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Jungfraujoch/tests/RotationScaleWalkTest.cpp
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v1.0.0-rc.178 (#88)
* 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>
2026-10-21 11:20:01 +02:00

255 lines
13 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <cmath>
#include <catch2/catch_all.hpp>
#include "../rugnux/Rugnux.h"
#include "../image_analysis/scale_merge/RotationScaleMerge.h"
namespace {
// A synthetic sweep whose stage turned `true_scale` times the stored angles. Scored at a scale k,
// the validation spots stay on the lattice as long as the angles track the rotation, and the share
// that does falls off with the relative rate error; a wrong spindle angle keeps half a percent.
struct SyntheticSweep {
double true_scale;
int64_t spots = 35000;
int index_calls = 0;
int refit_calls = 0;
ValidationSpotEvidence IndexAt(float k) {
++index_calls;
const double error = std::fabs(true_scale / k - 1.0);
const double on = 0.9 * std::max(0.0, 1.0 - 30.0 * error);
return ValidationSpotEvidence{spots, std::llround(on * spots), std::llround(0.005 * spots)};
}
// The post-refinement at k, relative to k. It reads only 70 % of the error that is left: it
// sees only the frames the angles at k still track.
std::optional<double> RefitAt(float k) {
++refit_calls;
return 1.0 + 0.7 * (true_scale / k - 1.0);
}
RotationScaleWalk Walk(double first_fit, int64_t sweep_images = 3600) {
return WalkRotationScale(first_fit, [this](float k) { return IndexAt(k); },
[this](float k) { return RefitAt(k); }, 8, sweep_images);
}
};
}
TEST_CASE("ValidationEvidencePrefers", "[RotationScale]") {
const ValidationSpotEvidence base{10000, 3000, 50};
// 1 % more of the spots beyond chance is under the noise of two 30 % shares over 10000 spots
// (sqrt(2 * 0.3 * 0.7 / 10000) = 0.65 %, times 3.29); 5 % is well over it.
CHECK_FALSE(ValidationEvidencePrefers(base, {10000, 3100, 50}));
CHECK(ValidationEvidencePrefers(base, {10000, 3500, 50}));
// A candidate is judged against its own null: more spots on the lattice bought by a null that
// rose just as much is no gain.
CHECK_FALSE(ValidationEvidencePrefers(base, {10000, 3500, 550}));
// Never against itself, and nothing that scored nothing wins.
CHECK_FALSE(ValidationEvidencePrefers(base, base));
CHECK_FALSE(ValidationEvidencePrefers(base, {}));
CHECK(ValidationEvidencePrefers({}, base));
}
TEST_CASE("WalkRotationScale_ReachesTheFixedPoint", "[RotationScale]") {
// A stage 3 % slow. The first fit reads 70 % of that; each refit at the adopted scale reads 70 %
// of what is left, and the walk goes on as long as the validation frames prefer the new scale.
SyntheticSweep sweep{0.97};
const auto walk = sweep.Walk(sweep.RefitAt(1.0f).value());
CHECK(walk.scale == Catch::Approx(0.97).margin(0.001));
CHECK(walk.scale != 1.0f);
CHECK(walk.evidence.on_lattice > sweep.IndexAt(1.0f).on_lattice);
CHECK(sweep.refit_calls > 2);
CHECK_FALSE(walk.trail.empty());
}
TEST_CASE("WalkRotationScale_StopsWhereTheNextStepIsUnderHalfAFrame", "[RotationScale]") {
// Spots enough for the validation frames to prefer every step: what ends the walk is the step the
// contraction predicts, measured against the sweep. Each refit reads 70 % of the error left, so the
// steps contract by 0.3.
SyntheticSweep short_sweep{0.97};
short_sweep.spots = 1000000000;
const auto a = short_sweep.Walk(short_sweep.RefitAt(1.0f).value(), 360);
SyntheticSweep long_sweep{0.97};
long_sweep.spots = 1000000000;
const auto b = long_sweep.Walk(long_sweep.RefitAt(1.0f).value(), 36000);
CHECK(short_sweep.refit_calls < long_sweep.refit_calls);
// Where it stops, what is left of the error moves the end of the sweep by under a frame.
CHECK(std::fabs(a.scale - 0.97) * 360 < 1.0);
CHECK(std::fabs(b.scale - 0.97) * 36000 < 1.0);
}
TEST_CASE("WalkRotationScale_StoredAnglesStand", "[RotationScale]") {
SECTION("A healthy stage: a fit off by noise scores no better than the stored angles") {
SyntheticSweep sweep{1.0};
const auto walk = sweep.Walk(1.0002);
CHECK(walk.scale == 1.0f);
CHECK(sweep.index_calls == 2); // the stored angles and the fit, nothing more
CHECK(sweep.refit_calls == 0);
}
SECTION("A real but small error the spots cannot resolve beyond their noise") {
SyntheticSweep sweep{0.999};
sweep.spots = 400;
const auto walk = sweep.Walk(0.9993);
CHECK(walk.scale == 1.0f);
}
SECTION("A fit that tracks something other than the rotation scores worse, and is refused") {
SyntheticSweep sweep{1.0};
const auto walk = sweep.Walk(0.98);
CHECK(walk.scale == 1.0f);
CHECK(sweep.refit_calls == 0);
}
SECTION("A fit of exactly one asks for no probe at all") {
SyntheticSweep sweep{1.0};
const auto walk = sweep.Walk(1.0);
CHECK(walk.scale == 1.0f);
CHECK(walk.trail.empty());
CHECK(sweep.index_calls == 0);
}
}
TEST_CASE("SmoothLogScale_FollowsInformationBridgesGaps", "[RotationScale]") {
const int n = 60;
// A ramp is no curvature, so any amount of smoothing keeps it exactly.
std::vector<double> ramp(n), J(n, 1.0);
for (int f = 0; f < n; ++f) ramp[f] = -0.1 * f;
auto x = RotationScaleMerge::SmoothLogScale(ramp, J, 1e6);
for (int f = 0; f < n; ++f) CHECK(x[f] == Catch::Approx(ramp[f]).margin(1e-6));
// A stretch with no information is bridged by the straight line through its neighbours.
std::vector<double> Jgap(J);
for (int f = 20; f < 40; ++f) Jgap[f] = 0.0;
x = RotationScaleMerge::SmoothLogScale(ramp, Jgap, 1.0);
CHECK(x[30] == Catch::Approx(-3.0).margin(1e-6));
// A frame with far more information than its neighbours keeps its own value.
std::vector<double> y(n, 0.0), Jone(n, 1.0);
y[30] = 1.0; Jone[30] = 1e6;
x = RotationScaleMerge::SmoothLogScale(y, Jone, 10.0);
CHECK(x[30] == Catch::Approx(1.0).margin(1e-3));
// Fewer than two frames with information: nothing to smooth against.
std::vector<double> Jsingle(n, 0.0);
Jsingle[5] = 1.0;
CHECK(RotationScaleMerge::SmoothLogScale(y, Jsingle, 1.0) == y);
}
TEST_CASE("ChooseLogScaleSmoothing_SmoothsNoiseFollowsSignal", "[RotationScale]") {
const int n = 400;
std::vector<double> J(n, 1.0), noisy(n), step(n);
// Deterministic noise about a flat scale: the chosen curve is close to flat.
for (int f = 0; f < n; ++f) noisy[f] = 0.3 * std::sin(12.9898 * f) * std::cos(78.233 * f);
const double l_noise = RotationScaleMerge::ChooseLogScaleSmoothing(noisy, J, 1);
const auto flat = RotationScaleMerge::SmoothLogScale(noisy, J, l_noise);
double rms = 0.0;
for (double v : flat) rms += v * v;
CHECK(std::sqrt(rms / n) < 0.05);
// A precise slow wave is followed.
for (int f = 0; f < n; ++f) step[f] = 2.0 * std::sin(f / 30.0);
const double l_wave = RotationScaleMerge::ChooseLogScaleSmoothing(step, J, 1);
const auto wave = RotationScaleMerge::SmoothLogScale(step, J, l_wave);
CHECK(wave[47] == Catch::Approx(step[47]).margin(0.01));
CHECK(l_wave < l_noise);
}
TEST_CASE("ValidationEvidenceBeatsChance_ExchangeableArrangements", "[RotationScale]") {
// Four reflections taken at the recorded angles and none at any wrong one: (1/6)^4 < 0.001.
CHECK(ValidationEvidenceBeatsChance({.reflections = 4, .reflections_by_chance = 0}));
CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 3, .reflections_by_chance = 0}));
// The same four with two more spread over the wrong angles is what chance does once in ~100.
CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 4, .reflections_by_chance = 2}));
CHECK_FALSE(ValidationEvidenceBeatsChance({}));
// A real lattice: thousands against a handful.
CHECK(ValidationEvidenceBeatsChance({.reflections = 3000, .reflections_by_chance = 250}));
// As many at the recorded angles as at an average wrong one is no lattice.
CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 100, .reflections_by_chance = 500}));
}
TEST_CASE("ValidationEvidenceBeatsChance_NoCrystalSignificance", "[RotationScale]") {
// A handful of stray reflections passes 0.001 but not the no-crystal test's own level.
CHECK(ValidationEvidenceBeatsChance({.reflections = 5, .reflections_by_chance = 1}));
CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 5, .reflections_by_chance = 1}, NO_CRYSTAL_SIGNIFICANCE));
// Against two by chance it takes 15 (tail 10^-9.7), and 14 is not enough (10^-8.96).
CHECK(ValidationEvidenceBeatsChance({.reflections = 15, .reflections_by_chance = 2}, NO_CRYSTAL_SIGNIFICANCE));
CHECK_FALSE(ValidationEvidenceBeatsChance({.reflections = 14, .reflections_by_chance = 2}, NO_CRYSTAL_SIGNIFICANCE));
// A weak real lattice on a few frames is still tens of decades past it.
CHECK(ValidationEvidenceBeatsChance({.reflections = 115, .reflections_by_chance = 4}, NO_CRYSTAL_SIGNIFICANCE));
}
TEST_CASE("ValidationEvidenceLog10Tail_Exact", "[RotationScale]") {
CHECK(ValidationEvidenceLog10Tail({.reflections = 4, .reflections_by_chance = 2}) == Catch::Approx(-2.0604).margin(1e-4));
CHECK(ValidationEvidenceLog10Tail({.reflections = 5, .reflections_by_chance = 2}) == Catch::Approx(-2.6981).margin(1e-4));
// Far below the smallest double, still finite.
CHECK(ValidationEvidenceLog10Tail({.reflections = 1354, .reflections_by_chance = 777}) == Catch::Approx(-509.691).margin(1e-3));
CHECK(ValidationEvidenceLog10Tail({}) == 0.0);
}
namespace {
// A frame of `strong` reflections at I/sigma 10, `up` and `down` at +4 and -4 (noise in both
// tails), and enough at +-0.5 to make 200 in all, every one on a background of `bkg`.
IntegrationOutcome FrameOf(int strong, float bkg, int up = 0, int down = 0) {
IntegrationOutcome io;
auto add = [&](float z) {
Reflection r{};
r.I = z;
r.sigma = 1.0f;
r.bkg = bkg;
io.reflections.push_back(r);
};
for (int i = 0; i < strong; ++i) add(10.0f);
for (int i = 0; i < up; ++i) add(4.0f);
for (int i = 0; i < down; ++i) add(-4.0f);
for (int i = strong + up + down; i < 200; ++i) add(i % 2 ? 0.5f : -0.5f);
return io;
}
}
TEST_CASE("TrimBlankSweepEnds_ShutterEndsOnly", "[RotationScale]") {
std::vector<IntegrationOutcome> sweep;
sweep.push_back(FrameOf(0, 0.0f)); // 0: the shutter not yet open
sweep.push_back(FrameOf(20, 3.0f)); // 1: partly exposed - it recorded something, so it stays
for (int f = 2; f < 37; ++f) // 20: no beam inside the sweep - the ledger's, not ours
sweep.push_back(f == 20 ? FrameOf(0, 0.0f) : FrameOf(40, 10.0f));
sweep.push_back(FrameOf(0, 2.0f)); // 37: closed; a dark level, as a CCD leaves
sweep.push_back(FrameOf(0, 0.0f, 4, 4)); // 38: closed, noise in both tails
sweep.emplace_back(); // 39: nothing integrated - passed over, not counted
const auto [at_start, at_end] = TrimBlankSweepEnds(sweep, 2);
CHECK(at_start == 1);
CHECK(at_end == 2);
CHECK(sweep[0].reflections.empty());
CHECK(sweep[1].reflections.size() == 200);
CHECK(sweep[20].reflections.size() == 200);
CHECK(sweep[36].reflections.size() == 200);
CHECK(sweep[37].reflections.empty());
CHECK(sweep[38].reflections.empty());
}
TEST_CASE("TrimBlankSweepEnds_CrystalOutOfTheBeamStays", "[RotationScale]") {
// No diffraction at the end, but the beam was on - the background is still there. That is the crystal
// leaving the beam, which the sweep ledger reports; it is not a shutter.
std::vector<IntegrationOutcome> sweep;
for (int f = 0; f < 36; ++f)
sweep.push_back(FrameOf(40, 10.0f));
for (int f = 36; f < 40; ++f)
sweep.push_back(FrameOf(0, 8.0f));
const auto [at_start, at_end] = TrimBlankSweepEnds(sweep, 2);
CHECK(at_start == 0);
CHECK(at_end == 0);
CHECK(sweep.back().reflections.size() == 200);
}
TEST_CASE("TrimBlankSweepEnds_WeakCrystalKeepsItsEnds", "[RotationScale]") {
// Three strong reflections a frame: one frame cannot tell this crystal from no crystal, so even a
// frame without beam at an end is not called.
std::vector<IntegrationOutcome> sweep;
sweep.push_back(FrameOf(0, 0.0f));
for (int f = 1; f < 39; ++f)
sweep.push_back(FrameOf(3, 10.0f));
sweep.push_back(FrameOf(0, 0.0f));
const auto [at_start, at_end] = TrimBlankSweepEnds(sweep, 2);
CHECK(at_start == 0);
CHECK(at_end == 0);
CHECK(sweep.front().reflections.size() == 200);
CHECK(sweep.back().reflections.size() == 200);
}