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feat: add abstract and concrete classes for negative controls and regions #81

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Merged
merged 12 commits into from
Dec 11, 2024
Merged

feat: add abstract and concrete classes for negative controls and regions #81

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4fb6bb2
feat(negative-controls): implement negative control strategies and re…
jjjermiah Dec 11, 2024
80b1981
update notebooks
jjjermiah Dec 11, 2024
1ee3e05
refactor(negative-controls): clean up code formatting and improve rea…
jjjermiah Dec 11, 2024
6396861
docs(negative-controls): add README to explain negative control proce…
jjjermiah Dec 11, 2024
ae8dcdf
update notebook
jjjermiah Dec 11, 2024
75b3d20
docs: correct region strategy description in Negative Control Process…
strixy16 Dec 11, 2024
e0a28d6
docs: update sampled and randomized class descriptions for specificity
strixy16 Dec 11, 2024
0d334ce
refactor(negative-controls): enhance region strategies with detailed …
jjjermiah Dec 11, 2024
36ccbe2
docs(negative-controls): improve docstring for NonROIWithBorderRegion…
jjjermiah Dec 11, 2024
7ca26b3
chore: format
jjjermiah Dec 11, 2024
748bdf4
refactor(negative-controls): rename TypeVar to ImageInput for clarity…
jjjermiah Dec 11, 2024
3edf54e
chore: remove old pyproject
jjjermiah Dec 11, 2024
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3 changes: 2 additions & 1 deletion config/ruff.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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375 changes: 375 additions & 0 deletions notebooks/viz_neg_4D.ipynb
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404 changes: 404 additions & 0 deletions notebooks/viz_neg_controls.ipynb
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