rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG
The rc178 branch continued after #88 was squash-merged; this is its content fromb9ada7914(the tree #88 squashed) to094eee31a, as one change on main. The individual commits stay on the rc178 branch: - still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes - AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets - DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked - tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout - Dense per-pixel maps through the panel table (panel layout stage 1) - Panel id on spots and the panel table in the start message - Viewer and preview show a panel detector as it lies on the detector plane - Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster - Panel layout stage 2: prediction and Bragg integration through the panel table - XTC reader: frames handed up as stored, streams indexed in parallel - XFEL reader: integer frames stay integer, one gain, placement by panel - EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery" - still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed - float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count - CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them - Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table - Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane - still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good - still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file - still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition - stills fixed cost: geometry refinement and pre-scan do the same work in less wall time - stills geometry sample and trial spot finding run as many workers as the image pass - Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame - StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's - MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in) - Stills given a cell: the written cell is the mean over the frames that are merged - Stills: the radial curvature correction decided per run on the same empty apertures - StillsPartialityRefine: measure the run width only on shells with signal - Stills pre-scan: report the paired z of the radial-correction comparison - module placement: the five concurrent fits each keep every thread - still battery: score R-free against the deposited data through the same dimple protocol - still battery: the R-free target is the lower of the deposition's dimple and published values - Stills: background clip follows the radial curve; signal disk from the lattice spacing - Stills keep an overloaded observation as a lower bound instead of dropping it - Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip - battery: R-free against the deposition without refinement only, one protocol for rotation and stills - still battery: EuXFEL sets run on a 2,000-image subset for now - stills geometry refinement: fit the detector distance and the cell together - stills geometry refinement: a distance given with --detector-distance is held in the joint fit - Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count - Metal integration test: the CPU comparison runs on a rotation experiment - Stills: kept overloads go back to the drop where they are not concentrated at low resolution - stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated - battery results: XFEL still battery 20261022-1358 on rc1780cf62452c- 12 sets, cold, R_free unrefined - battery results: still summary gains the resolution of our merge and of the deposition - Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value - Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed - XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock - stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes - rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid - stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree - CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get - broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4) - frontend: Mol* viewer of the placed model and its density on the Rugnux live page - writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does - rugnux live maps: one unit cell centred on the model; the viewer opens on all of it - Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer - Mol* viewer: open with the maps drawn within 10 A of the centre of view - Mol* viewer: aaredb's structure-viewer setup, on a black stage - rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons - Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2) - ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI) - stills tilt decision: the modules stay where the run placed them - still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it - battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC - Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons - BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it - ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization - BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain - ShadowFinder: measure the modulation robustly under a wide one-sided shadow - ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation - ShadowFinder: back to the predicted polarization factor, in the plane the background shows - MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again - battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables - XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel - stills geometry trial: the hypotheses a search asks are indexed side by side - stills tilt decision: the fits start beside the pre-scan and the geometry trial - XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache - XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step - GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block - GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart - docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts - battery: doc_check.py cross-checks the manifests against the dataset pages - stills module placement: the placement fit gets half the threads, each held-out fit an eighth - still battery: the EuXFEL sets run on all their frames, as the published still runs did - battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table - macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
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@@ -720,6 +720,7 @@ TEST_CASE("StillsPartialityRefine_RecoversTheTilt") {
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Reflection r{};
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r.h = h; r.k = k; r.l = l;
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r.d = 1.0f / dstar;
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r.dist_ewald = std::fabs((q + S0).Length() - 1.0f / WAVELENGTH);
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r.I = static_cast<float>(G * p_true * full_I(h, k, l));
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r.sigma = static_cast<float>(1.0 + 0.01 * r.I);
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r.prescaling_corr = 1.0f;
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@@ -745,7 +746,7 @@ TEST_CASE("StillsPartialityRefine_RecoversTheTilt") {
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const double after = mean_abs_error();
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CHECK(mean_tilt > 0.015);
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CHECK(mean_tilt < 0.06);
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CHECK(after < 0.6 * before); // measured 0.54: the prior holds the larger tilts back
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CHECK(after < 0.6 * before); // measured 0.41 (0.54 with the per-crystal window width): the prior holds the larger tilts back
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}
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namespace {
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@@ -914,3 +915,116 @@ TEST_CASE("MergeOnTheFly_RsplitKeepsEveryFrameWhole") {
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CHECK(sh.r_split == Catch::Approx(expected).epsilon(1e-5));
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CHECK_FALSE(SerialShellTable(stats).empty());
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}
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// The run's rocking width is measured on the crystals, not on the prediction window: reflections spread
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// evenly across a window four times wider than the curve, each recording I_full * p(de), give back the
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// curve's gamma0 and angular width, while the plain moment of de would return the window's.
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TEST_CASE("StillsPartialityRefine_MeasureRunWidth") {
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constexpr double GAMMA0 = 1.0e-4, GAMMA_E = 0.035 * M_PI / 180.0;
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DiffractionExperiment x;
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x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
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std::mt19937 rng(5);
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std::uniform_real_distribution<double> unit(0.0, 1.0);
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std::exponential_distribution<double> wilson(1.0);
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std::normal_distribution<double> gauss(0.0, 1.0);
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std::vector<IntegrationOutcome> outcomes(200);
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for (auto &o: outcomes) {
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o.image_scale_g = 0.5 + unit(rng);
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for (int j = 0; j < 200; ++j) {
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const double d = 1.5 + 8.0 * unit(rng);
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const double dstar = 1.0 / d;
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const double s = std::sqrt(GAMMA0 * GAMMA0 + GAMMA_E * GAMMA_E * dstar * dstar);
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const double window = 4.0 * std::sqrt(GAMMA0 * GAMMA0 + GAMMA_E * GAMMA_E / (1.5 * 1.5));
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const double de = window * (2.0 * unit(rng) - 1.0);
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Reflection r{};
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r.h = j; r.k = 1; r.l = 1;
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r.d = static_cast<float>(d);
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r.dist_ewald = static_cast<float>(std::fabs(de));
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r.I = static_cast<float>(*o.image_scale_g * 1000.0 * wilson(rng) * std::exp(-0.5 * de * de / (s * s))
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+ 5.0 * gauss(rng));
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r.sigma = 5.0f;
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r.prescaling_corr = 1.0f;
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r.partiality = 1.0f;
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r.image_scale_corr = static_cast<float>(1.0 / *o.image_scale_g);
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o.reflections.push_back(r);
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}
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}
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const auto width = StillsPartialityRefine(x).MeasureRunWidth(outcomes, std::nullopt);
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REQUIRE(width.has_value());
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CHECK(width->gamma0 == Catch::Approx(GAMMA0).epsilon(0.3));
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CHECK(width->gamma_e == Catch::Approx(GAMMA_E).epsilon(0.1));
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CHECK(width->bandwidth_sigma < 1e-3);
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}
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// Outlier rejection on the stills merge: one observation at ten times its reflection's intensity among
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// nineteen consistent ones is dropped, and nothing else is.
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TEST_CASE("MergeOnTheFly_RejectsAnOutlierInTheBand") {
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DiffractionExperiment x;
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x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
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ScalingSettings s = x.GetScalingSettings();
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s.OutlierRejectNsigma(6.0);
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x.ImportScalingSettings(s);
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std::mt19937 rng(3);
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std::normal_distribution<float> gauss(0.0f, 1.0f);
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std::vector<IntegrationOutcome> outcomes(20);
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for (size_t i = 0; i < outcomes.size(); ++i) {
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for (int h = 1; h <= 50; ++h) {
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Reflection r{};
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r.h = h; r.k = 2; r.l = 3;
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r.d = 2.0f;
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const float I_true = 100.0f * static_cast<float>(h);
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r.I = I_true * (1.0f + 0.1f * gauss(rng)) + 3.0f * gauss(rng);
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if (i == 7 && h == 25)
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r.I = 10.0f * I_true;
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r.sigma = 3.0f;
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r.prescaling_corr = 1.0f;
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r.partiality = 1.0f;
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r.image_scale_corr = 1.0f;
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outcomes[i].reflections.push_back(r);
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}
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}
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MergeOnTheFly merge(x);
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merge.RefineErrorModel(outcomes);
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REQUIRE(merge.ErrorModelActive());
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merge.AddImages(outcomes);
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CHECK(merge.RejectedCount() == 1);
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}
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// The capture term widens the sigma of a partial by (c (1 - p) <I>): a partial merges at a lower weight
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// than a full of the same intensity, and not at all differently with c = 0.
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TEST_CASE("MergeOnTheFly_CaptureTermDownweightsPartials") {
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auto merged_I = [](double c) {
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DiffractionExperiment x;
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x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
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ScalingSettings s = x.GetScalingSettings();
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s.CaptureUncertaintyCoeff(c);
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x.ImportScalingSettings(s);
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std::mt19937 rng(9);
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std::normal_distribution<float> gauss(0.0f, 1.0f);
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std::vector<IntegrationOutcome> outcomes(40);
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for (size_t i = 0; i < outcomes.size(); ++i)
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for (int h = 1; h <= 40; ++h) {
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Reflection r{};
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r.h = h; r.k = 1; r.l = 1;
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r.d = 2.0f;
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// Every other image records the reflection as a 30 % partial that reads 20 % high.
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const bool partial = i % 2 == 1;
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r.partiality = partial ? 0.3f : 1.0f;
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r.image_scale_corr = 1.0f / r.partiality;
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r.I = r.partiality * 100.0f * static_cast<float>(h) * (partial ? 1.2f : 1.0f) * (1.0f + 0.05f * gauss(rng));
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r.sigma = 2.0f;
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r.prescaling_corr = 1.0f;
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outcomes[i].reflections.push_back(r);
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}
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MergeOnTheFly merge(x);
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merge.RefineErrorModel(outcomes);
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merge.AddImages(outcomes);
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const auto m = merge.ExportReflections();
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return m.at(10).I / (100.0f * static_cast<float>(m.at(10).h));
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};
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const float without = merged_I(0.0), with = merged_I(1.0);
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CHECK(with < without);
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CHECK(with < 1.08f);
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}
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