Avoid eager C-order copy in NibabelReader (fixes #8107)

[aymuos15]

Summary

• NibabelReader._get_array_data forced np.asanyarray(img.dataobj, order="C"), triggering a full dense memory reorder on every load on top of the file read/decompression step. This is the hot path reported in Very Slow Loading of NIfTI (.nii.gz) Files Compared to SimpleITK #8107.
• Drop the forced C-order conversion and keep nibabel's native (F-order) layout. This aligns the CPU path with the existing GPU/cupy branch just above, which already returns F-order via .reshape(data_shape, order="F").
• Downstream MONAI conversion paths (convert_to_tensor/convert_to_numpy in monai/utils/type_conversion.py, monai/data/image_writer.py, recon utils) already call ascontiguousarray where they actually need C-contiguous memory, so the reader does not need to pay that cost eagerly at load time.

Biggest wins are on uncompressed .nii, where nibabel's memmap view is returned lazily rather than being materialized by a forced reorder. Compressed .nii.gz still pays the decompression cost but skips the subsequent reorder pass, which matches the "twice as long" observation from @ericspod in the issue thread.

Compatibility note

The returned array's memory layout changes from C-contiguous to whatever nibabel provides (typically F-contiguous). Any external caller consuming reader.get_data(...)[0] directly via .tobytes() or a raw C-extension buffer without first calling ascontiguousarray would see a different byte order. All in-repo consumers already guard themselves.

Test plan

• New regression test in tests/data/test_init_reader.py loads a small NIfTI through NibabelReader for both .nii and .nii.gz, asserts array equality, and asserts the returned data is not C-contiguous (i.e. no eager C copy).
• pytest tests/data/test_init_reader.py passes locally.
• runtests.sh-equivalent checks: ruff, black --skip-magic-trailing-comma --check, isort --check, pycln, pre-commit hooks — all clean on touched files.

Fixes #8107

[coderabbitai]

📝 Walkthrough

Walkthrough

The change removes the explicit order="C" argument from np.asanyarray(img.dataobj) in the NibabelReader's _get_array_data method, allowing NumPy to use its default memory layout handling instead of forcing C-contiguous conversion. A new test was added to verify that loaded NIfTI data is not C-contiguous, confirming the optimization avoids unnecessary data copying.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly summarizes the main change: removing eager C-order conversion in NibabelReader and references the fixed issue.
Description check	✅ Passed	Description includes comprehensive summary, rationale, compatibility notes, and test plan matching the template structure.
Linked Issues check	✅ Passed	Code changes directly address issue #8107: removes forced C-order conversion causing slow NIfTI load times and adds regression tests.
Out of Scope Changes check	✅ Passed	All changes are in-scope: one-line fix in image_reader.py and new regression test in test_init_reader.py directly related to issue #8107.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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🧹 Nitpick comments (1)

tests/data/test_init_reader.py (1)

84-84: Add a docstring to the new test method.

Line 84 introduces a new definition without a docstring; add a short Google-style docstring.

As per coding guidelines, "Docstrings should be present for all definition which describe each variable, return value, and raised exception in the appropriate section of the Google-style of docstrings."

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@tests/data/test_init_reader.py` at line 84, Add a Google-style docstring to
the test function test_nibabel_reader_avoids_eager_c_order_copy describing what
the test verifies (that the nibabel reader avoids an eager C-order copy),
include a short "Args:" section only if the test takes parameters (omit
otherwise), and include a "Raises:" or "Returns:" section only if the test
explicitly raises or returns something (omit otherwise); place the docstring
immediately under the def line in triple quotes.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@tests/data/test_init_reader.py`:
- Line 84: Add a Google-style docstring to the test function
test_nibabel_reader_avoids_eager_c_order_copy describing what the test verifies
(that the nibabel reader avoids an eager C-order copy), include a short "Args:"
section only if the test takes parameters (omit otherwise), and include a
"Raises:" or "Returns:" section only if the test explicitly raises or returns
something (omit otherwise); place the docstring immediately under the def line
in triple quotes.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro

Run ID: be4e5a1e-b10b-4097-a28d-5d3c9fda14f0

📥 Commits

Reviewing files that changed from the base of the PR and between 5a2d0a7 and f1873ec.

📒 Files selected for processing (2)

• monai/data/image_reader.py
• tests/data/test_init_reader.py