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v1.0.0-rc.164 (#74) 
* rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction.
* rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are.
* rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log.
* rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4.
* rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning.
* rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities.
* rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present.
* rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file.
* rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware.
* Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere.
* Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged.
* The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot.
* The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel.
* A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave.
* A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted.
* A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires.
* `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent.
* The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged.
* The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count.
* `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible.
* `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so.
* The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents.

Reviewed-on: #74
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-08-26 22:47:00 +02:00

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# jfjoch-client
API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).
Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.
Jungfraujoch uses FPGA boards to acquire data at high data rates.
# License Clarification
While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**
when this file is used solely to generate OpenAPI clients or when implementing applications that
interact with the API. Generated client code and applications using this API definition are not
subject to the GPL license requirements and may be distributed under terms of your choosing.
This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and
the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that
user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not
derivative works of the kernel and are not subject to the terms of the GPL.
This exception is intended to allow wider use of this API specification without imposing GPL
requirements on applications that merely interact with the API, regardless of whether they
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.164
- Package version: 1.0.0-rc.164
- Generator version: 7.20.0
- Build package: org.openapitools.codegen.languages.PythonClientCodegen
## Requirements.
Python 3.9+
## Installation & Usage
### pip install
If the python package is hosted on a repository, you can install directly using:
```sh
pip install git+https://gitea.psi.ch/mx/jungfraujoch.git
```
(you may need to run `pip` with root permission: `sudo pip install git+https://gitea.psi.ch/mx/jungfraujoch.git`)
Then import the package:
```python
import jfjoch_client
```
### Setuptools
Install via [Setuptools](http://pypi.python.org/pypi/setuptools).
```sh
python setup.py install --user
```
(or `sudo python setup.py install` to install the package for all users)
Then import the package:
```python
import jfjoch_client
```
### Tests
Execute `pytest` to run the tests.
## Getting Started
Please follow the [installation procedure](#installation--usage) and then run the following:
```python
import jfjoch_client
from jfjoch_client.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:5232
# See configuration.py for a list of all supported configuration parameters.
configuration = jfjoch_client.Configuration(
host = "http://localhost:5232"
)
# Enter a context with an instance of the API client
with jfjoch_client.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = jfjoch_client.DefaultApi(api_client)
try:
# Cancel running data collection
api_instance.cancel_post()
except ApiException as e:
print("Exception when calling DefaultApi->cancel_post: %s\n" % e)
```
## Documentation for API Endpoints
All URIs are relative to *http://localhost:5232*
Class | Method | HTTP request | Description
------------ | ------------- | ------------- | -------------
*DefaultApi* | [**cancel_post**](docs/DefaultApi.md#cancel_post) | **POST** /cancel | Cancel running data collection
*DefaultApi* | [**config_azim_int_get**](docs/DefaultApi.md#config_azim_int_get) | **GET** /config/azim_int | Get azimuthal integration configuration
*DefaultApi* | [**config_azim_int_put**](docs/DefaultApi.md#config_azim_int_put) | **PUT** /config/azim_int | Configure azimuthal integration
*DefaultApi* | [**config_bragg_integration_get**](docs/DefaultApi.md#config_bragg_integration_get) | **GET** /config/bragg_integration | Get Bragg integration configuration
*DefaultApi* | [**config_bragg_integration_put**](docs/DefaultApi.md#config_bragg_integration_put) | **PUT** /config/bragg_integration | Change Bragg integration settings
*DefaultApi* | [**config_dark_mask_get**](docs/DefaultApi.md#config_dark_mask_get) | **GET** /config/dark_mask | Get settings for dark data collection to calculate mask
*DefaultApi* | [**config_dark_mask_put**](docs/DefaultApi.md#config_dark_mask_put) | **PUT** /config/dark_mask | Set configuration for dark data collection to calculate mask
*DefaultApi* | [**config_detector_get**](docs/DefaultApi.md#config_detector_get) | **GET** /config/detector | Get detector configuration
*DefaultApi* | [**config_detector_put**](docs/DefaultApi.md#config_detector_put) | **PUT** /config/detector | Change detector configuration
*DefaultApi* | [**config_file_writer_get**](docs/DefaultApi.md#config_file_writer_get) | **GET** /config/file_writer | Get file writer settings
*DefaultApi* | [**config_file_writer_put**](docs/DefaultApi.md#config_file_writer_put) | **PUT** /config/file_writer | Change file writer settings
*DefaultApi* | [**config_image_format_conversion_post**](docs/DefaultApi.md#config_image_format_conversion_post) | **POST** /config/image_format/conversion | Configure format for data collection with full conversion
*DefaultApi* | [**config_image_format_get**](docs/DefaultApi.md#config_image_format_get) | **GET** /config/image_format | Get image output format
*DefaultApi* | [**config_image_format_put**](docs/DefaultApi.md#config_image_format_put) | **PUT** /config/image_format | Change image output format
*DefaultApi* | [**config_image_format_raw_post**](docs/DefaultApi.md#config_image_format_raw_post) | **POST** /config/image_format/raw | Configure format for raw data collection
*DefaultApi* | [**config_indexing_get**](docs/DefaultApi.md#config_indexing_get) | **GET** /config/indexing | Get indexing configuration
*DefaultApi* | [**config_indexing_put**](docs/DefaultApi.md#config_indexing_put) | **PUT** /config/indexing | Change indexing algorithm settings
*DefaultApi* | [**config_instrument_get**](docs/DefaultApi.md#config_instrument_get) | **GET** /config/instrument | Get instrument metadata
*DefaultApi* | [**config_instrument_put**](docs/DefaultApi.md#config_instrument_put) | **PUT** /config/instrument | Change instrument metadata
*DefaultApi* | [**config_internal_generator_image_put**](docs/DefaultApi.md#config_internal_generator_image_put) | **PUT** /config/internal_generator_image | Load binary image for internal FPGA generator
*DefaultApi* | [**config_internal_generator_image_tiff_put**](docs/DefaultApi.md#config_internal_generator_image_tiff_put) | **PUT** /config/internal_generator_image.tiff | Load TIFF image for internal FPGA generator
*DefaultApi* | [**config_mask_get**](docs/DefaultApi.md#config_mask_get) | **GET** /config/mask | Get mask of the detector (binary)
*DefaultApi* | [**config_mask_tiff_get**](docs/DefaultApi.md#config_mask_tiff_get) | **GET** /config/mask.tiff | Get mask of the detector (TIFF)
*DefaultApi* | [**config_roi_get**](docs/DefaultApi.md#config_roi_get) | **GET** /config/roi | Get ROI definitions
*DefaultApi* | [**config_roi_put**](docs/DefaultApi.md#config_roi_put) | **PUT** /config/roi | Upload ROI definitions
*DefaultApi* | [**config_select_detector_get**](docs/DefaultApi.md#config_select_detector_get) | **GET** /config/select_detector | List available detectors
*DefaultApi* | [**config_select_detector_put**](docs/DefaultApi.md#config_select_detector_put) | **PUT** /config/select_detector | Select detector
*DefaultApi* | [**config_spot_finding_get**](docs/DefaultApi.md#config_spot_finding_get) | **GET** /config/spot_finding | Get data processing configuration
*DefaultApi* | [**config_spot_finding_put**](docs/DefaultApi.md#config_spot_finding_put) | **PUT** /config/spot_finding | Configure spot finding
*DefaultApi* | [**config_user_mask_get**](docs/DefaultApi.md#config_user_mask_get) | **GET** /config/user_mask | Detector must be Initialized. Get user mask of the detector (binary)
*DefaultApi* | [**config_user_mask_put**](docs/DefaultApi.md#config_user_mask_put) | **PUT** /config/user_mask | Upload user mask of the detector (binary)
*DefaultApi* | [**config_user_mask_tiff_get**](docs/DefaultApi.md#config_user_mask_tiff_get) | **GET** /config/user_mask.tiff | Detector must be Initialized. Get user mask of the detector (TIFF)
*DefaultApi* | [**config_user_mask_tiff_put**](docs/DefaultApi.md#config_user_mask_tiff_put) | **PUT** /config/user_mask.tiff | Upload user mask of the detector
*DefaultApi* | [**config_zeromq_metadata_get**](docs/DefaultApi.md#config_zeromq_metadata_get) | **GET** /config/zeromq_metadata | Get ZeroMQ metadata socket settings
*DefaultApi* | [**config_zeromq_metadata_put**](docs/DefaultApi.md#config_zeromq_metadata_put) | **PUT** /config/zeromq_metadata | Set ZeroMQ metadata settings
*DefaultApi* | [**config_zeromq_preview_get**](docs/DefaultApi.md#config_zeromq_preview_get) | **GET** /config/zeromq_preview | Get ZeroMQ preview settings
*DefaultApi* | [**config_zeromq_preview_put**](docs/DefaultApi.md#config_zeromq_preview_put) | **PUT** /config/zeromq_preview | Set ZeroMQ preview settings
*DefaultApi* | [**deactivate_post**](docs/DefaultApi.md#deactivate_post) | **POST** /deactivate | Prepare detector to turn off
*DefaultApi* | [**detector_status_get**](docs/DefaultApi.md#detector_status_get) | **GET** /detector/status | Get detector status
*DefaultApi* | [**fpga_status_get**](docs/DefaultApi.md#fpga_status_get) | **GET** /fpga_status | Get status of FPGA devices
*DefaultApi* | [**image_buffer_clear_post**](docs/DefaultApi.md#image_buffer_clear_post) | **POST** /image_buffer/clear | Clear image buffer
*DefaultApi* | [**image_buffer_image_cbor_get**](docs/DefaultApi.md#image_buffer_image_cbor_get) | **GET** /image_buffer/image.cbor | Get image message in CBOR format
*DefaultApi* | [**image_buffer_image_jpeg_get**](docs/DefaultApi.md#image_buffer_image_jpeg_get) | **GET** /image_buffer/image.jpeg | Get preview image in JPEG format using custom settings
*DefaultApi* | [**image_buffer_image_tiff_get**](docs/DefaultApi.md#image_buffer_image_tiff_get) | **GET** /image_buffer/image.tiff | Get preview image in TIFF format
*DefaultApi* | [**image_buffer_start_cbor_get**](docs/DefaultApi.md#image_buffer_start_cbor_get) | **GET** /image_buffer/start.cbor | Get Start message in CBOR format
*DefaultApi* | [**image_buffer_status_get**](docs/DefaultApi.md#image_buffer_status_get) | **GET** /image_buffer/status | Get status of the image buffers
*DefaultApi* | [**image_pusher_status_get**](docs/DefaultApi.md#image_pusher_status_get) | **GET** /image_pusher/status | Get status of image pusher
*DefaultApi* | [**initialize_post**](docs/DefaultApi.md#initialize_post) | **POST** /initialize | Initialize detector and data acquisition
*DefaultApi* | [**pedestal_post**](docs/DefaultApi.md#pedestal_post) | **POST** /pedestal | Collect dark current for the detector
*DefaultApi* | [**preview_pedestal_tiff_get**](docs/DefaultApi.md#preview_pedestal_tiff_get) | **GET** /preview/pedestal.tiff | Get pedestal in TIFF format
*DefaultApi* | [**preview_plot_bin_get**](docs/DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn&#39;t transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
*DefaultApi* | [**preview_plot_get**](docs/DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
*DefaultApi* | [**result_scan_get**](docs/DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
*DefaultApi* | [**start_post**](docs/DefaultApi.md#start_post) | **POST** /start | Start detector
*DefaultApi* | [**statistics_calibration_get**](docs/DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics
*DefaultApi* | [**statistics_data_collection_get**](docs/DefaultApi.md#statistics_data_collection_get) | **GET** /statistics/data_collection | Get data collection statistics
*DefaultApi* | [**statistics_get**](docs/DefaultApi.md#statistics_get) | **GET** /statistics | Get general statistics
*DefaultApi* | [**status_get**](docs/DefaultApi.md#status_get) | **GET** /status | Get Jungfraujoch status
*DefaultApi* | [**trigger_post**](docs/DefaultApi.md#trigger_post) | **POST** /trigger | Send soft trigger to the detector
*DefaultApi* | [**version_get**](docs/DefaultApi.md#version_get) | **GET** /version | Get Jungfraujoch version of jfjoch_broker
*DefaultApi* | [**wait_till_done_post**](docs/DefaultApi.md#wait_till_done_post) | **POST** /wait_till_done | Wait for acquisition done
*DefaultApi* | [**wait_until_running_post**](docs/DefaultApi.md#wait_until_running_post) | **POST** /wait_until_running | Wait for acquisition running
*DefaultApi* | [**xfel_event_code_get**](docs/DefaultApi.md#xfel_event_code_get) | **GET** /xfel/event_code | Return XFEL event codes for the current data acquisition
*DefaultApi* | [**xfel_pulse_id_get**](docs/DefaultApi.md#xfel_pulse_id_get) | **GET** /xfel/pulse_id | Return XFEL pulse IDs for the current data acquisition
## Documentation For Models
- [AzimIntSettings](docs/AzimIntSettings.md)
- [BraggIntegrationSettings](docs/BraggIntegrationSettings.md)
- [BrokerStatus](docs/BrokerStatus.md)
- [CalibrationStatisticsInner](docs/CalibrationStatisticsInner.md)
- [DarkMaskSettings](docs/DarkMaskSettings.md)
- [DatasetSettings](docs/DatasetSettings.md)
- [DatasetSettingsSmargon](docs/DatasetSettingsSmargon.md)
- [DatasetSettingsXrayFluorescenceSpectrum](docs/DatasetSettingsXrayFluorescenceSpectrum.md)
- [Detector](docs/Detector.md)
- [DetectorList](docs/DetectorList.md)
- [DetectorListElement](docs/DetectorListElement.md)
- [DetectorModule](docs/DetectorModule.md)
- [DetectorModuleDirection](docs/DetectorModuleDirection.md)
- [DetectorPowerState](docs/DetectorPowerState.md)
- [DetectorSelection](docs/DetectorSelection.md)
- [DetectorSettings](docs/DetectorSettings.md)
- [DetectorState](docs/DetectorState.md)
- [DetectorStatus](docs/DetectorStatus.md)
- [DetectorTiming](docs/DetectorTiming.md)
- [DetectorType](docs/DetectorType.md)
- [ErrorMessage](docs/ErrorMessage.md)
- [FileWriterFormat](docs/FileWriterFormat.md)
- [FileWriterSettings](docs/FileWriterSettings.md)
- [FpgaStatusInner](docs/FpgaStatusInner.md)
- [GeomRefinementAlgorithm](docs/GeomRefinementAlgorithm.md)
- [GridScan](docs/GridScan.md)
- [ImageBufferStatus](docs/ImageBufferStatus.md)
- [ImageFormatSettings](docs/ImageFormatSettings.md)
- [ImagePusherStatus](docs/ImagePusherStatus.md)
- [ImagePusherType](docs/ImagePusherType.md)
- [IndexingAlgorithm](docs/IndexingAlgorithm.md)
- [IndexingSettings](docs/IndexingSettings.md)
- [InstrumentMetadata](docs/InstrumentMetadata.md)
- [IntegrationModel](docs/IntegrationModel.md)
- [JfjochSettings](docs/JfjochSettings.md)
- [JfjochStatistics](docs/JfjochStatistics.md)
- [MeasurementStatistics](docs/MeasurementStatistics.md)
- [PcieDevicesInner](docs/PcieDevicesInner.md)
- [PixelMaskStatistics](docs/PixelMaskStatistics.md)
- [Plot](docs/Plot.md)
- [PlotUnitX](docs/PlotUnitX.md)
- [Plots](docs/Plots.md)
- [RoiAzimList](docs/RoiAzimList.md)
- [RoiAzimuthal](docs/RoiAzimuthal.md)
- [RoiBox](docs/RoiBox.md)
- [RoiBoxList](docs/RoiBoxList.md)
- [RoiCircle](docs/RoiCircle.md)
- [RoiCircleList](docs/RoiCircleList.md)
- [RoiDefinitions](docs/RoiDefinitions.md)
- [RotationAxis](docs/RotationAxis.md)
- [ScanResult](docs/ScanResult.md)
- [ScanResultImagesInner](docs/ScanResultImagesInner.md)
- [SpotFindingSettings](docs/SpotFindingSettings.md)
- [StandardDetectorGeometry](docs/StandardDetectorGeometry.md)
- [TcpSettings](docs/TcpSettings.md)
- [UnitCell](docs/UnitCell.md)
- [ZeromqMetadataSettings](docs/ZeromqMetadataSettings.md)
- [ZeromqPreviewSettings](docs/ZeromqPreviewSettings.md)
- [ZeromqSettings](docs/ZeromqSettings.md)
<a id="documentation-for-authorization"></a>
## Documentation For Authorization
Endpoints do not require authorization.
## Author
filip.leonarski@psi.ch
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