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Thresholds Modules

Functions for calculating thresholds.

_get_threshold(method='otsu')

Creator component which determines which threshold method to use.

Parameters

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

Returns

function Returns function appropriate for the required threshold method.

Raises

ValueError Unsupported methods result in ValueError.

Source code in topostats/thresholds.py 
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def _get_threshold(method: str = "otsu") -> Callable:
    """
    Creator component which determines which threshold method to use.

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

    Returns
    -------
    function
        Returns function appropriate for the required threshold method.

    Raises
    ------
    ValueError
        Unsupported methods result in ValueError.
    """
    if method == "otsu":
        return _threshold_otsu
    if method == "mean":
        return _threshold_mean
    if method == "minimum":
        return _threshold_minimum
    if method == "yen":
        return _threshold_yen
    if method == "triangle":
        return _threshold_triangle
    raise ValueError(method)

_threshold_mean(image, otsu_threshold_multiplier=None, **kwargs)

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>_.

Parameters

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

Returns

float Threshold to be used in masking heights.

Source code in topostats/thresholds.py 
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def _threshold_mean(image: npt.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>`_.

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

    Returns
    -------
    float
        Threshold to be used in masking heights.
    """
    return threshold_mean(image, **kwargs)

_threshold_minimum(image, otsu_threshold_multiplier=None, **kwargs)

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>_.

Parameters

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

Returns

float Threshold to be used in masking heights.

Source code in topostats/thresholds.py 
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def _threshold_minimum(image: npt.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>`_.

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

    Returns
    -------
    float
        Threshold to be used in masking heights.
    """
    return threshold_minimum(image, **kwargs)

_threshold_otsu(image, otsu_threshold_multiplier=None, **kwargs)

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>_.

Parameters

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

Returns

float Threshold to be used in masking heights.

Source code in topostats/thresholds.py 
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def _threshold_otsu(image: npt.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>`_.

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

    Returns
    -------
    float
        Threshold to be used in masking heights.
    """
    return threshold_otsu(image, **kwargs) * otsu_threshold_multiplier

_threshold_triangle(image, otsu_threshold_multiplier=None, **kwargs)

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>_.

Parameters

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

Returns

float Threshold to be used in masking heights.

Source code in topostats/thresholds.py 
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def _threshold_triangle(image: npt.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>`_.

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

    Returns
    -------
    float
        Threshold to be used in masking heights.
    """
    return threshold_triangle(image, **kwargs)

_threshold_yen(image, otsu_threshold_multiplier=None, **kwargs)

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>_.

Parameters

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

Returns

float Threshold to be used in masking heights.

Source code in topostats/thresholds.py 
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def _threshold_yen(image: npt.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>`_.

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

    Returns
    -------
    float
        Threshold to be used in masking heights.
    """
    return threshold_yen(image, **kwargs)

threshold(image, method=None, otsu_threshold_multiplier=None, **kwargs)

Thresholding for producing masks.

Parameters

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

Returns

float Threshold of image using specified method.

Source code in topostats/thresholds.py 
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def threshold(image: npt.NDArray, method: str = None, otsu_threshold_multiplier: float = None, **kwargs: dict) -> float:
    """
    Thresholding for producing masks.

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

    Returns
    -------
    float
        Threshold of image using specified method.
    """
    thresholder = _get_threshold(method)
    return thresholder(image, otsu_threshold_multiplier=otsu_threshold_multiplier, **kwargs)

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