leonarski_fandClaude Opus 5
bb5aaca68e
--export-unmerged now writes one row per reflection with its partials summed, which is how a rotation dataset is normally handed to a scaling program. The previous behaviour is still available as --export-unmerged-partials. Partials made the file's usefulness depend on the reading program's partial-assembly settings. On an orthorhombic case only 31% of partial sets passed aimless's default PARTIALS test, so it merged 2% of the file: multiplicity 4.7 against our own 12.4, CC1/2 0.788, and CC against our merged intensities 0.806. Summed, aimless uses 89% of the file and rejects nothing: multiplicity 12.5, CC1/2 0.931, completeness 96.1 to 98.0, pointless Laue confidence 0.669 to 0.792, CC 0.848. The other two test crystals are ties overall and win their outer shells, and the anomalous signal comes out stronger from the fulls. iotbx.merging_statistics, which never assembled partials at all, now reports real merging statistics rather than statistics of parts. Events are grouped by Combine()'s own rule so the file and the merge assemble exactly the same reflections; the sum is plain with variances in quadrature and no partiality division, which reproduces the merge's full times FRACTIONCALC to a few percent. Per-part metadata is combined on a partiality-weighted centroid rather than an intensity-weighted one: 8-41% of events have parts summing to zero or less, where intensity weights are undefined or sign-flipped, and 10-21% of intensity-weighted centroids fall outside the event's own frame range. Events below --min-partiality are not written. Declaring a reflection whose rocking curve caught a thousandth of itself as a complete measurement gives a scaling program noise with a small sigma and it weights it heavily; there is no partial test to catch it once it is a full. This is the same constant already applied to the same quantity in the merge, and it is what takes the orthorhombic case from CC 0.219 to 0.848. --min-partiality 0 writes every event. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P
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.