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v1.0.0-rc.85

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This commit is contained in:
leonarski_f
2025-09-24 22:52:31 +02:00
parent 961d6b42a0
commit 5bb8898a0e
146 changed files with 258 additions and 202 deletions
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56
reader/JFJochHDF5Reader.cpp
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@@ -75,12 +75,23 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
dataset->efficiency = master_file->ReadVector<float>(
"/entry/instrument/detector/detectorSpecific/data_collection_efficiency_image");
dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/nPeaks");
dataset->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
if (master_file->Exists("/entry/MX")) {
if (master_file->Exists("/entry/MX/peakCountUnfiltered"))
dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/peakCountUnfiltered");
else
dataset->spot_count = master_file->ReadOptVector<float>("/entry/MX/nPeaks");
dataset->spot_count_low_res = master_file->ReadOptVector<float>("/entry/MX/peakCountLowRes");
dataset->spot_count_indexed = master_file->ReadOptVector<float>("/entry/MX/peakCountIndexed");
dataset->spot_count_ice_rings = master_file->ReadOptVector<float>("/entry/MX/peakCountIceRing");
dataset->indexing_result = master_file->ReadOptVector<float>("/entry/MX/imageIndexed");
dataset->bkg_estimate = master_file->ReadOptVector<float>("/entry/MX/bkgEstimate");
dataset->resolution_estimate = master_file->ReadOptVector<float>("/entry/MX/resolutionEstimate");
dataset->profile_radius = master_file->ReadOptVector<float>("/entry/MX/profileRadius");
dataset->b_factor = master_file->ReadOptVector<float>("/entry/MX/bFactor");
}
if (master_file->Exists("/entry/image"))
dataset->max_value = master_file->ReadOptVector<int64_t>("/entry/image/max_value");
} else if (master_file->Exists("/entry/data/data_000001")) {
@@ -123,11 +134,28 @@ void JFJochHDF5Reader::ReadFile(const std::string& filename) {
data_file, "/entry/detector/data_collection_efficiency_image",
number_of_images, fimages);
}
if (data_file.Exists("/entry/MX")) {
ReadVector(dataset->spot_count,
data_file, "/entry/MX/nPeaks",
number_of_images, fimages);
if (data_file.Exists("/entry/MX/peakCountUnfiltered"))
ReadVector(dataset->spot_count,
data_file, "/entry/MX/peakCountUnfiltered",
number_of_images, fimages);
else
ReadVector(dataset->spot_count,
data_file, "/entry/MX/nPeaks",
number_of_images, fimages);
ReadVector(dataset->spot_count_ice_rings,
data_file, "/entry/MX/peakCountIceRingRes",
number_of_images, fimages);
ReadVector(dataset->spot_count_low_res,
data_file, "/entry/MX/peakCountLowRes",
number_of_images, fimages);
ReadVector(dataset->spot_count_indexed,
data_file, "/entry/MX/peakCountIndexed",
number_of_images, fimages);
ReadVector(dataset->indexing_result,
data_file, "/entry/MX/imageIndexed",
@@ -370,9 +398,11 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
message.image = LoadImageDataset(buffer, *source_file, image_id);
message.number = image_number;
if ((dataset->spot_count.size() > image_number)
&& (dataset->spot_count[image_number] > 0)) {
size_t spot_count = std::lround(dataset->spot_count[image_number]);
auto spot_count_opt = source_file->ReadElement<uint32_t>("/entry/MX/nPeaks", image_id);
if (spot_count_opt.has_value() && spot_count_opt.value() > 0) {
size_t spot_count = spot_count_opt.value();
auto spot_x = source_file->ReadVector<float>(
"/entry/MX/peakXPosRaw",
{(hsize_t) image_id, 0},

4
reader/JFJochHttpReader.cpp
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@@ -99,6 +99,10 @@ std::shared_ptr<JFJochReaderDataset> JFJochHttpReader::UpdateDataset_i() {
dataset->bkg_estimate = GetPlot_i("bkg_estimate");
dataset->spot_count = GetPlot_i("spot_count");
dataset->spot_count_ice_rings = GetPlot_i("spot_count_ice");
dataset->spot_count_low_res = GetPlot_i("spot_count_low_res");
dataset->spot_count_indexed = GetPlot_i("spot_count_indexed");
dataset->indexing_result = GetPlot_i("indexing_rate");
dataset->profile_radius = GetPlot_i("profile_radius");
dataset->b_factor = GetPlot_i("b_factor");

4
reader/JFJochReaderDataset.h
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@@ -27,6 +27,10 @@ struct JFJochReaderDataset {
size_t q_bins = 0;
std::vector<float> spot_count;
std::vector<float> spot_count_indexed;
std::vector<float> spot_count_low_res;
std::vector<float> spot_count_ice_rings;
std::vector<float> indexing_result;
std::vector<float> bkg_estimate;
std::vector<float> resolution_estimate;