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John Henry BealeandClaude Sonnet 5 5841a31d1b Add crystfel/0.12.0 Millepede detector calibration pipeline

Staged pipeline (coarse -> level0 -> level1 -> tilt -> camera_length) for
detector geometry refinement using CrystFEL's Millepede-based align_detector,
replacing the old crystfel/0.10.2 detector-shift workflow. Each stage
iterates indexamajig + align_detector to convergence before advancing, and
the run produces four diagnostic plots (per-stage convergence, per-panel
refinement support, indexed pattern count, unit-cell before/after).

The coarse stage falls back to crystfel/0.10.2's predict_refine/det_shift
(dead in 0.12.0, always reports 0.000/0.000) to bring badly-off starting
geometries within Millepede's ~100-300um working range before handing off,
since this crystfel/0.12.0 build has no --big-errors flag to relax its
default reject threshold. Validated end-to-end on p23523's previously-failing
geometry (99.4% reject rate without coarse pre-alignment).

crystfel_split_mille.py and millepede-refine are the supporting indexing/
alignment helpers the pipeline reuses; replot_pipeline_v2.py regenerates the
four plots from an already-completed run's on-disk data, for recovery if a
run crashes after the expensive cluster work is done.

SESSION_SUMMARY.md documents the investigation findings behind this work.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

2026-09-02 08:23:14 +02:00

cta

added extra bit so that all BS files are used when making the lists.

2026-06-15 10:54:28 +02:00

data

added comments to submit_results_clara.sh

2025-06-13 14:04:33 +02:00

det_calib

Add crystfel/0.12.0 Millepede detector calibration pipeline

2026-09-02 08:23:14 +02:00

edge_scan

updated scipy import - now numpy