omni.io#

Read/write functions for various omni outputs.

Functions

`convert_affine_file`(output, filename, ...[, ...])	Converts input affine file to output affine file of another type.
`convert_framewise_affine_to_rigid_body`(...)	Converts framewise affine file to rigid body.
`load_interaction_spec`(model)	Parse the interaction model input.
`load_target_source`(target, source)	Conveinence function for loading two images (target/source).
`read_affine_file`(filename)	Loads affine file from disk.
`read_afni_affine`(filename)	Loads the afni affine matrix file.
`read_afni_framewise_affine`(filename)	Loads in a framewise affine from afni
`read_omni_affine`(filename)	Read omni format affine matrix from disk.
`write_affine_file`(filename, affine_mat, atype)	Write affine file.
`write_afni_affine`(filename, affine_mat)	Writes an afni affine matrix file to disk.
`write_fsl_affine`(filename, affine_mat)	Writes fsl format affine matrix to disk.
`write_omni_affine`(filename, affine_mat)	Writes omni format affine matrix to disk.
`write_rb_params`(filename, rb_params)	Writes rigid body params to disk.
`write_regress_params`(filename, regress_params)	Writes regression parameters to disk.

omni.io.convert_affine_file(output: str, filename: str, output_atype: str, invert: bool = False, target: Optional[str] = None, source: Optional[str] = None) → None[source]#

Converts input affine file to output affine file of another type.

Parameters:

output: str: Path/name of output affine file.
filename: str: Affine file to convert.
output_atype: str: Type of affine to output (omni/afni/fsl).
invert: bool: Controls whether the affine should be inverted.
target: str: Path to target image affine is transformed to (required for fsl conversion).
source: str: Path to source image affine is applying transform to (required for fsl conversion).

omni.io.convert_framewise_affine_to_rigid_body(output: str, filename: str) → None[source]#

Converts framewise affine file to rigid body.

Parameters:

output: str: Path/name of output rigid body parames file.
filename: str: Affine file to convert.

omni.io.load_interaction_spec(model: str) → str[source]#: Parse the interaction model input.

omni.io.load_target_source(target: str, source: str) → Tuple[Nifti1Image, Nifti1Image][source]#: Conveinence function for loading two images (target/source).

omni.io.read_affine_file(filename: str) → Tuple[ndarray, str][source]#

Loads affine file from disk.

Parameters:

filename: str: Affine filename to load.

Returns:

np.ndarray: 4x4 affine matrix.
str: Type of affine file loaded (omni/afni/fsl).

omni.io.read_afni_affine(filename: str) → ndarray[source]#: Loads the afni affine matrix file.

omni.io.read_afni_framewise_affine(filename: str) → ndarray[source]#

Loads in a framewise affine from afni

Parameters:

filename: str: Multi frame affine file to load.

Returns:

np.ndarray: n x 16 array of affines

omni.io.read_omni_affine(filename: str) → ndarray[source]#: Read omni format affine matrix from disk.

omni.io.write_affine_file(filename: str, affine_mat: ndarray, atype: str) → None[source]#

Write affine file.

Parameters:

filename: str: Filename of affine file to write.
affine_mat: np.ndarray: 4x4 affine matrix.
atype: str: Type of affine file to write (omni/afni/fsl).

omni.io.write_afni_affine(filename: str, affine_mat: ndarray) → None[source]#: Writes an afni affine matrix file to disk.

omni.io.write_fsl_affine(filename: str, affine_mat: ndarray) → None[source]#: Writes fsl format affine matrix to disk.

omni.io.write_omni_affine(filename: str, affine_mat: ndarray) → None[source]#: Writes omni format affine matrix to disk.

omni.io.write_rb_params(filename: str, rb_params: ndarray) → None[source]#

Writes rigid body params to disk.

Parameters:

filename: str: Rigid body params file to write.
rb_params: str: n x 6 ndarray containing rigid body parameters.

omni.io.write_regress_params(filename: str, regress_params: ndarray) → None[source]#: Writes regression parameters to disk.