The same frame mismatch as the rot2/rot3 fix, in the other two fields. Our pixel
coordinates are pixel-centred - 948.0 is the CENTRE of pixel 948 - while pyFAI
measures from the edge of the sensor and puts the centre of pixel i at (i + 0.5) *
pixel size. Poni1/Poni2 went out as beam * pixel size, so anything reading the
file placed the pattern half a pixel (37.5 um at 75 um pixels) off ours. The
previous commit's "Poni1/Poni2 need no such change" was right about the axis
directions and wrong about the origin.
The proof was already in the tree. The pyFAI reference values in
DiffractionGeometryTest were computed for a .poni with Poni2: 0.150 and a 75 um
pixel, which the tests translate to beam_x = 2000 - but pyFAI's numbers are
reproduced only at 1999.5. At 2000 every one of them is out by 2.6e-3 nm^-1, which
the 1e-2 tolerance hid. The tests now use the beam centre those headers actually
mean, and agree with pyFAI to 1e-6 - float precision - across untilted q, azimuth,
rot1, rot1+rot2, rot3, rot1+rot2+rot3 and the solid-angle correction. Tolerances
drop to 1e-4 (1e-5 for solid angle): ~100x the observed float noise, and 26x
tighter than the half pixel they were blind to.
The viewer's calibration window printed "PONI x = ... mm" from the un-offset value
beside the path of the file it disagreed with; it now matches the file.
Also moves the viewer's beam-centre cross half a pixel down and right, where the
spot, prediction, top-pixel and saturation markers already are. Our coordinates
are pixel-centred and the Qt scene's are pixel-cornered, so the map between them
is +0.5, and DrawBeamCenter was the one overlay missing it.
The convention itself is now written down in docs/DETECTOR_GEOMETRY.md, with the
conversions to XDS ORGX/ORGY and to the edge-of-sensor programs, this being the
second bug to come out of it.
Only exported and displayed values change; the fitted geometry, spot positions and
integration were always self-consistent. A .poni written by an earlier build is
half a pixel off.
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.
* Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation.
* jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window.
* rugnux: Accept an absolute `-o` output prefix in offline processing.
* Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed).
* Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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.
* Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4)
* jfjoch_viewer: Improve image render performance
Reviewed-on: #44
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis.
If things go wrong with analysis, it is better to revert to 1.0.0-rc.124.
* jfjoch_broker: Improve logic on switching on/off spot finding
* jfjoch_broker: Increase maximum spot count for FFBIDX to 65536
* jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD)
* jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis
* jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection
* jfjoch_writer: Save more information about each reflection
Reviewed-on: #32
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5