2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	d412306c77	beam stop: a shadow does not have to touch the direct beam ... The shadow finder kept only the low region connected to the beam centre, flooding outward from seeds within 4 px of it. That is written for the beam stop and its holder arm, an object that touches the direct beam. Hardware that stands in the beam further out - a pin, a loop - casts a shadow that begins some way out in radius, with lit detector between it and the stop, and no bridge crosses that gap. On a sweep where such a shadow covers 38 % of the detector the per-ring test found the whole of it and connectivity then discarded 950 k pixels, leaving the beam-stop disk alone; those pixels went into integration as measured-and-near-zero. What makes the test specific instead is size: keep the connected components that hold at least MIN_SHADOW_PIXELS core pixels. A shadow is cast by something physical and is correspondingly large, while the background wanders a pixel or two at a time. Measured on five clean in-house sweeps spanning 0.05 to 9.5 counts/px/frame of background, every one returns exactly one such component - the beam stop - and the largest spurious candidate anywhere is 74 pixels, a 27x margin. MIN_EXPECTED_COUNTS becomes a Poisson significance. A ratio says nothing when the background behind it is a handful of photons, so the deficit is now required to be significant against its own scatter, sqrt(2 (E - N + N ln(N/E))) over the pooled counts. This is what makes the comparison scale-free rather than tuned to one exposure: rebuilt from six frames of a low-background sweep, the same thresholds without it mask three quarters of the detector and with it mask none of it. The index of dispersion, measured over the frames, does NOT do this job - it is 1.0 inside the shadow and 1.0 outside it, because a shadowed pixel is Poisson at a low rate and a lit one is Poisson at a high rate. Only the rate relative to the ring separates them. The rest follows: the core ratio moves 0.35 -> 0.50 and the half-shadow reach 0.72 within 14 px -> 0.75 within 30 px, since a pin's penumbra is much wider than a beam stop edge's; the ring walk that finds the rings lying wholly inside the stop keeps its own threshold so the central disk does not move; and those rings join the region after the size filter rather than being asked to be large themselves. On the shadowed sweep this takes the mask from 16,587 px (0.66 %) to 818,184 px (32.32 %), against 956,705 px (37.79 %) for the reference implementation, at a precision of 0.92 against it. Clean sweeps move from 0.60 % to 0.82 %, the width of the same arm. One thing this costs: an empty mask used to be a statement about the beam centre, because the seeds were placed at it. It no longer is, and a centre wrong by a couple of hundred pixels now draws the rings across the background's own fall-off and returns a large spurious mask instead of an empty one. The log message says so. The fix is ordering - the centre is measured from this same projection a moment later - and is not attempted here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-13 07:36:57 +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