5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	2629f3821c	XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin ... Plugin: - Module-edge (bit 30) and chip-edge (bit 31) pixels are marked -2 (untrusted). Chip-edge pixels are split from a larger pixel with integer division and read low at low counts; feeding them to XDS as real pixels was what made the three plugins disagree in CI. - A saturated pixel in a signed image (INTx_MAX) is passed through with its value, so XDS counts it as an overload; only the error marker (INTx_MIN / UINTx_MAX) becomes -1. - Release version 1.1.0 set in CMake (library name and start message). VERSION_* in plugin.h stay 0: XDS refuses a plugin whose info-array major version is not 0. - Built and packaged on Linux only; the untested macOS archive is dropped. - The XDS linking permission is removed from LICENSE; the plugin is GPL-3.0. CI: - XDS.INP beam centre corrected to 1091/1137 (ORGY was 7.7 px off, which put IDXREF on a knife edge where one plugin's run fell into a false minimum). - Each XDS case must reach CORRECT, IDXREF spot SD must be < 2 px, and all file layouts read by the same plugin must give identical SPOT.XDS. Docs: recommend Durin (PSI or Global Phasing build); mask-bit table rewritten from measurement. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-08 10:56:34 +02:00
leonarski_fandClaude Opus 5.5	07ae3c3a40	XDS plugin: GPL linking permission, own tgz with its notices, macOS build; one portable CI build ... LICENSE: the section-7 addendum is rewritten as numbered additional permissions. CUDA libraries are treated as System Libraries (Intel MKL dropped - never linked). New: the XDS plugin may be linked with the closed-source XDS, valid only while it contains no third-party GPL code. The plugin links HDF5, zlib-ng, Zstandard and Compression (LZ4, Bitshuffle, Bitshuffle h-perf) and nothing else - no FFTW. In a portable (viewer-only) build it is its own CPack component, shipped as jfjoch_xds_plugin-<version>-<os>-<arch>.tar.gz with LICENSE, a short xds-plugin/THIRD_PARTY_NOTICES.md and only those six licence texts. On macOS it now exports only plugin_* (--exclude-libs does the same on Linux). The RPM/DEB packaging is unchanged. The viewer-only build already compiled everything rugnux needs, so it now packs one archive per program: Linux three .tar.gz (viewer, rugnux, plugin); macOS the viewer .dmg plus rugnux and plugin .tar.gz, each generator getting its components through CPACK_PROJECT_CONFIG_FILE. CI merges build-viewer-tgz + build-rugnux-tgz into build-portable-tgz (cuda and nocuda, so Linux rugnux gains a -cpu archive) and the two macOS jobs into build-macos. Both check that FFTW is neither on the plugin's link line nor in its symbol table and that it exports only plugin_*. The bare .so upload from the RPM job is dropped. RUGNUX_ONLY stays for aarch64 and Windows. Verified locally (Linux, CPU, CI flags): three tarballs, the plugin link line is exactly the list above, 0 FFTW symbols, four exports, system-only dynamic deps; XDS loads the packaged plugin. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>	2026-10-07 20:29:19 +02:00
leonarski_f	30b6800289	v1.0.0-rc.171 (#81) ... * Rugnux: basic support for CCD images (marCCD, SMV) and for gzipped miniCBF. * `jfjoch_viewer`: opens the CCD formats, and fixes to the dataset plots. * Documentation updates. Reviewed-on: #81 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-17 14:42:52 +02:00
leonarski_fandjungfrau	4dc2534dbf	v1.0.0.rc-162 (#72) ... **Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one. * HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected. * HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it. * HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset. * HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts. * HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout. * A grid scan and a goniometer axis can both be set; they are no longer alternatives. * `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000. * The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned. * The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer. * rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it. * rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`. * rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way. * rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound. * rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached. * rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use. * rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own. * rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement. * rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged. * rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged. * Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged. * A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses. * rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given. * CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer. * The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2. * Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact. **Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`): * `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file. * `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them. --------- Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch> Reviewed-on: #72 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 08:21:39 +02:00
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43	2026-04-09 13:30:47 +02:00