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Jungfraujoch/reader/HDF5MetadataSource.cpp
T
leonarski_fandClaude Opus 5 61a7c91b90 Ice: detect it on two channels, and only handle it when it is there 
The per-image ice score was read off the PLAIN azimuthal profile. That profile is a
per-ring mean, so a few strong Bragg reflections landing in a ring's q bin lift it
exactly as ice would. Measured over 37 rotation crystals, that did not merely add
noise - it INVERTED the metric: the two highest-scoring crystals had no ice at all
(4.23 and 4.06), while a clean control read 1.57. A decoy null - the identical
statistic evaluated at q positions where hexagonal ice cannot be - reaches 1.51 at its
99th percentile and 2.70 at its maximum, so that metric cannot support any absolute
threshold whatsoever.

The adaptive spot finder already computes the right input for its own threshold: a
sigma-clipped per-resolution-ring background, in the same bins. A powder ring is
azimuthally smooth and survives the clip; Bragg peaks do not. On the clipped profile
the clean population tightens to 1.00-1.22 and the crystals with confirmed ice sit at
2.08-2.37, against a decoy null that never exceeds 1.29.

That channel is blind to one thing: ice in large crystallites diffracts as DISCRETE
spots and leaves the radial profile flat. So a second channel counts found spots on the
rings against the same q width of ice-free flanks beside them. The two barely overlap -
the smooth-ice crystals read 2.1-2.4 / ~1.0 and the textured ones ~1.1 / 3.8-17.6,
while a clean crystal reads 1.04 on both.

Both are then used as a GATE (--ice-min-score 1.5, --ice-min-spot-ratio 2.0, both
calibrated on the battery, 0 disables): the eleven fixed hexagonal bands cover 16-26 %
of the unique reflections at typical resolutions whether or not the crystal has ice, so
flagging, the exclusion from the scale fit and the merge-time CC1/2 ring mask are now
all skipped when neither channel sees any. The gate is applied in the full pipeline and
in --scale, which reads the stored per-image values back out of the _process.h5.

Also fixes the merge-time mask's control: the shoulder now excludes reflections that
are themselves on an ice ring. The rings are not evenly spaced - 1.947/1.916/1.882 A
sit 0.05-0.06 apart in q - so for those three the [w,3w) shoulder landed squarely on
the neighbours and the test compared ice against ice. Measured, that is the only thing
this changes: it removes firings on those three rings and leaves every other firing's
CC pair identical to three decimals.

And the online ice half-width, which was 0.02 in the API against 0.03 offline, so the
same data got a narrower band online than the measured ~0.06 ring FWHM justifies.

Battery (37 rotation crystals, against the previous behaviour): space groups 34/37 in
both and NO crystal's space group changes; 6 crystals gain unique reflections, 1 loses.
Best of them gains 7082 unique reflections with R_meas 16.0 -> 14.3, CC1/2 95.9 -> 97.3
and ISa 13.7 -> 19.0; another goes R_meas 54.9 -> 42.9, CC1/2 84.0 -> 90.4, ISa
3.9 -> 5.5; a third reaches CC1/2 99.4 from 95.7 at an unchanged reflection count. The
one crystal that loses reflections improves on both R_meas and CC1/2.

Not done here: the ScanResult/API/plot-type/frontend/viewer layers for the new
spot_count_ice_control (they need the OpenAPI regeneration). Message, CBOR, HDF5
write/read and the receiver plots are.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-06 16:17:23 +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 <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/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();
}
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;
}
bool ReadReflectionsFromGroup(HDF5Object &file,
const std::string &image_group_name,
std::vector<Reflection> &reflections) {
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");
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++) {
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];
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 = h.at(i),
.k = k.at(i),
.l = l.at(i),
.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),
.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");
}
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->experiment.DetectIceRings(
master_file->GetOptBool("/entry/instrument/detector/detectorSpecific/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 = master_file->GetFloat("/entry/instrument/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);
if (master_file->Exists("/entry/sample/transformations")) {
if (master_file->Exists("/entry/sample/transformations/omega")) {
auto omega = ReadAxis(master_file.get(), "omega");
dataset->experiment.Goniometer(omega);
} else 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"));
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);
// 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(master_file->GetInt("/entry/instrument/detector/saturation_value"));
// 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);
dataset->experiment.FrameTime(
std::chrono::duration_cast<std::chrono::nanoseconds>(
std::chrono::duration<float>(
master_file->GetFloat("/entry/instrument/detector/frame_time"))),
std::chrono::duration_cast<std::chrono::nanoseconds>(
std::chrono::duration<float>(
master_file->GetFloat("/entry/instrument/detector/count_time")))
);
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.
for (auto &m : vds_data_mappings)
m.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 = CrystalLattice(tmp);
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))
ReadReflectionsFromGroup(*source_file, source_reflection_group_name, message.reflections);
if (!message.reflections.empty()) {
CalcISigma(message);
CalcWilsonBFactor(message, !message.b_factor.has_value());
}
}
std::optional<GoniometerAxis> HDF5MetadataSource::ReadAxis(HDF5Object *file, const std::string &name) {
std::string dname = "/entry/sample/transformations/" + name;
if (!file->Exists(dname))
return {};
HDF5DataSet dataset(*file, dname);
std::vector<double> angle;
dataset.ReadVector(angle);
if (angle.size() < 2)
return {};
std::vector<double> end = file->ReadOptVector<double>(dname + "_end");
double start = angle[0];
double incr = angle[1] - angle[0];
if (dataset.ReadAttrStr("transformation_type") != "rotation")
return {};
std::vector<double> axis_vec = dataset.ReadAttrVec("vector");
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");
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);
// ── 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 = CrystalLattice(lattice_vec);
} 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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