- Motivation no longer frames the format as serial-only: Jungfraujoch serves
both rotation and serial MX, and the two-layout rationale (per-image CXI
spots vs. dataset-wide NXreflections) is presented for both.
- Document the <prefix>_process.h5 reprocessing output of jfjoch_process: an
integrated-format master whose /entry/data/data is a VDS linking back to the
original images (all results, no image copies).
- Add a section on the header_appendix / image_appendix (user_data) mechanism:
how the free-form JSON flows through the start/image CBOR messages and how an
"hdf5" sub-object is persisted to /entry/user, with an example.
- Link the niggliClass row to International Tables for Crystallography A,
Table 3.1.3.1.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
New docs/HDF5.md documents the on-disk HDF5/NeXus format produced by the
writer: a FAIR/derived-metadata rationale (CXI-style per-image spot layout,
NXreflections for integration), the master/data-file layout and the three
NXmx format variants, the NXmx-standard fields that are populated, and every
Jungfraujoch extension group (/entry/MX, /entry/reflections, /entry/azint,
/entry/roi, /entry/image, /entry/profiling, /entry/detector, /entry/xfel,
detectorSpecific, calibration, fluorescence, user). Content is derived from
writer/HDF5NXmx.cpp and writer/HDF5DataFilePlugin*.cpp and cross-checked
against the NXmx and NXreflections definitions.
JFJOCH_WRITER.md's stale, partial structure table is replaced by a pointer to
the new doc; HDF5 is added to the Sphinx toctree.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8