[fix] TestDetermineZPosition in z_localization_test.py

[K4rishma]

Fix the z_stack_step_size value and add a folder path for images such that test cases can be run any path.

[Copilot]

Pull request overview

This PR updates the z-localization unit test to use an absolute path for test images (so it can run from any working directory) and adjusts the z-stack step size/precision used by the assertions.

Changes:

• Updated z_stack_step_size and derived PRECISION for TestDetermineZPosition.
• Introduced IMG_PATH and updated image loads to use that path instead of CWD-relative paths.

Comments suppressed due to low confidence (1)

src/odemis/acq/align/test/z_localization_test.py:114

• This block says it changes the range so “warning 6 is raised”, but the subsequent assertion expects warning 4. Please update the comment to match the behavior being tested (or adjust the assertion if the comment is correct).

        # Change the range so warning 6 is raised with an image which is just above focus
        calib_data_limited_range = CALIB_DATA.copy()
        calib_data_limited_range["z_calibration_range"] = (-1e-10, 1e-10)
        image = read_data(IMG_PATH + "super_z_single_beed_aprox_500nm_above_focus.tif")[0]
        expected_outcome_image_3 = 420.6e-9  # Value determined using the function determine_z_position
        z, warning = determine_z_position(image, calib_data_limited_range)
        # Since the range is set to small the detected feature is to big and warning raised should be 4
        self.assertEqual(warning, 4)

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: ce8f4144-f931-4fb1-9d3a-391dfa355249

📥 Commits

Reviewing files that changed from the base of the PR and between f854ecf and 3078238.

📒 Files selected for processing (1)

• src/odemis/acq/align/test/z_localization_test.py

🚧 Files skipped from review as they are similar to previous changes (1)

• src/odemis/acq/align/test/z_localization_test.py

---

📝 Walkthrough

Walkthrough

The test file z_localization_test.py was updated to introduce an IMG_PATH constant and centralize image file references by updating all read_data calls to use IMG_PATH. A numeric literal for z_stack_step_size was clarified from 50*10-9 to 50e-9. Several test expected outcomes (signs and values in meters) were adjusted to match the new path usage and conventions. No public APIs or function signatures were changed.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately summarizes the main changes: fixing TestDetermineZPosition in z_localization_test.py, which aligns with the z_stack_step_size fix and image path improvements.
Description check	✅ Passed	The description directly addresses the changeset by explaining both key fixes: the z_stack_step_size value correction and the addition of a folder path for images.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

📝 Coding Plan

• Generate coding plan for human review comments

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

Tip

You can disable sequence diagrams in the walkthrough.

Disable the reviews.sequence_diagrams setting to disable sequence diagrams in the walkthrough.

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

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

Inline comments:
In `@src/odemis/acq/align/test/z_localization_test.py`:
- Around line 55-56: The test's z resolution is too coarse: update the constants
so z_stack_step_size and PRECISION match the dataset ("step50nm") and production
convergence threshold (50 nm). Change z_stack_step_size from 10e-6 to 50e-9 (50
nm) and set PRECISION to that same 50e-9 (or to a slightly tighter fraction of
z_stack_step_size, e.g., 0.9 * z_stack_step_size) so the test will catch real
localization regressions; update the symbols z_stack_step_size and PRECISION
accordingly.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: ce45ca74-db76-42e7-8e01-d0f7dcb2ef1d

📥 Commits

Reviewing files that changed from the base of the PR and between c1b1ff1 and f854ecf.

📒 Files selected for processing (1)

• src/odemis/acq/align/test/z_localization_test.py

[tepals]

I think it is easier to read if you use os.path.join here as well. So update line 57 to:

IMG_PATH = os.path.join(os.path.dirname(__file__), "images")

and then in the test cases use:

Suggested change

	image = read_data(IMG_PATH + "super_z_single_beed_aprox_500nm_under_focus.tif")[0]
	image = read_data(os.path.join(IMG_PATH, "super_z_single_beed_aprox_500nm_under_focus.tif"))[0]

[tepals]

@K4rishma did you see this comment?

[pieleric]

Looks good to me... assuming you implement the suggestions by Thera and copilot.