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* 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>
99 lines
5.4 KiB
C++
99 lines
5.4 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, 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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