leonarski_fandClaude Opus 5
ea667cb306
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--scale did none of the ice handling the run that wrote the _process.h5 had
done, so re-scaling a stored dataset silently produced a different - and
flatteringly more complete - answer than the pipeline it was meant to
reproduce. Three separate gaps:
* --detect-ice-rings was accepted and ignored. The --scale block returns
before the line that applies it.
* Reflections were never flagged as sitting on an ice ring, so the per-image
scale fit included them. The flag is not stored per reflection, so it has
to be recomputed from the resolution.
* RotationScaleMerge was constructed with the ice half-width hardcoded to
zero. That is what turns a resolution into a ring index, so every ice test
inside the merge was a no-op whatever was passed to it.
The CC1/2 ring test that decides which rings to drop moves into
FindDecorrelatedIceRings, shared with the full pipeline so both reach the same
verdict on the same data, and --scale now re-merges with the mask the way the
pipeline does. The stills branch re-runs only the merge: the scaling has
already been applied to the reflections and repeating it would compound it.
Measured on a rotation dataset with three decorrelated rings, --scale went
from 8765 unique / 36.3% completeness / R-meas 18.5% / <I/sig> 1.1 to
7638 / 31.6% / 18.0% / 1.3, against the full pipeline's 7692 / 31.8% / 17.9% /
1.3 - the reported completeness had been inflated by reflections the pipeline
drops. The full pipeline is bit-identical across the refactor.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.