leonarski_fandClaude Opus 5
84d14696b1
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Three changes to the rotation path, all in the same first-pass block. Input. Rugnux now holds a JFJochReader rather than the concrete HDF5 reader, so a sweep can come from a directory of miniCBF as well as from a master file; the CLI picks by looking at the file. Only the _process.h5 image links need the concrete reader and they ask for it by dynamic_cast - there is nothing for a virtual dataset to point at in a directory of CBFs, so that file writes its images instead of linking to them. --mode scale refuses a CBF sweep, there being no stored reflections to re-scale. Search bound. A reference cell longer than the FFT bound cannot be represented by the search meant to find it, so the run reported "found no lattice" - strictly worse than not giving the cell at all. Raise the bound to cover a given cell (margin 1.3, as DIALS uses when a cell is known), and raise it in the long-axis rescue too, where it costs nothing: that pass already coarsens the resolution to 3.5 A, which shrinks the transform by 1.75x, so spending it back on reach leaves the rescue at 1.14x the standard pass. The rescue's constrained re-index gets a pool wide enough to hold what the coarse pass recovered, which it did not before. ROTATION ONLY - stills fire the FFT once per image across every worker and routinely run with a known cell, so widening the transform there would cost the whole serial run for nothing. Clamped rather than throwing: the rescue can recover an implausible axis, and a bad candidate must not take the run down with it. Axis sign. The rotation-axis sign is a convention the input often cannot settle - a miniCBF header names the axis but gives no direction, and an NXmx vector is only meaningful together with the detector orientation, which nothing here reads. It is decidable from the data, though: the wrong sign does not index at all (measured on one sweep, changing nothing else: every frame indexed one way, none the other). So after a poor first pass, try the other sign and keep whichever indexes more validation frames - the same count the scheme choice already uses, so no new metric and no new threshold. It flips the AXIS, not the angles, because prediction reads the axis too; the decision then holds for the rest of the run. Runs before the long-axis rescue, since with the sign wrong every candidate lattice is wrong. Only after a poor pass, so a correctly-signed file costs nothing, and spot finding is not repeated. 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.