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Coordinates

Model definitions

Affine

Definition of an affine transform 3x4 matrix

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

Atlas

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)

AtlasCoordinate

A point in an Atlas

Field Type Title (Description)
coordinate_system Atlas Atlas
translation List[float] Translation parameters
frame TransformFrame Reference frame

Axis

Linked direction and axis

Field Type Title (Description)
name AxisName Axis
direction Direction Direction (Direction of positive values along the axis)

CoordinateSystem

Definition of a coordinate system

Field Type Title (Description)
name str Name
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)

Handedness

Coordinate system handedness

Name Value
RIGHT right
LEFT left

NonlinearTransform

Definition of a nonlinear transform

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

Rotation

Rotation

Rotations are applied as Euler angles in the specified axis order.

The default convention is fixed global axes, right-hand rule (positive angles rotate counter-clockwise when looking toward the origin from the positive axis), xyz axis order, pivoting around the global origin.

Field Type Title (Description)
angles List[float] Angles and axes in 3D space (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.)
frame TransformFrame Reference frame (Whether to rotate around global axes or local axes (which rotate with the device))
rotation_direction RotationDirection Rotation direction (Right-hand rule: positive angles rotate CCW when looking toward the origin from the positive axis)
pivot TransformFrame Rotation pivot (Whether to rotate around the global origin or the local origin of the device)

RotationDirection

Rotation direction convention

Name Value
RIGHT_HAND right_hand
LEFT_HAND left_hand

Scale

Scale

Field Type Title (Description)
scale List[float] Scale parameters
pivot Optional[TransformFrame] Scale pivot (Whether to scale around the global origin or the local origin of the device)

TransformFrame

Reference frame for applying transforms

Name Value
GLOBAL global
LOCAL local

Translation

Translation

Field Type Title (Description)
translation List[float] Translation parameters
frame TransformFrame Reference frame