leonarski_f
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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: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
396 lines
13 KiB
C++
396 lines
13 KiB
C++
// SPDX-FileCopyrightText: 2024 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 "../../common/JFJochMath.h"
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#include "LatticeSearch.h"
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#include <gemmi/cellred.hpp>
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#include <cmath>
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#include <optional>
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// How close the reduced beta has to be to 90 degrees for the two Niggli types to be genuinely
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// interchangeable (see the retry at the end of LatticeSearch). Not the angle tolerance: that is how
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// far a metric may sit from an ideal one and still be called it, which is far too generous here - a
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// cell 2 degrees off the boundary is a real type-1 cell, and presenting it in the obtuse setting
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// promotes a general triclinic lattice to C-centred monoclinic on residuals of ~2 degrees. Measured:
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// the crystal this was found on sits 0.07 degrees from the boundary and matches on 0.006 to 0.135;
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// the triclinic cell that must not be promoted sits 2.0 degrees from it.
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constexpr double NIGGLI_TYPE_BOUNDARY_DEG = 0.5;
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struct NiggliClass {
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int number;
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int type;
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bool cond_AB;
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bool cond_BC;
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double cond_D;
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double cond_E;
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double cond_F;
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bool cond_DEF;
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bool cond_2DF;
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gemmi::Mat33 reindex;
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gemmi::CrystalSystem system;
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char centering;
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};
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LatticeSearchResult LatticeSearch(const CrystalLattice &L, double dist_tolerance, double angle_tolerance) {
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UnitCell uc = L.GetUnitCell();
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gemmi::UnitCell g_uc(uc.a, uc.b, uc.c, uc.alpha, uc.beta, uc.gamma);
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gemmi::GruberVector g_vec(g_uc, 'P', true);
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g_vec.niggli_reduce();
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CrystalLattice L_niggli = L;
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if (g_vec.change_of_basis)
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L_niggli = L.Multiply(gemmi::rot_as_mat33(g_vec.change_of_basis->rot).transpose());
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double A = g_vec.A;
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double B = g_vec.B;
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double C = g_vec.C;
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double D = g_vec.xi / 2;
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double E = g_vec.eta / 2;
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double F = g_vec.zeta / 2;
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// D, E, F are parameters so the table can also be built for the type-flipped setting below.
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auto make_classes = [&](double D, double E, double F) {
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return std::vector<NiggliClass>{
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{
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1, 1,
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true, true, A / 2, A / 2, A / 2, false, false,
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gemmi::Mat33{1, -1, 1, 1, 1, -1, -1, 1, 1},
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gemmi::CrystalSystem::Cubic, 'F'
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},
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{
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2, 1,
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true, true, D, D, D, false, false,
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{1, -1, 0, -1, 0, 1, -1, -1, -1},
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gemmi::CrystalSystem::Trigonal, 'R'
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},
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{
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3, 2,
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true, true, 0, 0, 0, false, false,
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gemmi::Mat33{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Cubic, 'P'
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},
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{
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5, 2,
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true, true, -A / 3, -A / 3, -A / 3, false, false,
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gemmi::Mat33{1, 0, 1, 1, 1, 0, 0, 1, 1},
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gemmi::CrystalSystem::Cubic, 'I'
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},
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{
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4, 2,
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true, true, D, D, D, false, false,
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{1, -1, 0, -1, 0, 1, -1, -1, -1},
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gemmi::CrystalSystem::Trigonal, 'R'
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},
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{
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6, 2,
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true, true, D, D, F, true, false,
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{0, 1, 1, 1, 0, 1, 1, 1, 0},
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gemmi::CrystalSystem::Tetragonal, 'I'
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},
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{
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7, 2,
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true, true, D, E, E, true, false,
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{1, 0, 1, 1, 1, 0, 0, 1, 1},
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gemmi::CrystalSystem::Tetragonal, 'I'
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},
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{
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8, 2,
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true, true, D, E, F, true, false,
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{-1, -1, 0, -1, 0, -1, 0, -1, -1},
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gemmi::CrystalSystem::Orthorhombic, 'I'
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},
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{
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9, 1,
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true, false, A / 2, A / 2, A / 2, false, false,
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{1, 0, 0, -1, 1, 0, -1, -1, 3},
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gemmi::CrystalSystem::Trigonal, 'R'
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},
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{
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10, 1,
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true, false, D, D, F, false, false,
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{1, 1, 0, 1, -1, 0, 0, 0, -1},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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11, 2,
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true, false, 0, 0, 0, false, false,
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{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Tetragonal, 'P'
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},
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{
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12, 2,
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true, false, 0, 0, -A / 2, false, false,
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{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Hexagonal, 'P'
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},
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{
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13, 2,
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true, false, 0, 0, F, false, false,
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{1, 1, 0, -1, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Orthorhombic, 'C'
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},
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{
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15, 2,
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true, false, -A / 2, -A / 2, 0, false, false,
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{1, 0, 0, 0, 1, 0, 1, 1, 2},
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gemmi::CrystalSystem::Tetragonal, 'I'
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},
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{
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16, 2,
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true, false, D, D, F, true, false,
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{-1, -1, 0, 1, -1, 0, 1, 1, 2},
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gemmi::CrystalSystem::Orthorhombic, 'F'
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},
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{
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14, 2,
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true, false, D, D, F, false, false,
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{1, 1, 0, -1, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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17, 2,
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true, false, D, E, F, true, false,
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{1, -1, 0, 1, 1, 0, -1, 0, -1},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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18, 1,
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false, true, A / 4, A / 2, A / 2, false, false,
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{0, -1, 1, 1, -1, -1, 1, 0, 0},
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gemmi::CrystalSystem::Tetragonal, 'I'
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},
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{
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19, 1,
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false, true, D, A / 2, A / 2, false, false,
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{-1, 0, 0, 0, -1, 1, -1, 1, 1},
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gemmi::CrystalSystem::Orthorhombic, 'I'
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},
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{
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20, 1,
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false, true, D, E, E, false, false,
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{0, 1, 1, 0, 1, -1, -1, 0, 0},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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21, 2,
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false, true, 0, 0, 0, false, false,
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{0, 1, 0, 0, 0, 1, 1, 0, 0},
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gemmi::CrystalSystem::Tetragonal, 'P'
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},
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{
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22, 2,
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false, true, -B / 2, 0, 0, false, false,
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{0, 1, 0, 0, 0, 1, 1, 0, 0},
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gemmi::CrystalSystem::Hexagonal, 'P'
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},
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{
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23, 2,
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false, true, D, 0, 0, false, false,
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{0, 1, 1, 0, -1, 1, 1, 0, 0},
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gemmi::CrystalSystem::Orthorhombic, 'C'
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},
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{
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24, 2,
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false, true, D, -A / 3, -A / 3, true, false,
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{1, 2, 1, 0, -1, 1, 1, 0, 0},
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gemmi::CrystalSystem::Trigonal, 'R'
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},
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{
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25, 2,
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false, true, D, E, E, false, false,
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{0, 1, 1, 0, -1, 1, 1, 0, 0},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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26, 1,
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false, false, A / 4, A / 2, A / 2, false, false,
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{1, 0, 0, -1, 2, 0, -1, 0, 2},
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gemmi::CrystalSystem::Orthorhombic, 'F'
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},
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{
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27, 1,
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false, false, D, A / 2, A / 2, false, false,
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{-1, 2, 0, -1, 0, 0, 0, -1, 1},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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28, 1,
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false, false, D, A / 2, 2 * D, false, false,
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{-1, 0, 0, -1, 0, 2, 0, 1, 0},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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29, 1,
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false, false, D, 2 * D, A / 2, false, false,
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{1, 0, 0, 1, -2, 0, 0, 0, -1},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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30, 1,
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false, false, B / 2, E, 2 * E, false, false,
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{0, 1, 0, 0, 1, -2, -1, 0, 0},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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31, 1,
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false, false, D, E, F, false, false,
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{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Triclinic, 'P'
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},
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{
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32, 2,
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false, false, 0, 0, 0, false, false,
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{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Orthorhombic, 'P'
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},
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{
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40, 2,
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false, false, -B / 2, 0, 0, false, false,
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{0, -1, 0, 0, 1, 2, -1, 0, 0},
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gemmi::CrystalSystem::Orthorhombic, 'C'
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},
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{
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35, 2,
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false, false, D, 0, 0, false, false,
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{0, -1, 0, -1, 0, 0, 0, 0, -1},
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gemmi::CrystalSystem::Monoclinic, 'P'
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},
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{
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36, 2,
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false, false, 0, -A / 2, 0, false, false,
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{1, 0, 0, -1, 0, -2, 0, 1, 0},
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gemmi::CrystalSystem::Orthorhombic, 'C'
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},
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{
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33, 2,
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false, false, 0, E, 0, false, false,
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{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Monoclinic, 'P'
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},
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{
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38, 2,
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false, false, 0, 0, -A / 2, false, false,
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{-1, 0, 0, 1, 2, 0, 0, 0, -1},
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gemmi::CrystalSystem::Orthorhombic, 'C'
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},
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{
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34, 2,
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false, false, 0, 0, F, false, false,
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{-1, 0, 0, 0, 0, -1, 0, -1, 0},
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gemmi::CrystalSystem::Monoclinic, 'P'
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},
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{
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42, 2,
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false, false, -B / 2, -A / 2, 0, false, false,
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{-1, 0, 0, 0, -1, 0, 1, 1, 2},
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gemmi::CrystalSystem::Orthorhombic, 'I'
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},
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{
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41, 2,
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false, false, -B / 2, E, 0, false, false,
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{0, -1, -2, 0, -1, 0, -1, 0, 0},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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37, 2,
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false, false, D, -A / 2, 0, false, false,
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{1, 0, 2, 1, 0, 0, 0, 1, 0},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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39, 2,
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false, false, D, 0, -A / 2, false, false,
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{-1, -2, 0, -1, 0, 0, 0, 0, -1},
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gemmi::CrystalSystem::Monoclinic, 'C'
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},
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{
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44, 2,
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false, false, D, E, F, false, false,
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{1, 0, 0, 0, 1, 0, 0, 0, 1},
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gemmi::CrystalSystem::Triclinic, 'P'
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}
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};
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};
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auto match = [&](const CrystalLattice &latt, double D, double E, double F)
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-> std::optional<LatticeSearchResult> {
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const auto uc_reduced = latt.GetUnitCell();
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for (const auto &c: make_classes(D, E, F)) {
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if (c.type == 1 && uc_reduced.beta >= 90 - angle_tolerance )
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continue;
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bool ok = true;
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if (c.cond_AB && fabs((uc_reduced.a - uc_reduced.b) / (0.5 * (uc_reduced.a + uc_reduced.b))) > dist_tolerance)
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ok = false;
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if (c.cond_BC && fabs((uc_reduced.b - uc_reduced.c) / (0.5 * (uc_reduced.b + uc_reduced.c))) > dist_tolerance)
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ok = false;
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double expected_alpha = acos(c.cond_D / sqrt(B*C)) * 180 / PI;
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double expected_beta = acos(c.cond_E / sqrt(A*C)) * 180 / PI;
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double expected_gamma = acos(c.cond_F / sqrt(A*B)) * 180 / PI;
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if (fabs(expected_alpha - uc_reduced.alpha) > angle_tolerance)
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ok = false;
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if (fabs(expected_beta - uc_reduced.beta) > angle_tolerance)
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ok = false;
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if (fabs(expected_gamma - uc_reduced.gamma) > angle_tolerance)
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ok = false;
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double tmp1 = 2.0 * fabs(D + E + F);
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double tmp2 = A + B;
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if (c.cond_DEF && fabs((tmp1 - tmp2) / (0.5 * (tmp1 + tmp2))) > dist_tolerance)
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ok = false;
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if (ok) {
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return LatticeSearchResult{
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.niggli_class = c.number,
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.primitive_reduced = latt,
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.conventional = latt.Multiply(c.reindex),
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.system = c.system,
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.centering = c.centering,
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.reindex = c.reindex,
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};
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}
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}
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return std::nullopt;
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};
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// Character 44 fits any cell, so a match is always found - "nothing fits" is reported as triclinic.
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auto found = match(L_niggli, D, E, F);
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if (found && found->system != gemmi::CrystalSystem::Triclinic)
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return *found;
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// A reduced cell whose beta is 90 to within NIGGLI_TYPE_BOUNDARY_DEG sits ON the boundary between the two
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// Niggli types: the same lattice reduces to an all-acute cell or an all-obtuse one according to the
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// last digits of whatever refinement produced it. The type-1 characters are skipped for such a cell
|
|
// (just above) and the type-2 ones are stated for the obtuse setting, so an acute cell can match none
|
|
// of them and comes back triclinic. Present it in the obtuse setting and try once more - negating a
|
|
// and c keeps the lattice and beta and turns alpha and gamma into their supplements. Measured on a
|
|
// C-centred monoclinic crystal whose reduced beta sits 0.07 deg from 90: its centring was read or
|
|
// missed according to the sign of that 0.07 deg, and with it the space group of the whole run.
|
|
if (L_niggli.GetUnitCell().beta >= 90 - NIGGLI_TYPE_BOUNDARY_DEG && D > 0 && E > 0 && F > 0) {
|
|
const gemmi::Mat33 obtuse(-1, 0, 0, 0, 1, 0, 0, 0, -1);
|
|
const auto flipped = match(L_niggli.Multiply(obtuse), -D, E, -F);
|
|
if (flipped && flipped->system != gemmi::CrystalSystem::Triclinic)
|
|
return *flipped;
|
|
}
|
|
|
|
if (found)
|
|
return *found;
|
|
|
|
return LatticeSearchResult{
|
|
.niggli_class = 44,
|
|
.primitive_reduced = L_niggli,
|
|
.conventional = L_niggli,
|
|
.system = gemmi::CrystalSystem::Triclinic,
|
|
.centering = 'P',
|
|
.reindex = gemmi::Mat33(1, 0, 0, 0, 1, 0, 0, 0, 1),
|
|
};
|
|
}
|