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brainhops.io.base.nifti

The shared NIfTI-reading and NIfTI-writing machinery behind every NIfTI-based image and transformation format.

Classes

NiftiParser magic 

NiftiParser(
    image: Nifti1Image | None = None,
    _header: Nifti1Header | None = None,
)

Bases: DataModelBase, BinaryFileParserWriter

Base class for objects that are encoded by a NIfTI file.

This class is a base for NiftiBasedImage and NiftiBasedTransformation.

Attributes

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.

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

File extensions handled by this parser, e.g. (".nii", ".nii.gz").

Used as a first, cheap dispatch pass. When several parsers match, the longest matching extension wins, so a parser declaring ".nii.gz" takes precedence over one declaring ".gz".

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.

Methods:

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

Build the object from bytes in NIfTI format.

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.

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_bytes 
to_bytes(**kwargs) -> bytes

Return the uncompressed NIfTI-1 encoding of the object.

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

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

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_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.

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 classmethod 
sniff(
    file: FileOrContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

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

Parameters:

Name Type Description Default
file FileOrContentLike

The file to sniff.

 required
error bool | type[Exception]

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

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the file is of this type, in [0, 1].
sniff_file classmethod 
sniff_file(
    file: FileLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

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

Parameters:

Name Type Description Default
file FileLike

The file to sniff.

 required
error bool | type[Exception]

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

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the file is of this type, in [0, 1].
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_content classmethod 
sniff_content(
    content: ContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

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

Parameters:

Name Type Description Default
content ContentLike

The content to sniff.

 required
error bool | type[Exception]

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

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the content is of this type, in [0, 1].
sniff_text classmethod 
sniff_text(
    text: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

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

Parameters:

Name Type Description Default
text str

The text to sniff.

 required
error bool | type[Exception]

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

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the text is of this type, in [0, 1].
sniff_lines classmethod 
sniff_lines(
    lines: Iterable[str],
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given lines are of the type that this parser can handle.

Parameters:

Name Type Description Default
lines Iterable[str]

The lines to sniff.

 required
error bool | type[Exception]

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

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the lines is of this type, in [0, 1].
sniff_line classmethod 
sniff_line(
    line: str,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

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

Parameters:

Name Type Description Default
line str

The line to sniff.

 required
error bool | type[Exception]

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

 False
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
float

Confidence that the line is of this type, in [0, 1].
load classmethod 
load(other: FileOrContentLike, **kwargs) -> Self

Build an object from a file (path, file-like object or iterable of lines).

This is the generic front door to the from_* family: it looks at what it was handed and calls the right one.

A str is always a path, whether or not the file exists, so a missing file raises FileNotFoundError whichever way its path was spelled. Text held in memory is read with from_text or from_content.

Parameters:

Name Type Description Default
other FileOrContentLike

Input file, or its content.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.

Raises:

Type Description
ParserExistsError

If other is a path to a file that does not exist. It is a FileNotFoundError.
from_spec classmethod 
from_spec(spec: SourceSpec, **kwargs) -> Self

Build an object from an unqualified structured source.

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

Build an object from a file content (bytes, str, or iterable of lines).

Parameters:

Name Type Description Default
content ContentLike

The content to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_text classmethod 
from_text(text: str, **kwargs) -> Self

Build an object from a text representation of a file.

Parameters:

Name Type Description Default
text str

The text to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

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

Build an object from an iterable of lines (e.g., the content of a file).

Parameters:

Name Type Description Default
lines Iterable[str]

The lines to sniff.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
from_line classmethod 
from_line(line: str, **kwargs) -> Self

Build an object from a single line of text.

Parameters:

Name Type Description Default
line str

The line to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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_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_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: Self, *args, **kwargs) -> Self

Create an instance of the class from an instance of a similar class.

Only attributes of the other instance that match keyword-like fields of this class will be used. An attribute that is None is unset, and leaves the default of this class in place.

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

Unless the other instance is already an instance of this class, an attribute naming a field that this class fixes (a field that cannot be passed to its constructor) is checked instead of used: an instance that sets it to anything other than None or the value of this class is refused with a ValueError. A generic Axis whose orientation is right-to-left, for example, cannot be read as a LeftToRightAxis.

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

Create an instance of the class from any object that can be interpreted as a dictionary, or an instance of a similar class, or an arguments to be passed to the constructor.

A similar class is this class or one of its parents within the data model, or another member of a polymorphic family this class belongs to: calling a polymorphic class such as Axis builds the subclass its arguments select, so a "generic" axis is usually an instance of a sibling (a RightToLeftAxis, a TimeAxis) rather than of a parent. Any other object, including an instance of a parent that is not a data model (such as a plain object), is passed to the constructor.

Unlike from_dict, a dictionary with a key that matches no field of this class is refused with a TypeError naming the keys, so that a misspelt key is not silently dropped.