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Jungfraujoch/reader/HDF5MetadataSource.cpp
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leonarski_fandClaude Opus 5 f0cdb027e1 Ice: default the merge mask off, gate the radial background on smooth ice, and pick detection by geometry 
Three defaults, each settled by measurement rather than by argument. The
arbiter throughout is structure-referenced - anomalous peak height where a
crystal can carry it, and otherwise the agreement of the ice bands with a fixed
external model against resolution-matched DECOY bands carrying no ice. The
band-versus-decoy contrast is used because R-free here tracks completeness, and
every one of these switches moves completeness.

The damage is real and it localizes: over the rotation battery the ice bands'
excess amplitude reaches +9.6% on a smooth-ice crystal and +35% on the worst,
while a clean control sits at +0.6% (z +0.45). On the worst crystal, nine of the
ten largest excess peaks in a q scan land on hexagonal ring positions. Turning
ice handling off leaves the contrast unchanged and forcing it on a clean crystal
does not create one, so it is the ice and not the machinery.

MERGE-TIME RING MASK -> OFF. It deletes reflections, which no other program does
by default - AIMLESS, DIALS, xia2, XDS and CrystFEL all keep ice-band
reflections in the merge and exclude them only from the model fit; autoPROC is
the sole exception. On the one battery crystal where the mask fires and an
anomalous arbiter can score it, dropping the band moved the mean peak height at
the known sites by -0.001 +- 0.018 sigma, 2% of the site height, while removing
1149 unique reflections whose mean I/sigma was 3.62 against the dataset's own
3.05 - better than average data - and costing 17 completeness points in that
shell. It fires on 5 of 37 crystals, changes no space group, and those 5
disagree in sign: it clearly helps the two most heavily iced, is a wash on two
and costs a third. So it stays as a switch, worth setting by hand on a badly
iced crystal where it shows in the high shell, but it is not a default.

RADIAL BACKGROUND -> AUTO, gated per image. The correction models the background
as a function of radius alone, and that is exactly when it works. On a crystal
with pure smooth powder ice it removes 43% of the bands' excess amplitude, with
the improvement 7x larger inside the bands than outside; on a crystal whose ice
is discrete crystallite spots - no smooth ring to model - the excess amplitude
GREW by half; on clean data it is inert to four decimals. The two ice channels
already separate those morphologies, so --background-radial takes on|off|auto
and auto applies it to an image when that image's peak-excluded score reaches
--ice-min-score. Auto never engages without such a score, because the plain
profile carries the Bragg peaks and cannot support an absolute threshold.

Per image rather than per run, and that was tested rather than assumed: the
gate fires on 100% and 94% of frames on the two crystals that want it, and on
1.5% of frames - 32 blocks, 23 of them single frames - on the textured-ice
crystal. A seam statistic against off + f*(on - off) is null on both mixed runs,
every merge statistic is bracketed by the pure arms, and the textured crystal's
auto arm lands on `off` rather than on `on`'s harm. A run-level gate would need
the score before the pass that integrates, i.e. rotation-only plumbing, and buys
nothing measurable.

The kernel was already built unconditionally, so flipping the flag per image is
free - except on the GPU, where the launches were gated on a construction-time
n_rad. That is why the buffers are now allocated whenever the correction could
run, and Run() decides per image.

DETECTION -> the geometry's default when the file is silent: on for rotation,
off for stills, with the command line and then the file taking precedence. A
rotation sweep sits on the same rings for the whole run, so ice there is a
coherent systematic and the presence gate keeps it inert on a clean crystal; a
serial stills run has too few spots per image to spend any on flagging. The
master file's key is kept as written rather than collapsed to a bool, so "the
file said nothing" is distinguishable from "the file said no" - it used to fall
silently to off, taking the exclusion from the scale fit with it.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-06 19:06:30 +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->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 = 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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