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Fix calibration bugs and clean up solvers, UDFs, UI and packaging - #69

Merged

uellue merged 34 commits into

LiberTEM:mainfrom

uellue:cleanup

Oct 14, 2026

Merged

Fix calibration bugs and clean up solvers, UDFs, UI and packaging#69
uellue merged 34 commits into
LiberTEM:mainfrom
uellue:cleanup

Commits on Oct 12, 2026
- Check the fitted detector rotation in the overfocus optimizer test
  
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- Compare inverted rays with the inverted model's center in test_invert_focus
  
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- Dispatch cos/sin on the argument type instead of always using SymPy
  
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  f22dd3a
- Remove value check from adjust_flip_factor() so that it works with jax.jit()
  
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  3342ff2
- Fix lambdify(args=...), which always raised a TypeError
  
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  dd69cc8
- Implement Model4DSTEM.derive() with dataclasses.replace()
  
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  b08c68d
- Pass _one from trace() to _components() for consistency
  
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  7f3ce2f
- Pass fix points to solvers as float64 instead of float32
  
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  bf4a7df
- Fit both flip factors in solve_coords_points() instead of a continuous one
  
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  7be6c92
- Fit camera length with the model's diffraction geometry in solve_camera_length()
  
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  269ad1c
- Reject strings in Model4DSTEM.normalize_types() and name the field in errors
  
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  05e4121
- Seed random test inputs per test and relax descan deviation tolerance
  
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  1659c81
- Share the least-squares call of the solvers in one helper
  
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  f0646b4
- Remove duplicated regression residual and descan error code from the solvers
  
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  e391d0c
- Reject too few points in the point-based solvers instead of returning arbitrary values
  
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  1216c7a
- Document the solvers and annotate their return types
  
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  38f5d46
- Calculate the UDF transformation matrices per task instead of in __init__
  
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  86c6fa3
- Clean up the overfocus UDFs
  
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  f1828a8
Commits on Oct 13, 2026
- Replace the backend dispatch of cos/sin with lambdify() at the call sites
  
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  c2e741c
- Update the Apptainer image and its pinned requirements to Python 3.14
  
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  3089b0c
- Move the coverage configuration to pyproject.toml and remove stale files
  
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  2abde36
- Move optax to the test extra and drop Numba constraints for old Python versions
  
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  bf582e6
- Read DM4 tags once per file in jeol_dm4 and test it with fake tags
  
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  ea48329
- Calculate the affine maps of the Numba kernels with one shared helper
  
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  d2ea398
- Check the number of reflections in test_twothetas instead of truncating
  
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  55c11c7
- Include underfocus in the random_model test fixture
  
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  0b1a538
- Combine the test_correct variants with shared helpers and non-square shapes
  
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  54804e5
Commits on Oct 14, 2026
- Treat semiconv consistently as the slope at the source
  
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  96c9aae
- Split CoordinateCorrectionLayout.__init__() into state, figures, widgets and events
  
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  7b29c0a
- Share the row handling of the two fix point tables in the calibration UI
  
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  1b31bd1
- Move the calculations of the calibration UI into tested functions
  
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  99efb9a
- Move the instruction texts of the calibration UI layout to module constants
  
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  daaec93
- Move CalibratedDataset to its own module so jeol_dm4 doesn't import the GUI
  
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  aaa32f5
- Fix the instructions of the calibration UI and order the sections accordingly
  
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  7daa7ae

Commits

Commits on Oct 12, 2026

Commits on Oct 13, 2026

Commits on Oct 14, 2026