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v1.0.0-rc.81

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leonarski_f
2025-09-21 19:27:51 +02:00
parent 3ded4cd3ce
commit 5d9d2de4a4
243 changed files with 3401 additions and 935 deletions
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18
reader/JFJochHDF5Reader.cpp
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@@ -52,6 +52,7 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
try {
auto dataset = std::make_shared<JFJochReaderDataset>();
master_file = std::make_unique<HDF5ReadOnlyFile>(filename);
dataset->experiment.DetectIceRings(true);
std::filesystem::path fsPath(filename);
dataset->experiment.FilePrefix(dataset_name(filename));
@@ -171,6 +172,10 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFBIDX);
}
auto ring_current_A = master_file->GetOptFloat("/entry/source/current");
if (ring_current_A) dataset->experiment.RingCurrent_mA(ring_current_A.value() * 1000.0);
dataset->experiment.DetectIceRings(master_file->GetOptBool("/entry/instrument/detector/detectorSpecific/detect_ice_rings").value_or(false));
dataset->experiment.PoniRot1_rad(master_file->GetOptFloat("/entry/instrument/detector/transformations/rot1").value_or(0.0));
dataset->experiment.PoniRot2_rad(master_file->GetOptFloat("/entry/instrument/detector/transformations/rot2").value_or(0.0));
dataset->experiment.PoniRot3_rad(master_file->GetOptFloat("/entry/instrument/detector/transformations/rot3").value_or(0.0));
@@ -254,6 +259,14 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
}
}
// Read fluorescence spectrum if present
if (master_file->Exists("/entry/instrument/fluorescence")) {
auto energy = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/energy");
auto data = master_file->ReadOptVector<float>("/entry/instrument/fluorescence/data");
if (!energy.empty() && energy.size() == data.size())
dataset->experiment.FluorescenceSpectrum(XrayFluorescenceSpectrum(energy, data));
}
auto detector_name = master_file->GetString("/entry/instrument/detector/description");
DetectorSetup detector = DetDECTRIS(image_size_x, image_size_y, detector_name, {});
@@ -431,6 +444,11 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
s.ice_ring = (spot_ice.at(i) != 0);
message.spots.emplace_back(s);
}
message.spot_count = source_file->ReadElement<uint32_t>("/entry/MX/peakCountUnfiltered", image_id);
message.spot_count_ice_rings = source_file->ReadElement<uint32_t>("/entry/MX/peakCountIceRingRes", image_id);
message.spot_count_low_res = source_file->ReadElement<uint32_t>("/entry/MX/peakCountLowRes", image_id);
message.spot_count_indexed = source_file->ReadElement<uint32_t>("/entry/MX/peakCountIndexed", image_id);
}
if (!dataset->az_int_bin_to_q.empty()) {