Migrating to v4¶

v4 is a clean break from v2/v3: new package layout, new Python API, one CLI. The algorithms are the same (and better tested); the interface was redesigned.

CLI¶

Eleven separate scripts became subcommands of one binary:

v2 script	v4 command
`zscore-normalize img.nii -m mask.nii`	`intensity-normalize zscore img.nii.gz -m mask.nii.gz`
`fcm-normalize`	`intensity-normalize fcm`
`kde-normalize`	`intensity-normalize kde`
`ws-normalize`	`intensity-normalize whitestripe`
`nyul-normalize dir/ -m masks/ -ssh s.npy`	`intensity-normalize nyul dir/ -m masks/ --save-state s.npz`
`nyul-normalize dir/ -lsh s.npy`	`intensity-normalize nyul dir/ --load-state s.npz`
`lsq-normalize`	`intensity-normalize lsq`
`ravel-normalize`	`intensity-normalize ravel`
`tissue-membership`	`intensity-normalize tissue-membership`
`plot-histograms`	`intensity-normalize plot-histograms`
`preprocess`	`intensity-normalize preprocess`
`coregister`	`intensity-normalize coregister`

Single-image and directory CLIs were unified: individual methods accept one image, several images, or a directory. Saved transform state moved from .npy to stamped .npz (old .npy files are not loadable — refit them).

Python API¶

Classes with setup/teardown and a modality keyword became:

individual methods: plain functions — inorm.whitestripe(img, mask=mask)
population methods: fit returns a fitted transform — tx = inorm.nyul.fit(imgs); tx(new_img); tx.save("x.npz")

# v2
from intensity_normalization.normalize.whitestripe import WhiteStripeNormalize

ws = WhiteStripeNormalize(norm_value=1.0)
normalized = ws(image, mask)

# v4
import intensity_normalization as inorm

normalized = inorm.whitestripe(image, mask=mask)

Notable changes:

pymedio images are gone; pass numpy arrays or nibabel images and get the same type back.
scikit-fuzzy is gone; fuzzy c-means is implemented in-house (seeded, deterministic by default).
Modality/TissueType enums became plain validated strings ("t1", "wm").
The normalize_image(method="...") dispatcher (v3) was removed; call the method by name.
antspy/matplotlib are optional extras as before, now imported lazily: [ants], [plot].