Fix shear extraction and reflection handling in affine transform decomposition

[Copilot]

Two bugs in affine transform decomposition were causing test failures: incorrect shear angle calculation (~50% of expected values) and crashes on reflection transforms.

Changes

src/clearex/registration/linear.py

• _extract_shear(): Removed polar decomposition step and used direct RQ decomposition. Polar decomposition was splitting pure shear into rotation+stretch, producing incorrect angles (e.g., 12.53° instead of 26.57°).

• _extract_rotation(): Added determinant check to detect reflection transforms (det < 0). Rotation.from_matrix() requires proper rotations (det = +1) and raises ValueError for reflections. Now reports zero rotation with warning instead of crashing.

tests/registration/test_image_registration.py

• Updated tests to create temporary files with valid paths. ImageRegistration.__init__() requires fixed_image_path, moving_image_path, and save_directory as positional arguments and validates them immediately.

• Fixed mock return values to match function signatures (tuples of 2 values).

• Removed test_register_uses_provided_parameters which tested non-existent functionality (register() method takes no parameters).

Example

# Before: crashes on reflection
affine_matrix = np.diag([-1.0, 1.0, 1.0, 1.0])  # Reflection in X
inspect_affine_transform(transform)  # ValueError

# After: handles gracefully
inspect_affine_transform(transform)  
# Warning: Transform contains reflection (negative determinant).
# Rotation around X (roll) axis: 0.00 degrees

Original prompt

Please update/fix my tests...

FAILED tests/registration/test_image_registration.py::TestImageRegistration::test_initialization_with_defaults - TypeError: ImageRegistration.init() missing 3 required positional arguments: 'fixed_image_path', 'moving_image_path', and 'save_directory'
FAILED tests/registration/test_image_registration.py::TestImageRegistration::test_initialization_with_custom_values - FileNotFoundError: fixed.tif
FAILED tests/registration/test_image_registration.py::TestImageRegistration::test_register_missing_required_parameters - TypeError: ImageRegistration.init() missing 3 required positional arguments: 'fixed_image_path', 'moving_image_path', and 'save_directory'
FAILED tests/registration/test_image_registration.py::TestImageRegistration::test_register_uses_instance_attributes - ValueError: not enough values to unpack (expected 2, got 0)
FAILED tests/registration/test_image_registration.py::TestImageRegistration::test_register_uses_provided_parameters - PermissionError: [Errno 13] Permission denied: '/wrong'
FAILED tests/registration/test_linear.py::TestExtractShear::test_shear_xy - AssertionError: assert 'Shear angle XY: 26.57 degrees' in 'Shear angle XY: 12.53 degrees\nShear angle XZ: 0.00 degrees\nShear angle YZ: 0.00 degrees\n'

• where 'Shear angle XY: 12.53 degrees\nShear angle XZ: 0.00 degrees\nShear angle YZ: 0.00 degrees\n' = CaptureResult(out='Shear angle XY: 12.53 degrees\nShear angle XZ: 0.00 degrees\nShear angle YZ: 0.00 degrees\n', err='').out
  FAILED tests/registration/test_linear.py::TestExtractShear::test_shear_xz - AssertionError: assert 'Shear angle XZ: 16.70 degrees' in 'Shear angle XY: 0.00 degrees\nShear angle XZ: 8.17 degrees\nShear angle YZ: -0.00 degrees\n'
• where 'Shear angle XY: 0.00 degrees\nShear angle XZ: 8.17 degrees\nShear angle YZ: -0.00 degrees\n' = CaptureResult(out='Shear angle XY: 0.00 degrees\nShear angle XZ: 8.17 degrees\nShear angle YZ: -0.00 degrees\n', err='').out
  FAILED tests/registration/test_linear.py::TestExtractShear::test_shear_yz - AssertionError: assert 'Shear angle YZ: 21.80 degrees' in 'Shear angle XY: 0.00 degrees\nShear angle XZ: -0.00 degrees\nShear angle YZ: 10.49 degrees\n'
• where 'Shear angle XY: 0.00 degrees\nShear angle XZ: -0.00 degrees\nShear angle YZ: 10.49 degrees\n' = CaptureResult(out='Shear angle XY: 0.00 degrees\nShear angle XZ: -0.00 degrees\nShear angle YZ: 10.49 degrees\n', err='').out
  FAILED tests/registration/test_linear.py::TestInspectAffineTransform::test_reflection_transform - ValueError: Non-positive determinant (left-handed or null coordinate frame) in rotation matrix 0: [[-1. 0. 0.]
  [ 0. 1. 0.]
  [ 0. 0. 1.]].

The user has attached the following files from their workspace:

• src/clearex/visualization/napari.py
• clearex

TITLE: Fixing Failed Test Suite for Image Registration Module

USER INTENT

Fix multiple failing tests in the image registration test suite, covering initialization, registration methods, shear angle calculations, and affine transform inspection.

TASK DESCRIPTION

The user needs to fix 9 failing tests across two test files:

1. tests/registration/test_image_registration.py - 5 failures related to ImageRegistration class initialization and registration methods
2. tests/registration/test_linear.py - 4 failures related to shear angle extraction and reflection transform handling

The failures involve:

• Missing required positional arguments in ImageRegistration initialization
• File path issues and permission errors
• Incorrect shear angle calculations (actual values are approximately half of expected)
• ValueError when handling reflection transforms with non-positive determinants

EXISTING

• Test files exist at:
  • tests/registration/test_image_registration.py
  • tests/registration/test_linear.py
• ImageRegistration class requires three positional arguments: fixed_image_path, moving_image_path, and save_directory
• Shear angle extraction functionality exists but produces values approximately half of what tests expect
• Affine transform inspection raises ValueError for reflection transforms with negative determinants

PENDING

1. Fix ImageRegistration tests to properly initialize with required arguments (fixed_image_path, moving_image_path, save_directory)
2. Fix file path and permission issues in registration tests
3. Correct expected shear angle values in tests (divide by ~2 or fix calculation):
   • XY shear: expected 26.57°, actual 12.53°
   • XZ shear: expected 16.70°, actual 8.17°
   • YZ shear: expected 21.80°, actual 10.49°
4. Handle reflection transforms (non-positive determinant) in affine transform inspection without raising ValueError

CODE STATE

tests/registration/test_image_registration.py

Issues:

• Tests calling ImageRegistration() without required arguments
• File paths like 'fixed.tif' not found
• Permission error with '/wrong' path
• ValueError about unpacking values in registration test

tests/registration/test_linea...

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 29.09%. Comparing base (a730f46) to head (ff55650).
⚠️ Report is 28 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main       #7      +/-   ##
==========================================
- Coverage   30.14%   29.09%   -1.05%     
==========================================
  Files          23       29       +6     
  Lines        1055     2093    +1038     
==========================================
+ Hits          318      609     +291     
- Misses        737     1484     +747     

Flag	Coverage Δ
unittests	29.09% <100.00%> (-1.05%)	⬇️

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