make_contiguous

make_contiguous(im, mode='keep_zeros')[source]

Take an image with arbitrary greyscale values and adjust them to ensure all values fall in a contiguous range starting at 0.

Parameters
  • im (array_like) – An ND array containing greyscale values

  • mode (string) –

    Controls how the ranking is applied in the presence of numbers less than or equal to 0.

    ’keep_zeros’

    (default) Voxels equal to 0 remain 0, and all other numbers are ranked starting at 1, include negative numbers, so [-1, 0, 4] becomes [1, 0, 2]

    ’symmetric’

    Negative and positive voxels are ranked based on their respective distances to 0, so [-4, -1, 0, 5] becomes [-2, -1, 0, 1]

    ’clipped’

    Voxels less than or equal to 0 are set to 0, while all other numbers are ranked starting at 1, so [-3, 0, 2] becomes [0, 0, 1].

    ’none’

    Voxels are ranked such that the smallest or most negative number becomes 1, so [-4, 2, 0] becomes [1, 3, 2]. This is equivalent to calling scipy.stats.rankdata directly, and reshaping the result to match im.

Returns

image – An ndarray the same size as im but with all values in contiguous order.

Return type

ndarray

Examples

>>> import porespy as ps
>>> import scipy as sp
>>> im = np.array([[0, 2, 9], [6, 8, 3]])
>>> im = ps.tools.make_contiguous(im)
>>> print(im)
[[0 1 5]
 [3 4 2]]

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