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Jungfraujoch/tests/CBORTest.cpp
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leonarski_fandClaude Opus 5 307987c865 rugnux: the mounting's cost is computed exactly from the measured group, not guessed from an angle 
Offline, a merged rotation run has what a still lacks - a determined point group and an exact
indexed orientation - so the run-level number no longer needs the pessimistic presumed-diad
bound, and it no longer uses the nearest-axis angle either. That 15-deg warning heuristic was
wrong in both directions: an aligned in-plane 2-fold of a dihedral group is repaired by the
principal axis, a cubic group is never severe in any orientation, and a lone diad perpendicular
to the spindle is severe with no axis anywhere near the spindle at all.

The group's proper rotations are applied to the sweep's blind double cone in the crystal's
actual orientation, and what no operator maps onto measured territory is counted, weighted by
each shell's own cone width so the result is a fraction of unique reflections to this run's
resolution limit. Friedel and the improper operators need no separate handling - the cone and
the measured region are both inversion-symmetric. The number is machine-readable on purpose:
SPINDLE_LOST_UNIQUE_FRACTION in the report (0-1, a bare number a pipeline can act on) and
/entry/MX/spindleLostUniqueFraction in the master, with the warning prose only on top of it,
fired when the group recovers less than half the cone's content. REPORT_VERSION stays 7: the
format's own rule is that adding a key does not move it.

This also settles what the nearest-axis keys hedged: with the measured group the mounting is
cleared or convicted exactly, so their documentation now calls them descriptive and points at
the new key for the verdict. Verified against Monte Carlo: P1 loses 2.0% of unique reflections
at theta_max = 15 deg with nothing repaired; a lone diad on or perpendicular to the spindle
repairs nothing; an axis of order >= 3 perpendicular to the spindle repairs everything; 622
with an in-plane diad on the spindle loses nothing; cubic loses nothing in any orientation.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
2026-09-04 10:59:05 +02:00

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// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include "../frame_serialize/CBORStream2Serializer.h"
#include "../frame_serialize/CBORStream2Deserializer.h"
#include "../compression/JFJochCompressor.h"
#include "../frame_serialize/CborUtil.h"
#include "../common/DiffractionExperiment.h" // kImageMetadataHeadroom
TEST_CASE("CBORSerialize_Start", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
StartMessage message{
.detector_distance = 0.0005,
.beam_center_x = 456.6,
.beam_center_y = 124.3,
.direct_beam_x = 461.2,
.direct_beam_y = 129.9,
.number_of_images = 34567,
.image_size_x = 456,
.image_size_y = 457,
.bit_depth_image = 32,
.bit_depth_readout = 16,
.pixel_signed = true,
.countrate_correction_enabled = true,
.incident_energy = 12400,
.incident_wavelength = 0.988,
.beam_size_x = 8e-5,
.beam_size_y = 3e-5,
.frame_time = 0.0001,
.count_time = 0.000098,
.saturation_value = 65534,
.error_value = 65535,
.pixel_size_x = 0.000075,
.pixel_size_y = 0.000075,
.sensor_thickness = 0.0005,
.sensor_material = "Si",
.unit_cell = UnitCell{.a = 45, .b = 37, .c = 45, .alpha = 90, .beta = 108, . gamma = 120},
.space_group_number = 154,
.max_spot_count = 250,
.storage_cell_number = 16,
.storage_cell_delay_ns = 15345,
.pixel_mask_enabled = true,
.arm_date = "abc",
.sample_name = "test_sample",
.file_prefix = "test_sample/dir/file",
.images_per_file = 12345,
.channels = {"default", "sc2"},
.detector_description = "EIGER 16M",
.detector_serial_number = "123",
.run_name = "bla",
.run_number = 4567,
.gain_file_names = {"abc", "def", "/dsadasdsa/dadsadas/dsadsa/M056.bin"},
.detector_translation = {0.5f, 0.0f, 0.5f},
.source_type = "Synchrotron X-ray Source",
.source_name = "Swiss Light Source",
.instrument_name = "X06SA",
.summation = 567,
.az_int_bin_to_q = {0.1, 0.2, 0.3, 0.5},
.az_int_q_bin_count = 35,
.az_int_phi_bin_count = 120,
.total_flux = 123,
.attenuator_transmission = 0.345,
.write_master_file = true,
.user_data = R"({"pi":3.1415, "z":"string"})"_json,
.data_reduction_factor_serialmx = 0.75,
.experiment_group = "p10001",
.jfjoch_release = "1.4.98",
.socket_number = 3,
.writer_notification_zmq_addr = "tcp://1.2.3.4:5678",
.jungfrau_conversion_enabled = true,
.jungfrau_conversion_factor = 17.56f,
.geometry_transformation_enabled = false,
.overwrite = true,
.file_format = FileWriterFormat::NXmxVDS,
.ring_current_mA = 123,
.sample_temperature_K = 345,
.indexing_algorithm = IndexingAlgorithmEnum::FFT
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
CHECK(output_message.images_per_file == message.images_per_file);
CHECK(output_message.detector_distance == Catch::Approx(message.detector_distance));
CHECK(output_message.beam_center_x == Catch::Approx(message.beam_center_x));
CHECK(output_message.beam_center_y == Catch::Approx(message.beam_center_y));
// The PONI (beam_center_*) and the direct beam are different points on a tilted detector, so the
// round trip has to keep them apart, not merely keep two floats.
REQUIRE(output_message.direct_beam_x);
REQUIRE(output_message.direct_beam_y);
CHECK(output_message.direct_beam_x.value() == Catch::Approx(message.direct_beam_x.value()));
CHECK(output_message.direct_beam_y.value() == Catch::Approx(message.direct_beam_y.value()));
CHECK(output_message.number_of_images == message.number_of_images);
CHECK(output_message.image_size_x == message.image_size_x);
CHECK(output_message.image_size_y == message.image_size_y);
CHECK(output_message.bit_depth_image == message.bit_depth_image);
CHECK(output_message.bit_depth_readout == message.bit_depth_readout);
CHECK(output_message.incident_energy == Catch::Approx(message.incident_energy));
CHECK(output_message.incident_wavelength == Catch::Approx(message.incident_wavelength));
CHECK(output_message.frame_time == Catch::Approx(message.frame_time));
CHECK(output_message.count_time == Catch::Approx(message.count_time));
CHECK(output_message.saturation_value == message.saturation_value);
CHECK(output_message.error_value == message.error_value);
CHECK(output_message.pixel_size_x == Catch::Approx(message.pixel_size_x));
CHECK(output_message.pixel_size_y == Catch::Approx(message.pixel_size_y));
CHECK(output_message.sensor_thickness == Catch::Approx(message.sensor_thickness));
CHECK(output_message.sensor_material == message.sensor_material);
CHECK(output_message.pixel_mask_enabled == message.pixel_mask_enabled);
CHECK(output_message.space_group_number == message.space_group_number);
CHECK(output_message.arm_date == message.arm_date);
CHECK(output_message.storage_cell_number == message.storage_cell_number);
CHECK(output_message.storage_cell_delay_ns == message.storage_cell_delay_ns);
CHECK(output_message.pixel_signed == message.pixel_signed);
CHECK(output_message.sample_name == message.sample_name);
CHECK(output_message.file_prefix == message.file_prefix);
CHECK(output_message.max_spot_count == message.max_spot_count);
CHECK(output_message.channels == message.channels);
CHECK(output_message.detector_description == message.detector_description);
CHECK(output_message.detector_serial_number == message.detector_serial_number);
CHECK(output_message.run_name == message.run_name);
CHECK(output_message.run_number == message.run_number);
CHECK(output_message.source_type == message.source_type);
CHECK(output_message.source_name == message.source_name);
CHECK(output_message.instrument_name == message.instrument_name);
CHECK(output_message.az_int_q_bin_count == message.az_int_q_bin_count);
CHECK(output_message.az_int_phi_bin_count == message.az_int_phi_bin_count);
CHECK(output_message.summation == message.summation);
CHECK(output_message.az_int_bin_to_q == message.az_int_bin_to_q);
for (int i = 0; i < 3; i++)
CHECK(output_message.detector_translation[i] == message.detector_translation[i]);
CHECK(output_message.unit_cell);
CHECK(output_message.unit_cell->a == message.unit_cell->a);
CHECK(output_message.unit_cell->b == message.unit_cell->b);
CHECK(output_message.unit_cell->c == message.unit_cell->c);
CHECK(output_message.unit_cell->alpha == message.unit_cell->alpha);
CHECK(output_message.unit_cell->beta == message.unit_cell->beta);
CHECK(output_message.unit_cell->gamma == message.unit_cell->gamma);
REQUIRE(output_message.beam_size_x);
CHECK(output_message.beam_size_x.value() == message.beam_size_x.value());
REQUIRE(output_message.beam_size_y);
CHECK(output_message.beam_size_y.value() == message.beam_size_y.value());
REQUIRE(output_message.total_flux);
CHECK(output_message.total_flux.value() == message.total_flux.value());
REQUIRE(output_message.attenuator_transmission);
CHECK(output_message.attenuator_transmission.value() == message.attenuator_transmission.value());
CHECK(output_message.user_data == message.user_data);
REQUIRE(output_message.user_data.is_object());
CHECK(output_message.user_data.size() == 2);
CHECK(output_message.gain_file_names == message.gain_file_names);
CHECK(output_message.countrate_correction_enabled == message.countrate_correction_enabled);
CHECK(output_message.flatfield_enabled == message.flatfield_enabled);
CHECK(output_message.write_master_file == message.write_master_file);
CHECK(output_message.data_reduction_factor_serialmx == message.data_reduction_factor_serialmx);
CHECK(output_message.experiment_group == message.experiment_group);
CHECK(output_message.jfjoch_release == message.jfjoch_release);
CHECK(output_message.socket_number == message.socket_number);
CHECK(output_message.writer_notification_zmq_addr == message.writer_notification_zmq_addr);
CHECK(output_message.geometry_transformation_enabled == message.geometry_transformation_enabled);
CHECK(output_message.jungfrau_conversion_enabled == message.jungfrau_conversion_enabled);
CHECK(output_message.jungfrau_conversion_factor == message.jungfrau_conversion_factor);
CHECK(output_message.overwrite == message.overwrite);
CHECK(output_message.file_format == message.file_format);
CHECK(output_message.sample_temperature_K == message.sample_temperature_K);
CHECK(output_message.ring_current_mA == message.ring_current_mA);
CHECK(output_message.indexing_algorithm == message.indexing_algorithm);
}
TEST_CASE("CBORSerialize_Start_GoniometerAxis", "[CBOR]") {
GoniometerAxis axis("z", 115, 0.456, {1, 2, 3}, Coord{50, 20, 30});
axis.ScreeningWedge(0.01);
StartMessage message{
.goniometer = axis
};
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
REQUIRE(output_message.goniometer.has_value());
CHECK(output_message.goniometer->GetName() == axis.GetName());
CHECK(output_message.goniometer->GetStart_deg() == axis.GetStart_deg());
CHECK(output_message.goniometer->GetIncrement_deg() == axis.GetIncrement_deg());
CHECK(output_message.goniometer->GetAxis().x == Catch::Approx(axis.GetAxis().x));
CHECK(output_message.goniometer->GetAxis().y == Catch::Approx(axis.GetAxis().y));
CHECK(output_message.goniometer->GetAxis().z == Catch::Approx(axis.GetAxis().z));
REQUIRE(output_message.goniometer->GetHelicalStep());
CHECK(output_message.goniometer->GetHelicalStep() == axis.GetHelicalStep());
REQUIRE(output_message.goniometer->GetScreeningWedge());
CHECK(output_message.goniometer->GetScreeningWedge() == axis.GetScreeningWedge());
}
TEST_CASE("CBORSerialize_Start_GridScan", "[CBOR]") {
GridScanSettings grid(123, 0.1, 34.0, true, true);
StartMessage message{
.grid_scan = grid
};
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
REQUIRE(!output_message.goniometer.has_value());
REQUIRE(output_message.grid_scan.has_value());
CHECK(output_message.grid_scan->GetNFast() == grid.GetNFast());
CHECK(output_message.grid_scan->IsVerticalScan() == grid.IsVerticalScan());
CHECK(output_message.grid_scan->IsSnakeScan() == grid.IsSnakeScan());
CHECK(output_message.grid_scan->GetGridElemFast_um() == Catch::Approx(grid.GetGridElemFast_um()));
CHECK(output_message.grid_scan->GetGridElemSlow_um() == Catch::Approx(grid.GetGridElemSlow_um()));
}
// A grid scan and a goniometer axis travel together on the wire: the axis with increment 0 is how
// the angle the spindle stood at reaches the file.
TEST_CASE("CBORSerialize_Start_GridScanAtStationaryAxis", "[CBOR]") {
GridScanSettings grid(20, 5.0, 5.0, false, false);
GoniometerAxis axis("omega", 90.0f, 0.0f, Coord(-1, 0, 0), {});
StartMessage message{
.grid_scan = grid,
.goniometer = axis
};
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
REQUIRE(output_message.grid_scan.has_value());
CHECK(output_message.grid_scan->GetNFast() == grid.GetNFast());
REQUIRE(output_message.goniometer.has_value());
CHECK(output_message.goniometer->GetName() == "omega");
CHECK(!output_message.goniometer->IsScanning());
CHECK(output_message.goniometer->GetStart_deg() == Catch::Approx(90.0f));
}
TEST_CASE("CBORSerialize_Start_ThresholdEnergy", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
StartMessage message{};
message.threshold_energy["thr1"] = 12500;
message.threshold_energy["thr2"] = 17000;
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
REQUIRE(output_message.threshold_energy.size() == 2);
REQUIRE(output_message.threshold_energy == message.threshold_energy);
}
TEST_CASE("CBORSerialize_Start_Fluorescence", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
StartMessage message{};
// prepare fluorescence spectrum
std::vector<float> energy{1.0f, 2.0f, 3.0f};
std::vector<float> data{10.0f, 20.0f, 15.0f};
message.fluorescence_spectrum = XrayFluorescenceSpectrum(energy, data);
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
const StartMessage &out = *deserialized->start_message;
REQUIRE(!out.fluorescence_spectrum.empty());
CHECK(out.fluorescence_spectrum.GetEnergy_eV() == energy);
CHECK(out.fluorescence_spectrum.GetData() == data);
}
TEST_CASE("CBORSerialize_Start_Smargon", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
StartMessage message{};
SmargonPosition smargon;
smargon.phi_deg = 45.0f;
smargon.chi_deg = 30.0f;
smargon.phi_axis = {0, -1, 0};
smargon.chi_axis = {0, 0, 1};
message.smargon_position = smargon;
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
const StartMessage &out = *deserialized->start_message;
REQUIRE(out.smargon_position.has_value());
CHECK(out.smargon_position->phi_deg == 45.0f);
CHECK(out.smargon_position->chi_deg == 30.0f);
CHECK(out.smargon_position->phi_axis == Coord{0, -1, 0});
CHECK(out.smargon_position->chi_axis == Coord{0, 0, 1});
}
TEST_CASE("CBORSerialize_ROI", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
StartMessage message{
.rois = {
ROIConfig{
.type = ROIConfig::ROIType::Circle,
.name = "roi1",
.circle = ROIConfigCircle{
.r = 3.0,
.x = 5.0,
.y = 4.0
}
},
ROIConfig{
.type = ROIConfig::ROIType::Box,
.name = "roi2",
.box = ROIConfigBox{
.xmin = 5,
.xmax = 12,
.ymin = 7,
.ymax = 3
}
},
ROIConfig{
.type = ROIConfig::ROIType::Azim,
.name = "roi3",
.azim = ROIConfigAzim{
.qmin = 4.0,
.qmax = 5.0,
.phi_min = 30.0f,
.phi_max = 90.0f
}
},
ROIConfig{
.type = ROIConfig::ROIType::Azim,
.name = "roi4",
.azim = ROIConfigAzim{
.qmin = 1.0,
.qmax = 2.0,
.phi_min = 0.0f,
.phi_max = 0.0f
}
}
}
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
REQUIRE(output_message.rois.size() == 4);
for (int i = 0; i < 4; i++) {
CHECK(output_message.rois[i].name == message.rois[i].name);
CHECK(output_message.rois[i].type == message.rois[i].type);
}
CHECK(output_message.rois[0].circle.x == message.rois[0].circle.x);
CHECK(output_message.rois[0].circle.y == message.rois[0].circle.y);
CHECK(output_message.rois[0].circle.r == message.rois[0].circle.r);
CHECK(output_message.rois[1].box.xmin == message.rois[1].box.xmin);
CHECK(output_message.rois[1].box.xmax == message.rois[1].box.xmax);
CHECK(output_message.rois[1].box.ymin == message.rois[1].box.ymin);
CHECK(output_message.rois[1].box.ymax == message.rois[1].box.ymax);
CHECK(output_message.rois[2].azim.qmin == message.rois[2].azim.qmin);
CHECK(output_message.rois[2].azim.qmax == message.rois[2].azim.qmax);
CHECK(output_message.rois[2].azim.phi_min == 30.0f);
CHECK(output_message.rois[2].azim.phi_max == 90.0f);
// Full ring: phi_min == phi_max round-trips (no sector emitted)
CHECK(output_message.rois[3].azim.phi_min == output_message.rois[3].azim.phi_max);
}
TEST_CASE("CBORSerialize_Start_EmptyString", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
StartMessage message{
.sample_name = "",
.file_prefix = ""
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
CHECK(output_message.file_prefix.empty());
CHECK(output_message.sample_name.empty());
CHECK(output_message.arm_date.empty());
}
TEST_CASE("CBORSerialize_Start_PixelMask", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<uint32_t> mask_0(456 * 457, 15);
std::vector<uint32_t> mask_1(456 * 457, 12);
StartMessage message{
.image_size_x = 456,
.image_size_y = 457,
.pixel_mask = {{"default", mask_0}, {"mask_1", mask_1}}
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
StartMessage &output_message = *deserialized->start_message;
REQUIRE(output_message.pixel_mask.size() == 2);
REQUIRE(output_message.pixel_mask.contains("default"));
REQUIRE(output_message.pixel_mask.contains("mask_1"));
REQUIRE(output_message.pixel_mask["default"].size() == 456*457);
REQUIRE(output_message.pixel_mask["mask_1"].size() == 456*457);
REQUIRE(output_message.pixel_mask["default"] == mask_0);
REQUIRE(output_message.pixel_mask["mask_1"] == mask_1);
}
TEST_CASE("CBORSerialize_Calibration", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<float> calib1(256);
for (int i = 0; i < 256; i++) {
calib1[i] = i * 34.567;
}
CompressedImage image1(calib1, 16, 16);
image1.Channel("calib1");
REQUIRE_NOTHROW(serializer.SerializeCalibration(image1));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::CALIBRATION);
REQUIRE(deserialized->calibration);
CompressedImage &output_message = *deserialized->calibration;
CHECK(output_message.GetMode() == CompressedImageMode::Float32);
CHECK(output_message.GetWidth() == 16);
CHECK(output_message.GetHeight() == 16);
CHECK(output_message.GetChannel() == "calib1");
CHECK(memcmp(output_message.GetCompressed(), calib1.data(), 256 * sizeof(float)) == 0);
}
TEST_CASE("CBORSerialize_End", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
EndMessage message{
.max_image_number = 57789,
.images_collected_count = 50000,
.images_sent_to_write_count = 40000,
.max_receiver_delay = 3456,
.efficiency = 0.99,
.spindle_blind_fraction = 0.31f,
.spindle_lost_unique_fraction = 0.021f,
.end_date = "ccc",
.run_name = "bla5",
.run_number = 45676782,
.rotation_lattice_type = LatticeMessage{
.centering = 'R',
.niggli_class = 22,
.crystal_system = gemmi::CrystalSystem::Tetragonal,
},
.rotation_lattice = CrystalLattice(40, 50, 60, 90, 90, 90),
.v_spindle_blind_fraction = {0.25f, NAN, 1.0f}
};
REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::END);
REQUIRE(deserialized->end_message);
EndMessage &output_message = *deserialized->end_message;
REQUIRE(output_message.max_receiver_delay == message.max_receiver_delay);
REQUIRE(output_message.max_image_number == message.max_image_number);
REQUIRE(output_message.images_collected_count == message.images_collected_count);
REQUIRE(output_message.images_sent_to_write_count == message.images_sent_to_write_count);
REQUIRE(output_message.efficiency);
REQUIRE(output_message.efficiency == Catch::Approx(message.efficiency.value()));
REQUIRE(output_message.end_date == message.end_date);
REQUIRE(output_message.run_number == message.run_number);
REQUIRE(output_message.run_name == message.run_name);
REQUIRE(output_message.az_int_result.empty());
REQUIRE(output_message.rotation_lattice_type.has_value());
CHECK(output_message.rotation_lattice_type->centering == 'R');
CHECK(output_message.rotation_lattice_type->crystal_system == gemmi::CrystalSystem::Tetragonal);
CHECK(output_message.rotation_lattice_type->niggli_class == 22);
REQUIRE(output_message.rotation_lattice.has_value());
CHECK(output_message.rotation_lattice->GetUnitCell().c == Catch::Approx(60.0));
REQUIRE(output_message.spindle_blind_fraction == message.spindle_blind_fraction);
REQUIRE(output_message.spindle_lost_unique_fraction == message.spindle_lost_unique_fraction);
// The per-image vector holds NaN where a frame had no value (CANNOT SAY); the hole must
// survive the round trip as a hole, not as a number.
REQUIRE(output_message.v_spindle_blind_fraction.size() == 3);
CHECK(output_message.v_spindle_blind_fraction[0] == Catch::Approx(0.25f));
CHECK(std::isnan(output_message.v_spindle_blind_fraction[1]));
CHECK(output_message.v_spindle_blind_fraction[2] == Catch::Approx(1.0f));
}
TEST_CASE("CBORSerialize_End_SpaceGroup", "[CBOR]") {
// The determined group travels as both spellings. Only the name keeps the setting, so a
// non-reference setting has to survive the round trip as itself and not as its number's group.
const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name("P 1 1 2");
REQUIRE(sg != nullptr);
REQUIRE(gemmi::find_spacegroup_by_number(sg->number)->xhm() != sg->xhm());
std::vector<uint8_t> buffer(1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
EndMessage message{};
message.max_image_number = 0;
message.space_group_name = sg->xhm();
message.space_group_number = static_cast<uint64_t>(sg->number);
REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->end_message);
const EndMessage &out = *deserialized->end_message;
REQUIRE(out.space_group_name.has_value());
CHECK(*out.space_group_name == sg->xhm());
REQUIRE(out.space_group_number.has_value());
CHECK(*out.space_group_number == static_cast<uint64_t>(sg->number));
}
TEST_CASE("CBORSerialize_End_SpaceGroupNumberOnly", "[CBOR]") {
// A sender written before the name existed fills in only the number; the message still arrives
// and the missing name is absent rather than empty, so a reader can tell it apart.
std::vector<uint8_t> buffer(1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
EndMessage message{};
message.max_image_number = 0;
message.space_group_number = 96;
REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->end_message);
const EndMessage &out = *deserialized->end_message;
CHECK_FALSE(out.space_group_name.has_value());
REQUIRE(out.space_group_number.has_value());
CHECK(*out.space_group_number == 96);
}
TEST_CASE("CBORSerialize_End_RadIntResult", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
EndMessage message{
.max_image_number = 57789,
.max_receiver_delay = 3456,
.efficiency = 0.99,
.end_date = "ccc",
.run_name = "bla5",
.run_number = 45676782
};
message.az_int_result["avg"] = {11.0, 12.0, 13.0};
message.az_int_result["file0"] = {56.0, 75.0, 34.0};
REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::END);
EndMessage &output_message = *deserialized->end_message;
REQUIRE(output_message.az_int_result.size() == 2);
REQUIRE(output_message.az_int_result.contains("avg"));
REQUIRE(output_message.az_int_result.contains("file0"));
CHECK(message.az_int_result["avg"] == output_message.az_int_result["avg"]);
CHECK(message.az_int_result["file0"] == output_message.az_int_result["file0"]);
}
TEST_CASE("CBORSerialize_End_ADUHistogram", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
EndMessage message{
.max_image_number = 57789,
.max_receiver_delay = 3456,
.efficiency = 0.99,
.end_date = "ccc",
.run_name = "bla5",
.run_number = 45676782,
.adu_histogram_bin_width = 55
};
message.adu_histogram["avg"] = {11, 12, 13};
message.adu_histogram["file0"] = {56, 75, 34};
REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::END);
REQUIRE(deserialized->end_message);
EndMessage &output_message = *deserialized->end_message;
REQUIRE(output_message.adu_histogram.size() == 2);
REQUIRE(output_message.adu_histogram.contains("avg"));
REQUIRE(output_message.adu_histogram.contains("file0"));
CHECK(message.adu_histogram["avg"] == output_message.adu_histogram["avg"]);
CHECK(message.adu_histogram["file0"] == output_message.adu_histogram["file0"]);
CHECK(message.adu_histogram_bin_width == output_message.adu_histogram_bin_width);
}
TEST_CASE("CBORSerialize_Image", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
std::vector<uint16_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 256, 2);
DataMessage message{
.number = 456,
.image = image,
.image_collection_efficiency = 0.11,
.spots = spots,
.spot_count_ice_rings = 157,
.bkg_estimate = 12.345f,
.spindle_blind_fraction = 0.62f,
.indexing_result = true,
.indexing_unit_cell = UnitCell{.a = 123, .b = 145, .c = 67.5, .alpha = 90, .beta = 120, .gamma = 134},
.adu_histogram = {3, 4, 5, 8},
.timestamp = 1ul << 27 | 1ul << 35,
.exptime = 1000,
.run_name = "bla2",
.run_number = 4567678,
.saturated_pixel_count = 378,
.error_pixel_count = 123,
.strong_pixel_count = 1234,
.min_viable_pixel_value = 123,
.max_viable_pixel_value = 6789,
.user_data = R"({"pi":3.1415, "z":"string"})"_json,
.jf_info = UINT32_MAX,
.receiver_aq_dev_delay = 2323,
.storage_cell = 0xF,
.xfel_pulse_id = UINT64_MAX - 5678,
.xfel_event_code = UINT64_MAX - 123,
.original_number = 12789
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.image.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION);
REQUIRE(image_array.image.GetWidth() == 256);
REQUIRE(image_array.image.GetHeight() == 2);
REQUIRE(image_array.image.GetMode() == CompressedImageMode::Uint16);
REQUIRE(image_array.image.GetChannel() == "default");
REQUIRE(image_array.image.GetCompressedSize() == test.size() * sizeof(uint16_t));
REQUIRE(image_array.indexing_result == message.indexing_result);
REQUIRE(image_array.number == 456);
REQUIRE(image_array.run_number == message.run_number);
REQUIRE(image_array.run_name == message.run_name);
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size() * sizeof(uint16_t)) == 0);
REQUIRE(image_array.xfel_pulse_id == message.xfel_pulse_id);
REQUIRE(image_array.xfel_event_code == message.xfel_event_code);
REQUIRE(image_array.jf_info == message.jf_info);
REQUIRE(image_array.timestamp == message.timestamp);
REQUIRE(image_array.storage_cell == message.storage_cell);
REQUIRE(image_array.exptime == message.exptime);
REQUIRE(image_array.receiver_aq_dev_delay == image_array.receiver_aq_dev_delay);
REQUIRE(image_array.adu_histogram == message.adu_histogram);
REQUIRE(image_array.saturated_pixel_count == message.saturated_pixel_count);
REQUIRE(image_array.error_pixel_count == message.error_pixel_count);
REQUIRE(image_array.strong_pixel_count == message.strong_pixel_count);
REQUIRE(image_array.bkg_estimate == message.bkg_estimate);
REQUIRE(image_array.spindle_blind_fraction == message.spindle_blind_fraction);
REQUIRE(image_array.image_collection_efficiency == message.image_collection_efficiency);
REQUIRE(image_array.user_data == message.user_data);
REQUIRE(image_array.original_number == message.original_number);
REQUIRE(image_array.spot_count_ice_rings == message.spot_count_ice_rings);
REQUIRE(image_array.indexing_unit_cell.has_value());
REQUIRE(image_array.indexing_unit_cell.value().a == message.indexing_unit_cell.value().a);
REQUIRE(image_array.indexing_unit_cell.value().b == message.indexing_unit_cell.value().b);
REQUIRE(image_array.indexing_unit_cell.value().c == message.indexing_unit_cell.value().c);
REQUIRE(image_array.indexing_unit_cell.value().alpha == message.indexing_unit_cell.value().alpha);
REQUIRE(image_array.indexing_unit_cell.value().beta == message.indexing_unit_cell.value().beta);
REQUIRE(image_array.indexing_unit_cell.value().gamma == message.indexing_unit_cell.value().gamma);
REQUIRE(image_array.min_viable_pixel_value == message.min_viable_pixel_value);
REQUIRE(image_array.max_viable_pixel_value == message.max_viable_pixel_value);
}
TEST_CASE("CBORSerialize_Image_CrystalLattice", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
std::vector<uint16_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 256, 2);
std::vector<float> latt = {1, 2, 3, 4, 5, 6, 7, 8, 9};
DataMessage message{
.image = image,
.indexing_lattice = CrystalLattice(latt)
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(deserialized->data_message->indexing_lattice);
REQUIRE(deserialized->data_message->indexing_lattice->GetVector() == latt);
}
TEST_CASE("CBORSerialize_Image_2", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
std::vector<uint8_t> test(512 * 1024);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 1024, 512);
DataMessage message{
.number = 480,
.image = image,
.spots = spots,
.indexing_result = true
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.image.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION);
REQUIRE(image_array.image.GetWidth() == 1024);
REQUIRE(image_array.image.GetHeight() == 512);
REQUIRE(image_array.image.GetMode() == CompressedImageMode::Uint8);
REQUIRE(image_array.image.GetChannel() == "default");
REQUIRE(image_array.image.GetCompressedSize() == test.size());
REQUIRE(image_array.indexing_result == message.indexing_result);
REQUIRE(image_array.number == 480);
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size()) == 0);
REQUIRE(!image_array.original_number);
}
TEST_CASE("CBORSerialize_Image_Float", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
std::vector<float> test(512 * 1024);
for (int i = 0; i < test.size(); i++)
test[i] = i * 0.1f;
CompressedImage image(test, 1024, 512);
DataMessage message{
.number = 480,
.image = image,
.spots = spots,
.indexing_result = false
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.image.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION);
REQUIRE(image_array.image.GetWidth() == 1024);
REQUIRE(image_array.image.GetHeight() == 512);
REQUIRE(image_array.image.GetMode() == CompressedImageMode::Float32);
REQUIRE(image_array.image.GetChannel() == "default");
REQUIRE(image_array.image.GetCompressedSize() == test.size() * sizeof(float));
REQUIRE(image_array.indexing_result == message.indexing_result);
REQUIRE(image_array.number == 480);
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size() * sizeof(float)) == 0);
}
TEST_CASE("CBORSerialize_Image_Rgb", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
std::vector<rgb> test(512 * 1024);
for (int i = 0; i < test.size(); i++) {
test[i].r = (i / 256) % 256;
test[i].g = i % 256;
test[i].b = (i / 771) % 256;
}
CompressedImage image(test, 1024, 512);
DataMessage message{
.number = 480,
.image = image,
.spots = spots,
.indexing_result = false
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.image.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION);
REQUIRE(image_array.image.GetWidth() == 1024);
REQUIRE(image_array.image.GetHeight() == 512);
REQUIRE(image_array.image.GetMode() == CompressedImageMode::RGB);
REQUIRE(image_array.image.GetChannel() == "default");
REQUIRE(image_array.image.GetCompressedSize() == test.size() * sizeof(rgb));
REQUIRE(image_array.indexing_result == message.indexing_result);
REQUIRE(image_array.number == 480);
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size() * sizeof(rgb)) == 0);
}
TEST_CASE("CBORSerialize_Image_Compressed", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
std::vector<uint8_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 256, 2, CompressedImageMode::Int32, CompressionAlgorithm::BSHUF_LZ4);
DataMessage message{
.number = 456,
.image = image,
.spots = spots
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.image.GetCompressionAlgorithm() == CompressionAlgorithm::BSHUF_LZ4);
REQUIRE(image_array.image.GetWidth() == 256);
REQUIRE(image_array.image.GetHeight() == 2);
REQUIRE(image_array.image.GetMode() == CompressedImageMode::Int32);
REQUIRE(image_array.image.GetChannel() == "default");
REQUIRE(image_array.image.GetCompressedSize() == test.size());
REQUIRE(image_array.number == 456);
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size()) == 0);
}
TEST_CASE("CBORSerialize_Image_Rad_Int_Profile", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<uint16_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 256, 2);
DataMessage message{
.number = 789,
.image = image,
.az_int_profile = {4.0, 5.0, 7.0, 12.0, 13.25, 0.125},
.az_int_profile_std = {1.0, 0.0, NAN, NAN, 8.0, 12.0},
.az_int_profile_count = {3,2,0,1,5,7}
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.number == 789);
REQUIRE(image_array.image.GetCompressedSize() == test.size() * sizeof(uint16_t));
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size() * sizeof(uint16_t)) == 0);
REQUIRE(image_array.az_int_profile == message.az_int_profile);
REQUIRE(image_array.az_int_profile_std.size() == message.az_int_profile_std.size());
for (int i = 0; i < image_array.az_int_profile_std.size(); i++) {
if (std::isnan(message.az_int_profile_std[i]))
CHECK(std::isnan(image_array.az_int_profile_std[i]));
else
CHECK(message.az_int_profile_std[i] == Catch::Approx(image_array.az_int_profile_std[i]));
}
REQUIRE(image_array.az_int_profile_count == message.az_int_profile_count);
}
TEST_CASE("CBORSerialize_Start_AzintMap", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<uint16_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
std::vector<uint16_t> azint_map(32 * 15, 57);
azint_map[0] = 123;
azint_map[32*14] = UINT16_MAX;
StartMessage msg{
.image_size_x = 32,
.image_size_y = 15,
.az_int_map = azint_map
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(msg));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
CHECK(deserialized->start_message->az_int_map == azint_map);
}
TEST_CASE("CBORSerialize_Start_ROIMap", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<uint16_t> roi_map(32 * 15, 0);
roi_map[0] = (1 << 0) | (1 << 3);
roi_map[32 * 14] = (1 << 2);
StartMessage msg{
.image_size_x = 32,
.image_size_y = 15,
.roi_map = roi_map
};
REQUIRE_NOTHROW(serializer.SerializeSequenceStart(msg));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::START);
REQUIRE(deserialized->start_message);
CHECK(deserialized->start_message->roi_map == roi_map);
}
TEST_CASE("CBORSerialize_Image_Spots", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<SpotToSave> spots;
spots.push_back(SpotToSave{.x = 7, .y = 8, .intensity = 34, .indexed = false});
spots.push_back(SpotToSave{.x = 37, .y = 48, .intensity = 123, .indexed = true});
std::vector<uint16_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 256, 2);
DataMessage message{
.number = 789,
.image = image,
.spots = spots
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.number == 789);
REQUIRE(image_array.image.GetCompressedSize() == test.size() * sizeof(uint16_t));
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size() * sizeof(uint16_t)) == 0);
REQUIRE(image_array.spots.size() == 2);
REQUIRE(image_array.spots[0].intensity == 34);
REQUIRE(!image_array.spots[0].indexed);
REQUIRE(image_array.spots[1].x == 37);
REQUIRE(image_array.spots[1].y == 48);
REQUIRE(image_array.spots[1].intensity == 123);
REQUIRE(image_array.spots[1].indexed);
}
TEST_CASE("CBORSerialize_Image_Reflections") {
// Prepare a few reflections with distinct values
std::vector<Reflection> refs_in;
// Every float is given a distinct value: a field the encoder forgets reads back as 0 and fails
// here. var_bkg was added to Reflection and to the HDF5 writer but not to the CBOR map, so every
// broker-written file carried a zeroed background_variance until this test was widened to see it.
refs_in.push_back(Reflection{
.h = 1, .k = 0, .l = -1,
.image_number = 789.0f, .delta_phi_deg = 0.125f,
.predicted_x = 1024.5f, .predicted_y = 768.25f,
.observed_x = 1024.75f, .observed_y = 768.5f,
.d = 2.345f, .I = 1234.5f, .bkg = 3.25f, .var_bkg = 41.5f, .sigma = 37.125f,
.dist_ewald = 0.0025f, .rlp = 1.75f, .partiality = 0.875f, .zeta = 0.625f,
.image_scale_corr = 1.125f
});
refs_in.push_back(Reflection{
.h = -3, .k = 2, .l = 7,
.image_number = 790.0f, .delta_phi_deg = -0.25f,
.predicted_x = 5.0f, .predicted_y = 10.0f,
.observed_x = 5.5f, .observed_y = 10.5f,
.d = 4.0f, .I = 12.0f, .bkg = 0.5f, .var_bkg = 6.75f, .sigma = 4.25f,
.dist_ewald = -0.001f, .rlp = 2.5f, .partiality = 0.5f, .zeta = 0.25f,
.image_scale_corr = 0.875f
});
refs_in.push_back(Reflection{
.h = 0, .k = 0, .l = 1,
.image_number = 791.0f, .delta_phi_deg = 0.0f,
.predicted_x = 0.0f, .predicted_y = 0.0f,
.observed_x = 0.25f, .observed_y = 0.5f,
.d = 10.0f, .I = -1.5f, .bkg = 0.125f, .var_bkg = 0.875f, .sigma = 1.5f,
.dist_ewald = 0.0f, .rlp = 1.0f, .partiality = 1.0f, .zeta = 1.0f,
.image_scale_corr = 1.0f
});
// Minimal DataMessage carrying reflections
std::vector<uint16_t> test(512);
CompressedImage image(test, 256, 2);
DataMessage msg_in{
.number = 789,
.image = image,
.reflections = refs_in
};
// Serialize
std::vector<uint8_t> buffer(1 << 20); // 1 MB buffer for safety
CBORStream2Serializer ser(buffer.data(), buffer.size());
ser.SerializeImage(msg_in);
// Deserialize
auto deserialized = CBORStream2Deserialize(buffer.data(), ser.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &msg_out = *deserialized->data_message;
// Check reflections
REQUIRE(msg_out.reflections.size() == refs_in.size());
for (size_t i = 0; i < refs_in.size(); ++i) {
const auto &a = refs_in[i];
const auto &b = msg_out.reflections[i];
CHECK(a.h == b.h);
CHECK(a.k == b.k);
CHECK(a.l == b.l);
CHECK(b.predicted_x == Catch::Approx(a.predicted_x).margin(1e-6f));
CHECK(b.predicted_y == Catch::Approx(a.predicted_y).margin(1e-6f));
CHECK(b.observed_x == Catch::Approx(a.observed_x).margin(1e-6f));
CHECK(b.observed_y == Catch::Approx(a.observed_y).margin(1e-6f));
CHECK(b.d == Catch::Approx(a.d).margin(1e-6f));
CHECK(b.image_number == Catch::Approx(a.image_number).margin(1e-6f));
CHECK(b.delta_phi_deg == Catch::Approx(a.delta_phi_deg).margin(1e-6f));
CHECK(b.I == Catch::Approx(a.I).margin(1e-6f));
CHECK(b.bkg == Catch::Approx(a.bkg).margin(1e-6f));
CHECK(b.var_bkg == Catch::Approx(a.var_bkg).margin(1e-6f));
CHECK(b.sigma == Catch::Approx(a.sigma).margin(1e-6f));
CHECK(b.dist_ewald == Catch::Approx(a.dist_ewald).margin(1e-6f));
CHECK(b.rlp == Catch::Approx(a.rlp).margin(1e-6f));
CHECK(b.partiality == Catch::Approx(a.partiality).margin(1e-6f));
CHECK(b.zeta == Catch::Approx(a.zeta).margin(1e-6f));
CHECK(b.image_scale_corr == Catch::Approx(a.image_scale_corr).margin(1e-6f));
}
}
TEST_CASE("CBORSerialize_Image_MetadataHeadroom", "[CBOR]") {
// The receiver serializes the per-image CBOR metadata (spots, reflections,
// azimuthal profile, ...) into the same buffer slot as the compressed image, and
// DiffractionExperiment::GetImageBufferLocationSize() reserves
// kImageMetadataHeadroom on top of GetMaxCompressedSize() for it. A frame whose
// metadata exceeds that headroom is dropped by the receiver. This test guards that
// even the largest possible metadata still fits, so ordinary frames are never
// dropped: the kOnlineMaxReflections (10000, BraggPrediction.h) reflection cap, the
// API maximum of 2000 spots (jfjoch_api.yaml), and the 65534-bin azimuthal cap
// (AzimuthalIntegrationMapping, UINT16_MAX - 1), all serialized together. Take the
// headroom from the constant rather than restate it: written down twice, the two
// drifted apart and this test kept passing against the value the code had left.
constexpr size_t max_reflections = 10000;
constexpr size_t max_spots = 2000;
constexpr size_t max_az_bins = 65534;
constexpr size_t headroom = DiffractionExperiment::kImageMetadataHeadroom;
std::vector<Reflection> reflections(max_reflections);
for (size_t i = 0; i < reflections.size(); ++i)
reflections[i] = Reflection{
.h = static_cast<int32_t>(i % 200) - 100,
.k = static_cast<int32_t>(i % 200) - 100,
.l = static_cast<int32_t>(i % 200) - 100,
.image_number = 789.0f, .delta_phi_deg = 0.123f,
.predicted_x = 1234.5f, .predicted_y = 678.9f,
.observed_x = 1234.0f, .observed_y = 678.0f,
.d = 2.345f, .I = 1234.5f, .bkg = 12.3f, .sigma = 35.6f,
.dist_ewald = 0.001f, .rlp = 0.5f, .partiality = 0.9f,
.zeta = 0.3f, .image_scale_corr = 1.1f};
std::vector<SpotToSave> spots(max_spots);
for (size_t i = 0; i < spots.size(); ++i)
spots[i] = SpotToSave{
.x = 1234.5f, .y = 678.9f, .intensity = 1234.5f, .maxc = 5000,
.lattice = 0, .image = 789,
.h = static_cast<int64_t>(i % 200) - 100,
.k = static_cast<int64_t>(i % 200) - 100,
.l = static_cast<int64_t>(i % 200) - 100,
.dist_ewald_sphere = 0.01f, .indexed = true};
DataMessage message{
.number = 789,
.image = CompressedImage(nullptr, 0, 4000, 4000,
CompressedImageMode::Uint32, CompressionAlgorithm::BSHUF_LZ4),
.spots = spots,
.az_int_profile = std::vector<float>(max_az_bins, 1.0f),
.az_int_profile_std = std::vector<float>(max_az_bins, 1.0f),
.az_int_profile_count = std::vector<uint64_t>(max_az_bins, 1),
.reflections = reflections};
std::vector<uint8_t> buffer(16 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
REQUIRE_NOTHROW(serializer.SerializeImage(message));
// GetImageAppendOffset() is where the compressed image is appended, i.e. the size
// of everything-but-the-image; it must stay below the metadata headroom.
INFO("worst-case metadata size = " << serializer.GetImageAppendOffset() << " B");
CHECK(serializer.GetImageAppendOffset() < headroom);
}
TEST_CASE("CBORSerialize_Image_ROI", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<uint16_t> test(512);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(test, 256, 2);
DataMessage message{
.number = 789,
.image = image,
};
message.roi["roi0"] = {
.sum = -876, .sum_square = 89998, .max_count = -1, .pixels = 4567, .x_weighted = 123, .y_weighted = 122
};
message.roi["roi1"] = {
.sum = 876, .sum_square = 998, .max_count = 12, .pixels = 234, .x_weighted = -11222233443123LL, .y_weighted = -5
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.number == 789);
REQUIRE(image_array.roi.size() == 2);
REQUIRE(image_array.roi.contains("roi0"));
REQUIRE(image_array.roi.contains("roi1"));
CHECK(image_array.roi["roi0"].sum == message.roi["roi0"].sum);
CHECK(image_array.roi["roi0"].sum_square == message.roi["roi0"].sum_square);
CHECK(image_array.roi["roi0"].max_count == message.roi["roi0"].max_count);
CHECK(image_array.roi["roi0"].pixels == message.roi["roi0"].pixels);
CHECK(image_array.roi["roi0"].x_weighted == message.roi["roi0"].x_weighted);
CHECK(image_array.roi["roi0"].y_weighted == message.roi["roi0"].y_weighted);
CHECK(image_array.roi["roi1"].sum == message.roi["roi1"].sum);
CHECK(image_array.roi["roi1"].sum_square == message.roi["roi1"].sum_square);
CHECK(image_array.roi["roi1"].max_count == message.roi["roi1"].max_count);
CHECK(image_array.roi["roi1"].pixels == message.roi["roi1"].pixels);
CHECK(image_array.roi["roi1"].x_weighted == message.roi["roi1"].x_weighted);
CHECK(image_array.roi["roi1"].y_weighted == message.roi["roi1"].y_weighted);
}
TEST_CASE("CBORSerialize_Image_Append", "[CBOR]") {
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
std::vector<uint8_t> test(512 * 1024);
for (int i = 0; i < test.size(); i++)
test[i] = (i * 253 + 56) % 256;
CompressedImage image(nullptr, 0, 1024, 512, CompressedImageMode::Uint8, CompressionAlgorithm::BSHUF_LZ4);
DataMessage message{
.number = 480,
.image = image
};
REQUIRE_NOTHROW(serializer.SerializeImage(message));
memcpy(buffer.data() + serializer.GetImageAppendOffset(), test.data(), 512 * 1024);
//REQUIRE_THROWS(serializer.AppendImage(16*1024*1024));
REQUIRE_NOTHROW(serializer.AppendImage(512 * 1024));
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::IMAGE);
REQUIRE(deserialized->data_message);
DataMessage &image_array = *deserialized->data_message;
REQUIRE(image_array.image.GetCompressionAlgorithm() == CompressionAlgorithm::BSHUF_LZ4);
REQUIRE(image_array.image.GetWidth() == 1024);
REQUIRE(image_array.image.GetHeight() == 512);
REQUIRE(image_array.image.GetMode() == CompressedImageMode::Uint8);
REQUIRE(image_array.image.GetChannel() == "default");
REQUIRE(image_array.image.GetCompressedSize() == test.size());
REQUIRE(image_array.indexing_result == message.indexing_result);
REQUIRE(image_array.number == 480);
REQUIRE(memcmp(image_array.image.GetCompressed(), test.data(), test.size()) == 0);
}
TEST_CASE("CBORSerialize_Metadata", "[CBOR]") {
MetadataMessage msgs;
CompressedImage image(nullptr, 0, 123, 145, CompressedImageMode::Uint8,
CompressionAlgorithm::BSHUF_LZ4);
msgs.images.push_back(DataMessage{.number = 172, .image = image, .bkg_estimate = 45});
msgs.images.push_back(DataMessage{.number = 173, .image = image, .bkg_estimate = 48});
//msgs.push_back(DataMessage{.number = 174, .image = CompressedImage{.GetWidth() = 123, .GetHeight() = 145}, .bkg_estimate = 48});
std::vector<uint8_t> buffer(8 * 1024 * 1024);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
REQUIRE_NOTHROW(serializer.SerializeMetadata(msgs));
REQUIRE(serializer.GetBufferSize() > 0);
auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(deserialized);
REQUIRE(deserialized->msg_type == CBORImageType::METADATA);
REQUIRE(deserialized->metadata);
REQUIRE(deserialized->metadata->images.size() == 2);
CHECK(deserialized->metadata->images.at(0).number == 172);
CHECK(deserialized->metadata->images.at(0).bkg_estimate == 45);
CHECK(!deserialized->metadata->images.at(0).spindle_blind_fraction.has_value());
CHECK(deserialized->metadata->images.at(0).image.GetWidth() == 0);
CHECK(deserialized->metadata->images.at(1).number == 173);
CHECK(deserialized->metadata->images.at(1).bkg_estimate == 48);
CHECK(deserialized->metadata->images.at(1).image.GetWidth() == 0);
}
TEST_CASE("CBORSerialize_Image_LatticeType", "[CBOR][Lattice]") {
std::vector<uint8_t> buffer(1 << 20);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
// Prepare an image with lattice_type set
std::vector<uint16_t> pixels(16, 0);
CompressedImage img(pixels, 4, 4);
DataMessage in_msg{
.number = 1,
.image = img
};
// Case 1: Tetragonal, body-centered -> expect same after round trip
in_msg.lattice_type = LatticeMessage{
.centering = 'I',
.niggli_class = 25,
.crystal_system = gemmi::CrystalSystem::Tetragonal
};
REQUIRE_NOTHROW(serializer.SerializeImage(in_msg));
auto out = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
REQUIRE(out);
REQUIRE(out->msg_type == CBORImageType::IMAGE);
REQUIRE(out->data_message);
// LatticeMessage present
REQUIRE(out->data_message->lattice_type.has_value());
const auto lm = out->data_message->lattice_type.value();
CHECK(lm.centering == 'I');
CHECK(lm.niggli_class == 25);
CHECK(lm.crystal_system == gemmi::CrystalSystem::Tetragonal);
// Case 2: Absent lattice_type should remain absent
CBORStream2Serializer serializer2(buffer.data(), buffer.size());
DataMessage in_msg2{
.number = 2,
.image = img
};
REQUIRE_NOTHROW(serializer2.SerializeImage(in_msg2));
auto out2 = CBORStream2Deserialize(buffer.data(), serializer2.GetBufferSize());
REQUIRE(out2);
REQUIRE(out2->msg_type == CBORImageType::IMAGE);
REQUIRE(out2->data_message);
CHECK_FALSE(out2->data_message->lattice_type.has_value());
// Case 3: Various systems/centerings sanity round-trip
struct Case {
gemmi::CrystalSystem cs;
char ctr;
};
std::vector<Case> cases = {
{gemmi::CrystalSystem::Triclinic, 'P'},
{gemmi::CrystalSystem::Monoclinic, 'C'},
{gemmi::CrystalSystem::Orthorhombic, 'F'},
{gemmi::CrystalSystem::Orthorhombic, 'A'},
{gemmi::CrystalSystem::Tetragonal, 'P'},
{gemmi::CrystalSystem::Trigonal, 'R'},
{gemmi::CrystalSystem::Hexagonal, 'P'},
{gemmi::CrystalSystem::Cubic, 'I'},
};
int i = 0;
for (const auto &c: cases) {
CBORStream2Serializer ser(buffer.data(), buffer.size());
DataMessage m{
.number = 3,
.image = img
};
m.lattice_type = LatticeMessage{.centering = c.ctr, .niggli_class = i, .crystal_system = c.cs};
REQUIRE_NOTHROW(ser.SerializeImage(m));
auto d = CBORStream2Deserialize(buffer.data(), ser.GetBufferSize());
REQUIRE(d);
REQUIRE(d->msg_type == CBORImageType::IMAGE);
REQUIRE(d->data_message);
REQUIRE(d->data_message->lattice_type.has_value());
auto l = d->data_message->lattice_type.value();
CHECK(l.centering == c.ctr);
CHECK(l.niggli_class == i);
CHECK(l.crystal_system == c.cs);
i++;
}
}
// The chain is sent as an ARRAY because the mounting order has to survive, and a CBOR map's order
// carries no guarantee - RFC 8949 requires deterministic encoders to sort map keys. This asserts the
// order round trips, not merely the contents, and that a moving axis keeps one value per image
// while a stationary one keeps a single value.
TEST_CASE("CBORSerialize_End_Transformations", "[CBOR]") {
EndMessage message{};
message.max_image_number = 4;
message.transformations = {
DetectorTransformation("grid_scan_x", TransformationType::Translation, {1, 0, 0})
.Values({0.0f, 1e-4f, 2e-4f, 3e-4f}),
DetectorTransformation("omega", TransformationType::Rotation, {-1, 0, 0})
.DependsOn("grid_scan_x").Values({95.0f, 95.1f, 95.2f, 95.3f}),
DetectorTransformation("chi", TransformationType::Rotation, {0, 0, 1})
.DependsOn("omega").Value(12.5f),
DetectorTransformation("phi", TransformationType::Rotation, {1, 0, 0})
.DependsOn("chi").Value(-7.25f).Offset({1, 2, 3}),
};
std::vector<uint8_t> buffer(MESSAGE_SIZE_FOR_START_END);
CBORStream2Serializer serializer(buffer.data(), buffer.size());
REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
buffer.resize(serializer.GetBufferSize());
auto output = CBORStream2Deserialize(buffer.data(), buffer.size());
REQUIRE(output->end_message.has_value());
const auto &chain = output->end_message->transformations;
REQUIRE(chain.size() == message.transformations.size());
for (size_t i = 0; i < chain.size(); i++) {
const auto &got = chain[i];
const auto &want = message.transformations[i];
CHECK(got.GetName() == want.GetName());
CHECK(got.IsRotation() == want.IsRotation());
CHECK(got.GetUnits() == want.GetUnits());
CHECK(got.GetDependsOn() == want.GetDependsOn());
CHECK(got.GetVector().x == Catch::Approx(want.GetVector().x));
CHECK(got.GetVector().y == Catch::Approx(want.GetVector().y));
CHECK(got.GetVector().z == Catch::Approx(want.GetVector().z));
CHECK(got.GetOffset().x == Catch::Approx(want.GetOffset().x));
CHECK(got.IsConstant() == want.IsConstant());
REQUIRE(got.GetValues().size() == want.GetValues().size());
for (size_t j = 0; j < got.GetValues().size(); j++)
CHECK(got.GetValues()[j] == Catch::Approx(want.GetValues()[j]).margin(1e-4));
}
// The base of the chain names no parent.
CHECK(chain[0].GetDependsOn().empty());
CHECK(!chain[1].IsConstant());
CHECK(chain[2].IsConstant());
}
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