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brainhops.io.base.arrays

Format-independent readers for generic array containers.

Several formats store a bare numeric array in a generic container: a delimited text file, a NumPy .npy / .npz file, or a MATLAB .mat file. This module reads those containers into NumPy arrays and knows nothing about what the arrays mean, so that every format built on one of them (FLIRT matrices, plain affine matrices, and later the generic array readers) shares one parser.

It has two layers:

  • Functions (read_text_array, read_npy, read_npz, read_mat, ...) that parse the content of one container.
  • Parsers, one per container, deriving from the abstract ArrayParser. Each implements the usual from_* / sniff_* entry points of its kind of content (from_lines for text, from_bytes for binary), and hands the array it read to from_array, which a format class implements (with the private hooks _accepts_array and _array_confidence). A format mixes one of them in per container, as in class NpyMatrixAffine(NpyArrayParser, MatrixAffine).

Text (built on TextFileParser):

Binary (built on BinaryFileParser):

The text readers build on the shared text plumbing (decoding, and declining content that does not decode) and differ by their separator: whitespace, commas or tabs. AFNI .1D and generic .dat files are whitespace-separated columns with # comments, so they are extensions of TxtArrayParser rather than formats of their own. MatArrayParser dispatches between the two unrelated MATLAB containers: its sniff_bytes scores the best of its variants', and its from_bytes reads a file with the variant whose container it is.

Every reader takes the whole file content as bytes (or text lines), never a path, so that it works the same on files, streams and in-memory content. Nothing here unpickles: NumPy containers are read with allow_pickle=False, and MATLAB cell arrays or structs are skipped.

Classes

ArrayContainerError

Bases: ValueError

Raised when a container cannot be read as (numeric) arrays.

ArrayParser

Bases: FileParser

Abstract base of the readers of one generic array container.

A concrete subclass reads one container through the usual entry points: from_lines / sniff_lines for a text container, from_bytes / sniff_bytes for a binary one. It declares its EXTENSIONS, HINTS and CONTAINER. What the array means is left to a format class, which mixes the container parser in and implements:

  • from_array: how to build the object from the array;
  • _accepts_array: which arrays it can read, used to pick one in a container that holds several;
  • _array_confidence: how sure it is that the array is its own.

Abstract: it reads no container, and is never registered as a format.

Selecting an array: in a container that holds several (.npz, .mat), key= (or its alias variable=) names the array to read. By default, the container must hold exactly one array that _accepts_array accepts. Single-array containers ignore it.

Attributes

CONTAINER class-attribute 
CONTAINER: str = ''

A short name for the container, e.g. "npy".

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

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_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

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

Score an open file, reading at most SNIFF_LIMIT bytes.

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_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_bytes classmethod 
sniff_bytes(
    content: BinaryContentLike,
    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
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.

 {}

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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

Build an object from a file-like object.

The default implementation reads the whole stream and hands its content to from_content (hence to from_bytes for binary streams). Parsers that only need part of the stream (e.g., a header) should override this method; from_bytes then falls back to it.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_bytes classmethod 
from_bytes(content: BinaryContentLike, **kwargs) -> Self

Build an object from a binary representation of a file.

If the class implements from_fileobj itself, the bytes are wrapped in an io.BytesIO stream and handed to from_fileobj. Otherwise, this raises ParserNotImplementedError: the default from_fileobj delegates to from_bytes, so falling back to it would recurse. A from_fileobj override that only forwards to super().from_fileobj should be decorated with _passthrough_from_fileobj; if it is not, the loop is still detected when from_bytes is re-entered for the same class, and ParserNotImplementedError is raised.

Parameters:

Name Type Description Default
content BinaryContentLike

The content to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.

Raises:

Type Description
ParserNotImplementedError

If neither from_bytes nor from_fileobj is implemented.
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.

TextArrayParser

Bases: ArrayParser, TextFileParser

Base of the readers of a 2-D array stored as delimited text.

One row per line; # starts a comment; blank lines are skipped. All rows must have the same length. Decoding is the shared text plumbing of TextFileParser: content that does not decode (or holds a NUL byte) is not text, and scores NO.

This base splits values on any run of whitespace, commas or semicolons, and declares no extension or hint: it is not a format. The concrete readers fix the separator and the file names:

Sniffing. A file whose name ends in one of a reader's EXTENSIONS and whose content it reads scores at least NAMED_CONFIDENCE: the name says "plain numbers", which no content check can. Without such a name, a reader also requires its signature, so that one content is claimed by one reader only: CSV needs a comma, TSV a tab, and whitespace text yields tab-separated content to TSV.

Attributes

SEPARATORS class-attribute 
SEPARATORS: str | None = None

The regular expression that separates values (see read_text_rows). None accepts whitespace, commas and semicolons.

NAMED_CONFIDENCE class-attribute 
NAMED_CONFIDENCE: float = Confidence.LIKELY

The least score of a text array whose file name has one of the reader's extensions.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

Methods:

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

TxtArrayParser

Bases: TextArrayParser

Reader for a 2-D array stored as whitespace-separated text (.txt).

Values are separated by spaces or tabs, as numpy.loadtxt and numpy.savetxt do by default. This is also the layout of AFNI .1D files (whitespace-separated columns, # comments) and of the conventionless .dat files many tools write, so both are read here rather than by readers of their own.

Its signature is anything but tab-separated values: unnamed content that TsvArrayParser reads is left to it.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

NAMED_CONFIDENCE class-attribute 
NAMED_CONFIDENCE: float = Confidence.LIKELY

The least score of a text array whose file name has one of the reader's extensions.

Methods:

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

CsvArrayParser

Bases: TextArrayParser

Reader for a 2-D array stored as comma-separated values (.csv).

Values are separated by commas, with optional spaces around them. Its signature is a comma.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

NAMED_CONFIDENCE class-attribute 
NAMED_CONFIDENCE: float = Confidence.LIKELY

The least score of a text array whose file name has one of the reader's extensions.

Methods:

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

TsvArrayParser

Bases: TextArrayParser

Reader for a 2-D array stored as tab-separated values (.tsv).

Values are separated by one tab, with optional spaces around it. Its signature is a tab.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

NAMED_CONFIDENCE class-attribute 
NAMED_CONFIDENCE: float = Confidence.LIKELY

The least score of a text array whose file name has one of the reader's extensions.

Methods:

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

NpyArrayParser

Bases: _BinaryArrayParser

Reader for the single array of a NumPy .npy file, without unpickling.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

Methods:

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

Score an open file, reading at most SNIFF_LIMIT bytes.

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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

Build an object from a file-like object.

The default implementation reads the whole stream and hands its content to from_content (hence to from_bytes for binary streams). Parsers that only need part of the stream (e.g., a header) should override this method; from_bytes then falls back to it.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

NpzArrayParser

Bases: _BinaryArrayParser

Reader for one array of a NumPy .npz archive, selected by key=, without unpickling.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

Methods:

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

Score an open file, reading at most SNIFF_LIMIT bytes.

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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

Build an object from a file-like object.

The default implementation reads the whole stream and hands its content to from_content (hence to from_bytes for binary streams). Parsers that only need part of the stream (e.g., a header) should override this method; from_bytes then falls back to it.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

MatArrayParser

Bases: _BinaryArrayParser

Reader for one variable of a MATLAB .mat file of any version, selected by key= (or variable=).

MATLAB has two unrelated containers behind one extension, each read by a subclass:

This class dispatches between its VARIANTS: sniff_bytes scores the best of theirs, and from_bytes reads a file with the variant whose container it is. The variants override both, so they read their own container only. It declares the hint "mat", which the subclasses inherit; the v7.3 reader adds "mat73" and "73" (so "mat.73").

A format built on this one (as in MatMatrixAffine) declares its own VARIANTS, so that dispatch returns objects of its own variant classes. Register the variants for dispatch, not the dispatcher: it would only ever tie with (and lose to) its own subclasses.

Attributes

VARIANTS class-attribute 
VARIANTS: tuple[type, ...] = ()

The readers this class dispatches to: the v4-v7 reader, then the v7.3 reader.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

Methods:

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

Score an open file, reading at most SNIFF_LIMIT bytes.

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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

Build an object from a file-like object.

The default implementation reads the whole stream and hands its content to from_content (hence to from_bytes for binary streams). Parsers that only need part of the stream (e.g., a header) should override this method; from_bytes then falls back to it.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

MatLegacyArrayParser

Bases: MatArrayParser

Reader for one variable of a MATLAB v4 or v5-v7 .mat file, selected by key= (or variable=), read with scipy.io.loadmat.

A v5-v7 file is recognized by its header; a v4 file has none, so it is any binary content that scipy.io reads. Only numeric variables are considered. It adds no hint to "mat".

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

VARIANTS class-attribute 
VARIANTS: tuple[type, ...] = ()

The readers this class dispatches to: the v4-v7 reader, then the v7.3 reader.

Methods:

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

Score an open file, reading at most SNIFF_LIMIT bytes.

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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

Build an object from a file-like object.

The default implementation reads the whole stream and hands its content to from_content (hence to from_bytes for binary streams). Parsers that only need part of the stream (e.g., a header) should override this method; from_bytes then falls back to it.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

Mat73ArrayParser

Bases: MatArrayParser

Reader for one variable of a MATLAB v7.3 .mat file, selected by key= (or variable=).

A v7.3 file is an HDF5 file with a MATLAB header. It is read with h5py, imported only then. HDF5 stores MATLAB's column-major arrays transposed, which is undone. Only numeric variables are considered. It adds the hints "mat73" and "73" to "mat", so "mat.73" selects it.

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.

SNIFF_CONFIDENCE class-attribute 
SNIFF_CONFIDENCE: float = Confidence.WEAK

The score of content whose container and array are both readable.

A generic container says nothing about what its array means, so the default is WEAK: any format that recognizes the file positively wins. A format raises it in _array_confidence when the array itself identifies it.

SNIFF_LIMIT class-attribute 
SNIFF_LIMIT: int | None = None

The largest file, in bytes, that sniffing reads. A larger file is turned down without being read whole. None means no limit.

VARIANTS class-attribute 
VARIANTS: tuple[type, ...] = ()

The readers this class dispatches to: the v4-v7 reader, then the v7.3 reader.

Methods:

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

Score an open file, reading at most SNIFF_LIMIT bytes.

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

Build an object from a file (path or file-like object).

Parameters:

Name Type Description Default
file FileLike

The file to parse.

 required
**kwargs

Parser-specific options.

 {}

Returns:

Type Description
obj

The parsed object.
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

Build an object from a file-like object.

The default implementation reads the whole stream and hands its content to from_content (hence to from_bytes for binary streams). Parsers that only need part of the stream (e.g., a header) should override this method; from_bytes then falls back to it.

Parameters:

Name Type Description Default
file IO

A file object open for reading.

 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_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.
from_array classmethod 
from_array(
    array: ndarray, key: str | None = None, **kwargs
) -> Self

Build the object from the array read from the container. Implemented by the format class.

Functions:

detect_container 

detect_container(content: bytes) -> str | None

Identify a binary array container from its magic number.

Parameters:

Name Type Description Default
content bytes

The file content, or at least its first 1 KiB.

 required

Returns:

Name Type Description
kind {npy, npz, mat5, mat73, hdf5} | None

"mat5" is a MATLAB v5-v7 file, "mat73" a MATLAB v7.3 (HDF5) file and "hdf5" an HDF5 file without a MATLAB header. None means no magic number was recognized: the content may be text, a MATLAB v4 file (which has no magic number), or anything else.

read_text_rows 

read_text_rows(
    lines: Iterable[str],
    comments: str | Sequence[str] | None = "#",
    separators: str | None = None,
) -> list[list[float]]

Read rows of floats from delimited text.

Blank lines (after removing comments) are skipped. Rows may have different lengths; use read_text_array to require a rectangle.

Parameters:

Name Type Description Default
lines Iterable[str]

The lines of text.

 required
comments str | Sequence[str] | None

Markers that start a comment running to the end of the line. None or an empty sequence disables comments.

 '#'
separators str | None

A regular expression matching value separators. The default accepts whitespace (spaces, tabs), commas and semicolons.

 None

Returns:

Name Type Description
rows list[list[float]]

Raises:

Type Description
ArrayContainerError

If a value is not a number, or a line holds a NUL byte (binary content that happens to decode).

read_text_array 

read_text_array(
    lines: Iterable[str],
    comments: str | Sequence[str] | None = "#",
    separators: str | None = None,
) -> ndarray

Read a 2D array of floats from delimited text.

See read_text_rows for the accepted syntax.

Raises:

Type Description
ArrayContainerError

If the text is empty, holds a non-numeric value, or its rows do not all have the same length.

read_npy 

read_npy(content: bytes) -> ndarray

Read the array stored in .npy content, without unpickling.

read_npz 

read_npz(content: bytes) -> dict[str, ndarray]

Read every array stored in .npz content, without unpickling.

read_mat 

read_mat(content: bytes) -> dict[str, ndarray]

Read the numeric arrays stored in MATLAB .mat content.

MATLAB v4 and v5-v7 files are read with scipy.io.loadmat. MATLAB v7.3 files are HDF5 files and are read with h5py, imported only when needed. HDF5 stores MATLAB's column-major arrays with their axes reversed, so v7.3 arrays are transposed back to MATLAB's shape.

Only top-level numeric (or logical) arrays are returned; structs, cells, strings and objects are skipped.

Raises:

Type Description
ArrayContainerError

If the content is not a readable MATLAB file.
ImportError

If the file is v7.3 and h5py is not installed.

read_mat73 

read_mat73(content: bytes) -> dict[str, ndarray]

Read the numeric arrays stored in MATLAB v7.3 (HDF5) .mat content.

The file is read with h5py, imported only now. HDF5 stores MATLAB's column-major arrays with their axes reversed, so arrays are transposed back to MATLAB's shape. Only top-level numeric (or logical) datasets are returned.

Raises:

Type Description
ArrayContainerError

If the content is not a readable HDF5 file.
ImportError

If h5py is not installed.

is_numeric_array 

is_numeric_array(value: Any) -> bool

Whether value is a real numeric (or boolean) NumPy array.

select_array 

select_array(
    arrays: Mapping[str, ndarray],
    name: str | None = None,
    predicate: Callable[[ndarray], bool] | None = None,
    what: str = "array",
) -> tuple[str, ndarray]

Pick one array from a named collection.

Parameters:

Name Type Description Default
arrays Mapping[str, ndarray]

Named arrays, e.g. the variables of a .mat or the keys of a .npz.

 required
name str

The name to select. By default, the collection must hold exactly one array that satisfies predicate.

 None
predicate callable

Which arrays may be selected by default (ignored when name is given). By default, any numeric array.

 None
what str

How to call the arrays in error messages.

 'array'

Returns:

Name Type Description
name str
array ndarray

Raises:

Type Description
ArrayContainerError

If name is missing, or no single array can be chosen.