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brainhops.io.transformations.nifti

Readers and writers for transformations stored in NIfTI files.

Fields of RAS displacements and of RAS coordinates

The NIfTI-1 standard (nifti1.h) gives a field of vectors two intent codes, and they do not mean the same map:

A displacement field maps x -> x + u(x); a coordinates field maps a voxel to the position its vector holds. Reading one as the other moves every point by the whole world position of its voxel, so the intent code decides between them.

DISPVECT is read as RAS displacements in millimetres, as ITK 5.4 and later reads it. A field of coordinates is written as VECTOR, with the intent name "Mapping", which is what SPM writes for its y_ deformations -- the same kind of field. POINTSET (1008) would name the content better ("the vector value at each voxel is really a spatial coordinate"), but the standard ties it to a flat list of points (dim[2] = dim[3] = dim[4] = 1), and readers -- brainhops included -- lay out its axes as one, so a grid written with it would be misread.

Coordinates fields written by brainhops before this change

Older versions of brainhops wrote fields of RAS coordinates with the DISPVECT intent and nothing else to mark them. Such a file is byte-for-byte a standard displacement field, so it is now read as one. Nothing in the file tells the two apart, and guessing from the values would be just that, so read them explicitly: load(path, hint="nifti.coordinates"), or NiftiRASCoordinatesField.from_file(path). Saving the result rewrites it with the VECTOR intent.

Classes

NiftiRASToVoxel 

NiftiRASToVoxel(
    *,
    _input: CoordinateSystem = RASmm(),
    _output: CoordinateSystem = VoxelCoordinateSystem(),
)

Bases: RASToVoxel, _NiftiAffine

Affine transformation from RAS space to voxel space, derived from a NIfTI header.

Not a registered format

A NIfTI header encodes voxel-to-RAS; RAS-to-voxel is its inverse, computed rather than stored. The two are indistinguishable by content -- same container, same extension, same confidence -- so registering both would make every .nii an ambiguity. Reach this one through NiftiVoxelToRAS.inverse().

Attributes

PREFIXES class-attribute 
PREFIXES: tuple[str, ...] = ()

Filename prefixes required by this parser, e.g. ("y_", "iy_").

An empty tuple means "no constraint". A parser that constrains the prefix is more specific than one that does not, and wins ties.

Declaring EXTENSIONS and PREFIXES separately states the cross-product implicitly, which is how these conventions actually work: SPM's four names are {y_, iy_} x {.nii, .nii.gz}.

PRIORITY class-attribute 
PRIORITY: int = 0

Explicit tie-breaker, consulted only when specificity cannot decide. Higher wins. Leave at 0 unless two parsers genuinely collide.

header property writable 
header: Nifti1Header | None

The NIfTI header associated with this object.

If a header was explicitly set by the user (at construction or later), this will be pointing to that header.

Otherwise, if the object was created from a NIfTI header, this will be pointing to that header.

Otherwise, if the object was created from a NIfTI image, this will be pointing to the header of that image.

Example

    import nibabel as nb
    image1 = nb.load("image1.nii")
    image2 = nb.load("image2.nii")
    NiftiParser(image1).header                        # `image1.header`
    NiftiParser(header=image2.header).header          # `image2.header`
    NiftiParser(image1, header=image2.header).header  # `image2.header`
    obj = NiftiParser(image1)
    obj.header = image2.header
    obj.header                                        # `image2.header`
system property writable 
system: CoordinateSystem | None

The voxel coordinate system, derived from header, unless it has been set explicitly.

The axes that the intent code marks as irrelevant are dropped. None when there is no header to derive it from.

matrix property 
matrix: ArrayProtocol | None

The affine matrix, of shape (No, Ni + 1), whose last column is the translation component.

homogeneous_matrix property 
homogeneous_matrix: ArrayProtocol

The homogeneous matrix of the affine transformation, of shape (No + 1, Ni + 1). The last row of the homogeneous matrix is [0, 0, ..., 1].

data property writable 
data: ndarray | None

The stored affine matrix, which the matrix view reads.

It is derived from the header, unless it has been set explicitly. It takes the name of the NIfTI parser's image data (the file holds no voxels of interest, only the header's affine), but not its storage: an explicit matrix has a slot of its own, so that reading the image through the parser never stands in for it.

Methods:

sniff classmethod 
sniff(
    file: FileOrContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read file. On a concrete format, score how confident it is that file, in any supported form, is its own.

sniff_file classmethod 
sniff_file(
    file: FileLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the file (path or file-like object). On a concrete format, score how confident it is that the file is its own.

sniff_filename classmethod 
sniff_filename(
    filename: FilenameLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given filename is of the type that this parser can handle.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to sniff.

 required
error bool | type[Exception]

If not False, raise an error if the filename cannot be sniffed.

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the filename is of this type, in [0, 1].
sniff_fileobj classmethod 
sniff_fileobj(
    file: IO,
    error: bool | Type[Exception] = False,
    *,
    version: int | None = None,
    **kwargs,
) -> float

Score how confident the class is that an open file object holds a NIfTI-1 or NIfTI-2 header, or a header of the given version when one is passed.

sniff_content classmethod 
sniff_content(
    content: ContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the content (text or bytes). On a concrete format, score how confident it is that the content is its own.

sniff_bytes classmethod 
sniff_bytes(
    data: bytes,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that bytes hold a NIfTI-1 or NIfTI-2 header.

sniff_text classmethod 
sniff_text(
    text: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the text. On a concrete format, score how confident it is that the text is its own.

sniff_lines classmethod 
sniff_lines(
    lines: Iterable[str],
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the lines. On a concrete format, score how confident it is that the lines are its own.

sniff_line classmethod 
sniff_line(
    line: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the line. On a concrete format, score how confident it is that the line is its own.

load classmethod 
load(other: FileOrContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from other. On a concrete format, build an instance of this class from other, in any supported form.

from_spec classmethod 
from_spec(spec: SourceSpec, **kwargs) -> Self

Load a structured source specification through this dispatcher.

from_file classmethod 
from_file(file: FileLike, **kwargs) -> Self

Build the object from a NIfTI file.

A local path is handed to nibabel by name, so that it owns the file handle and can memory-map the voxels: its array proxy reads them lazily, long after the call returns. A remote path is opened through its own backend instead, since nibabel would take its name for a local file. See _load_nifti.

from_filename classmethod 
from_filename(filename: FilenameLike, **kwargs) -> Self

Build an object from a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_fileobj classmethod 
from_fileobj(fileobj: BinaryIO, **kwargs) -> Self

Build the object from an open NIfTI file object, image data included when the stream allows reading it.

from_content classmethod 
from_content(content: ContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the content (text or bytes). On a concrete format, build an instance of this class from the content.

from_bytes classmethod 
from_bytes(data: bytes, **kwargs) -> Self

Build the object from bytes in NIfTI format.

from_text classmethod 
from_text(text: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the text. On a concrete format, build an instance of this class from the text.

from_lines classmethod 
from_lines(lines: Iterable[str], **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the lines. On a concrete format, build an instance of this class from the lines.

from_line classmethod 
from_line(line: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the line. On a concrete format, build an instance of this class from the line.

save 
save(file: FileLike, **kwargs) -> None

Write the object to a file (path or file-like object).

This is the generic front door to the to_* family. It is named save rather than to because to already means something else on the data models these parsers are mixed into: Transformation.to converts an object to another type. A writer's to was shadowed by it on every writable transformation.

Parameters:

Name Type Description Default
file FileLike

The file to write to.

 required
**kwargs

Parser-specific options.

 {}
to_file 
to_file(file: FileLike, **kwargs) -> None

Write the object to a NIfTI file.

A path is written gzipped when its name ends in .gz: a local path is handed to nibabel by name, and a remote one is opened through its own backend. See _save_nifti. A file-like object is written the uncompressed NIfTI bytes.

to_filename 
to_filename(filename: FilenameLike, **kwargs) -> None

Write the object to a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to write to.

 required
**kwargs

Parser-specific options.

 {}
to_fileobj 
to_fileobj(file: IO, **kwargs) -> None

Write the uncompressed NIfTI-1 encoding of the object to an open file object.

to_bytes 
to_bytes(**kwargs) -> bytes

Return the uncompressed NIfTI-1 encoding of the object.

to_text 
to_text(**kwargs) -> str

Return a text version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A text version of the file.
to_lines 
to_lines(**kwargs) -> Iterator[str]

Return a text version of the file as an iterable of lines.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
Iterator[str]

An iterable of lines representing the object.
to_line 
to_line(**kwargs) -> str

Return a line representing the object.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A line representing the object.
from_dict classmethod 
from_dict(other: Mapping, *args, **kwargs) -> Self

Create an instance of the class from a dictionary-like object.

Only keys in the dictionary that match keyword-like fields of this class, or the keywords its constructor takes without storing them (its InitVars, such as the matrix= of an Affine), will be used. Other keys are ignored, but see from_other, which refuses them.

Additional positional and/or keyword arguments can be provided, and will take precedence over the values in the dictionary.

A key naming a field that this class fixes (a field that cannot be passed to its constructor) is checked instead of used: a dictionary that sets it to anything other than None or the value of this class is refused with a ValueError.

from_instance classmethod 
from_instance(other: Any, *args, **kwargs) -> Self

Create an instance from an instance of a similar class.

See DataModelBase.from_instance. The map of an Affine is copied through its matrix view, not its stored data, which a lazy wrapper derives and a tangent (log=True) stores as its logarithm. A tangent is copied into a tangent through its data.

from_other classmethod 
from_other(other: Any, *args, **kwargs) -> Self

Create an instance from a file, or from anything the data model reads.

A path (str or os.PathLike), an open file, bytes or a structured source (SourceSpec) is read with load: on a dispatcher such as FileBasedImage, the best-matching registered format reads it, and on a concrete format, that format does. Any other value is handed to the data model's own from_other, which reads a mapping field by field, copies an instance of a similar class, and passes anything else to the constructor.

Parameters:

Name Type Description Default
other Any

A file, its content, a mapping, or an instance of a similar class.

 required
*args

Constructor arguments. A file is read with keyword options only.

 ()
**kwargs

Format-specific options when reading a file, and field values otherwise.

 {}

Returns:

Type Description
obj

The object that was built.

Raises:

Type Description
TypeError

If positional arguments come with a file to read.
from_nibabel classmethod 
from_nibabel(nifti: _NiftiObject, **kwargs) -> Self

Build the object from an already-loaded nibabel header or image.

to_nibabel 
to_nibabel(
    like: Any = None, **overrides
) -> Nifti1Image | Nifti2Image

Build a nibabel image whose affine is this transformation.

NIfTI stores an affine only as the geometry of a data array, so a single-voxel placeholder volume carries it. The voxel-to-RAS matrix becomes both the sform and the qform, under the code the source header recorded.

When like is given, non-encoding header fields are copied from it. Keyword arguments override header fields last. The geometry always comes from this transformation.

sniff_nibabel classmethod 
sniff_nibabel(
    nifti: _NiftiObject,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that an already-loaded nibabel header or image matches this format.

The header's magic number is checked first. A header that passes is then scored for how well it matches this particular format, as opposed to another kind of NIfTI-based format.

compute 
compute(
    mode: ModeLike = True,
    *,
    simplify: SimplifyLike = "analytic",
    factor: bool = False,
) -> Self

Compute the transformation, downcasting it to the cheapest compatible kind.

A concrete transformation holds a parameter, so it simplifies to the simplest compatible kind, whose compatibility can be detected with (almost) no overhead. For example, a transformation whose parameter is set to None is treated as an identity.

Parameters:

Name Type Description Default
mode [list of] name or type

Ignored on a leaf. mode gates which kinds compose, and a leaf has nothing to compose; its downcast is gated only by simplify (simplification is decoupled from the compose mode).

 True
simplify simplify policy

How hard this leaf may be looked at. The resolved SimplifyPolicy decides whether the kind-checks run structure-only (analytic) or read values (numeric), or are skipped entirely (none).

 "analytic"
factor bool

Whether to factor this leaf into its axis-group normal form. A leaf factors by wrapping itself in a one-element sequence, so a diagonal affine (say) splits into its per-axis blocks. Off by default.

 False
simplify 
simplify(
    policy: SimplifyLike = "analytic",
    *,
    compute: ModeLike | bool | None = False,
) -> Self

Simplify this transformation under a per-kind policy.

Convenience sugar for compute: t.simplify(policy, compute=mode) is t.compute(mode, simplify=policy).

By default simplify() does no computation at all: compute=False maps to mode=False, which composes nothing (no matrices multiplied, no fields sampled, no lazy inverse materialized). It only downcasts each leaf under policy (analytic by default). Pass an explicit compute=<mode> to also compose that kind.

Parameters:

Name Type Description Default
policy simplify policy

The simplify policy, in the grammar compute accepts.

 "analytic"
compute [list of] name or type

The compose mode. The default, False, composes nothing (mode=False in compute); None would compose every kind. A real mode passes straight through.

 False
square 
square(compute: bool = False, **kwargs) -> Transformation

Return the square of this transformation, self @ self.

The square is the sequence [self, self], which composes when it is computed. It is defined for a transformation that maps a space to itself.

Parameters:

Name Type Description Default
compute bool

Whether to compute the result now rather than return it lazily.

 False
**kwargs

Passed to compute when compute is true.

 {}

Raises:

Type Description
DomainError

If the transformation does not map a space to itself.
to 
to(
    cls: Type[Self] | None = None,
    *,
    lossy: bool = False,
    error: Type[Exception] | Exception | bool = True,
    **kwargs,
) -> Self

Convert this transformation to a different type.

Conversion can be

  • between type: linear.to(Affine) ; or
  • within type: displacement.to(coeff=True) ; or
  • both: coords.to(DisplacementField, coeff=True) .

Parameters:

Name Type Description Default
cls type

The type to convert to. If None, keep the current type.

 None
lossy bool

Whether to allow lossy conversions.

 False
error bool or Exception

Whether to raise an error if the conversion fails:

  • If an Exception, raise it.
  • If True, raise the original error.
  • Otherwise, return the value of error.
 True
**kwargs dict

Attributes to override in the converted transform. This allows transformations to be modified within their type. For example, a DisplacementField can be converted from a field of values to a field of spline coefficients by setting coeff=True in kwargs: a change of encoding flag re-encodes the stored data, and keeps the map. A view's name (field=, matrix=, ...) sets the map, as values, and it is stored in the encoding of the result; data= is stored as given.

 {}

Returns:

Type Description
Transformation

The converted transformation.
inverse 
inverse(compute: bool = False, **kwargs) -> VoxelToRAS

The inverse transformation, from RAS space to voxel space.

NiftiVoxelToRAS 

NiftiVoxelToRAS(
    *,
    _input: CoordinateSystem = VoxelCoordinateSystem(),
    _output: CoordinateSystem = RASmm(),
)

Bases: VoxelToRAS, _NiftiAffine

Affine transformation from voxel space to RAS space, derived from a NIfTI header.

Attributes

PREFIXES class-attribute 
PREFIXES: tuple[str, ...] = ()

Filename prefixes required by this parser, e.g. ("y_", "iy_").

An empty tuple means "no constraint". A parser that constrains the prefix is more specific than one that does not, and wins ties.

Declaring EXTENSIONS and PREFIXES separately states the cross-product implicitly, which is how these conventions actually work: SPM's four names are {y_, iy_} x {.nii, .nii.gz}.

PRIORITY class-attribute 
PRIORITY: int = 0

Explicit tie-breaker, consulted only when specificity cannot decide. Higher wins. Leave at 0 unless two parsers genuinely collide.

header property writable 
header: Nifti1Header | None

The NIfTI header associated with this object.

If a header was explicitly set by the user (at construction or later), this will be pointing to that header.

Otherwise, if the object was created from a NIfTI header, this will be pointing to that header.

Otherwise, if the object was created from a NIfTI image, this will be pointing to the header of that image.

Example

    import nibabel as nb
    image1 = nb.load("image1.nii")
    image2 = nb.load("image2.nii")
    NiftiParser(image1).header                        # `image1.header`
    NiftiParser(header=image2.header).header          # `image2.header`
    NiftiParser(image1, header=image2.header).header  # `image2.header`
    obj = NiftiParser(image1)
    obj.header = image2.header
    obj.header                                        # `image2.header`
system property writable 
system: CoordinateSystem | None

The voxel coordinate system, derived from header, unless it has been set explicitly.

The axes that the intent code marks as irrelevant are dropped. None when there is no header to derive it from.

matrix property 
matrix: ArrayProtocol | None

The affine matrix, of shape (No, Ni + 1), whose last column is the translation component.

homogeneous_matrix property 
homogeneous_matrix: ArrayProtocol

The homogeneous matrix of the affine transformation, of shape (No + 1, Ni + 1). The last row of the homogeneous matrix is [0, 0, ..., 1].

data property writable 
data: ndarray | None

The stored affine matrix, which the matrix view reads.

It is derived from the header, unless it has been set explicitly. It takes the name of the NIfTI parser's image data (the file holds no voxels of interest, only the header's affine), but not its storage: an explicit matrix has a slot of its own, so that reading the image through the parser never stands in for it.

Methods:

sniff classmethod 
sniff(
    file: FileOrContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read file. On a concrete format, score how confident it is that file, in any supported form, is its own.

sniff_file classmethod 
sniff_file(
    file: FileLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the file (path or file-like object). On a concrete format, score how confident it is that the file is its own.

sniff_filename classmethod 
sniff_filename(
    filename: FilenameLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given filename is of the type that this parser can handle.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to sniff.

 required
error bool | type[Exception]

If not False, raise an error if the filename cannot be sniffed.

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the filename is of this type, in [0, 1].
sniff_fileobj classmethod 
sniff_fileobj(
    file: IO,
    error: bool | Type[Exception] = False,
    *,
    version: int | None = None,
    **kwargs,
) -> float

Score how confident the class is that an open file object holds a NIfTI-1 or NIfTI-2 header, or a header of the given version when one is passed.

sniff_content classmethod 
sniff_content(
    content: ContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the content (text or bytes). On a concrete format, score how confident it is that the content is its own.

sniff_bytes classmethod 
sniff_bytes(
    data: bytes,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that bytes hold a NIfTI-1 or NIfTI-2 header.

sniff_text classmethod 
sniff_text(
    text: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the text. On a concrete format, score how confident it is that the text is its own.

sniff_lines classmethod 
sniff_lines(
    lines: Iterable[str],
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the lines. On a concrete format, score how confident it is that the lines are its own.

sniff_line classmethod 
sniff_line(
    line: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the line. On a concrete format, score how confident it is that the line is its own.

load classmethod 
load(other: FileOrContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from other. On a concrete format, build an instance of this class from other, in any supported form.

from_spec classmethod 
from_spec(spec: SourceSpec, **kwargs) -> Self

Load a structured source specification through this dispatcher.

from_file classmethod 
from_file(file: FileLike, **kwargs) -> Self

Build the object from a NIfTI file.

A local path is handed to nibabel by name, so that it owns the file handle and can memory-map the voxels: its array proxy reads them lazily, long after the call returns. A remote path is opened through its own backend instead, since nibabel would take its name for a local file. See _load_nifti.

from_filename classmethod 
from_filename(filename: FilenameLike, **kwargs) -> Self

Build an object from a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_fileobj classmethod 
from_fileobj(fileobj: BinaryIO, **kwargs) -> Self

Build the object from an open NIfTI file object, image data included when the stream allows reading it.

from_content classmethod 
from_content(content: ContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the content (text or bytes). On a concrete format, build an instance of this class from the content.

from_bytes classmethod 
from_bytes(data: bytes, **kwargs) -> Self

Build the object from bytes in NIfTI format.

from_text classmethod 
from_text(text: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the text. On a concrete format, build an instance of this class from the text.

from_lines classmethod 
from_lines(lines: Iterable[str], **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the lines. On a concrete format, build an instance of this class from the lines.

from_line classmethod 
from_line(line: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the line. On a concrete format, build an instance of this class from the line.

save 
save(file: FileLike, **kwargs) -> None

Write the object to a file (path or file-like object).

This is the generic front door to the to_* family. It is named save rather than to because to already means something else on the data models these parsers are mixed into: Transformation.to converts an object to another type. A writer's to was shadowed by it on every writable transformation.

Parameters:

Name Type Description Default
file FileLike

The file to write to.

 required
**kwargs

Parser-specific options.

 {}
to_file 
to_file(file: FileLike, **kwargs) -> None

Write the object to a NIfTI file.

A path is written gzipped when its name ends in .gz: a local path is handed to nibabel by name, and a remote one is opened through its own backend. See _save_nifti. A file-like object is written the uncompressed NIfTI bytes.

to_filename 
to_filename(filename: FilenameLike, **kwargs) -> None

Write the object to a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to write to.

 required
**kwargs

Parser-specific options.

 {}
to_fileobj 
to_fileobj(file: IO, **kwargs) -> None

Write the uncompressed NIfTI-1 encoding of the object to an open file object.

to_bytes 
to_bytes(**kwargs) -> bytes

Return the uncompressed NIfTI-1 encoding of the object.

to_text 
to_text(**kwargs) -> str

Return a text version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A text version of the file.
to_lines 
to_lines(**kwargs) -> Iterator[str]

Return a text version of the file as an iterable of lines.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
Iterator[str]

An iterable of lines representing the object.
to_line 
to_line(**kwargs) -> str

Return a line representing the object.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A line representing the object.
from_dict classmethod 
from_dict(other: Mapping, *args, **kwargs) -> Self

Create an instance of the class from a dictionary-like object.

Only keys in the dictionary that match keyword-like fields of this class, or the keywords its constructor takes without storing them (its InitVars, such as the matrix= of an Affine), will be used. Other keys are ignored, but see from_other, which refuses them.

Additional positional and/or keyword arguments can be provided, and will take precedence over the values in the dictionary.

A key naming a field that this class fixes (a field that cannot be passed to its constructor) is checked instead of used: a dictionary that sets it to anything other than None or the value of this class is refused with a ValueError.

from_instance classmethod 
from_instance(other: Any, *args, **kwargs) -> Self

Create an instance from an instance of a similar class.

See DataModelBase.from_instance. The map of an Affine is copied through its matrix view, not its stored data, which a lazy wrapper derives and a tangent (log=True) stores as its logarithm. A tangent is copied into a tangent through its data.

from_other classmethod 
from_other(other: Any, *args, **kwargs) -> Self

Create an instance from a file, or from anything the data model reads.

A path (str or os.PathLike), an open file, bytes or a structured source (SourceSpec) is read with load: on a dispatcher such as FileBasedImage, the best-matching registered format reads it, and on a concrete format, that format does. Any other value is handed to the data model's own from_other, which reads a mapping field by field, copies an instance of a similar class, and passes anything else to the constructor.

Parameters:

Name Type Description Default
other Any

A file, its content, a mapping, or an instance of a similar class.

 required
*args

Constructor arguments. A file is read with keyword options only.

 ()
**kwargs

Format-specific options when reading a file, and field values otherwise.

 {}

Returns:

Type Description
obj

The object that was built.

Raises:

Type Description
TypeError

If positional arguments come with a file to read.
from_nibabel classmethod 
from_nibabel(nifti: _NiftiObject, **kwargs) -> Self

Build the object from an already-loaded nibabel header or image.

to_nibabel 
to_nibabel(
    like: Any = None, **overrides
) -> Nifti1Image | Nifti2Image

Build a nibabel image whose affine is this transformation.

NIfTI stores an affine only as the geometry of a data array, so a single-voxel placeholder volume carries it. The voxel-to-RAS matrix becomes both the sform and the qform, under the code the source header recorded.

When like is given, non-encoding header fields are copied from it. Keyword arguments override header fields last. The geometry always comes from this transformation.

sniff_nibabel classmethod 
sniff_nibabel(
    nifti: _NiftiObject,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that an already-loaded nibabel header or image matches this format.

The header's magic number is checked first. A header that passes is then scored for how well it matches this particular format, as opposed to another kind of NIfTI-based format.

compute 
compute(
    mode: ModeLike = True,
    *,
    simplify: SimplifyLike = "analytic",
    factor: bool = False,
) -> Self

Compute the transformation, downcasting it to the cheapest compatible kind.

A concrete transformation holds a parameter, so it simplifies to the simplest compatible kind, whose compatibility can be detected with (almost) no overhead. For example, a transformation whose parameter is set to None is treated as an identity.

Parameters:

Name Type Description Default
mode [list of] name or type

Ignored on a leaf. mode gates which kinds compose, and a leaf has nothing to compose; its downcast is gated only by simplify (simplification is decoupled from the compose mode).

 True
simplify simplify policy

How hard this leaf may be looked at. The resolved SimplifyPolicy decides whether the kind-checks run structure-only (analytic) or read values (numeric), or are skipped entirely (none).

 "analytic"
factor bool

Whether to factor this leaf into its axis-group normal form. A leaf factors by wrapping itself in a one-element sequence, so a diagonal affine (say) splits into its per-axis blocks. Off by default.

 False
simplify 
simplify(
    policy: SimplifyLike = "analytic",
    *,
    compute: ModeLike | bool | None = False,
) -> Self

Simplify this transformation under a per-kind policy.

Convenience sugar for compute: t.simplify(policy, compute=mode) is t.compute(mode, simplify=policy).

By default simplify() does no computation at all: compute=False maps to mode=False, which composes nothing (no matrices multiplied, no fields sampled, no lazy inverse materialized). It only downcasts each leaf under policy (analytic by default). Pass an explicit compute=<mode> to also compose that kind.

Parameters:

Name Type Description Default
policy simplify policy

The simplify policy, in the grammar compute accepts.

 "analytic"
compute [list of] name or type

The compose mode. The default, False, composes nothing (mode=False in compute); None would compose every kind. A real mode passes straight through.

 False
square 
square(compute: bool = False, **kwargs) -> Transformation

Return the square of this transformation, self @ self.

The square is the sequence [self, self], which composes when it is computed. It is defined for a transformation that maps a space to itself.

Parameters:

Name Type Description Default
compute bool

Whether to compute the result now rather than return it lazily.

 False
**kwargs

Passed to compute when compute is true.

 {}

Raises:

Type Description
DomainError

If the transformation does not map a space to itself.
to 
to(
    cls: Type[Self] | None = None,
    *,
    lossy: bool = False,
    error: Type[Exception] | Exception | bool = True,
    **kwargs,
) -> Self

Convert this transformation to a different type.

Conversion can be

  • between type: linear.to(Affine) ; or
  • within type: displacement.to(coeff=True) ; or
  • both: coords.to(DisplacementField, coeff=True) .

Parameters:

Name Type Description Default
cls type

The type to convert to. If None, keep the current type.

 None
lossy bool

Whether to allow lossy conversions.

 False
error bool or Exception

Whether to raise an error if the conversion fails:

  • If an Exception, raise it.
  • If True, raise the original error.
  • Otherwise, return the value of error.
 True
**kwargs dict

Attributes to override in the converted transform. This allows transformations to be modified within their type. For example, a DisplacementField can be converted from a field of values to a field of spline coefficients by setting coeff=True in kwargs: a change of encoding flag re-encodes the stored data, and keeps the map. A view's name (field=, matrix=, ...) sets the map, as values, and it is stored in the encoding of the result; data= is stored as given.

 {}

Returns:

Type Description
Transformation

The converted transformation.
inverse 
inverse(compute: bool = False, **kwargs) -> RASToVoxel

The inverse transformation, from RAS space to voxel space.

NiftiBasedTransformation 

NiftiBasedTransformation(
    data_fields: ClassVar[tuple[str, ...]] = (),
    metadata_fields: ClassVar[tuple[str, ...]] = (),
    derived_fields: ClassVar[tuple[str, ...]] = (),
    *,
    _input: CoordinateSystem | None = None,
    _output: CoordinateSystem | None = None,
)

Bases: WritableFileBasedTransformation, NiftiParser

A transformation that is stored in a NIfTI file.

Abstract: it is not decorated with @register_format, so it never takes part in dispatch. Concrete NIfTI transformations inherit from it and register themselves.

Attributes

PREFIXES class-attribute 
PREFIXES: tuple[str, ...] = ()

Filename prefixes required by this parser, e.g. ("y_", "iy_").

An empty tuple means "no constraint". A parser that constrains the prefix is more specific than one that does not, and wins ties.

Declaring EXTENSIONS and PREFIXES separately states the cross-product implicitly, which is how these conventions actually work: SPM's four names are {y_, iy_} x {.nii, .nii.gz}.

PRIORITY class-attribute 
PRIORITY: int = 0

Explicit tie-breaker, consulted only when specificity cannot decide. Higher wins. Leave at 0 unless two parsers genuinely collide.

header property writable 
header: Nifti1Header | None

The NIfTI header associated with this object.

If a header was explicitly set by the user (at construction or later), this will be pointing to that header.

Otherwise, if the object was created from a NIfTI header, this will be pointing to that header.

Otherwise, if the object was created from a NIfTI image, this will be pointing to the header of that image.

Example

    import nibabel as nb
    image1 = nb.load("image1.nii")
    image2 = nb.load("image2.nii")
    NiftiParser(image1).header                        # `image1.header`
    NiftiParser(header=image2.header).header          # `image2.header`
    NiftiParser(image1, header=image2.header).header  # `image2.header`
    obj = NiftiParser(image1)
    obj.header = image2.header
    obj.header                                        # `image2.header`
data property writable 
data: ArrayProtocol | None

The image data, read lazily from image and cached, unless it has been set explicitly.

The axes that the intent code marks as irrelevant, such as a singleton axis before a vector's components, are dropped.

system property writable 
system: CoordinateSystem | None

The voxel coordinate system, derived from header, unless it has been set explicitly.

The axes that the intent code marks as irrelevant are dropped. None when there is no header to derive it from.

Methods:

sniff classmethod 
sniff(
    file: FileOrContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read file. On a concrete format, score how confident it is that file, in any supported form, is its own.

sniff_file classmethod 
sniff_file(
    file: FileLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the file (path or file-like object). On a concrete format, score how confident it is that the file is its own.

sniff_filename classmethod 
sniff_filename(
    filename: FilenameLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given filename is of the type that this parser can handle.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to sniff.

 required
error bool | type[Exception]

If not False, raise an error if the filename cannot be sniffed.

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the filename is of this type, in [0, 1].
sniff_fileobj classmethod 
sniff_fileobj(
    file: IO,
    error: bool | Type[Exception] = False,
    *,
    version: int | None = None,
    **kwargs,
) -> float

Score how confident the class is that an open file object holds a NIfTI-1 or NIfTI-2 header, or a header of the given version when one is passed.

sniff_content classmethod 
sniff_content(
    content: ContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the content (text or bytes). On a concrete format, score how confident it is that the content is its own.

sniff_bytes classmethod 
sniff_bytes(
    data: bytes,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that bytes hold a NIfTI-1 or NIfTI-2 header.

sniff_text classmethod 
sniff_text(
    text: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the text. On a concrete format, score how confident it is that the text is its own.

sniff_lines classmethod 
sniff_lines(
    lines: Iterable[str],
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the lines. On a concrete format, score how confident it is that the lines are its own.

sniff_line classmethod 
sniff_line(
    line: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the line. On a concrete format, score how confident it is that the line is its own.

load classmethod 
load(other: FileOrContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from other. On a concrete format, build an instance of this class from other, in any supported form.

from_spec classmethod 
from_spec(spec: SourceSpec, **kwargs) -> Self

Load a structured source specification through this dispatcher.

from_file classmethod 
from_file(file: FileLike, **kwargs) -> Self

Build the object from a NIfTI file.

A local path is handed to nibabel by name, so that it owns the file handle and can memory-map the voxels: its array proxy reads them lazily, long after the call returns. A remote path is opened through its own backend instead, since nibabel would take its name for a local file. See _load_nifti.

from_filename classmethod 
from_filename(filename: FilenameLike, **kwargs) -> Self

Build an object from a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_fileobj classmethod 
from_fileobj(fileobj: BinaryIO, **kwargs) -> Self

Build the object from an open NIfTI file object, image data included when the stream allows reading it.

from_content classmethod 
from_content(content: ContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the content (text or bytes). On a concrete format, build an instance of this class from the content.

from_bytes classmethod 
from_bytes(data: bytes, **kwargs) -> Self

Build the object from bytes in NIfTI format.

from_text classmethod 
from_text(text: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the text. On a concrete format, build an instance of this class from the text.

from_lines classmethod 
from_lines(lines: Iterable[str], **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the lines. On a concrete format, build an instance of this class from the lines.

from_line classmethod 
from_line(line: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the line. On a concrete format, build an instance of this class from the line.

save 
save(file: FileLike, **kwargs) -> None

Write the object to a file (path or file-like object).

This is the generic front door to the to_* family. It is named save rather than to because to already means something else on the data models these parsers are mixed into: Transformation.to converts an object to another type. A writer's to was shadowed by it on every writable transformation.

Parameters:

Name Type Description Default
file FileLike

The file to write to.

 required
**kwargs

Parser-specific options.

 {}
to_file 
to_file(file: FileLike, **kwargs) -> None

Write the object to a NIfTI file.

A path is written gzipped when its name ends in .gz: a local path is handed to nibabel by name, and a remote one is opened through its own backend. See _save_nifti. A file-like object is written the uncompressed NIfTI bytes.

to_filename 
to_filename(filename: FilenameLike, **kwargs) -> None

Write the object to a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to write to.

 required
**kwargs

Parser-specific options.

 {}
to_fileobj 
to_fileobj(file: IO, **kwargs) -> None

Write the uncompressed NIfTI-1 encoding of the object to an open file object.

to_bytes 
to_bytes(**kwargs) -> bytes

Return the uncompressed NIfTI-1 encoding of the object.

to_text 
to_text(**kwargs) -> str

Return a text version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A text version of the file.
to_lines 
to_lines(**kwargs) -> Iterator[str]

Return a text version of the file as an iterable of lines.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
Iterator[str]

An iterable of lines representing the object.
to_line 
to_line(**kwargs) -> str

Return a line representing the object.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A line representing the object.
from_dict classmethod 
from_dict(other: Mapping, *args, **kwargs) -> Self

Create an instance of the class from a dictionary-like object.

Only keys in the dictionary that match keyword-like fields of this class, or the keywords its constructor takes without storing them (its InitVars, such as the matrix= of an Affine), will be used. Other keys are ignored, but see from_other, which refuses them.

Additional positional and/or keyword arguments can be provided, and will take precedence over the values in the dictionary.

A key naming a field that this class fixes (a field that cannot be passed to its constructor) is checked instead of used: a dictionary that sets it to anything other than None or the value of this class is refused with a ValueError.

from_instance classmethod 
from_instance(other: Any, *args, **kwargs) -> Self

Create an instance from an instance of a similar class.

The data model copies the fields both classes share, by name. A field that a file format declares for its own use -- such as the nibabel image and header of the NIfTI and MGH formats -- is only copied from an object of that same format: from any other object, a field of the same name holds something else (a NIfTI image is no MGH image), so this class's default is kept instead. Saving a NIfTI image to MGH, or the converse, therefore converts the data model only, and the format-specific state is rebuilt by the writer.

from_other classmethod 
from_other(other: Any, *args, **kwargs) -> Self

Create an instance from a file, or from anything the data model reads.

A path (str or os.PathLike), an open file, bytes or a structured source (SourceSpec) is read with load: on a dispatcher such as FileBasedImage, the best-matching registered format reads it, and on a concrete format, that format does. Any other value is handed to the data model's own from_other, which reads a mapping field by field, copies an instance of a similar class, and passes anything else to the constructor.

Parameters:

Name Type Description Default
other Any

A file, its content, a mapping, or an instance of a similar class.

 required
*args

Constructor arguments. A file is read with keyword options only.

 ()
**kwargs

Format-specific options when reading a file, and field values otherwise.

 {}

Returns:

Type Description
obj

The object that was built.

Raises:

Type Description
TypeError

If positional arguments come with a file to read.
from_nibabel classmethod 
from_nibabel(nifti: _NiftiObject, **kwargs) -> Self

Build the object from an already-loaded nibabel header or image.

to_nibabel 
to_nibabel(**kwargs) -> Nifti1Image

Build the nibabel image that encodes this object.

Each concrete NIfTI format overrides this method to describe how its own contents map onto a NIfTI image. The other writer methods are defined in terms of this one.

sniff_nibabel classmethod 
sniff_nibabel(
    nifti: _NiftiObject,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that an already-loaded nibabel header or image matches this format.

The header's magic number is checked first. A header that passes is then scored for how well it matches this particular format, as opposed to another kind of NIfTI-based format.

compute 
compute(
    mode: ModeLike = True,
    *,
    simplify: SimplifyLike = "analytic",
    factor: bool = False,
) -> Self

Compute the transformation, if it is not already fully defined.

Parameters:

Name Type Description Default
mode [list of] name or type

Which kinds of transformations to materialize. True (the default) admits every kind. On a leaf transformation, if a mode is given and this leaf is not admitted by it, the leaf is returned unchanged. Keys are transformation types, names or symbols (e.g., "affine", "Aff", "rigid", "SO(3)").

 True
simplify SimplifyLike
"analytic"
What

Whether to simplify the transformation prior if possible, and how hard to try to simplify them. * "analytic" (the default) looks at the type structure only; * "numeric" looks at the numeric values of the transformation; * False/"none"/None disables simplification.

 required
factor bool

Whether to rewrite the transformation into its axis-group normal form, splitting it into independent factors that each act on a group of axes that transform together. Off by default, so a plain compute() result is unchanged. Nothing is ever composed across axis groups; mode still decides whether the restricted pieces inside a group compose.

 False
simplify 
simplify(
    policy: SimplifyLike = "analytic",
    *,
    compute: ModeLike | bool | None = False,
) -> Self

Simplify this transformation under a per-kind policy.

Convenience sugar for compute: t.simplify(policy, compute=mode) is t.compute(mode, simplify=policy).

By default simplify() does no computation at all: compute=False maps to mode=False, which composes nothing (no matrices multiplied, no fields sampled, no lazy inverse materialized). It only downcasts each leaf under policy (analytic by default). Pass an explicit compute=<mode> to also compose that kind.

Parameters:

Name Type Description Default
policy simplify policy

The simplify policy, in the grammar compute accepts.

 "analytic"
compute [list of] name or type

The compose mode. The default, False, composes nothing (mode=False in compute); None would compose every kind. A real mode passes straight through.

 False
inverse 
inverse(compute: bool = False, **kwargs) -> Self

Return the inverse of this transformation.

Some classes of transformations return a lazy inverse by default, which is only evaluated when the compute() method is called. This allows for efficient composition of transformations. Or the inverse can be computed immediately by setting compute=True.

The inverse can also be obtained using the __invert__ operator: T.inverse() is equivalent to ~T.

square 
square(compute: bool = False, **kwargs) -> Transformation

Return the square of this transformation, self @ self.

The square is the sequence [self, self], which composes when it is computed. It is defined for a transformation that maps a space to itself.

Parameters:

Name Type Description Default
compute bool

Whether to compute the result now rather than return it lazily.

 False
**kwargs

Passed to compute when compute is true.

 {}

Raises:

Type Description
DomainError

If the transformation does not map a space to itself.
sqrt 
sqrt(compute: bool = False, **kwargs) -> Transformation

Return the principal square root of this transformation.

The square root S of T is the transformation with S @ S == T, the half-transformation. The principal one, whose linear part has its eigenvalues in the open right half-plane, is unique, and it is of the same kind as T: the square root of a rotation is a rotation, of a translation a translation, of a scaling a scaling, of an affine an affine. The square root of a permutation is a Linear transformation.

The square root is lazy: an Sqrt wrapper is returned, and computed when it is applied, computed or converted. A transformation that needs no wrapper (an identity) is returned as is. A Sequence is reduced first (see Sequence.sqrt).

Parameters:

Name Type Description Default
compute bool

Whether to compute the result now rather than return it lazily.

 False
**kwargs

Passed to compute when compute is true.

 {}

Raises:

Type Description
DomainError

If the transformation does not map a space to itself, or, when the result is computed, if its linear part has an eigenvalue on the closed negative real axis (a reflection, a rotation by a half turn, a singular matrix), so that it has no real principal square root.
NotImplementedError

If brainhops does not compute the square root of this kind of transformation. A displacement field has one only when it is a stationary velocity field (log=True), whose square root halves its velocity.
to 
to(
    cls: Type[Self] | None = None,
    *,
    lossy: bool = False,
    error: Type[Exception] | Exception | bool = True,
    **kwargs,
) -> Self

Convert this transformation to a different type.

Conversion can be

  • between type: linear.to(Affine) ; or
  • within type: displacement.to(coeff=True) ; or
  • both: coords.to(DisplacementField, coeff=True) .

Parameters:

Name Type Description Default
cls type

The type to convert to. If None, keep the current type.

 None
lossy bool

Whether to allow lossy conversions.

 False
error bool or Exception

Whether to raise an error if the conversion fails:

  • If an Exception, raise it.
  • If True, raise the original error.
  • Otherwise, return the value of error.
 True
**kwargs dict

Attributes to override in the converted transform. This allows transformations to be modified within their type. For example, a DisplacementField can be converted from a field of values to a field of spline coefficients by setting coeff=True in kwargs: a change of encoding flag re-encodes the stored data, and keeps the map. A view's name (field=, matrix=, ...) sets the map, as values, and it is stored in the encoding of the result; data= is stored as given.

 {}

Returns:

Type Description
Transformation

The converted transformation.

NiftiRASCoordinatesField 

NiftiRASCoordinatesField(
    *,
    _input: CoordinateSystem = VoxelCoordinateSystem(),
    _output: CoordinateSystem = RASmm(),
)

Bases: RASCoordinatesField, NiftiBasedTransformation

Field of RAS coordinates, stored in a NIfTI file.

Attributes

PREFIXES class-attribute 
PREFIXES: tuple[str, ...] = ()

Filename prefixes required by this parser, e.g. ("y_", "iy_").

An empty tuple means "no constraint". A parser that constrains the prefix is more specific than one that does not, and wins ties.

Declaring EXTENSIONS and PREFIXES separately states the cross-product implicitly, which is how these conventions actually work: SPM's four names are {y_, iy_} x {.nii, .nii.gz}.

PRIORITY class-attribute 
PRIORITY: int = 0

Explicit tie-breaker, consulted only when specificity cannot decide. Higher wins. Leave at 0 unless two parsers genuinely collide.

header property writable 
header: Nifti1Header | None

The NIfTI header associated with this object.

If a header was explicitly set by the user (at construction or later), this will be pointing to that header.

Otherwise, if the object was created from a NIfTI header, this will be pointing to that header.

Otherwise, if the object was created from a NIfTI image, this will be pointing to the header of that image.

Example

    import nibabel as nb
    image1 = nb.load("image1.nii")
    image2 = nb.load("image2.nii")
    NiftiParser(image1).header                        # `image1.header`
    NiftiParser(header=image2.header).header          # `image2.header`
    NiftiParser(image1, header=image2.header).header  # `image2.header`
    obj = NiftiParser(image1)
    obj.header = image2.header
    obj.header                                        # `image2.header`
system property writable 
system: CoordinateSystem | None

The voxel coordinate system, derived from header, unless it has been set explicitly.

The axes that the intent code marks as irrelevant are dropped. None when there is no header to derive it from.

data property writable 
data: ArrayProtocol | None

The field of RAS coordinates, as an (X, Y, Z, 3) array.

It is the image data that the NIfTI parser reads from the file, and the array this field stores: its field view reads it. NIfTI stores a vector field as (X, Y, Z, 1, 3), with the components in the fifth axis, and SPM writes its y_ fields that way. The singleton axis before the components is dropped, or the field would be sampled as a 4-D grid of 3-vectors.

Methods:

sniff classmethod 
sniff(
    file: FileOrContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read file. On a concrete format, score how confident it is that file, in any supported form, is its own.

sniff_file classmethod 
sniff_file(
    file: FileLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the file (path or file-like object). On a concrete format, score how confident it is that the file is its own.

sniff_filename classmethod 
sniff_filename(
    filename: FilenameLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given filename is of the type that this parser can handle.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to sniff.

 required
error bool | type[Exception]

If not False, raise an error if the filename cannot be sniffed.

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the filename is of this type, in [0, 1].
sniff_fileobj classmethod 
sniff_fileobj(
    file: IO,
    error: bool | Type[Exception] = False,
    *,
    version: int | None = None,
    **kwargs,
) -> float

Score how confident the class is that an open file object holds a NIfTI-1 or NIfTI-2 header, or a header of the given version when one is passed.

sniff_content classmethod 
sniff_content(
    content: ContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the content (text or bytes). On a concrete format, score how confident it is that the content is its own.

sniff_bytes classmethod 
sniff_bytes(
    data: bytes,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that bytes hold a NIfTI-1 or NIfTI-2 header.

sniff_text classmethod 
sniff_text(
    text: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the text. On a concrete format, score how confident it is that the text is its own.

sniff_lines classmethod 
sniff_lines(
    lines: Iterable[str],
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the lines. On a concrete format, score how confident it is that the lines are its own.

sniff_line classmethod 
sniff_line(
    line: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the line. On a concrete format, score how confident it is that the line is its own.

load classmethod 
load(other: FileOrContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from other. On a concrete format, build an instance of this class from other, in any supported form.

from_spec classmethod 
from_spec(spec: SourceSpec, **kwargs) -> Self

Load a structured source specification through this dispatcher.

from_file classmethod 
from_file(file: FileLike, **kwargs) -> Self

Build the object from a NIfTI file.

A local path is handed to nibabel by name, so that it owns the file handle and can memory-map the voxels: its array proxy reads them lazily, long after the call returns. A remote path is opened through its own backend instead, since nibabel would take its name for a local file. See _load_nifti.

from_filename classmethod 
from_filename(filename: FilenameLike, **kwargs) -> Self

Build an object from a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_fileobj classmethod 
from_fileobj(fileobj: BinaryIO, **kwargs) -> Self

Build the object from an open NIfTI file object, image data included when the stream allows reading it.

from_content classmethod 
from_content(content: ContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the content (text or bytes). On a concrete format, build an instance of this class from the content.

from_bytes classmethod 
from_bytes(data: bytes, **kwargs) -> Self

Build the object from bytes in NIfTI format.

from_text classmethod 
from_text(text: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the text. On a concrete format, build an instance of this class from the text.

from_lines classmethod 
from_lines(lines: Iterable[str], **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the lines. On a concrete format, build an instance of this class from the lines.

from_line classmethod 
from_line(line: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the line. On a concrete format, build an instance of this class from the line.

save 
save(file: FileLike, **kwargs) -> None

Write the object to a file (path or file-like object).

This is the generic front door to the to_* family. It is named save rather than to because to already means something else on the data models these parsers are mixed into: Transformation.to converts an object to another type. A writer's to was shadowed by it on every writable transformation.

Parameters:

Name Type Description Default
file FileLike

The file to write to.

 required
**kwargs

Parser-specific options.

 {}
to_file 
to_file(file: FileLike, **kwargs) -> None

Write the object to a NIfTI file.

A path is written gzipped when its name ends in .gz: a local path is handed to nibabel by name, and a remote one is opened through its own backend. See _save_nifti. A file-like object is written the uncompressed NIfTI bytes.

to_filename 
to_filename(filename: FilenameLike, **kwargs) -> None

Write the object to a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to write to.

 required
**kwargs

Parser-specific options.

 {}
to_fileobj 
to_fileobj(file: IO, **kwargs) -> None

Write the uncompressed NIfTI-1 encoding of the object to an open file object.

to_bytes 
to_bytes(**kwargs) -> bytes

Return the uncompressed NIfTI-1 encoding of the object.

to_text 
to_text(**kwargs) -> str

Return a text version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A text version of the file.
to_lines 
to_lines(**kwargs) -> Iterator[str]

Return a text version of the file as an iterable of lines.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
Iterator[str]

An iterable of lines representing the object.
to_line 
to_line(**kwargs) -> str

Return a line representing the object.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A line representing the object.
from_dict classmethod 
from_dict(other: Mapping, *args, **kwargs) -> Self

Create an instance of the class from a dictionary-like object.

Only keys in the dictionary that match keyword-like fields of this class, or the keywords its constructor takes without storing them (its InitVars, such as the matrix= of an Affine), will be used. Other keys are ignored, but see from_other, which refuses them.

Additional positional and/or keyword arguments can be provided, and will take precedence over the values in the dictionary.

A key naming a field that this class fixes (a field that cannot be passed to its constructor) is checked instead of used: a dictionary that sets it to anything other than None or the value of this class is refused with a ValueError.

from_instance classmethod 
from_instance(other: Any, *args, **kwargs) -> Self

Create an instance from an instance of a similar class.

See DataModelBase.from_instance. A lazy wrapper derives its data and its flags, so they are read through their public names.

from_other classmethod 
from_other(other: Any, *args, **kwargs) -> Self

Create an instance from a file, or from anything the data model reads.

A path (str or os.PathLike), an open file, bytes or a structured source (SourceSpec) is read with load: on a dispatcher such as FileBasedImage, the best-matching registered format reads it, and on a concrete format, that format does. Any other value is handed to the data model's own from_other, which reads a mapping field by field, copies an instance of a similar class, and passes anything else to the constructor.

Parameters:

Name Type Description Default
other Any

A file, its content, a mapping, or an instance of a similar class.

 required
*args

Constructor arguments. A file is read with keyword options only.

 ()
**kwargs

Format-specific options when reading a file, and field values otherwise.

 {}

Returns:

Type Description
obj

The object that was built.

Raises:

Type Description
TypeError

If positional arguments come with a file to read.
from_nibabel classmethod 
from_nibabel(nifti: _NiftiObject, **kwargs) -> Self

Build the object from an already-loaded nibabel header or image.

sniff_nibabel classmethod 
sniff_nibabel(
    nifti: _NiftiObject,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that an already-loaded nibabel header or image matches this format.

The header's magic number is checked first. A header that passes is then scored for how well it matches this particular format, as opposed to another kind of NIfTI-based format.

compute 
compute(
    mode: ModeLike = True,
    *,
    simplify: SimplifyLike = "analytic",
    factor: bool = False,
) -> Self

Compute the transformation, downcasting it to the cheapest compatible kind.

A concrete transformation holds a parameter, so it simplifies to the simplest compatible kind, whose compatibility can be detected with (almost) no overhead. For example, a transformation whose parameter is set to None is treated as an identity.

Parameters:

Name Type Description Default
mode [list of] name or type

Ignored on a leaf. mode gates which kinds compose, and a leaf has nothing to compose; its downcast is gated only by simplify (simplification is decoupled from the compose mode).

 True
simplify simplify policy

How hard this leaf may be looked at. The resolved SimplifyPolicy decides whether the kind-checks run structure-only (analytic) or read values (numeric), or are skipped entirely (none).

 "analytic"
factor bool

Whether to factor this leaf into its axis-group normal form. A leaf factors by wrapping itself in a one-element sequence, so a diagonal affine (say) splits into its per-axis blocks. Off by default.

 False
simplify 
simplify(
    policy: SimplifyLike = "analytic",
    *,
    compute: ModeLike | bool | None = False,
) -> Self

Simplify this transformation under a per-kind policy.

Convenience sugar for compute: t.simplify(policy, compute=mode) is t.compute(mode, simplify=policy).

By default simplify() does no computation at all: compute=False maps to mode=False, which composes nothing (no matrices multiplied, no fields sampled, no lazy inverse materialized). It only downcasts each leaf under policy (analytic by default). Pass an explicit compute=<mode> to also compose that kind.

Parameters:

Name Type Description Default
policy simplify policy

The simplify policy, in the grammar compute accepts.

 "analytic"
compute [list of] name or type

The compose mode. The default, False, composes nothing (mode=False in compute); None would compose every kind. A real mode passes straight through.

 False
square 
square(compute: bool = False, **kwargs) -> Transformation

Return the square of this transformation, self @ self.

The square is the sequence [self, self], which composes when it is computed. It is defined for a transformation that maps a space to itself.

Parameters:

Name Type Description Default
compute bool

Whether to compute the result now rather than return it lazily.

 False
**kwargs

Passed to compute when compute is true.

 {}

Raises:

Type Description
DomainError

If the transformation does not map a space to itself.
to 
to(
    cls: Type[Self] | None = None,
    *,
    lossy: bool = False,
    error: Type[Exception] | Exception | bool = True,
    **kwargs,
) -> Self

Convert this transformation to a different type.

Conversion can be

  • between type: linear.to(Affine) ; or
  • within type: displacement.to(coeff=True) ; or
  • both: coords.to(DisplacementField, coeff=True) .

Parameters:

Name Type Description Default
cls type

The type to convert to. If None, keep the current type.

 None
lossy bool

Whether to allow lossy conversions.

 False
error bool or Exception

Whether to raise an error if the conversion fails:

  • If an Exception, raise it.
  • If True, raise the original error.
  • Otherwise, return the value of error.
 True
**kwargs dict

Attributes to override in the converted transform. This allows transformations to be modified within their type. For example, a DisplacementField can be converted from a field of values to a field of spline coefficients by setting coeff=True in kwargs: a change of encoding flag re-encodes the stored data, and keeps the map. A view's name (field=, matrix=, ...) sets the map, as values, and it is stored in the encoding of the result; data= is stored as given.

 {}

Returns:

Type Description
Transformation

The converted transformation.
field 
field() -> ArrayProtocol | None

The field, as values: an array of shape (*shape, ndim).

It is data itself when coeff is false, and data decoded from spline coefficients (once, then cached) when it is true.

to_nibabel 
to_nibabel(
    like: Any = None, **overrides
) -> Nifti1Image | Nifti2Image

Build the nibabel image that encodes this field of RAS coordinates.

The field array becomes the NIfTI data array, and the header carries the VECTOR (1007) intent code, with SPM's intent name "Mapping", that marks the file as a field of coordinates rather than a plain image. DISPVECT (1006) is not used: the standard reserves it for displacements, and ITK and brainhops read it as such. The voxel-to-RAS affine of the grid is taken from the source header when the field was read from one, and is the identity otherwise.

The field array keeps its own array backend. A cupy or dask array is passed through rather than coerced into numpy. When like is given, non-encoding header fields are copied from it. Keyword arguments override header fields last, so an explicit value wins.

NiftiRASDisplacementField magic 

NiftiRASDisplacementField(
    *, log: bool = False, steps: int | None = None
)

Bases: ImmutableSequence, NiftiBasedTransformation

Field of RAS displacements, stored in a NIfTI file.

This is the DISPVECT (1006) field of the NIfTI-1 standard: each voxel holds the displacement, in RAS millimetres, of the point at its centre, and the field maps RAS to RAS as x -> x + u(x). It is how ITK 5.4 and later reads and writes a DISPVECT image.

A DisplacementField adds its values in the units of its own grid, so the field is the ImmutableSequence of three named slots:

Slot Transformation
ras2voxel RAS world coordinates to the field's voxels
displacement the displacement field, in voxel units
voxel2ras the field's voxels back to RAS world

The displacements are interpolated linearly and extended with the nearest value outside the grid, as ITK's DisplacementFieldTransform does by default.

The file may hold a stationary velocity instead, whose flow at time one is the map: the standard has no code for one, so it is said with the log option (warp.nii.gz|displacements|log:true, or its alias warp.nii.gz|svf; in Python, load(path, log=True)). The displacement slot is then a StationaryVelocityField, integrated with steps squaring steps (|svf|steps:6). The field is written in the encoding the options say: a velocity when log is set, and otherwise the displacement, which a velocity is integrated into.

Attributes

PREFIXES class-attribute 
PREFIXES: tuple[str, ...] = ()

Filename prefixes required by this parser, e.g. ("y_", "iy_").

An empty tuple means "no constraint". A parser that constrains the prefix is more specific than one that does not, and wins ties.

Declaring EXTENSIONS and PREFIXES separately states the cross-product implicitly, which is how these conventions actually work: SPM's four names are {y_, iy_} x {.nii, .nii.gz}.

PRIORITY class-attribute 
PRIORITY: int = 0

Explicit tie-breaker, consulted only when specificity cannot decide. Higher wins. Leave at 0 unless two parsers genuinely collide.

header property writable 
header: Nifti1Header | None

The NIfTI header associated with this object.

If a header was explicitly set by the user (at construction or later), this will be pointing to that header.

Otherwise, if the object was created from a NIfTI header, this will be pointing to that header.

Otherwise, if the object was created from a NIfTI image, this will be pointing to the header of that image.

Example

    import nibabel as nb
    image1 = nb.load("image1.nii")
    image2 = nb.load("image2.nii")
    NiftiParser(image1).header                        # `image1.header`
    NiftiParser(header=image2.header).header          # `image2.header`
    NiftiParser(image1, header=image2.header).header  # `image2.header`
    obj = NiftiParser(image1)
    obj.header = image2.header
    obj.header                                        # `image2.header`
data property writable 
data: ArrayProtocol | None

The image data, read lazily from image and cached, unless it has been set explicitly.

The axes that the intent code marks as irrelevant, such as a singleton axis before a vector's components, are dropped.

system property writable 
system: CoordinateSystem | None

The voxel coordinate system, derived from header, unless it has been set explicitly.

The axes that the intent code marks as irrelevant are dropped. None when there is no header to derive it from.

degree class-attribute 
degree: int = 1

The spline degree used to interpolate the field.

bound class-attribute 
bound: BoundaryCondition = BoundaryCondition.nearest

The boundary condition used outside of the field of view.

ras2voxel property 
ras2voxel: Transformation | None

The affine from RAS world coordinates to the field's voxels.

displacement property 
displacement: Transformation | None

The displacement field, in the voxel units of its grid (a velocity, with log).

voxel2ras property 
voxel2ras: Transformation | None

The affine from the field's voxels back to RAS world.

Methods:

sniff classmethod 
sniff(
    file: FileOrContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read file. On a concrete format, score how confident it is that file, in any supported form, is its own.

sniff_file classmethod 
sniff_file(
    file: FileLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the file (path or file-like object). On a concrete format, score how confident it is that the file is its own.

sniff_filename classmethod 
sniff_filename(
    filename: FilenameLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given filename is of the type that this parser can handle.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to sniff.

 required
error bool | type[Exception]

If not False, raise an error if the filename cannot be sniffed.

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the filename is of this type, in [0, 1].
sniff_fileobj classmethod 
sniff_fileobj(
    file: IO,
    error: bool | Type[Exception] = False,
    *,
    version: int | None = None,
    **kwargs,
) -> float

Score how confident the class is that an open file object holds a NIfTI-1 or NIfTI-2 header, or a header of the given version when one is passed.

sniff_content classmethod 
sniff_content(
    content: ContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the content (text or bytes). On a concrete format, score how confident it is that the content is its own.

sniff_bytes classmethod 
sniff_bytes(
    data: bytes,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that bytes hold a NIfTI-1 or NIfTI-2 header.

sniff_text classmethod 
sniff_text(
    text: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the text. On a concrete format, score how confident it is that the text is its own.

sniff_lines classmethod 
sniff_lines(
    lines: Iterable[str],
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the lines. On a concrete format, score how confident it is that the lines are its own.

sniff_line classmethod 
sniff_line(
    line: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> type | None

On a dispatcher, identify which registered format would read the line. On a concrete format, score how confident it is that the line is its own.

load classmethod 
load(other: FileOrContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from other. On a concrete format, build an instance of this class from other, in any supported form.

from_spec classmethod 
from_spec(spec: SourceSpec, **kwargs) -> Self

Load a structured source specification through this dispatcher.

from_filename classmethod 
from_filename(filename: FilenameLike, **kwargs) -> Self

Build an object from a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_content classmethod 
from_content(content: ContentLike, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the content (text or bytes). On a concrete format, build an instance of this class from the content.

from_bytes classmethod 
from_bytes(data: bytes, **kwargs) -> Self

Build the object from bytes in NIfTI format.

from_text classmethod 
from_text(text: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the text. On a concrete format, build an instance of this class from the text.

from_lines classmethod 
from_lines(lines: Iterable[str], **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the lines. On a concrete format, build an instance of this class from the lines.

from_line classmethod 
from_line(line: str, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the line. On a concrete format, build an instance of this class from the line.

save 
save(file: FileLike, **kwargs) -> None

Write the object to a file (path or file-like object).

This is the generic front door to the to_* family. It is named save rather than to because to already means something else on the data models these parsers are mixed into: Transformation.to converts an object to another type. A writer's to was shadowed by it on every writable transformation.

Parameters:

Name Type Description Default
file FileLike

The file to write to.

 required
**kwargs

Parser-specific options.

 {}
to_file 
to_file(file: FileLike, **kwargs) -> None

Write the object to a NIfTI file.

A path is written gzipped when its name ends in .gz: a local path is handed to nibabel by name, and a remote one is opened through its own backend. See _save_nifti. A file-like object is written the uncompressed NIfTI bytes.

to_filename 
to_filename(filename: FilenameLike, **kwargs) -> None

Write the object to a filename.

Parameters:

Name Type Description Default
filename FilenameLike

The filename to write to.

 required
**kwargs

Parser-specific options.

 {}
to_fileobj 
to_fileobj(file: IO, **kwargs) -> None

Write the uncompressed NIfTI-1 encoding of the object to an open file object.

to_bytes 
to_bytes(**kwargs) -> bytes

Return the uncompressed NIfTI-1 encoding of the object.

to_text 
to_text(**kwargs) -> str

Return a text version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A text version of the file.
to_lines 
to_lines(**kwargs) -> Iterator[str]

Return a text version of the file as an iterable of lines.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
Iterator[str]

An iterable of lines representing the object.
to_line 
to_line(**kwargs) -> str

Return a line representing the object.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
str

A line representing the object.
from_dict classmethod 
from_dict(other: Mapping, *args, **kwargs) -> Self

Create an instance of the class from a dictionary-like object.

Only keys in the dictionary that match keyword-like fields of this class, or the keywords its constructor takes without storing them (its InitVars, such as the matrix= of an Affine), will be used. Other keys are ignored, but see from_other, which refuses them.

Additional positional and/or keyword arguments can be provided, and will take precedence over the values in the dictionary.

A key naming a field that this class fixes (a field that cannot be passed to its constructor) is checked instead of used: a dictionary that sets it to anything other than None or the value of this class is refused with a ValueError.

from_other classmethod 
from_other(other: Any, *args, **kwargs) -> Self

Create an instance from a file, or from anything the data model reads.

A path (str or os.PathLike), an open file, bytes or a structured source (SourceSpec) is read with load: on a dispatcher such as FileBasedImage, the best-matching registered format reads it, and on a concrete format, that format does. Any other value is handed to the data model's own from_other, which reads a mapping field by field, copies an instance of a similar class, and passes anything else to the constructor.

Parameters:

Name Type Description Default
other Any

A file, its content, a mapping, or an instance of a similar class.

 required
*args

Constructor arguments. A file is read with keyword options only.

 ()
**kwargs

Format-specific options when reading a file, and field values otherwise.

 {}

Returns:

Type Description
obj

The object that was built.

Raises:

Type Description
TypeError

If positional arguments come with a file to read.
from_nibabel classmethod 
from_nibabel(nifti: _NiftiObject, **kwargs) -> Self

Build the object from an already-loaded nibabel header or image.

sniff_nibabel classmethod 
sniff_nibabel(
    nifti: _NiftiObject,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Score how confident the class is that an already-loaded nibabel header or image matches this format.

The header's magic number is checked first. A header that passes is then scored for how well it matches this particular format, as opposed to another kind of NIfTI-based format.

compute 
compute(
    mode: ModeLike = True,
    *,
    simplify: SimplifyLike = "analytic",
    factor: bool = False,
) -> Transformation

Compute the resulting transform of the sequence of transformations.

Assuming that mode=True:

  • If all transformations in the sequence are affine-like transformations, compute() returns an affine-like transform.

  • If the first (= rightmost) transform in the sequence is a coordinate field, compute() returns a coordinate field.

  • If the first (= rightmost) transform in the sequence is an affine-like transform, and the sequence contains at least one non-affine-like transform, compute() returns a sequence of two transformations:

  • the composition of all affine-like transformations that appear before the first non-affine-like transform in the sequence, and

  • the composition of all transformations in the sequence, starting from the first non-affine-like transform in the sequence.
Parameters

mode : [list of] name or type, optional Kinds of transformations to compose. * If True (default): compose every kind in the sequence. * If False: compose nothing (simplify-only). * If a (list of) transformation type(s): compose only pairs of transformations of these kinds. simplify : simplify policy, default="analytic" Whether to simplify sub-transformations prior to composition, and how hard to try to simplify them. * "analytic" (the default) looks at the type structure only; * "numeric" looks at the numeric values of the transformation; * False/"none"/None disables simplification. factor : bool, default=False Whether to rewrite the sequence into its axis-group normal form [grid?, F_1..F_m, Pi_perm?]: a leading grid (if any), one axis-preserving subspace factor per group of axes that transform together, and a trailing reindex permutation. Off by default, so the result is byte-for-byte the plain compute() result. Nothing is ever composed across groups; mode still decides whether the restricted pieces inside a group compose. A chain that creates or drops axes is left unfactored. With mode=False nothing is computed, so factor has nothing to act on and is ignored.

simplify 
simplify(
    policy: SimplifyLike = "analytic",
    *,
    compute: ModeLike | bool | None = False,
) -> Self

Simplify this transformation under a per-kind policy.

Convenience sugar for compute: t.simplify(policy, compute=mode) is t.compute(mode, simplify=policy).

By default simplify() does no computation at all: compute=False maps to mode=False, which composes nothing (no matrices multiplied, no fields sampled, no lazy inverse materialized). It only downcasts each leaf under policy (analytic by default). Pass an explicit compute=<mode> to also compose that kind.

Parameters:

Name Type Description Default
policy simplify policy

The simplify policy, in the grammar compute accepts.

 "analytic"
compute [list of] name or type

The compose mode. The default, False, composes nothing (mode=False in compute); None would compose every kind. A real mode passes straight through.

 False
square 
square(compute: bool = False, **kwargs) -> Transformation

Return the square of this transformation, self @ self.

The square is the sequence [self, self], which composes when it is computed. It is defined for a transformation that maps a space to itself.

Parameters:

Name Type Description Default
compute bool

Whether to compute the result now rather than return it lazily.

 False
**kwargs

Passed to compute when compute is true.

 {}

Raises:

Type Description
DomainError

If the transformation does not map a space to itself.
sqrt 
sqrt(compute: bool = False, **kwargs) -> Transformation

Return the principal square root of this chain.

The chain is first simplified, which costs nothing. A chain [P, *X, P^-1], where P^-1 is the lazy inverse of P, or both are affines whose product is exactly the identity, is a change of coordinates around X, and its square root is [P, sqrt(X), P^-1]: a field stored in voxels between a world-to-voxel affine and its lazy inverse keeps that form. Any other chain is composed now, and the square root of the transformation it composes to is returned.

Raises:

Type Description
DomainError

If the chain does not map a space to itself, or if the square root of what it reduces to is not defined.
NotImplementedError

If the chain does not compose to a single transformation.
to 
to(
    cls: Type[Transformation] | None = None, **kwargs
) -> Transformation

Convert this chain to a different type or encoding.

See Transformation.to. A chain has no tangent of its own -- the tangent of a composition is not the sum of the tangents -- so log= re-encodes the transformation it reduces to, and anything else is refused before it is computed:

  • a chain that simplifies to one transformation is that one;
  • a change of coordinates [P, *X, P^-1] (see sqrt) keeps its ends, and re-encodes X: the flow of a velocity commutes with the conjugation, so this is exact. A velocity read between a world-to-voxel affine and its inverse (|svf) is turned into its displacement that way;
  • a chain of affines is composed, which is cheap and exact.

Any other chain -- one with a field, between ends that do not undo each other -- raises ConversionError.

from_instance classmethod 
from_instance(other: Any, *args, **kwargs) -> Self

Create an instance from an instance of a similar class.

The chain of another transformation is carried over, rather than re-read from a NIfTI header that comes with it and says something else (a NiftyReg file holds positions, say). Its encoding is not: log and steps are this format's options, so a velocity copied here is written as its displacement unless log=True is given -- to this copy, or to save.

input 
input() -> CoordinateSystem | None

The anatomical space the field maps from.

output 
output() -> CoordinateSystem | None

The anatomical space the field maps to.

transformations 
transformations() -> tuple[Transformation, ...]

The chain of transformations that the field encodes.

It is built from the NIfTI header and data on first access, and cached. Assigning to it overrides the derived chain, which is how a field that was not read from a file is built. Either way it is a tuple, and the field refuses in-place edits: its slots name fixed positions in the chain, so a copy with other slots is made with replace.

to_nibabel 
to_nibabel(
    like: Any = None, log: bool | None = None, **overrides
) -> Nifti1Image | Nifti2Image

Build the nibabel image that encodes this field of displacements.

The displacements are rotated from voxel units into RAS millimetres and written as a DISPVECT (1006) image of shape (X, Y, Z, 1, 3), whose voxel-to-RAS affine is the grid's. With log (this field's own, unless one is given here, as in save(path, log=True)), the velocity is written instead; otherwise a velocity is integrated into its displacement.

When like is given, non-encoding header fields are copied from it. Keyword arguments override header fields last.