Develop/betapipe #254

jjjermiah · 2025-03-06T15:47:19Z

coderabbitai · 2025-03-06T15:47:32Z

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…nctions.

…nto develop/betapipe

…rror with structlog

…nto develop/betapipe

… fields stuff

…adata attr after transforms.

…nto develop/betapipe

…et=True)

…ix/SEG_Compatability

…nal ROI index remapping

@skim2257

@skim2257 Have you ever aligned a SEG when its size doesn't match source?

JoshuaSiraj · 2025-03-19T19:52:31Z

@jjjermiah I tried adding tqdm like you do, but it no workie

…y as arg (#267)

jjjermiah

@JoshuaSiraj @skim2257

is there a single commit for just the logger namespace changes that we can cherrypick into develop/hackathon so this feature isnt 55 file changes?

JoshuaSiraj · 2025-03-20T15:26:15Z

@JoshuaSiraj @skim2257

is there a single commit for just the logger namespace changes that we can cherrypick into develop/hackathon so this feature isnt 55 file changes?

a051924

This branch should also get merged ASAP

jjjermiah · 2025-03-20T15:52:24Z

@JoshuaSiraj @skim2257
is there a single commit for just the logger namespace changes that we can cherrypick into develop/hackathon so this feature isnt 55 file changes?

a051924

This branch should also get merged ASAP

@JoshuaSiraj why asap?

JoshuaSiraj · 2025-03-20T15:54:04Z

@JoshuaSiraj @skim2257
is there a single commit for just the logger namespace changes that we can cherrypick into develop/hackathon so this feature isnt 55 file changes?

a051924
This branch should also get merged ASAP

@JoshuaSiraj why asap?

Because a lot of the PRs being merged to this, really should be merged to the main hackathon branch

skim2257 · 2025-03-20T16:10:59Z

@JoshuaSiraj @skim2257

is there a single commit for just the logger namespace changes that we can cherrypick into develop/hackathon so this feature isnt 55 file changes?

it already got merged into this branch way up there

… multiprocessing

jjjermiah · 2025-03-21T14:45:00Z

@JoshuaSiraj @skim2257
is there a single commit for just the logger namespace changes that we can cherrypick into develop/hackathon so this feature isnt 55 file changes?

it already got merged into this branch way up there

yeah I'd like to have it as its own commit when merging into the release branch, also cleans up this PR to hopefully not be 55 file changes

…etapipe

Co-authored-by: Jermiah Joseph <[email protected]>

WIP: BetaPipeline

886e480

jjjermiah added the hackathon label Mar 6, 2025

JoshuaSiraj and others added 5 commits March 10, 2025 18:27

Merge branch 'develop/hackathon' into develop/betapipe

6bb96bb

fix(dicom): circular import

9716934

chore: crawler force = True for example

06dc05a

fix: circular import in SampleInput and remove resample_[modality] fu…

a0c074d

…nctions.

Merge branch 'develop/betapipe' of github.com:bhklab/med-imagetools i…

63cbec2

…nto develop/betapipe

skim2257 marked this pull request as ready for review March 10, 2025 23:37

skim2257 requested a review from JoshuaSiraj March 10, 2025 23:38

skim2257 and others added 20 commits March 10, 2025 19:38

feat: betapipeline with decent code, breaking on windows

d8f12f1

refactor(SampleInput): made class callanle as default

595a7d4

fix: changed logging module to loggers to avoid circular import e…

a051924

…rror with structlog

Merge remote-tracking branch 'refs/remotes/origin/develop/betapipe' i…

90a8647

…nto develop/betapipe

feat(SampleOutput): temporary default context keys + update meta data…

030b12a

… fields stuff

chore(SampleOutput): update doc string

8738db0

fix(Segmentation): sparse mark generation

2fa753d

feat: working nnunet output

5017cf1

refactor(SampleOutput): change CaseID to SampleID for consitency

7c5db1d

chore(nnUNetOutput): remove unused imports

74be3a8

feat(SampleOutput): better context key init

fe30e14

Merge branch 'develop/betapipe' into JoshuaSiraj/nnUNetOutput

5772639

feat(nnUNetOutput): better context key init

94c7a56

chore(nnUNetOutput): remove old type hint

fe6e7a6

chore(SampleOutput): remove old type hint

c749654

fix: working Transformer. Scan/Dose/PET/Segmentation doesn't lose met…

577bfa6

…adata attr after transforms.

feat(writers): new nnUNet Output (#261)

b5e949a

fix: Segmentation not saving

a5bd7e8

Merge branch 'develop/betapipe' of github.com:bhklab/med-imagetools i…

400977c

…nto develop/betapipe

chore(SampleOutput): remove commented code

493b267

JoshuaSiraj and others added 12 commits March 17, 2025 13:30

chore: remove field in default for now

7a3465c

feat(Betapipeline): skip sample if not all ROI's in Segmentation(nnun…

494f50f

…et=True)

Merge branch 'JoshuaSiraj/feat/nnunet_in_betapipe' into JoshuaSiraj/f…

76eab8d

…ix/SEG_Compatability

feat(SEG): updated regex search to full match

21440eb

refactor(Betapipeline): clean nnunet usage in beta pipeline

7efa190

refactor(Segmentation): improve generate_sparse_mask to support optio…

7135787

…nal ROI index remapping

feat(Betapipeline): add tqdm progress bar and update docstring

b2ae436

feat(SEG): handle fractional segmentation type

8a869be

feat: nnunet flag in betapipeline (#264)

a220246

Merge branch 'develop/betapipe' into JoshuaSiraj/fix/SEG_Compatability

1b6a76d

feat: SEG compatibility for >1 segments (#262)

5c1d778

@skim2257 Have you ever aligned a SEG when its size doesn't match source?

chore: add docstrings and apply ruff fixes

b7c8dbb

fix(SampleInput): use absolute path, now requiring data root director…

dc32979

…y as arg (#267)

jjjermiah commented Mar 20, 2025

View reviewed changes

fix(Betapipeline): tqdm when n_jobs>1

e530a5b

JoshuaSiraj added 2 commits March 20, 2025 14:04

fix(betapipeline): remove crawl as self variable to allow pickling in…

ab9158a

… multiprocessing

feat(Betapipeline): add try except block in process_one_sample

6aa91ab

JoshuaSiraj and others added 7 commits March 21, 2025 11:21

chore(SEG): docstring + ruff + mypy

369779b

betapipeline misc changes (#270)

2fc7cb2

feat: enable autopipeline cli via __main__

2a292ea

fix: f-string error

86a5d8b

Merge remote-tracking branch 'origin/develop/betapipe' into develop/b…

8932db7

…etapipe

Develop/add autopipeline cli (#276)

25acde1

feat: os-agnostic crawl (#260)

edbc861

Co-authored-by: Jermiah Joseph <[email protected]>

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Develop/betapipe #254

Develop/betapipe #254

jjjermiah commented Mar 6, 2025

coderabbitai bot commented Mar 6, 2025 •

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Develop/betapipe #254

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Develop/betapipe #254

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