216 lines
9.8 KiB
C++
216 lines
9.8 KiB
C++
// Copyright (2019-2023) Paul Scherrer Institute
|
|
|
|
#include "HDF5DataFile.h"
|
|
#include "../compression/JFJochCompressor.h"
|
|
|
|
HDF5DataFile::HDF5DataFile(const std::string &in_filename, int64_t width, int64_t height,
|
|
int64_t pixel_depth_byte, bool is_signed, const std::vector<float>& in_rad_int_bin_to_q,
|
|
CompressionAlgorithm compression,
|
|
size_t in_max_spots) : data_type(pixel_depth_byte, is_signed),
|
|
max_spots(in_max_spots), rad_int_bin_to_q(in_rad_int_bin_to_q) {
|
|
max_image_number = 0;
|
|
nimages = 0;
|
|
|
|
if (max_spots > 256)
|
|
throw JFJochException(JFJochExceptionCategory::ArrayOutOfBounds, "Max spot count must be less than 256 for performance reasons");
|
|
|
|
filename = in_filename;
|
|
|
|
xpixel = width;
|
|
ypixel = height;
|
|
|
|
dcpl.SetCompression(compression, pixel_depth_byte, JFJochBitShuffleCompressor::DefaultBlockSize);
|
|
dcpl.SetChunking( {1, ypixel, xpixel});
|
|
if (is_signed) {
|
|
if (pixel_depth_byte == 2)
|
|
dcpl.SetFillValue16(INT16_MIN);
|
|
else
|
|
dcpl.SetFillValue32(INT32_MIN);
|
|
}
|
|
}
|
|
|
|
HDF5DataFile::~HDF5DataFile() {
|
|
if (data_file) {
|
|
HDF5Group group_exp(*data_file, "/entry/jungfrau");
|
|
group_exp.NXClass("NXcollection");
|
|
|
|
group_exp.SaveVector("info", jf_info);
|
|
group_exp.SaveVector("timestamp", timestamp);
|
|
group_exp.SaveVector("storage_cell", storage_cell);
|
|
group_exp.SaveVector("exptime", exptime);
|
|
group_exp.SaveVector("receiverAqDevDelay", receiver_aq_dev_delay);
|
|
|
|
data_file->SaveVector("/entry/result/strongPixelCount", strong_pixel_count);
|
|
if (!resolution_estimation.empty())
|
|
data_file->SaveVector("/entry/result/resolutionEstimation", resolution_estimation);
|
|
}
|
|
}
|
|
|
|
void HDF5DataFile::CreateFile() {
|
|
SetupSWMRFile();
|
|
|
|
data_file = std::make_unique<HDF5File>(filename, false, true);
|
|
data_set = std::make_unique<HDF5DataSet>(*data_file, "/entry/data/data");
|
|
data_set_spot_x = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakXPosRaw");
|
|
data_set_spot_y = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakYPosRaw");
|
|
data_set_spot_int = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakTotalIntensity");
|
|
data_set_spot_indexed = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/peakIndexed");
|
|
data_set_spot_npeaks = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/nPeaks");
|
|
data_set_xfel_event_code = std::make_unique<HDF5DataSet>(*data_file, "/entry/xfel/eventCode");
|
|
data_set_xfel_pulseid = std::make_unique<HDF5DataSet>(*data_file, "/entry/xfel/pulseID");
|
|
data_set_indexed = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/imageIndexed");
|
|
data_set_indexed_lattice = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/latticeIndexed");
|
|
if (!rad_int_bin_to_q.empty())
|
|
data_set_az_int = std::make_unique<HDF5DataSet>(*data_file, "/entry/result/azimIntegration");
|
|
}
|
|
|
|
void HDF5DataFile::Write(const DataMessage &msg, uint64_t image_number) {
|
|
std::lock_guard<std::mutex> lock(hdf5_mutex);
|
|
bool new_file = false;
|
|
|
|
if (!data_file) {
|
|
CreateFile();
|
|
new_file = true;
|
|
}
|
|
|
|
if (new_file || (static_cast<int64_t>(image_number) > max_image_number)) {
|
|
max_image_number = image_number;
|
|
data_set->SetExtent({max_image_number+1, ypixel, xpixel});
|
|
data_set_spot_x->SetExtent({max_image_number+1, max_spots});
|
|
data_set_spot_y->SetExtent({max_image_number+1, max_spots});
|
|
data_set_spot_int->SetExtent({max_image_number+1, max_spots});
|
|
data_set_spot_indexed->SetExtent({max_image_number+1, max_spots});
|
|
data_set_spot_npeaks->SetExtent({max_image_number+1});
|
|
data_set_xfel_pulseid->SetExtent({max_image_number+1});
|
|
data_set_xfel_event_code->SetExtent({max_image_number+1});
|
|
data_set_indexed->SetExtent({max_image_number + 1});
|
|
data_set_indexed_lattice->SetExtent({max_image_number + 1, 9});
|
|
if (!rad_int_bin_to_q.empty())
|
|
data_set_az_int->SetExtent({max_image_number + 1, rad_int_bin_to_q.size()});
|
|
|
|
strong_pixel_count.resize(max_image_number + 1);
|
|
jf_info.resize(max_image_number + 1);
|
|
receiver_aq_dev_delay.resize(max_image_number + 1);
|
|
timestamp.resize(max_image_number + 1);
|
|
exptime.resize(max_image_number + 1);
|
|
storage_cell.resize(max_image_number + 1);
|
|
|
|
if (msg.resolution_estimation)
|
|
resolution_estimation.resize(max_image_number + 1);
|
|
}
|
|
|
|
nimages++;
|
|
data_set->WriteDirectChunk(msg.image.data, msg.image.size, {image_number, 0, 0});
|
|
|
|
uint32_t cnt = std::min(msg.spots.size(), max_spots);
|
|
|
|
std::vector<float> spot_x(max_spots), spot_y(max_spots), spot_intensity(max_spots);
|
|
std::vector<uint8_t> spot_indexed(max_spots);
|
|
for (int i = 0; i < cnt; i++) {
|
|
spot_x[i] = msg.spots[i].x;
|
|
spot_y[i] = msg.spots[i].y;
|
|
spot_intensity[i] = msg.spots[i].intensity;
|
|
spot_indexed[i] = msg.spots[i].indexed;
|
|
}
|
|
data_set_spot_x->WriteVec(spot_x, {image_number, 0}, {1, max_spots});
|
|
data_set_spot_y->WriteVec(spot_y, {image_number, 0}, {1, max_spots});
|
|
data_set_spot_int->WriteVec(spot_intensity, {image_number, 0}, {1, max_spots});
|
|
data_set_spot_indexed->WriteVec(spot_indexed, {image_number, 0}, {1, max_spots});
|
|
data_set_spot_npeaks->WriteScalar(cnt, {image_number});
|
|
|
|
data_set_xfel_event_code->WriteScalar(msg.xfel_event_code, {image_number});
|
|
data_set_xfel_pulseid->WriteScalar(msg.xfel_bunch_id, {image_number});
|
|
|
|
data_set_indexed->WriteScalar((uint8_t) msg.indexing_result, {image_number});
|
|
if (msg.indexing_lattice.size() == 9)
|
|
data_set_indexed_lattice->WriteVec(msg.indexing_lattice, {image_number, 0}, {1, 9});
|
|
|
|
strong_pixel_count[image_number] = msg.strong_pixel_count;
|
|
jf_info[image_number] = msg.jf_info;
|
|
receiver_aq_dev_delay[image_number] = msg.receiver_aq_dev_delay;
|
|
timestamp[image_number] = msg.timestamp;
|
|
storage_cell[image_number] = msg.storage_cell;
|
|
exptime[image_number] = msg.exptime;
|
|
|
|
if (msg.resolution_estimation)
|
|
resolution_estimation[image_number] = msg.resolution_estimation.value();
|
|
|
|
if (!msg.az_int_profile.empty() && (msg.az_int_profile.size() == rad_int_bin_to_q.size()))
|
|
data_set_az_int->WriteVec(msg.az_int_profile, {image_number, 0}, {1, rad_int_bin_to_q.size()});
|
|
|
|
auto now_time = std::chrono::system_clock::now();
|
|
auto time_diff = now_time - (last_flush + swmr_flush_period);
|
|
if (time_diff.count() >= 0) {
|
|
data_set->Flush();
|
|
data_set_spot_x->Flush();
|
|
data_set_spot_y->Flush();
|
|
data_set_spot_int->Flush();
|
|
data_set_spot_indexed->Flush();
|
|
data_set_spot_npeaks->Flush();
|
|
data_set_xfel_event_code->Flush();
|
|
data_set_xfel_pulseid->Flush();
|
|
data_set_indexed->Flush();
|
|
data_set_indexed_lattice->Flush();
|
|
if (!rad_int_bin_to_q.empty())
|
|
data_set_az_int->Flush();
|
|
|
|
last_flush = now_time;
|
|
}
|
|
}
|
|
|
|
HDF5DataFileStatistics HDF5DataFile::GetStatistics() const {
|
|
HDF5DataFileStatistics ret;
|
|
ret.max_image_number = max_image_number;
|
|
ret.total_images = nimages;
|
|
ret.filename = filename;
|
|
return ret;
|
|
}
|
|
|
|
size_t HDF5DataFile::GetNumImages() const {
|
|
return nimages;
|
|
}
|
|
|
|
void HDF5DataFile::SetupSWMRFile() {
|
|
HDF5File data_file_local(filename, true, true);
|
|
HDF5Group(data_file_local, "/entry").NXClass("NXentry");
|
|
HDF5Group(data_file_local, "/entry/data").NXClass("NXdata");
|
|
|
|
HDF5Group(data_file_local, "/entry/xfel").NXClass("NXcollection");
|
|
HDF5Group(data_file_local, "/entry/result").NXClass("NXcollection");
|
|
|
|
HDF5DataSpace data_space({1, ypixel, xpixel}, {H5S_UNLIMITED, ypixel, xpixel});
|
|
HDF5DataSet(data_file_local, "/entry/data/data", data_type, data_space, dcpl);
|
|
|
|
HDF5DataSpace data_space_spots({1, max_spots}, {H5S_UNLIMITED, max_spots});
|
|
HDF5Dcpl dcpl_spots;
|
|
dcpl_spots.SetChunking({1, max_spots});
|
|
HDF5DataSet(data_file_local, "/entry/result/peakXPosRaw", HDF5DataType(0.0f), data_space_spots, dcpl_spots);
|
|
HDF5DataSet(data_file_local, "/entry/result/peakYPosRaw", HDF5DataType(0.0f), data_space_spots, dcpl_spots);
|
|
HDF5DataSet(data_file_local, "/entry/result/peakTotalIntensity", HDF5DataType(0.0f), data_space_spots, dcpl_spots);
|
|
HDF5DataSet(data_file_local, "/entry/result/peakIndexed", HDF5DataType(1, false), data_space_spots, dcpl_spots);
|
|
|
|
HDF5DataSpace data_space_linear({2}, {H5S_UNLIMITED});
|
|
HDF5Dcpl dcpl_linear;
|
|
dcpl_linear.SetChunking({1});
|
|
HDF5DataSet(data_file_local, "/entry/result/nPeaks", HDF5DataType(4, false), data_space_linear, dcpl_linear).SetExtent({1});
|
|
HDF5DataSet(data_file_local, "/entry/xfel/pulseID", HDF5DataType(8, false), data_space_linear, dcpl_linear).SetExtent({1});
|
|
HDF5DataSet(data_file_local, "/entry/xfel/eventCode", HDF5DataType(4, false), data_space_linear, dcpl_linear).SetExtent({1});
|
|
HDF5DataSet(data_file_local, "/entry/result/imageIndexed", HDF5DataType(1, false), data_space_linear, dcpl_linear).SetExtent({1});
|
|
|
|
HDF5DataSpace data_space_lattice({1, 9}, {H5S_UNLIMITED, 9});
|
|
HDF5Dcpl dcpl_lattice;
|
|
dcpl_lattice.SetChunking({1, 9});
|
|
HDF5DataSet(data_file_local, "/entry/result/latticeIndexed", HDF5DataType(0.0f), data_space_lattice, dcpl_lattice);
|
|
|
|
if (!rad_int_bin_to_q.empty()) {
|
|
data_file_local.SaveVector("/entry/result/azimIntegrationBinToQ", rad_int_bin_to_q);
|
|
|
|
HDF5DataSpace data_space_rad_int({1, rad_int_bin_to_q.size()}, {H5S_UNLIMITED, rad_int_bin_to_q.size()});
|
|
HDF5Dcpl dcpl_rad_int;
|
|
dcpl_rad_int.SetChunking({1, rad_int_bin_to_q.size()});
|
|
HDF5DataSet(data_file_local, "/entry/result/azimIntegration", HDF5DataType(0.0f), data_space_rad_int,
|
|
dcpl_rad_int);
|
|
}
|
|
last_flush = std::chrono::system_clock::now();
|
|
}
|