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Jungfraujoch/writer/HDF5NXmx.cpp
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leonarski_fandClaude Opus 5 77c6d0f4ec Report the stored image depth in bit_depth_readout, and write underload_value 
NXmx has no field for the depth of the stored image - only bit_depth_readout,
"how many bits the electronics record per pixel". The two diverge exactly when
summation is used: the readout keeps the detector's native width while the
summed image must be wider to hold the sum.

Every NXmx reader nonetheless takes bit_depth_readout as the width of the stored
pixel. dxtbx ignores the non-standard bit_depth_image entirely for a generic
NXmx file, derives its masking markers from bit_depth_readout, and raises
"Unsupported integer dtype uint32" for a 32-bit image when the field is absent.
Reporting the electronic value there would mislead precisely where it differs.

So report the image depth in both fields, and drop the machinery that existed to
carry the electronic one for a DECTRIS detector: the SIMPLON read, the
DetectorSetup setter, and the receiver-side propagation of a key that the DECTRIS
stream2 protocol does not even define. JUNGFRAU and PSI EIGER keep their readout
depth, which the FPGA acquisition genuinely needs.

Also write NXmx underload_value, the lowest valid value. Without it a reader
takes the trusted minimum to be -0x7FFFFFFF, so the error-pixel marker sits
inside the trusted range and is consumed as an intensity. Measured with DIALS
3.27 on a written file: trusted_range goes from (-2147483647, 32766) to
(-32767, 32766), so the INT16_MIN gap pixels are now masked.

Third fix in the same area: JFJochReceiverLite::Configure took the image width
from the incoming stream but not the sign, while the image itself is forwarded
byte-for-byte. A detector sending int32 was re-declared uint32, and the VDS
master was typed unsigned over signed data files. Take pixel_signed from the
stream too - it and the width are both carried by the one image_dtype key.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-22 18:15:44 +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));
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);
}
}
std::unique_ptr<HDF5DataSet> NXmx::VDS(const StartMessage &start,
const std::string &name,
const std::vector<hsize_t> &dim,
const HDF5DataType &data_type) {
return VDS(start, name, name, dim, data_type);
}
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) {
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]});
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/rot3");
// 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};
SaveScalar(transformations, "translation", vector_length)->
Transformation("m", ".", "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)};
SaveScalar(transformations, "rot1", rot1)->
Transformation("rad",
"/entry/instrument/detector/transformations/translation",
"detector", "detector_arm",
"rotation",
std::vector<double>{1.0, 0.0, 0.0});
SaveScalar(transformations, "rot2", rot2)->
Transformation("rad",
"/entry/instrument/detector/transformations/rot1",
"detector", "detector_arm",
"rotation",
std::vector<double>{0.0, -1.0, 0.0});
SaveScalar(transformations, "rot3", rot3)->
Transformation("rad",
"/entry/instrument/detector/transformations/rot2",
"detector", "detector_arm",
"rotation",
std::vector<double>{0.0, 0.0, -1.0});
DetectorModule("module", origin, size, {-1,0,0}, {0,-1,0}, "rot3",
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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