omni.interfaces.common#

Functions

`append_suffix`(filename, suffix)	Appends a suffix to a given filename.
`create_fov_masks`(ref_img, source_img, affine)	Creates FOV masks for reference/source images.
`get_path_and_prefix`(filename)	Gets prefix but leaves in the path.
`get_prefix`(filename)	A convenient function for getting the filename without extension.
`normalize`(data)	Normalize an array.
`repath`(dirname, filename)	Changes the directory of a given filename.
`replace_suffix`(filename, suffix)	Replaces the last suffix in the given filename.
`run_process`(process_string[, stdout])	Runs an outside terminal process.

omni.interfaces.common.append_suffix(filename: str, suffix: str) → str[source]#

Appends a suffix to a given filename.

Parameters:

filename: str: Name of file to get the prefix and path.
suffix: str: Suffix to add to filename

Returns:

str: Name of file with suffix

omni.interfaces.common.create_fov_masks(ref_img: str, source_img: str, affine: str, ref_mask_path: Optional[str] = None, source_mask_path: Optional[str] = None)[source]#

Creates FOV masks for reference/source images.

This function generates FOV masks, defining the extents of the reference and source images provided.

Parameters:

ref_img: str: Path to reference image.
source_img: str: Path to source image.
affine: str: Affine transform (afni).
ref_mask_path: str: Path to output reference mask. If None it will create a mask with a random name in the /tmp folder.
source_mask_path: str: Path to output source mask. If None it will create a mask with a random name in the /tmp folder.

Returns:

str: Path to output reference mask.
str: Path to output source mask.

omni.interfaces.common.get_path_and_prefix(filename: str) → str[source]#

Gets prefix but leaves in the path.

Parameters:

filename: str: Name of file to get the prefix and path.

Returns:

str: prefix of file with path.

omni.interfaces.common.get_prefix(filename: str) → str[source]#

A convenient function for getting the filename without extension.

Parameters:

filename: str: Name of file to get the prefix.

Returns:

str: prefix of file.

omni.interfaces.common.normalize(data: ndarray) → ndarray[source]#

Normalize an array.

Parameters:

data: np.ndarray: Data to 0/1 normalize.

Returns:

np.ndarray: Normalized data.

omni.interfaces.common.repath(dirname: str, filename: str) → str[source]#

Changes the directory of a given filename.

Parameters:

dirname: str: Directory name to use.
filename: str: Filename whose path to change.

Returns:

str: Filename with changed path.

omni.interfaces.common.replace_suffix(filename: str, suffix: str) → str[source]#

Replaces the last suffix in the given filename.

Parameters:

filename: str: Name of file to get the prefix and path.
suffix: str: Suffix to replace in the filename

Returns:

str: Name of file with new suffix

omni.interfaces.common.run_process(process_string: str, stdout: bool = True) → str[source]#

Runs an outside terminal process.

Parameters:

process_string: str: A string containing a valid terminal command to run.
stdout: bool: Indicates whether the process string should be directed to stdout through the logging module.

Returns:

str: The formatted process_string.