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Merge branch 'worktree-agent-a4c58d76a0be29dd6' into grid-scan-integration

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# Conflicts:
#	rugnux/rugnux_cli.cpp
This commit is contained in:
leonarski_f
2026-09-08 07:55:31 +02:00
parent 36a082c2f8 c08e37443a
commit cb1d88dd4d
50 changed files with 2125 additions and 72 deletions
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reader/HDF5MetadataSource.cpp
+47
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@@ -798,6 +798,53 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
}
if (master_file->Exists("/entry/MX")) {
// The analysis that wrote the file, kept as provenance only. It is deliberately not pushed
// onto the experiment: what a stored file was produced by is not what the next run should
// do, and letting it decide would be exactly the implicitness the mode exists to remove.
dataset->file_analysis_mode =
AnalysisModeFromName(master_file->GetString("/entry/MX/analysis_mode", ""));
// Grid-scan crystals: parallel 1-D datasets, one per field, all of length N. nx sets N and
// the rest are read into that length, so a file written by a build that had one field
// fewer still re-opens with the crystals it does have.
if (master_file->Exists("/entry/MX/crystals/nx")) {
auto nx = master_file->ReadOptVector<float>("/entry/MX/crystals/nx");
auto ny = master_file->ReadOptVector<float>("/entry/MX/crystals/ny");
auto x_um = master_file->ReadOptVector<float>("/entry/MX/crystals/xUm");
auto y_um = master_file->ReadOptVector<float>("/entry/MX/crystals/yUm");
auto image_number = master_file->ReadOptVector<int64_t>("/entry/MX/crystals/imageNumber");
auto major_um = master_file->ReadOptVector<float>("/entry/MX/crystals/majorUm");
auto minor_um = master_file->ReadOptVector<float>("/entry/MX/crystals/minorUm");
auto angle_deg = master_file->ReadOptVector<float>("/entry/MX/crystals/angleDeg");
auto score = master_file->ReadOptVector<float>("/entry/MX/crystals/score");
auto ice_score = master_file->ReadOptVector<float>("/entry/MX/crystals/iceScore");
auto res_A = master_file->ReadOptVector<float>("/entry/MX/crystals/resA");
auto n_images = master_file->ReadOptVector<int64_t>("/entry/MX/crystals/nImages");
const size_t n = nx.size();
auto f = [n](const std::vector<float> &v, size_t i) { return v.size() == n ? v[i] : 0.0f; };
auto i64 = [n](const std::vector<int64_t> &v, size_t i) {
return v.size() == n ? v[i] : int64_t(0);
};
dataset->grid_crystals.resize(n);
for (size_t i = 0; i < n; i++) {
auto &c = dataset->grid_crystals[i];
c.nx = nx[i];
c.ny = f(ny, i);
c.x_um = f(x_um, i);
c.y_um = f(y_um, i);
c.image_number = i64(image_number, i);
c.major_um = f(major_um, i);
c.minor_um = f(minor_um, i);
c.angle_deg = f(angle_deg, i);
c.score = f(score, i);
c.ice_score = f(ice_score, i);
c.res_A = f(res_A, i);
c.n_images = i64(n_images, i);
}
}
auto indexing = master_file->GetString("/entry/MX/indexing_algorithm", "none");
if (indexing == "fft" || indexing == "FFT (CUDA)" || indexing == "FFT (FFTW)")
dataset->experiment.IndexingAlgorithm(IndexingAlgorithmEnum::FFT);