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
99 lines
5.5 KiB
C++
99 lines
5.5 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <catch2/catch_all.hpp>
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#include <cmath>
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#include <random>
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#include <vector>
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#include "../common/DiffractionGeometry.h"
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#include "../image_analysis/SensorAbsorption.h"
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#include "../image_analysis/bragg_integration/SpotWidth.h"
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namespace {
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constexpr int W = 3000, H = 3000, C = 1500;
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constexpr double DIST_MM = 100.0, PIXEL_MM = 0.075, LAMBDA_A = 1.0;
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constexpr double THICKNESS_UM = 450.0;
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constexpr double ANGULAR_SIGMA = 1.5e-4; // rad: divergence and crystal, the same in every direction
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// Spots on an untilted detector, each an elliptical Gaussian with its long axis along the radius:
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// the isotropic angular width, the bandwidth's radial streak 2 tan(theta) sigma, and the sensor
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// parallax - a conversion depth z moves the photon by z tan(psi) along the radius, and on an
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// untilted detector psi = 2theta. Worked out here from the flat-detector geometry, independently
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// of the estimator's own Jacobians: R = D tan(2theta), so one radian of 2theta is D/cos^2(2theta)
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// along the radius and one radian across the scattering plane D/cos(2theta) across it. Painted
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// with 4x4 sub-pixel sampling so each pixel carries the box it integrates, and Poisson noise.
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void PaintSpots(std::vector<int32_t> &image, std::vector<DiffractionSpot> &spots, double bw_fwhm,
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int offset, std::mt19937 &rng) {
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const double sigma_bw = bw_fwhm / 2.3548;
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const double L_um = sensor_absorption::AttenuationLength_um("Si", LAMBDA_A);
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std::vector<double> mean(image.size(), 3.0);
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for (int cy = 40 + offset; cy < H - 40; cy += 60)
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for (int cx = 40 + offset; cx < W - 40; cx += 60) {
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const double rx = (cx - C) * PIXEL_MM, ry = (cy - C) * PIXEL_MM, r = std::hypot(rx, ry);
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if (r < 8.0) continue;
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const double tt = std::atan2(r, DIST_MM), c2 = std::cos(tt);
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const double jr = DIST_MM / (PIXEL_MM * c2 * c2), jt = DIST_MM / (PIXEL_MM * c2);
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const double depth_var = sensor_absorption::ConversionDepthVariance_um2(L_um * c2, THICKNESS_UM);
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const double par = depth_var * std::tan(tt) * std::tan(tt) / (PIXEL_MM * 1000.0 * PIXEL_MM * 1000.0);
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const double streak = 2.0 * std::tan(tt / 2.0) * sigma_bw;
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const double var_u = jr * jr * (ANGULAR_SIGMA * ANGULAR_SIGMA + streak * streak) + par;
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const double var_v = jt * jt * ANGULAR_SIGMA * ANGULAR_SIGMA;
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const double ux = rx / r, uy = ry / r;
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const double total = 20000.0;
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const double norm = total / (2.0 * M_PI * std::sqrt(var_u * var_v) * 16.0);
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for (int dy = -14; dy <= 14; dy++)
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for (int dx = -14; dx <= 14; dx++) {
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double v = 0.0;
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for (int sy = 0; sy < 4; sy++)
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for (int sx = 0; sx < 4; sx++) {
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const double px = dx - 0.375 + 0.25 * sx, py = dy - 0.375 + 0.25 * sy;
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const double u = px * ux + py * uy, t = -px * uy + py * ux;
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v += std::exp(-0.5 * (u * u / var_u + t * t / var_v));
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}
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mean[static_cast<size_t>(cy + dy) * W + cx + dx] += norm * v;
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}
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spots.emplace_back(static_cast<uint32_t>(cx), static_cast<uint32_t>(cy),
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static_cast<int64_t>(total));
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}
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for (size_t i = 0; i < image.size(); i++)
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image[i] = std::poisson_distribution<int32_t>(mean[i])(rng);
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}
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std::optional<spot_width::BandwidthEstimate> Estimate(double bw_fwhm) {
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DiffractionGeometry geometry;
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geometry.BeamX_pxl(C).BeamY_pxl(C).DetectorDistance_mm(DIST_MM).PixelSize_mm(PIXEL_MM)
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.Wavelength_A(LAMBDA_A);
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std::mt19937 rng(7);
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std::vector<spot_width::FluxCurve> curves;
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for (int offset : {0, 20, 40}) {
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ImagePreprocessorBuffer image(static_cast<size_t>(W) * H);
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std::vector<DiffractionSpot> spots;
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PaintSpots(image.getBuffer(), spots, bw_fwhm, offset, rng);
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MeasureSpotFluxCurves(image, W, H, geometry, DetectorModules(), spots, curves);
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}
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return spot_width::EstimateBandwidth(curves, sensor_absorption::AttenuationLength_um("Si", LAMBDA_A),
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THICKNESS_UM, PIXEL_MM * 1000.0);
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}
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}
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// A 0.45 % FWHM bandwidth - a multilayer's - on a thick silicon sensor, whose parallax elongates the
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// spots along the radius as well and grows with angle much as the bandwidth does. The estimator has
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// to take the parallax out from the sensor's physics and return the bandwidth, significantly.
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TEST_CASE("BandwidthEstimate_RecoversBandwidthPastParallax", "[SpotWidth]") {
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const auto e = Estimate(0.0045);
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REQUIRE(e.has_value());
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CHECK(e->spots >= spot_width::BANDWIDTH_MIN_SPOTS);
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CHECK(e->fwhm == Catch::Approx(0.0045).margin(0.0006));
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CHECK(e->z > spot_width::BANDWIDTH_Z);
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}
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// The same spots from a monochromatic beam: the parallax alone must not read as a bandwidth.
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TEST_CASE("BandwidthEstimate_MonochromaticIsNotSignificant", "[SpotWidth]") {
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const auto e = Estimate(0.0);
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REQUIRE(e.has_value());
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CHECK(e->z < spot_width::BANDWIDTH_Z);
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CHECK(std::abs(e->fwhm) < 0.0015);
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}
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