v1.0.0-rc.175 (#85)

* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`).
* Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection.
* Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS).
* Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead.
* Rugnux: On macOS, Bragg integration runs on the Apple GPU.
* Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand.
* Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`.
* Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit.
* Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed.
* Rugnux: The beam-stop shadow is found correctly on tilted detectors.
* Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement.
* jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps.
* jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection.
* jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images.
* Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges.

---------

Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home>
Reviewed-on: #85
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

tests/RotationScaleWalkTest.cpp

@@ -31,9 +31,9 @@ namespace {
             return 1.0 + 0.7 * (true_scale / k - 1.0);
         }
 
-        RotationScaleWalk Walk(double first_fit) {
+        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);
+                                     [this](float k) { return RefitAt(k); }, 8, sweep_images);
         }
     };
 }
@@ -65,6 +65,22 @@ TEST_CASE("WalkRotationScale_ReachesTheFixedPoint", "[RotationScale]") {
     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};
@@ -134,3 +150,35 @@ TEST_CASE("ChooseLogScaleSmoothing_SmoothsNoiseFollowsSignal", "[RotationScale]"
     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);
+}