Jungfraujoch (1.0.0-rc.29)

For standard synchrotron data collection - this is number of images collected per one TTL trigger For XFEL (pulsed source) - this number is ignored and set to 1 For storage cell mode - this number is ignored and set to number of storage cells

Number of TTL trigger that the detector is expected to receive during data collection

Image time. If not provided (or zero value) the frame time is assumed as default. Image time must be multiple of frame time; max value is 256 * frame_time.
In XFEL mode: summation happens for frames collected with multiple triggers. Ignored for storage cells and if raw data are saved.

/entry/detector/beam_center_x in NXmx Beam center in X direction [pixels]

/entry/detector/beam_center_y in NXmx Beam center in X direction [pixels]

/entry/detector/distance in NXmx Detector distance [mm]

Used to calculate /entry/beam/incident_wavelength in NXmx Incident particle (photon, electron) energy in keV

Prefix for filenames. If left empty, no file will be saved.

Number of files in a single HDF5 data file (0 = write all images to a single data file).

Number of space group for the crystal. Currently used solely as metadata, not relevant for image processing done in Jungfraujoch.

/entry/sample/name in NXmx Sample name

Compression type for the images transferred over ZeroMQ and saved to HDF5 file.

/entry/beam/total_flux in NXmx Flux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]

/entry/instrument/attenuator/attenuator_transmission Transmission of attenuator (filter) [no units]

Definition of a crystal rotation axis

Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON) In general, it is not saved in HDF5 file.

However, if values are placed in "hdf5" object, jfjoch_writer will write them in /entry/data of the HDF5 file. This applies solely to string and number (double floating-point). No arrays/sub-objects is allowed. For example {"hdf5": {"val1":1, "val2":"xyz"}}, will write /entry/user/val1 and /entry/user/val2.

Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON) Not saved in HDF5 file

Rate at which non-indexed images are accepted to be forwarded to writer. Value of 1.0 (default) means that all images are written. Values below zero mean that non-indexed images will be accepted with a given probability.

Set all counts lower than the value to zero. When the value is set, negative numbers other than error pixel value are always set to zero. Setting to zero is equivalent to turning the option off.

Number of run within an experimental session. Transferred over CBOR stream as "series ID", though not saved in HDF5 file. It is highly recommended to keep this number unique for each data collection during experimental series. If not provided, the number will be automatically incremented.

Unique ID of run. Transferred over CBOR stream as "unique series ID", though not saved in HDF5 file. It is highly recommended to keep this name unique for each data collection during experimental series. If not provided, the name will be automatically generated as number + colon + file_prefix.

Name of group owning the data (e.g. p-group or proposal number). Transferred over CBOR stream, though not saved in HDF5 file.

Enable lossy compression of pixel values that preserves Poisson statistics. Requires to provide a numerical factor SQ. Pixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer. Compression is turned off if the value is missing or it is set to zero.

Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments and to turn off for other experiments.

Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer. If parameter is not provided calibration will be saved only if more than 4 images are recorded.

Interval between consecutive frames. This is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number. For EIGER detector this is default frame time, not used otherwise

Integration time of the detector. If not provided count time will be set to maximum value for a given frame time.

Use internal frame generator in FPGA instead of getting data from a real detector

Number of images stored in the internal frame generator.

Delay between TTL trigger and acquisition start [ns]

Threshold for the EIGER detector. If value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy. If value is not provided, threshold will be determined on start of acquisition as half of incident energy. This might lead to increased start time.

Bit depth of EIGER read-out. If value is not provided bit depth is adjusted automatically based on the image time.

Minimum number of collected images for pedestal to consider it viable

Delay between two storage cells [ns]

Fix gain to G1 (can be useful for storage cells)

Type of radiation source. NXmx gives a fixed dictionary, though Jungfraujoch is not enforcing compliance. https://manual.nexusformat.org/classes/base_classes/NXsource.html#nxsource NXsource allows the following:

Spallation Neutron Source Pulsed Reactor Neutron Source Reactor Neutron Source Synchrotron X-ray Source Pulsed Muon Source Rotating Anode X-ray Fixed Tube X-ray UV Laser Free-Electron Laser Optical Laser Ion Source UV Plasma Source Metal Jet X-ray

Settings specific to XFEL (e.g., every image has to come from TTL trigger, save pulse ID and event code)

Enable summation of images to a given image_time If disabled images are saved according to original detector speed, but image count is adjusted

Place module read-out into their location on composed detector and extend multipixels

Convert pixel value in ADU to photon counts/energy Only affects JUNGFRAU detector

Used to convert energy deposited into pixel to counts If not provided incident_energy_keV is used

Bit depth of resulting image (it doesn't affect the detector read-out value) If not provided value is adjusted automatically

Controls if pixels have signed output If not provided value is adjusted automatically

Mask 1 pixel on the module boundary

Mask multipixels on chip boundary

JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1. This should be turned off for cases, where detector is operated at room temperature with long exposure time.

Masked pixels are set to special value in the images produced by Jungfraujoch

Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. Even if disabled spot finding information will still be send and written, though always with zero spots.

Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.

Filter spots which form powder rings (e.g., ice rings)

Minimum number of spots to consider a thin resolution shell (0.01 A^-1) a powder ring and filter out.

If polarization factor is provided, than polarization correction is enabled.

Apply solid angle correction for radial integration

ZeroMQ preview socket is enabled.

Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. If set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection). This has no effect on HTTP based preview, which updates always at rate of 1 second.

ZeroMQ metadata socket is enabled.

Period for generating metadata package sent to the ZeroMQ interface in milliseconds.

List of box ROIs