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
149 lines
6.8 KiB
C++
149 lines
6.8 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 <vector>
|
|
|
|
#include "../common/CUDAWrapper.h"
|
|
#include "../common/DiffractionExperiment.h"
|
|
#include "../common/PixelMask.h"
|
|
#include "../writer/HDF5Objects.h"
|
|
#include "../image_analysis/bragg_integration/SpotWidth.h"
|
|
#include "../image_analysis/image_preprocessing/ImagePreprocessorCPU.h"
|
|
#include "../image_analysis/spot_finding/ImageSpotFinderCPU.h"
|
|
#ifdef JFJOCH_USE_CUDA
|
|
#include "../image_analysis/image_preprocessing/ImagePreprocessorBufferGPU.h"
|
|
#endif
|
|
|
|
// The pre-scan measures the spot width and the footprint on squares cut out about each spot instead
|
|
// of the whole frame (MeasureSpotsOnTiles). That is only allowed because it gives the whole frame's
|
|
// answer to the bit, so this checks exactly that on real diffraction frames - including the spots
|
|
// whose footprint window walks off its square and is measured again, on a larger square or on the
|
|
// frame, and the frame whose squares would be more than the frame itself.
|
|
namespace {
|
|
|
|
struct Frame {
|
|
DiffractionExperiment x;
|
|
ImagePreprocessorBuffer image;
|
|
std::vector<DiffractionSpot> spots;
|
|
};
|
|
|
|
std::vector<Frame> ReadFrames() {
|
|
HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
|
|
HDF5DataSet dataset(data, "/entry/data/data");
|
|
HDF5DataSpace file_space(dataset);
|
|
const auto dim = file_space.GetDimensions();
|
|
|
|
DiffractionExperiment x(DetDECTRIS(dim[2], dim[1], "Test", {}));
|
|
x.PixelSigned(true).DetectorDistance_mm(75).BeamY_pxl(1136).BeamX_pxl(1090).IncidentEnergy_keV(12.4);
|
|
const PixelMask mask(x);
|
|
ImagePreprocessorCPU preprocessor(x, mask);
|
|
ImageSpotFinderCPU finder(static_cast<int32_t>(x.GetXPixelsNumConv()), static_cast<int32_t>(x.GetYPixelsNumConv()));
|
|
|
|
std::vector<Frame> frames;
|
|
std::vector<int16_t> raw(dim[1] * dim[2]);
|
|
for (hsize_t i = 0; i < dim[0]; i += 4) {
|
|
dataset.ReadVector(raw, {i, 0, 0}, {1, dim[1], dim[2]});
|
|
Frame f{x, ImagePreprocessorBuffer(x.GetPixelsNum()), {}};
|
|
preprocessor.Analyze(f.image, reinterpret_cast<const uint8_t *>(raw.data()), CompressedImageMode::Int16);
|
|
f.spots = finder.Run(f.image, SpotFindingSettings{});
|
|
frames.push_back(std::move(f));
|
|
}
|
|
return frames;
|
|
}
|
|
|
|
bool Same(const std::vector<spot_width::FluxCurve> &a, const std::vector<spot_width::FluxCurve> &b) {
|
|
if (a.size() != b.size()) return false;
|
|
for (size_t k = 0; k < a.size(); k++) {
|
|
const auto &p = a[k], &q = b[k];
|
|
if (p.d_A != q.d_A || p.c != q.c || p.shape.valid != q.shape.valid || p.shape.two_theta != q.shape.two_theta
|
|
|| p.shape.jr != q.shape.jr || p.shape.jt != q.shape.jt || p.shape.m_rad != q.shape.m_rad
|
|
|| p.shape.m_tan != q.shape.m_tan || p.shape.cos_psi != q.shape.cos_psi
|
|
|| p.shape.par_u != q.shape.par_u || p.shape.par_v != q.shape.par_v)
|
|
return false;
|
|
}
|
|
return true;
|
|
}
|
|
|
|
bool Same(const std::vector<FootprintSpot> &a, const std::vector<FootprintSpot> &b) {
|
|
if (a.size() != b.size()) return false;
|
|
for (size_t k = 0; k < a.size(); k++)
|
|
if (a[k].r_px != b[k].r_px || a[k].sigma_rad != b[k].sigma_rad || a[k].sigma_tan != b[k].sigma_tan)
|
|
return false;
|
|
return true;
|
|
}
|
|
|
|
// Every frame through MeasureSpotsOnTiles on `image(f)`, against the whole frame; the misses summed.
|
|
template <class Image>
|
|
SpotTileMisses CheckFrames(std::vector<Frame> &frames, Image &&image, int half, int footprint_half) {
|
|
SpotTileMisses total;
|
|
size_t curves = 0, footprints = 0;
|
|
for (auto &f : frames) {
|
|
const int width = static_cast<int>(f.x.GetXPixelsNumConv()), height = static_cast<int>(f.x.GetYPixelsNumConv());
|
|
const auto &g = f.x.GetDiffractionGeometry();
|
|
std::vector<spot_width::FluxCurve> c_frame, c_tiles;
|
|
std::vector<FootprintSpot> f_frame, f_tiles;
|
|
MeasureSpotFluxCurves(f.image, width, height, g, DetectorModules(), f.spots, c_frame);
|
|
std::vector<float> sx, sy;
|
|
for (const auto &s : f.spots) {
|
|
sx.push_back(s.RawCoord().x);
|
|
sy.push_back(s.RawCoord().y);
|
|
}
|
|
MeasureFootprintSpots(f.image.data(), width, height, g.GetBeamX_pxl(), g.GetBeamY_pxl(), sx, sy, f_frame);
|
|
|
|
const auto misses = MeasureSpotsOnTiles(image(f), width, height, g, DetectorModules(), f.spots, c_tiles, f_tiles,
|
|
half, footprint_half);
|
|
CHECK(Same(c_frame, c_tiles));
|
|
CHECK(Same(f_frame, f_tiles));
|
|
total.larger += misses.larger;
|
|
total.whole_frame += misses.whole_frame;
|
|
curves += c_frame.size();
|
|
footprints += f_frame.size();
|
|
}
|
|
// Something was measured, or the comparison says nothing.
|
|
CHECK(curves > 0);
|
|
CHECK(footprints > 100);
|
|
return total;
|
|
}
|
|
|
|
} // namespace
|
|
|
|
TEST_CASE("SpotTiles_MatchWholeFrame", "[SpotWidth]") {
|
|
auto frames = ReadFrames();
|
|
REQUIRE(!frames.empty());
|
|
const auto host = [](Frame &f) -> ImagePreprocessorBuffer & { return f.image; };
|
|
|
|
// As the pre-scan reads them.
|
|
CheckFrames(frames, host, SPOT_TILE_HALF, FOOTPRINT_TILE_HALF);
|
|
// Squares too small for the footprint: its spots are measured again on the larger squares...
|
|
CHECK(CheckFrames(frames, host, spot_width::R_BKG_OUT, spot_width::R_BKG_OUT + 1).larger > 0);
|
|
// ... and on the frame, where the larger squares would be more than it.
|
|
CHECK(CheckFrames(frames, host, spot_width::R_BKG_OUT, 4000).whole_frame > 0);
|
|
// Squares so large that the frame is read instead from the start.
|
|
CHECK(CheckFrames(frames, host, 1000, FOOTPRINT_TILE_HALF).whole_frame == 0);
|
|
}
|
|
|
|
#ifdef JFJOCH_USE_CUDA
|
|
// The same with the squares cut out on the card, from a device image the host never holds.
|
|
TEST_CASE("SpotTiles_MatchWholeFrame_GPU", "[SpotWidth][GPU]") {
|
|
if (get_gpu_count() == 0)
|
|
SKIP("No GPU");
|
|
auto frames = ReadFrames();
|
|
REQUIRE(!frames.empty());
|
|
ImagePreprocessorBufferGPU device(frames.front().x.GetPixelsNum(), /*host_mirror=*/false);
|
|
const auto upload = [&](Frame &f) -> ImagePreprocessorBuffer & {
|
|
REQUIRE(cudaMemcpy(device.getGPUBuffer(), f.image.data(), f.image.size() * sizeof(int32_t),
|
|
cudaMemcpyHostToDevice) == cudaSuccess);
|
|
// From pageable memory cudaMemcpy may return before the copy has landed, and the buffer cuts
|
|
// its squares on a non-blocking stream that does not wait for the NULL stream.
|
|
REQUIRE(cudaDeviceSynchronize() == cudaSuccess);
|
|
return device;
|
|
};
|
|
CheckFrames(frames, upload, SPOT_TILE_HALF, FOOTPRINT_TILE_HALF);
|
|
CHECK(CheckFrames(frames, upload, spot_width::R_BKG_OUT, spot_width::R_BKG_OUT + 1).larger > 0);
|
|
CHECK(CheckFrames(frames, upload, spot_width::R_BKG_OUT, 4000).whole_frame > 0);
|
|
CheckFrames(frames, upload, 1000, FOOTPRINT_TILE_HALF);
|
|
}
|
|
#endif
|