leonarski_f
84228bf8be
* jfjoch_broker: Optional per-dataset authentication - statistics, images and plots can require a bearer token, which jfjoch_viewer supports. * jfjoch_viewer: Dark mode and a theme-matched colour scheme, a magnifier panel, and simpler contrast and background controls. * Rugnux: Multiple performance improvements on GPU and CPU (CPU-only processing up to 40% faster, faster image decoding on ARM), with unchanged results. * Rugnux: `--model` rigid-body refinement runs on the GPU, and the model-validation check is faster and more reliable. * Rugnux: Improved scaling and merging - error model, outlier rejection, absorption correction and French-Wilson amplitudes now agree more closely with XDS and ctruncate. * Rugnux: Improved integration - radial background on powder and ice rings, crowded rotation data keep their reflections, and CPU-only builds integrate large unit cells as GPU builds do. * Rugnux: More robust detector geometry - measured beam centre, X-ray bandwidth and goniometer rate, and geometry refinement accepted only on significant evidence. * Rugnux: Merged files are written in the standard setting, or in the setting of a reference MTZ, structure-factor mmCIF or model, with its free-R flags. * Rugnux: Richer report - ice and powder rings, further lattices, superstructure candidates and mosaicity, with warnings worded as prompts to check. * Rugnux: Clear error messages when a data set needs more GPU or host memory than is available. Reviewed-on: #83 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Large reference test datasets (git-LFS)
The [large] Catch tests in tests/ run the full analysis/processing pipeline over real
JUNGFRAU datasets that are too big to keep as ordinary git blobs. They are tracked with
git-LFS (see the tests/data/*.h5 rule in the top-level .gitattributes).
These files are not required to build or to run the normal test suite: every test that
needs them resolves the path through jfjoch_test::LargeDataFile() (tests/TestData.h) and
SKIP()s when the file is absent or is still an unfetched LFS pointer. jfjoch_test also
prints, at start-up, whether this directory is populated.
Fetching
git lfs install
git lfs pull # or: git lfs pull --include "tests/data/*.h5"
Datasets
| File | Dataset | Shipped |
|---|---|---|
rotation_master.h5 |
protein rotation series (~1800 images) | yes (LFS) |
rotation_master.h5 (plus its _data_NNNNNN.h5 files) is fetched by git lfs pull and
drives Rugnux_Rotation, and its first four frames Portable_Rugnux_RotationWedge (the
[portable] end-to-end check, which skips on the macOS/Windows jobs because they do not pull LFS). A separate serial dataset is intentionally not shipped
to keep the repository small — the rotation series can be run in serial mode (full analysis
without rotation indexing) to exercise that path. To add your own dataset, drop the master + its
data files here as real files (not symlinks, if you intend to commit them via LFS); the master
references its data files by relative name, so keep them side by side.