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* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`). * Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels. * Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL. * jfjoch_viewer: Opens the same XFEL file formats. * Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL. * Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded. * jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start. Reviewed-on: #88 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
255 lines
13 KiB
C++
255 lines
13 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, int64_t sweep_images = 3600) {
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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, sweep_images);
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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_StopsWhereTheNextStepIsUnderHalfAFrame", "[RotationScale]") {
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// Spots enough for the validation frames to prefer every step: what ends the walk is the step the
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// contraction predicts, measured against the sweep. Each refit reads 70 % of the error left, so the
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// steps contract by 0.3.
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SyntheticSweep short_sweep{0.97};
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short_sweep.spots = 1000000000;
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const auto a = short_sweep.Walk(short_sweep.RefitAt(1.0f).value(), 360);
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SyntheticSweep long_sweep{0.97};
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long_sweep.spots = 1000000000;
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const auto b = long_sweep.Walk(long_sweep.RefitAt(1.0f).value(), 36000);
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CHECK(short_sweep.refit_calls < long_sweep.refit_calls);
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// Where it stops, what is left of the error moves the end of the sweep by under a frame.
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CHECK(std::fabs(a.scale - 0.97) * 360 < 1.0);
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CHECK(std::fabs(b.scale - 0.97) * 36000 < 1.0);
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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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TEST_CASE("ValidationEvidenceBeatsChance_ExchangeableArrangements", "[RotationScale]") {
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// Four reflections taken at the recorded angles and none at any wrong one: (1/6)^4 < 0.001.
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CHECK(ValidationEvidenceBeatsChance({.reflections = 4, .reflections_by_chance = 0}));
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CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 3, .reflections_by_chance = 0}));
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// The same four with two more spread over the wrong angles is what chance does once in ~100.
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CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 4, .reflections_by_chance = 2}));
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CHECK_FALSE(ValidationEvidenceBeatsChance({}));
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// A real lattice: thousands against a handful.
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CHECK(ValidationEvidenceBeatsChance({.reflections = 3000, .reflections_by_chance = 250}));
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// As many at the recorded angles as at an average wrong one is no lattice.
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CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 100, .reflections_by_chance = 500}));
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}
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TEST_CASE("ValidationEvidenceBeatsChance_NoCrystalSignificance", "[RotationScale]") {
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// A handful of stray reflections passes 0.001 but not the no-crystal test's own level.
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CHECK(ValidationEvidenceBeatsChance({.reflections = 5, .reflections_by_chance = 1}));
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CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 5, .reflections_by_chance = 1}, NO_CRYSTAL_SIGNIFICANCE));
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// Against two by chance it takes 15 (tail 10^-9.7), and 14 is not enough (10^-8.96).
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CHECK(ValidationEvidenceBeatsChance({.reflections = 15, .reflections_by_chance = 2}, NO_CRYSTAL_SIGNIFICANCE));
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CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 14, .reflections_by_chance = 2}, NO_CRYSTAL_SIGNIFICANCE));
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// A weak real lattice on a few frames is still tens of decades past it.
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CHECK(ValidationEvidenceBeatsChance({.reflections = 115, .reflections_by_chance = 4}, NO_CRYSTAL_SIGNIFICANCE));
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}
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TEST_CASE("ValidationEvidenceLog10Tail_Exact", "[RotationScale]") {
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CHECK(ValidationEvidenceLog10Tail({.reflections = 4, .reflections_by_chance = 2}) == Catch::Approx(-2.0604).margin(1e-4));
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CHECK(ValidationEvidenceLog10Tail({.reflections = 5, .reflections_by_chance = 2}) == Catch::Approx(-2.6981).margin(1e-4));
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// Far below the smallest double, still finite.
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CHECK(ValidationEvidenceLog10Tail({.reflections = 1354, .reflections_by_chance = 777}) == Catch::Approx(-509.691).margin(1e-3));
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CHECK(ValidationEvidenceLog10Tail({}) == 0.0);
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}
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namespace {
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// A frame of `strong` reflections at I/sigma 10, `up` and `down` at +4 and -4 (noise in both
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// tails), and enough at +-0.5 to make 200 in all, every one on a background of `bkg`.
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IntegrationOutcome FrameOf(int strong, float bkg, int up = 0, int down = 0) {
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IntegrationOutcome io;
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auto add = [&](float z) {
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Reflection r{};
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r.I = z;
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r.sigma = 1.0f;
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r.bkg = bkg;
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io.reflections.push_back(r);
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};
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for (int i = 0; i < strong; ++i) add(10.0f);
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for (int i = 0; i < up; ++i) add(4.0f);
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for (int i = 0; i < down; ++i) add(-4.0f);
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for (int i = strong + up + down; i < 200; ++i) add(i % 2 ? 0.5f : -0.5f);
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return io;
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}
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}
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TEST_CASE("TrimBlankSweepEnds_ShutterEndsOnly", "[RotationScale]") {
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std::vector<IntegrationOutcome> sweep;
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sweep.push_back(FrameOf(0, 0.0f)); // 0: the shutter not yet open
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sweep.push_back(FrameOf(20, 3.0f)); // 1: partly exposed - it recorded something, so it stays
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for (int f = 2; f < 37; ++f) // 20: no beam inside the sweep - the ledger's, not ours
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sweep.push_back(f == 20 ? FrameOf(0, 0.0f) : FrameOf(40, 10.0f));
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sweep.push_back(FrameOf(0, 2.0f)); // 37: closed; a dark level, as a CCD leaves
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sweep.push_back(FrameOf(0, 0.0f, 4, 4)); // 38: closed, noise in both tails
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sweep.emplace_back(); // 39: nothing integrated - passed over, not counted
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const auto [at_start, at_end] = TrimBlankSweepEnds(sweep, 2);
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CHECK(at_start == 1);
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CHECK(at_end == 2);
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CHECK(sweep[0].reflections.empty());
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CHECK(sweep[1].reflections.size() == 200);
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CHECK(sweep[20].reflections.size() == 200);
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CHECK(sweep[36].reflections.size() == 200);
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CHECK(sweep[37].reflections.empty());
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CHECK(sweep[38].reflections.empty());
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}
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TEST_CASE("TrimBlankSweepEnds_CrystalOutOfTheBeamStays", "[RotationScale]") {
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// No diffraction at the end, but the beam was on - the background is still there. That is the crystal
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// leaving the beam, which the sweep ledger reports; it is not a shutter.
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std::vector<IntegrationOutcome> sweep;
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for (int f = 0; f < 36; ++f)
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sweep.push_back(FrameOf(40, 10.0f));
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for (int f = 36; f < 40; ++f)
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sweep.push_back(FrameOf(0, 8.0f));
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const auto [at_start, at_end] = TrimBlankSweepEnds(sweep, 2);
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CHECK(at_start == 0);
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CHECK(at_end == 0);
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CHECK(sweep.back().reflections.size() == 200);
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}
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TEST_CASE("TrimBlankSweepEnds_WeakCrystalKeepsItsEnds", "[RotationScale]") {
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// Three strong reflections a frame: one frame cannot tell this crystal from no crystal, so even a
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// frame without beam at an end is not called.
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std::vector<IntegrationOutcome> sweep;
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sweep.push_back(FrameOf(0, 0.0f));
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for (int f = 1; f < 39; ++f)
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sweep.push_back(FrameOf(3, 10.0f));
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sweep.push_back(FrameOf(0, 0.0f));
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const auto [at_start, at_end] = TrimBlankSweepEnds(sweep, 2);
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CHECK(at_start == 0);
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CHECK(at_end == 0);
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CHECK(sweep.front().reflections.size() == 200);
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CHECK(sweep.back().reflections.size() == 200);
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}
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