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* Rugnux: Performance improvements on GPU and CPU (more of the pre-scan and of scaling on the GPU, faster CPU spot finding and crystal refinement), with unchanged results. * Rugnux: More robust processing - patches of persistently hot pixels are masked, an inconsistent merge triggers a retry at the measured beam centre, and builds targeting different CPU levels give the same results. * Rugnux: Improved scaling and merging - reflections with an overloaded pixel are dropped, as in XDS, sparse rotation sweeps are scaled more reliably, and French-Wilson amplitudes use an anisotropic Wilson prior. * Rugnux: Improved space-group determination - glide planes in groups without a centre of symmetry, screw axes from short or weak axial rows kept when a higher group is adopted, and more reliable decisions on twinned and pseudo-symmetric crystals. * Rugnux: Improved small-molecule processing - spots that grow wider than the integration disk and split spots are integrated over their measured footprint, sparse lattices are integrated on every frame, and the `.hkl` file holds unmerged scaled reflections (SHELX HKLF 4). * Rugnux: Reads Rigaku d*TREK SMV images (Saturn CCD), including detector 2theta and encoded pixel overflows; home-source (rotating-anode) datasets were added to the validation battery. * jfjoch_viewer: Fixed processing failing at the end with "Wrong JPEG library version" on Linux; the merge window shows the space group with proper subscripts and a checklist of crystal pathologies. Reviewed-on: #84 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
137 lines
6.3 KiB
C++
137 lines
6.3 KiB
C++
// SPDX-FileCopyrightText: 2026 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 <catch2/catch_all.hpp>
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#include "../rugnux/Rugnux.h"
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#include "../image_analysis/scale_merge/RotationScaleMerge.h"
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namespace {
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// A synthetic sweep whose stage turned `true_scale` times the stored angles. Scored at a scale k,
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// the validation spots stay on the lattice as long as the angles track the rotation, and the share
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// that does falls off with the relative rate error; a wrong spindle angle keeps half a percent.
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struct SyntheticSweep {
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double true_scale;
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int64_t spots = 35000;
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int index_calls = 0;
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int refit_calls = 0;
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ValidationSpotEvidence IndexAt(float k) {
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++index_calls;
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const double error = std::fabs(true_scale / k - 1.0);
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const double on = 0.9 * std::max(0.0, 1.0 - 30.0 * error);
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return ValidationSpotEvidence{spots, std::llround(on * spots), std::llround(0.005 * spots)};
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}
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// The post-refinement at k, relative to k. It reads only 70 % of the error that is left: it
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// sees only the frames the angles at k still track.
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std::optional<double> RefitAt(float k) {
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++refit_calls;
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return 1.0 + 0.7 * (true_scale / k - 1.0);
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}
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RotationScaleWalk Walk(double first_fit) {
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return WalkRotationScale(first_fit, [this](float k) { return IndexAt(k); },
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[this](float k) { return RefitAt(k); }, 8);
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}
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};
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}
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TEST_CASE("ValidationEvidencePrefers", "[RotationScale]") {
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const ValidationSpotEvidence base{10000, 3000, 50};
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// 1 % more of the spots beyond chance is under the noise of two 30 % shares over 10000 spots
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// (sqrt(2 * 0.3 * 0.7 / 10000) = 0.65 %, times 3.29); 5 % is well over it.
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CHECK_FALSE(ValidationEvidencePrefers(base, {10000, 3100, 50}));
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CHECK(ValidationEvidencePrefers(base, {10000, 3500, 50}));
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// A candidate is judged against its own null: more spots on the lattice bought by a null that
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// rose just as much is no gain.
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CHECK_FALSE(ValidationEvidencePrefers(base, {10000, 3500, 550}));
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// Never against itself, and nothing that scored nothing wins.
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CHECK_FALSE(ValidationEvidencePrefers(base, base));
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CHECK_FALSE(ValidationEvidencePrefers(base, {}));
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CHECK(ValidationEvidencePrefers({}, base));
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}
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TEST_CASE("WalkRotationScale_ReachesTheFixedPoint", "[RotationScale]") {
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// A stage 3 % slow. The first fit reads 70 % of that; each refit at the adopted scale reads 70 %
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// of what is left, and the walk goes on as long as the validation frames prefer the new scale.
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SyntheticSweep sweep{0.97};
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const auto walk = sweep.Walk(sweep.RefitAt(1.0f).value());
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CHECK(walk.scale == Catch::Approx(0.97).margin(0.001));
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CHECK(walk.scale != 1.0f);
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CHECK(walk.evidence.on_lattice > sweep.IndexAt(1.0f).on_lattice);
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CHECK(sweep.refit_calls > 2);
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CHECK_FALSE(walk.trail.empty());
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}
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TEST_CASE("WalkRotationScale_StoredAnglesStand", "[RotationScale]") {
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SECTION("A healthy stage: a fit off by noise scores no better than the stored angles") {
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SyntheticSweep sweep{1.0};
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const auto walk = sweep.Walk(1.0002);
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CHECK(walk.scale == 1.0f);
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CHECK(sweep.index_calls == 2); // the stored angles and the fit, nothing more
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CHECK(sweep.refit_calls == 0);
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}
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SECTION("A real but small error the spots cannot resolve beyond their noise") {
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SyntheticSweep sweep{0.999};
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sweep.spots = 400;
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const auto walk = sweep.Walk(0.9993);
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CHECK(walk.scale == 1.0f);
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}
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SECTION("A fit that tracks something other than the rotation scores worse, and is refused") {
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SyntheticSweep sweep{1.0};
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const auto walk = sweep.Walk(0.98);
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CHECK(walk.scale == 1.0f);
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CHECK(sweep.refit_calls == 0);
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}
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SECTION("A fit of exactly one asks for no probe at all") {
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SyntheticSweep sweep{1.0};
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const auto walk = sweep.Walk(1.0);
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CHECK(walk.scale == 1.0f);
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CHECK(walk.trail.empty());
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CHECK(sweep.index_calls == 0);
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}
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}
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TEST_CASE("SmoothLogScale_FollowsInformationBridgesGaps", "[RotationScale]") {
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const int n = 60;
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// A ramp is no curvature, so any amount of smoothing keeps it exactly.
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std::vector<double> ramp(n), J(n, 1.0);
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for (int f = 0; f < n; ++f) ramp[f] = -0.1 * f;
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auto x = RotationScaleMerge::SmoothLogScale(ramp, J, 1e6);
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for (int f = 0; f < n; ++f) CHECK(x[f] == Catch::Approx(ramp[f]).margin(1e-6));
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// A stretch with no information is bridged by the straight line through its neighbours.
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std::vector<double> Jgap(J);
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for (int f = 20; f < 40; ++f) Jgap[f] = 0.0;
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x = RotationScaleMerge::SmoothLogScale(ramp, Jgap, 1.0);
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CHECK(x[30] == Catch::Approx(-3.0).margin(1e-6));
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// A frame with far more information than its neighbours keeps its own value.
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std::vector<double> y(n, 0.0), Jone(n, 1.0);
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y[30] = 1.0; Jone[30] = 1e6;
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x = RotationScaleMerge::SmoothLogScale(y, Jone, 10.0);
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CHECK(x[30] == Catch::Approx(1.0).margin(1e-3));
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// Fewer than two frames with information: nothing to smooth against.
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std::vector<double> Jsingle(n, 0.0);
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Jsingle[5] = 1.0;
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CHECK(RotationScaleMerge::SmoothLogScale(y, Jsingle, 1.0) == y);
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}
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TEST_CASE("ChooseLogScaleSmoothing_SmoothsNoiseFollowsSignal", "[RotationScale]") {
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const int n = 400;
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std::vector<double> J(n, 1.0), noisy(n), step(n);
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// Deterministic noise about a flat scale: the chosen curve is close to flat.
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for (int f = 0; f < n; ++f) noisy[f] = 0.3 * std::sin(12.9898 * f) * std::cos(78.233 * f);
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const double l_noise = RotationScaleMerge::ChooseLogScaleSmoothing(noisy, J, 1);
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const auto flat = RotationScaleMerge::SmoothLogScale(noisy, J, l_noise);
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double rms = 0.0;
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for (double v : flat) rms += v * v;
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CHECK(std::sqrt(rms / n) < 0.05);
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// A precise slow wave is followed.
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for (int f = 0; f < n; ++f) step[f] = 2.0 * std::sin(f / 30.0);
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const double l_wave = RotationScaleMerge::ChooseLogScaleSmoothing(step, J, 1);
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const auto wave = RotationScaleMerge::SmoothLogScale(step, J, l_wave);
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CHECK(wave[47] == Catch::Approx(step[47]).margin(0.01));
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CHECK(l_wave < l_noise);
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}
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