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Jungfraujoch/tests/BraggIntegrationEngineMetalTest.cpp
leonarski_fandFilip Leonarski 19b135186d
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v1.0.0-rc.175 (#85)
* 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>
2026-10-16 15:34:43 +02:00

266 lines
12 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>
#ifdef __APPLE__
#include <bit>
#include <cmath>
#include <cstdint>
#include <random>
#include <vector>
#include "../common/BraggIntegrationSettings.h"
#include "../common/DetectorSetup.h"
#include "../common/DiffractionExperiment.h"
#include "../common/PixelMask.h"
#include "../common/Reflection.h"
#include "../image_analysis/bragg_integration/BraggIntegrationEngineCPU.h"
#include "../image_analysis/bragg_integration/BraggIntegrationEngineMetal.h"
// The Metal engine's whole claim is that it IS the CPU engine, bit for bit (BraggIntegrationEngineMetal.h).
// So nothing here has a tolerance: every float of every reflection is compared as a bit pattern, and
// every count as an integer. A Mac without a Metal device fails rather than skips - the macOS CI job is
// the only place this can be checked, and a skip there would check nothing.
namespace {
struct Frame {
std::vector<int32_t> image;
std::vector<Reflection> predicted;
};
// A crowded random frame: predictions at random sub-pixel positions (so the pixel classification meets
// every kind of rounding near the stencil boundaries), a quarter of them on whole and half pixels (so it
// meets exact ties with the radii too), with random partialities (rocking-curve tails and flux, which
// mask the rings differently), about a third of them with a spot, overlapping where they fall close. On
// a background that rises with the radius (the radial correction has a curve to fit) with noise that
// takes it below zero near the beam, as a pedestal-subtracted detector does (a negative pixel is what
// carries into the high word of the GPU's 64-bit radial sums), hot pixels in the rings (so the
// background clip rejects something), and unreadable pixels: some in the run's mask, some saturated,
// some unreadable on this frame alone (both read as an overload), inside spots as well as between them.
Frame RandomFrame(const DiffractionExperiment &x, uint32_t seed, const std::vector<size_t> &masked) {
const int W = static_cast<int>(x.GetXPixelsNum()), H = static_cast<int>(x.GetYPixelsNum());
const float beam_x = x.GetBeamX_pxl(), beam_y = x.GetBeamY_pxl();
std::mt19937 rng(seed);
std::uniform_real_distribution<float> U(0.0f, 1.0f);
Frame f;
f.image.resize(static_cast<size_t>(W) * H);
for (int y = 0; y < H; ++y)
for (int x_ = 0; x_ < W; ++x_) {
const float r = std::hypot(x_ - beam_x, y - beam_y);
const float mean = 0.5f + 0.01f * r;
f.image[static_cast<size_t>(y) * W + x_] = static_cast<int32_t>(std::lround(mean + (U(rng) - 0.5f) * 8.0f));
}
const int nrefl = W * H / 400;
int hkl = 1;
for (int n = 0; n < nrefl; ++n) {
Reflection r{};
r.h = hkl; r.k = -hkl; r.l = hkl % 7; ++hkl;
r.predicted_x = 2.0f + U(rng) * (W - 4);
r.predicted_y = 2.0f + U(rng) * (H - 4);
if (n % 4 == 1) {
r.predicted_x = std::round(r.predicted_x * 2.0f) / 2.0f;
r.predicted_y = std::round(r.predicted_y);
}
const float u = U(rng);
r.partiality = u < 0.3f ? 0.01f * u : u; // a third of them rocking-curve tails
r.d = 1.2f + 3.0f * U(rng);
r.prescaling_corr = 1.0f;
f.predicted.push_back(r);
if (U(rng) < 0.35f) {
const float amp = 20.0f + 3000.0f * U(rng) * U(rng);
const float s = 0.8f + 1.4f * U(rng);
for (int dy = -8; dy <= 8; ++dy)
for (int dx = -8; dx <= 8; ++dx) {
const int px = static_cast<int>(std::lround(r.predicted_x)) + dx;
const int py = static_cast<int>(std::lround(r.predicted_y)) + dy;
if (px < 0 || py < 0 || px >= W || py >= H) continue;
const float ex = px - r.predicted_x, ey = py - r.predicted_y;
f.image[static_cast<size_t>(py) * W + px] += static_cast<int32_t>(
std::lround(amp * std::exp(-(ex * ex + ey * ey) / (2.0f * s * s))));
}
}
}
std::uniform_int_distribution<size_t> P(0, f.image.size() - 1);
for (int k = 0; k < W * H / 500; ++k)
f.image[P(rng)] += 200 + static_cast<int32_t>(5000 * U(rng)); // hot pixels
for (int k = 0; k < W * H / 3000; ++k)
f.image[P(rng)] = U(rng) < 0.5f ? INT32_MIN : INT32_MAX; // unreadable on this frame
for (size_t i = 0; i < f.predicted.size(); i += 13) { // ... inside spots too
const auto &r = f.predicted[i];
const size_t idx = static_cast<size_t>(std::lround(r.predicted_y)) * W + std::lround(r.predicted_x) + i % 3;
if (idx < f.image.size()) f.image[idx] = i % 2 ? INT32_MIN : INT32_MAX;
}
for (size_t idx : masked)
f.image[idx] = INT32_MIN; // what the run's mask holds
return f;
}
struct Case {
IntegratorMode mode = IntegratorMode::ProfileGaussian;
OverlapMode overlap = OverlapMode::Exclude;
bool radial = false;
std::optional<float> bandwidth;
float stencil_k = 0.0f;
bool footprint = false;
float clip_nsigma = 4.0f;
};
DiffractionExperiment MakeExperiment(const DetectorSetup &det, const Case &c) {
DiffractionExperiment x(det);
x.DetectorDistance_mm(100.0f).IncidentEnergy_keV(WVL_1A_IN_KEV)
.BeamX_pxl(0.4f * static_cast<float>(x.GetXPixelsNum()))
.BeamY_pxl(0.55f * static_cast<float>(x.GetYPixelsNum()));
x.BandwidthFWHM(c.bandwidth);
BraggIntegrationSettings s;
s.Integrator(c.mode).Overlap(c.overlap).BackgroundRadialCorrection(c.radial).StencilKSigma(c.stencil_k)
.BackgroundClipNSigma(c.clip_nsigma);
if (c.footprint) {
// Wider than the r1 disk can hold from the middle out, so both stencils occur on one frame.
SpotFootprint fp;
fp.bin_px = 100.0f;
for (int b = 0; b < 8; ++b) {
fp.sigma_rad.push_back(0.9f + 0.35f * b);
fp.sigma_tan.push_back(0.8f + 0.3f * b);
}
s.Footprint(fp);
}
x.ImportBraggIntegrationSettings(s);
return x;
}
uint32_t Bits(float f) { return std::bit_cast<uint32_t>(f); }
void RequireSame(const std::vector<Reflection> &cpu, const std::vector<Reflection> &metal) {
REQUIRE(metal.size() == cpu.size());
for (size_t i = 0; i < cpu.size(); ++i) {
const Reflection &a = cpu[i], &b = metal[i];
INFO("reflection " << i << " hkl " << a.h << " " << a.k << " " << a.l
<< " I " << a.I << " / " << b.I << " bkg " << a.bkg << " / " << b.bkg);
REQUIRE(a.h == b.h);
REQUIRE(a.k == b.k);
REQUIRE(a.l == b.l);
REQUIRE(Bits(a.image_number) == Bits(b.image_number));
REQUIRE(Bits(a.I) == Bits(b.I));
REQUIRE(Bits(a.sigma) == Bits(b.sigma));
REQUIRE(Bits(a.bkg) == Bits(b.bkg));
REQUIRE(Bits(a.var_bkg) == Bits(b.var_bkg));
REQUIRE(Bits(a.observed_x) == Bits(b.observed_x));
REQUIRE(Bits(a.observed_y) == Bits(b.observed_y));
REQUIRE(Bits(a.image_scale_corr) == Bits(b.image_scale_corr));
REQUIRE(Bits(a.prescaling_corr) == Bits(b.prescaling_corr));
REQUIRE(a.observed == b.observed);
REQUIRE(a.overloaded == b.overloaded);
}
}
void RequireSame(const BraggIntegrationCounts &a, const BraggIntegrationCounts &b) {
CHECK(a.predicted == b.predicted);
CHECK(a.bkg_starved == b.bkg_starved);
CHECK(a.bkg_starved_by_neighbour == b.bkg_starved_by_neighbour);
CHECK(a.profile_fallback == b.profile_fallback);
CHECK(a.overlapped == b.overlapped);
CHECK(a.overlapped_major == b.overlapped_major);
}
// Three frames through one pair of engines - so whatever the Metal engine keeps between frames (its
// masks, its buffers) has to be left as the CPU engine leaves its own - each compared exactly.
// Returns how many reflections came out, so a case can show it was not vacuous.
size_t CompareFrames(const DetectorSetup &det, const Case &c) {
const DiffractionExperiment x = MakeExperiment(det, c);
REQUIRE(BraggIntegrationEngineMetal::Available(x));
const size_t W = x.GetXPixelsNum();
// A few pixels of the run's mask, under spots and between them: unreadable there, but not overloads.
PixelMask mask(x);
std::vector<uint32_t> user(x.GetPixelsNum(), 0);
std::vector<size_t> masked;
for (size_t k = 0; k < x.GetPixelsNum(); k += 7919) {
user[k] = 1;
masked.push_back(k);
}
mask.LoadUserMask(x, user);
BraggIntegrationEngineCPU cpu(x, mask);
BraggIntegrationEngineMetal metal(x, mask);
ImagePreprocessorBuffer image(x.GetPixelsNum());
size_t n_out = 0;
for (uint32_t frame = 0; frame < 3; ++frame) {
INFO("frame " << frame);
const Frame f = RandomFrame(x, 1000 * frame + static_cast<uint32_t>(W), masked);
std::copy(f.image.begin(), f.image.end(), image.data());
// The auto radial mode switches per image; here it is on for the radial cases, every image.
cpu.BackgroundRadial(c.radial);
metal.BackgroundRadial(c.radial);
const auto out_cpu = cpu.Run(image, f.predicted, f.predicted.size(), frame);
const auto out_metal = metal.Run(image, f.predicted, f.predicted.size(), frame);
RequireSame(out_cpu, out_metal);
n_out += out_cpu.size();
}
RequireSame(cpu.Counts(), metal.Counts());
// Not the CPU engine compared with itself: every frame went through the kernels.
REQUIRE(metal.FramesOnGPU() == 3);
return n_out;
}
} // namespace
TEST_CASE("BraggIntegrationEngineMetal_BitIdenticalToCPU", "[portable][Integration][Metal]") {
// A JUNGFRAU 1M, and a small odd-sized detector, where most boxes meet an edge.
const DetectorSetup large = DetJF(2);
const DetectorSetup small = DetDECTRIS(211, 197, "small", {});
std::vector<std::pair<std::string, Case>> cases;
for (IntegratorMode mode : {IntegratorMode::BoxSum, IntegratorMode::ProfileGaussian, IntegratorMode::ProfileEmpirical})
for (OverlapMode overlap : {OverlapMode::Off, OverlapMode::Reject, OverlapMode::Exclude})
for (bool radial : {false, true}) {
Case c;
c.mode = mode;
c.overlap = overlap;
c.radial = radial;
cases.emplace_back("mode " + std::to_string(static_cast<int>(mode)) + " overlap "
+ std::to_string(static_cast<int>(overlap)) + (radial ? " radial" : ""), c);
}
// Rings elongated by the bandwidth, and the measured footprint: per-reflection stencils.
Case broadband;
broadband.bandwidth = 0.01f;
broadband.stencil_k = 3.0f;
broadband.radial = true;
cases.emplace_back("broadband stencil radial", broadband);
Case footprint;
footprint.footprint = true;
footprint.radial = true;
cases.emplace_back("footprint radial", footprint);
Case footprint_box = footprint;
footprint_box.mode = IntegratorMode::BoxSum;
cases.emplace_back("footprint box sum", footprint_box);
// No clip: the plain ring mean, and no clip kernel at all.
Case no_clip;
no_clip.clip_nsigma = 0.0f;
cases.emplace_back("no clip", no_clip);
for (const auto &[name, c] : cases) {
DYNAMIC_SECTION(name) {
CHECK(CompareFrames(large, c) > 1000);
CHECK(CompareFrames(small, c) > 50);
}
}
}
// The trimmed-mean background sorts each ring, which only the CPU engine does: such a run keeps the CPU
// engine (MXAnalysisWithoutFPGA asks Available).
TEST_CASE("BraggIntegrationEngineMetal_TrimmedMeanStaysOnCPU", "[portable][Integration][Metal]") {
Case trim;
trim.clip_nsigma = 0.0f;
DiffractionExperiment x = MakeExperiment(DetJF(2), trim);
BraggIntegrationSettings s = x.GetBraggIntegrationSettings();
s.BackgroundTrimFraction(0.1f);
x.ImportBraggIntegrationSettings(s);
CHECK(!BraggIntegrationEngineMetal::Available(x));
}
#endif