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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@@ -9,27 +9,14 @@
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#include "../image_analysis/geom_refinement/GeometryRefiner.h"
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#include "../image_analysis/bragg_prediction/BraggPrediction.h"
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// A detector of four modules (the quadrants around the beam), each displaced by a known rigid move: the
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// bundle adjustment with module placement must find the moves, and the fit without it must be worse.
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TEST_CASE("RefineGlobalGeometry_ModulePlacement") {
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DiffractionExperiment exp;
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exp.IncidentEnergy_keV(WVL_1A_IN_KEV).BeamX_pxl(1000).BeamY_pxl(1000).DetectorDistance_mm(150);
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const DiffractionGeometry geom = exp.GetDiffractionGeometry();
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namespace {
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// Moves that hold none of what the gauge takes away: zero in sum, in turn and outwards.
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std::vector<ModuleShift> truth(4);
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const double centre[4][2] = {{500, 500}, {1500, 500}, {500, 1500}, {1500, 1500}};
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const double move[4][3] = {{2.0, -2.0, 0.2}, {2.0, 2.0, -0.2}, {-2.0, -2.0, 0.1}, {-2.0, 2.0, -0.1}};
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for (int m = 0; m < 4; m++) {
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truth[m].x0 = centre[m][0];
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truth[m].y0 = centre[m][1];
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truth[m].dx = move[m][0];
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truth[m].dy = move[m][1];
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truth[m].rot_rad = move[m][2] * PI / 180.0;
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}
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// Frames of a 50/60/70 A orthorhombic crystal in random orientations on a detector of four modules (the
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// quadrants around the beam at 1000, 1000), each displaced by the rigid move `truth` gives it: the spots are
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// where the image shows them, each indexed as predicted.
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std::vector<GeomRefineFrame> FramesOnMovedModules(const DiffractionExperiment &exp, const CrystalLattice &latt,
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const std::vector<ModuleShift> &truth) {
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auto module_of = [](double x, double y) { return (x < 1000 ? 0 : 1) + (y < 1000 ? 0 : 2); };
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const CrystalLattice latt(50, 60, 70, 90, 90, 90);
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BraggPredictionSettings settings{.high_res_A = 2.0, .ewald_dist_cutoff = 0.001};
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std::mt19937 rng(7);
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std::uniform_real_distribution<float> u(-1.0f, 1.0f);
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@@ -62,6 +49,31 @@ TEST_CASE("RefineGlobalGeometry_ModulePlacement") {
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if (frame.spots.size() >= 20)
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frames.push_back(frame);
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}
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return frames;
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}
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} // namespace
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// A detector of four modules (the quadrants around the beam), each displaced by a known rigid move: the
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// bundle adjustment with module placement must find the moves, and the fit without it must be worse.
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TEST_CASE("RefineGlobalGeometry_ModulePlacement") {
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DiffractionExperiment exp;
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exp.IncidentEnergy_keV(WVL_1A_IN_KEV).BeamX_pxl(1000).BeamY_pxl(1000).DetectorDistance_mm(150);
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const DiffractionGeometry geom = exp.GetDiffractionGeometry();
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// Moves that hold none of what the gauge takes away: zero in sum, in turn and outwards.
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std::vector<ModuleShift> truth(4);
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const double centre[4][2] = {{500, 500}, {1500, 500}, {500, 1500}, {1500, 1500}};
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const double move[4][3] = {{2.0, -2.0, 0.2}, {2.0, 2.0, -0.2}, {-2.0, -2.0, 0.1}, {-2.0, 2.0, -0.1}};
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for (int m = 0; m < 4; m++) {
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truth[m].x0 = centre[m][0];
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truth[m].y0 = centre[m][1];
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truth[m].dx = move[m][0];
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truth[m].dy = move[m][1];
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truth[m].rot_rad = move[m][2] * PI / 180.0;
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}
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const CrystalLattice latt(50, 60, 70, 90, 90, 90);
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const std::vector<GeomRefineFrame> frames = FramesOnMovedModules(exp, latt, truth);
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REQUIRE(frames.size() > 30);
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GeometryRefinerSettings st;
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@@ -91,4 +103,117 @@ TEST_CASE("RefineGlobalGeometry_ModulePlacement") {
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CHECK(placed.beam_x_px == Catch::Approx(1000).margin(0.1));
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CHECK(placed.beam_y_px == Catch::Approx(1000).margin(0.1));
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CHECK(placed.distance_mm == Catch::Approx(150).margin(0.05));
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// The distance held (it shares a block with the beam): it stays exactly where it was given.
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GeometryRefinerSettings held_distance = st;
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held_distance.refine_distance = false;
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const auto fixed = RefineGlobalGeometry(geom, latt.GetUnitCell(), frames, held_distance);
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REQUIRE(fixed.ok);
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CHECK(fixed.distance_mm == geom.GetDetectorDistance_mm());
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CHECK(fixed.modules[0].dx == Catch::Approx(truth[0].dx).margin(0.1));
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// Only the orientations moved, on the modules as placed: the spots fit as well as in the placement.
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GeometryRefinerSettings ev = st;
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ev.refine_modules = false;
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ev.refine_beam_distance = false;
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ev.modules = placed.modules;
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const auto scored = RefineGlobalGeometry(geom, latt.GetUnitCell(), frames, ev);
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REQUIRE(scored.ok);
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CHECK(scored.median_residual_px < 0.1);
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CHECK(scored.distance_mm == geom.GetDetectorDistance_mm());
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}
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// The coarse search ahead of the placement: a module off by several pixels is found near where it is, and the
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// search gives the same answer on any number of threads.
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TEST_CASE("ScanModuleShifts_FindsShiftedModule") {
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DiffractionExperiment exp;
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exp.IncidentEnergy_keV(WVL_1A_IN_KEV).BeamX_pxl(1000).BeamY_pxl(1000).DetectorDistance_mm(150);
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const DiffractionGeometry geom = exp.GetDiffractionGeometry();
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std::vector<ModuleShift> truth(4), given(4);
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const double centre[4][2] = {{500, 500}, {1500, 500}, {500, 1500}, {1500, 1500}};
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for (int m = 0; m < 4; m++) {
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truth[m].x0 = given[m].x0 = centre[m][0];
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truth[m].y0 = given[m].y0 = centre[m][1];
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}
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truth[1].dx = 6.0;
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truth[1].dy = -4.0;
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const CrystalLattice latt(50, 60, 70, 90, 90, 90);
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std::vector<GeomRefineFrame> frames = FramesOnMovedModules(exp, latt, truth);
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REQUIRE(frames.size() > 30);
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// The module's spots did not index where it was given: the search sees them as unindexed.
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for (auto &f: frames)
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for (auto &s: f.spots)
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if (s.module == 1) {
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s.h = s.k = s.l = 0;
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f.unindexed.push_back(s);
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}
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for (auto &f: frames)
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std::erase_if(f.spots, [](const GeomRefineSpot &s) { return s.module == 1; });
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const auto one = ScanModuleShifts(geom, frames, given, 25.0, 1);
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const auto many = ScanModuleShifts(geom, frames, given, 25.0, 4);
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REQUIRE(one.size() == 4);
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// Coarse: a spot is on its lattice within 0.15 of an index, here ~4 px of the spacing, so the search lands
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// within that of the true shift and the placement takes it from there.
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CHECK(one[1].dx == Catch::Approx(6.0).margin(4.0));
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CHECK(one[1].dy == Catch::Approx(-4.0).margin(4.0));
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CHECK(one[1].on_lattice_at_best > 2 * one[1].on_lattice_at_zero);
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for (int m = 0; m < 4; m++) {
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CHECK(many[m].dx == one[m].dx);
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CHECK(many[m].dy == one[m].dy);
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CHECK(many[m].on_lattice_at_best == one[m].on_lattice_at_best);
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CHECK(many[m].on_lattice_at_zero == one[m].on_lattice_at_zero);
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}
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}
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// A tilted detector, one panel: started from the untilted geometry with the beam where the beam really lands
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// (the direct beam, which is what a beam-centre measurement gives), the refinement with the tilt must find it
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// and put the PONI where the tilt has it - 10 px from the direct beam here, further than the beam's 8 px box
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// would reach in PONI terms - and the fit with the tilt held must be worse. With the image mirrored and turned
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// as well, the direct beam has to be taken through the image orientation.
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TEST_CASE("RefineGlobalGeometry_Tilt") {
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for (const auto &orientation : {DetectorOrientation(), DetectorOrientation(true, 1)}) {
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DiffractionExperiment exp;
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exp.IncidentEnergy_keV(WVL_1A_IN_KEV).BeamX_pxl(1000).BeamY_pxl(1000).DetectorDistance_mm(150)
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.PoniRot1_rad(0.3 * PI / 180.0).PoniRot2_rad(-0.2 * PI / 180.0);
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exp.Detector().ImageOrientation(orientation);
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const DiffractionGeometry truth = exp.GetDiffractionGeometry();
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const auto [direct_x, direct_y] = truth.GetDirectBeam_pxl();
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REQUIRE(std::hypot(direct_x - 1000, direct_y - 1000) > 10);
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// One module covering the whole image: the frames' spots, each where the tilted detector shows it.
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ModuleShift whole;
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whole.x0 = 1000;
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whole.y0 = 1000;
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const CrystalLattice latt(50, 60, 70, 90, 90, 90);
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std::vector<GeomRefineFrame> frames = FramesOnMovedModules(exp, latt, {whole, whole, whole, whole});
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REQUIRE(frames.size() > 30);
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for (auto &f: frames)
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for (auto &s: f.spots)
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s.module = -1;
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DiffractionGeometry nominal = truth;
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nominal.PoniRot1_rad(0).PoniRot2_rad(0).BeamX_pxl(direct_x).BeamY_pxl(direct_y);
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GeometryRefinerSettings st;
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st.crystal_system = gemmi::CrystalSystem::Orthorhombic;
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st.num_threads = 2;
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const auto held = RefineGlobalGeometry(nominal, latt.GetUnitCell(), frames, st);
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REQUIRE(held.ok);
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CHECK(held.rot1_rad == 0);
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CHECK(held.rot2_rad == 0);
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st.refine_tilt = true;
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const auto tilted = RefineGlobalGeometry(nominal, latt.GetUnitCell(), frames, st);
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REQUIRE(tilted.ok);
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CHECK(tilted.rot1_rad * 180.0 / PI == Catch::Approx(0.3).margin(0.01));
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CHECK(tilted.rot2_rad * 180.0 / PI == Catch::Approx(-0.2).margin(0.01));
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CHECK(tilted.beam_x_px == Catch::Approx(1000).margin(0.2));
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CHECK(tilted.beam_y_px == Catch::Approx(1000).margin(0.2));
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CHECK(tilted.distance_mm == Catch::Approx(150).margin(0.05));
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CHECK(tilted.median_residual_px < 0.1);
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CHECK(tilted.capped_rms_px < held.capped_rms_px);
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}
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}
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