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Brings in the following enhancements from smx_beamtime: - New clustering tools (cluster2, index2) - Geometry refinement capabilities - Cake plot preparation utilities - Reflection subsampling and clustering in small_cell indexing - Various powder plotting enhancements These changes enable advanced small-cell crystallography workflows including geometry refinement and multi-stage clustering.
This script is no longer needed and has been superseded by other tools. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
These experimental indexing and clustering algorithms are specific to the smx_findexer workflow and have been moved to that dedicated branch. The smx_small_cell_processing branch now contains only general small-cell features: - geometry_refiner.py: Geometry refinement functionality - powder_refine_geometry.py: Powder-based geometry refinement tool - powder_util.py: General powder pattern utilities - small_cell.py: Core small-cell processing with reflection subsampling The experimental clustering/indexing algorithms (cluster2.py, index2.py) are now on the smx_findexer branch along with the smx_statistics worker that supports them. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
…ents This allows users to stop plotting after a specified number of experiments, useful when working with large datasets. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Remove the superseded angle_histogram feature entirely: the angle() and create_pairwise_plots() top-level functions, the per-experiment and per-reflection angle accumulation code, and the post-loop histogram plot. Also remove import itertools (only used by that code) and the duplicate import numpy as np. Fix n_max off-by-one: change i>n_max to i>=n_max so that n_max=10 processes exactly 10 experiments (indices 0-9).
…ounter, relaxed tolerances
…mx_small_cell_processing
dwpaley
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Apr 17, 2026
Replace flex.sorted with numpy.partition for the Tukey hinge indices, dropping the cost of the #3 hottest function in indexing. Preserves the exact Tukey hinge index logic (numpy.percentile is not equivalent for many array sizes).
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Experimental PR 3: accumulated changes from NERSC