2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	a8c559bf6b	tests: jfjoch_portable_test, quick [portable] checks for the macOS and Windows jobs ... A Catch2 executable that builds in the portable configurations (JFJOCH_VIEWER_ONLY / JFJOCH_RUGNUX_ONLY) and links only what those build - JFJochRugnux, JFJochReader, JFJochImageAnalysis, JFJochWriter, JFJochCommon - so it can run on the macOS arm64 and Windows x64 jobs, where the receiver/broker/FPGA/HLS sources are not built and there is no GPU. EXCLUDE_FROM_ALL, so a product build does not pay for it; catch2 is now made available in the portable configure as well (it is EXCLUDE_FROM_ALL too). The cases tagged [portable] cover what depends on the architecture, the compiler or the standard library: bitshuffle/LZ4/zstd, HDF5 read-back (legacy/VDS/integrated, the direct-chunk path), miniCBF/marCCD/SMV header parsing, CBOR, CPU spot finding, azimuthal mapping, Bragg prediction/integration, gemmi MTZ/mmCIF. New in tests/PortableTest.cpp: - a golden FNV-1a hash of two frames of compression_benchmark.h5, decoded from the raw chunk by the hperf and the classic bitshuffle and through the HDF5 filter (x86 hashes affea29c511b6ec2 / e46913009c95a1f1); - a golden hash of a bitshuffle/LZ4 encode (the writer must produce the same bytes everywhere); - the shipped bitshuffle block selector against the classic reference over elem 1/2/4/8 and block tails; - the FFTW indexer, named explicitly, on a synthetic orthorhombic lattice (the existing FFT indexer lattice tests run only under CUDA); - a 4-frame end-to-end rugnux run on the git-LFS rotation dataset (HDF5 via external links, CPU spot finding, indexing, integration); SKIPs when LFS was not pulled. All 45 take ~4 s on Linux (~2 s without the LFS case), CPU-only build. M_PI replaced by PI (common/JFJochMath.h) in the two tagged files that used it, as MSVC does not define M_PI. The CBF gzip test shells out to gzip and is left untagged. CI: build and run jfjoch_portable_test "[portable]" in build-windows (both variants), build-rugnux-windows, build-macos-viewer and build-rugnux-macos, after the build and before packaging. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C	2026-09-27 23:44:53 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... 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. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-13 13:54:03 +02:00