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>

tests/RotationScaleWalkTest.cpp

@@ -182,3 +182,73 @@ TEST_CASE("ValidationEvidenceLog10Tail_Exact", "[RotationScale]") {
     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);
+}