pseudo_electrostatic_packing

pseudo_electrostatic_packing(shape: List = None, im: Buffer | _SupportsArray[dtype[Any]] | _NestedSequence[_SupportsArray[dtype[Any]]] | bool | int | float | complex | str | bytes | _NestedSequence[bool | int | float | complex | str | bytes] = None, r: int = 5, sites=None, clearance: int = 0, protrusion: int = 0, edges: Literal['extended', 'contained'] = 'extended', phi: float = 1.0, maxiter: int = 1000, seed: int = None, smooth: bool = True, compactness: float = 1.0, value: int = 1)[source]

Iterativley inserts spheres as close to the given sites as possible.

Parameters:

  • shape (list) – The shape of the image to create. This is equivalent to passing an array of False values of the desired size to im.

  • im (ndarray) – Image with False indicating the voxels where spheres should be inserted. This can be used to insert spheres into an image that already has some features (e.g. half filled with larger spheres, or a cylindrical plug).

  • r (int) – Radius of spheres to insert.

  • sites (ndarray (optional)) – An image with True values indicating the electrostatic attraction points. If this is not given then the peaks in the distance transform of im are used, which corresponds to the center of the image for a blank input.

  • clearance (int (optional, default=0)) – The amount of space to put between each sphere. Negative values are acceptable to create overlaps, but abs(clearance) < r.

  • protrusion (int (optional, default=0)) – The amount that spheres are allowed to protrude beyond the active phase. A negative number will create clearance between spheres and the background.

  • maxiter (int (optional, default=1000)) – The maximum number of spheres to insert.

  • phi (float (default is 1.0)) – The “solid volume fraction” of spheres to add (considering spheres as solid). This is used to calculate the discrete number of spheres, N, required based on the total volume of the image. If N is less than maxiter then maxiter will be set to N. Note that this number is not quite accurate when the edges=’extended’ since it’s not possible to know how much of the sphere will be cutoff by the edge.

  • edges (string (default is 'contained')) –

    Controls how spheres at the edges of the image are handled. Options are:

    edges

    description

    ’contained’

    Spheres are all completely within the image

    ’extended’

    Spheres are allowed to extend beyond the edge of the image. In this mode the volume fraction will be less that requested since some spheres extend beyond the image, but their entire volume is counted as added for computational efficiency.

  • seed (int, optional, default = None) – The seed to supply to the random number generator. Because this function uses numba for speed, calling the normal numpy.random.seed(<seed>) has no effect. To get a repeatable image, the seed must be passed to the function so it can be initialized the way numba requires. The default is None, which means each call will produce a new realization.

  • compactness (float) – Controls how tightly the spheres are grouped together. A value of 1.0 (default) results in the tighest possible grouping while values < 1.0 give more loosely or imperfectly packed spheres.

  • value (int, default = 1) – The value of insert for the spheres. The default is 1, which puts holes into to the background. Values other than 1 (Foreground) make it easy to add spheres repeated and identify which were added on each step.

Returns:

im – An image with inserted spheres indicated by True

Return type:

ndarray

Examples

Click here to view online example.