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