leonarski_fandClaude Opus 5
659ba0d5b9
Nothing constrained the tilted geometry. Every existing test is either self-consistent or moves one angle at a time, and every file CI writes has zero tilt - where a swapped axis, a reversed composition order and a wrong pivot all give exactly the same answer. Two real bugs lived in that gap. Two checks, because there are two things to guard. DiffractionGeometry_Tilted_vs_PyFAI_and_DIALS pins the model itself: all three PONI angles non-zero and of mixed sign, compared per pixel against reference positions from pyFAI (an independent implementation of the convention) and from DIALS, to 2 um. Because the references are quoted in their own frames and the test applies the documented mappings - pyFAI (t1,t2,t3) -> our (x,y,z), and imgCIF = ours turned 180 degrees about x - it pins those relations too, not just the arithmetic. The comment gives the snippets to regenerate both sets. tests/nxmx_geometry_dials_test.py guards the writer, which is where the bugs actually were and which the unit test cannot reach. CI writes a master, patches the geometry in and asks DIALS where the panel is. Only the angle VALUES are patched; the axis vectors, the depends_on chain and the pivot stay as the writer emitted them, so they remain under test. Verified to fail on the pre-fix encoding: 7.3 mm, exit 1, naming the chain as the thing to look at. Recorded in both, because it cost an hour: compare via get_origin() and the fast/slow axes, NOT get_pixel_lab_coord(), which applies a parallax correction from the sensor thickness that Jungfraujoch does not model - about 0.1 mm at the detector edge, easily mistaken for a geometry error. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
105 lines
4.5 KiB
Python
105 lines
4.5 KiB
Python
#!/usr/bin/env python
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"""Check that DIALS places a TILTED detector where Jungfraujoch does.
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Run under the DIALS environment:
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source /opt/dials-v3-27-0/dials_env.sh
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dials.python tests/nxmx_geometry_dials_test.py <master.h5>
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Why this exists: the NXmx transformation chain the writer produces is only exercised by the rest of
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CI at zero tilt, where every plausible encoding of the tilt - right axes or swapped, right
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composition order or reversed, right pivot or not - gives exactly the same answer. The errors are
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second order and only appear with two angles non-zero at once, or with a non-zero distance being
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rotated. A previous encoding placed the detector 40 mm out at a few degrees of tilt while passing
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every zero-tilt check.
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The reference positions below are the same ones pinned in
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tests/DiffractionGeometryTest.cpp ("DiffractionGeometry_Tilted_vs_PyFAI_and_DIALS"), which checks
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them against pyFAI as well; that comment explains how to regenerate them. Keep the two in step.
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The script patches the geometry into an existing master rather than requiring the writing tool to
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take tilt options: the angle VALUES are just scalars, while the axis vectors, the depends_on chain
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and the pivot - the parts that were wrong - stay exactly as the writer emitted them, so they remain
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under test.
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"""
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import shutil
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import sys
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import h5py
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import numpy as np
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from dxtbx.model.experiment_list import ExperimentListFactory
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# Geometry to impose. Mixed signs on purpose, and all three angles non-zero.
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BEAM_X, BEAM_Y, DISTANCE_M = 1000.0, 1275.0, 0.150
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ROT1, ROT2, ROT3 = 0.05, -0.03, 0.02
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# Expected lab position per pixel, in the imgCIF frame DIALS reports (mm).
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EXPECTED = {
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(0, 0): (-69.399544982, 98.819979800, -150.623559832),
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(1000, 1275): (7.405508016, 4.642730847, -149.745128473),
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(300, 1800): (-44.232877406, -35.676610671, -153.548927191),
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(1700, 400): (58.519164629, 71.195014535, -145.153947836),
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}
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# 2 um, matching the C++ test. A wrong axis, order or pivot is a millimetre-scale error.
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TOLERANCE_MM = 2e-3
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def main(master):
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patched = "geometry_check_master.h5"
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shutil.copy(master, patched)
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with h5py.File(patched, "r+") as h:
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det = h["/entry/instrument/detector"]
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det["beam_center_x"][()] = BEAM_X
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det["beam_center_y"][()] = BEAM_Y
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det["distance"][()] = DISTANCE_M
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transformations = det["transformations"]
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transformations["rot1"][()] = ROT1
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transformations["rot2"][()] = ROT2
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transformations["rot3"][()] = ROT3
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# The writer derives the translation from the beam centre and the distance, so it has to be
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# recomputed here - both the magnitude and the direction it points in.
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pixel_m = float(det["x_pixel_size"][()])
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vector = np.array([BEAM_X * pixel_m, BEAM_Y * pixel_m, DISTANCE_M])
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length = np.linalg.norm(vector)
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transformations["translation"][()] = length
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transformations["translation"].attrs["vector"] = vector / length
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panel = ExperimentListFactory.from_filenames([patched])[0].detector[0]
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origin = np.array(panel.get_origin())
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fast = np.array(panel.get_fast_axis())
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slow = np.array(panel.get_slow_axis())
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pixel_mm = panel.get_pixel_size()[0]
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# Deliberately NOT get_pixel_lab_coord(): it applies a parallax correction from the sensor
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# thickness and material that Jungfraujoch does not model, worth ~0.1 mm at the detector edge.
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failures = []
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for (x, y), expected in sorted(EXPECTED.items()):
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got = origin + x * pixel_mm * fast + y * pixel_mm * slow
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error = np.max(np.abs(got - np.array(expected)))
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status = "ok" if error <= TOLERANCE_MM else "FAILED"
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print(f" pixel ({x:5d},{y:5d}): max error {error:.2e} mm {status}")
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if error > TOLERANCE_MM:
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failures.append(f"pixel ({x},{y}): got {got}, expected {expected}")
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if failures:
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print("\nDIALS does not place the tilted detector where Jungfraujoch does:")
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for failure in failures:
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print(" " + failure)
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print("\nThe NXmx transformation chain in writer/HDF5NXmx.cpp is the thing to look at: the "
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"rot1/rot2/rot3 axis vectors, the order of the depends_on chain, and whether "
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"translation sits inside the rotations so the tilt pivots about the sample.")
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return 1
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print(f"\nAll {len(EXPECTED)} pixels agree within {TOLERANCE_MM} mm.")
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return 0
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if __name__ == "__main__":
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if len(sys.argv) != 2:
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print(__doc__)
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sys.exit(2)
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sys.exit(main(sys.argv[1]))
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