spaces

ngtools.spaces

Utilities to manipulate spaces (ng.CoordinateSpace) in neuroglancer.

Functions:

Name	Description
`convert_space`	Convert units of a coordinate space.
`normalize_space`	Ensure that dimensions have SI units (without prefix).
`name_compact2full`	Convert a compact axis name (`"RAS"`) to a list of full axis names (`["anterior", "posterior", "superior"]`).
`space_is_compatible`	Check whether two standard spaces can map to/from each other.
`space_to_name`	Get neurospace name from spatial axis names.

Attributes:

Name	Type	Description
`default`	`CoordinateSpace`	Default display space (`"xyz"`).
`defaultnames`	`list[str]`	List of all default orientations (`"xyz"`, `"zyx"`, etc).
`defaultspaces`	`dict[str, CoordinateSpace]`	Mapping to all neuroglancer standard spaces (xyz, zyx, etc).
`letter2full`	`dict[str, str]`	Mapping from short to long axis names.
`neuronames`	`list[str]`	List of all existing neuroimaging orientations (`"ras"`, `"lpi"`, etc).
`neurospaces`	`dict[str, CoordinateSpace]`	Mapping to all known neuroimaging-oriented spaced (RAS, LPI, etc), as well as all neuroglancer standard spaces (xyz, zyx, etc).
`neurotransforms`	`dict[tuple[str, str], CoordinateSpaceTransform]`	Mapping to transforms between neuroimaging spaces. The keys are either pairs of `str`, or pairs of `ng.CoordinateSpace` instances from the `neurospaces` dictionary.

name_compact2full

name_compact2full(name)

Convert compact axes name to long list of names.

Examples:

compact2full("ras") -> ["right", "anterior", "posterior"] compact2full("xyz") -> ["x", "y", "z"]

space_is_compatible

space_is_compatible(src, dst)

Check whether two spaces can map to/from each other.

True if both spaces describe the same set of 3 axes.

convert_space

convert_space(space, units='base', *, names=None)

Convert units of a coordinate space.

Example

ABC

Ensure that all axes have SI unit (without prefix)

new_space = convert_space(space)
# or
new_space = convert_space(space, "base")
# or
new_space = convert_space(space, ["m", "s", "hz", "rad/s"])
# or
new_space = normalize_space(space)

Ensure that spatial axes have millimeter unit

new_space = convert_space(space, "mm")

Ensure that specific axes have specific unit

new_space = convert_space(space, {"x": "mm", "y": "mm", "t": "ms"})
# or
new_space = convert_space(space, {("x", "y"): "mm", "t": "ms"})
# or
new_space = convert_space(space, {("x", "y", "t"): ["mm", "ms"]})

normalize_space

normalize_space(space)

Ensure that dimensions have SI units (without prefix).

space_to_name

space_to_name(space, compact=False)

Get spatial axis name from coordinate space.

Name	Type	Description	Default
`space`	`CoordinateSpace`	Coordinate space to convert.	required
`units`	`str \| list[str] \| dict[str \| tuple[str], str \| list[str]]`	Output unit(s). If `"base"`, convert all units to their zero-exponent basis (`{"m", "s", "hz", "rad/s"}`). If a dictionary, it should map axis name(s) to target unit(s).	`'base'`
`names`	`str \| list[str] \| dict[str, str] \| None`	Name(s) of axis to convert. If `None`, all axes that have compatible units. Cannot be used if `units` is a dictionary.	`None`