4 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Fable 5	70c4d871b6	Documentation sweep: Rugnux naming, repository citations, defect pass ... - Capitalize Rugnux as a proper noun throughout the prose; the command stays lowercase `rugnux` in code font. RUGNUX_OVERVIEW.md is retitled "What Rugnux does". - ACKNOWLEDGEMENT.md cites the raw-data repositories only: dataset counts and DOI prefixes moved out (EXTERNAL_TEST_DATA.md owns them), the ESRF data portal gains its citation (Dimper et al. 2019), and MXRDR remains name + link - it has no canonical citation paper. - RUGNUX_FORMATS.md: the CCD formats (marCCD, SMV) are supported as-is with very limited scope, and per-panel XFEL data is not read. - Fix wrong facts a reader would act on: nonexistent `make jfjoch` targets, invalid udev rules, PUSH sockets documented as PULL, swapped writer width/height, underload semantics, the transposed pixel-mask numpy example (the server checks width and height separately), the Durin/Neggia mask-bit table, FPGA threshold register addresses and the mailbox bit field, the I2C core's document number (PG090), an inverted MODEL_FIT_SIGMA formula, a self-inconsistent worked report example, and 11 cross-page anchors whose slugs carry MyST section numbers. - Unify CC1/2 spelling in prose; math notation and report keys unchanged. - Sweep grammar, typos and editing residue across the FPGA, deployment, streaming and analysis pages, including historical CHANGELOG typos. - rugnux_cli.cpp: the -S usage/error examples pair 96 with P43212; 92 names a different group. - Root THIRD_PARTY_NOTICES.md: scope the GPL-compatibility claim (CUDA EULA) and the vendored-table intro (traccc); the docs copy regenerates via update_version.sh. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>	2026-09-17 08:07:45 +02:00
leonarski_fandClaude Opus 5	2ab8c55dfa	rugnux and the viewer read SMV and gzipped miniCBF ... Two more of the formats deposited data actually arrives in, found by processing a corpus of it: every PETRA III EMBL set is .cbf.gz, and NSRRC and the whole ADSC Quantum era are SMV. Both were previously "no native input". SMV is an ASCII "KEY=value;" block between braces, then the pixels - no container, no compression, nothing to decode by offset - so reader/SMV.{h,cpp} and JFJochSMVReader are a smaller job than the marCCD pair they sit beside, and need no new dependency at all. Two things the format does not give us, both said out loud rather than papered over: * It states no saturation value, so overloads are judged on the 16-bit container alone. That can only fail to call a pixel saturated, never condemn a good one, but a CCD at the top of its range does saturate, so the reader warns once. * Its beam centre is in MILLIMETRES and which of X/Y is the fast direction is a convention rather than a rule. Measured on one ALS ADSC sweep the file's value is TRANSPOSED: as stated it indexes 2/60 frames, and the run's own beam-centre measurement (which adopts the right one automatically) indexes 60/60. Swapping it here would fit that writer and might break another, so the header is read as the format defines it and the measurement stays the arbiter. Revisit with a second vendor's SMV in hand. .cbf.gz needed only Slurp() in MiniCBF.cpp, through which every read already passes: it sniffs the two-byte gzip magic - not the file name - and takes a zlib path when it is there, leaving the plain path free of zlib's buffer copy. zlib-ng is already in the build, so this is a link line, not a dependency. The sweep template grew a suffix, because ".cbf" and ".cbf.gz" are separate sweeps and std::filesystem cannot split the double extension on its own. The viewer's single cbf_reader becomes three, dispatched by CanRead() in the same order as rugnux. Dispatch is by CONTENT in both: ".img" is used by miniCBF, marCCD AND SMV depending on the writer, and a PDB detector label has now been wrong about the format four times, so an extension decides nothing. Measured, de novo, no flags: 9fcg (1800 gzipped frames) gives P4 and a cell 0.06% from the deposited one at 1.37 A against a deposited 1.54; 6oel (ADSC SMV) gives F4132 - 96 operations, the most a protein space group can have - and a cell 0.05% out, 100% indexed. Tests cover both formats and the transposed-beam-centre case with fixtures written byte for byte, so they need no external data. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-16 22:35:05 +02:00
leonarski_fandClaude Opus 5	a1889c45e9	rugnux reads marCCD sweeps natively ... A decade of deposited CCD data is archived as marCCD - what Rayonix MX-series and mar Mosaic detectors write - and rugnux could not open any of it. reader/ had two formats, NXmx/HDF5 and PILATUS miniCBF, and rugnux_cli dispatched on the one CanRead(); this adds the third. The format needs no new dependency: a marCCD file is an ordinary uncompressed TIFF whose 3072-byte instrument header sits in the gap between the TIFF header and the pixels, so libtiff - already fetched for JFJochPreview in every build mode - reads the image, and the header is a fixed-offset block of little-endian int32. Two things differ from the miniCBF path and are worth naming: * The pixel size is NOT rounded to whole micrometres. A PILATUS pixel is exactly 172 um so the existing reader can afford lround(); a MAR300 pixel is 73.242 um, and rounding it to 73 is a 0.33% scale error on every cell edge reported. * The sweep template is the last run of digits in the whole file name rather than in the stem, which covers both schemes these detectors use - a numbered stem (xtal_1_00042.mccd) and the frame number as the extension (D1.042). A CCD frame marks no untrusted pixels, so the sweep starts with nothing masked, and the format has nowhere to state the rotation axis' direction, so the run settles its sign from the data exactly as it does for a miniCBF carrying no axis table. Measured on one deposited 300-frame Rayonix MX-300 sweep, de novo with no flags: 100% indexing, the deposited point group, cell within 0.045%, 99.5% complete at multiplicity 3.4, in 26 s. The chosen sweep is confirmed against the instrument header before it is opened, so a directory of ordinary TIFFs is refused rather than read with a pixel size of zero - a unit test covers that, both naming schemes, and the geometry conversion. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-16 19:31:58 +02:00
leonarski_f	680c36c20d	v1.0.0-rc.166 (#76) ... * `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-02 21:17:31 +02:00