// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute // SPDX-License-Identifier: GPL-3.0-only #include "HDF5DataFilePluginMX.h" #define RESERVE_IMAGES 1000 HDF5DataFilePluginMX::HDF5DataFilePluginMX(const StartMessage& msg) : max_spots(msg.max_spot_count) { } void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg) { bkg_estimate.reserve(RESERVE_IMAGES); if (max_spots == 0) return; spot_x.reserve(max_spots * RESERVE_IMAGES); spot_y.reserve(max_spots * RESERVE_IMAGES); spot_int.reserve(max_spots * RESERVE_IMAGES); spot_indexed.reserve(max_spots * RESERVE_IMAGES); spot_ice_ring.reserve(max_spots * RESERVE_IMAGES); spot_h.reserve(max_spots * RESERVE_IMAGES); spot_k.reserve(max_spots * RESERVE_IMAGES); spot_l.reserve(max_spots * RESERVE_IMAGES); spot_dist_ewald.reserve(max_spots * RESERVE_IMAGES); beam_corr_x.reserve(RESERVE_IMAGES); beam_corr_y.reserve(RESERVE_IMAGES); npeaks.reserve(RESERVE_IMAGES); strong_pixel_count.reserve(RESERVE_IMAGES); indexed.reserve(RESERVE_IMAGES); profile_radius.reserve(RESERVE_IMAGES); b_factor.reserve(RESERVE_IMAGES); indexed_lattice.reserve(9 * RESERVE_IMAGES); resolution_estimate.reserve(RESERVE_IMAGES); spot_count_total.reserve(RESERVE_IMAGES); spot_count_ice.reserve(RESERVE_IMAGES); spot_count_indexed.reserve(RESERVE_IMAGES); spot_count_low_res.reserve(RESERVE_IMAGES); } void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number) { if (msg.bkg_estimate.has_value()) bkg_estimate[image_number] = msg.bkg_estimate.value(); if (max_spots == 0) return; if (image_number >= max_image_number) { max_image_number = image_number; spot_x.resize(max_spots * (max_image_number + 1)); spot_y.resize(max_spots * (max_image_number + 1)); spot_int.resize(max_spots * (max_image_number + 1)); spot_indexed.resize(max_spots * (max_image_number + 1)); spot_ice_ring.resize(max_spots * (max_image_number + 1)); spot_h.resize(max_spots * (max_image_number + 1)); spot_k.resize(max_spots * (max_image_number + 1)); spot_l.resize(max_spots * (max_image_number + 1)); spot_dist_ewald.resize(max_spots * (max_image_number + 1)); indexed_lattice.resize((max_image_number + 1) * 9); } uint32_t spot_cnt = std::min(msg.spots.size(), max_spots); for (int i = 0; i < spot_cnt; i++) { spot_x[max_spots * image_number + i] = msg.spots[i].x; spot_y[max_spots * image_number + i] = msg.spots[i].y; spot_int[max_spots * image_number + i] = msg.spots[i].intensity; spot_indexed[max_spots * image_number + i] = msg.spots[i].indexed; spot_ice_ring[max_spots * image_number + i] = msg.spots[i].ice_ring; spot_h[max_spots * image_number + i] = msg.spots[i].h; spot_k[max_spots * image_number + i] = msg.spots[i].k; spot_l[max_spots * image_number + i] = msg.spots[i].l; spot_dist_ewald[max_spots * image_number + i] = msg.spots[i].dist_ewald_sphere; } npeaks[image_number] = spot_cnt; if (msg.strong_pixel_count.has_value()) strong_pixel_count[image_number] = msg.strong_pixel_count.value(); if (msg.indexing_result.has_value()) indexed[image_number] = msg.indexing_result.value(); if (msg.profile_radius.has_value()) profile_radius[image_number] = msg.profile_radius.value(); if (msg.b_factor.has_value()) b_factor[image_number] = msg.b_factor.value(); if (msg.resolution_estimate.has_value()) resolution_estimate[image_number] = msg.resolution_estimate.value(); if (msg.beam_corr_x) beam_corr_x[image_number] = msg.beam_corr_x.value(); if (msg.beam_corr_y) beam_corr_y[image_number] = msg.beam_corr_y.value(); if (msg.spot_count) spot_count_total[image_number] = msg.spot_count.value(); if (msg.spot_count_ice_rings) spot_count_ice[image_number] = msg.spot_count_ice_rings.value(); if (msg.spot_count_low_res) spot_count_low_res[image_number] = msg.spot_count_low_res.value(); if (msg.spot_count_indexed) spot_count_indexed[image_number] = msg.spot_count_indexed.value(); if (msg.indexing_lattice) { auto tmp = msg.indexing_lattice->GetVector(); for (int i = 0; i < 9; i++) indexed_lattice[image_number * 9 + i] = tmp[i]; } } void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) { HDF5Group(data_file, "/entry/MX").NXClass("NXcollection"); if (!spot_x.empty()) { data_file.SaveVector("/entry/MX/peakXPosRaw", spot_x, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakYPosRaw", spot_y, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakTotalIntensity", spot_int, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakIndexed", spot_indexed, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakIceRingRes", spot_ice_ring, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/nPeaks", npeaks.vec()); data_file.SaveVector("/entry/MX/peakH", spot_h, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakK", spot_k, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakL", spot_l, {(hsize_t) (max_image_number + 1), max_spots}); data_file.SaveVector("/entry/MX/peakDistEwaldSphere", spot_dist_ewald, {(hsize_t) (max_image_number + 1), max_spots}); } if (!strong_pixel_count.empty()) data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count.vec()); if (!spot_count_ice.empty()) data_file.SaveVector("/entry/MX/peakCountIceRingRes", spot_count_ice.vec()); if (!spot_count_indexed.empty()) data_file.SaveVector("/entry/MX/peakCountIndexed", spot_count_indexed.vec()); if (!spot_count_low_res.empty()) data_file.SaveVector("/entry/MX/peakCountLowRes", spot_count_low_res.vec()); if (!spot_count_total.empty()) data_file.SaveVector("/entry/MX/peakCountUnfiltered", spot_count_total.vec()); if (!indexed.empty()) data_file.SaveVector("/entry/MX/imageIndexed", indexed.vec()); if (!indexed_lattice.empty()) data_file.SaveVector("/entry/MX/latticeIndexed", indexed_lattice, {(hsize_t) (max_image_number + 1), 9}); if (!bkg_estimate.empty()) data_file.SaveVector("/entry/MX/bkgEstimate", bkg_estimate.vec()); if (!profile_radius.empty()) data_file.SaveVector("/entry/MX/profileRadius", profile_radius.vec())->Units("Angstrom^-1"); if (!b_factor.empty()) data_file.SaveVector("/entry/MX/bFactor", b_factor.vec())->Units("Angstrom^2"); if (!beam_corr_x.empty()) data_file.SaveVector("/entry/MX/beam_corr_x", beam_corr_x.vec())->Units("pixel"); if (!beam_corr_y.empty()) data_file.SaveVector("/entry/MX/beam_corr_y", beam_corr_y.vec())->Units("pixel"); if (!resolution_estimate.empty()) data_file.SaveVector("/entry/MX/resolutionEstimate", resolution_estimate.vec())->Units("Angstrom"); }