omni.affine#

Functions that pertain to affine matrix manipulation.

Functions

`afni_affine_to_rigid_body`(affines)	Convert multiple lines of afni transforms to rigid body
`convert_affine`(input_affine, input_atype, ...)	Converts input affine to output affine of another type.
`deoblique`(in_img, **kwargs)	Load and deoblique image.
`generate_rigid_transform`([ang_x, ang_y, ...])	Generates a rigid-body transformation.

omni.affine.afni_affine_to_rigid_body(affines: ndarray) → ndarray[source]#

Convert multiple lines of afni transforms to rigid body

Parameters:

affines: np.ndarray: n x 16 matrix of affine transforms

Returns:

np.ndarray: n x 6 matrix of rigid body transforms

omni.affine.convert_affine(input_affine: ndarray, input_atype: str, output_atype: str, invert: bool = False, target: Optional[Nifti1Image] = None, source: Optional[Nifti1Image] = None) → ndarray[source]#

Converts input affine to output affine of another type.

Parameters:

input_affine: np.ndarray: 4x4 affine matrix to convert.
input_atype: str: Type of affine that is input (omni/afni/fsl).
output_atype: str: Type of affine to output (omni/afni/fsl).
invert: bool: Controls whether the affine should be inverted.
target: nib.Nifti1Image: Target image affine is transformed to (required for fsl conversion).
source: nib.Nifti1Image: Source image affine is applying transform to (required for fsl conversion).

Returns:

np.ndarray: 4x4 affine matrix in output_atype format.

omni.affine.deoblique(in_img: Nifti1Image, **kwargs) → Nifti1Image[source]#

Load and deoblique image.

Parameters:

in_img: nib.Nifti1Image: Input image to deoblique.

Returns:

nib.Nifti1Image: Deobliqued image.

omni.affine.generate_rigid_transform(ang_x: float = 0, ang_y: float = 0, ang_z: float = 0, translate: Tuple[float, float, float] = [0, 0, 0]) → ndarray[source]#

Generates a rigid-body transformation.

Parameters:

ang_x: float: Angle over x-axis (degrees).
ang_y: float: Angle over y-axis (degrees).
ang_z: float: Angle over z-axis (degrees).
translate: Tuple[float, float, float]: Length 3 tuple specifying translation (mm) for x, y, and z-axis.

Returns:

np.ndarray: 4x4 affine matrix for given rigid-bdy transform.