flyscan_data`#

A flyscan NeXus master file (*.hdf) holds its primary product in the /entry/flyscan_data group: the in-scan image substack plus the per-frame motor positions. That group is written at run end only when the area-detector image file is reachable from the master file’s directory through the image-files symlink ({detector}_files, e.g. eiger2_files).

If the symlink was missing or mis-shaped at run end, the master will have /entry/images (the external link) but no /entry/flyscan_data, and a WARNING will be in the run log. Once the symlink is fixed, recover the group with the repair tool.

Step 1 – fix the image-files symlink#

From the directory that contains the master file, create the symlink pointing at the workstation mount where the detector’s image files are visible. For an eiger2 detector whose files are mounted at /net/s3data/export/sector3/s3ida/XRD/:

cd /path/to/your/run/directory
ln -s /net/s3data/export/sector3/s3ida/XRD/ eiger2_files
ls -l eiger2_files          # should show 'eiger2_files -> .../XRD/'
ls eiger2_files/ | head     # should list at least one entry

The symlink must map directly to the image-file root. A common mistake is creating a directory eiger2_files/ that contains a child symlink (e.g. eiger2_files/XRD -> .../XRD); that adds an extra path level and the external link will not resolve.

Step 2 – run the repair tool#

id3c-flyscan-repair /path/to/your/run/20260618-...-S00024-....hdf

The tool:

reads the run uid from the master’s /entry/entry_identifier;
locates the area-detector file from the master’s /entry/images external link (or, if absent, composes it from the ad_file_path / ad_file_name start metadata);
recomputes the per-frame pairing from the authoritative area-detector file; and
writes /entry/flyscan_data (replacing any existing copy) and sets /entry@default = "flyscan_data".

Preview without writing#

id3c-flyscan-repair --dry-run /path/to/.../master.hdf

Point at a specific area-detector file#

If the master cannot resolve the area-detector path (or you want to override it), pass it explicitly:

id3c-flyscan-repair --external-file /net/.../XRDS4_..._000001.h5 \
    /path/to/.../master.hdf

Add -v for INFO-level logging.

When repair is not possible#

The tool exits non-zero and explains the cause if:

the master has no run uid (/entry/entry_identifier);
the area-detector file cannot be located or does not resolve (most often the symlink from Step 1 is still wrong);
the area-detector file is not openable; or
pairing produces zero in-scan frames.

The repair reads only the area-detector file (the lossless, authoritative per-frame source). It never falls back to a lossy source, so a repaired /entry/flyscan_data is always the full-count result.

Repair a flyscan master file missing /entry/flyscan_data#