111 lines
4.4 KiB
C++
111 lines
4.4 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(size_t in_max_spots) : max_spots(in_max_spots) {}
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void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg) {
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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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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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mosaicity.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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spot_count_rings.reserve(RESERVE_IMAGES);
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bkg_estimate.reserve(RESERVE_IMAGES);
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resolution_estimate.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 (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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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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}
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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.mosaicity.has_value())
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mosaicity[image_number] = msg.mosaicity.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.bkg_estimate.has_value())
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bkg_estimate[image_number] = msg.bkg_estimate.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.spot_count_in_rings)
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spot_count_rings[image_number] = msg.spot_count_in_rings.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/nPeaks", npeaks.vec());
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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_rings.empty())
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data_file.SaveVector("/entry/MX/nPeaksRingFiltered", spot_count_rings.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 (!mosaicity.empty())
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data_file.SaveVector("/entry/MX/mosaicity", mosaicity.vec());
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if (!b_factor.empty())
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data_file.SaveVector("/entry/MX/bFactor", b_factor.vec());
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if (!resolution_estimate.empty())
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data_file.SaveVector("/entry/MX/resolutionEstimate", resolution_estimate.vec());
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}
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