space_group_name; // Hermann-Mauguin short symbol, for display
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std::string point_group; // point-group symbol, for the consistency check
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std::string used_column;
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char used_column_type = '\0';
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bool squared = false; // an 'F' column was squared to an intensity
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bool default_column = true; // column was auto-selected, not user-specified
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std::vector<ReferenceMtzColumn> candidate_columns;
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double d_min = 0.0;
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double d_max = 0.0;
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};
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// Load reference reflections from an MTZ. With no column requested the smart default is used:
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// a calculated structure factor F-model (squared to an intensity), else a merged/observed
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// intensity column (IMEAN/I/IOBS/...), else any mean-intensity (J) column - this also lets
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// PixelRefine be self-seeded from the data's own previous merge. A requested column overrides
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// the default (an 'F'-type column is squared, a 'J'-type used directly). Throws if the requested
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// column is missing or no usable column exists.
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ReferenceMtzData LoadReferenceMtz(const std::string& path,
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const std::optional<std::string>& column = std::nullopt);
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// Compare a loaded reference against the data it will scale. Returns an empty string when they are
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// consistent (or when the data cell / space group is unknown, so nothing can be said); otherwise a
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// one-line, human-readable description of the mismatch to warn the user about. Reference intensities
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// keyed in a different point group or cell do not correspond to the data, so this is the check that
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// makes reference-based scaling and CCref trustworthy.
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std::string ReferenceConsistencyWarning(const ReferenceMtzData& reference,
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const std::optional<UnitCell>& data_cell,
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std::optional<int> data_space_group_number);
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