leonarski_f
680c36c20d
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* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
63 lines
2.7 KiB
C++
63 lines
2.7 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 "../gemmi_gph/gemmi/math.hpp"
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#include "../gemmi_gph/gemmi/symmetry.hpp"
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#include <vector>
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#include <array>
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#include "Coord.h"
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#include "UnitCell.h"
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// Below this a basis counts as coplanar. 0.02 is 1.1 deg off flat: an order of magnitude below the
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// flattest basis a real indexing candidate has been seen to reach, and three orders above the point
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// where float cell angles stop carrying even the SIGN of the metric determinant.
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constexpr float MIN_BASIS_VOLUME_FRACTION = 0.02f;
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class CrystalLattice {
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Coord vec[3];
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void FixHandedness();
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// Throws if the basis is too flat to have a reciprocal cell. Everything that builds a lattice
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// rejects one this flat, so reaching it means a degenerate basis got through somewhere.
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void CheckHasReciprocal() const;
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public:
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void ReorderABEqual();
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void ReorderMonoclinic();
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CrystalLattice() = default;
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explicit CrystalLattice(const UnitCell &cell);
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explicit CrystalLattice(const std::vector<float>& input);
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CrystalLattice(float a, float b, float c, float alpha, float beta, float gamma);
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CrystalLattice(const Coord &a, const Coord &b, const Coord &c);
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[[nodiscard]] float CalcVolume() const;
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// |V| / (|a| |b| |c|) - the cell volume made scale-free: 1 for an orthogonal basis, 0 for three
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// coplanar rows. This is the test for a degenerate basis, not CalcVolume(): three nearly-coplanar
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// 300 A rows still enclose hundreds of A^3, so an absolute volume cannot see them, and a basis
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// that flat has no usable reciprocal cell (1/V blows up) whatever its size.
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[[nodiscard]] float VolumeFraction() const;
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[[nodiscard]] const Coord &Vec0() const;
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[[nodiscard]] const Coord &Vec1() const;
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[[nodiscard]] const Coord &Vec2() const;
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[[nodiscard]] Coord Astar() const;
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[[nodiscard]] Coord Bstar() const;
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[[nodiscard]] Coord Cstar() const;
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[[nodiscard]] UnitCell GetUnitCell() const;
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[[nodiscard]] std::vector<float> GetVector() const;
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CrystalLattice FromPrimitive(char centering) const;
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CrystalLattice ToPrimitive(char centering) const;
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CrystalLattice Multiply(const RotMatrix &input) const;
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CrystalLattice Multiply(const gemmi::Mat33 &input) const;
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void Sort();
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void Regularize(const gemmi::CrystalSystem &input);
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[[nodiscard]] std::vector<float> GetUBMatrix() const;
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CrystalLattice NiggliReduce() const;
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void FlipSign(size_t i1);
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};
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inline std::ostream &operator<<( std::ostream &output, const CrystalLattice &in ) {
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output << in.Vec0() << std::endl << in.Vec1() << std::endl << in.Vec2() << std::endl;
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return output;
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}
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