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Jungfraujoch/reader/JFJochHDF5Reader.cpp
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v1.0.0-rc.140 (#50) 
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.

* jfjoch_broker: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection
* jfjoch_broker: Minor bug fixes for rare conditions

Reviewed-on: #50
2026-04-29 21:40:22 +02:00

841 lines
38 KiB
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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochHDF5Reader.h"
#include "spdlog/fmt/fmt.h"
#include "../image_analysis/bragg_integration/CalcISigma.h"
#include "../image_analysis/spot_finding/SpotUtils.h"
#include "../common/GridScanSettings.h"
inline std::pair<gemmi::CrystalSystem, char> parse_niggli_class(int64_t val) {
switch (val) {
case 1: return {gemmi::CrystalSystem::Cubic, 'F'};
case 2: return {gemmi::CrystalSystem::Trigonal, 'R'};
case 3: return {gemmi::CrystalSystem::Cubic, 'P'};
case 5: return {gemmi::CrystalSystem::Cubic, 'I'};
case 4: return {gemmi::CrystalSystem::Trigonal, 'R'};
case 6: return {gemmi::CrystalSystem::Tetragonal, 'I'};
case 7: return {gemmi::CrystalSystem::Tetragonal, 'I'};
case 9: return {gemmi::CrystalSystem::Trigonal, 'R'};
case 10: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 11: return {gemmi::CrystalSystem::Tetragonal, 'P'};
case 12: return {gemmi::CrystalSystem::Hexagonal, 'P'};
case 13: return {gemmi::CrystalSystem::Orthorhombic, 'C'};
case 15: return {gemmi::CrystalSystem::Tetragonal, 'I'};
case 16: return {gemmi::CrystalSystem::Orthorhombic, 'F'};
case 14: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 17: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 18: return {gemmi::CrystalSystem::Tetragonal, 'I'};
case 19: return {gemmi::CrystalSystem::Orthorhombic, 'I'};
case 20: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 21: return {gemmi::CrystalSystem::Tetragonal, 'P'};
case 22: return {gemmi::CrystalSystem::Hexagonal, 'P'};
case 23: return {gemmi::CrystalSystem::Orthorhombic, 'C'};
case 24: return {gemmi::CrystalSystem::Trigonal, 'R'};
case 25: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 26: return {gemmi::CrystalSystem::Orthorhombic, 'F'};
case 27: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 28: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 29: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 30: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 31: return {gemmi::CrystalSystem::Triclinic, 'P'};
case 32: return {gemmi::CrystalSystem::Orthorhombic, 'P'};
case 40: return {gemmi::CrystalSystem::Orthorhombic, 'C'};
case 35: return {gemmi::CrystalSystem::Monoclinic, 'P'};
case 36: return {gemmi::CrystalSystem::Orthorhombic, 'C'};
case 33: return {gemmi::CrystalSystem::Monoclinic, 'P'};
case 38: return {gemmi::CrystalSystem::Orthorhombic, 'C'};
case 34: return {gemmi::CrystalSystem::Monoclinic, 'P'};
case 42: return {gemmi::CrystalSystem::Orthorhombic, 'I'};
case 41: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 37: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 39: return {gemmi::CrystalSystem::Monoclinic, 'C'};
case 44: return {gemmi::CrystalSystem::Triclinic, 'P'};
default: return {gemmi::CrystalSystem::Triclinic, 'P'};
}
}
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;
}
template <class T>
void JFJochHDF5Reader::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 = path;
int pos = file.rfind('/');
if (pos != std::string::npos)
file = file.substr(pos+1);
file = removeSuffix(file, "_master.h5");
// If previous suffix was not found, try removing this one
file = removeSuffix(file, ".h5");
return file;
}
void JFJochHDF5Reader::ReadFile(const std::string& filename) {
std::unique_lock ul(hdf5_mutex);
try {
auto dataset = std::make_shared<JFJochReaderDataset>();
master_file = std::make_shared<HDF5ReadOnlyFile>(filename);
dataset->experiment = default_experiment;
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"))
format = FileWriterFormat::NXmxVDS;
else if (master_file->Exists("/entry/data/data_000001")) {
format = FileWriterFormat::NXmxLegacy;
}
if (format == FileWriterFormat::NXmxVDS ) {
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 (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->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
dataset->mosaicity_deg = master_file->ReadOptVector<float>("/entry/MX/mosaicity");
dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
}
if (master_file->Exists("/entry/image"))
dataset->max_value = master_file->ReadOptVector<int64_t>("/entry/image/max_value");
} else if (format == FileWriterFormat::NXmxLegacy) {
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 = master_file->GetLinkedFileName(dname);
if (!directory.empty())
fname = fmt::format("{}/{}", directory.string(), fname);
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->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")
dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFT);
else if (indexing == "ffbidx")
dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
dataset->scale_factor = master_file->ReadOptVector<float>("/entry/MX/imageScaleFactor");
}
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);
dataset->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / master_file->GetFloat("/entry/instrument/beam/incident_wavelength"));
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 = std::vector<uint32_t>(image_size_x * image_size_y);
dataset->pixel_mask = PixelMask(mask_tmp);
}
dataset->experiment.ImagesPerTrigger(number_of_images);
SetStartMessage(dataset);
} catch (const std::exception& e) {
master_file = {};
number_of_images = 0;
SetStartMessage({});
throw;
}
}
uint64_t JFJochHDF5Reader::GetNumberOfImages() const {
std::unique_lock ul(hdf5_mutex);
return number_of_images;
}
CompressedImage JFJochHDF5Reader::LoadImageDataset(std::vector<uint8_t> &tmp, HDF5Object &file, hsize_t number) {
std::vector<hsize_t> start = {static_cast<hsize_t>(number), 0, 0};
const std::string dataset_name = "/entry/data/data";
HDF5DataSet dataset(file, dataset_name);
HDF5DataSpace dataspace(dataset);
HDF5DataType datatype(dataset);
HDF5Dcpl dcpl(dataset);
if (dataspace.GetNumOfDimensions() != 3)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"/entry/data/data dataset must be 3D");
auto dim = dataspace.GetDimensions();
CompressionAlgorithm algorithm = CompressionAlgorithm::NO_COMPRESSION;
auto chunk_size = dcpl.GetChunking();
if ((chunk_size.size() == 3) && (chunk_size[0] == 1) && (chunk_size[1] == dim[1]) && (chunk_size[2] == dim[2])) {
dataset.ReadDirectChunk(tmp, start);
algorithm = dcpl.GetCompression();
} else {
dataset.ReadVectorToU8(tmp, start, {1, dim[1], dim[2]});
algorithm = CompressionAlgorithm::NO_COMPRESSION;
}
if (datatype.IsFloat())
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,"Float datasets not supported at this time");
return {tmp, dim[2], dim[1],
CalcImageMode(datatype.GetElemSize(), datatype.IsFloat(), datatype.IsSigned()),
algorithm};
}
std::pair<std::shared_ptr<HDF5ReadOnlyFile>, uint32_t> JFJochHDF5Reader::GetImageLocation(int64_t image_number) {
if (image_number >= number_of_images || image_number < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Image out of bounds");
uint32_t image_id;
std::shared_ptr<HDF5ReadOnlyFile> data_file;
if (format == FileWriterFormat::NXmxLegacy) {
uint32_t file_id = image_number / images_per_file;
image_id = image_number % images_per_file;
data_file = std::make_shared<HDF5ReadOnlyFile>(legacy_format_files.at(file_id));
} else {
image_id = image_number;
data_file = master_file;
}
return {std::move(data_file), image_id};
}
std::shared_ptr<JFJochReaderRawImage> JFJochHDF5Reader::GetRawImage(int64_t image_number) {
std::unique_lock ul(hdf5_mutex);
if (!master_file)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Cannot load image if file not loaded");
auto [source_file, image_id] = GetImageLocation(image_number);
auto ret = std::make_shared<JFJochReaderRawImage>();
ret->image = LoadImageDataset(ret->image_buffer, *source_file, image_id);
return ret;
}
bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
DataMessage &message,
std::vector<uint8_t> &buffer,
int64_t image_number,
bool update_dataset) {
std::unique_lock ul(hdf5_mutex);
if (!dataset)
return {};
if (!master_file)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Cannot load image if file not loaded");
auto [source_file, image_id] = GetImageLocation(image_number);
message.image = LoadImageDataset(buffer, *source_file, image_id);
message.number = image_number;
auto spot_count_opt = source_file->ReadElement<uint32_t>("/entry/MX/nPeaks", image_id);
if (spot_count_opt.has_value() && spot_count_opt.value() > 0) {
size_t spot_count = spot_count_opt.value();
auto spot_x = source_file->ReadVector<float>(
"/entry/MX/peakXPosRaw",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_y = source_file->ReadVector<float>(
"/entry/MX/peakYPosRaw",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_intensity = source_file->ReadVector<float>(
"/entry/MX/peakTotalIntensity",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_indexed = source_file->ReadOptVector<uint8_t>(
"/entry/MX/peakIndexed",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_ice = source_file->ReadOptVector<uint8_t>(
"/entry/MX/peakIceRingRes",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_h = source_file->ReadOptVector<int32_t>(
"/entry/MX/peakH",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_k = source_file->ReadOptVector<int32_t>(
"/entry/MX/peakK",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_l = source_file->ReadOptVector<int32_t>(
"/entry/MX/peakL",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto spot_dist_ewald_sphere = source_file->ReadOptVector<float>(
"/entry/MX/peakDistEwaldSphere",
{(hsize_t) image_id, 0},
{1, spot_count}
);
auto geom = dataset->experiment.GetDiffractionGeometry();
for (int i = 0; i < spot_count; i++) {
auto x = spot_x.at(i);
auto y = spot_y.at(i);
auto d = geom.PxlToRes(x, y);
SpotToSave s{
.x = x,
.y = y,
.intensity = spot_intensity.at(i),
.d_A = d,
.image = image_number
};
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);
message.spots.emplace_back(s);
}
if (source_file->Exists("/entry/MX/peakCountUnfiltered"))
message.spot_count = source_file->ReadElement<uint32_t>("/entry/MX/peakCountUnfiltered", image_id);
else
message.spot_count = source_file->ReadElement<uint32_t>("/entry/MX/nPeaks", image_id);
if (source_file->Exists("/entry/MX/peakCountIceRingRes"))
message.spot_count_ice_rings = source_file->ReadElement<uint32_t>("/entry/MX/peakCountIceRingRes", image_id);
if (source_file->Exists("/entry/MX/peakCountLowRes"))
message.spot_count_low_res = source_file->ReadElement<uint32_t>("/entry/MX/peakCountLowRes", image_id);
if (source_file->Exists("/entry/MX/peakCountIndexed"))
message.spot_count_indexed = source_file->ReadElement<uint32_t>("/entry/MX/peakCountIndexed", image_id);
GenerateSpotPlot(message, 1.5);
}
if (source_file->Exists("/entry/MX/integratedReflections"))
message.integrated_reflections = source_file->ReadElement<float>("/entry/MX/integratedReflections", image_id);
if (!dataset->az_int_bin_to_q.empty()) {
if (dataset->azimuthal_bins == 0)
message.az_int_profile = source_file->ReadOptVector<float>(
"/entry/azint/image",
{(hsize_t) image_id, 0},
{1, dataset->az_int_bin_to_q.size()}
);
else {
message.az_int_profile.resize(dataset->azimuthal_bins * dataset->q_bins, 0);
message.az_int_profile = source_file->ReadOptVector<float>(
"/entry/azint/image",
{(hsize_t) image_id, 0, 0},
{1, dataset->azimuthal_bins, dataset->q_bins}
);
}
}
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->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->indexing_result.size() > image_number
&& dataset->indexing_result[image_number] != 0
&& source_file->Exists("/entry/MX")
&& source_file->Exists("/entry/MX/latticeIndexed")) {
std::vector<float> tmp = source_file->ReadVector<float>(
"/entry/MX/latticeIndexed",
{(hsize_t) image_id, 0},
{1, 9}
);
message.indexing_lattice = CrystalLattice(tmp);
std::optional<uint32_t> niggli_opt = source_file->ReadElement<uint32_t>("/entry/MX/niggli_class", image_id);
if (niggli_opt) {
auto symm_info = parse_niggli_class(niggli_opt.value());
message.lattice_type = LatticeMessage{
.centering = symm_info.second,
.niggli_class = static_cast<int64_t>(niggli_opt.value()),
.crystal_system = symm_info.first,
};
}
}
std::string image_group_name = fmt::format("/entry/reflections/image_{:06d}", image_id);
if (source_file->Exists("/entry/reflections") && source_file->Exists(image_group_name)) {
auto h = source_file->ReadOptVector<int32_t>(image_group_name + "/h");
auto k = source_file->ReadOptVector<int32_t>(image_group_name + "/k");
auto l = source_file->ReadOptVector<int32_t>(image_group_name + "/l");
auto predicted_x = source_file->ReadOptVector<float>(image_group_name + "/predicted_x");
auto predicted_y = source_file->ReadOptVector<float>(image_group_name + "/predicted_y");
auto d = source_file->ReadOptVector<float>(image_group_name + "/d");
auto int_sum = source_file->ReadOptVector<float>(image_group_name + "/int_sum");
auto int_err = source_file->ReadOptVector<float>(image_group_name + "/int_err");
auto bkg = source_file->ReadOptVector<float>(image_group_name + "/background_mean");
auto lp = source_file->ReadOptVector<float>(image_group_name + "/lp");
auto partiality = source_file->ReadOptVector<float>(image_group_name + "/partiality");
auto phi = source_file->ReadOptVector<float>(image_group_name + "/delta_phi");
auto zeta = source_file->ReadOptVector<float>(image_group_name + "/zeta");
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())
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];
Reflection r{
.h = h.at(i),
.k = k.at(i),
.l = l.at(i),
.delta_phi_deg = delta_phi_val,
.predicted_x = predicted_x.at(i),
.predicted_y = predicted_y.at(i),
.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
};
message.reflections.emplace_back(r);
}
CalcISigma(message);
CalcWilsonBFactor(message, !message.b_factor.has_value());
}
return true;
}
void JFJochHDF5Reader::Close() {
std::unique_lock ul(hdf5_mutex);
master_file = {};
number_of_images = 0;
legacy_format_files.clear();
SetStartMessage({});
}
std::optional<GoniometerAxis> JFJochHDF5Reader::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 JFJochHDF5Reader::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};
}
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