bidsschematools.types.protocols¶

BIDS validation context definitions

The classes in this module are used to define the context for BIDS validation. The context is a namespace that contains relevant information about the dataset as a whole and an individual file to be validated.

These classes are used to define the structure of the context, but they cannot be instantiated directly. Conforming subtypes need only match the structure of these classes, and do not need to inherit from them. It is recommended to import this module in an if TYPE_CHECKING block to avoid import costs.

The classes use @property decorators to indicate that subtypes need only provide read access to the attributes, and may restrict writing, for example, when calculating attributes dynamically based on other attributes.

Note that some type checkers will not match classes that use functools.cached_property. To permit this, add the following to your module:

if TYPE_CHECKING:
    cached_property = property
else:
    from functools import cached_property

This module has been auto-generated from the BIDS schema version 1.2.0-dev.

Classes

class bidsschematools.types.protocols.Aslcontext(*args, **kwargs)¶

Bases: Protocol

ASL context file

property n_rows: int¶: Number of rows in aslcontext.tsv

property path: str¶: Path to associated aslcontext file

property volume_type: Sequence[str] | None¶: Contents of the volume_type column

class bidsschematools.types.protocols.Associations(*args, **kwargs)¶

Bases: Protocol

Associated files, indexed by suffix, selected according to the inheritance principle

property aslcontext: Aslcontext | None¶: ASL context file

property bval: Bval | None¶: B value file

property bvec: Bvec | None¶: B vector file

property channels: Channels | None¶: Channels file

property coordsystem: Coordsystem | None¶: Coordinate system file

property electrodes: Electrodes | None¶: Electrodes file

property events: Events | None¶: Events file

property m0scan: M0scan | None¶: M0 scan file

property magnitude: Magnitude | None¶: Magnitude image file

property magnitude1: Magnitude1 | None¶: Magnitude1 image file

class bidsschematools.types.protocols.Bval(*args, **kwargs)¶

Bases: Protocol

B value file

property n_cols: int¶: Number of columns in bval file

property n_rows: int¶: Number of rows in bval file

property path: str¶: Path to associated bval file

property values: Sequence[float]¶: B-values contained in bval file

class bidsschematools.types.protocols.Bvec(*args, **kwargs)¶

Bases: Protocol

B vector file

property n_cols: int¶: Number of columns in bvec file

property n_rows: int¶: Number of rows in bvec file

property path: str¶: Path to associated bvec file

class bidsschematools.types.protocols.Channels(*args, **kwargs)¶

Bases: Protocol

Channels file

property path: str¶: Path to associated channels file

property sampling_frequency: Sequence[str] | None¶: Contents of the sampling_frequency column

property short_channel: Sequence[str] | None¶: Contents of the short_channel column

property type: Sequence[str] | None¶: Contents of the type column

class bidsschematools.types.protocols.Context(*args, **kwargs)¶

Bases: Protocol

property associations: Associations¶: Associated files, indexed by suffix, selected according to the inheritance principle

property columns: Mapping[str, Any] | None¶: TSV columns, indexed by column header, values are arrays with column contents

property dataset: Dataset¶: Properties and contents of the entire dataset

property datatype: str | None¶: Datatype of current file, for examples, anat

property entities: Mapping[str, Any] | None¶: Entities parsed from the current filename

property extension: str | None¶: Extension of current file including initial dot

property gzip: Gzip | None¶: Parsed contents of gzip header

property json: Mapping[str, Any] | None¶: Contents of the current JSON file

property modality: str | None¶: Modality of current file, for examples, MRI

property nifti_header: NiftiHeader | None¶: Parsed contents of NIfTI header referenced elsewhere in schema.

property ome: Ome | None¶: Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files

property path: str¶: Path of the current file

property schema: Mapping[str, Any]¶: The BIDS specification schema

property sidecar: Mapping[str, Any]¶: Sidecar metadata constructed via the inheritance principle

property size: int¶: Length of the current file in bytes

property subject: Subject | None¶: Properties and contents of the current subject

property suffix: str | None¶: Suffix of current file

property tiff: Tiff | None¶: TIFF file format metadata

class bidsschematools.types.protocols.Coordsystem(*args, **kwargs)¶

Bases: Protocol

Coordinate system file

property path: str¶: Path to associated coordsystem file

class bidsschematools.types.protocols.Dataset(*args, **kwargs)¶

Bases: Protocol

Properties and contents of the entire dataset

property dataset_description: Mapping[str, Any]¶: Contents of /dataset_description.json

property datatypes: Sequence[str]¶: Data types present in the dataset

property ignored: Sequence[str]¶: Set of ignored files

property modalities: Sequence[str]¶: Modalities present in the dataset

property subjects: Subjects¶: Collections of subjects in dataset

property tree: Mapping[str, Any]¶: Tree view of all files in dataset

class bidsschematools.types.protocols.DimInfo(*args, **kwargs)¶

Bases: Protocol

Metadata about dimensions data.

property freq: int¶: These fields encode which spatial dimension (1, 2, or 3).

property phase: int¶: Corresponds to which acquisition dimension for MRI data.

property slice: int¶: Slice dimensions.

class bidsschematools.types.protocols.Electrodes(*args, **kwargs)¶

Bases: Protocol

Electrodes file

property path: str¶: Path to associated electrodes.tsv file

class bidsschematools.types.protocols.Events(*args, **kwargs)¶

Bases: Protocol

Events file

property onset: Sequence[str] | None¶: Contents of the onset column

property path: str¶: Path to associated events file

class bidsschematools.types.protocols.Gzip(*args, **kwargs)¶

Bases: Protocol

Parsed contents of gzip header

property comment: str | None¶: Comment

property filename: str | None¶: Filename

property timestamp: float¶: Modification time, unix timestamp

class bidsschematools.types.protocols.M0scan(*args, **kwargs)¶

Bases: Protocol

M0 scan file

property path: str¶: Path to associated M0 scan file

class bidsschematools.types.protocols.Magnitude(*args, **kwargs)¶

Bases: Protocol

Magnitude image file

property path: str¶: Path to associated magnitude file

class bidsschematools.types.protocols.Magnitude1(*args, **kwargs)¶

Bases: Protocol

Magnitude1 image file

property path: str¶: Path to associated magnitude1 file

class bidsschematools.types.protocols.NiftiHeader(*args, **kwargs)¶

Bases: Protocol

Parsed contents of NIfTI header referenced elsewhere in schema.

property axis_codes: Sequence[Literal['R', 'L', 'A', 'P', 'S', 'I']]¶: Orientation labels indicating primary direction of data axes defined with respect to the object of interest.

property dim: Sequence[int]¶: Data seq dimensions.

property dim_info: DimInfo¶: Metadata about dimensions data.

property mrs: Mapping[str, Any] | None¶: NIfTI-MRS JSON fields

property pixdim: Sequence[float]¶: Grid spacings (unit per dimension).

property qform_code: int¶: Use of the quaternion fields.

property sform_code: int¶: Use of the affine fields.

property shape: Sequence[int]¶

dim[0] + 1]

Type:: Data array shape, equal to dim[1

property voxel_sizes: Sequence[float]¶

dim[0] + 1]

Type:: Voxel sizes, equal to pixdim[1

property xyzt_units: XyztUnits¶: Units of pixdim[1..4]

class bidsschematools.types.protocols.Ome(*args, **kwargs)¶

Bases: Protocol

Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files

property PhysicalSizeX: float | None¶: Pixels / @PhysicalSizeX

property PhysicalSizeXUnit: str | None¶: Pixels / @PhysicalSizeXUnit

property PhysicalSizeY: float | None¶: Pixels / @PhysicalSizeY

property PhysicalSizeYUnit: str | None¶: Pixels / @PhysicalSizeYUnit

property PhysicalSizeZ: float | None¶: Pixels / @PhysicalSizeZ

property PhysicalSizeZUnit: str | None¶: Pixels / @PhysicalSizeZUnit

class bidsschematools.types.protocols.Sessions(*args, **kwargs)¶

Bases: Protocol

Collections of sessions in subject

property ses_dirs: Sequence[str]¶: Sessions as determined by ses-* directories

property session_id: Sequence[str] | None¶: The session_id column of sessions.tsv

class bidsschematools.types.protocols.Subject(*args, **kwargs)¶

Bases: Protocol

Properties and contents of the current subject

property sessions: Sessions¶: Collections of sessions in subject

class bidsschematools.types.protocols.Subjects(*args, **kwargs)¶

Bases: Protocol

Collections of subjects in dataset

property participant_id: Sequence[str] | None¶: The participant_id column of participants.tsv

property sub_dirs: Sequence[str]¶: Subjects as determined by sub-* directories

class bidsschematools.types.protocols.Tiff(*args, **kwargs)¶

Bases: Protocol

TIFF file format metadata

property version: int¶: TIFF file format version (the second 2-byte block)

class bidsschematools.types.protocols.XyztUnits(*args, **kwargs)¶

Bases: Protocol

Units of pixdim[1..4]

property t: Literal['unknown', 'sec', 'msec', 'usec']¶: String representing the unit of inter-volume intervals.

property xyz: Literal['unknown', 'meter', 'mm', 'um']¶: String representing the unit of voxel spacing.