Source code for topostats.tracing.skeletonize
"""Skeletonize molecules"""
import logging
from typing import Callable
import numpy as np
from skimage.morphology import medial_axis, skeletonize, thin
from topostats.logs.logs import LOGGER_NAME
LOGGER = logging.getLogger(LOGGER_NAME)
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def get_skeleton(image: np.ndarray, method: str) -> np.ndarray:
"""Factory method for skeletonizing molecules.
Parameters
----------
image : np.ndarray
Image of molecule to be skeletonized.
method : str
Method to use, default is 'zhang' other options are 'lee', 'medial_axis' and 'thin'.
Returns
-------
np.ndarray
Skeletonised version of the image.all($0)
Notes
-----
This is a thin wrapper to the methods provided
by the `skimage.morphology
<https://scikit-image.org/docs/stable/api/skimage.morphology.html?highlight=skeletonize>`_
module. See also the `examples
<https://scikit-image.org/docs/stable/auto_examples/edges/plot_skeleton.html>_
"""
skeletonizer = _get_skeletonize(method)
return skeletonizer(image)
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def _get_skeletonize(method: str = "zhang") -> Callable:
"""Creator component which determines which skeletonize method to use.
Parameters
----------
method: str
Method to use for skeletonizing, methods are 'zhang' (default), 'lee', 'medial_axis', and 'thin'.
Returns
-------
Callable
Returns the function appropriate for the required skeletonizing method.
"""
if method == "zhang":
return _skeletonize_zhang
if method == "lee":
return _skeletonize_lee
if method == "medial_axis":
return _skeletonize_medial_axis
if method == "thin":
return _skeletonize_thin
raise ValueError(method)
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def _skeletonize_zhang(image: np.ndarray) -> np.ndarray:
return skeletonize(image, method="zhang")
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def _skeletonize_lee(image: np.ndarray) -> np.ndarray:
return skeletonize(image, method="lee")
[docs]
def _skeletonize_thin(image: np.ndarray) -> np.ndarray:
return thin(image)