porespy.networks.skeleton#

porespy.networks.skeleton(im, surface=False, parallel_kw=None)#

Takes the skeleton of an image. This function ensures that no shells are found in the resulting skeleton by trimming floating solids from the image beforehand and by checking for shells after taking the skeleton. The skeleton is taken using Lee’s method as available in scikit-image. For faster skeletonization, a parallel mode is available.

Parameters:

  • im (ndarray) – A binary image of porous media with ‘True’ values indicating phase of interest.

  • surface (boolean) –

    If False disconnected solid at the surface of the image is NOT

    trimmed. This is the default mode. However, if True, disconnected solid at the surface of the image is trimmed. Note that disconnected solids are NOT removed if a 2D image is passed.

    parallel_kwdict

    Dictionary containing the settings for parallelization by chunking. If None is provided, parallelization does not occur. The default is None.

    The optional settings include divs (scalar or list of scalars, default = [2, 2, 2]), overlap (scalar or list of scalars, optional), and cores (scalar, default is all available cores).

    divs is the number of times to divide the image for parallel processing. If 1 then parallel processing does not occur. 2 is equivalent to [2, 2, 2] for a 3D image. If a list is provided, each respective axis will be divided by its corresponding number in the list. For example, [2, 3, 4] will divide z, y, and x axis to 2, 3, and 4 respectively.

    overlap is the amount of overlap to include when dividing up the image. This value will almost always be the size (i.e. raduis) of the structuring element. If not specified then the amount of overlap is inferred from the size of the structuring element, in which case the strel_arg must be specified.

    cores is the number of cores that will be used to parallel process all domains. If None then all cores will be used but user can specify any integer values to control the memory usage. Setting value to 1 will effectively process the chunks in serial to minimize memory usage.

Returns:

  • sk (ndarray) – Skeleton of image

  • im (ndarray) – The image used to take the skeleton, the same as the input image except for floating solids removed if the image supplied is 3D

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