[METEOR-1766] [feature] Add lens metadata to change refractive index factor

[K4rishma]

No description provided.

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request adds support for a refractive index mismatch correction metadata key and uses it in correlation Z-corrections. A new metadata constant MD_RIM_COR was added. Two simulation Optical Objective YAML files gained RIM_COR: 0.495 in their metadata. The CorrelationPointsController now reads the lens metadata into an instance attribute refractive_scale (falling back to a default 0.495) and uses it for Z-correction instead of the previous module-level constant.

Possibly related PRs

• [config] METEOR Tescan FIBSEM was missing some components #3280: Adds Optical Objective object declarations to simulation YAML files, which this PR extends by introducing RIM_COR metadata fields.

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Description check	❓ Inconclusive	No pull request description was provided by the author, so there is no content to evaluate.	Add a pull request description explaining the motivation, implementation details, and any testing performed for this metadata addition.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: adding lens metadata (MD_RIM_COR) to enable dynamic configuration of the refractive index mismatch correction factor.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing touches

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@src/odemis/gui/cont/multi_point_correlation.py`:
- Around line 171-172: The code assumes self._main_data_model.lens exists before
calling lens.getMetadata(), which can be None; update the block around lens_md
and self.refractive_scale to defensively handle a missing lens by first checking
self._main_data_model.lens (or using a conditional expression) so lens_md falls
back to an empty dict when lens is None, then call .get(model.MD_RIM_COR,
REFRACTIVE_SCALE) to assign self.refractive_scale; target the code that uses
self._main_data_model.lens.getMetadata(), self.refractive_scale,
model.MD_RIM_COR and REFRACTIVE_SCALE to implement this null-safe behavior.

🧹 Nitpick comments (2)

install/linux/usr/share/odemis/sim/meteor-fibsem-sim.odm.yaml (1)

118-121: Minor formatting inconsistency and clarify comment.

1. There's a space before the colon in RIM_COR : (line 120) which is inconsistent with other YAML entries in this file (e.g., na: 0.85, ri: 1.0).

2. The comment references "50x lens" and "100x0.9 na" values, but the lens magnification in the init block is 84.0. Consider updating the comment to clarify which value applies to this 84x configuration.

Suggested fix

     metadata: {
         # Refractive index mismatch correction factor
-        RIM_COR : 0.495,  # generally for 50x lens use 0.495, 100x0.9 na use 0.6
+        RIM_COR: 0.495,  # for this 84x lens configuration
     },

install/linux/usr/share/odemis/sim/meteor-tfs3-sim.odm.yaml (1)

73-76: Same formatting and comment issues as the other YAML file.

Apply the same fix for consistency: remove the space before the colon and clarify the comment for the 84x lens configuration.

Suggested fix

     metadata: {
         # Refractive index mismatch correction factor
-        RIM_COR : 0.495,  # generally for 50x lens use 0.495, 100x0.9 na use 0.6
+        RIM_COR: 0.495,  # for this 84x lens configuration
     },