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Jungfraujoch/tests/SpindleCuspLossTest.cpp
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v1.0.0-rc.167 (#77)
* `rugnux --model` reports CC(model, data) - the correlation of the merged intensities with the placed, scaled model - by resolution shell, on the same shells as CC1/2, with the reflection count and a significance for each.
* `rugnux --model` fits the model's scale, anisotropic B and bulk-solvent parameters on the working reflections only, so the R-free it reports is measured against a model no free reflection helped scale.
* The bulk-solvent parameters of `rugnux --model` are searched over their physically meaningful range instead of being fitted without bounds, so a model is never scaled with a solvent term that has silently switched itself off.
* The rigid-body placement of `rugnux --model` uses the same bounded bulk solvent as the reported fit, so a model is no longer placed against a target carrying a solvent term with no physical meaning.
* `rugnux --model` puts the model into the data's own description of the lattice before placing it, so a model whose cell is written on other axes - I-centred where the run indexed C-centred, a different unique axis, a permuted orthorhombic cell - is placed rather than scored where it was read; `MODEL_CHANGE_OF_BASIS=` and `MODEL_SETTING_AS_READ=` report it when it happens.
* The rugnux results report opens with a summary - `VERDICT=` (`OK`, `WARNINGS`, `UNUSABLE`, `FAILED`), `VERDICT_TEXT=`, `PATHOLOGY_FLAGS=` with one closed-vocabulary code per condition that warned, and the `WARNING:` lines, which used to close the file - and the sections after it are renumbered 1-5 with no gaps.
* `rugnux --developer` writes the full results report - the pipeline-internal keys and the long explanations the default report now leaves out - and `--finalist-ledger` adds the evidence for every space group the search considered, not only the one it adopted.
* The results report warns when the merged data carry no usable signal and when too little of reciprocal space was measured inside the fitted resolution, and omits `FITTED_RESOLUTION` where the CC1/2 curve it is fitted on never falls off.
* rugnux detects translational pseudo-symmetry and reports it under the `PSEUDO_TRANSLATION` flag as `TNCS_DETECTED=` and the `TNCS_*` keys - a translation the merged data are exactly invariant under is reported as `UNDECLARED_LATTICE_TRANSLATION=` under `LATTICE_TRANSLATION` instead - and a detected pseudo-translation can no longer buy a false screw axis in the space-group search or hide a twin from the L-test (`L_TEST_VS_TNCS=`).
* The space-group search determines glide planes from zonal systematic absences, so a non-Sohncke space group such as P 2_1/c or Pbca is named where the run previously stopped at its Sohncke subgroup; `SOHNCKE_SPACE_GROUP=` carries the best Sohncke group beside it on every run that searched, and a centre of symmetry is never claimed.
* Where the cell metric carries more rotational symmetry than the Bravais class the indexer named, the extra rotations are put to the intensities and the space-group search is asked again on the metric's own cell - adopted only where the intensities confirm the higher symmetry - so a lattice that is nearly but not exactly hexagonal, or whose reduction landed in a sub-cell, still reaches its true point group.
* Systematic-absence calls rest on the evidence rather than on counts: a screw axis whose absent class the data show extinct is no longer refused because a handful of reflections in it read as present, and `SPACE_GROUP_ALTERNATIVES=` no longer drops a candidate that differs only on a zone the sweep never measured.
* A reference correlation measured on too few reflections is refused instead of scored zero, so a run given a reference MTZ is no longer reindexed on an operator that mapped almost everything outside the reference's coverage.
* A frame counts as indexed from 6 spots on its lattice rather than 9, so a weakly diffracting crystal whose frames cannot carry 9 is no longer refused the lattice it fits; `--min-indexed-spots` overrides it.
* `-C` accepts a known cell in any equivalent description - conventional or primitive, centred or not - instead of only the reduced primitive form, so a centred cell given the way it is published no longer makes the run report that it found no lattice.
* Each reflection is corrected for the sensor's quantum efficiency at the angle it meets the detector (attenuation lengths from the NIST tables, which also fixes the spot-width parallax term on CdTe) and for the attenuation of the flight path between the sample and its pixel; `--flight-path air|helium|vacuum` declares the medium - default air, since no file states it - and the report says what was assumed and what it was worth. The unmerged MTZ records the factors in new `QE` and `FLIGHT` columns beside `LP`, so raw counts are `I / LP * QE * FLIGHT`, and `_process.h5` in new optional `qe` and `flight` datasets.
* Rotation geometry post-refinement fits the crystal and the detector at once, against the observed spot positions and the observed rocking angles together, so the refined distance depends far less on how wrong the file's distance was.
* A coarsely sliced sweep integrates correctly: partials are joined into one rocking event by angle rather than by frame count, so two crossings of the Ewald sphere are no longer summed into one full, and at 0.5 degrees per image or coarser the per-frame geometry refinement accepts a spot whose miss the exposure's own rotation accounts for.
* `rugnux --mode scale` reports the detector tilt and direct beam of the geometry it re-scaled at, instead of zeros that read as a flat detector, and no longer warns that no image was indexed on a run whose lattice came from its input file.
* Every rotation run that determined a space group and merged reports what the mounting cost: `SPINDLE_LOST_UNIQUE_FRACTION=` is the fraction (0-1) of unique reflections the mounting made unmeasurable under the measured point group, also written to the master as `/entry/MX/spindleLostUniqueFraction` and what the mounting warning fires on; `SPINDLE_SYMMETRY_AXIS_ANGLE_DEG=` / `SPINDLE_SYMMETRY_AXIS_ORDER=` describe the mounting in the `--developer` report.
* Stills and grid scans carry a per-image `spindle_blind_fraction` - how much of a rotation sweep's blind cone this orientation would make unrecoverable, 0.5 and above calling for a second orientation - through the CBOR stream, HDF5 (`/entry/MX/spindleBlindFraction`), the plot and scan-result APIs, and the viewer and frontend plots; an absent value means the frame could not be assessed and is not a 0.
* The results report's `REPORT_VERSION` is 7.

Reviewed-on: #77
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-09-09 07:25:13 +02:00

94 lines
4.9 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
#include "../rugnux/SpindleCuspLoss.h"
using Catch::Matchers::WithinAbs;
namespace {
// lambda = 1 A against d_min = 1 / (2 sin 15 deg) puts theta_max at exactly 15 deg.
constexpr double WVL = 1.0;
const double D_MIN = 1.0 / (2.0 * std::sin(15.0 * M_PI / 180.0));
Coord Perpendicular(const Coord &v) {
const Coord seed = std::fabs(v.Normalize().x) < 0.9f ? Coord(1, 0, 0) : Coord(0, 1, 0);
return (v % seed).Normalize();
}
}
TEST_CASE("SpindleCuspLoss_Orbit", "[Rugnux][Spindle]") {
SECTION("P1 repairs nothing, anywhere") {
const CrystalLattice latt(UnitCell{40, 50, 60, 83, 95, 102});
const auto r = SpindleUnrepairedFraction(*gemmi::find_spacegroup_by_name("P 1"), latt,
Coord(0.3f, -0.5f, 0.8f), WVL, D_MIN);
REQUIRE(r.has_value());
CHECK_THAT(r->cone_fraction, WithinAbs(1.0, 1e-9));
// Radially weighted double-cone content at theta_max = 15 deg (verified by Monte Carlo).
CHECK_THAT(r->lost_unique_fraction, WithinAbs(0.0203, 0.0005));
CHECK_THAT(r->theta_max_deg, WithinAbs(15.0, 1e-6));
}
SECTION("a lone diad on the spindle, and one perpendicular to it, both lose the whole cone") {
const CrystalLattice latt(UnitCell{40, 50, 60, 90, 100, 90}); // P2, unique axis b
const auto &sg = *gemmi::find_spacegroup_by_name("P 2");
const Coord diad = latt.Vec1(); // b is perpendicular to a and c, so it IS the axis
const auto on = SpindleUnrepairedFraction(sg, latt, diad, WVL, D_MIN);
REQUIRE(on.has_value());
CHECK_THAT(on->cone_fraction, WithinAbs(1.0, 1e-4));
const auto perp = SpindleUnrepairedFraction(sg, latt, Perpendicular(diad), WVL, D_MIN);
REQUIRE(perp.has_value());
CHECK_THAT(perp->cone_fraction, WithinAbs(1.0, 1e-4));
}
SECTION("the same diad at 60 deg from the spindle loses nothing") {
const CrystalLattice latt(UnitCell{40, 50, 60, 90, 100, 90});
const Coord diad = latt.Vec1().Normalize();
const Coord spindle = diad * 0.5f + Perpendicular(diad) * static_cast<float>(std::sqrt(0.75));
const auto r = SpindleUnrepairedFraction(*gemmi::find_spacegroup_by_name("P 2"), latt,
spindle, WVL, D_MIN);
REQUIRE(r.has_value());
CHECK_THAT(r->lost_unique_fraction, WithinAbs(0.0, 1e-9));
}
SECTION("an axis of order >= 3 perpendicular to the spindle repairs the cone completely") {
// The situation the per-image worst-case bound must flag but the known group clears.
const CrystalLattice latt(UnitCell{50, 50, 60, 90, 90, 120});
const Coord three_fold = latt.Vec2(); // c, the 3-fold of P3
const auto r = SpindleUnrepairedFraction(*gemmi::find_spacegroup_by_name("P 3"), latt,
Perpendicular(three_fold), WVL, D_MIN);
REQUIRE(r.has_value());
CHECK_THAT(r->lost_unique_fraction, WithinAbs(0.0, 1e-9));
}
SECTION("a dihedral group repairs an in-plane diad the warning heuristic used to flag") {
// 622 with an in-plane 2-fold exactly on the spindle: the old any-axis-within-15-deg rule
// warned here, but the principal 6-fold maps the cone off itself and nothing is lost.
const CrystalLattice latt(UnitCell{50, 50, 60, 90, 90, 120});
const auto r = SpindleUnrepairedFraction(*gemmi::find_spacegroup_by_name("P 6 2 2"), latt,
latt.Vec0(), WVL, D_MIN);
REQUIRE(r.has_value());
CHECK_THAT(r->lost_unique_fraction, WithinAbs(0.0, 1e-9));
}
SECTION("a cubic group is never severe, whatever the mounting") {
const CrystalLattice latt(UnitCell{60, 60, 60, 90, 90, 90});
const auto &sg = *gemmi::find_spacegroup_by_name("P 4 3 2");
for (const auto &spindle : {Coord(1, 0, 0), Coord(0.3f, -0.5f, 0.8f), Coord(1, 1, 1)}) {
const auto r = SpindleUnrepairedFraction(sg, latt, spindle, WVL, D_MIN);
REQUIRE(r.has_value());
CHECK_THAT(r->lost_unique_fraction, WithinAbs(0.0, 1e-9));
}
}
SECTION("no spindle, no wavelength or no resolution gives no answer") {
const CrystalLattice latt(UnitCell{40, 50, 60, 90, 90, 90});
const auto &sg = *gemmi::find_spacegroup_by_name("P 1");
CHECK_FALSE(SpindleUnrepairedFraction(sg, latt, Coord(0, 0, 0), WVL, D_MIN).has_value());
CHECK_FALSE(SpindleUnrepairedFraction(sg, latt, Coord(0, 0, 1), 0.0, D_MIN).has_value());
CHECK_FALSE(SpindleUnrepairedFraction(sg, latt, Coord(0, 0, 1), WVL, 0.0).has_value());
}
}