feat: add abstract and concrete classes for negative controls and reg…

…ions (#81) # 4D-Lung ![combined](https://github.com/user-attachments/assets/17d071d5-5738-4b08-ac72-d0a7b46e254a) # Order of operations 1. `negative_control_strategy(image, mask=mask, region=region_strategy)` 2. runs the `__call__` on the `negative_control_strategy` 3. which runs the `__call__` of `region(image_array, mask_array)` 4. the result of which is used to figure out what indices of the original image to apply the `transform` method of the `NegativeControlStrategy` concrete classes to 5. only replace the region indices `image_array[mask_indices] = transformed_values` Resource on Strategy Pattern: https://refactoring.guru/design-patterns/strategy/python/example --------- Co-authored-by: Katy Scott <[email protected]>
bhklab · Dec 11, 2024 · c10a568 · c10a568
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diff --git a/config/ruff.toml b/config/ruff.toml
@@ -3,7 +3,8 @@ cache-dir = "~/.cache/ruff"
 # iteratively adding files to the include list
 include = [
   "src/readii/loaders.py",
-  "src/readii/feature_extraction.py"
+  "src/readii/feature_extraction.py",
+  "src/readii/negative_controls_refactor/**.py",
 ]
 
 # extend-exclude is used to exclude directories from the flake8 checks

diff --git a/notebooks/viz_neg_4D.ipynb b/notebooks/viz_neg_4D.ipynb
diff --git a/notebooks/viz_neg_controls.ipynb b/notebooks/viz_neg_controls.ipynb
diff --git a/old_pyproject.toml b/old_pyproject.toml