121 feature non atlas centric preprocessing pipeline

[MarcelRosier]

No description provided.

[Copilot]

Pull Request Overview

This PR refactors the preprocessing pipeline to support multiple processing paradigms by introducing a non-atlas-centric approach alongside the existing atlas-centric preprocessing. The changes create a more modular architecture with specialized preprocessors for different use cases.

• Implementation of a new native space preprocessing pipeline that operates without atlas registration
• Refactoring of the existing preprocessor into separate atlas-centric and base preprocessor classes
• Addition of enhanced defacing capabilities with optional atlas registration for improved performance

Reviewed Changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
brainles_preprocessing/preprocessor/preprocessor.py	Introduces BasePreprocessor abstract class with common preprocessing functionality
brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py	Refactored atlas-centric preprocessor inheriting from BasePreprocessor
brainles_preprocessing/preprocessor/native_space_preprocessor.py	New native space preprocessor for processing without atlas registration
brainles_preprocessing/preprocessor/init.py	Module initialization with backward compatibility for deprecated Preprocessor class
brainles_preprocessing/modality.py	Enhanced modality classes with improved defacing support and flexible input handling
brainles_preprocessing/defacing/quickshear/quickshear.py	Enhanced QuickshearDefacer with configurable atlas registration
tests/test_preprocessor.py	Updated tests to use new AtlasCentricPreprocessor class
example/example_atlas_centric_preprocessor.py	New example demonstrating atlas-centric preprocessing
example/example_native_space_preprocessor.py	New example demonstrating native space preprocessing
example/example_modality_centric_preprocessor.py	Removed outdated example file

Comments suppressed due to low confidence (2)

brainles_preprocessing/preprocessor/atlas_centric_preprocessor.py:209

• This comment and the following code block (lines 209-211) appear to be duplicated from the base class. Consider removing this duplication since the base class already handles this logic in the run_coregistration method.

        transformation_matrix = self.center_modality.register(

example/example_native_space_preprocessor.py:93

• The output directory name 'mni_native_space_preprocessed_{subject}' is misleading since this is native space preprocessing, not MNI space. Consider renaming to 'native_space_preprocessed_{subject}'.

        output_dir=Path(

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