Coordinates¶

Model definitions¶

Definition of an NxN+1 affine transform matrix

Field	Type	Title (Description)
`affine_transform`	`List[List[float]]`	Affine transform matrix

Definition an atlas

Field	Type	Title (Description)
`name`	AtlasName	Atlas name
`version`	`str`	Atlas version
`size`	`List[float]`	Size
`size_unit`	SizeUnit	Size unit
`resolution`	`List[float]`	Resolution
`resolution_unit`	SizeUnit	Resolution unit
`origin`	MouseAnatomyModel	Origin (Defines the position of (0,0,0) in the coordinate system)
`axes`	List[Axis]	Axis names (Axis names and directions)
`axis_unit`	SizeUnit	Size unit
`handedness`	Optional[Handedness]	Handedness (Whether the coordinate system is right-handed or left-handed)

A point in an Atlas

Field	Type	Title (Description)
`coordinate_system`	Atlas	Atlas
`translation`	`List[float]`	Translation parameters
`reference_coordinate_system`	ReferenceCoordinateSystem	Reference coordinate system (Whether to translate on the global or local coordinate system axes)

Linked direction and axis

Field	Type	Title (Description)
`name`	AxisName	Axis name (Note: axis names do not influence order or orientation)
`direction`	Direction	Direction (Direction of positive values along the axis)

Definition of a coordinate system

Field	Type	Title (Description)
`name`	`str`	Name (Convention is to use _<POS_X_DIR><POS_Y_DIR><POS_Z_DIR> etc)
`origin`	MouseAnatomyModel	Origin (Defines the position of (0,0,0) in the coordinate system)
`axes`	List[Axis]	Axis names (Axis names and directions)
`axis_unit`	SizeUnit	Size unit
`handedness`	Optional[Handedness]	Handedness (Whether the coordinate system is right-handed or left-handed)

Coordinate system handedness

Name	Value
`RIGHT`	`right`
`LEFT`	`left`

Definition of a nonlinear transform

Field	Type	Title (Description)
`path`	`AssetPath`	Path to nonlinear transform file (Relative path from metadata json to file)

Reference coordinate system for applying transforms

Name	Value
`GLOBAL`	`global`
`LOCAL`	`local`

Rotation

Rotations should be applied as Euler angles in the specified axis order.

Field	Type	Title (Description)
`angles`	`List[float]`	Angles (Right-hand rule, positive angles rotate CCW)
`angles_unit`	AngleUnit	Angle unit
`axis_order`	`str`	Axis order (Order of rotation axes as a string (e.g. ‘xyz’, ‘zyx’). Must match the length of angles.)
`reference_coordinate_system`	ReferenceCoordinateSystem	Reference coordinate system (Whether to rotate around the global or local coordinate system axes)
`rotation_direction`	RotationDirection	Rotation direction (Right-hand rule: positive angles rotate CCW when looking toward the origin from the positive axis)
`pivot`	ReferenceCoordinateSystem	Rotation pivot (Whether to rotate around the global or local coordinate system origin)

Rotation direction convention

Name	Value
`RIGHT_HAND`	`right_hand`
`LEFT_HAND`	`left_hand`

Scale

Field	Type	Title (Description)
`scale`	`List[float]`	Scale parameters
`pivot`	ReferenceCoordinateSystem	Scale pivot (Whether to scale around the global or local coordinate system origin)

Translation

Field	Type	Title (Description)
`translation`	`List[float]`	Translation parameters
`reference_coordinate_system`	ReferenceCoordinateSystem	Reference coordinate system (Whether to translate on the global or local coordinate system axes)