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Improvements before MAX IV test

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leonarski_f
2024-04-25 20:11:58 +02:00
parent 2c8e1fd83d
commit ea70b27e85
80 changed files with 1835 additions and 1781 deletions
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75
writer/HDF5DataFilePluginMX.cpp
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@@ -1,6 +1,7 @@
// Copyright (2019-2024) Paul Scherrer Institute
#include "HDF5DataFilePluginMX.h"
#define RESERVE_IMAGES 1000
HDF5DataFilePluginMX::HDF5DataFilePluginMX(size_t in_max_spots) : max_spots(in_max_spots) {}
@@ -8,55 +9,47 @@ void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg)
if (max_spots == 0)
return;
HDF5Group(data_file, "/entry/MX").NXClass("NXcollection");
spot_x.reserve(max_spots * RESERVE_IMAGES);
spot_y.reserve(max_spots * RESERVE_IMAGES);
spot_int.reserve(max_spots * RESERVE_IMAGES);
npeaks.reserve(RESERVE_IMAGES);
strong_pixel_count.reserve(RESERVE_IMAGES);
indexed.reserve(RESERVE_IMAGES);
indexed_lattice.reserve(9 * RESERVE_IMAGES);
HDF5DataSpace data_space_spots({1, max_spots}, {H5S_UNLIMITED, max_spots});
HDF5Dcpl dcpl_spots;
dcpl_spots.SetChunking({1, max_spots});
data_set_spot_x = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakXPosRaw", HDF5DataType(0.0f),
data_space_spots, dcpl_spots);
data_set_spot_y = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakYPosRaw", HDF5DataType(0.0f),
data_space_spots, dcpl_spots);
data_set_spot_int = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakTotalIntensity", HDF5DataType(0.0f),
data_space_spots, dcpl_spots);
data_set_spot_indexed = std::make_unique<HDF5DataSet>(data_file, "/entry/MX/peakIndexed", HDF5DataType(1, false),
data_space_spots, dcpl_spots);
indexing_drift_beam_center_x_pxl.reserve(RESERVE_IMAGES);
indexing_drift_beam_center_y_pxl.reserve(RESERVE_IMAGES);
indexing_drift_detector_distance_mm.reserve(RESERVE_IMAGES);
}
void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number) {
if (max_spots == 0)
return;
size_t image_number = msg.number;
if (image_number >= max_image_number) {
max_image_number = image_number;
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});
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));
npeaks.resize(max_image_number + 1);
strong_pixel_count.resize(max_image_number + 1);
indexed.resize(max_image_number + 1);
indexed_lattice.resize((max_image_number + 1) * 9);
}
std::vector<float> spot_x(max_spots), spot_y(max_spots), spot_intensity(max_spots);
std::vector<uint8_t> spot_indexed(max_spots);
indexing_drift_beam_center_x_pxl.resize(max_image_number + 1);
indexing_drift_beam_center_y_pxl.resize(max_image_number + 1);
indexing_drift_detector_distance_mm.resize(max_image_number + 1);
}
uint32_t spot_cnt = std::min(msg.spots.size(), max_spots);
for (int i = 0; i < spot_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;
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;
}
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});
npeaks[image_number] = spot_cnt;
strong_pixel_count[image_number] = msg.strong_pixel_count;
@@ -65,15 +58,33 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg) {
for (int i = 0; i < 9; i++)
indexed_lattice[image_number * 9 + i] = msg.indexing_lattice[i];
}
if (msg.corr_beam_x_pxl) {
indexing_drift_beam_center_x_pxl[image_number] = msg.corr_beam_x_pxl.value();
indexing_drift_beam_center_y_pxl[image_number] = msg.corr_beam_y_pxl.value();
indexing_drift_detector_distance_mm[image_number] = msg.corr_det_dist_mm.value();
}
}
void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
if (!npeaks.empty())
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/nPeaks", npeaks);
if (!strong_pixel_count.empty())
data_file.SaveVector("/entry/MX/strongPixels", strong_pixel_count);
}
if (!indexed.empty())
data_file.SaveVector("/entry/MX/imageIndexed", indexed);
if (!indexed_lattice.empty())
data_file.SaveVector("/entry/MX/latticeIndexed", indexed_lattice, {(hsize_t) (max_image_number + 1), 9});
if (!indexing_drift_beam_center_x_pxl.empty()) {
data_file.SaveVector("/entry/MX/indexingDriftBeamCenterX", indexing_drift_beam_center_x_pxl)->Units("pxl");
data_file.SaveVector("/entry/MX/indexingDriftBeamCenterY", indexing_drift_beam_center_y_pxl)->Units("pxl");
data_file.SaveVector("/entry/MX/indexingDriftDetectorDistance", indexing_drift_detector_distance_mm)->Units("mm");
}
}