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brainhops.io.base

The format-independent base shared by every file-based object, whatever its kind.

Classes

BinaryFileBasedObject

Bases: BinaryFileParser, FileBasedObject

An object that is stored in a binary file.

Attributes

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:

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,
    **kwargs,
) -> type | None

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

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

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

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

On a dispatcher, pick the best-matching registered format and build an instance of it from the file (path or file-like object). On a concrete format, build an instance of this class from the file.

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(file: IO, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the open file object. On a concrete format, build an instance of this class from the file 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(content: BinaryContentLike, **kwargs) -> Self

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

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.

FileBasedObject

Bases: FormatDispatcher

An object that is stored in a file.

Subclasses decorated with @format_registry become dispatchers for their own kind of object (images, transformations, ...). Concrete parsers decorated with @register_format land in every ancestor registry, so both the scoped and the generic entry points see them. The dispatching itself is described in FormatDispatcher.

Attributes

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:

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,
    **kwargs,
) -> type | None

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

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

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

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

On a dispatcher, pick the best-matching registered format and build an instance of it from the file (path or file-like object). On a concrete format, build an instance of this class from the file.

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(file: IO, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the open file object. On a concrete format, build an instance of this class from the file 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(content: BinaryContentLike, **kwargs) -> Self

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

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.

TextFileBasedObject

Bases: TextFileParser, FileBasedObject

An object that is stored in a text file.

Attributes

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:

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,
    **kwargs,
) -> float

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

A text stream decodes as it is read, so content that is not text -- a binary file that shares an extension with a text format -- fails there. That is a "no", not a failure to sniff.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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(
    content: BinaryContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given bytes are of the type that this parser can handle, by decoding them to text and delegating to sniff_text. Bytes that do not decode are not text, so they score NO.

Parameters:

Name Type Description Default
content BinaryContentLike

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, plus encoding (default "utf-8") for decoding content.

 {}

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,
) -> 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

On a dispatcher, pick the best-matching registered format and build an instance of it from the file (path or file-like object). On a concrete format, build an instance of this class from the file.

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(file: IO, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the open file object. On a concrete format, build an instance of this class from the file 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(content: BinaryContentLike, **kwargs) -> Self

Build an object from bytes, by decoding them to text and delegating to from_text.

Parameters:

Name Type Description Default
content BinaryContentLike

The content to parse.

 required
**kwargs

Parser-specific options, plus encoding (default "utf-8") for decoding content.

 {}

Returns:

Type Description
obj

The parsed object.
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.

WritableBinaryFileBasedObject

Bases: BinaryFileParserWriter, WritableFileBasedObject

An object that is stored in a binary file and can be written back.

Attributes

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:

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,
    **kwargs,
) -> type | None

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

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

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

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

On a dispatcher, pick the best-matching registered format and build an instance of it from the file (path or file-like object). On a concrete format, build an instance of this class from the file.

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(file: IO, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the open file object. On a concrete format, build an instance of this class from the file 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(content: BinaryContentLike, **kwargs) -> Self

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

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 file (path or file-like object).

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

Write the object to a file-like object open for writing.

Parameters:

Name Type Description Default
file IO

A file object open for writing.

 required
**kwargs

Parser-specific options.

 {}
to_bytes 
to_bytes(**kwargs) -> bytes

Return a binary version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
bytes

A binary version of the file.
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.

WritableFileBasedObject

Bases: FileParserWriter, FileBasedObject

An object that is stored in a file and can be written back.

Attributes

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:

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,
    **kwargs,
) -> type | None

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

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

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

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

On a dispatcher, pick the best-matching registered format and build an instance of it from the file (path or file-like object). On a concrete format, build an instance of this class from the file.

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(file: IO, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the open file object. On a concrete format, build an instance of this class from the file 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(content: BinaryContentLike, **kwargs) -> Self

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

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 file (path or file-like object).

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

Write the object to a file-like object open for writing.

Parameters:

Name Type Description Default
file IO

A file object open for writing.

 required
**kwargs

Parser-specific options.

 {}
to_bytes 
to_bytes(**kwargs) -> bytes

Return a binary version of the file.

Parameters:

Name Type Description Default
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
bytes

A binary version of the file.
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.

WritableTextFileBasedObject

Bases: TextFileParserWriter, WritableFileBasedObject

An object that is stored in a text file and can be written back.

Attributes

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:

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,
    **kwargs,
) -> float

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

A text stream decodes as it is read, so content that is not text -- a binary file that shares an extension with a text format -- fails there. That is a "no", not a failure to sniff.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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(
    content: BinaryContentLike,
    error: bool | Type[Exception] = False,
    **kwargs,
) -> float

Determine if the given bytes are of the type that this parser can handle, by decoding them to text and delegating to sniff_text. Bytes that do not decode are not text, so they score NO.

Parameters:

Name Type Description Default
content BinaryContentLike

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, plus encoding (default "utf-8") for decoding content.

 {}

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,
) -> 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

On a dispatcher, pick the best-matching registered format and build an instance of it from the file (path or file-like object). On a concrete format, build an instance of this class from the file.

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(file: IO, **kwargs) -> Self

On a dispatcher, pick the best-matching registered format and build an instance of it from the open file object. On a concrete format, build an instance of this class from the file 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(content: BinaryContentLike, **kwargs) -> Self

Build an object from bytes, by decoding them to text and delegating to from_text.

Parameters:

Name Type Description Default
content BinaryContentLike

The content to parse.

 required
**kwargs

Parser-specific options, plus encoding (default "utf-8") for decoding content.

 {}

Returns:

Type Description
obj

The parsed object.
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 file (path or file-like object).

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

Write the object to a file-like object open for writing.

Parameters:

Name Type Description Default
file IO

A file object open for writing.

 required
**kwargs

Parser-specific options.

 {}
to_bytes 
to_bytes(**kwargs) -> bytes

Convert the object to bytes, by converting it to text and encoding the result.

Parameters:

Name Type Description Default
**kwargs

Writer-specific options, plus encoding (default "utf-8") for encoding the text.

 {}

Returns:

Type Description
bytes

The byte representation 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.

ImageSpec magic 

ImageSpec(path: ConvertTo[Path], hints: tuple[str, ...] = (), options: dict[str, str | SourceSpec])

Bases: SourceSpec

A structured source specification for an image.

Methods:

from_arg classmethod 
from_arg(text: str) -> Self

Parse path|hint|key:value CLI syntax.

Brackets delimit a nested source specification. Colons are syntax only in modifier segments, so URI schemes in source values remain intact. A literal pipe must be percent-encoded as %7C because | is always structural.

OperationSpec magic 

OperationSpec(name: str)

Bases: Magic

A validated operation attached to a structured source.

Methods:

from_arg classmethod 
from_arg(text: str) -> Self

Parse this operation's segment from a source argument.

apply 
apply(value: Any) -> Any

Apply this operation to a loaded source value.

Parser magic 

Parser(value: Any)

Bases: Magic

Annotated metadata selecting the parser for a field.

The value may be a registered target type or a parser callable/class. An explicit Parser always takes precedence over registry lookup.

SourceSpec magic 

SourceSpec(path: ConvertTo[Path], hints: tuple[str, ...] = (), options: dict[str, str | SourceSpec])

Bases: Magic

A source path plus format hints and typed named options.

Methods:

from_arg classmethod 
from_arg(text: str) -> Self

Parse path|hint|key:value CLI syntax.

Brackets delimit a nested source specification. Colons are syntax only in modifier segments, so URI schemes in source values remain intact. A literal pipe must be percent-encoded as %7C because | is always structural.

TransformationSpec magic 

TransformationSpec(path: ConvertTo[Path], hints: tuple[str, ...] = (), options: dict[str, str | SourceSpec], operations: tuple[OperationSpec, ...] = ())

Bases: SourceSpec

A transformation source with validated transformation operations.

The hint svf is an alias of displacements|log:true: a field of displacements that holds the stationary velocity of the map. It combines with other options, as in warp.nii.gz|svf|steps:6.

Methods:

from_arg classmethod 
from_arg(text: str) -> Self

Parse path|hint|key:value CLI syntax (see SourceSpec.from_arg), expanding the svf alias.

register_operation classmethod 
register_operation(
    name: str,
) -> Callable[[Type[OperationSpec]], Type[OperationSpec]]

Register an operation understood by this source-spec class.

apply_operations 
apply_operations(value: Any) -> Any

Apply registered operations in their written order.

Functions:

format_registry 

format_registry(cls: Type[_T]) -> Type[_T]

Give a class its own registry of file formats.

A class decorated with @format_registry becomes a dispatcher: sniff* reports the best score among its registered formats, and load/from_* pick the best one and delegate to it. Use it on the base class of a kind of object -- FileBasedImage, FileBasedTransformation -- and on the root, FileBasedObject.

A dispatcher is not itself a format, so it is never registered into its ancestors' registries; only @register_format classes are.

register_format 

register_format(cls: Type[_T]) -> Type[_T]

Register a format into the registries of all its ancestors.

A concrete reader is registered into every registry above it, so a NiftiImage is found both by images.load and by the generic load. Registering twice is a no-op, so re-importing is harmless.

Dispatchers are not formats

Registries are flat. A concrete format is registered into every registry above it, and dispatchers are registered into none, so each format is tried exactly once per load. Registering a dispatcher as a format would break that: every format below it would be tried twice -- once directly, once through the dispatcher -- and FileBasedObject.load would recurse into itself, since the dispatcher's registry would contain a class whose load re-enters dispatch.

Order does not matter

The registry is an unordered set, deliberately: registration order is import order, which is neither stable nor meaningful. Dispatch never falls back on it -- candidates that cannot be separated on merit raise AmbiguousFormatError instead.

Parameters:

Name Type Description Default
cls type

The format to register.

 required

Returns:

Name Type Description
cls type

The same class, unchanged.

Raises:

Type Description
TypeError

If cls owns a registry of its own.

load 

load(
    filelike: FileOrContentLike,
    brute: bool = False,
    **kwargs,
) -> FileBasedObject

Read an object from a file, whatever its kind and format.

Every registered format is a candidate, whether it builds an image, a transformation or anything else. Formats score how well the content matches them, so a NIfTI whose intent code says "displacement field" is read as a transformation, while a plain one is read as an image.

Prefer the scoped entry points when you know the kind

images.load and transformations.load only consider formats of the kind you asked for, which is both faster and unambiguous.

Parameters:

Name Type Description Default
filelike FileOrContentLike

Input file, or its content.

 required
brute bool

If no format recognizes the input, try every registered reader.

 False
**kwargs

Format-specific options.

 {}

Returns:

Name Type Description
obj FileBasedObject

The object that was read.

sniff 

sniff(filelike: FileOrContentLike, **kwargs) -> type | None

Identify which format would read this file, without reading it.

The file is only inspected, never parsed, so this is a prediction of what load would reach for rather than a guarantee.

Parameters:

Name Type Description Default
filelike FileOrContentLike

Input file, or its content.

 required
**kwargs

Format-specific options.

 {}

Returns:

Name Type Description
format type | None

The best match among all registered formats, or None if no single one stands out.

save 

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

Write an object to a file, in the format the file name calls for.

The format is chosen from the registered writable formats, in three steps.

  1. The file name. The formats that declare the longest of the extensions the name ends with are the candidates, so a.ome.zarr asks for OME-Zarr and a.zarr for any Zarr format. A format that requires a prefix is a candidate only when the name has one of its prefixes.
  2. The object's own format. If obj already is of one of the candidates, it is written as it is.
  3. A format that can hold the object. Otherwise, a candidate can hold obj if it is a file-backed version of the very data model obj is an instance of, and takes every field that data model has (NiftiImage and ZarrImage are file-backed SingleScaleImages). obj is converted to it, which neither loses nor changes anything. When several can, the most specific is used, by the rules reading uses: the longest prefix, then the narrowest declaration, then PRIORITY. Two that are equally specific are an ambiguity, and nothing is written.

No conversion beyond the file format

obj is never converted to another data model on the way. A Scaling is not turned into an Affine, and a general Affine is not turned into the voxel-to-RAS affine a NIfTI file holds, since it would come back meaning something it did not say. Build the format you want when that is what the file should hold: NiftiVoxelToRAS.from_other(affine).save(file).

Parameters:

Name Type Description Default
obj Any

The object to write.

 required
file FileLike

The file to write to: a path, or a file object opened for writing. An unnamed file object, such as a buffer, has no name to choose a format from, so obj must already be of a writable format, and is written in that format.

 required
**kwargs

Format-specific options, passed on to the chosen format's save.

 {}

Raises:

Type Description
AmbiguousFormatError

If several equally specific formats can hold obj.
WriterError

If no registered format claims the file name, or none of those that do can hold obj, or the chosen format cannot write it.

format_hints 

format_hints(cls: type) -> FrozenSet[str]

Collect leaf and qualified hints along semantic inheritance branches.

parser_for 

parser_for(annotation: Any) -> Any | None

Resolve explicit parser metadata or the best registered parser.

register_parser 

register_parser(target: Hashable) -> Callable[[Any], Any]

Register a default parser for target as a class decorator.