leonarski_f
75e401f0e5
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63
1163 lines
53 KiB
C++
1163 lines
53 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <cmath>
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#include <set>
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#include "HDF5MetadataSource.h"
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#include "spdlog/fmt/fmt.h"
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#include "../image_analysis/bragg_integration/CalcISigma.h"
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#include "../image_analysis/spot_finding/SpotUtils.h"
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#include "../common/GridScanSettings.h"
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#include "../common/JFJochMath.h"
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#include "../common/ROIDefinition.h"
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inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::string &val) {
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if (val.empty())
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return {gemmi::CrystalSystem::Triclinic, 'P'};
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if (val.size() != 2)
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throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong Bravais lattice encoding");
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gemmi::CrystalSystem cs;
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char centering = val[1];
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std::set<char> allowed_centering;
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switch (val[0]) {
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case 'a':
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cs = gemmi::CrystalSystem::Triclinic;
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allowed_centering = {'P'};
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break;
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case 'm':
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cs = gemmi::CrystalSystem::Monoclinic;
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allowed_centering = {'P', 'A', 'B', 'C'};
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break;
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case 'o':
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cs = gemmi::CrystalSystem::Orthorhombic;
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allowed_centering = {'P', 'A', 'B', 'C', 'I', 'F'};
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break;
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case 't':
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cs = gemmi::CrystalSystem::Tetragonal;
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allowed_centering = {'P', 'I'};
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break;
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case 'h':
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if (centering == 'P')
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cs = gemmi::CrystalSystem::Hexagonal;
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else if (centering == 'R')
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cs = gemmi::CrystalSystem::Trigonal;
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allowed_centering = {'P', 'R'};
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break;
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case 'c':
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cs = gemmi::CrystalSystem::Cubic;
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allowed_centering = {'P', 'F', 'I'};
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break;
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default:
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// allowed_centering is empty and exception will be always thrown
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break;
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}
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if (!allowed_centering.contains(centering))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Invalid lattice encoding " + val);
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return {cs, centering};
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}
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std::vector<hsize_t> GetDimension(HDF5Object &object, const std::string &path) {
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const auto dim = object.GetDimension(path);
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if (dim.size() != 3)
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throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong dimension of /entry/data/data");
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return dim;
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}
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std::vector<HDF5VirtualDatasetMapping> ReadVDSImageMappings(HDF5Object &file,
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const std::string &dataset_name) {
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HDF5DataSet dataset(file, dataset_name);
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HDF5Dcpl dcpl(dataset);
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auto mappings = dcpl.GetVirtualMappings();
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if (mappings.empty())
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throw JFJochException(JFJochExceptionCategory::HDF5,
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dataset_name + " is not a virtual dataset");
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for (const auto &mapping: mappings) {
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if (mapping.dataset.empty())
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throw JFJochException(JFJochExceptionCategory::HDF5,
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"VDS mapping has empty source dataset name");
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if (mapping.virtual_start.size() != 3)
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throw JFJochException(JFJochExceptionCategory::HDF5,
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"Only 3D image VDS mappings are supported");
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}
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return mappings;
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}
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std::string ResolveRelativeToMaster(const std::string &directory,
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const std::string &filename) {
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std::filesystem::path path(filename);
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if (path.is_absolute() || directory.empty())
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return filename;
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return (std::filesystem::path(directory) / path).string();
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}
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template<class T>
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void ReadVector(std::vector<T> &v,
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HDF5Object &file,
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const std::string &dataset_name,
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size_t image0,
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size_t nimages) {
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try {
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auto tmp = file.ReadOptVector<T>(dataset_name);
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if (tmp.size() <= nimages) {
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v.resize(image0 + nimages);
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for (int i = 0; i < tmp.size(); i++)
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v[image0 + i] = tmp[i];
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}
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} catch (JFJochException &e) {
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}
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}
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std::string removeSuffix(const std::string &s, const std::string &suffix) {
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if (s.ends_with(suffix))
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return s.substr(0, s.size() - suffix.size());
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return s;
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}
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std::string dataset_name(const std::string &path) {
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std::string file = std::filesystem::path(path).filename().string();
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file = removeSuffix(file, "_master.h5");
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// If previous suffix was not found, try removing this one
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file = removeSuffix(file, ".h5");
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return file;
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}
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bool ReadReflectionsFromGroup(HDF5Object &file,
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const std::string &image_group_name,
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std::vector<Reflection> &reflections) {
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if (!file.Exists("/entry/reflections") || !file.Exists(image_group_name))
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return false;
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auto h = file.ReadOptVector<int32_t>(image_group_name + "/h");
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auto k = file.ReadOptVector<int32_t>(image_group_name + "/k");
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auto l = file.ReadOptVector<int32_t>(image_group_name + "/l");
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auto predicted_x = file.ReadOptVector<float>(image_group_name + "/predicted_x");
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auto predicted_y = file.ReadOptVector<float>(image_group_name + "/predicted_y");
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auto obs_x = file.ReadOptVector<float>(image_group_name + "/observed_x");
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auto obs_y = file.ReadOptVector<float>(image_group_name + "/observed_y");
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auto d = file.ReadOptVector<float>(image_group_name + "/d");
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auto int_sum = file.ReadOptVector<float>(image_group_name + "/int_sum");
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auto int_err = file.ReadOptVector<float>(image_group_name + "/int_err");
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auto bkg = file.ReadOptVector<float>(image_group_name + "/background_mean");
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auto lp = file.ReadOptVector<float>(image_group_name + "/lp");
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auto partiality = file.ReadOptVector<float>(image_group_name + "/partiality");
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auto phi = file.ReadOptVector<float>(image_group_name + "/delta_phi");
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auto zeta = file.ReadOptVector<float>(image_group_name + "/zeta");
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auto image_scale_corr = file.ReadOptVector<float>(image_group_name + "/image_scale_corr");
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if (h.size() != l.size() || h.size() != k.size() || h.size() != d.size()
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|| h.size() != predicted_x.size() || h.size() != predicted_y.size()
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|| h.size() != int_sum.size() || h.size() != int_err.size() || h.size() != bkg.size())
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throw JFJochException(JFJochExceptionCategory::HDF5, "Wrong size of reflections dataset");
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for (size_t i = 0; i < h.size(); i++) {
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float lp_val = 0.0;
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if (lp.size() > i && lp[i] != 0.0f)
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lp_val = 1.0f / lp[i];
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float partiality_val = -1.0f;
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if (partiality.size() > i && partiality[i] >= 0.0f)
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partiality_val = partiality[i];
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float delta_phi_val = NAN;
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if (phi.size() > i)
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delta_phi_val = phi[i];
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float zeta_val = NAN;
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if (zeta.size() > i)
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zeta_val = zeta[i];
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float image_scale_corr_val = 1.0f; // Default is 1.0, if we don't know any better
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if (image_scale_corr.size() > i)
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image_scale_corr_val = image_scale_corr[i];
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float obs_x_val = NAN;
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float obs_y_val = NAN;
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if (obs_x.size() > i && obs_y.size() > i) {
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obs_x_val = obs_x[i];
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obs_y_val = obs_y[i];
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}
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Reflection r{
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.h = h.at(i),
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.k = k.at(i),
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.l = l.at(i),
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.delta_phi_deg = delta_phi_val,
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.predicted_x = predicted_x.at(i),
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.predicted_y = predicted_y.at(i),
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.observed_x = obs_x_val,
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.observed_y = obs_y_val,
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.d = d.at(i),
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.I = int_sum.at(i),
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.bkg = bkg.at(i),
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.sigma = int_err.at(i),
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.rlp = lp_val,
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.partiality = partiality_val,
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.zeta = zeta_val,
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.image_scale_corr = image_scale_corr_val
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};
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reflections.emplace_back(r);
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}
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return true;
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}
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template<class T>
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std::optional<T> ReadElementMasterFirst(HDF5Object &master_file,
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HDF5Object &source_file,
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const std::string &path,
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hsize_t master_image,
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hsize_t source_image) {
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if (master_file.Exists(path))
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return master_file.ReadElement<T>(path, master_image);
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if (source_file.Exists(path))
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return source_file.ReadElement<T>(path, source_image);
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return {};
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}
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template<class T>
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std::vector<T> ReadVectorMasterFirst(HDF5Object &master_file,
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HDF5Object &source_file,
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const std::string &path,
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const std::vector<hsize_t> &master_start,
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const std::vector<hsize_t> &source_start,
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const std::vector<hsize_t> &size) {
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if (master_file.Exists(path))
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return master_file.ReadOptVector<T>(path, master_start, size);
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if (source_file.Exists(path))
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return source_file.ReadOptVector<T>(path, source_start, size);
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return {};
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}
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void HDF5MetadataSource::ReadROIMetadata(HDF5ReadOnlyFile &file, JFJochReaderDataset &dataset) const {
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// ROI definitions live in /entry/roi_defs (kept separate from the per-image ROI
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// results in /entry/roi so that older readers, which iterate /entry/roi, are not
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// disturbed by the bitmap and definition subgroups).
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if (!file.Exists("/entry/roi_defs"))
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return;
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if (file.Exists("/entry/roi_defs/roi_map")) {
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auto dim = file.GetDimension("/entry/roi_defs/roi_map"); // [y, x]
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if (dim.size() == 2)
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dataset.roi_map = file.ReadOptVector<uint16_t>("/entry/roi_defs/roi_map",
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{0, 0}, {dim[0], dim[1]});
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}
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ROIDefinition defs;
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for (const auto &name: file.FindLeafs("/entry/roi_defs")) {
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const std::string base = "/entry/roi_defs/" + name;
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// Skip the roi_map bitmask; only named ROI subgroups carry a definition.
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if (name == "roi_map" || !file.Exists(base + "/type"))
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continue;
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dataset.roi_bit_index[name] = static_cast<uint16_t>(file.GetInt(base + "/bit_index"));
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const std::string type = file.GetString(base + "/type");
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if (type == "box")
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defs.boxes.emplace_back(name, file.GetInt(base + "/min_x_pxl"), file.GetInt(base + "/max_x_pxl"),
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file.GetInt(base + "/min_y_pxl"), file.GetInt(base + "/max_y_pxl"));
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else if (type == "circle")
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defs.circles.emplace_back(name, file.GetFloat(base + "/center_x_pxl"), file.GetFloat(base + "/center_y_pxl"),
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file.GetFloat(base + "/radius_pxl"));
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else if (type == "azim") {
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const float qmin = file.GetFloat(base + "/q_min_recipA");
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const float qmax = file.GetFloat(base + "/q_max_recipA");
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float phi_min = 0, phi_max = 0;
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if (file.Exists(base + "/phi_min_deg") && file.Exists(base + "/phi_max_deg")) {
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phi_min = file.GetFloat(base + "/phi_min_deg");
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phi_max = file.GetFloat(base + "/phi_max_deg");
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}
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const float d_min = (qmax == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmax;
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const float d_max = (qmin == 0.0f) ? 0.0f : 2.0f * static_cast<float>(PI) / qmin;
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defs.azimuthal.emplace_back(name, d_min, d_max, phi_min, phi_max);
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}
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}
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if (!defs.boxes.empty() || !defs.circles.empty() || !defs.azimuthal.empty())
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dataset.experiment.ROI().SetROI(defs);
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}
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HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filename,
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const DiffractionExperiment &default_experiment) {
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try {
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auto dataset = std::make_shared<JFJochReaderDataset>();
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master_file = std::make_shared<HDF5ReadOnlyFile>(filename);
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master_filename = filename;
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dataset->experiment = default_experiment;
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// Image-layout state is accumulated locally while parsing, then handed to image_locator_
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// at the end. format stays NoFile if the master carries no image data.
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FileWriterFormat format = FileWriterFormat::NoFile;
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HDF5DataSetLayout data_layout = HDF5DataSetLayout::CONTIGUOUS;
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std::vector<std::string> legacy_format_files;
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std::vector<HDF5VirtualDatasetMapping> vds_data_mappings;
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size_t images_per_file = 1;
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std::filesystem::path master_path(filename);
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std::string master_file_directory = master_path.parent_path().string();
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dataset->arm_date = master_file->GetString("/entry/start_time");
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dataset->experiment.FilePrefix(dataset_name(filename));
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// JFJochReader is always using int32_t
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dataset->experiment.BitDepthImage(32);
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dataset->experiment.PixelSigned(true);
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size_t image_size_x = 0;
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size_t image_size_y = 0;
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if (master_file->Exists("/entry/data/data")) {
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HDF5DataSet data_dataset(*master_file, "/entry/data/data");
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HDF5Dcpl dcpl(data_dataset);
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data_layout = dcpl.GetLayout();
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auto dim = GetDimension(*master_file, "/entry/data/data");
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number_of_images = dim[0];
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image_size_y = dim[1];
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image_size_x = dim[2];
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images_per_file = number_of_images;
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if (data_layout == HDF5DataSetLayout::VIRTUAL)
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vds_data_mappings = ReadVDSImageMappings(*master_file, "/entry/data/data");
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if (master_file->Exists("/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image"))
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dataset->efficiency = master_file->ReadVector<float>(
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"/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image");
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else
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dataset->efficiency = std::vector<float>(number_of_images, 1.0);
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if (master_file->Exists("/entry/roi"))
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dataset->roi = master_file->FindLeafs("/entry/roi");
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for (const auto &s: dataset->roi) {
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dataset->roi_max.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/max"));
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dataset->roi_sum.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum"));
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dataset->roi_sum_sq.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/sum_sq"));
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dataset->roi_npixel.emplace_back(master_file->ReadVector<int64_t>("/entry/roi/" + s + "/npixel"));
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dataset->roi_x.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/x"));
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dataset->roi_y.emplace_back(master_file->ReadVector<float>("/entry/roi/" + s + "/y"));
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}
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if (master_file->Exists("/entry/MX")) {
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if (master_file->Exists("/entry/MX/peakCountUnfiltered"))
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dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/peakCountUnfiltered");
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else
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dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/nPeaks");
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dataset->spot_count_low_res = master_file->ReadOptVector<float>("/entry/MX/peakCountLowRes");
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dataset->spot_count_indexed = master_file->ReadOptVector<float>("/entry/MX/peakCountIndexed");
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dataset->spot_count_ice_rings = master_file->ReadOptVector<float>("/entry/MX/peakCountIceRingRes");
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dataset->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
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dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
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dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
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dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
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// Master files write indexedLatticeCount; data files / the per-file MX
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// plugin use indexingLatticeCount. Accept either for backward compatibility.
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dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexedLatticeCount");
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if (dataset->indexing_lattice_count.empty())
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dataset->indexing_lattice_count = master_file->ReadOptVector<float>("/entry/MX/indexingLatticeCount");
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dataset->mosaicity_deg = master_file->ReadOptVector<float>("/entry/MX/mosaicity");
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dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
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dataset->image_scale_factor = master_file->ReadOptVector<float>("/entry/MX/imageScaleFactor");
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|
dataset->image_scale_cc = master_file->ReadOptVector<float>("/entry/MX/imageScaleCC");
|
|
dataset->image_scale_b = master_file->ReadOptVector<float>("/entry/MX/imageScaleBFactor");
|
|
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_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->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"));
|
|
dataset->experiment.TotalFlux(master_file->GetOptFloat("/entry/instrument/beam/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);
|
|
detector.SaturationLimit(master_file->GetInt("/entry/instrument/detector/saturation_value"));
|
|
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 = 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,
|
|
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, 1.5);
|
|
}
|
|
|
|
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(), 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->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_b.size() > image_number)
|
|
message.image_scale_b_factor = dataset->image_scale_b[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);
|
|
|
|
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 live in the same file as the image pixels,
|
|
// at the source-local index (the locator keeps the data-file handle cached).
|
|
const auto loc = ResolveMeta(static_cast<int64_t>(img));
|
|
HDF5Object *meta_file = loc.file.get();
|
|
const size_t meta_image_id = loc.local_index;
|
|
|
|
// ── reflections ──────────────────────────────────────────────────────
|
|
const std::string refl_group = fmt::format("/entry/reflections/image_{:06d}", meta_image_id);
|
|
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,
|
|
tmp_message);
|
|
|
|
return tmp_message.spots;
|
|
}
|