9 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 4.8	4cda46c6b0	Wire BraggIntegrationEngine into the pipeline; deterministic prediction; integration_model API ... Replace the free functions BraggIntegrate2D/ProfileIntegrate2D with the BraggIntegrationEngine (CPU/GPU) as the live integrator. - IndexAndRefine no longer holds the integrator: ProcessImage takes a per-worker BraggIntegrateFn callback (ProcessImage is called concurrently by the shared IndexAndRefine, so the stateful engine must not be a member). - WithoutFPGA/jfjoch_process: owns a GPU engine when a GPU is present, else CPU, and passes the GPU-resident preprocessed buffer so integration runs on-device. - AfterFPGA: forces CPU and integrates straight off the assembled CompressedImage via a templated per-pixel sampler - only the reflection-disk pixels are read, no whole-image copy (the FPGA host runs up to 36 GB/s). Sampler maps type min/max to INT32_MIN/INT32_MAX on read; special/saturation only, no +/-1 band. - Remove BraggIntegrate2D/ProfileIntegrate2D and their test; keep IntegratorMode. Prediction: buffer up to 20000 candidates but return the 10000 closest to the Ewald sphere (deterministic partial_sort on |dist_ewald|, hkl tiebreak) instead of the GPU atomic-fill order. Serialized output stays <=10000, so the frame transport headroom and its CBOR guard are unchanged. integration_model exposed via OpenAPI (bragg_integration_settings schema, /config/bragg_integration PUT/GET, added to jfjoch_settings and jfjoch_statistics) and the frontend (BraggIntegrationSettings dropdown). Regenerated C++/TS clients and redoc. Validated old-vs-new on all 18 /data/rotation_test crystals: indexing rate and space group bit-identical; ISa/CC identical on 16/18 (one improved, EcwtAL500 ISa 0.0->6.7); new CompressedImage-vs-buffer and GPU-vs-CPU parity tests pass. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-03 14:35:20 +02:00
leonarski_fandClaude Opus 4.8	711216e116	scan_result: short "ice" field + global Bravais lattice type ... Two per-object scan_result API tweaks (C++ internal names unchanged): - Rename the per-image scan_result field ice_ring_score -> ice (it is serialized once per image, so keep it short). Only the OpenAPI property and its regenerated C++/TS clients change; the DataMessage/EndMessage/CBOR/HDF5 field stays ice_ring_score, and the ice_ring_score plot_type enum is untouched. - Add a global rotation_bravais string (crystal-system letter + centering, e.g. "tP", "cF", "hR") to scan_result, alongside rotation_unit_cell / rotation_crystal_lattice. It comes from the RotationIndexer result (LatticeSearchResult system+centering) via the receiver, formatted by a new BravaisSymbol() helper in ScanResult.h. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-07-02 21:00:12 +02:00
leonarski_fandClaude Fable 5	5737d2e1d0	ice score: measure against a smooth whole-profile background, not shoulders ... The score's baseline was two adjacent shoulder bins with a bin-overlap bug - the ring's edge bins were counted in both the ring and the shoulder, since GetMeanValueOfBins is inclusive. At the typical (coarse) azint binning (dq ~ 0.05 in q, wider than the 0.03 ring half-width) a shoulder is only ~1 bin, so the ratio was noisy and poorly separated. Replace it with the ring intensity over a smooth whole-profile background: a running median of the non-ice bins, interpolated under each ring. Clean crystals now sit at ~1.0 and ice separates far more cleanly on /data/rotation_test: cytC 1.06->1.03, lysoC 1.23->2.77, EP_cs_01-17 1.67->4.51 (max 11.4). A z-score / abnormality probability was tried but is uninformative here - with many photons any real ice ring is highly significant, so the useful discriminator is the ice magnitude (this ratio), noted in CPU_DATA_ANALYSIS.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 17:05:39 +02:00
leonarski_fandClaude Fable 5	f422988cd2	ice score: per-image ice-ring indicator plumbed through all layers ... A single per-image ice_ring_score - the strongest hexagonal-ice ring band/shoulder intensity ratio from the azimuthal profile (1 = no ice) - computed in the CPU and FPGA analysis paths and the offline azint worker, then plumbed through every layer: DataMessage/EndMessage, CBOR (frame_serialize), HDF5 (/entry/MX/iceRingScore), ScanResult, receiver plots (PlotType::IceRingScore), the OpenAPI spec (plot_type + scan_result schema, with regenerated broker/gen and frontend client) and OpenAPIConvert, the reader + Qt viewer, and the React frontend plot. Documented in docs/CBOR.md, docs/HDF5.md and docs/CPU_DATA_ANALYSIS.md, with the general "add a per-image quantity" recipe added to CLAUDE.md. Verified in HDF5: lysoC (weak ice) mean 1.23, EP_cs_01-17 (heavy ice) mean 1.67 / max 2.23. This is a monitoring quantity - it does not gate scaling (which already excludes all ice rings) or merging (handled by the CC1/2 ring mask). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-07-02 16:37:12 +02:00
leonarski_f	ab2176960f	OpenAPI: Fix smargon descriptions	2026-07-01 14:12:09 +02:00
leonarski_fandClaude Opus 4.8	b7613c559c	smargon: write chi/phi goniometer position into NXmx transformations ... Add an optional Smargon static positioner (chi/phi angles + rotation axes) that is reconstructed into the NXmx sample transformation chain. Chi/phi are appended at the innermost end of the chain (closest to the sample) for both the goniometer and grid-scan branches, with axes defaulting to chi {0,0,1} and phi = omega default {1,0,0}. - SmargonPosition gains chi_axis/phi_axis (common/JFJochMessages.h) - OpenAPI: optional phi_axis/chi_axis arrays; clients regenerated - OpenAPIConvert wires Dataset_settings.smargon -> DatasetSettings - CBOR serializer/deserializer round-trip the axes - tests: CBORSerialize_Start_Smargon Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>	2026-07-01 11:45:08 +02:00
leonarski_fandClaude Opus 4.8	809f6f92a3	Regenerate OpenAPI clients for bszstd_rlehuf compression value ... update_version.sh regenerated the TypeScript client (types.gen.ts, zod.gen.ts) and Redoc docs to include the new "bszstd_rlehuf" compression enum value added to jfjoch_api.yaml; the package-lock version field follows VERSION. The C++ server model treats compression as a plain string, so it needed no change. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>	2026-06-27 14:52:12 +02:00
leonarski_f	6136f858af	v1.0.0-rc.154 (#64) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Fix to TCP file pusher (remove kernel zero copy to improve reliability) Reviewed-on: #64 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-25 18:12:00 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +02:00