leonarski_fandClaude Opus 4.8
1caa57744a
Split the naming: rugnux = data-processing subsystem, Jungfraujoch = streaming/acquisition. Executables jfjoch_process -> rugnux (source tools/rugnux_cli.cpp) and jfjoch_scale -> rugnux_scale; the processing library process/ -> rugnux/ with class/target JFJochProcess -> Rugnux (JFJochProcessObserver -> RugnuxObserver, JFJochProcessCommandLine -> RugnuxCommandLine). Doc JFJOCH_PROCESS.md -> RUGNUX.md, reconciled with the live usage message (drop dead -P/--partiality, -w/--wedge; --process-as-stills -> --force-still; add the real rot3d scaling knobs). New docs/NAMING.md explains both names, with pronunciation and a note on Romansh. rugnux now scales and merges rotation data automatically (implicit -M); stills still require an explicit -M. jfjoch_viewer and its classes keep their names (rename deferred); only their references to the renamed library are updated. The _process.h5 output suffix and ProcessConfig/Mode/Result are kept. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
1.5 KiB
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 |
|---|---|---|
lyso_rotation_master.h5 |
lysozyme rotation series (~1800 images) | yes (LFS) |
lyso_rotation_master.h5 (plus its _data_NNNNNN.h5 files) is fetched by git lfs pull and
drives Rugnux_LysoRotation. 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.