Get rid of passing directory paths and introduce data classes for these use cases - #99

Merged

PolarBean merged 82 commits into

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interpolate-volume-refactor

Jun 8, 2026

Commits on Mar 31, 2026

fix: correct coordinate system for interpolate_volume with BrainGlobeAtlas

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4f1eb84
create read segmentation and read image dir functions
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760a397
update interpolate volume to use image series and registration
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ae2346e
create volume result data class
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da8b12b
fix test failure
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5c69105
save volume niftis takes atlas object
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df8f3bc
update function name
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220f1a9
fix docstring
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9405efb
demo files
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631224a
allow interpolate volume to take colour from segmentation
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b062568
fix: update tests broken during cherry-pick onto volume-refactor

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06eed58
fix failing test
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4949c7c
fix: regenerate volume NIfTI fixtures for default ASR orientation

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1fa3e06

Commits on Apr 23, 2026

Merge branch 'simplify-api' into interpolate-volume-refactor

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36fe540
Harden atlas resolution parsing after merge

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bba8d28
Align commented Q3 colour ordering in validator test

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2e324a6
Document why Q3 validator scenario stays disabled

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5107f06
remove lazy loading
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52869f6
fix merge conflict
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f050941
remove old demo
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b0b9e7d
remove empty file
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2e1fc4d
improve demo readability
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c3083bd
improve demo formatting
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65aa798
remove test data not used for this pr
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f6e11a0
reduce duplicated code
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0b9ec84
add warning of shadowing
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12bad18
ensure either image or path is provided
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427a899
fix docstrings, revert test data to match main, test if output is None before writing
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9cf7563
fix interpolate output
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b6693a8
remove useless comment
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16aaabf
formatting
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e72a78e
Update PyNutil/processing/pipeline/batch_processor.py

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469f0a5
Update PyNutil/image_series.py

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11d99b1
Defer section image loading to worker threads

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bf66e7a
Annotate worker helper in batch processor

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e18214f
fix gui workers.py
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116f760
Add return annotation to worker helper

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0ae5fc0
Type batch processor worker with generic return

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93d46f6
Refine typing for deferred section worker helper

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169fd21
Pass worker dependencies explicitly in batch loop

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d46683a
Annotate section adapter type in worker helper

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9d2757c
Merge remote-tracking branch 'origin/main' into interpolate-volume-refactor
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3b57404
add typing and reintroduce test case
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3ad1c2b

Commits on Apr 27, 2026

Move code changes from documentation branch into refactor PR

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a3ffba8
Bring remaining code fixes from documentation branch

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91c596c
Restore nutil_validator alignment JSON test fixtures

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e77feff
Remove docstring-only improvements from refactor PR

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f6fa9e7
Rewrite public API docstrings to NumPy style

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4f07517
remove unused test data
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7249192
reintroduce initial downlaod
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6573db9
Split inline read_segmentation_dir/read_image_dir calls into separate lines

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e27759f
Set with_damage once at read time via SectionResult.has_damage

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b67fc06
Use None sentinel for undamaged mask instead of explicit with_damage flag

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565c8df
remove lazy loading
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0de6cc3
fix brainglobe atlas imports
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de99ca1
fix bugs found in review
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24659ad
address feedback
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c6b1974
update tests to new api
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b5452e0
temporary patch since column is now filtered properly
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2681445
fix circular import
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b119a7b
remove redundant with damage flag
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388f37a
use none instead of explicit flag
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bd279d9
update test
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c346e04
sync atlasdata with brainglobe atlasapi
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f9f632d
fix volumes inadvertently brought over
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bc47778
fix docstring
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b3489ac
restore classifiers
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f6e8f6c
sync test helpers.py with main
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6a9bbf7

Commits on Apr 28, 2026

fix regression!
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bc6205d
remove conditional import
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7d1f002
reintroduce to prevent circular improt
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9a32ad1

Commits on May 8, 2026

update resolve atlas to mimic bg atlasapi
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f98d5ef

Commits on May 15, 2026

Commits on Jun 4, 2026

Commits on Jun 8, 2026

implement igors suggestions
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67f012e
removed unused imports
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453e763
add type hinting to docstrings
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85dd00a