80 lines
3.5 KiB
C++
80 lines
3.5 KiB
C++
// Copyright (2019-2024) Paul Scherrer Institute
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#include "HDF5DataFilePluginMX.h"
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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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HDF5Group(data_file, "/entry/MX").NXClass("NXcollection");
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HDF5DataSpace data_space_spots({1, max_spots}, {H5S_UNLIMITED, max_spots});
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HDF5Dcpl dcpl_spots;
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dcpl_spots.SetChunking({1, max_spots});
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data_set_spot_x = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakXPosRaw", HDF5DataType(0.0f),
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data_space_spots, dcpl_spots);
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data_set_spot_y = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakYPosRaw", HDF5DataType(0.0f),
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data_space_spots, dcpl_spots);
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data_set_spot_int = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakTotalIntensity", HDF5DataType(0.0f),
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data_space_spots, dcpl_spots);
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data_set_spot_indexed = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakIndexed", HDF5DataType(1, false),
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data_space_spots, dcpl_spots);
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}
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void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
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if (max_spots == 0)
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return;
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size_t image_number = msg.number;
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if (image_number >= max_image_number) {
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max_image_number = image_number;
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data_set_spot_x->SetExtent({max_image_number+1, max_spots});
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data_set_spot_y->SetExtent({max_image_number+1, max_spots});
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data_set_spot_int->SetExtent({max_image_number+1, max_spots});
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data_set_spot_indexed->SetExtent({max_image_number+1, max_spots});
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npeaks.resize(max_image_number + 1);
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strong_pixel_count.resize(max_image_number + 1);
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indexed.resize(max_image_number + 1);
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indexed_lattice.resize((max_image_number + 1) * 9);
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}
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std::vector<float> spot_x(max_spots), spot_y(max_spots), spot_intensity(max_spots);
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std::vector<uint8_t> spot_indexed(max_spots);
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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[i] = msg.spots[i].x;
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spot_y[i] = msg.spots[i].y;
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spot_intensity[i] = msg.spots[i].intensity;
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spot_indexed[i] = msg.spots[i].indexed;
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}
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data_set_spot_x->WriteVec(spot_x, {image_number, 0}, {1, max_spots});
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data_set_spot_y->WriteVec(spot_y, {image_number, 0}, {1, max_spots});
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data_set_spot_int->WriteVec(spot_intensity, {image_number, 0}, {1, max_spots});
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data_set_spot_indexed->WriteVec(spot_indexed, {image_number, 0}, {1, max_spots});
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npeaks[image_number] = spot_cnt;
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strong_pixel_count[image_number] = msg.strong_pixel_count;
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indexed[image_number] = msg.indexing_result;
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if (msg.indexing_lattice.size() == 9) {
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for (int i = 0; i < 9; i++)
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indexed_lattice[image_number * 9 + i] = msg.indexing_lattice[i];
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}
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}
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void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
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if (!npeaks.empty())
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data_file.SaveVector("/entry/MX/nPeaks", npeaks);
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if (!strong_pixel_count.empty())
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data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count);
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if (!indexed.empty())
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data_file.SaveVector("/entry/MX/imageIndexed", indexed);
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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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}
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