Which way the detector's rows run was decided once, in the module assembly, and
never stated again: not on the wire, not in the file, nowhere a consumer could
read it. mirror_y was consumed inside the DetectorGeometryModular constructor and
discarded. It is now a declared property of the detector setup, carried into the
start message, written to HDF5 under detectorSpecific, and read back. Absence
means true, which is the MX convention and the only thing Jungfraujoch has ever
produced.
Deliberately a boolean and not a corner enum: the assembled image can only be
flipped in Y, so a four-corner value would encode states that cannot occur.
DECTRIS stream2 has no field for this - checked against the specification - so
the key is new rather than an extension of theirs, and a consumer that does not
know it skips it and behaves exactly as before.
The .poni file gains pyFAI's orientation. Without it pyFAI applies its own
default, 3 (bottom left), and believes increasing row means physically upwards.
The numbers still agreed - a mirror preserves 2theta, so radial integration was
never affected - but the azimuth came out with the opposite sense, which matters
for cake and sector integration.
Declaring orientation 2 is not a one-line addition: it re-anchors Poni1 to the
top edge and reverses rot2 and rot3, a row flip being improper. Measured against
pyFAI 2026.5.0 by searching all four orientations, both Poni1 anchorings and all
eight sign combinations: exactly two combinations reproduce the lab position
DiffractionGeometry computes to 1.4e-17 m - the unlabelled form written before,
and (orientation 2, Poni1 = height-1-beam_y, +rot1/+rot2/-rot3), which is now
written. Calibration_PoniFileAxisConvention pins it.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
NXmx has no field for the depth of the stored image - only bit_depth_readout,
"how many bits the electronics record per pixel". The two diverge exactly when
summation is used: the readout keeps the detector's native width while the
summed image must be wider to hold the sum.
Every NXmx reader nonetheless takes bit_depth_readout as the width of the stored
pixel. dxtbx ignores the non-standard bit_depth_image entirely for a generic
NXmx file, derives its masking markers from bit_depth_readout, and raises
"Unsupported integer dtype uint32" for a 32-bit image when the field is absent.
Reporting the electronic value there would mislead precisely where it differs.
So report the image depth in both fields, and drop the machinery that existed to
carry the electronic one for a DECTRIS detector: the SIMPLON read, the
DetectorSetup setter, and the receiver-side propagation of a key that the DECTRIS
stream2 protocol does not even define. JUNGFRAU and PSI EIGER keep their readout
depth, which the FPGA acquisition genuinely needs.
Also write NXmx underload_value, the lowest valid value. Without it a reader
takes the trusted minimum to be -0x7FFFFFFF, so the error-pixel marker sits
inside the trusted range and is consumed as an intensity. Measured with DIALS
3.27 on a written file: trusted_range goes from (-2147483647, 32766) to
(-32767, 32766), so the INT16_MIN gap pixels are now masked.
Third fix in the same area: JFJochReceiverLite::Configure took the image width
from the incoming stream but not the sign, while the image itself is forwarded
byte-for-byte. A detector sending int32 was re-declared uint32, and the VDS
master was typed unsigned over signed data files. Take pixel_signed from the
stream too - it and the width are both carried by the one image_dtype key.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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.
* jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing
* jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files
* jfjoch_broker: Add ROI calculation in non-FPGA workflow
* jfjoch_broker: Fixes to TCP image pusher
* jfjoch_broker: Remove NUMA bindings
* jfjoch_broker: Improvements to indexing
* jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values
* jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors
* jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs
* jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results
Reviewed-on: #63
This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.
* jfjoch_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin
Reviewed-on: #58
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
jfjoch_broker: Avoid copying gain calibration together with DiffractionExperiment
Reviewed-on: #53
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.
* jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start`
* jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start'
* jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time
* jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received
* jfjoch_broker: Use nanoseconds internally for frame/image/readout time
* jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished)
* jfojch_broker: Improve profiling of different data analysis steps
* jfjoch_broker: Record integration reflection count
* jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds)
* jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked
* jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets
**Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time.
Reviewed-on: #49
leonarski_fandClaude Opus 5