3 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	a8d289e7cf	Powder calibration: write Poni1/Poni2 in pyFAI's frame, not ours ... 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>	2026-08-08 03:55:42 +02:00
leonarski_fandClaude Opus 5	a72ba82f48	Powder calibration: write rot2/rot3 in pyFAI's frame, not ours ... The .poni file carried rot2 and rot3 with our sign, which is not pyFAI's. pyFAI has the slow axis increasing bottom to top; the MX convention runs top to bottom, so the two frames differ by a reflection in y. Conjugating a rotation by a reflection gives R(n, theta) -> R(Mn, -theta), so for rot2 (about x) and rot3 (about the beam) the sense reverses, while for rot1 the axis IS y and the axis and the sense reverse together and cancel. Negate the first two, leave rot1 alone. Poni1/Poni2 are unaffected: they are distances from pixel (0, 0) along each axis, which the direction the axis runs in does not change. Caught by integrating a LaB6 image in pyFAI with the file we had just written. Unflipped, the rings come out BROADER than they do with no tilt at all - peak height 42 against 30, mean ring-position error 0.0045 1/A against 0.0027 - which is the signature of a tilt applied the wrong way. Flipped, they sharpen to 132 and 0.0005, and flipping rot1 as well makes it far worse (peak 5), so the asymmetry is real and not a fitting artefact. The unit test pinned the old signs, so it passed throughout. It now pins the verified ones and says why, since the stored values and the written ones disagreeing looks like a bug unless the reason is written down. Only the exported file was wrong. Nothing internal changes: the fitted geometry and everything downstream of it in Jungfraujoch were always self-consistent. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-07 12:04:41 +02:00
leonarski_fandClaude Opus 5	6468dd13be	rugnux: --mode, and detector calibration from powder rings ... --azint-only and --scale are replaced by --mode mx|azint|scale|calibration, with mx the default. The old flags are removed rather than aliased. Calibration mode fits the detector geometry - PONI x/y, the two tilts and the distance - to a calibrant's powder rings and writes a pyFAI .poni alongside a report of how far each parameter moved from the header. Bragg data constrain the beam centre worst, because it is gauge-coupled to the crystal orientation; a powder ring has no orientation to couple to. --calibrant takes lab6, agbh, ceo2, si or ice. A calibrant is a list of ring positions rather than a unit cell, because hexagonal ice is P6_3/mmc: rings enumerated from its cell would include systematically absent ones. So the crystalline standards generate their rings from a cell and ice carries the measured list, and RingsFromAzimuthalProfile, GuessGeometry and OptimizeGeometry all take ring q. The calibrant table is shared with the viewer's powder panel, which previously carried its own copy. --calibration picks how the rings are measured: rings (default) sums the (q x azimuth) profile over every processed image and fits the arcs in it; spots pools the found spots and fits those. Both use the whole run, with -s/-e/-t selecting images. rings defaults --azim-phi-bins to 32, since a profile with one azimuthal bin has averaged the ring over every direction and cannot locate it. Two fixes this exposed: The extraction window is capped at half the gap to the neighbouring ring. The background under a peak is taken from the ends of its window, so a window wider than half that gap measures the next ring's flank as this ring's background - and hexagonal ice has three rings within 0.06 1/A. Ice calibration was 3.5 px out before this and 0.29 px after; LaB6 is unaffected. RingOptimizer holds rot1/rot2 fixed when only one ring is present. A tilt and a centre offset both move a ring as cos(phi) and are separated only by the tilt's amplitude growing as the ring radius squared, so on a single ring they are exactly degenerate. Measured. LaB6 at five distances: the fitted direct beam is within 0.36 px of an independent implementation out to 300 mm, and D = -0.046 + 1.000788 dtz with an rms of 0.011 mm. At 500 mm one ring is fully on the detector and a second only clips the corners, which is not enough to constrain a tilt - restricting the q range to the resolved ring recovers 0.06 px. Ice: 5.53 -> 0.29 px on one crystal and 4.71 -> 0.80 px on another, against XDS's refined direct beam. On an ice-free crystal the fit is worse than the header, which is the correct outcome. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-07 10:00:03 +02:00