SPINEPS 2.0: usability, error-proofing, batched inference, segment() API + CLI cleanup - #64

Merged

Hendrik-code merged 42 commits into

mainfrom

Aug 27, 2026

Commits on Nov 10, 2025

bug fixes, add more paramter options - robert
robert-graf
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8b017cc

Commits on Jun 10, 2026

added prepare vertexact
Hendrik-code
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79d6777
fix: prepare_vertexact VERTEX-head fallback used a wrong-sized vector

Hendrik-code
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claude
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54d1113
refactor: replace user-input asserts with descriptive exceptions + cleanups

Hendrik-code
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claude
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ba0cc3c
perf: batched instance inference (one forward per chunk of cutouts)

Hendrik-code
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claude
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a6e6bbf
refactor!: rename process_img_nii -> segment_image and Segmentation_Model* -> PascalCase

Hendrik-code
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claude
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0e526f7
feat: high-level spineps.segment() API + grouped config dataclasses

Hendrik-code
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claude
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fc0aa37
refactor!: kebab-case CLI flags, positive-polarity booleans, --batch-size; fix -h crash

Hendrik-code
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claude
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e2461ad
docs: add MIGRATION.md and update README/docs for the 2.0 API and CLI

Hendrik-code
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claude
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4a945a8

Commits on Jun 11, 2026

feat: wire --amp, --step-size, --tta/--no-tta speed knobs end to end

Hendrik-code
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claude
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5426944
feat: apply --tta/--no-tta to auto-resolved dataset models

Hendrik-code
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claude
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330be2f
Merge origin/main into ccleanup (2.0 work)

Hendrik-code
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claude
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00aed3b

Commits on Jun 17, 2026

add endplate support
robert-graf
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210f0af

Commits on Jun 29, 2026

build: require TPTBox ^0.7.3 (numpy 2); drop unused INP001 noqa; simplify test

Hendrik-code
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claude
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c913a67
docs: align docs/README with the 2.0 code; document the high-level API

Hendrik-code
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claude
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ae93caa

Commits on Jun 30, 2026

Merge branch 'labelingupdate' into ccleanup
robert-graf
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653d84a
push ants version
robert-graf
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743786e
remove unused imports
robert-graf
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bf590ae
Merge branch 'loading' into ccleanup
robert-graf
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004d774
update crop
robert-graf
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9a7da9e

Commits on Jul 1, 2026

adaptive nnunet version depending on python >=3.10 or not
Hendrik-code
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d03eb1e
fix test
Hendrik-code
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3ae4ad2
move to newest tptbox version
Hendrik-code
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83301bb
move to newest tptbox version
Hendrik-code
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d91d474
fix versioning issue
Hendrik-code
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819baae
changed to arbitrary blosc2 version
Hendrik-code
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c709785
ruff happy
Hendrik-code
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ecbed44
some cleanup to newest tptbox, also acvl-utils
Hendrik-code
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a04bc9e

Commits on Jul 2, 2026

Commits on Jul 3, 2026

cleanup and sync
Hendrik-code
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948ee11
fixed 3.9 generic alias issue
Hendrik-code
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557ebc3

Commits on Aug 10, 2026

bug fixes
robert-graf
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5fe1dc6
Merge branch 'ccleanup' of github.com:Hendrik-code/spineps into ccleanup
robert-graf
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9aedae4

Commits on Aug 17, 2026

prepare new Models
robert-graf
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0802b47

Commits on Aug 18, 2026

find newest model
robert-graf
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c2529a5

Commits on Aug 25, 2026

ruff issues.
robert-graf
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927dfe4

Commits on Aug 27, 2026

feat(labeling): solve the label path on the 26-class VertExactClass axis

Hendrik-code
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claude
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6f6af19
fix: address Copilot review on the batched instance path and CLI docs

Hendrik-code
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claude
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c61a35c
ci: pin antspyx 0.5.4 on python <3.10 so the Windows 3.9 job installs

Hendrik-code
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claude
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0c5e940
ci: drop the windows/3.9 job and stop PowerShell masking pytest failures

Hendrik-code
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5944971
test: accept the Windows errno for a file used as a directory component

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a44dd25