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Migrating from v1 to v2

This guide covers every breaking change between TorchIO v1 and v2.

!!! note "Report bugs or request features"

Hit a snag migrating, or have an idea to improve TorchIO? Please
[start a discussion](https://github.com/TorchIO-project/torchio/discussions)
or [open an issue](https://github.com/TorchIO-project/torchio/issues) on
GitHub to report bugs or request features.

Quick checklist

  • Replace Random* transform names with their base names (RandomFlip → Flip)
  • Pass explicit ranges for augmentation (renamed transforms are a no-op without arguments): RandomAffine() → Affine(degrees=(-10, 10), scales=(0.9, 1.1))
  • Replace path= with positional arg or source= in Image constructors
  • Replace .affine (numpy array) with .affine.data where a raw array is needed
  • Replace RescaleIntensity(out_min_max=...) with Normalize(out_min=..., out_max=...)
  • Replace SubjectsDataset with any Dataset passed to SubjectsLoader
  • Replace GridAggregator with PatchAggregator
  • Rewrite custom transforms to accept a SubjectsBatch in make_params(batch) and apply_transform(batch, params)

Image construction

v1:

image = tio.ScalarImage(path="t1.nii.gz")
image = tio.ScalarImage(tensor=tensor, affine=affine_array)

v2:

image = tio.ScalarImage("t1.nii.gz")
image = tio.ScalarImage(tensor, affine=tio.AffineMatrix(affine_array))

Changes:

  • First positional argument accepts a path, tensor, numpy array, NiBabel image, SimpleITK image, or bytes. The path and tensor keyword names are gone: use positional or source=.
  • type parameter removed. Use ScalarImage or LabelMap directly.
  • affine accepts AffineMatrix objects in addition to arrays.
  • New channels_last parameter for tensor sources shaped (I, J, K, C).

Affine access

v1:

affine_array = image.affine           # np.ndarray (4, 4)
spacing = image.spacing               # tuple
direction = image.direction            # 9-tuple of floats

v2:

affine_obj = image.affine             # AffineMatrix object
affine_array = image.affine.data      # np.ndarray (4, 4)
spacing = image.spacing               # tuple (unchanged)
orientation = image.affine.orientation # e.g. ("R", "A", "S")

The .affine property now returns an AffineMatrix object. Use .affine.data when you need the raw 4×4 numpy array.

Subject construction

v1:

subject = tio.Subject({"t1": image, "seg": label})  # dict positional arg
subject = tio.Subject(t1=image, seg=label)

v2:

subject = tio.Subject(t1=image, seg=label)  # keyword args only

The positional dictionary form is removed. Use keyword arguments.

Transform naming

v2 removes the Random* prefix. Stochasticity is controlled by parameter type: a scalar is deterministic, a tuple samples uniformly, and a Distribution or Choice gives full control.

!!! warning "Renaming a Random* transform changes its default behavior" In v1, RandomAffine() (no arguments) applied random augmentation. In v2, the renamed Affine() (no arguments) is a deterministic identity (no-op) that emits a warning (randomness is opt-in). Pass a range like (a, b) for random augmentation, or a scalar for a fixed effect. Transforms that draw a random realisation rather than sampling a scalar parameter (e.g. Noise, BiasField, ElasticDeformation, Swap) still apply with their default parameters.

v1 v2
RandomFlip Flip
RandomAffine Affine
RandomElasticDeformation ElasticDeformation
RandomNoise Noise
RandomBlur Blur
RandomMotion Motion
RandomGhosting Ghosting
RandomBiasField BiasField
RandomGamma Gamma
RandomSpike Spike
RandomSwap Swap
RandomAnisotropy Anisotropy
RandomLabelsToImage LabelsToImage
RescaleIntensity Normalize (alias RescaleIntensity available)
ZNormalization Standardize (alias ZNormalization available)

Transform parameter changes

Flip

flip_probability default changed from 0.5 to 1.0. If you relied on the old default, set it explicitly:

# v1 (implicit 0.5)
tio.RandomFlip(axes=(0, 1, 2))

# v2 (explicit 0.5)
tio.Flip(axes=(0, 1, 2), flip_probability=0.5)

Affine

scales and degrees now expect explicit ranges instead of half-widths:

# v1: scales=0.1 means range (0.9, 1.1)
tio.RandomAffine(scales=0.1, degrees=10)

# v2: specify the range directly
tio.Affine(scales=(0.9, 1.1), degrees=(-10, 10))

Normalize (was RescaleIntensity)

Tuple parameters are split into individual keyword arguments:

# v1
tio.RescaleIntensity(
    out_min_max=(0, 1),
    percentiles=(0.5, 99.5),
)

# v2
tio.Normalize(
    out_min=0,
    out_max=1,
    percentile_low=0.5,
    percentile_high=99.5,
)

Each parameter can independently be a scalar (fixed), a tuple (uniform range), a Distribution, or a Choice.

HistogramStandardization

Landmark computation is now a standalone function instead of a classmethod:

# v1
landmarks = tio.HistogramStandardization.train(paths)
transform = tio.HistogramStandardization({"t1": landmarks})

# v2
from torchio.transforms.intensity.histogram_standardization import (
    compute_histogram_landmarks,
)
landmarks = compute_histogram_landmarks(images)
transform = tio.HistogramStandardization(landmarks, include=["t1"])

One instance per modality. For multi-modal subjects, compose:

tio.Compose([
    tio.HistogramStandardization(t1_landmarks, include=["t1"]),
    tio.HistogramStandardization(t2_landmarks, include=["t2"]),
])

Custom transforms

Rewrite the transform hooks

In v1, custom transforms implemented a subject-level hook:

# v1
def apply_transform(self, subject: tio.Subject) -> tio.Subject:
    ...

In v2, parameter creation and application are separate batch-level hooks:

# v2
def make_params(self, batch: tio.SubjectsBatch) -> dict[str, Any]:
    ...

def apply_transform(
    self,
    batch: tio.SubjectsBatch,
    params: dict[str, Any],
) -> tio.SubjectsBatch:
    ...

Call the transform normally rather than calling either hook yourself. For a single subject, TorchIO performs this conversion automatically:

Subject -> SubjectsBatch -> apply_transform -> Subject

The following complete transform works for both a single Subject and a SubjectsBatch:

from typing import Any

import torch
import torchio as tio


class AddValue(tio.Transform):
    """Add a fixed value to every batched image."""

    def __init__(self, value: float) -> None:
        super().__init__()
        self.value = value
        self.received_shape: tuple[int, ...] | None = None

    def make_params(self, batch: tio.SubjectsBatch) -> dict[str, Any]:
        """Return the value to add."""
        return {"value": self.value}

    def apply_transform(
        self,
        batch: tio.SubjectsBatch,
        params: dict[str, Any],
    ) -> tio.SubjectsBatch:
        """Add the value to every image tensor."""
        for image_batch in batch.images.values():
            self.received_shape = tuple(image_batch.data.shape)
            image_batch.data = image_batch.data + params["value"]
        return batch


subject = tio.Subject(image=tio.ScalarImage(torch.zeros(1, 2, 3, 4)))
transform = AddValue(2)
result = transform(subject)
assert isinstance(result, tio.Subject)
assert transform.received_shape == (1, 1, 2, 3, 4)
assert result.image.data.shape == (1, 2, 3, 4)
assert torch.all(result.image.data == 2)

The image is 4D (C, I, J, K) before and after the public call, but it is 5D (B, C, I, J, K) inside apply_transform. For a single subject, B is 1.

!!! warning "apply_transform is not a public replay method" It is the low-level batch kernel. Calling it directly bypasses wrapping, copying, probability handling, history recording, and output-type restoration. Pass a supported input to the transform itself instead.

Migrate metadata access

In v1, subject metadata values were scalars or arbitrary objects. In a v2 batch, each metadata key maps to a list containing one value per element:

import torch
import torchio as tio

subjects = [
    tio.Subject(
        image=tio.ScalarImage(torch.zeros(1, 2, 3, 4)),
        site="A",
        age=30,
    ),
    tio.Subject(
        image=tio.ScalarImage(torch.ones(1, 2, 3, 4)),
        site="B",
        age=40,
    ),
]
batch = tio.SubjectsBatch.from_subjects(subjects)
assert batch.metadata == {"site": ["A", "B"], "age": [30, 40]}

Treat batch.metadata as dict[str, list[Any]]. Metadata transforms must keep each list aligned with the batch dimension. Subjects in one batch must have equivalent image names and metadata keys. The first subject determines the shared key order; later subjects may use a different local order, but custom transforms should preserve the batch schema rather than adding, removing, or renaming keys for only some elements.

Choose deterministic or per-instance behavior

A fixed scalar is not sampled: transforms such as Gamma use that value for every batch element. For built-in stochastic transforms that support per-instance sampling, ranges and distributions produce independent parameters for each batch element by default. Set per_instance=False to share one sampled parameter set:

import torchio as tio

independent = tio.Gamma(log_gamma=(-0.3, 0.3))
shared = tio.Gamma(log_gamma=(-0.3, 0.3), per_instance=False)
deterministic = tio.Gamma(log_gamma=0.2)

Custom transforms do not gain per-instance sampling automatically. Unless a transform explicitly implements and advertises that capability, its parameters remain batch-shared. See Per-instance augmentation for the capability contract and stochastic-realisation caveats.

Migrate inherently per-subject logic

Prefer vectorized operations on 5D tensors or metadata lists. If logic must call a subject-oriented external API, the current low-level escape hatch is to unbatch, process every subject without changing its schema, restack, and adopt the prior history:

from typing import Any

import torch
import torchio as tio


class StripIdentifier(tio.Transform):
    """Strip whitespace from subject identifiers."""

    def make_params(self, batch: tio.SubjectsBatch) -> dict[str, Any]:
        """Return no parameters."""
        return {}

    def apply_transform(
        self,
        batch: tio.SubjectsBatch,
        params: dict[str, Any],
    ) -> tio.SubjectsBatch:
        """Process metadata one subject at a time."""
        subjects = batch.unbatch()
        for subject in subjects:
            identifier = subject.metadata["identifier"]
            subject.metadata["identifier"] = identifier.strip()
        rebuilt = tio.SubjectsBatch.from_subjects(subjects)
        rebuilt.adopt_history(batch, subjects)
        return rebuilt


subject = tio.Subject(
    image=tio.ScalarImage(torch.zeros(1, 2, 3, 4)),
    identifier=" sub-01 ",
)
result = StripIdentifier()(subject)
assert result.identifier == "sub-01"

This pattern is more expensive than vectorized code and requires every resulting subject to retain a compatible image and metadata schema. A supported mapping utility is planned, but it is not part of the current API.

New features

Choice

Sample from a discrete set of values:

tio.Affine(degrees=tio.Choice([-90, 0, 90, 180]))

SomeOf

Apply a random subset of transforms:

tio.SomeOf(
    [tio.Flip(axes=(0,)), tio.Noise(std=0.1), tio.Gamma(log_gamma=(-0.3, 0.3))],
    num_transforms=(1, 2),
)

Operator sugar

pipeline = tio.Flip(axes=(0,)) + tio.Noise(std=0.1)  # Compose
artifact = tio.Ghosting(intensity=(0.5, 1)) | tio.Spike(intensity=(1, 3))  # OneOf

Compose copy control

Compose deep-copies the input once, then all inner transforms operate in-place. Disable with copy=False for nested pipelines:

inner = tio.Compose([tio.Flip(axes=(0,))], copy=False)
outer = tio.Compose([inner, tio.Noise(std=0.1)])

Data loading

SubjectsDataset removed

v1 required wrapping subjects in SubjectsDataset. v2 removes this class. Pass any Dataset returning Subject instances to SubjectsLoader:

# v1
dataset = tio.SubjectsDataset(subjects, transform=augment)
loader = DataLoader(dataset, batch_size=4)

# v2
loader = tio.SubjectsLoader(subjects, transform=augment, batch_size=4)

Queue

# v1
dataset = tio.SubjectsDataset(subjects)
sampler = tio.UniformSampler(patch_size=96)
queue = tio.Queue(dataset, max_length=300, samples_per_volume=10)

# v2
queue = tio.Queue(
    subjects,
    patch_sampler=tio.UniformSampler(patch_size=96),
    max_length=300,
    patches_per_volume=10,
)

PatchAggregator (was GridAggregator)

# v1
aggregator = tio.GridAggregator(sampler)

# v2
aggregator = tio.PatchAggregator(sampler)

Transform history

v2 simplifies the history API:

# Both versions
restored = subject.apply_inverse_transform()
inverse = subject.get_inverse_transform()

# v1 only (removed in v2)
subject.history
subject.get_applied_transforms()
subject.get_composed_history()

Imports

All transforms are available at the top level:

# v1
from torchio.transforms import RandomFlip, RandomAffine
from torchio.transforms.augmentation.intensity import RandomNoise

# v2
import torchio as tio
tio.Flip
tio.Affine
tio.Noise

New exports in v2:

  • AffineMatrix: the affine matrix class
  • Points, BoundingBoxes, BoundingBoxFormat: annotation types
  • SubjectsBatch, ImagesBatch: batch containers
  • Choice: discrete parameter sampling utility
  • SomeOf: random subset composition
  • PatchAggregator: renamed from GridAggregator
  • apply_inverse_transform: standalone inverse function