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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
120 lines
3.9 KiB
C++
120 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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#include <cmath>
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#include "BraggIntegrationSettings.h"
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#include "JFJochException.h"
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#define check_max(param, val, max) if ((val) > (max)) throw JFJochException(JFJochExceptionCategory::InputParameterAboveMax, param)
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#define check_min(param, val, min) if ((val) < (min)) throw JFJochException(JFJochExceptionCategory::InputParameterBelowMin, param)
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#define check_finite(param, val) if (!std::isfinite(val)) throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, param)
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BraggIntegrationSettings &BraggIntegrationSettings::R1(float input) {
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check_finite("Integration radius R1", input);
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check_min("Integration radius R1", input, 0.1);
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check_max("Integration radius R1", input, 20.0);
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r_1 = input;
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return *this;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::R2(float input) {
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check_finite("Background inner radius R2", input);
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check_min("Background inner radius R2", input, 0.1);
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check_max("Background inner radius R2", input, 30.0);
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if (input <= r_1)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Background inner radius (R2) must be larger than integration radius (R1)");
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r_2 = input;
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return *this;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::R3(float input) {
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check_finite("Background outer radius R3", input);
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check_min("Background outer radius R3", input, 0.1);
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check_max("Background outer radius R3", input, 40.0);
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if (input <= r_2)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"Background outer radius (R3) must be larger than background inner radius (R2)");
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r_3 = input;
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return *this;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::DMinLimit_A(float input) {
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check_finite("Minimum d-spacing", input);
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check_min("Minimum d-spacing", input, 0.5);
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check_max("Minimum d-spacing", input, 100.0);
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d_min_limit_A = input;
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return *this;
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}
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BraggIntegrationSettings & BraggIntegrationSettings::FixedProfileRadius_recipA(std::optional<float> input) {
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if (input) {
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check_finite("Profile radius", input.value());
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check_min("Profile radius [A^-1]", input.value(), 0.000001);
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check_max("Profile radius [A^-1]", input.value(), 0.01);
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}
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fixed_profile_radius = input;
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return *this;
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}
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std::optional<float> BraggIntegrationSettings::GetFixedProfileRadius_recipA() const {
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return fixed_profile_radius;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::Integrator(IntegratorMode input) {
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integrator_mode = input;
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return *this;
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}
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IntegratorMode BraggIntegrationSettings::GetIntegrator() const {
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return integrator_mode;
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}
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float BraggIntegrationSettings::GetR1() const {
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return r_1;
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}
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float BraggIntegrationSettings::GetR2() const {
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return r_2;
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}
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float BraggIntegrationSettings::GetR3() const {
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return r_3;
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}
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float BraggIntegrationSettings::GetDMinLimit_A() const {
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return d_min_limit_A;
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}
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float BraggIntegrationSettings::GetMinimumSigmaInRegardsToI() const {
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return minimum_sigma_in_regards_to_i;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::StillPartiality(bool input) {
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still_partiality = input;
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return *this;
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}
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bool BraggIntegrationSettings::GetStillPartiality() const {
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return still_partiality;
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}
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BraggIntegrationSettings &BraggIntegrationSettings::BackgroundTrimFraction(float input) {
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check_finite("Background trim fraction", input);
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check_min("Background trim fraction", input, 0.0);
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check_max("Background trim fraction", input, 0.49); // must leave a central majority after trimming
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bkg_trim_fraction = input;
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return *this;
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}
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float BraggIntegrationSettings::GetBackgroundTrimFraction() const {
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return bkg_trim_fraction;
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}
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