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leonarski_f 54f2de31bb grid scan: say how the stationary spindle angle is stated, and pin it 
A grid scan is a set of stills at a stationary spindle, and the angle it stood
at is what relates one grid to another taken elsewhere on the circle. Users were
finding an all-zero omega in the file and concluding the angle could not be
recorded at all.

It already can, and has since the goniometer and the grid scan stopped being
alternatives: send the axis with step 0 and its start angle, and that angle is
written per image into the NXmx sample chain, read back by reader/, and taken by
dials.import as a set of stills. Measured on a generated 12-image grid: the
placeholder file carries omega = 0 x 12, the same file with the axis sent at
step 0 carries omega = 90 x 12, and dials.import reports "still: 1, sweep: 0"
for both. Nothing in the code needed changing, so nothing was; what was missing
was that nobody could tell, and that no test held the behaviour down.

So: the API and the HDF5 documentation now say it in as many words, and three
tests pin the three legs the value crosses - the OpenAPI request (which used to
drop the grid scan whenever an axis was present, unpinned until now), the CBOR
start message, and the file round trip.

Also corrects a claim two comments and the HDF5 page were making. NXmx can
express "no rotation" perfectly well - a sample may depend_on "." - so the
placeholder is not there for the standard's sake. It is there because dxtbx
cannot read a sample chain of translations alone: strip the rotation axis from a
grid scan master and dials.import dies in get_dxtbx_goniometer with a matmul
dimension mismatch. Recorded so nobody removes the placeholder on the strength
of the standard.

One thing the change does not fix, because it cannot: a stationary angle is
invisible to DIALS when a grid scan is present. dxtbx picks the first varying
axis as the scan axis, which is a grid translation, so the oscillation reads
(0, 0); and with exactly one rotation axis in the chain it builds a single-axis
goniometer whose fixed rotation is the identity, never consulting the angle. The
same angle IS visible when it is the only candidate (oscillation reads (90, 0))
or when a Smargon head puts a second rotation axis in the chain (the setting
rotation then carries it). The value is in the file and correct either way.
2026-09-02 11:04:29 +02:00
..
docs
grid scan: say how the stationary spindle angle is stated, and pin it
2026-09-02 11:04:29 +02:00
README.md
docs: publish the powder calibration schemas in the python client docs
2026-08-31 19:02:12 +02:00

README.md

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 project:

  • API version: 1.0.0-rc.166
  • Package version: 1.0.0-rc.166
  • 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:

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:

import jfjoch_client

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import jfjoch_client

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:


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 POST /cancel Cancel running data collection
DefaultApi config_azim_int_get GET /config/azim_int Get azimuthal integration configuration
DefaultApi config_azim_int_put PUT /config/azim_int Configure azimuthal integration
DefaultApi config_bragg_integration_get GET /config/bragg_integration Get Bragg integration configuration
DefaultApi config_bragg_integration_put PUT /config/bragg_integration Change Bragg integration settings
DefaultApi config_dark_mask_get GET /config/dark_mask Get settings for dark data collection to calculate mask
DefaultApi config_dark_mask_put PUT /config/dark_mask Set configuration for dark data collection to calculate mask
DefaultApi config_detector_get GET /config/detector Get detector configuration
DefaultApi config_detector_put PUT /config/detector Change detector configuration
DefaultApi config_file_writer_get GET /config/file_writer Get file writer settings
DefaultApi config_file_writer_put PUT /config/file_writer Change file writer settings
DefaultApi config_image_format_conversion_post POST /config/image_format/conversion Configure format for data collection with full conversion
DefaultApi config_image_format_get GET /config/image_format Get image output format
DefaultApi config_image_format_put PUT /config/image_format Change image output format
DefaultApi config_image_format_raw_post POST /config/image_format/raw Configure format for raw data collection
DefaultApi config_indexing_get GET /config/indexing Get indexing configuration
DefaultApi config_indexing_put PUT /config/indexing Change indexing algorithm settings
DefaultApi config_instrument_get GET /config/instrument Get instrument metadata
DefaultApi config_instrument_put PUT /config/instrument Change instrument metadata
DefaultApi config_internal_generator_image_put PUT /config/internal_generator_image Load binary image for internal FPGA generator
DefaultApi config_internal_generator_image_tiff_put PUT /config/internal_generator_image.tiff Load TIFF image for internal FPGA generator
DefaultApi config_mask_get GET /config/mask Get mask of the detector (binary)
DefaultApi config_mask_tiff_get GET /config/mask.tiff Get mask of the detector (TIFF)
DefaultApi config_roi_get GET /config/roi Get ROI definitions
DefaultApi config_roi_put PUT /config/roi Upload ROI definitions
DefaultApi config_select_detector_get GET /config/select_detector List available detectors
DefaultApi config_select_detector_put PUT /config/select_detector Select detector
DefaultApi config_spot_finding_get GET /config/spot_finding Get data processing configuration
DefaultApi config_spot_finding_put PUT /config/spot_finding Configure spot finding
DefaultApi config_user_mask_get GET /config/user_mask Detector must be Initialized. Get user mask of the detector (binary)
DefaultApi config_user_mask_put PUT /config/user_mask Upload user mask of the detector (binary)
DefaultApi 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 PUT /config/user_mask.tiff Upload user mask of the detector
DefaultApi config_zeromq_metadata_get GET /config/zeromq_metadata Get ZeroMQ metadata socket settings
DefaultApi config_zeromq_metadata_put PUT /config/zeromq_metadata Set ZeroMQ metadata settings
DefaultApi config_zeromq_preview_get GET /config/zeromq_preview Get ZeroMQ preview settings
DefaultApi config_zeromq_preview_put PUT /config/zeromq_preview Set ZeroMQ preview settings
DefaultApi deactivate_post POST /deactivate Prepare detector to turn off
DefaultApi detector_status_get GET /detector/status Get detector status
DefaultApi fpga_status_get GET /fpga_status Get status of FPGA devices
DefaultApi image_buffer_clear_post POST /image_buffer/clear Clear image buffer
DefaultApi image_buffer_image_cbor_get GET /image_buffer/image.cbor Get image message in CBOR format
DefaultApi 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 GET /image_buffer/image.tiff Get preview image in TIFF format
DefaultApi image_buffer_start_cbor_get GET /image_buffer/start.cbor Get Start message in CBOR format
DefaultApi image_buffer_status_get GET /image_buffer/status Get status of the image buffers
DefaultApi image_pusher_status_get GET /image_pusher/status Get status of image pusher
DefaultApi initialize_post POST /initialize Initialize detector and data acquisition
DefaultApi pedestal_post POST /pedestal Collect dark current for the detector
DefaultApi preview_pedestal_tiff_get GET /preview/pedestal.tiff Get pedestal in TIFF format
DefaultApi 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't transmit information about X-axis, only values, so it is of limited use for azimuthal integration.
DefaultApi preview_plot_get GET /preview/plot Generate 1D plot from Jungfraujoch
DefaultApi result_scan_get GET /result/scan Get full scan result
DefaultApi start_post POST /start Start detector
DefaultApi statistics_calibration_get GET /statistics/calibration Get calibration statistics
DefaultApi statistics_data_collection_get GET /statistics/data_collection Get data collection statistics
DefaultApi statistics_get GET /statistics Get general statistics
DefaultApi status_get GET /status Get Jungfraujoch status
DefaultApi trigger_post POST /trigger Send soft trigger to the detector
DefaultApi version_get GET /version Get Jungfraujoch version of jfjoch_broker
DefaultApi wait_till_done_post POST /wait_till_done Wait for acquisition done
DefaultApi wait_until_running_post POST /wait_until_running Wait for acquisition running
DefaultApi xfel_event_code_get GET /xfel/event_code Return XFEL event codes for the current data acquisition
DefaultApi xfel_pulse_id_get GET /xfel/pulse_id Return XFEL pulse IDs for the current data acquisition

Documentation For Models

Documentation For Authorization

Endpoints do not require authorization.

Author

filip.leonarski@psi.ch

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