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
137 lines
5.2 KiB
C++
137 lines
5.2 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 "../common/CUDAWrapper.h"
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#ifdef JFJOCH_USE_CUDA
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#include <map>
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#include <string>
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#include <vector>
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#include "../image_analysis/roi/ROIIntegrationCPU.h"
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#include "../image_analysis/roi/ROIIntegrationGPU.h"
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#include "../image_analysis/image_preprocessing/ImagePreprocessorBufferGPU.h"
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#include "../common/DiffractionExperiment.h"
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namespace {
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DiffractionExperiment make_roi_experiment() {
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DiffractionExperiment experiment(DetJF(1));
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// Overlapping boxes so some pixels belong to several ROIs at once (multi-bit
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// mask), exercising the per-bit accumulation that has to match between CPU and GPU.
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// ROIBox is (name, x_min, x_max, y_min, y_max), kept within the JF module bounds.
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experiment.ROI().SetROI(ROIDefinition{.boxes = {
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ROIBox("roiA", 10, 210, 20, 220),
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ROIBox("roiB", 100, 300, 100, 300),
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ROIBox("roiC", 0, 150, 0, 150),
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ROIBox("roiD", 50, 250, 50, 250),
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}});
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return experiment;
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}
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void compare_results(const std::map<std::string, ROIMessage> &cpu,
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const std::map<std::string, ROIMessage> &gpu) {
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REQUIRE(cpu.size() == gpu.size());
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for (const auto &[name, c] : cpu) {
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INFO("ROI " << name);
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REQUIRE(gpu.contains(name));
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const auto &g = gpu.at(name);
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CHECK(g.sum == c.sum);
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CHECK(g.sum_square == c.sum_square);
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CHECK(g.max_count == c.max_count);
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CHECK(g.pixels == c.pixels);
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CHECK(g.x_weighted == c.x_weighted);
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CHECK(g.y_weighted == c.y_weighted);
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CHECK(g.pixels_masked == c.pixels_masked);
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}
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}
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void run_and_compare(const DiffractionExperiment &experiment) {
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const auto roi_map = experiment.ExportROIMap();
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const size_t npixel = roi_map.size();
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const uint16_t roi_count = experiment.ROI().size();
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REQUIRE(roi_count > 0);
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// Deterministic image with both positive and negative values; negatives exercise
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// the signed weighted-sum path (val * x can be negative).
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std::vector<int32_t> values(npixel);
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for (size_t i = 0; i < npixel; i++)
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values[i] = static_cast<int32_t>((i * 2654435761u) % 1000) - 500;
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// Inject one saturated (INT32_MAX) and one masked (INT32_MIN) pixel into every ROI
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// so both the "max only, not summed" and "fully excluded" branches are covered.
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for (uint16_t r = 0; r < roi_count; r++) {
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bool injected_sat = false, injected_mask = false;
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for (size_t i = 0; i < npixel && !(injected_sat && injected_mask); i++) {
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if (!(roi_map[i] & (1u << r)))
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continue;
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if (!injected_sat) { values[i] = INT32_MAX; injected_sat = true; }
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else if (!injected_mask) { values[i] = INT32_MIN; injected_mask = true; }
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}
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REQUIRE(injected_sat);
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REQUIRE(injected_mask);
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}
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// CPU reference
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ImagePreprocessorBuffer cpu_image(npixel);
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for (size_t i = 0; i < npixel; i++)
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cpu_image[i] = values[i];
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ROIIntegrationCPU cpu(experiment);
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std::map<std::string, ROIMessage> out_cpu;
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cpu.Run(cpu_image, out_cpu);
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// GPU under test — identical input uploaded to the device
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auto stream = std::make_shared<CudaStream>();
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ImagePreprocessorBufferGPU gpu_image(npixel);
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for (size_t i = 0; i < npixel; i++)
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gpu_image[i] = values[i];
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REQUIRE(cudaMemcpyAsync(gpu_image.getGPUBuffer(),
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gpu_image.getBuffer().data(),
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npixel * sizeof(int32_t),
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cudaMemcpyHostToDevice,
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*stream) == cudaSuccess);
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ROIIntegrationGPU gpu(experiment, stream);
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std::map<std::string, ROIMessage> out_gpu;
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gpu.Run(gpu_image, out_gpu);
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compare_results(out_cpu, out_gpu);
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}
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} // namespace
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// The GPU kernel reduces with atomics and two's-complement unsigned accumulators,
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// while the CPU path is a plain serial loop. On identical input every per-ROI
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// statistic must be bit-for-bit identical, so we run both and compare.
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TEST_CASE("ROIIntegrationGPU_MatchesCPU") {
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if (get_gpu_count() == 0) {
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WARN("No CUDA GPU present. Skipping ROIIntegrationGPU_MatchesCPU");
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return;
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}
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run_and_compare(make_roi_experiment());
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}
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// The same with a panel table: the centre of mass is summed per panel and placed on the plane. Two panels
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// stacked in the image, the second turned by 180 degrees and moved by a fraction of a pixel; a strip of
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// rows below them is on no panel.
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TEST_CASE("ROIIntegrationGPU_MatchesCPU_Panels") {
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if (get_gpu_count() == 0) {
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WARN("No CUDA GPU present. Skipping ROIIntegrationGPU_MatchesCPU_Panels");
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return;
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}
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DetectorModule a = DetectorModule::AsImaged(0, 0, 256, 128);
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DetectorModule b = DetectorModule::AsImaged(0, 128, 256, 128);
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b.ox = 300.25; b.oy = 400.5; b.fx = -1; b.sy = -1;
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DiffractionExperiment experiment(DetDECTRIS(256, 300, "panels", ""));
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experiment.Modules(DetectorModules({a, b}));
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experiment.ROI().SetROI(ROIDefinition{.boxes = {
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ROIBox("roiA", 10, 210, 20, 220),
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ROIBox("roiB", 0, 255, 0, 299),
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}});
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run_and_compare(experiment);
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}
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#endif
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