The full processing workflow no longer lives in the CLIs. New process/JFJochProcess
encapsulates it for jfjoch_process, jfjoch_azint and (later) the viewer:
- ProcessMode {AzimuthalIntegration, FullAnalysis}; ProcessConfig carries run control
(range, threads, output prefix, spot finding, rotation + scaling options, reference
data) while the DiffractionExperiment carries all algorithm settings.
- Run() executes setup -> optional two-pass rotation pre-pass -> parallel per-image loop
(std::thread) -> optional scaling/merging post-pass -> NXmxIntegrated _process.h5 that
links back to the original images. ProcessResult returns stats + merge text.
- Cancel() / std::atomic<bool> (receiver style), checked between images; the CLIs install
a SIGINT handler that calls it (fixes the previous Ctrl+C gap), the viewer will use the
same hook. JFJochProcessObserver streams progress / per-image results for a live GUI.
jfjoch_process.cpp and jfjoch_azint.cpp are now thin: argument parsing + experiment
configuration, then JFJochProcess::Run + stats printing. Behaviour and usage messages
are unchanged.
Adds JFJochProcessTest (azimuthal integration round-trip, no-output run, pre-cancel) over
a small generated dataset.
Verified: tests/jfjoch_test [HDF5] (83 cases / 1854 assertions); jfjoch_azint and
jfjoch_process run end-to-end on lyso_test (azint 20 images; full analysis recovers the
lysozyme cell at 25% indexing).
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
