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>

docs/python_client/README.md

@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.161
-- Package version: 1.0.0-rc.161
+- API version: 1.0.0-rc.162
+- Package version: 1.0.0-rc.162
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 

docs/python_client/docs/DatasetSettings.md

@@ -13,7 +13,7 @@ Name | Type | Description | Notes
 **detector_distance_mm** | **float** | /entry/detector/distance in NXmx Detector distance [mm] | 
 **incident_energy_ke_v** | **float** | Used to calculate /entry/beam/incident_wavelength in NXmx Incident particle (photon, electron) energy in keV  | 
 **file_prefix** | **str** | Prefix for filenames. If left empty, no file will be saved. | [optional] [default to '']
-**images_per_file** | **int** | Number of files in a single HDF5 data file (0 = write all images to a single data file). | [optional] [default to 1000]
+**images_per_file** | **int** | Number of images in a single HDF5 data file, taken literally when given. If omitted, it is chosen from the acquisition: a rotation sweep of at most 20000 images goes into a single data file, so the dataset stays readable by programs that follow only the first data file of a legacy master; a grid scan is split on a whole number of fast-axis rows; anything else (stills, serial) uses 1000.  | [optional] 
 **space_group_number** | **int** | Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch. | [optional] 
 **sample_name** | **str** | /entry/sample/name in NXmx Sample name  | [optional] [default to '']
 **compression** | **str** | Compression type for the images transferred over ZeroMQ and saved to HDF5 file.  | [optional] [default to 'bslz4']

docs/python_client/docs/FileWriterSettings.md

@@ -6,7 +6,7 @@
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
 **overwrite** | **bool** | Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.  | [optional] [default to False]
-**format** | [**FileWriterFormat**](FileWriterFormat.md) |  | [optional] [default to FileWriterFormat.NXMXLEGACY]
+**format** | [**FileWriterFormat**](FileWriterFormat.md) |  | [optional] [default to FileWriterFormat.NXMXVDS]
 
 ## Example
 

docs/python_client/docs/GridScan.md

@@ -1,6 +1,6 @@
 # GridScan
 
-Definition of a grid scan (mutually exclusive with `rotation_axis`)
+Definition of a grid scan. May be combined with a goniometer axis: a grid is often collected at a particular head position, and a stationary axis records where that was. 
 
 ## Properties