v1.0.0.rc-161 (#71)

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: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice.
* **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster.
* **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory.
* **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again.

**Breaking change to the rugnux command line:**
* `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one.
* `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride.

**Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional:
* `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve.
* `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing.

**Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional:
* The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more.
* `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.**

Reviewed-on: #71
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

docs/python_client/docs/SpotFindingSettings.md

@@ -11,12 +11,14 @@ Name | Type | Description | Notes
 **photon_count_threshold** | **int** |  | 
 **min_pix_per_spot** | **int** |  | 
 **max_pix_per_spot** | **int** |  | 
-**high_resolution_limit** | **float** | High resolution limit for spot finding [Angstrom] | 
-**low_resolution_limit** | **float** | Low resolution limit for spot finding [Angstrom] | 
+**high_resolution_limit** | **float** | High resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding extends as far as the detector reaches, i.e. the detection is not clipped in resolution.  | [optional] 
+**low_resolution_limit** | **float** | Low resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding is not clipped at the low-resolution end. A value of 0 is accepted and means the same thing.  | [optional] 
 **high_resolution_limit_for_spot_count_low_res** | **float** | High resolution threshold to consider spot \"low resolution\" [Angstrom] | 
 **quick_integration** | **bool** | Quick integration of Bragg spots in diffraction images. If enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate. (experimental feature)  | [default to False]
-**ice_ring_width_q_recip_a** | **float** | Width of ice ring in q-space in reciprocal space | [default to 0.02]
+**ice_ring_width_q_recip_a** | **float** | Half-width of the ice ring band in q (1/A). Matches the offline default in image_analysis/spot_finding/SpotFindingSettings.h, which was set from a measured ring FWHM of ~0.06; the two must agree or the same data gets a narrower ice band online. | [default to 0.03]
 **high_res_gap_q_recip_a** | **float** | This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector. If there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter. This option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.  | [optional] [default to 1.5]
+**adaptive_threshold** | **bool** | Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring threshold derived from each image's own noise, so the same setting works across datasets without per-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the operating point instead. Only available on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow). The JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold, so enabling this there is rejected rather than silently ignored.  | [optional] [default to False]
+**false_pixels_per_frame** | **float** | Operating point of the adaptive threshold: the number of noise pixels tolerated per frame. About 100 suits a multi-megapixel detector. Ignored unless adaptive_threshold is set.  | [optional] [default to 100.0]
 
 ## Example