topostats.thresholds
====================

.. py:module:: topostats.thresholds

.. autoapi-nested-parse::

   Functions for calculating thresholds.

   ..
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Attributes
----------

.. autoapisummary::

   topostats.thresholds.LOGGER


Functions
---------

.. autoapisummary::

   topostats.thresholds.threshold
   topostats.thresholds._get_threshold
   topostats.thresholds._threshold_otsu
   topostats.thresholds._threshold_mean
   topostats.thresholds._threshold_minimum
   topostats.thresholds._threshold_yen
   topostats.thresholds._threshold_triangle


Module Contents
---------------

.. py:data:: LOGGER

.. py:function:: threshold(image: numpy.typing.NDArray, method: str = None, otsu_threshold_multiplier: float = None, **kwargs: dict) -> float

   
   Thresholding for producing masks.

   :param image: 2-D Numpy array of image for thresholding.
   :type image: npt.NDArray
   :param method: Method to use for thresholding, currently supported methods are otsu (default), mean and minimum.
   :type method: str
   :param otsu_threshold_multiplier: Factor for scaling the Otsu threshold.
   :type otsu_threshold_multiplier: float
   :param \*\*kwargs: Additional keyword arguments to pass to skimage methods.
   :type \*\*kwargs: dict

   :returns: Threshold of image using specified method.
   :rtype: float















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.. py:function:: _get_threshold(method: str = 'otsu') -> collections.abc.Callable

   
   Creator component which determines which threshold method to use.

   :param method: Threshold method to use, currently supports otsu (default), mean, minimum, mean yen, and triangle.
   :type method: str

   :returns: Returns function appropriate for the required threshold method.
   :rtype: function

   :raises ValueError: Unsupported methods result in ValueError.















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.. py:function:: _threshold_otsu(image: numpy.typing.NDArray, otsu_threshold_multiplier: float = None, **kwargs) -> float

   
   Calculate the Otsu threshold.

   For more information see `skimage.filters.threshold_otsu()
   <https://scikit-image.org/docs/stable/api/skimage.filters.html#skimage.filters.threshold_otsu>`_.

   :param image: 2-D Numpy array of image for thresholding.
   :type image: npt.NDArray
   :param otsu_threshold_multiplier: Factor for scaling Otsu threshold.
   :type otsu_threshold_multiplier: float
   :param \*\*kwargs: Dictionary of keyword arguments to pass to 'skimage.filters.threshold_otsu(**kwargs)'.
   :type \*\*kwargs: dict

   :returns: Threshold to be used in masking heights.
   :rtype: float















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.. py:function:: _threshold_mean(image: numpy.typing.NDArray, otsu_threshold_multiplier: float = None, **kwargs) -> float

   
   Calculate the Mean threshold.

   For more information see `skimage.filters.threshold_mean()
   <https://scikit-image.org/docs/stable/api/skimage.filters.html#skimage.filters.threshold_mean>`_.

   :param image: 2-D Numpy array of image for thresholding.
   :type image: npt.NDArray
   :param otsu_threshold_multiplier: Factor for scaling (not used).
   :type otsu_threshold_multiplier: float
   :param \*\*kwargs: Dictionary of keyword arguments to pass to 'skimage.filters.threshold_mean(**kwargs)'.
   :type \*\*kwargs: dict

   :returns: Threshold to be used in masking heights.
   :rtype: float















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.. py:function:: _threshold_minimum(image: numpy.typing.NDArray, otsu_threshold_multiplier: float = None, **kwargs) -> float

   
   Calculate the Minimum threshold.

   For more information see `skimage.filters.threshold_minimum()
   <https://scikit-image.org/docs/stable/api/skimage.filters.html#skimage.filters.threshold_minimum>`_.

   :param image: 2-D Numpy array of image for thresholding.
   :type image: npt.NDArray
   :param otsu_threshold_multiplier: Factor for scaling (not used).
   :type otsu_threshold_multiplier: float
   :param \*\*kwargs: Dictionary of keyword arguments to pass to 'skimage.filters.threshold_minimum(**kwargs)'.
   :type \*\*kwargs: dict

   :returns: Threshold to be used in masking heights.
   :rtype: float















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.. py:function:: _threshold_yen(image: numpy.typing.NDArray, otsu_threshold_multiplier: float = None, **kwargs) -> float

   
   Calculate the Yen threshold.

   For more information see `skimage.filters.threshold_yen()
   <https://scikit-image.org/docs/stable/api/skimage.filters.html#skimage.filters.threshold_yen>`_.

   :param image: 2-D Numpy array of image for thresholding.
   :type image: npt.NDArray
   :param otsu_threshold_multiplier: Factor for scaling (not used).
   :type otsu_threshold_multiplier: float
   :param \*\*kwargs: Dictionary of keyword arguments to pass to 'skimage.filters.threshold_yen(**kwargs)'.
   :type \*\*kwargs: dict

   :returns: Threshold to be used in masking heights.
   :rtype: float















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.. py:function:: _threshold_triangle(image: numpy.typing.NDArray, otsu_threshold_multiplier: float = None, **kwargs) -> float

   
   Calculate the triangle threshold.

   For more information see `skimage.filters.threshold_triangle()
   <https://scikit-image.org/docs/stable/api/skimage.filters.html#skimage.filters.threshold_triangle>`_.

   :param image: 2-D Numpy array of image for thresholding.
   :type image: npt.NDArray
   :param otsu_threshold_multiplier: Factor for scaling (not used).
   :type otsu_threshold_multiplier: float
   :param \*\*kwargs: Dictionary of keyword arguments to pass to 'skimage.filters.threshold_triangle(**kwargs)'.
   :type \*\*kwargs: dict

   :returns: Threshold to be used in masking heights.
   :rtype: float















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