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Jungfraujoch/tests/RugnuxTest.cpp
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leonarski_fandClaude Opus 5.5 2c1123c267 rugnux: calibration re-bin sums every image; clean out-of-host-memory failures 
Calibration (--mode calibration): RebinAndRefit gave each worker one
AzimuthalIntegrationProfile that AzIntEngineCPU::Run clears on every
image, so the re-binned profile held only the last image each worker
read, added in completion order - on a 1800-frame LaB6 run the re-binned
fit changed with -N (197 / 181 / 205 ring points at rms ~7 px). Each
fixed block of images is now summed in image order into its own slot
(ParallelBlocks) and the slots added in block order, so the profile is
the sum over every image and the same at any thread count (rms 0.93 px,
identical at -N 1, 7 and 32). On the LaB6 runs with a sane header the
first pass still wins and the .poni is unchanged; with a header 100 px
off the re-binned fit is now adopted (218 vs 140 ring points). New test
Rugnux_CalibrationRebinsEveryImage spreads the rings over six frames
and fails on the old code (241 vs 141 points at -N 1 vs -N 4).

Host memory: out-of-memory now ends with "Processing failed: out of
host memory (...) - this data set needs more RAM than is available" and
exit 1. Tested with ulimit -v and an LD_PRELOAD allocator that refuses
allocations from a chosen phase (CPU and GPU builds, image loop through
merging and writing, calibration mode). Paths that crashed instead:
- PostIndexingRefinement ran candidate blocks on bare std::threads, so
  a bad_alloc there called std::terminate (seen: "terminate called
  recursively", SIGABRT); now std::async futures.
- FFTW aborts on its own failed allocation (CK(p) in kernel/alloc.c,
  also inside buffered transforms: BeamCenterFFTCPU, FFTIndexerCPU);
  rugnux now defines fftwf_assertion_failed to report it and exit 1.
- libjpeg's default error_exit calls exit() from the diagnostic-JPEG
  thread ("Insufficient memory (case 12)"); WriteJPEGToMem now
  longjmps back and throws (bad_alloc for JERR_OUT_OF_MEMORY).
- WorkerPool construction that fails to start a thread destroyed
  joinable threads (terminate); it now joins them and rethrows.
Also: length_error counts as a fatal resource error, pinned host
allocation failure is MemAllocFailed, and the GPU scaling fail-fast
message says the CPU path needs a lot of host memory.

Docs: very large cells and what running out of host memory looks like
(including the OOM killer) in RUGNUX_INSTALL.md, pointer in RUGNUX.md.

Validation: myob, cytc, lyso, sparse md5-identical to 82e6583e0 on
both GPU and CPU builds.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
2026-09-28 23:25:54 +02:00

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// 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 <filesystem>
#include "../common/DiffractionExperiment.h"
#include "../common/ScanResultGenerator.h"
#include "../writer/FileWriter.h"
#include "../reader/JFJochHDF5Reader.h"
#include "../rugnux/Rugnux.h"
#include "../rugnux/RugnuxCommandLine.h"
#include "../rugnux/SpotWidth.h"
#include "../image_analysis/geom_refinement/Calibrants.h"
namespace {
// Write a small VDS dataset of `n` flat images and return nothing (prefix_master.h5 +
// prefix_data_000001.h5 land in the test working directory).
void WriteTestDataset(const std::string &prefix, int n) {
RegisterHDF5Filter();
DiffractionExperiment x(DetJF(1));
x.FilePrefix(prefix).ImagesPerTrigger(n).OverwriteExistingFiles(true);
x.BitDepthImage(16).ImagesPerFile(n).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true);
x.Compression(CompressionAlgorithm::NO_COMPRESSION);
x.BeamX_pxl(512).BeamY_pxl(256).DetectorDistance_mm(150).IncidentEnergy_keV(WVL_1A_IN_KEV)
.FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
std::vector<int16_t> image(x.GetPixelsNum(), 5);
StartMessage start_message;
x.FillMessage(start_message);
FileWriter file_set(start_message);
ScanResultGenerator generator(x);
for (int i = 0; i < n; i++) {
DataMessage message{};
message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
message.number = i;
REQUIRE_NOTHROW(file_set.WriteHDF5(message));
generator.Add(message);
}
EndMessage end_message;
end_message.max_image_number = n;
generator.FillEndMessage(end_message);
file_set.WriteHDF5(end_message);
file_set.Finalize();
}
}
TEST_CASE("Rugnux_AzInt", "[HDF5][Full]") {
WriteTestDataset("process_azint_in", 8);
JFJochHDF5Reader reader;
REQUIRE_NOTHROW(reader.ReadFile("process_azint_in_master.h5"));
auto dataset = reader.GetDataset();
REQUIRE(dataset);
ProcessConfig config;
config.mode = ProcessMode::AzimuthalIntegration;
config.nthreads = 2;
config.output_prefix = "process_azint_out";
Rugnux process(reader, dataset->experiment, *dataset->pixel_mask, config);
ProcessResult result;
REQUIRE_NOTHROW(result = process.Run());
CHECK_FALSE(result.cancelled);
CHECK(result.images_processed == 8);
REQUIRE(result.written_master_path.has_value());
{
// The _process.h5 links back to the source images and carries an azimuthal profile per image.
JFJochHDF5Reader out;
REQUIRE_NOTHROW(out.ReadFile("process_azint_out_process.h5"));
CHECK(out.GetNumberOfImages() == 8);
std::shared_ptr<JFJochReaderImage> img;
REQUIRE_NOTHROW(img = out.LoadImage(0));
REQUIRE(img);
CHECK_FALSE(img->ImageData().az_int_profile.empty());
}
reader.Close();
remove("process_azint_in_master.h5");
remove("process_azint_in_data_000001.h5");
remove("process_azint_out_process.h5");
REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("Rugnux_NoOutput", "[HDF5][Full]") {
WriteTestDataset("process_noout_in", 6);
JFJochHDF5Reader reader;
REQUIRE_NOTHROW(reader.ReadFile("process_noout_in_master.h5"));
auto dataset = reader.GetDataset();
// Empty output prefix => process without writing any file.
ProcessConfig config;
config.mode = ProcessMode::AzimuthalIntegration;
config.nthreads = 3;
Rugnux process(reader, dataset->experiment, *dataset->pixel_mask, config);
auto result = process.Run();
CHECK_FALSE(result.cancelled);
CHECK(result.images_processed == 6);
CHECK_FALSE(result.written_master_path.has_value());
reader.Close();
remove("process_noout_in_master.h5");
remove("process_noout_in_data_000001.h5");
REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("Rugnux_Cancel", "[HDF5][Full]") {
WriteTestDataset("process_cancel_in", 8);
JFJochHDF5Reader reader;
REQUIRE_NOTHROW(reader.ReadFile("process_cancel_in_master.h5"));
auto dataset = reader.GetDataset();
ProcessConfig config;
config.mode = ProcessMode::AzimuthalIntegration;
config.nthreads = 2;
Rugnux process(reader, dataset->experiment, *dataset->pixel_mask, config);
process.Cancel(); // cancel before running: the worker loop stops immediately
auto result = process.Run();
CHECK(result.cancelled);
CHECK(result.images_processed == 0);
CHECK_FALSE(result.written_master_path.has_value());
reader.Close();
remove("process_cancel_in_master.h5");
remove("process_cancel_in_data_000001.h5");
REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
// A calibration re-integrates its images binned about the geometry it fitted, and fits again. That
// second profile must be the sum over every image: here each of six frames carries a different sixth
// of the LaB6 rings, so a profile missing a frame is missing rings. The header's beam centre is 5 px
// out, far enough that the first pass's smeared profile loses to the re-binned one - so the geometry
// that comes out is the one fitted on the re-binned sum, and it must not depend on the thread count.
TEST_CASE("Rugnux_CalibrationRebinsEveryImage", "[HDF5][DetGeomCalib]") {
RegisterHDF5Filter();
constexpr int n = 6;
constexpr float true_beam_x = 1090.0f, true_beam_y = 1100.0f;
const std::vector<float> rings_q = CalibrantRings("lab6");
DiffractionExperiment x(DetJF4M());
x.FilePrefix("process_calib_in").ImagesPerTrigger(n).OverwriteExistingFiles(true);
x.BitDepthImage(16).ImagesPerFile(n).SetFileWriterFormat(FileWriterFormat::NXmxVDS).PixelSigned(true);
x.Compression(CompressionAlgorithm::NO_COMPRESSION);
x.BeamX_pxl(true_beam_x).BeamY_pxl(true_beam_y).DetectorDistance_mm(100).IncidentEnergy_keV(WVL_1A_IN_KEV)
.FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
const DiffractionGeometry geom_true = x.GetDiffractionGeometry();
x.BeamX_pxl(true_beam_x + 5.0f); // what the header says
// Radii of the rings the beam reaches, in pixels about the true centre.
std::vector<float> ring_radius;
for (const float q : rings_q) {
const float d = static_cast<float>(2.0 * PI) / q;
if (d > geom_true.GetWavelength_A() / 2.0f)
ring_radius.push_back(geom_true.ResToPxl(d));
}
{
StartMessage start_message;
x.FillMessage(start_message);
FileWriter file_set(start_message);
ScanResultGenerator generator(x);
std::vector<int16_t> image(x.GetPixelsNum());
for (int i = 0; i < n; i++) {
for (int64_t p = 0; p < x.GetPixelsNum(); p++) {
const float px = static_cast<float>(p % x.GetXPixelsNum());
const float py = static_cast<float>(p / x.GetXPixelsNum());
const float r = std::hypot(px - true_beam_x, py - true_beam_y);
float v = 5.0f;
for (size_t k = i; k < ring_radius.size(); k += n) {
const float dr = r - ring_radius[k];
v += 400.0f * std::exp(-0.5f * dr * dr / (1.5f * 1.5f));
}
image[p] = static_cast<int16_t>(std::lround(v));
}
DataMessage message{};
message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
message.number = i;
REQUIRE_NOTHROW(file_set.WriteHDF5(message));
generator.Add(message);
}
EndMessage end_message;
end_message.max_image_number = n;
generator.FillEndMessage(end_message);
file_set.WriteHDF5(end_message);
file_set.Finalize();
}
JFJochHDF5Reader reader;
REQUIRE_NOTHROW(reader.ReadFile("process_calib_in_master.h5"));
auto dataset = reader.GetDataset();
REQUIRE(dataset);
DiffractionExperiment experiment(dataset->experiment);
auto azint = experiment.GetAzimuthalIntegrationSettings();
azint.AzimuthalBinCount(32);
experiment.ImportAzimuthalIntegrationSettings(azint);
std::vector<CalibrationResult> results;
for (const int nthreads : {1, 4}) {
ProcessConfig config;
config.mode = ProcessMode::Calibration;
config.calibrant_ring_q = rings_q;
config.nthreads = nthreads;
config.write_process_h5 = false;
config.beam_center_check = false;
config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
config.spot_finding.indexing = false;
Rugnux process(reader, experiment, *dataset->pixel_mask, config);
ProcessResult result;
REQUIRE_NOTHROW(result = process.Run());
REQUIRE(result.calibration.has_value());
results.push_back(*result.calibration);
}
for (const auto &cal : results) {
CHECK(cal.converged);
CHECK(cal.geometry.GetBeamX_pxl() == Catch::Approx(true_beam_x).margin(0.5));
CHECK(cal.geometry.GetBeamY_pxl() == Catch::Approx(true_beam_y).margin(0.5));
}
CHECK(results[0].ring_points == results[1].ring_points);
CHECK(results[0].rms_radial_pxl == results[1].rms_radial_pxl);
CHECK(results[0].geometry.GetBeamX_pxl() == results[1].geometry.GetBeamX_pxl());
CHECK(results[0].geometry.GetBeamY_pxl() == results[1].geometry.GetBeamY_pxl());
CHECK(results[0].geometry.GetDetectorDistance_mm() == results[1].geometry.GetDetectorDistance_mm());
reader.Close();
remove("process_calib_in_master.h5");
remove("process_calib_in_data_000001.h5");
REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
}
TEST_CASE("RugnuxCommandLine_Full", "[process]") {
DiffractionExperiment x(DetJF(1));
IndexingSettings idx;
idx.Algorithm(IndexingAlgorithmEnum::FFT);
idx.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
x.ImportIndexingSettings(idx);
x.SpaceGroupNumber(96);
ProcessConfig config;
config.mode = ProcessMode::FullAnalysis;
config.nthreads = 8;
config.output_prefix = "run1";
config.end_image = 500;
config.rotation_indexing = true;
config.two_pass_rotation = true;
config.rotation_indexing_image_count = 30;
config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
const std::string cmd = RugnuxCommandLine(config, x, "/data/test_master.h5");
CHECK(cmd.rfind("rugnux", 0) == 0);
CHECK(cmd.find("-N 8") != std::string::npos);
CHECK(cmd.find("-e 500") != std::string::npos);
CHECK(cmd.find("-o run1") != std::string::npos);
CHECK(cmd.find("-X fft") != std::string::npos);
CHECK(cmd.find("-S 96") != std::string::npos);
// -R takes an optional argument, so its value must be attached (-R30); a separate "-R 30" token
// would not re-parse (getopt would leave 30 as a positional and drop the count).
CHECK(cmd.find("-R30") != std::string::npos);
CHECK(cmd.find("-R 30") == std::string::npos);
CHECK(cmd.find("/data/test_master.h5") != std::string::npos);
}
TEST_CASE("RugnuxCommandLine_AzInt", "[process]") {
DiffractionExperiment x(DetJF(1));
AzimuthalIntegrationSettings a;
a.AzimuthalBinCount(4);
x.ImportAzimuthalIntegrationSettings(a);
ProcessConfig config;
config.mode = ProcessMode::AzimuthalIntegration;
config.nthreads = 2;
config.output_prefix = "az";
const std::string cmd = RugnuxCommandLine(config, x, "in.h5");
CHECK(cmd.rfind("rugnux", 0) == 0);
CHECK(cmd.find("--mode azint") != std::string::npos);
CHECK(cmd.find("--azim-phi-bins 4") != std::string::npos);
CHECK(cmd.find("--azim-min-q") != std::string::npos);
CHECK(cmd.find("in.h5") != std::string::npos);
}
namespace {
// A field of identical round Gaussian spots on three rings, so that the width estimator sees
// several resolution bands with the same true width and its 1/d fit has to come back flat.
void PaintGaussianSpots(ImagePreprocessorBuffer &image, int w, double sigma, double total_counts,
std::vector<DiffractionSpot> &spots) {
constexpr int BKG = 3;
for (size_t i = 0; i < image.size(); i++) image[i] = BKG;
const double amp = total_counts / (2.0 * M_PI * sigma * sigma);
for (int radius : {150, 350, 550})
for (int k = 0; k < 20; k++) {
const double phi = 2.0 * M_PI * k / 20.0 + 0.1 * radius;
const int cx = static_cast<int>(std::lround(600 + radius * std::cos(phi)));
const int cy = static_cast<int>(std::lround(600 + radius * std::sin(phi)));
for (int dy = -14; dy <= 14; dy++)
for (int dx = -14; dx <= 14; dx++)
image[static_cast<size_t>(cy + dy) * w + (cx + dx)] +=
static_cast<int32_t>(std::lround(
amp * std::exp(-(dx * dx + dy * dy) / (2.0 * sigma * sigma))));
spots.emplace_back(static_cast<uint32_t>(cx), static_cast<uint32_t>(cy),
static_cast<int64_t>(total_counts));
}
}
}
// The width the adaptive integration radius is set from. A round Gaussian of width sigma holds 80 %
// of its flux inside sqrt(2 ln 5) * sigma = 1.794 * sigma, and that is what the estimator has to
// return - over an aperture that owes nothing to the integrator's r1, which is the whole point of
// measuring it here rather than reading the integrator's own second moment.
TEST_CASE("SpotWidth_Gaussian", "[process]") {
constexpr int W = 1200, H = 1200;
DiffractionGeometry geometry;
geometry.BeamX_pxl(600).BeamY_pxl(600).DetectorDistance_mm(200).PixelSize_mm(0.075)
.Wavelength_A(1.0);
for (double sigma : {1.0, 2.2}) {
ImagePreprocessorBuffer image(static_cast<size_t>(W) * H);
std::vector<DiffractionSpot> spots;
PaintGaussianSpots(image, W, sigma, 20000.0, spots);
std::vector<spot_width::FluxCurve> curves;
MeasureSpotFluxCurves(image, W, H, geometry, spots, curves);
REQUIRE(curves.size() >= 45);
const auto r80 = spot_width::R80AtReference(curves);
REQUIRE(r80.has_value());
CHECK(*r80 == Catch::Approx(1.794 * sigma).margin(0.3));
}
// The rule the measurement drives: the shipped radius below the line, the capped one above it.
CHECK(spot_width::R1ForWidth(1.0f) == 4.0f);
CHECK(spot_width::R1ForWidth(1.794f) == 4.0f);
CHECK(spot_width::R1ForWidth(2.4f) == 5.0f);
CHECK(spot_width::R1ForWidth(3.947f) == 6.0f);
CHECK(spot_width::R1ForWidth(9.0f) == 6.0f);
}
// The beam-centre arbitration between a first pass at the file's centre and one at the measured
// centre. Two arms on the same lattice are two geometries of one hypothesis: they are judged on the
// signal each measured, not on a CC1/2 that reads the same on both.
TEST_CASE("MeasuredCentreWins", "[process]") {
const auto arm = [](const UnitCell &cell, gemmi::CrystalSystem system, double cc_half, int64_t strong) {
ProcessResult r;
r.has_merge_statistics = true;
r.consensus_cell = cell;
r.consensus_centering = 'P';
r.rotation_lattice_type = LatticeMessage{'P', 0, system};
r.search_merge_cc_half = cc_half;
r.search_merge_strong_reflections = strong;
r.search_merge_reflections = 40000;
return r;
};
const UnitCell triclinic{40.0f, 41.0f, 100.0f, 86.0f, 84.0f, 72.0f};
// The same lattice in the setting with a and b exchanged, as a noisy a ~ b can come out.
const UnitCell swapped{41.02f, 39.98f, 100.1f, 84.0f, 86.0f, 72.0f};
const auto tri = gemmi::CrystalSystem::Triclinic;
const ProcessResult file = arm(triclinic, tri, 0.87, 9000);
REQUIRE(ArmsHoldSameLattice(file, arm(swapped, tri, 0.87, 9000)));
// Same lattice, same CC1/2: the arm that measured more signal wins, whichever centre it is...
CHECK(!MeasuredCentreWins(file, arm(swapped, tri, 0.87, 9500)).empty());
CHECK(MeasuredCentreWins(file, arm(swapped, tri, 0.87, 8500)).empty());
// ...a tie keeps the file's centre, and a higher CC1/2 alone does not move it.
CHECK(MeasuredCentreWins(file, arm(swapped, tri, 0.99, 9000)).empty());
// Different lattices: the metric question, decided on the search merges.
const UnitCell monoclinic{57.0f, 42.0f, 100.0f, 90.0f, 95.0f, 90.0f};
const auto mono = gemmi::CrystalSystem::Monoclinic;
REQUIRE(!ArmsHoldSameLattice(file, arm(monoclinic, mono, 0.87, 9000)));
CHECK(!MeasuredCentreWins(file, arm(monoclinic, mono, 0.95, 9000)).empty());
CHECK(MeasuredCentreWins(file, arm(monoclinic, mono, 0.88, 20000)).empty());
}
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