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Jungfraujoch/writer/HDF5NXmx.cpp
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leonarski_fandClaude Opus 5 259b43154e Writer: refuse a mistyped stream, and mark unreadable VDS frames 
Two ways the written files could misdescribe themselves without anyone noticing.

The pixel format is stated twice and the two were never compared: each image
carries its own type as a CBOR tag, which is what the data files are written
with, while the master is typed from the start message. A stream whose header
contradicts its images produced data files of one type under a master declaring
another, and with NXmxVDS, HDF5 then converts silently on every read.
HDF5DataFile::CreateFile now checks the two agree and refuses the run otherwise -
the point where the values first meet, so it covers every path into the writer.

Two test fixtures were relying on exactly that inconsistency. The HDF5 writer
tests wrote uint16 buffers under a JUNGFRAU experiment, which converts to photon
counts by default and so declares int16; they never read the pixels back, so it
went unnoticed. The receiver-lite tests feed frames from
compression_benchmark.h5, which really are signed int16, through a DECTRIS
experiment, which declares unsigned by default - the same class of bug the
pixel_signed propagation fixed on the live path. Both now declare what they send.

Second: a virtual dataset whose source file is absent reads as the fill value,
and HDF5 defaults that to zero, so a data file that was not copied alongside the
master is indistinguishable from frames of genuine zero counts. Measured with
DIALS on a four-file set with one file removed: 25 frames of pure zeros, no error
and no warning. The image VDS is now filled with the error marker instead, which
sits outside underload_value..saturation_value, so a reader masks those frames.
Same measurement after the change: -32768 throughout, which DIALS excludes.

Only the images ask for a fill value; the per-image metadata datasets keep the
default.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-22 21:44:04 +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 <algorithm>
#include <cmath>
#include "HDF5NXmx.h"
#include "../common/GitInfo.h"
#include "../include/spdlog/fmt/fmt.h"
#include "MakeDirectory.h"
#include "../common/time_utc.h"
#include "gemmi/symmetry.hpp"
std::string HDF5Metadata::MasterFileName(const StartMessage &start) {
if (start.master_suffix.has_value())
return fmt::format("{:s}_{:s}.h5", start.file_prefix, start.master_suffix.value());
return fmt::format("{:s}_master.h5", start.file_prefix);
}
NXmx::NXmx(const StartMessage &start)
: start_message(start),
filename(HDF5Metadata::MasterFileName(start)) {
uint64_t tmp_suffix;
try {
if (!start.arm_date.empty())
tmp_suffix = parse_UTC_to_ms(start.arm_date);
} catch (...) {
tmp_suffix = std::chrono::system_clock::now().time_since_epoch().count();
}
tmp_filename = fmt::format("{}.{:08x}.tmp", filename, tmp_suffix);
if (start.overwrite.has_value())
overwrite = start.overwrite.value();
MakeDirectory(filename);
bool v1_10 = (start.file_format == FileWriterFormat::NXmxVDS)
|| !start.hdf5_source_data.empty();
hdf5_file = std::make_shared<HDF5File>(tmp_filename, v1_10);
hdf5_file->Attr("file_name", filename);
hdf5_file->Attr("HDF5_Version", hdf5_version());
HDF5Group(*hdf5_file, "/entry").NXClass("NXentry").SaveScalar("definition", "NXmx");
hdf5_file->SaveScalar("/entry/start_time", start.arm_date);
Facility(start);
Detector(start);
Beam(start);
Attenuator(start);
UserData(start);
MX(start);
ROI(start);
Fluorescence(start);
}
NXmx::~NXmx() {
try {
if (hdf5_file) {
hdf5_file.reset();
std::error_code ec;
std::filesystem::remove(tmp_filename, ec);
}
} catch (...) {}
}
std::string HDF5Metadata::DataFileName(const StartMessage &msg, int64_t file_number) {
if (file_number < 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"File number cannot be negative");
if (msg.source_name == "SwissFEL") {
if (file_number >= 10000)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Format doesn't allow for 10'000 or more files");
else if (msg.detector_serial_number.empty())
return fmt::format("{:s}{:04d}.JF.h5", msg.file_prefix, file_number + 1);
else
return fmt::format("{:s}{:04d}.{:s}.h5", msg.file_prefix, file_number + 1, msg.detector_serial_number);
} else {
if (file_number >= 1000000)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Format doesn't allow for 1 million or more files");
else
return fmt::format("{:s}_data_{:06d}.h5", msg.file_prefix, file_number + 1);
}
}
void NXmx::LinkToData(const StartMessage &start, const EndMessage &end) {
hsize_t total_images = end.max_image_number;
hsize_t images_per_file = start.images_per_file;
hsize_t file_count = 0;
if (start.images_per_file > 0) {
file_count = total_images / images_per_file;
if (total_images % images_per_file > 0)
file_count++;
}
HDF5Group(*hdf5_file, "/entry/data").NXClass("NXdata");
for (uint32_t file_id = 0; file_id < file_count; file_id++) {
char buff[32];
snprintf(buff,32,"/entry/data/data_%06d", file_id+1);
hdf5_file->ExternalLink(HDF5Metadata::DataFileName(start, file_id),
"/entry/data/data",
std::string(buff));
}
}
void NXmx::LinkToData_VDS(const StartMessage &start, const EndMessage &end) {
hsize_t total_images = end.max_image_number;
hsize_t width = start.image_size_x;
hsize_t height = start.image_size_y;
if (total_images > 0) {
HDF5Group(*hdf5_file, "/entry/data").NXClass("NXdata");
auto data_dataset = VDS(start,
"/entry/data/data",
{total_images, height, width},
HDF5DataType(start.bit_depth_image / 8, start.pixel_signed),
start.error_value);
data_dataset->Attr("image_nr_low", (int32_t) 1)
.Attr("image_nr_high",(int32_t) total_images);
if (start.max_spot_count > 0) {
VDS(start, "/entry/MX/peakXPosRaw",{total_images, start.max_spot_count}, HDF5DataType(0.0f));
VDS(start, "/entry/MX/peakYPosRaw",{total_images, start.max_spot_count}, HDF5DataType(0.0f));
VDS(start, "/entry/MX/peakTotalIntensity",{total_images, start.max_spot_count}, HDF5DataType(0.0f));
VDS(start, "/entry/MX/peakIceRingRes", {total_images, start.max_spot_count}, HDF5DataType(static_cast<int8_t>(0)));
VDS(start, "/entry/MX/nPeaks", {total_images}, HDF5DataType((uint32_t) 0));
}
if (start.indexing_algorithm != IndexingAlgorithmEnum::None) {
VDS(start, "/entry/MX/peakIndexed", {total_images, start.max_spot_count}, HDF5DataType(static_cast<int8_t>(0)));
VDS(start, "/entry/MX/peakLattice", {total_images, start.max_spot_count}, HDF5DataType(static_cast<int8_t>(-1)));
VDS(start, "/entry/MX/peakH", {total_images, start.max_spot_count}, HDF5DataType((int32_t) 0));
VDS(start, "/entry/MX/peakK", {total_images, start.max_spot_count}, HDF5DataType((int32_t) 0));
VDS(start, "/entry/MX/peakL", {total_images, start.max_spot_count}, HDF5DataType((int32_t) 0));
VDS(start, "/entry/MX/peakDistEwaldSphere", {total_images, start.max_spot_count}, HDF5DataType((float) 0));
VDS(start, "/entry/MX/latticeIndexed", {total_images,9}, HDF5DataType((float) 0))->Units("Angstrom");
if (start.max_extra_lattices > 0)
VDS(start, "/entry/MX/latticeIndexedExtra", {total_images, start.max_extra_lattices, 9}, HDF5DataType((float) 0))->Units("Angstrom");
}
if (!start.az_int_bin_to_q.empty()) {
size_t azimuthal_bins = start.az_int_phi_bin_count.value_or(1);
size_t q_bins = start.az_int_q_bin_count.value_or(1);
if (q_bins > 0 && azimuthal_bins > 0) {
VDS(start, "/entry/azint/image",
{total_images, azimuthal_bins, q_bins},
HDF5DataType(0.0f));
VDS(start, "/entry/azint/image_count",
{total_images, azimuthal_bins, q_bins},
HDF5DataType(static_cast<uint64_t>(0UL)));
// We make the link if we don't know if st.dev is recorded
VDS(start, "/entry/azint/image_std",
{total_images, azimuthal_bins, q_bins},
HDF5DataType(0.0f));
}
}
if (!start.rois.empty()) {
// Per-image ROI results live in the data files; expose them in the master
// through virtual datasets, one /entry/roi/<name> group per ROI.
HDF5Group(*hdf5_file, "/entry/roi").NXClass("NXcollection");
for (const auto &r: start.rois) {
const std::string base = "/entry/roi/" + r.name;
HDF5Group(*hdf5_file, base);
VDS(start, base + "/max", {total_images}, HDF5DataType((int64_t) 0));
VDS(start, base + "/sum", {total_images}, HDF5DataType((int64_t) 0));
VDS(start, base + "/sum_sq", {total_images}, HDF5DataType((int64_t) 0));
VDS(start, base + "/npixel", {total_images}, HDF5DataType((int64_t) 0));
VDS(start, base + "/x", {total_images}, HDF5DataType((float) 0));
VDS(start, base + "/y", {total_images}, HDF5DataType((float) 0));
}
}
if (start.xfel_pulse_id.value_or(false)) {
HDF5Group(*hdf5_file, "/entry/xfel").NXClass("NXcollection");
VDS(start, "/entry/xfel/pulseID", {total_images}, HDF5DataType((uint64_t) 0));
VDS(start, "/entry/xfel/eventCode", {total_images}, HDF5DataType((uint32_t) 0));
}
if (start.storage_cell_number)
VDS(start,
"/entry/detector/storage_cell_image",
"/entry/instrument/detector/detectorSpecific/storage_cell_image",
{total_images},
HDF5DataType((uint8_t) 0));
LinkToReflections_VDS(start, end);
}
}
void NXmx::LinkToData_ProcessingVDS(const StartMessage &start, const EndMessage &end) {
if (start.hdf5_source_data.empty() || end.max_image_number == 0)
return;
const hsize_t total_images = end.max_image_number;
const hsize_t width = start.image_size_x;
const hsize_t height = start.image_size_y;
HDF5Group(*hdf5_file, "/entry/data").NXClass("NXdata");
HDF5DataSpace full_data_space({total_images, height, width});
HDF5Dcpl dcpl;
dcpl.SetChunking({1, height, width});
for (const auto &mapping: start.hdf5_source_data) {
if (mapping.image_count == 0)
continue;
// The mapping is built from the number of images the run intended to process, while
// total_images is the number it actually finished. A cancelled run, or one that skipped an
// unreadable frame, legitimately ends up with fewer - so map what was written and drop the
// rest. Rejecting the mismatch here would take the whole output file with it.
if (mapping.virtual_first_image >= total_images)
continue;
const hsize_t image_count = std::min(static_cast<hsize_t>(mapping.image_count),
total_images - mapping.virtual_first_image);
const std::string source_dataset = mapping.dataset.empty()
? "/entry/data/data"
: mapping.dataset;
HDF5DataSpace virtual_data_space({total_images, height, width});
virtual_data_space.SelectHyperslab(
{static_cast<hsize_t>(mapping.virtual_first_image), 0, 0},
{image_count, height, width}
);
const hsize_t source_extent_images = mapping.source_first_image + image_count;
HDF5DataSpace source_data_space({source_extent_images, height, width});
source_data_space.SelectHyperslab(
{static_cast<hsize_t>(mapping.source_first_image), 0, 0},
{image_count, height, width}
);
dcpl.SetVirtual(mapping.filename,
source_dataset,
source_data_space,
virtual_data_space);
}
auto data_dataset = std::make_unique<HDF5DataSet>(
*hdf5_file,
"/entry/data/data",
HDF5DataType(start.bit_depth_image / 8, start.pixel_signed),
full_data_space,
dcpl
);
data_dataset->Attr("image_nr_low", static_cast<int32_t>(1))
.Attr("image_nr_high", static_cast<int32_t>(total_images));
}
void NXmx::LinkToReflections_VDS(const StartMessage &start, const EndMessage &end) {
if (end.integrated_reflections.empty())
return;
HDF5Group(*hdf5_file, "/entry/reflections").NXClass("NXcollection");
for (size_t image = 0; image < end.integrated_reflections.size(); ++image) {
if (end.integrated_reflections[image] <= 0)
continue;
if (start.images_per_file <= 0)
continue;
const uint64_t file_id = image / static_cast<uint64_t>(start.images_per_file);
const uint64_t image_in_file = image % static_cast<uint64_t>(start.images_per_file);
const std::string local_name = fmt::format("/entry/reflections/image_{:06d}", image);
const std::string source_name = fmt::format("/entry/reflections/image_{:06d}", image_in_file);
hdf5_file->ExternalLink(HDF5Metadata::DataFileName(start, file_id),
source_name,
local_name);
}
}
namespace {
void SetFillValue(HDF5Dcpl &dcpl, const HDF5DataType &data_type,
const std::optional<int64_t> &fill_value) {
if (!fill_value.has_value())
return;
const int64_t value = fill_value.value();
if (data_type.IsSigned()) {
switch (data_type.GetElemSize()) {
case 1: dcpl.SetFillValue8(static_cast<int8_t>(value)); break;
case 2: dcpl.SetFillValue16(static_cast<int16_t>(value)); break;
case 4: dcpl.SetFillValue32(static_cast<int32_t>(value)); break;
default: break;
}
} else {
switch (data_type.GetElemSize()) {
case 1: dcpl.SetFillValueU8(static_cast<uint8_t>(value)); break;
case 2: dcpl.SetFillValueU16(static_cast<uint16_t>(value)); break;
case 4: dcpl.SetFillValueU32(static_cast<uint32_t>(value)); break;
default: break;
}
}
}
}
std::unique_ptr<HDF5DataSet> NXmx::VDS(const StartMessage &start,
const std::string &name,
const std::vector<hsize_t> &dim,
const HDF5DataType &data_type,
const std::optional<int64_t> &fill_value) {
return VDS(start, name, name, dim, data_type, fill_value);
}
std::unique_ptr<HDF5DataSet> NXmx::VDS(const StartMessage &start,
const std::string &name_src,
const std::string &name_dest,
const std::vector<hsize_t> &dim,
const HDF5DataType &data_type,
const std::optional<int64_t> &fill_value) {
if (dim.empty() || dim.size() > 3)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Dimension must be in range 1-3");
hsize_t images_per_file = start.images_per_file;
hsize_t file_count = 0;
if (start.images_per_file > 0) {
file_count = dim[0] / images_per_file;
if (dim[0] % images_per_file > 0)
file_count++;
}
HDF5DataSpace full_data_space(dim);
HDF5Dcpl dcpl;
if (dim.size() == 3)
dcpl.SetChunking({1, dim[1], dim[2]});
// Where a virtual dataset has no source file to read from, HDF5 hands back the fill value, and
// that defaults to zero - so a data file that was not copied alongside the master reads as
// frames of zero counts, with no error and no warning. Fill with the error marker instead: it is
// outside underload_value..saturation_value, so a reader masks those frames rather than
// integrating them.
SetFillValue(dcpl, data_type, fill_value);
for (hsize_t file_id = 0; file_id < file_count; file_id++) {
hsize_t images_in_file = images_per_file;
if (file_id == file_count - 1)
images_in_file = dim[0] - (file_count - 1) * images_per_file;
HDF5DataSpace virtual_data_space(dim);
auto dim_src = dim;
dim_src[0] = images_in_file;
HDF5DataSpace src_data_space(dim_src);
std::vector<hsize_t> start_dim(dim.size());
start_dim[0] = file_id * images_per_file;
virtual_data_space.SelectHyperslab(start_dim, dim_src);
dcpl.SetVirtual(HDF5Metadata::DataFileName(start, file_id),
name_src,src_data_space, virtual_data_space);
}
return std::make_unique<HDF5DataSet>(*hdf5_file, name_dest, data_type, full_data_space, dcpl);
}
void NXmx::Detector(const StartMessage &start) {
HDF5Group group(*hdf5_file, "/entry/instrument/detector");
group.NXClass("NXdetector");
SaveScalar(group, "depends_on", "/entry/instrument/detector/transformations/translation");
// beam_center_x/y and the transformations chain (translation + rot1/2/3) are the refinable geometry;
// they are written once at Finalize (see Metrology) from the values refined by the offline analysis.
SaveScalar(group, "distance", start.detector_distance)->Units("m");
SaveScalar(group, "detector_distance", start.detector_distance)->Units("m");
SaveScalar(group, "count_time", start.count_time)->Units("s");
SaveScalar(group, "frame_time", start.frame_time)->Units("s");
SaveScalar(group, "sensor_thickness", start.sensor_thickness)->Units("m");
if (start.threshold_energy.size() == 1)
SaveScalar(group, "threshold_energy", start.threshold_energy.begin()->second)->Units("eV");
SaveScalar(group, "x_pixel_size", start.pixel_size_x)->Units("m");
SaveScalar(group, "y_pixel_size", start.pixel_size_y)->Units("m");
SaveScalar(group, "sensor_material", start.sensor_material);
SaveScalar(group, "description", start.detector_description);
if (!start.detector_serial_number.empty()) {
SaveScalar(group, "detector_number", start.detector_serial_number);
SaveScalar(group, "serial_number", start.detector_serial_number);
}
SaveScalar(group, "bit_depth_image", start.bit_depth_image);
if (start.bit_depth_readout)
SaveScalar(group, "bit_depth_readout", start.bit_depth_readout.value());
SaveScalar(group, "saturation_value", start.saturation_value);
if (start.underload_value)
SaveScalar(group, "underload_value", start.underload_value.value());
if (start.error_value)
SaveScalar(group, "error_value", start.error_value.value()); // this is not NXmx
SaveScalar(group, "flatfield_applied", start.flatfield_enabled);
SaveScalar(group, "pixel_mask_applied", start.pixel_mask_enabled);
if (start.jungfrau_conversion_enabled)
SaveScalar(group, "jungfrau_conversion_applied", start.jungfrau_conversion_enabled.value());
if (start.jungfrau_conversion_factor)
SaveScalar(group, "jungfrau_conversion_factor", start.jungfrau_conversion_factor.value())->Units("eV");
SaveScalar(group, "geometry_transformation_applied", start.geometry_transformation_enabled.value_or(true));
SaveScalar(group, "acquisition_type", "triggered");
SaveScalar(group, "countrate_correction_applied", start.countrate_correction_enabled);
SaveScalar(group, "number_of_cycles", start.summation);
HDF5Group det_specific(group, "detectorSpecific");
det_specific.NXClass("NXcollection");
if (!start.jfjoch_release.empty())
SaveScalar(det_specific, "jfjoch_release", start.jfjoch_release);
SaveScalar(det_specific, "jfjoch_writer_release", jfjoch_version());
if (start.summation_mode.has_value())
SaveScalar(det_specific, "summation_mode", start.summation_mode.value());
if (start.detect_ice_rings.has_value())
SaveScalar(det_specific, "detect_ice_rings", start.detect_ice_rings.value());
SaveScalar(det_specific, "x_pixels_in_detector", static_cast<uint32_t>(start.image_size_x));
SaveScalar(det_specific, "y_pixels_in_detector", static_cast<uint32_t>(start.image_size_y));
SaveScalar(det_specific, "software_git_commit", jfjoch_git_sha1());
SaveScalar(det_specific, "software_git_date", jfjoch_git_date());
if (start.storage_cell_number) {
SaveScalar(det_specific, "storage_cell_number", static_cast<uint32_t>(start.storage_cell_number.value()));
if (start.storage_cell_number.value() > 1)
SaveScalar(det_specific, "storage_cell_delay", static_cast<uint32_t>(start.storage_cell_delay_ns))->Units(
"ns");
}
if (start.data_reduction_factor_serialmx)
det_specific.SaveScalar("data_reduction_factor_serialmx", start.data_reduction_factor_serialmx.value());
if (!start.gain_file_names.empty())
det_specific.SaveVector("gain_file_names", start.gain_file_names);
if (start.pixel_mask.size() == 1) {
// Currently only handling single pixel mask
CompressionAlgorithm mask_alg = CompressionAlgorithm::BSHUF_LZ4;
if (start.file_format == FileWriterFormat::NXmxLegacy)
mask_alg = CompressionAlgorithm::NO_COMPRESSION;
std::vector<hsize_t> dims = {start.image_size_y, start.image_size_x};
group.SaveVector("pixel_mask", start.pixel_mask.begin()->second, dims, mask_alg);
hdf5_file->HardLink("/entry/instrument/detector/pixel_mask",
"/entry/instrument/detector/detectorSpecific/pixel_mask");
}
}
void NXmx::Detector(const StartMessage &start, const EndMessage &end) {
if (start.images_per_trigger.has_value() && start.images_per_trigger.value() > 0) {
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/nimages", start.images_per_trigger.value());
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/ntrigger", (end.max_image_number + start.images_per_trigger.value() - 1)/ start.images_per_trigger.value());
} else {
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/nimages", end.max_image_number);
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/ntrigger", 1);
}
if (end.images_collected_count)
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/nimages_collected", end.images_collected_count.value());
if (end.images_sent_to_write_count)
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/nimages_written", end.images_sent_to_write_count.value());
if (end.efficiency)
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/data_collection_efficiency", end.efficiency.value());
if (end.max_receiver_delay)
SaveScalar(*hdf5_file, "/entry/instrument/detector/detectorSpecific/max_receiver_delay", end.max_receiver_delay.value());
}
void NXmx::MX(const StartMessage &start) {
HDF5Group(*hdf5_file, "/entry/MX").NXClass("NXcollection");
switch (start.indexing_algorithm) {
case IndexingAlgorithmEnum::FFBIDX:
hdf5_file->SaveScalar("/entry/MX/indexing_algorithm", "FFBIDX");
break;
case IndexingAlgorithmEnum::FFTW:
hdf5_file->SaveScalar("/entry/MX/indexing_algorithm", "FFT (FFTW)");
break;
case IndexingAlgorithmEnum::FFT:
hdf5_file->SaveScalar("/entry/MX/indexing_algorithm", "FFT (CUDA)");
break;
default:
break;
}
switch (start.geom_refinement_algorithm) {
case GeomRefinementAlgorithmEnum::BeamCenter:
hdf5_file->SaveScalar("/entry/MX/geom_refinement_algorithm", "beam_center");
break;
case GeomRefinementAlgorithmEnum::Flex:
hdf5_file->SaveScalar("/entry/MX/geom_refinement_algorithm", "flex");
break;
default:
break;
}
}
static void WriteROIDefinition(const HDF5Object &group, const ROIConfig &def) {
switch (def.type) {
case ROIConfig::ROIType::Box:
SaveScalar(group, "type", "box");
SaveScalar(group, "min_x_pxl", def.box.xmin);
SaveScalar(group, "max_x_pxl", def.box.xmax);
SaveScalar(group, "min_y_pxl", def.box.ymin);
SaveScalar(group, "max_y_pxl", def.box.ymax);
break;
case ROIConfig::ROIType::Circle:
SaveScalar(group, "type", "circle");
SaveScalar(group, "center_x_pxl", def.circle.x);
SaveScalar(group, "center_y_pxl", def.circle.y);
SaveScalar(group, "radius_pxl", def.circle.r);
break;
case ROIConfig::ROIType::Azim:
SaveScalar(group, "type", "azim");
SaveScalar(group, "q_min_recipA", def.azim.qmin);
SaveScalar(group, "q_max_recipA", def.azim.qmax);
// phi_min == phi_max means a full ring; only record a sector.
if (def.azim.phi_min != def.azim.phi_max) {
SaveScalar(group, "phi_min_deg", def.azim.phi_min);
SaveScalar(group, "phi_max_deg", def.azim.phi_max);
}
break;
}
}
void NXmx::ROI(const StartMessage &start) {
if (start.rois.empty())
return;
// ROI definitions go in /entry/roi_defs, kept separate from the per-image ROI
// results (/entry/roi, written by the data-file plugin) so that older readers
// iterating /entry/roi are not disturbed by the bitmap and definition subgroups.
HDF5Group roi_group(*hdf5_file, "/entry/roi_defs");
roi_group.NXClass("NXcollection");
if (!start.roi_map.empty()) {
// Per-pixel ROI bitmask: bit i (the bit_index below) marks pixels in ROI i.
CompressionAlgorithm roi_alg = (start.file_format == FileWriterFormat::NXmxLegacy)
? CompressionAlgorithm::NO_COMPRESSION
: CompressionAlgorithm::BSHUF_LZ4;
std::vector<hsize_t> dims = {start.image_size_y, start.image_size_x};
roi_group.SaveVector("roi_map", start.roi_map, dims, roi_alg);
}
for (size_t i = 0; i < start.rois.size(); i++) {
HDF5Group g(roi_group, start.rois[i].name);
SaveScalar(g, "bit_index", static_cast<uint16_t>(i));
WriteROIDefinition(g, start.rois[i]);
}
}
void NXmx::DetectorModule(const std::string &name, const std::vector<int32_t> &origin, const std::vector<int32_t> &size,
const std::vector<double> &fast_axis, const std::vector<double> &slow_axis,
const std::string &nx_axis, double pixel_size_mm) {
HDF5Group module_group(*hdf5_file, "/entry/instrument/detector/" + name);
module_group.NXClass("NXdetector_module");
module_group.SaveVector("data_origin", origin);
module_group.SaveVector("data_size", size);
SaveScalar(module_group, "fast_pixel_direction", pixel_size_mm)->
Transformation("m", "/entry/instrument/detector/transformations/" + nx_axis,
"", "", "translation", fast_axis,
{0,0,0}, "");
SaveScalar(module_group, "slow_pixel_direction", pixel_size_mm)->
Transformation("m", "/entry/instrument/detector/transformations/" + nx_axis,
"", "", "translation", slow_axis,
{0,0,0}, "");
SaveScalar(module_group, "module_offset", 0)->
Transformation("m", "/entry/instrument/detector/transformations/" + nx_axis,
"", "", "translation", {0,0,0});
}
void NXmx::Facility(const StartMessage &start) {
HDF5Group(*hdf5_file, "/entry/source").NXClass("NXsource");
SaveScalar(*hdf5_file, "/entry/source/name", start.source_name);
if (!start.source_type.empty())
SaveScalar(*hdf5_file, "/entry/source/type", start.source_type);
if (start.ring_current_mA) {
SaveScalar(*hdf5_file, "/entry/source/current", start.ring_current_mA.value() / 1000.0)->Units("A");
}
HDF5Group(*hdf5_file, "/entry/instrument").NXClass("NXinstrument");
SaveScalar(*hdf5_file, "/entry/instrument/name", start.instrument_name);
}
void NXmx::Beam(const StartMessage &start) {
HDF5Group group(*hdf5_file, "/entry/instrument/beam");
group.NXClass("NXbeam");
SaveScalar(group, "incident_wavelength", start.incident_wavelength)->Units("angstrom");
if (start.incident_wavelength_spread)
SaveScalar(group, "incident_wavelength_spread", start.incident_wavelength_spread.value())->Units("angstrom");
if (start.total_flux)
SaveScalar(group, "total_flux", start.total_flux.value())->Units("Hz");
}
void NXmx::Fluorescence(const StartMessage &start) {
if (start.fluorescence_spectrum.empty())
return;
HDF5Group group(*hdf5_file, "/entry/instrument/fluorescence");
group.NXClass("NXcollection");
group.SaveVector("energy", start.fluorescence_spectrum.GetEnergy_eV())->Units("eV");
group.SaveVector("data", start.fluorescence_spectrum.GetData());
}
void NXmx::Metrology(const StartMessage &start, const EndMessage &end) {
// The beam centre and detector rotations may have been refined by the offline analysis (rugnux).
// The master file is streamed but never read before Finalize, so the whole geometry is written
// once here, at the end, from the refined values when present and the StartMessage values
// otherwise - simpler than an open-time write followed by an in-place overwrite. The broker
// leaves the refined fields empty, so the user-provided StartMessage geometry is used unchanged.
const float beam_center_x = end.refined_beam_center_x.value_or(start.beam_center_x);
const float beam_center_y = end.refined_beam_center_y.value_or(start.beam_center_y);
const double rot1 = end.refined_poni_rot1.value_or(start.poni_rot1.value_or(0.0f));
const double rot2 = end.refined_poni_rot2.value_or(start.poni_rot2.value_or(0.0f));
const double rot3 = end.refined_poni_rot3.value_or(start.poni_rot3.value_or(0.0f));
HDF5Group detector(*hdf5_file, "/entry/instrument/detector");
SaveScalar(detector, "beam_center_x", beam_center_x)->Units("pixel");
SaveScalar(detector, "beam_center_y", beam_center_y)->Units("pixel");
HDF5Group transformations(*hdf5_file, "/entry/instrument/detector/transformations");
transformations.NXClass("NXtransformations");
std::vector<double> vector{beam_center_x * start.pixel_size_x,
beam_center_y * start.pixel_size_y,
start.detector_distance};
double vector_length = sqrt(vector[0] * vector[0] + vector[1] * vector[1] + vector[2] * vector[2]);
std::vector<double> vector_norm{vector[0] / vector_length, vector[1]/vector_length, vector[2]/vector_length};
// The translation hangs off rot1, not off ".", so the tilt pivots about the SAMPLE: the rotations
// then act on the whole sample->pixel vector including the distance, which is what
// DiffractionGeometry does (poni_rot * {dx, dy, distance}). With the translation at the root the
// panel origin stays put and only its orientation turns, displacing the origin by tens of mm at a
// degree of tilt.
SaveScalar(transformations, "translation", vector_length)->
Transformation("m", "/entry/instrument/detector/transformations/rot1",
"detector", "detector_arm", "translation", vector_norm);
// https://manual.nexusformat.org/classes/base_classes/NXdetector_module.html?highlight=nxdetector_module
// The order of indices (i, j or i, j, k) is slow to fast.
// though EIGER has is the other way round
// Confusing....
std::vector<int32_t> origin = {0, 0};
std::vector<int32_t> size = {static_cast<int32_t>(start.image_size_y),
static_cast<int32_t>(start.image_size_x)};
// Jungfraujoch holds the tilt in the PyFAI PONI convention, poni_rot = Rz(-rot3)*Rx(-rot2)*Ry(+rot1)
// (DiffractionGeometry::UpdatePoniRotMatrix), written in the internal frame: x along increasing
// column, y along increasing row, z along the beam. NXmx uses McStas, which is that frame turned
// 180 degrees about x - a proper rotation, not a mirror - so rotations about y and z reverse sense
// while those about x keep it. Hence the axis vectors below. A depends_on chain applies the
// DEEPEST dependency first, so rot3 sits at the root to make the product R_rot3*R_rot2*R_rot1.
SaveScalar(transformations, "rot1", rot1)->
Transformation("rad",
"/entry/instrument/detector/transformations/rot2",
"detector", "detector_arm",
"rotation",
std::vector<double>{0.0, -1.0, 0.0});
SaveScalar(transformations, "rot2", rot2)->
Transformation("rad",
"/entry/instrument/detector/transformations/rot3",
"detector", "detector_arm",
"rotation",
std::vector<double>{1.0, 0.0, 0.0});
SaveScalar(transformations, "rot3", rot3)->
Transformation("rad",
".",
"detector", "detector_arm",
"rotation",
std::vector<double>{0.0, 0.0, -1.0});
DetectorModule("module", origin, size, {-1,0,0}, {0,-1,0}, "translation",
start.pixel_size_x);
}
void SaveUnitCell( HDF5Group& group, const std::string& name, const UnitCell& unit_cell) {
std::vector<float> v = {unit_cell.a, unit_cell.b, unit_cell.c,
unit_cell.alpha, unit_cell.beta, unit_cell.gamma};
group.SaveVector(name, v);
}
void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
HDF5Group group(*hdf5_file, "/entry/sample");
group.NXClass("NXsample");
if (!start.sample_name.empty())
group.SaveScalar("name", start.sample_name);
// The offline analysis determines the space group only after merging, so it arrives on the end
// message; prefer it over the (usually empty) start-message value.
const auto space_group_number = end.space_group_number ? end.space_group_number
: start.space_group_number;
if (space_group_number) {
group.SaveScalar("space_group_number", space_group_number.value());
auto *sg = gemmi::find_spacegroup_by_number(space_group_number.value());
if (sg != nullptr)
group.SaveScalar("space_group", sg->short_name());
}
std::optional<UnitCell> unit_cell;
std::optional<UnitCell> input_unit_cell;
if (end.unit_cell)
unit_cell = end.unit_cell;
else if (end.rotation_lattice)
unit_cell = end.rotation_lattice->GetUnitCell();
else if (start.unit_cell) {
unit_cell = start.unit_cell;
input_unit_cell = start.unit_cell;
}
if (unit_cell)
SaveUnitCell(group, "unit_cell", unit_cell.value());
if (input_unit_cell)
SaveUnitCell(group, "input_unit_cell", input_unit_cell.value());
if (end.rotation_lattice) {
group.SaveVector("ub_matrix",
end.rotation_lattice->GetUBMatrix(),
{1, 3, 3})
->Units("Angstrom^-1");
}
if (start.sample_temperature_K)
group.SaveScalar("temperature", start.sample_temperature_K.value())->Units("K");
std::string depends_on = ".";
// Smargon chi/phi are static positioners closest to the sample, so they are appended
// at the innermost end of the transformation chain (whatever depends_on currently is).
auto write_smargon = [&start](HDF5Group& transformations, std::string& depends_on) {
if (!start.smargon_position)
return;
SaveScalar(transformations, "chi", start.smargon_position->chi_deg)->
Transformation("deg", depends_on, "", "", "rotation",
{start.smargon_position->chi_axis.x, start.smargon_position->chi_axis.y,
start.smargon_position->chi_axis.z}, {0, 0, 0}, "");
depends_on = "/entry/sample/transformations/chi";
SaveScalar(transformations, "phi", start.smargon_position->phi_deg)->
Transformation("deg", depends_on, "", "", "rotation",
{start.smargon_position->phi_axis.x, start.smargon_position->phi_axis.y,
start.smargon_position->phi_axis.z}, {0, 0, 0}, "");
depends_on = "/entry/sample/transformations/phi";
};
if ((end.max_image_number > 0) && start.goniometer) {
HDF5Group transformations(group, "transformations");
transformations.NXClass("NXtransformations");
hdf5_file->HardLink("/entry/sample/transformations","/entry/sample/goniometer");
// Prefer the rotation axis refined by the offline analysis (rugnux); the broker leaves it empty
// and the user-provided goniometer axis stands.
const std::vector<double> axis_vector = end.refined_rotation_axis
? std::vector<double>{end.refined_rotation_axis->x, end.refined_rotation_axis->y,
end.refined_rotation_axis->z}
: start.goniometer->GetAxisVector();
SaveVector(transformations, start.goniometer->GetName(),
start.goniometer->GetAngleContainer(end.max_image_number))->
Transformation("deg", depends_on, "", "",
"rotation", axis_vector, {0,0,0}, "");
SaveVector(transformations, start.goniometer->GetName() + "_end",
start.goniometer->GetAngleContainerEnd(end.max_image_number))
->Units("deg");
SaveScalar(transformations, start.goniometer->GetName() + "_range_average",
start.goniometer->GetIncrement_deg())
->Units("deg");
SaveScalar(transformations, start.goniometer->GetName() + "_range_total",
start.goniometer->GetIncrement_deg() * end.max_image_number)
->Units("deg");
depends_on = "/entry/sample/transformations/" + start.goniometer->GetName();
write_smargon(transformations, depends_on);
auto helical = start.goniometer->GetHelicalStep();
if (helical.has_value()) {
SaveVector(transformations,
start.goniometer->GetName() + "_helical_x",
start.goniometer->GetXContainer_m(end.max_image_number))->
Transformation("m", depends_on, "", "",
"translation", {1, 0, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_x";
SaveVector(transformations,
start.goniometer->GetName() + "_helical_y",
start.goniometer->GetYContainer_m(end.max_image_number))->
Transformation("m", depends_on, "", "",
"translation", {0, 1, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_y";
SaveVector(transformations,
start.goniometer->GetName() + "_helical_z",
start.goniometer->GetZContainer_m(end.max_image_number))->
Transformation("m", depends_on, "", "",
"translation", {0, 0, 1}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_z";
}
} else if (start.grid_scan.has_value()) {
HDF5Group grid_scan_group(group, "grid_scan");
grid_scan_group.NXClass("NXcollection");
SaveScalar(grid_scan_group, "snake_scan", start.grid_scan->IsSnakeScan());
SaveScalar(grid_scan_group, "vertical_scan", start.grid_scan->IsVerticalScan());
SaveScalar(grid_scan_group, "n_fast", start.grid_scan->GetNFast());
SaveScalar(grid_scan_group, "step_x", start.grid_scan->GetGridStepX_um() * 1e-6)->Units("m");
SaveScalar(grid_scan_group, "step_y", start.grid_scan->GetGridStepY_um() * 1e-6)->Units("m");
HDF5Group transformations(group, "transformations");
transformations.NXClass("NXtransformations");
hdf5_file->HardLink("/entry/sample/transformations","/entry/sample/goniometer");
// The position containers hold one entry per image; they are empty when the scan
// stopped at the first image (max_image_number == 0), so only write them otherwise.
if (end.max_image_number > 0) {
SaveVector(transformations,"grid_scan_x", start.grid_scan->GetXContainer_m(end.max_image_number))
->Transformation("m", depends_on, "", "",
"translation", {1, 0, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/grid_scan_x";
SaveVector(transformations,"grid_scan_y", start.grid_scan->GetYContainer_m(end.max_image_number))
->Transformation("m", depends_on, "", "",
"translation", {0, 1, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/grid_scan_y";
}
write_smargon(transformations, depends_on);
}
group.SaveScalar("depends_on", depends_on);
}
void NXmx::Attenuator(const StartMessage &start) {
if (start.attenuator_transmission) {
HDF5Group group(*hdf5_file, "/entry/instrument/attenuator");
group.NXClass("NXattenuator");
SaveScalar(group, "attenuator_transmission", start.attenuator_transmission.value());
}
}
void NXmx::WriteCalibration(const CompressedImage &image) {
if (!hdf5_file)
throw JFJochException(JFJochExceptionCategory::FileWriteError, "HDF5 file already closed");
if (!calibration_group_created) {
calibration_group_created = true;
HDF5Group(*hdf5_file, "/entry/instrument/detector/calibration").NXClass("NXcollection");
}
SaveCBORImage("/entry/instrument/detector/calibration/" + image.GetChannel(), image);
}
void NXmx::SaveCBORImage(const std::string &hdf5_path, const CompressedImage &image) {
std::vector<hsize_t> dims = {image.GetHeight(), image.GetWidth()};
HDF5DataType data_type(image.GetMode());
HDF5Dcpl dcpl;
if (image.GetCompressionAlgorithm() != CompressionAlgorithm::NO_COMPRESSION) {
dcpl.SetCompression(image.GetCompressionAlgorithm(), 0);
dcpl.SetChunking(dims);
}
HDF5DataSpace data_space(dims);
auto dataset = std::make_unique<HDF5DataSet>(*hdf5_file, hdf5_path, data_type, data_space, dcpl);
if (image.GetCompressionAlgorithm() == CompressionAlgorithm::NO_COMPRESSION)
dataset->Write(data_type, image.GetCompressed());
else
dataset->WriteDirectChunk(image.GetCompressed(), image.GetCompressedSize(), {0, 0});
dataset->Close();
}
void NXmx::AzimuthalIntegration(const StartMessage &start, const EndMessage &end) {
if (!start.az_int_bin_to_q.empty()) {
size_t phi_bins = start.az_int_phi_bin_count.value_or(1);
size_t q_bin = start.az_int_q_bin_count.value_or(1);
std::vector<hsize_t> dim = {phi_bins, q_bin};
HDF5Group az_int_group(*hdf5_file, "/entry/azint");
az_int_group.NXClass("NXcollection");
if (start.file_format != FileWriterFormat::NXmxIntegrated) {
az_int_group.SaveVector("bin_to_q", start.az_int_bin_to_q, dim)->Units("reciprocal Angstrom");
if (!start.az_int_bin_to_two_theta.empty())
az_int_group.SaveVector("bin_to_two_theta", start.az_int_bin_to_two_theta, dim)->Units("degrees");
if (!start.az_int_bin_to_phi.empty())
az_int_group.SaveVector("bin_to_phi", start.az_int_bin_to_phi, dim)->Units("degrees");
}
for (const auto &[x,y]: end.az_int_result) {
if (x != "image")
az_int_group.SaveVector(x, y, dim);
}
if (!start.az_int_map.empty() && start.az_int_map.size() == start.image_size_y * start.image_size_x)
az_int_group.SaveVector("map", start.az_int_map, {start.image_size_y, start.image_size_x},
CompressionAlgorithm::BSHUF_LZ4);
}
}
void NXmx::ADUHistogram(const EndMessage &end) {
if (!end.adu_histogram.empty()) {
HDF5Group adu_histo_group(*hdf5_file, "/entry/instrument/detector/detectorSpecific/adu_histogram");
adu_histo_group.SaveScalar("bin_width", end.adu_histogram_bin_width);
for (const auto &[x, y]: end.adu_histogram)
adu_histo_group.SaveVector(x, y);
}
}
template<class T>
void SaveVectorIfMissing(HDF5Object &object,
const std::string &path,
const std::vector<T> &values,
const std::string &units = "") {
if (values.empty() || object.Exists(path))
return;
auto dataset = object.SaveVector(path, values);
if (!units.empty())
dataset->Units(units);
}
void NXmx::Finalize(const EndMessage &end) {
try {
if (!hdf5_file)
throw JFJochException(JFJochExceptionCategory::FileWriteError, "HDF5 file already closed");
if (end.end_date) {
hdf5_file->Attr("file_time", end.end_date.value());
hdf5_file->SaveScalar("/entry/end_time", end.end_date.value());
hdf5_file->SaveScalar("/entry/end_time_estimated", end.end_date.value());
} else {
std::string time_now = time_UTC(std::chrono::system_clock::now());
hdf5_file->Attr("file_time", time_now);
hdf5_file->SaveScalar("/entry/end_time", time_now);
hdf5_file->SaveScalar("/entry/end_time_estimated", time_now);
}
Detector(start_message, end);
Sample(start_message, end);
// Write the refinable detector geometry (beam centre + transformations) now, from the values
// refined by the offline analysis when present and the StartMessage otherwise. The master file
// is never read before this point, so writing once here is simpler than an open-time write plus
// an in-place overwrite - and, unlike the old overwrite, it also updates the translation vector
// (which encodes the beam centre in the NXmx geometry chain).
Metrology(start_message, end);
AzimuthalIntegration(start_message, end);
ADUHistogram(end);
EndResultVectors(end);
switch (start_message.file_format.value_or(FileWriterFormat::NXmxLegacy)) {
case FileWriterFormat::NXmxLegacy:
LinkToData(start_message, end);
break;
case FileWriterFormat::NXmxVDS:
LinkToData_VDS(start_message, end);
break;
case FileWriterFormat::NXmxIntegrated:
if (!start_message.hdf5_source_data.empty())
LinkToData_ProcessingVDS(start_message, end);
break;
default:
break;
}
if (end.rotation_lattice)
SaveVector(*hdf5_file, "/entry/MX/rotationLatticeIndexed", end.rotation_lattice->GetVector())
->Units("Angstrom");
if (!end.rotation_extra_lattices.empty()) {
std::vector<float> latt_info(9 * end.rotation_extra_lattices.size());
for (int i = 0; i < end.rotation_extra_lattices.size(); i++) {
auto vec = end.rotation_extra_lattices[i].GetVector();
for (int j = 0; j < 9; j++)
latt_info[i * 9 + j] = vec[j];
}
SaveVector(*hdf5_file,
"/entry/MX/rotationLatticeIndexedExtra",
latt_info, {end.rotation_extra_lattices.size(), 9})
->Units("Angstrom");
}
if (end.rotation_lattice_type)
SaveScalar(*hdf5_file, "/entry/MX/rotationLatticeNiggliClass", end.rotation_lattice_type->niggli_class);
if (end.indexing_rate) {
SaveScalar(*hdf5_file, "/entry/MX/imageIndexedMean", end.indexing_rate.value());
}
if (end.bkg_estimate) {
SaveScalar(*hdf5_file, "/entry/MX/bkgEstimateMean", end.bkg_estimate.value());
}
if (end.ice_ring_score_mean) {
SaveScalar(*hdf5_file, "/entry/MX/iceRingScoreMean", end.ice_ring_score_mean.value());
}
hdf5_file->Close();
hdf5_file.reset();
} catch (const JFJochException &e) {
hdf5_file.reset();
std::error_code ec;
std::filesystem::remove(tmp_filename, ec);
throw;
}
if (std::filesystem::exists(filename) && !overwrite)
throw JFJochException(JFJochExceptionCategory::FileWriteError, "File already exists");
std::error_code ec;
std::filesystem::rename(tmp_filename, filename, ec);
if (ec)
throw JFJochException(JFJochExceptionCategory::FileWriteError,
"Cannot rename temporary HDF5 master file " + tmp_filename +
" to " + filename + ": " + ec.message());
}
void NXmx::UserData(const StartMessage &start) {
if (!start.user_data.empty()
&& start.user_data.contains("hdf5")
&& start.user_data["hdf5"].is_object()) {
HDF5Group group(*hdf5_file, "/entry/user");
group.NXClass("NXcollection");
for (const auto &[x,y]: start.user_data["hdf5"].items()) {
if (y.is_number())
group.SaveScalar(x, y.get<double>());
else if (y.is_string())
group.SaveScalar(x, y.get<std::string>());
}
}
}
std::shared_ptr<HDF5File> NXmx::GetFile() {
return hdf5_file;
}
void NXmx::EndResultVectors(const EndMessage &end) {
if (!end.data_collection_efficiency.empty()) {
HDF5Group det_specific(*hdf5_file, "/entry/instrument/detector/detectorSpecific");
det_specific.NXClass("NXcollection");
SaveVectorIfMissing(*hdf5_file,
"/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image",
end.data_collection_efficiency);
}
if (!end.max_viable_pixel_value.empty() ||
!end.min_viable_pixel_value.empty() ||
!end.error_pixel_count.empty() ||
!end.saturated_pixel_count.empty() ||
!end.pixel_sum.empty()) {
HDF5Group image_group(*hdf5_file, "/entry/image");
image_group.NXClass("NXcollection");
SaveVectorIfMissing(*hdf5_file, "/entry/image/max_value", end.max_viable_pixel_value);
SaveVectorIfMissing(*hdf5_file, "/entry/image/min_value", end.min_viable_pixel_value);
SaveVectorIfMissing(*hdf5_file, "/entry/image/error_pixels", end.error_pixel_count);
SaveVectorIfMissing(*hdf5_file, "/entry/image/saturated_pixels", end.saturated_pixel_count);
SaveVectorIfMissing(*hdf5_file, "/entry/image/pixel_sum", end.pixel_sum);
}
HDF5Group mx_group(*hdf5_file, "/entry/MX");
mx_group.NXClass("NXcollection");
SaveVectorIfMissing(*hdf5_file, "/entry/MX/peakCountIceRingRes", end.spot_count_ice_ring);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/peakCountIceRingControl", end.spot_count_ice_control);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/peakCountLowRes", end.spot_count_low_res);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/peakCountIndexed", end.spot_count_indexed);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/imageIndexed", end.image_indexed);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/indexedLatticeCount", end.indexed_lattice_count);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/bkgEstimate", end.v_bkg_estimate);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/iceRingScore", end.ice_ring_score);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/profileRadius", end.profile_radius, "Angstrom^-1");
SaveVectorIfMissing(*hdf5_file, "/entry/MX/mosaicity", end.mosaicity, "deg");
SaveVectorIfMissing(*hdf5_file, "/entry/MX/bFactor", end.bFactor, "Angstrom^2");
SaveVectorIfMissing(*hdf5_file, "/entry/MX/resolutionEstimate", end.resolution_estimate, "Angstrom");
SaveVectorIfMissing(*hdf5_file, "/entry/MX/imageScaleFactor", end.image_scale_factor);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/integratedReflections", end.integrated_reflections);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/imageScaleFactor", end.image_scale_factor);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/imageScaleCC", end.image_scale_cc);
SaveVectorIfMissing(*hdf5_file, "/entry/MX/imageScaleMosaicity", end.image_scale_mosaicity, "deg");
if (!end.niggli_class.empty())
SaveVectorIfMissing(*hdf5_file, "/entry/MX/niggliClass", end.niggli_class);
// Per-image sweep-quality code, with the vocabulary next to it so the codes can be read without
// this source: sweepQuality[i] == 0 means the image is in no flagged range, otherwise it indexes
// sweepQualityReasons from 1. Absent when the diagnostic did not run.
if (!end.sweep_quality.empty() && !end.sweep_quality_reasons.empty()) {
SaveVectorIfMissing(*hdf5_file, "/entry/MX/sweepQuality", end.sweep_quality);
if (!hdf5_file->Exists("/entry/MX/sweepQualityReasons"))
hdf5_file->SaveVector("/entry/MX/sweepQualityReasons", end.sweep_quality_reasons);
}
}
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