Files
Jungfraujoch/tests/BraggIntegrationEngineCompressedImageTest.cpp
leonarski_fandClaude Opus 5.5 37a8c8e24e Rotation merge: drop rocking events with an overloaded pixel; capture uncertainty in the merge variance
A saturated pixel in a spot means the brightest part of the reflection was
not measured. The integration used to drop the peak frame's partial (its
peak pixel is unreadable) and keep the flanks, so the combine extrapolated
the event from its tails by the partiality model: on a strongly
diffracting small-molecule crystal the strongest low-order reflections
read 2-3x low and were the largest SHELXL misfits. XDS drops such a
reflection (OVERLOAD); so does rugnux now.

- Integration (CPU + GPU engines): a reflection is `overloaded` when a
  signal-disk pixel is saturated, or unreadable on this frame but not in
  the run's pixel mask - EIGER/PILATUS write their error value for a
  pixel they could not count, which the preprocessor turns into a masked
  pixel like a gap's. The engines now receive the PixelMask to tell the
  two apart (an earlier attempt that re-classified the marker as
  saturation in the preprocessor broke a dataset whose gaps are not in
  the file's mask). An overloaded reflection is kept with its box sum,
  unfitted, only so its event can be recognised.
- Rotation combine (CPU + GPU): an event with any overloaded partial is
  dropped whole; counted in the log and the report
  (OBSERVATIONS_REJECTED_OVERLOAD=). The unmerged MTZ export drops it too.
- Everything else that reads reflections leaves an overloaded one out:
  AcceptReflection (stills merge, per-image scaling), the post-refinement
  gather, the axial-row sums.
- Capture uncertainty: the merge rebuilds each full's variance at the
  reflection's mean (counting_variance / ModelSigma) and dropped the
  capture term the combine had put into sigma, so a full extrapolated
  from part of its rocking curve merged at the weight of a whole one.
  Fulls now carry it (Obs::capture) and the rebuilt variance adds
  (capture * <I>)^2, host and device.

SHELXL R1 on rugnux's own integration (harness), median fix -> this:
citric acid .0648 -> .0420 (XDS .051; 221 events dropped, EXTI 1.02 -> 0.29),
HEPES .0396 -> .0381 (184), aspirin 20 keV .0387 -> .0385 (6),
aspirin 25 keV .0376 -> .0375 (5); metformin/nidppe/dnba/lalanine/cytidine
no overloads, unchanged. YAG .116 -> .128 (87 dropped; its scale loop does
not settle either way). Proteins and private subset: see the branch report.
Tests: BraggIntegrationEngineCPU_SaturatedPeakIsFlaggedNotDropped (new),
BraggIntegrationEngineGPU_MatchesCPU (overloaded flag compared),
AcceptReflection_ResolutionLimits, [write_reflections], [large].

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB
2026-10-04 21:01:40 +02:00

138 lines
6.1 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 <cmath>
#include <cstdint>
#include <vector>
#include "../common/BraggIntegrationSettings.h"
#include "../common/CompressedImage.h"
#include "../common/DetectorSetup.h"
#include "../common/DiffractionExperiment.h"
#include "../common/Reflection.h"
#include "../image_analysis/bragg_integration/BraggIntegrationEngineCPU.h"
#include "../image_analysis/image_preprocessing/ImagePreprocessorBuffer.h"
// The FPGA workflow integrates straight off the assembled CompressedImage (any pixel type) instead of
// a preprocessed int32 buffer, reading only the reflection disks. These tests pin that the typed
// sampler produces exactly the same intensities as the equivalent int32 preprocessed buffer - i.e. the
// zero-copy route is numerically identical to the buffer route, not merely close.
namespace {
struct Scene {
std::vector<int32_t> image; // INT32_MIN = masked, INT32_MAX = saturated
std::vector<Reflection> predicted;
};
Reflection MakeReflection(float x, float y, float d, int hkl) {
Reflection r{};
r.h = hkl; r.k = hkl; r.l = hkl;
r.predicted_x = x;
r.predicted_y = y;
r.d = d;
r.prescaling_corr = 1.0f;
r.partiality = 1.0f;
return r;
}
// A grid of clean Gaussian spots on a flat background, values kept well inside int16 range so the same
// scene can be represented as Int16 and Int32 without clipping. A few masked/saturated pixels exercise
// the sentinel handling.
Scene BuildScene(size_t width, size_t height) {
Scene s;
s.image.assign(width * height, 12);
const int margin = 45, spacing = 60;
int hkl = 1;
for (int gy = 0; margin + gy * spacing < static_cast<int>(height) - margin; ++gy)
for (int gx = 0; margin + gx * spacing < static_cast<int>(width) - margin; ++gx) {
const float cx = static_cast<float>(margin + gx * spacing) + 0.3f;
const float cy = static_cast<float>(margin + gy * spacing) - 0.2f;
const double amp = 150.0 + 40.0 * ((gx * 7 + gy * 13) % 20); // <= ~950, safe for int16
const double sigma = 1.3;
for (int dy = -6; dy <= 6; ++dy)
for (int dx = -6; dx <= 6; ++dx) {
const int x = static_cast<int>(std::lround(cx)) + dx;
const int y = static_cast<int>(std::lround(cy)) + dy;
if (x < 0 || y < 0 || x >= static_cast<int>(width) || y >= static_cast<int>(height)) continue;
const double ex = x - cx, ey = y - cy;
s.image[y * width + x] += static_cast<int32_t>(std::lround(amp * std::exp(-(ex * ex + ey * ey) / (2.0 * sigma * sigma))));
}
const float d = 1.4f + 0.12f * static_cast<float>((gx + gy) % 12);
s.predicted.push_back(MakeReflection(cx, cy, d, hkl++));
}
for (int k = 0; k < 20; ++k) {
const size_t idx = (static_cast<size_t>(k) * 2654435761u) % s.image.size();
s.image[idx] = (k % 2) ? INT32_MIN : INT32_MAX;
}
return s;
}
DiffractionExperiment MakeExperiment(IntegratorMode mode) {
DiffractionExperiment experiment(DetJF(2));
experiment.DetectorDistance_mm(100.0f).IncidentEnergy_keV(WVL_1A_IN_KEV).BeamX_pxl(400.0f).BeamY_pxl(400.0f);
BraggIntegrationSettings settings;
settings.Integrator(mode);
experiment.ImportBraggIntegrationSettings(settings);
return experiment;
}
void RequireIdentical(const std::vector<Reflection> &a, const std::vector<Reflection> &b) {
REQUIRE(a.size() == b.size());
REQUIRE(a.size() > 40);
for (size_t i = 0; i < a.size(); ++i) {
INFO("reflection " << i << " hkl " << a[i].h);
CHECK(a[i].h == b[i].h);
CHECK(a[i].I == b[i].I);
CHECK(a[i].sigma == b[i].sigma);
CHECK(a[i].bkg == b[i].bkg);
}
}
} // namespace
TEST_CASE("BraggIntegrationEngineCPU_CompressedImageMatchesBuffer", "[Integration][portable]") {
for (const auto mode : {IntegratorMode::BoxSum, IntegratorMode::ProfileGaussian, IntegratorMode::ProfileEmpirical}) {
const DiffractionExperiment experiment = MakeExperiment(mode);
const size_t W = experiment.GetXPixelsNum(), H = experiment.GetYPixelsNum();
const size_t npixel = experiment.GetPixelsNum();
const Scene scene = BuildScene(W, H);
REQUIRE(scene.image.size() == npixel);
BraggIntegrationEngineCPU engine(experiment, PixelMask(experiment));
// Route A: the preprocessed int32 buffer.
ImagePreprocessorBuffer buffer(npixel);
for (size_t i = 0; i < npixel; ++i) buffer[i] = scene.image[i];
const auto from_buffer = engine.Run(buffer, scene.predicted, scene.predicted.size(), 7);
SECTION("Int32 CompressedImage") {
const CompressedImage image(scene.image, W, H);
const auto from_image = engine.Run(image, scene.predicted, scene.predicted.size(), 7);
RequireIdentical(from_buffer, from_image);
}
SECTION("Int16 CompressedImage") {
// Same scene as int16 (masked -> INT16_MIN, saturated -> INT16_MAX) with a matching int32
// buffer built by the exact sampler mapping; the two must integrate identically.
std::vector<int16_t> img16(npixel);
std::vector<int32_t> buf32(npixel);
for (size_t i = 0; i < npixel; ++i) {
const int32_t v = scene.image[i];
if (v == INT32_MIN) { img16[i] = INT16_MIN; buf32[i] = INT32_MIN; }
else if (v == INT32_MAX) { img16[i] = INT16_MAX; buf32[i] = INT32_MAX; }
else { img16[i] = static_cast<int16_t>(v); buf32[i] = v; }
}
ImagePreprocessorBuffer buffer16(npixel);
for (size_t i = 0; i < npixel; ++i) buffer16[i] = buf32[i];
const auto ref16 = engine.Run(buffer16, scene.predicted, scene.predicted.size(), 7);
const CompressedImage image(img16, W, H);
const auto from_image = engine.Run(image, scene.predicted, scene.predicted.size(), 7);
RequireIdentical(ref16, from_image);
}
}
}