Add option for global image filtering before particle extraction

[mgiammar]

Resolves #99

[Copilot]

Pull Request Overview

This pull request adds an option for global image filtering before particle extraction as an alternative to the existing post-extraction filtering approach. The change allows users to choose between applying preprocessing filters to the full micrograph before cropping particles or to the individual cropped particle images after extraction.

Key changes:

• Added apply_global_filtering parameter with default value True to maintain backward compatibility
• Modified particle extraction workflow to conditionally apply filtering at different stages
• Updated manager classes to expose the new filtering option

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
src/leopard_em/pydantic_models/utils.py	Removed post-extraction filtering logic and added apply_global_filtering parameter
src/leopard_em/pydantic_models/managers/refine_template_manager.py	Added apply_global_filtering field and passed it to backend functions
src/leopard_em/pydantic_models/managers/optimize_template_manager.py	Added apply_global_filtering field and passed it to backend functions
src/leopard_em/pydantic_models/data_structures/particle_stack.py	Implemented conditional filtering logic in construct_image_stack method

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[jdickerson95]

I think we keep this open for a v1.2 since there will be significant changes with extraction from movies.
At the moment the filter stack is calculated based on the entire micrograph. This will change to allow local filtering for the movie extraction, so I think decisions about how to structure the filtering and pre-process and what control to expose to the user should be made when incorporating that.

[jdickerson95]

I've made some changes to this PR that is now here (https://github.com/Lucaslab-Berkeley/Leopard-EM/tree/mdg_global_whitening).

I propose making this a part of the v1.2 release. and starting a new branch and PR once the v1.1 is merged into main.

[mgiammar]

Stale PR, functionality discussed here in #103