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Jungfraujoch/tests/ROIIntegrationGPUTest.cpp
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leonarski_fandClaude Opus 5.5 0a515bb086 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 from b9ada7914 (the tree
#88 squashed) to 094eee31a, 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 rc178 0cf62452c - 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
2026-10-23 17:56:42 +02:00

137 lines
5.2 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include "../common/CUDAWrapper.h"
#ifdef JFJOCH_USE_CUDA
#include <map>
#include <string>
#include <vector>
#include "../image_analysis/roi/ROIIntegrationCPU.h"
#include "../image_analysis/roi/ROIIntegrationGPU.h"
#include "../image_analysis/image_preprocessing/ImagePreprocessorBufferGPU.h"
#include "../common/DiffractionExperiment.h"
namespace {
DiffractionExperiment make_roi_experiment() {
DiffractionExperiment experiment(DetJF(1));
// Overlapping boxes so some pixels belong to several ROIs at once (multi-bit
// mask), exercising the per-bit accumulation that has to match between CPU and GPU.
// ROIBox is (name, x_min, x_max, y_min, y_max), kept within the JF module bounds.
experiment.ROI().SetROI(ROIDefinition{.boxes = {
ROIBox("roiA", 10, 210, 20, 220),
ROIBox("roiB", 100, 300, 100, 300),
ROIBox("roiC", 0, 150, 0, 150),
ROIBox("roiD", 50, 250, 50, 250),
}});
return experiment;
}
void compare_results(const std::map<std::string, ROIMessage> &cpu,
const std::map<std::string, ROIMessage> &gpu) {
REQUIRE(cpu.size() == gpu.size());
for (const auto &[name, c] : cpu) {
INFO("ROI " << name);
REQUIRE(gpu.contains(name));
const auto &g = gpu.at(name);
CHECK(g.sum == c.sum);
CHECK(g.sum_square == c.sum_square);
CHECK(g.max_count == c.max_count);
CHECK(g.pixels == c.pixels);
CHECK(g.x_weighted == c.x_weighted);
CHECK(g.y_weighted == c.y_weighted);
CHECK(g.pixels_masked == c.pixels_masked);
}
}
void run_and_compare(const DiffractionExperiment &experiment) {
const auto roi_map = experiment.ExportROIMap();
const size_t npixel = roi_map.size();
const uint16_t roi_count = experiment.ROI().size();
REQUIRE(roi_count > 0);
// Deterministic image with both positive and negative values; negatives exercise
// the signed weighted-sum path (val * x can be negative).
std::vector<int32_t> values(npixel);
for (size_t i = 0; i < npixel; i++)
values[i] = static_cast<int32_t>((i * 2654435761u) % 1000) - 500;
// Inject one saturated (INT32_MAX) and one masked (INT32_MIN) pixel into every ROI
// so both the "max only, not summed" and "fully excluded" branches are covered.
for (uint16_t r = 0; r < roi_count; r++) {
bool injected_sat = false, injected_mask = false;
for (size_t i = 0; i < npixel && !(injected_sat && injected_mask); i++) {
if (!(roi_map[i] & (1u << r)))
continue;
if (!injected_sat) { values[i] = INT32_MAX; injected_sat = true; }
else if (!injected_mask) { values[i] = INT32_MIN; injected_mask = true; }
}
REQUIRE(injected_sat);
REQUIRE(injected_mask);
}
// CPU reference
ImagePreprocessorBuffer cpu_image(npixel);
for (size_t i = 0; i < npixel; i++)
cpu_image[i] = values[i];
ROIIntegrationCPU cpu(experiment);
std::map<std::string, ROIMessage> out_cpu;
cpu.Run(cpu_image, out_cpu);
// GPU under test — identical input uploaded to the device
auto stream = std::make_shared<CudaStream>();
ImagePreprocessorBufferGPU gpu_image(npixel);
for (size_t i = 0; i < npixel; i++)
gpu_image[i] = values[i];
REQUIRE(cudaMemcpyAsync(gpu_image.getGPUBuffer(),
gpu_image.getBuffer().data(),
npixel * sizeof(int32_t),
cudaMemcpyHostToDevice,
*stream) == cudaSuccess);
ROIIntegrationGPU gpu(experiment, stream);
std::map<std::string, ROIMessage> out_gpu;
gpu.Run(gpu_image, out_gpu);
compare_results(out_cpu, out_gpu);
}
} // namespace
// The GPU kernel reduces with atomics and two's-complement unsigned accumulators,
// while the CPU path is a plain serial loop. On identical input every per-ROI
// statistic must be bit-for-bit identical, so we run both and compare.
TEST_CASE("ROIIntegrationGPU_MatchesCPU") {
if (get_gpu_count() == 0) {
WARN("No CUDA GPU present. Skipping ROIIntegrationGPU_MatchesCPU");
return;
}
run_and_compare(make_roi_experiment());
}
// The same with a panel table: the centre of mass is summed per panel and placed on the plane. Two panels
// stacked in the image, the second turned by 180 degrees and moved by a fraction of a pixel; a strip of
// rows below them is on no panel.
TEST_CASE("ROIIntegrationGPU_MatchesCPU_Panels") {
if (get_gpu_count() == 0) {
WARN("No CUDA GPU present. Skipping ROIIntegrationGPU_MatchesCPU_Panels");
return;
}
DetectorModule a = DetectorModule::AsImaged(0, 0, 256, 128);
DetectorModule b = DetectorModule::AsImaged(0, 128, 256, 128);
b.ox = 300.25; b.oy = 400.5; b.fx = -1; b.sy = -1;
DiffractionExperiment experiment(DetDECTRIS(256, 300, "panels", ""));
experiment.Modules(DetectorModules({a, b}));
experiment.ROI().SetROI(ROIDefinition{.boxes = {
ROIBox("roiA", 10, 210, 20, 220),
ROIBox("roiB", 0, 255, 0, 299),
}});
run_and_compare(experiment);
}
#endif