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fed077e683feffc70a6f91b5cee03a0119f1eadb
Jungfraujoch/reader/HDF5MetadataSource.cpp
T
leonarski_fandClaude Opus 5 fed077e683 geometry: hold the detector plane as axis vectors, and give the discrete part its own home 
The detector plane was three PONI angles and nothing else, so the two things it
cannot express - an image mirrored in Y, and one mounted at a multiple of 90
degrees - had no home at all. They are now the DetectorOrientation carried by the
detector setup, composed with the PONI rotation into one orthogonal matrix whose
columns ARE the fast axis, the slow axis and the sample->PONI normal:

    lab = R(rot1, rot2, rot3) * Delta * ( (x-bx)*p , (y-by)*p , distance )

GetFastAxis/GetSlowAxis/GetNormalAxis read those columns and DetectorAxes() sets
the plane from them, decomposing back to the angles; PoniRotMatrix and
PoniAnglesFromMatrix are the conversion in both directions, exact on the canonical
branch (rot2 in [-pi/2, pi/2]) and with a stated convention at gimbal lock. The
angles stay stored rather than re-derived, so a geometry given as angles is
written back as the same angles, to the bit.

Delta is never inferred. In particular an arbitrary rot3 is NOT decomposed into a
quarter turn plus a residual: rot3 is a fitted quantity, and a least-squares step
must not be able to turn the stored image. It is set only where something states
it - the detector setup, --detector-mirror-y / --detector-quarter-turns, or the
value a file this system wrote records - and defaults to the identity, which makes
the whole change a no-op for every existing detector and every existing file.

It is a different setting from DetectorSetup::mirror_y, which flips the MODULE
LAYOUT while an image is assembled and so decides what the stored pixels are.
Merging the two would apply the mirror twice for every modular detector, or change
the pixel content of every file written; both are ruled out. The new one earns its
keep exactly where the old one is a no-op: a detector whose image arrives already
assembled has no layout to flip.

Both generators are signed permutations of the in-plane offset, so they preserve
the distance from the PONI. That is why almost nothing downstream changes:
everything needing an azimuth already goes through LabCoord, and everything that
does not needs only a radius. The two hand-written copies of the rotation -
XtalResidual and RingOptimizer - take the discrete part as four constants next to
cos_rot3/sin_rot3, since it acts in the detector frame where rot3 acts in the
laboratory and cannot be folded into it. RingOptimizer needs it despite being a
radial fit: it fits the tilt, and the discrete part changes which way the tilt
tips a ring.

Carried as two optional CBOR keys and two detectorSpecific datasets, both
back-compatible; the NXmx module axis vectors and the translation direction stop
being hardcoded and are computed from it, reproducing today's values exactly at
the identity. GetPoniRotMatrix is renamed GetDetectorMatrix, because it is no
longer only the PONI rotation.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Lc5JG6kJqZoCWaoZ43JGTW
2026-08-29 23:00:35 +02:00

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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <cmath>
#include <cstring>
#include <set>
#include "HDF5MetadataSource.h"
#include "spdlog/fmt/fmt.h"
#include "../image_analysis/bragg_integration/CalcISigma.h"
#include "../image_analysis/spot_finding/SpotUtils.h"
#include "../common/GridScanSettings.h"
#include "../common/JFJochMath.h"
#include "../common/Logger.h"
#include "../common/ROIDefinition.h"
inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::string &val) {
if (val.empty())
return {gemmi::CrystalSystem::Triclinic, 'P'};
if (val.size() != 2)
throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong Bravais lattice encoding");
gemmi::CrystalSystem cs;
char centering = val[1];
std::set<char> allowed_centering;
switch (val[0]) {
case 'a':
cs = gemmi::CrystalSystem::Triclinic;
allowed_centering = {'P'};
break;
case 'm':
cs = gemmi::CrystalSystem::Monoclinic;
allowed_centering = {'P', 'A', 'B', 'C'};
break;
case 'o':
cs = gemmi::CrystalSystem::Orthorhombic;
allowed_centering = {'P', 'A', 'B', 'C', 'I', 'F'};
break;
case 't':
cs = gemmi::CrystalSystem::Tetragonal;
allowed_centering = {'P', 'I'};
break;
case 'h':
if (centering == 'P')
cs = gemmi::CrystalSystem::Hexagonal;
else if (centering == 'R')
cs = gemmi::CrystalSystem::Trigonal;
allowed_centering = {'P', 'R'};
break;
case 'c':
cs = gemmi::CrystalSystem::Cubic;
allowed_centering = {'P', 'F', 'I'};
break;
default:
// allowed_centering is empty and exception will be always thrown
break;
}
if (!allowed_centering.contains(centering))
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Invalid lattice encoding " + val);
return {cs, centering};
}
std::vector<hsize_t> GetDimension(HDF5Object &object, const std::string &path) {
const auto dim = object.GetDimension(path);
if (dim.size() != 3)
throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/data/data");
return dim;
}
std::vector<HDF5VirtualDatasetMapping> ReadVDSImageMappings(HDF5Object &file,
const std::string &dataset_name) {
HDF5DataSet dataset(file, dataset_name);
HDF5Dcpl dcpl(dataset);
auto mappings = dcpl.GetVirtualMappings();
if (mappings.empty())
throw JFJochException(JFJochExceptionCategory::HDF5,
dataset_name + " is not a virtual dataset");
for (const auto &mapping: mappings) {
if (mapping.dataset.empty())
throw JFJochException(JFJochExceptionCategory::HDF5,
"VDS mapping has empty source dataset name");
if (mapping.virtual_start.size() != 3)
throw JFJochException(JFJochExceptionCategory::HDF5,
"Only 3D image VDS mappings are supported");
}
return mappings;
}
std::string ResolveRelativeToMaster(const std::string &directory,
const std::string &filename) {
std::filesystem::path path(filename);
if (path.is_absolute() || directory.empty())
return filename;
return (std::filesystem::path(directory) / path).string();
}
// DECTRIS Eiger firmware 1.x writes the same values under different names, and a file from that era
// is still what a repository hands you. The modern spelling is tried first; the legacy one is a pure
// fallback, and it is safe because every current Eiger master carries BOTH (measured on thirteen
// masters from ten facilities, firmware release-2020.2.1 through release-2024.1.1 - all of them
// write detector_distance and countrate_correction_count_cutoff beside the NXmx names). So this can
// never change what a modern file reads.
float ReadWithLegacyFallback(HDF5Object &file, const std::string &nxmx, const std::string &legacy) {
if (file.Exists(nxmx))
return file.GetFloat(nxmx);
if (file.Exists(legacy))
return file.GetFloat(legacy);
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot find " + nxmx + " (nor " + legacy + ")");
}
int64_t ReadIntWithLegacyFallback(HDF5Object &file, const std::string &nxmx, const std::string &legacy) {
if (file.Exists(nxmx))
return file.GetInt(nxmx);
if (file.Exists(legacy))
return file.GetInt(legacy);
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot find " + nxmx + " (nor " + legacy + ")");
}
// Where the goniometer axes live. NXmx puts them in /entry/sample/transformations; firmware 1.x put
// them in /entry/sample/goniometer and wrote no transformation_type and no vector on them. Getting
// this one wrong is not a missing value but a WRONG ANSWER: a goniometer is only ever set from this
// group, so a file whose axes are somewhere else is read as stills, silently.
//
// A hybrid file has both: an NXmx transformations group holding one empty subgroup per axis, which
// states the direction and nothing else, beside a legacy goniometer group holding all the angles.
// So present is not the same as usable - transformations is the angle source only if it holds an
// axis dataset, and an axis is always a dataset.
std::string GoniometerGroup(HDF5Object &file) {
if (file.Exists("/entry/sample/transformations")) {
for (const auto &name: file.FindLeafs("/entry/sample/transformations"))
if (file.IsDataSet("/entry/sample/transformations/" + name))
return "/entry/sample/transformations";
}
if (file.Exists("/entry/sample/goniometer"))
return "/entry/sample/goniometer";
return {};
}
template<class T>
void ReadVector(std::vector<T> &v,
HDF5Object &file,
const std::string &dataset_name,
size_t image0,
size_t nimages) {
try {
auto tmp = file.ReadOptVector<T>(dataset_name);
if (tmp.size() <= nimages) {
v.resize(image0 + nimages);
for (int i = 0; i < tmp.size(); i++)
v[image0 + i] = tmp[i];
}
} catch (JFJochException &e) {
}
}
std::string removeSuffix(const std::string &s, const std::string &suffix) {
if (s.ends_with(suffix))
return s.substr(0, s.size() - suffix.size());
return s;
}
std::string dataset_name(const std::string &path) {
std::string file = std::filesystem::path(path).filename().string();
file = removeSuffix(file, "_master.h5");
// If previous suffix was not found, try removing this one
file = removeSuffix(file, ".h5");
return file;
}
// Per-image reflections and lattices are written in the setting the images were INDEXED in; the
// unit cell, the run lattice and the space group beside them are in the setting the merge settled
// on, which the space-group search can re-seat to. /entry/MX/reindexMatrix is the integral change of
// basis between the two, so applying it here is what makes the file read as one consistent dataset.
// No matrix means the two settings are the same one.
CrystalLattice ApplyReindex(const CrystalLattice &latt, const std::optional<std::array<int32_t, 9>> &m) {
if (!m)
return latt;
const auto &v = *m;
return latt.Multiply(gemmi::Mat33(v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8]));
}
bool ReadReflectionsFromGroup(HDF5Object &file,
const std::string &image_group_name,
std::vector<Reflection> &reflections,
const std::optional<std::array<int32_t, 9>> &reindex) {
if (!file.Exists("/entry/reflections") || !file.Exists(image_group_name))
return false;
auto h = file.ReadOptVector<int32_t>(image_group_name + "/h");
auto k = file.ReadOptVector<int32_t>(image_group_name + "/k");
auto l = file.ReadOptVector<int32_t>(image_group_name + "/l");
auto image_number = file.ReadOptVector<float>(image_group_name + "/observed_frame");
auto predicted_x = file.ReadOptVector<float>(image_group_name + "/predicted_x");
auto predicted_y = file.ReadOptVector<float>(image_group_name + "/predicted_y");
auto obs_x = file.ReadOptVector<float>(image_group_name + "/observed_x");
auto obs_y = file.ReadOptVector<float>(image_group_name + "/observed_y");
auto d = file.ReadOptVector<float>(image_group_name + "/d");
auto int_sum = file.ReadOptVector<float>(image_group_name + "/int_sum");
auto int_err = file.ReadOptVector<float>(image_group_name + "/int_err");
auto bkg = file.ReadOptVector<float>(image_group_name + "/background_mean");
// Written since the merge stopped back-deriving it; older _process.h5 do not carry it.
auto var_bkg = file.ReadOptVector<float>(image_group_name + "/background_variance");
auto lp = file.ReadOptVector<float>(image_group_name + "/lp");
auto partiality = file.ReadOptVector<float>(image_group_name + "/partiality");
auto phi = file.ReadOptVector<float>(image_group_name + "/delta_phi");
auto zeta = file.ReadOptVector<float>(image_group_name + "/zeta");
auto image_scale_corr = file.ReadOptVector<float>(image_group_name + "/image_scale_corr");
if (h.size() != l.size() || h.size() != k.size() || h.size() != d.size()
|| h.size() != predicted_x.size() || h.size() != predicted_y.size()
|| h.size() != int_sum.size() || h.size() != int_err.size() || h.size() != bkg.size()
|| h.size() != image_number.size())
throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of reflections dataset");
for (size_t i = 0; i < h.size(); i++) {
int32_t hh = h.at(i), kk = k.at(i), ll = l.at(i);
if (reindex) {
const auto &m = *reindex;
const int32_t h0 = hh, k0 = kk, l0 = ll;
hh = m[0] * h0 + m[1] * k0 + m[2] * l0;
kk = m[3] * h0 + m[4] * k0 + m[5] * l0;
ll = m[6] * h0 + m[7] * k0 + m[8] * l0;
}
float lp_val = 0.0;
if (lp.size() > i && lp[i] != 0.0f)
lp_val = 1.0f / lp[i];
float partiality_val = -1.0f;
if (partiality.size() > i && partiality[i] >= 0.0f)
partiality_val = partiality[i];
float delta_phi_val = NAN;
if (phi.size() > i)
delta_phi_val = phi[i];
float zeta_val = NAN;
if (zeta.size() > i)
zeta_val = zeta[i];
// A file written before this dataset existed has to have the non-signal variance reconstructed,
// not zeroed. The combine takes var_bkg as the authoritative non-signal term, so a zero would
// leave it the signal alone and weight a weak reflection by ~1/I instead of ~1/sigma^2 - orders
// of magnitude too high, and worst exactly where the reflection is weakest. The integrator's own
// identity sigma^2 = I + var_bkg inverts to recover what the file does not store.
float var_bkg_val = std::max(0.0f, int_err.at(i) * int_err.at(i) - int_sum.at(i));
if (var_bkg.size() > i)
var_bkg_val = var_bkg[i];
float image_scale_corr_val = 1.0f; // Default is 1.0, if we don't know any better
if (image_scale_corr.size() > i)
image_scale_corr_val = image_scale_corr[i];
float obs_x_val = NAN;
float obs_y_val = NAN;
if (obs_x.size() > i && obs_y.size() > i) {
obs_x_val = obs_x[i];
obs_y_val = obs_y[i];
}
Reflection r{
.h = hh,
.k = kk,
.l = ll,
.image_number = image_number.at(i),
.delta_phi_deg = delta_phi_val,
.predicted_x = predicted_x.at(i),
.predicted_y = predicted_y.at(i),
.observed_x = obs_x_val,
.observed_y = obs_y_val,
.d = d.at(i),
.I = int_sum.at(i),
.bkg = bkg.at(i),
.var_bkg = var_bkg_val,
.sigma = int_err.at(i),
.rlp = lp_val,
.partiality = partiality_val,
.zeta = zeta_val,
.image_scale_corr = image_scale_corr_val
};
reflections.emplace_back(r);
}
return true;
}
template<class T>
std::optional<T> ReadElementMasterFirst(HDF5Object &master_file,
HDF5Object &source_file,
const std::string &path,
hsize_t master_image,
hsize_t source_image) {
if (master_file.Exists(path))
return master_file.ReadElement<T>(path, master_image);
if (source_file.Exists(path))
return source_file.ReadElement<T>(path, source_image);
return {};
}
template<class T>
std::vector<T> ReadVectorMasterFirst(HDF5Object &master_file,
HDF5Object &source_file,
const std::string &path,
const std::vector<hsize_t> &master_start,
const std::vector<hsize_t> &source_start,
const std::vector<hsize_t> &size) {
if (master_file.Exists(path))
return master_file.ReadOptVector<T>(path, master_start, size);
if (source_file.Exists(path))
return source_file.ReadOptVector<T>(path, source_start, size);
return {};
}
void HDF5MetadataSource::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const {
// ROI definitions live in /entry/roi_defs (kept separate from the per-image ROI
// results in /entry/roi so that older readers, which iterate /entry/roi, are not
// disturbed by the bitmap and definition subgroups).
if (!file.Exists("/entry/roi_defs"))
return;
if (file.Exists("/entry/roi_defs/roi_map")) {
auto dim = file.GetDimension("/entry/roi_defs/roi_map"); // [y, x]
if (dim.size() == 2)
dataset.roi_map = file.ReadOptVector<uint16_t>("/entry/roi_defs/roi_map",
{0, 0}, {dim[0], dim[1]});
}
ROIDefinition defs;
for (const auto &name: file.FindLeafs("/entry/roi_defs")) {
const std::string base = "/entry/roi_defs/" + name;
// Skip the roi_map bitmask; only named ROI subgroups carry a definition.
if (name == "roi_map" || !file.Exists(base + "/type"))
continue;
dataset.roi_bit_index[name] = static_cast<uint16_t>(file.GetInt(base + "/bit_index"));
const std::string type = file.GetString(base + "/type");
if (type == "box")
defs.boxes.emplace_back(name, file.GetInt(base + "/min_x_pxl"), file.GetInt(base + "/max_x_pxl"),
file.GetInt(base + "/min_y_pxl"), file.GetInt(base + "/max_y_pxl"));
else if (type == "circle")
defs.circles.emplace_back(name, file.GetFloat(base + "/center_x_pxl"), file.GetFloat(base + "/center_y_pxl"),
file.GetFloat(base + "/radius_pxl"));
else if (type == "azim") {
const float qmin = file.GetFloat(base + "/q_min_recipA");
const float qmax = file.GetFloat(base + "/q_max_recipA");
float phi_min = 0, phi_max = 0;
if (file.Exists(base + "/phi_min_deg") && file.Exists(base + "/phi_max_deg")) {
phi_min = file.GetFloat(base + "/phi_min_deg");
phi_max = file.GetFloat(base + "/phi_max_deg");
}
const float d_min = (qmax == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmax;
const float d_max = (qmin == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmin;
defs.azimuthal.emplace_back(name, d_min, d_max, phi_min, phi_max);
}
}
if (!defs.boxes.empty() || !defs.circles.empty() || !defs.azimuthal.empty())
dataset.experiment.ROI().SetROI(defs);
}
HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filename,
const DiffractionExperiment &default_experiment) {
try {
auto dataset = std::make_shared<JFJochReaderDataset>();
master_file = std::make_shared<HDF5ReadOnlyFile>(filename);
master_filename = filename;
dataset->experiment = default_experiment;
// Image-layout state is accumulated locally while parsing, then handed to image_locator_
// at the end. format stays NoFile if the master carries no image data.
FileWriterFormat format = FileWriterFormat::NoFile;
HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
std::vector<std::string> legacy_format_files;
std::vector<HDF5VirtualDatasetMapping> vds_data_mappings;
size_t images_per_file = 1;
std::filesystem::path master_path(filename);
std::string master_file_directory = master_path.parent_path().string();
dataset->arm_date = master_file->GetString("/entry/start_time");
dataset->experiment.FilePrefix(dataset_name(filename));
// JFJochReader is always using int32_t
dataset->experiment.BitDepthImage(32);
dataset->experiment.PixelSigned(true);
size_t image_size_x = 0;
size_t image_size_y = 0;
if (master_file->Exists("/entry/data/data")) {
HDF5DataSet data_dataset(*master_file, "/entry/data/data");
HDF5Dcpl dcpl(data_dataset);
data_layout = dcpl.GetLayout();
auto dim = GetDimension(*master_file, "/entry/data/data");
number_of_images = dim[0];
image_size_y = dim[1];
image_size_x = dim[2];
images_per_file = number_of_images;
if (data_layout == HDF5DataSetLayout::VIRTUAL)
vds_data_mappings = ReadVDSImageMappings(*master_file, "/entry/data/data");
if (master_file->Exists("/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image"))
dataset->efficiency = master_file->ReadVector<float>(
"/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image");
else
dataset->efficiency = std::vector<float>(number_of_images, 1.0);
if (master_file->Exists("/entry/roi"))
dataset->roi = master_file->FindLeafs("/entry/roi");
for (const auto &s: dataset->roi) {
dataset->roi_max.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/max"));
dataset->roi_sum.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum"));
dataset->roi_sum_sq.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum_sq"));
dataset->roi_npixel.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/npixel"));
dataset->roi_x.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/x"));
dataset->roi_y.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/y"));
}
if (master_file->Exists("/entry/MX")) {
if (master_file->Exists("/entry/MX/peakCountUnfiltered"))
dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/peakCountUnfiltered");
else
dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/nPeaks");
dataset->spot_count_low_res = master_file->ReadOptVector<float>("/entry/MX/peakCountLowRes");
dataset->spot_count_indexed = master_file->ReadOptVector<float>("/entry/MX/peakCountIndexed");
dataset->spot_count_ice_rings = master_file->ReadOptVector<float>("/entry/MX/peakCountIceRingRes");
dataset->spot_count_ice_control = master_file->ReadOptVector<float>("/entry/MX/peakCountIceRingControl");
dataset->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
dataset->ice_ring_score = master_file->ReadOptVector<float>("/entry/MX/iceRingScore");
dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
// Master files write indexedLatticeCount; data files / the per-file MX
// plugin use indexingLatticeCount. Accept either for backward compatibility.
dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexedLatticeCount");
if (dataset->indexing_lattice_count.empty())
dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexingLatticeCount");
dataset->mosaicity_deg = master_file->ReadOptVector<float>("/entry/MX/mosaicity");
dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
dataset->image_scale_factor = master_file->ReadOptVector<float>("/entry/MX/imageScaleFactor");
dataset->image_scale_cc = master_file->ReadOptVector<float>("/entry/MX/imageScaleCC");
dataset->integrated_reflections = master_file->ReadOptVector<float>("/entry/MX/integratedReflections");
dataset->sweep_quality = master_file->ReadOptVector<uint8_t>("/entry/MX/sweepQuality");
if (master_file->Exists("/entry/MX/sweepQualityReasons")) {
const auto dim = master_file->GetDimension("/entry/MX/sweepQualityReasons");
for (size_t i = 0; i < (dim.empty() ? 0 : dim[0]); i++)
dataset->sweep_quality_reasons.push_back(
master_file->ReadElement<std::string>("/entry/MX/sweepQualityReasons", i)
.value_or(""));
}
}
if (master_file->Exists("/entry/image"))
dataset->max_value = master_file->ReadOptVector<int64_t>("/entry/image/max_value");
format = FileWriterFormat::NXmxVDS;
} else if (master_file->Exists("/entry/data/data_000001")) {
format = FileWriterFormat::NXmxLegacy;
data_layout = HDF5DataSetLayout::CONTIGUOUS;
legacy_format_files.clear();
image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
//size_t expected_images = master_file->GetInt("/entry/instrument/detector/detectorSpecific/nimages");
images_per_file = 0;
number_of_images = 0;
uint32_t nfiles = 0;
std::filesystem::path file_path(filename);
std::filesystem::path directory = file_path.parent_path();
while (true) {
std::string dname = fmt::format("/entry/data/data_{:06d}", nfiles + 1);
if (!master_file->Exists(dname))
break;
size_t fimages = 0;
try {
auto fname = ResolveRelativeToMaster(directory.string(),
master_file->GetLinkedFileName(dname));
HDF5ReadOnlyFile data_file(fname);
fimages = GetDimension(data_file, "/entry/data/data")[0];
legacy_format_files.push_back(fname);
if (nfiles == 0 && data_file.Exists("/entry/roi"))
dataset->roi = data_file.FindLeafs("/entry/roi");
dataset->roi_max.resize(dataset->roi.size());
dataset->roi_npixel.resize(dataset->roi.size());
dataset->roi_sum.resize(dataset->roi.size());
dataset->roi_sum_sq.resize(dataset->roi.size());
dataset->roi_x.resize(dataset->roi.size());
dataset->roi_y.resize(dataset->roi.size());
for (int i = 0; i < dataset->roi.size(); i++) {
auto roi_name = dataset->roi[i];
ReadVector(dataset->roi_max.at(i),
data_file, "/entry/roi/" + roi_name + "/max",
number_of_images, fimages);
ReadVector(dataset->roi_npixel.at(i),
data_file, "/entry/roi/" + roi_name + "/npixel",
number_of_images, fimages);
ReadVector(dataset->roi_sum.at(i),
data_file, "/entry/roi/" + roi_name + "/sum",
number_of_images, fimages);
ReadVector(dataset->roi_sum_sq.at(i),
data_file, "/entry/roi/" + roi_name + "/sum_sq",
number_of_images, fimages);
ReadVector(dataset->roi_x.at(i),
data_file, "/entry/roi/" + roi_name + "/x",
number_of_images, fimages);
ReadVector(dataset->roi_y.at(i),
data_file, "/entry/roi/" + roi_name + "/y",
number_of_images, fimages);
}
if (data_file.Exists("/entry/detector")) {
ReadVector(dataset->efficiency,
data_file, "/entry/detector/data_collection_efficiency_image",
number_of_images, fimages);
}
if (data_file.Exists("/entry/MX")) {
if (data_file.Exists("/entry/MX/peakCountUnfiltered"))
ReadVector(dataset->spot_count,
data_file, "/entry/MX/peakCountUnfiltered",
number_of_images, fimages);
else
ReadVector(dataset->spot_count,
data_file, "/entry/MX/nPeaks",
number_of_images, fimages);
ReadVector(dataset->spot_count_ice_control,
data_file, "/entry/MX/peakCountIceRingControl",
number_of_images, fimages);
ReadVector(dataset->spot_count_ice_rings,
data_file, "/entry/MX/peakCountIceRingRes",
number_of_images, fimages);
ReadVector(dataset->spot_count_low_res,
data_file, "/entry/MX/peakCountLowRes",
number_of_images, fimages);
ReadVector(dataset->spot_count_indexed,
data_file, "/entry/MX/peakCountIndexed",
number_of_images, fimages);
ReadVector(dataset->indexing_result,
data_file, "/entry/MX/imageIndexed",
number_of_images, fimages);
ReadVector(dataset->bkg_estimate,
data_file, "/entry/MX/bkgEstimate",
number_of_images, fimages);
ReadVector(dataset->ice_ring_score,
data_file, "/entry/MX/iceRingScore",
number_of_images, fimages);
ReadVector(dataset->profile_radius,
data_file, "/entry/MX/profileRadius",
number_of_images, fimages);
ReadVector(dataset->indexing_lattice_count,
data_file, "/entry/MX/indexingLatticeCount",
number_of_images, fimages);
ReadVector(dataset->mosaicity_deg,
data_file, "/entry/MX/mosaicity",
number_of_images, fimages);
ReadVector(dataset->b_factor,
data_file, "/entry/MX/bFactor",
number_of_images, fimages);
ReadVector(dataset->resolution_estimate,
data_file, "/entry/MX/resolutionEstimate",
number_of_images, fimages);
}
if (data_file.Exists("/entry/image")) {
ReadVector(dataset->max_value,
data_file, "/entry/image/max_value",
number_of_images, fimages);
}
} catch (JFJochException &e) {
}
if (nfiles == 0)
images_per_file = fimages;
number_of_images += fimages;
nfiles++;
}
} else {
image_size_x = master_file->GetInt("/entry/instrument/detector/detectorSpecific/x_pixels_in_detector");
image_size_y = master_file->GetInt("/entry/instrument/detector/detectorSpecific/y_pixels_in_detector");
number_of_images = 0;
}
if (master_file->Exists("/entry/MX")) {
auto indexing = master_file->GetString("/entry/MX/indexing_algorithm", "none");
if (indexing == "fft" || indexing == "FFT (CUDA)" || indexing == "FFT (FFTW)")
dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFT);
else if (indexing == "ffbidx" || indexing == "FFBIDX")
dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
}
auto ring_current_A = master_file->GetOptFloat("/entry/source/current");
if (ring_current_A) dataset->experiment.RingCurrent_mA(ring_current_A.value() * 1000.0);
dataset->file_detect_ice_rings =
master_file->GetOptBool("/entry/instrument/detector/detectorSpecific/detect_ice_rings");
dataset->experiment.DetectIceRings(dataset->file_detect_ice_rings.value_or(false));
dataset->experiment.PoniRot1_rad(
master_file->GetOptFloat("/entry/instrument/detector/transformations/rot1").value_or(0.0));
dataset->experiment.PoniRot2_rad(
master_file->GetOptFloat("/entry/instrument/detector/transformations/rot2").value_or(0.0));
dataset->experiment.PoniRot3_rad(
master_file->GetOptFloat("/entry/instrument/detector/transformations/rot3").value_or(0.0));
dataset->experiment.SampleTemperature_K(master_file->GetOptFloat("/entry/sample/temperature"));
dataset->experiment.BeamX_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_x"));
dataset->experiment.BeamY_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_y"));
float det_distance = ReadWithLegacyFallback(*master_file,
"/entry/instrument/detector/distance",
"/entry/instrument/detector/detector_distance");
if (det_distance < 0.001)
det_distance = 0.1; // Set to 100 mm, if det distance is less than 1 mm
dataset->experiment.DetectorDistance_mm(det_distance * 1000.0);
const float incident_wavelength_A = master_file->GetFloat("/entry/instrument/beam/incident_wavelength");
dataset->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / incident_wavelength_A);
// NXmx incident_wavelength_spread is the absolute FWHM (Angstrom); store it
// as the relative bandwidth FWHM (dlambda/lambda) used internally.
if (const auto spread = master_file->GetOptFloat("/entry/instrument/beam/incident_wavelength_spread"))
if (incident_wavelength_A > 0.0f)
dataset->experiment.BandwidthFWHM(spread.value() / incident_wavelength_A);
dataset->error_value = master_file->GetOptInt("/entry/instrument/detector/error_value");
dataset->jfjoch_release = master_file->GetString("/entry/instrument/detector/detectorSpecific/jfjoch_release");
InstrumentMetadata metadata;
metadata.InstrumentName(master_file->GetString("/entry/instrument/name"));
metadata.SourceName(master_file->GetString("/entry/source/name"));
dataset->experiment.ImportInstrumentMetadata(metadata);
// The rotation axis is whatever the file calls it. The name is free-form throughout the API,
// the CBOR stream and the writer, so looking only for "omega" - as this did - read a sweep
// recorded as "phi" back as stills, silently. Prefer an axis that actually turns; fall back
// to a stationary one, which still says where the head was.
const std::string gonio_group = GoniometerGroup(*master_file);
if (!gonio_group.empty()) {
// A Smargon chi/phi is tagged with equipment_component - it is a head position, not the
// spindle. Recognised by that tag and not by name: phi is an ordinary spindle name in MX,
// so a file from anywhere else must not have its rotation axis read back as a head
// position, nor its spindle mistaken for one here.
auto is_smargon_axis = [this, &gonio_group](const std::string &name) {
const std::string dname = gonio_group + "/" + name;
if (!master_file->Exists(dname))
return false;
HDF5DataSet axis(*master_file, dname);
return axis.AttrExists("equipment_component")
&& (axis.ReadAttrStr("equipment_component") == "smargon");
};
std::optional<GoniometerAxis> stationary;
for (const auto &name: master_file->FindLeafs(gonio_group)) {
if (is_smargon_axis(name))
continue;
auto axis = ReadAxis(master_file.get(), name, gonio_group);
if (!axis.has_value())
continue;
if (axis->IsScanning()) {
dataset->experiment.Goniometer(axis);
stationary.reset();
break;
}
if (!stationary.has_value())
stationary = axis;
}
if (stationary.has_value())
dataset->experiment.Goniometer(stationary);
// chi and phi are ordinary stationary axes in the file; the settings still keep them in
// their own Smargon field, so put them back there. Without this a re-opened file lost
// the head position entirely - nothing in reader/ read it.
std::optional<GoniometerAxis> chi, phi;
if (is_smargon_axis("chi"))
chi = ReadAxis(master_file.get(), "chi", gonio_group);
if (is_smargon_axis("phi"))
phi = ReadAxis(master_file.get(), "phi", gonio_group);
if (chi.has_value() || phi.has_value()) {
SmargonPosition smargon;
if (chi.has_value()) {
smargon.chi_deg = chi->GetStart_deg();
smargon.chi_axis = chi->GetAxis();
}
if (phi.has_value()) {
smargon.phi_deg = phi->GetStart_deg();
smargon.phi_axis = phi->GetAxis();
}
dataset->experiment.Smargon(smargon);
}
}
// Independent of the axis: a grid scan can be taken at a given head position, so the two are
// not alternatives.
if (master_file->Exists("/entry/sample/grid_scan")) {
GridScanSettings grid(
master_file->GetInt("/entry/sample/grid_scan/n_fast"),
master_file->GetFloat("/entry/sample/grid_scan/step_x") * 1e6f,
master_file->GetFloat("/entry/sample/grid_scan/step_y") * 1e6f,
master_file->GetOptBool("/entry/sample/grid_scan/snake_scan").value_or(false),
master_file->GetOptBool("/entry/sample/grid_scan/vertical_scan").value_or(false)
);
grid.ImageNum(number_of_images);
dataset->experiment.GridScan(grid);
}
auto tmp = master_file->ReadOptVector<float>("/entry/sample/unit_cell");
if (tmp.size() == 6)
dataset->experiment.SetUnitCell(UnitCell{
.a = tmp[0],
.b = tmp[1],
.c = tmp[2],
.alpha = tmp[3],
.beta = tmp[4],
.gamma = tmp[5]
});
dataset->experiment.SpaceGroupNumber(master_file->GetOptInt("/entry/sample/space_group_number"));
// The setting the cell and space group just read are in, relative to the setting the per-image
// reflections and lattices were written in. Absent on every file written before the offline
// analysis started recording it, and on every run that never re-seated its lattice - both mean
// the identity, and both are read as such.
if (const auto m = master_file->ReadOptVector<int32_t>("/entry/MX/reindexMatrix"); m.size() == 9)
dataset->reindex_matrix = std::array<int32_t, 9>{m[0], m[1], m[2], m[3], m[4],
m[5], m[6], m[7], m[8]};
dataset->experiment.SampleName(master_file->GetString("/entry/sample/name"));
if (master_file->Exists("/entry/instrument/attenuator"))
dataset->experiment.AttenuatorTransmission(
master_file->GetOptFloat("/entry/instrument/attenuator/attenuator_transmission"));
auto total_flux = master_file->GetOptFloat("/entry/instrument/beam/total_flux");
if (total_flux.has_value() && total_flux.value() < 0)
total_flux.reset(); // negative value is an "unknown flux" sentinel; treat as absent
dataset->experiment.TotalFlux(total_flux);
if (master_file->Exists("/entry/azint") && master_file->Exists("/entry/azint/bin_to_q")) {
HDF5DataSet bin_to_q_dataset(*master_file, "/entry/azint/bin_to_q");
HDF5DataSpace bin_to_q_dataspace(bin_to_q_dataset);
auto dim = bin_to_q_dataspace.GetDimensions();
if (dim.size() == 1) {
dataset->azimuthal_bins = 0;
dataset->q_bins = dim[0];
bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q);
} else if (dim.size() == 2) {
dataset->azimuthal_bins = dim[0];
dataset->q_bins = dim[1];
dataset->az_int_bin_to_q.resize(dim[0] * dim[1]);
bin_to_q_dataset.ReadVector(dataset->az_int_bin_to_q, {0, 0}, dim);
} else
throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/azint/image dataset");
if (master_file->Exists("/entry/azint/bin_to_phi")) {
HDF5DataSet bin_to_phi_dataset(*master_file, "/entry/azint/bin_to_phi");
if (dataset->q_bins > 0) {
dataset->az_int_bin_to_phi.resize(dim[0] * dim[1]);
bin_to_phi_dataset.ReadVector(dataset->az_int_bin_to_phi, {0, 0}, dim);
} else {
bin_to_phi_dataset.ReadVector(dataset->az_int_bin_to_phi);
}
}
}
// Read fluorescence spectrum if present
if (master_file->Exists("/entry/instrument/fluorescence")) {
auto energy = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/energy");
auto data = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/data");
if (!energy.empty() && energy.size() == data.size())
dataset->experiment.FluorescenceSpectrum(XrayFluorescenceSpectrum(energy, data));
}
auto detector_name = master_file->GetString("/entry/instrument/detector/description");
DetectorSetup detector = DetDECTRIS(image_size_x, image_size_y, detector_name, {});
detector.PixelSize_um(master_file->GetFloat("/entry/instrument/detector/x_pixel_size") * 1e6);
// Whether the stored image is mirrored in Y. A file written before this was recorded is
// mirrored - that is the only thing Jungfraujoch has ever produced - so absence means true.
detector.MirrorY(master_file
->GetOptBool("/entry/instrument/detector/detectorSpecific/mirror_y")
.value_or(true));
// How the stored image sits in the detector plane. A different setting from mirror_y above,
// recorded separately by the writer; absence means the identity, which is what a file written
// before it existed - or by anything else - describes.
detector.ImageOrientation(DetectorOrientation(
master_file->GetOptBool(
"/entry/instrument/detector/detectorSpecific/detector_orientation_mirror_y")
.value_or(false),
master_file->GetOptInt(
"/entry/instrument/detector/detectorSpecific/detector_orientation_quarter_turns")
.value_or(0)));
// Sensor thickness/material drive the parallax/absorption model, so take them from the file
// rather than the DetectorSetup default (NXmx stores thickness in metres).
if (master_file->Exists("/entry/instrument/detector/sensor_thickness"))
detector.SensorThickness_um(master_file->GetFloat("/entry/instrument/detector/sensor_thickness") * 1e6);
if (master_file->Exists("/entry/instrument/detector/sensor_material"))
detector.SensorMaterial(master_file->GetString("/entry/instrument/detector/sensor_material"));
detector.SaturationLimit(SaturationLimitFromValue(
ReadIntWithLegacyFallback(*master_file,
"/entry/instrument/detector/saturation_value",
"/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff")));
// The reader hands every image out as signed int32 whatever the file stored (see PixelSigned
// below), so that is the container depth the rest of the code has to see. DetectorSetup defaults
// DECTRIS to 16 bits and GetByteDepthImage() prefers the detector's value over the image
// format's, so leaving it at the default computed the overflow as a 16-bit one and called every
// count above 32767 saturated - the integration accept gate then dropped the WHOLE reflection,
// silently removing the strongest reflections of a strong crystal (measured on a lysozyme set:
// max accepted pixel 32738 against a declared saturation of 108833). Taking bit_depth_image from
// the file instead does not work either: it describes an UNSIGNED container, so pairing it with
// signed pixels halves the range (a 16-bit file capped at 32767, an 8-bit one at 127). The real
// cap is the file's own saturation_value, set just above.
detector.BitDepthImage(32);
detector.MinFrameTime(std::chrono::microseconds(0));
detector.MinCountTime(std::chrono::microseconds(0));
detector.ReadOutTime(std::chrono::nanoseconds(0));
dataset->experiment.Detector(detector);
// frame_time is the period between frames, count_time the exposure within one. NXmx requires
// neither, and a master written outside the DECTRIS toolchain often carries only count_time;
// falling back to it says "no dead time", which is the honest reading of a file that does not
// state one. What is read here is metadata - the one place frame time is divided by is the
// JUNGFRAU summation, which a dataset read from a DECTRIS-style file never reaches.
const float count_time_s = master_file->GetFloat("/entry/instrument/detector/count_time");
dataset->experiment.FrameTime(
std::chrono::duration_cast<std::chrono::nanoseconds>(
std::chrono::duration<float>(
master_file->GetOptFloat("/entry/instrument/detector/frame_time")
.value_or(count_time_s))),
std::chrono::duration_cast<std::chrono::nanoseconds>(
std::chrono::duration<float>(count_time_s))
);
if (master_file->Exists("/entry/instrument/detector/calibration")) {
dataset->calibration_data = master_file->FindLeafs("/entry/instrument/detector/calibration");
std::sort(dataset->calibration_data.begin(), dataset->calibration_data.end());
}
if (image_size_x * image_size_y > 0) {
auto mask_tmp = master_file->ReadOptVector<uint32_t>(
"/entry/instrument/detector/pixel_mask",
{0, 0},
{image_size_y, image_size_x}
);
if (mask_tmp.empty())
mask_tmp = master_file->ReadOptVector<uint32_t>(
"/entry/instrument/detector/detectorSpecific/pixel_mask",
{0, 0},
{image_size_y, image_size_x}
);
if (mask_tmp.empty())
mask_tmp = std::vector<uint32_t>(image_size_x * image_size_y);
dataset->pixel_mask = std::make_shared<const PixelMask>(mask_tmp);
}
ReadROIMetadata(*master_file, *dataset);
// Resolve VDS mapping filenames to absolute paths so the image source's locator only ever
// deals with real paths, then report the layout to the caller. "." is HDF5's spelling for
// "the file this dataset is in", not a relative path - a master is allowed to compose its
// VDS over datasets in ITSELF, which are then external links to the data files. Resolved as
// a path it became <dir>/. and no image could be opened at all.
for (auto &m : vds_data_mappings)
m.filename = (m.filename == ".")
? master_filename
: ResolveRelativeToMaster(master_file_directory, m.filename);
dataset->experiment.ImagesPerTrigger(number_of_images);
cached_geom = dataset->experiment.GetDiffractionGeometry();
// Image-index -> original-image-number map (written as /entry/detector/number). When it is a
// genuine subset/strided selection, keep it so plots and per-image lookups use the original
// numbering; a plain 0..N-1 sequence is identity and left empty.
image_to_local_.clear();
auto numbers = master_file->ReadOptVector<uint64_t>("/entry/detector/number");
if (numbers.size() == number_of_images) {
bool identity = true;
for (size_t i = 0; i < numbers.size(); i++)
if (numbers[i] != i) { identity = false; break; }
if (!identity) {
dataset->source_image_number.assign(numbers.begin(), numbers.end());
for (size_t i = 0; i < numbers.size(); i++)
image_to_local_[static_cast<int64_t>(numbers[i])] = static_cast<int64_t>(i);
}
}
dataset_ = dataset;
return OpenResult{
.image_layout = HDF5ImageLocator::Layout{
.format = format,
.data_layout = data_layout,
.master_file = master_file,
.master_filename = master_filename,
.legacy_files = std::move(legacy_format_files),
.images_per_file = images_per_file,
.vds_mappings = std::move(vds_data_mappings)
},
.number_of_images = number_of_images
};
} catch (const std::exception &e) {
master_file = {};
master_filename.clear();
number_of_images = 0;
dataset_.reset();
cached_geom = DiffractionGeometry{};
throw;
}
}
HDF5ImageLocator::Location HDF5MetadataSource::ResolveMeta(int64_t global) const {
// Per-image metadata is co-located with the pixels for the original file (resolve via the
// shared image source); for an integrated _process.h5 snapshot it lives in this master at the
// global index.
if (image_source_)
return image_source_->Resolve(global);
return {master_file, static_cast<uint32_t>(global)};
}
std::optional<int64_t> HDF5MetadataSource::ToLocalIndex(int64_t image_number) const {
if (image_to_local_.empty())
return image_number; // 1:1 source (identity)
const auto it = image_to_local_.find(image_number);
if (it == image_to_local_.end())
return std::nullopt; // this source does not cover that image
return it->second;
}
// Reads spot data for a single image from the appropriate HDF5 source.
// master_image / source_image are the logical indices within master_file and
// source_file respectively (identical for NXmxVDS contiguous / integrated;
// differ for NXmxLegacy and NXmxVDS virtual layouts).
// Appends assembled SpotToSave entries to message.spots and fills the
// spot_count* fields; does NOT touch the image pixel data.
static void ReadSpotsFromFiles(HDF5Object &master_file,
HDF5Object &source_file,
hsize_t master_image,
hsize_t source_image,
int64_t image_number,
const DiffractionGeometry &geom,
float plot_d_min_A,
DataMessage &message) {
auto spot_count_opt = ReadElementMasterFirst<uint32_t>(master_file,
source_file,
"/entry/MX/nPeaks",
master_image,
source_image);
if (!spot_count_opt.has_value() || spot_count_opt.value() == 0)
return;
const size_t spot_count = spot_count_opt.value();
auto spot_x = ReadVectorMasterFirst<float>(
master_file, source_file,
"/entry/MX/peakXPosRaw",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_y = ReadVectorMasterFirst<float>(
master_file, source_file,
"/entry/MX/peakYPosRaw",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_intensity = ReadVectorMasterFirst<float>(
master_file, source_file,
"/entry/MX/peakTotalIntensity",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
if (spot_x.size() < spot_count || spot_y.size() < spot_count || spot_intensity.size() < spot_count)
throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of spot dataset");
auto spot_indexed = ReadVectorMasterFirst<uint8_t>(
master_file, source_file,
"/entry/MX/peakIndexed",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_ice = ReadVectorMasterFirst<uint8_t>(
master_file, source_file,
"/entry/MX/peakIceRingRes",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_h = ReadVectorMasterFirst<int32_t>(
master_file, source_file,
"/entry/MX/peakH",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_k = ReadVectorMasterFirst<int32_t>(
master_file, source_file,
"/entry/MX/peakK",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_l = ReadVectorMasterFirst<int32_t>(
master_file, source_file,
"/entry/MX/peakL",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_lattice = ReadVectorMasterFirst<int8_t>(
master_file, source_file,
"/entry/MX/peakLattice",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
auto spot_dist_ewald_sphere = ReadVectorMasterFirst<float>(
master_file, source_file,
"/entry/MX/peakDistEwaldSphere",
{master_image, 0}, {source_image, 0}, {1, spot_count}
);
message.spots.reserve(message.spots.size() + spot_count);
for (size_t i = 0; i < spot_count; i++) {
const auto x = spot_x.at(i);
const auto y = spot_y.at(i);
SpotToSave s{
.x = x,
.y = y,
.intensity = spot_intensity.at(i),
.image = image_number,
.d_A = geom.PxlToRes(x, y)
};
if (spot_indexed.size() > i)
s.indexed = (spot_indexed.at(i) != 0);
if (spot_h.size() > i)
s.h = spot_h.at(i);
if (spot_k.size() > i)
s.k = spot_k.at(i);
if (spot_l.size() > i)
s.l = spot_l.at(i);
if (spot_dist_ewald_sphere.size() > i)
s.dist_ewald_sphere = spot_dist_ewald_sphere.at(i);
if (spot_ice.size() > i)
s.ice_ring = (spot_ice.at(i) != 0);
if (spot_lattice.size() > i)
s.lattice = spot_lattice.at(i);
message.spots.emplace_back(s);
}
if (auto v = ReadElementMasterFirst<uint32_t>(master_file, source_file,
"/entry/MX/peakCountUnfiltered",
master_image, source_image); v)
message.spot_count = v;
else
message.spot_count = spot_count_opt;
message.spot_count_ice_rings = ReadElementMasterFirst<uint32_t>(
master_file, source_file, "/entry/MX/peakCountIceRingRes", master_image, source_image);
message.spot_count_low_res = ReadElementMasterFirst<uint32_t>(
master_file, source_file, "/entry/MX/peakCountLowRes", master_image, source_image);
message.spot_count_indexed = ReadElementMasterFirst<uint32_t>(
master_file, source_file, "/entry/MX/peakCountIndexed", master_image, source_image);
GenerateSpotPlot(message, message.spots, plot_d_min_A);
}
void HDF5MetadataSource::FillPerImage(DataMessage &message, int64_t requested_image,
const std::shared_ptr<const JFJochReaderDataset> &dataset) const {
const auto local_opt = ToLocalIndex(requested_image);
if (!local_opt)
return; // this metadata source does not cover the requested image
const int64_t image_number = *local_opt; // local index into this source (identity for 1:1)
auto loc = ResolveMeta(image_number);
auto &source_file = loc.file;
const uint32_t image_id = loc.local_index;
const auto master_image = static_cast<hsize_t>(image_number);
const auto source_image = static_cast<hsize_t>(image_id);
ReadSpotsFromFiles(*master_file, *source_file, master_image, source_image,
requested_image, dataset->experiment.GetDiffractionGeometry(),
dataset->experiment.GetDetectorMaxResolution_A(), message);
if (!dataset->az_int_bin_to_q.empty()) {
if (dataset->azimuthal_bins == 0) {
message.az_int_profile = ReadVectorMasterFirst<float>(
*master_file,
*source_file,
"/entry/azint/image",
{master_image, 0},
{source_image, 0},
{1, dataset->az_int_bin_to_q.size()}
);
} else {
message.az_int_profile = ReadVectorMasterFirst<float>(
*master_file,
*source_file,
"/entry/azint/image",
{master_image, 0, 0},
{source_image, 0, 0},
{1, dataset->azimuthal_bins, dataset->q_bins}
);
}
}
if (dataset->integrated_reflections.size() > image_number)
message.integrated_reflections = static_cast<int64_t>(std::lround(
dataset->integrated_reflections.at(image_number)));
if (dataset->resolution_estimate.size() > image_number)
message.resolution_estimate = dataset->resolution_estimate[image_number];
if (dataset->indexing_result.size() > image_number)
message.indexing_result = dataset->indexing_result[image_number];
if (dataset->indexing_lattice_count.size() > image_number)
message.indexing_lattice_count = dataset->indexing_lattice_count[image_number];
if (dataset->bkg_estimate.size() > image_number)
message.bkg_estimate = dataset->bkg_estimate[image_number];
if (dataset->ice_ring_score.size() > image_number)
message.ice_ring_score = dataset->ice_ring_score[image_number];
if (dataset->efficiency.size() > image_number)
message.image_collection_efficiency = dataset->efficiency[image_number];
if (dataset->profile_radius.size() > image_number)
message.profile_radius = dataset->profile_radius[image_number];
if (dataset->mosaicity_deg.size() > image_number)
message.mosaicity_deg = dataset->mosaicity_deg[image_number];
if (dataset->b_factor.size() > image_number)
message.b_factor = dataset->b_factor[image_number];
if (dataset->image_scale_factor.size() > image_number)
message.image_scale_factor = dataset->image_scale_factor[image_number];
if (dataset->image_scale_cc.size() > image_number)
message.image_scale_cc = dataset->image_scale_cc[image_number];
if (dataset->indexing_result.size() > image_number
&& dataset->indexing_result[image_number] != 0
&& (master_file->Exists("/entry/MX/latticeIndexed") ||
source_file->Exists("/entry/MX/latticeIndexed"))) {
std::vector<float> tmp = ReadVectorMasterFirst<float>(
*master_file,
*source_file,
"/entry/MX/latticeIndexed",
{master_image, 0},
{source_image, 0},
{1, 9}
);
if (tmp.size() == 9)
message.indexing_lattice = ApplyReindex(CrystalLattice(tmp), dataset->reindex_matrix);
std::optional<std::string> lattice;
if (master_file->Exists("/entry/MX/bravaisLattice"))
lattice = master_file->ReadElement<std::string>("/entry/MX/bravaisLattice", image_number);
else
lattice = source_file->ReadElement<std::string>("/entry/MX/bravaisLattice", image_id);
std::optional<uint32_t> niggli_opt;
if (master_file->Exists("/entry/MX/niggli_class"))
niggli_opt = master_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_number);
else if (master_file->Exists("/entry/MX/niggliClass"))
niggli_opt = master_file->ReadElement<uint32_t>("/entry/MX/niggliClass", image_number);
else if (source_file->Exists("/entry/MX/niggli_class"))
niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_id);
else if (source_file->Exists("/entry/MX/niggliClass"))
niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggliClass", image_id);
if (lattice && !lattice->empty()) {
auto symm_info = parse_bravais_lattice(lattice.value());
message.lattice_type = LatticeMessage{
.centering = symm_info.second,
.niggli_class = static_cast<int64_t>(niggli_opt.value_or(0)),
.crystal_system = symm_info.first,
};
}
}
const std::string master_reflection_group_name = fmt::format("/entry/reflections/image_{:06d}", image_number);
const std::string source_reflection_group_name = fmt::format("/entry/reflections/image_{:06d}", image_id);
if (!ReadReflectionsFromGroup(*master_file, master_reflection_group_name, message.reflections,
dataset->reindex_matrix))
ReadReflectionsFromGroup(*source_file, source_reflection_group_name, message.reflections,
dataset->reindex_matrix);
if (!message.reflections.empty()) {
CalcISigma(message);
CalcWilsonBFactor(message, !message.b_factor.has_value());
}
}
std::optional<GoniometerAxis> HDF5MetadataSource::ReadAxis(HDF5Object *file, const std::string &name,
const std::string &group) {
std::string dname = group + "/" + name;
// Not a dataset, not an axis: a hybrid file keeps a bare subgroup here for the direction alone.
if (!file->IsDataSet(dname))
return {};
HDF5DataSet dataset(*file, dname);
std::vector<double> angle;
dataset.ReadVector(angle);
if (angle.empty())
return {};
// Not everything in the group is an axis. The writer's own AXISNAME_end and the two rotation
// width scalars carry only units, and a file from anywhere else may hold whatever it likes.
// Missing attribute means "not a transformation", so skip it rather than throwing: the search
// for the goniometer walks every leaf and only stops early on an axis that turns, so a master
// whose axis was stationary reached omega_end and could not be opened at all.
// NXmx tags every axis; DECTRIS firmware 1.x tagged none of them, so absence has to mean two
// different things depending on the layout. In a transformations group it means "not an axis"
// (the writer's own AXISNAME_end and the rotation-width scalars live there and carry only units),
// and skipping is right. In the legacy goniometer group EVERY leaf is an axis and none is tagged,
// so skipping there would find no goniometer at all and the sweep would be read as stills.
const bool legacy_group = (group != "/entry/sample/transformations");
if (dataset.AttrExists("transformation_type")) {
if (dataset.ReadAttrStr("transformation_type") != "rotation")
return {};
} else if (!legacy_group) {
return {};
} else {
// The same companion datasets, recognised by name because there is no tag to go on. In the
// legacy layout each axis NAME carries five of them - AXIS_end, _start, _increment,
// _range_average, _range_total - and only the bare name is the axis itself. Matching the
// suffix rather than "contains an underscore" keeps a genuine two_theta axis readable.
static const char *const companions[] = {"_end", "_start", "_increment",
"_range_average", "_range_total"};
for (const char *suffix: companions)
if (name.size() > strlen(suffix)
&& name.compare(name.size() - strlen(suffix), strlen(suffix), suffix) == 0)
return {};
}
std::vector<double> end = file->ReadOptVector<double>(dname + "_end");
// A single value, or every value the same, is a stationary axis: it says where the head was
// rather than that anything turned. Increment 0 is the honest description of that, and
// GoniometerAxis::IsScanning is what separates it from a sweep.
double start = angle[0];
double incr = (angle.size() < 2) ? 0.0 : angle[1] - angle[0];
std::vector<double> axis_vec;
if (dataset.AttrExists("vector")) {
axis_vec = dataset.ReadAttrVec("vector");
} else if (legacy_group) {
// The angles carry no direction here, but a hybrid file still states one next door: an
// NXmx-shaped subgroup /entry/sample/transformations/AXIS, holding the vector attribute
// and no angles. That is the file speaking, so it beats the assumption below.
const std::string nxmx_axis = "/entry/sample/transformations/" + name;
if (file->Exists(nxmx_axis) && !file->IsDataSet(nxmx_axis)) {
HDF5Group nxmx_group(*file, nxmx_axis);
if (nxmx_group.AttrExists("vector"))
axis_vec = nxmx_group.ReadAttrVec("vector");
}
if (axis_vec.empty()) {
// Firmware 1.x stored no direction at all. Assume the one every DECTRIS master since has
// written, and say so - a wrong guess here does not index, so it is visible rather than
// silent, and the rotation first pass will try the opposite sign anyway.
axis_vec = {-1.0, 0.0, 0.0};
Logger("HDF5Reader").Warning("{} carries no axis direction (pre-NXmx layout); assuming "
"(-1,0,0), the direction current DECTRIS masters write", dname);
}
} else {
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
dname + " has no vector attribute");
}
if (axis_vec.size() != 3)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
dname + " Vector must have 3 elements");
Coord axis(axis_vec[0], axis_vec[1], axis_vec[2]);
GoniometerAxis g_axis(name, start, incr, axis, {});
if (!end.empty())
g_axis.ScreeningWedge(end[0] - angle[0]);
return g_axis;
}
CompressedImage HDF5MetadataSource::ReadCalibration(std::vector<uint8_t> &tmp, const std::string &name) const {
std::vector<hsize_t> start = {0, 0};
if (!master_file)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Master file not loaded");
if (!master_file->Exists("/entry/instrument/detector/calibration/" + name))
throw JFJochException(JFJochExceptionCategory::HDF5, "Calibration dataset not found");
HDF5DataSet dataset(*master_file, "/entry/instrument/detector/calibration/" + name);
HDF5DataSpace dataspace(dataset);
HDF5DataType datatype(dataset);
HDF5Dcpl dcpl(dataset);
if (dataspace.GetNumOfDimensions() != 2)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Calibration dataset must be 2D");
auto dim = dataspace.GetDimensions();
CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
dataset.ReadVectorToU8(tmp, start, {dim[0], dim[1]});
algorithm = CompressionAlgorithm::NO_COMPRESSION;
return {
tmp, dim[1], dim[0],
CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
algorithm
};
}
std::vector<IntegrationOutcome> HDF5MetadataSource::ReadReflections(size_t start_image,
std::optional<size_t> end_image) const {
if (start_image >= number_of_images)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"start_image must be less than number_of_images");
const size_t end_image_val = end_image.value_or(number_of_images - 1);
if (end_image_val < start_image)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"end_image must be greater or equal to start_image if provided");
if (end_image_val >= number_of_images)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"end_image must be less than number_of_images");
if (!master_file)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Cannot read reflections if file not loaded");
std::vector<IntegrationOutcome> ret;
ret.reserve(end_image_val - start_image + 1);
// A self-contained integrated _process.h5 keeps all reflections in this master (one group per
// indexed image), so a missing per-image group means that image simply has none - never fall
// back to the linked source pixel files (which may be absent, and never hold a snapshot's
// reflections). A legacy/VDS acquisition has no /entry/reflections in the master and resolves
// reflections lazily from the source data files instead.
const bool master_reflections_authoritative = master_file->Exists("/entry/reflections");
// Everything below comes out in the setting of the dataset's unit cell and space group, not in the
// setting it was written in (see ApplyReindex).
const auto &reindex = dataset_->reindex_matrix;
for (size_t img = start_image; img <= end_image_val; img++) {
IntegrationOutcome outcome;
// Generic (non-image-specific) detector geometry from experiment setup.
outcome.geom = cached_geom;
// Per-image reflections and MX metadata are stored in this master at the global index for a
// self-contained integrated _process.h5 snapshot, or co-located with the pixels in the source
// data file at the source-local index for a legacy/VDS dataset. Prefer the master (so an
// integrated snapshot reads without its linked source data present); fall back to the source.
HDF5ReadOnlyFile *meta_file = master_file.get();
size_t meta_image_id = img;
std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", img);
if (!master_reflections_authoritative && !master_file->Exists(refl_group)) {
const auto loc = ResolveMeta(static_cast<int64_t>(img));
meta_file = loc.file.get();
meta_image_id = loc.local_index;
refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
}
// ── reflections ──────────────────────────────────────────────────────
ReadReflectionsFromGroup(*meta_file, refl_group, outcome.reflections, reindex);
// ── per-image mosaicity ───────────────────────────────────────────────
if (meta_file->Exists("/entry/MX/mosaicity")) {
try {
outcome.mosaicity_deg =
meta_file->ReadElement<float>("/entry/MX/mosaicity", meta_image_id);
} catch (...) {
}
}
// ── indexed lattice (stored as 9-element row-major matrix) ────────────
if (meta_file->Exists("/entry/MX/latticeIndexed")) {
try {
auto lattice_vec = meta_file->ReadOptVector<float>(
"/entry/MX/latticeIndexed", {meta_image_id, 0}, {1, 9});
if (lattice_vec.size() == 9)
outcome.latt = ApplyReindex(CrystalLattice(lattice_vec), reindex);
} catch (...) {
}
}
ret.push_back(std::move(outcome));
}
return ret;
}
std::vector<SpotToSave> HDF5MetadataSource::ReadSpots(int64_t requested_image) const {
if (requested_image < 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"image number must be non-negative");
const auto local_opt = ToLocalIndex(requested_image);
if (!local_opt)
return {}; // this (subset) source does not cover the requested image
const int64_t image = *local_opt;
if (image >= number_of_images)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"image must be less than number_of_images");
if (!master_file)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Cannot read spots if file not loaded");
// Per-image spot/MX data, resolved the same way as the pixels (or in our own master at the
// local index for an integrated _process.h5 snapshot).
const auto loc = ResolveMeta(image);
HDF5Object *meta_file = loc.file.get();
const size_t meta_image_id = loc.local_index;
DataMessage tmp_message;
tmp_message.number = requested_image;
ReadSpotsFromFiles(*master_file, *meta_file,
image, meta_image_id,
requested_image,
cached_geom,
dataset_ ? dataset_->experiment.GetDetectorMaxResolution_A() : 0.0f,
tmp_message);
return tmp_message.spots;
}
bool HDF5MetadataSource::HasSpots() const {
// Stored spots (jungfraujoch spot finding) live under /entry/MX; a plain DECTRIS file has none,
// so ReadSpots would silently return nothing and the caller must find them itself. ReadSpots
// reads /entry/MX/nPeaks master-first-then-source, so check both: the integrated _process.h5
// keeps it in the master, while a VDS/legacy dataset keeps the per-image arrays in the data file.
if (!master_file || number_of_images == 0)
return false;
if (master_file->Exists("/entry/MX/nPeaks"))
return true;
const auto loc = ResolveMeta(0);
return loc.file && loc.file->Exists("/entry/MX/nPeaks");
}
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