leonarski_fandClaude Opus 5
c1b6030c4f
An image integrated in pyFAI through our .poni came out with every chi 180 degrees from where it belongs. pyFAI's in-plane axes are the negatives of ours, so Rot3 needs a half turn on top of the sign flip. Being a rotation about the beam it leaves 2theta alone - which is why radial integration was right all along and only the azimuth was wrong, and why a powder-ring check could never have caught it. The half turn is needed for the orientation-3 form written before rc.162 as well, so it is not an artefact of declaring the orientation - the file has been 180 degrees out for as long as it has been written. Verified against pyFAI 2026.5.0 on a tilted detector with an off-centre beam, against the lab positions of the NXmx chain: 2theta to 3.6e-15 deg and chi to 2.8e-14 deg. Then end to end, by integrating an image in jfjoch's own layout through a .poni the code actually writes: chi lands within 0.15 deg of physical truth on a 0.5 deg cake bin. Withdraws two changelog claims. The .poni does negate Rot3, and declaring orientation did not fix the azimuth: pyFAI's orientation is numerically inert here, so the file was relabelled and not corrected. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VfYvJT5Nb71suJCowRBn5z
3.8 KiB
Detector geometry
At the moment Jungfraujoch supports solely flat detectors. The default option is to place modules in their actual location vs. detector frame. It is not recommended to place detector modules stacked.
The simplest case is detector perpendicular to the beam. In this case it is enough to provide beam center, detector distance and wavelength.
For more complex case, one can provide tilt of the detector rotation in PyFAI convention.
This convention uses Point Of Nominal Interaction (PONI) definition. Beam X and Y would correspond to the location on the detector,
where beam from the sample is perpendicular to the detector surface and not to the actual direct beam location. Then tilt of the detector
is defined with three rotation angles: rot1 (rotating detector right), rot2 (rotating detector downwards), rot3 (rotating detector clockwise).
See PyFAI documentation for more details.
What a pixel coordinate means: (0, 0) is the centre of the first pixel
Pixel coordinates in Jungfraujoch and rugnux are 0-based and pixel-centred: an integer coordinate is the centre of that pixel, so pixel i covers [i − 0.5, i + 0.5) and the sensor spans −0.5 … width − 0.5. A beam centre of 948.0 × 546.0 sits in the middle of pixel [546][948], not on any of its corners; 948.5 is the boundary between pixel 948 and 949.
This holds throughout the code: spot and reflection centroids are intensity-weighted sums of the
integer pixel indices, the resolution and azimuthal-bin maps evaluate pixel (col, row) at exactly
(col, row), and a fractional coordinate is turned back into a pixel index by rounding, not by
truncation. The same convention applies to every coordinate the system exposes — the beam centre
(beam_x_pxl/beam_y_pxl in the API and broker configuration, --beam-x/--beam-y in rugnux,
beam_center_x/beam_center_y in NXmx and in the CBOR stream), the spot and predicted-reflection
positions written to HDF5, and the PONI reported by --mode calibration.
Other programs place the origin differently, and the difference is worth half a pixel — enough to matter when a geometry is copied between programs and then refined:
| Convention | Beam centre equivalent to our x = 948.0 |
|---|---|
| Jungfraujoch, rugnux | 948.0 |
XDS (ORGX/ORGY) |
949.0 — also pixel-centred, but pixels are numbered from 1 |
Measured from the edge of the sensor, in length units — pyFAI (Poni2, fast axis), DIALS/dxtbx |
(948.0 + 0.5) × pixel size, because the centre of pixel i is at (i + 0.5) × pixel size from the edge |
pyFAI Poni1 (slow axis) |
(height − 1 − y + 0.5) × pixel size — pyFAI measures the slow axis from the opposite edge, and the .poni declares orientation: 2 to say so |
The .poni file written by rugnux --mode calibration is in pyFAI's frame and so already carries
that half pixel; the pixel values the same run reports are ours. Rot3 in that file is our rot3
negated and turned by 180°: the half turn sets the azimuthal reference, because pyFAI's in-plane axes
are the negatives of ours. It leaves 2θ untouched, so it moves only the azimuth.
Macromolecular crystallography convention for the vertical direction
One place of confusion is the convention to have point (0,0) of the detector in the top left corner of the detector, with Y values increasing downwards. This is also consistent with computer image formats.
However, other techniques (as well as internal operation of PSI X-ray detectors) might follow convention, for point (0,0) being in the bottom left corner and Y values increasing upwards. Such a convention is used, for example, by PyFAI.
In general, convention is controlled in Jungfraujoch with a setting in the JSON configuration file, which allows mirroring detector in Y.
Extra care has to be taken by the user to ensure that no errors are made.