ants.math.get_neighborhood

Functions

get_neighborhood_at_voxel(image, center, kernel)	Get a hypercube neighborhood at a voxel.
get_neighborhood_in_mask(image, mask, radius)	Get neighborhoods for voxels within mask.

get_neighborhood_at_voxel(image, center, kernel, physical_coordinates=False)

Get a hypercube neighborhood at a voxel. Get the values in a local neighborhood of an image.

ANTsR function: getNeighborhoodAtVoxel

Parameters:

• image (ants.core.ANTsImage) – image to get values from.

• center (tuple/list) – indices for neighborhood center

• kernel (tuple/list) – either a collection of values for neighborhood radius (in voxels) or a binary collection of the same dimension as the image, specifying the shape of the neighborhood to extract

• physical_coordinates (bool) – whether voxel indices and offsets should be in voxel or physical coordinates

Returns:

valuesndarray

array of neighborhood values at the voxel

indicesndarray

matrix providing the coordinates for each value

Return type:

dictionary w/ following key-value pairs

Example

>>> import ants
>>> img = ants.image_read(ants.get_ants_data('r16'))
>>> center = (2,2)
>>> radius = (3,3)
>>> retval = ants.get_neighborhood_at_voxel(img, center, radius)

get_neighborhood_in_mask(image, mask, radius, physical_coordinates=False, boundary_condition=None, spatial_info=False, get_gradient=False)

Get neighborhoods for voxels within mask.

This converts a scalar image to a matrix with rows that contain neighbors around a center voxel

ANTsR function: getNeighborhoodInMask

Parameters:

• image (ants.core.ANTsImage) – image to get values from

• mask (ants.core.ANTsImage) – image indicating which voxels to examine. Each voxel > 0 will be used as the center of a neighborhood

• radius (tuple/list) – array of values for neighborhood radius (in voxels)

• physical_coordinates (bool) – whether voxel indices and offsets should be in voxel or physical coordinates

• boundary_condition (string (optional)) –

  how to handle voxels in a neighborhood, but not in the mask.

  None : fill values with NaN image : use image value, even if not in mask mean : use mean of all non-NaN values for that neighborhood

• spatial_info (bool) – whether voxel locations and neighborhood offsets should be returned along with pixel values.

• get_gradient (bool) – whether a matrix of gradients (at the center voxel) should be returned in addition to the value matrix (WIP)

Returns:

• if spatial_info is False –

  if get_gradient is False:

  ndarray

  an array of pixel values where the number of rows is the size of the neighborhood and there is a column for each voxel

  else if get_gradient is True:

  dictionary w/ following key-value pairs:

  valuesndarray

  array of pixel values where the number of rows is the size of the neighborhood and there is a column for each voxel.

  gradientsndarray

  array providing the gradients at the center voxel of each neighborhood

• else if spatial_info is True –

  dictionary w/ following key-value pairs:

  valuesndarray

  array of pixel values where the number of rows is the size of the neighborhood and there is a column for each voxel.

  indicesndarray

  array provinding the center coordinates for each neighborhood

  offsetsndarray

  array providing the offsets from center for each voxel in a neighborhood

Example

>>> import ants
>>> r16 = ants.image_read(ants.get_ants_data('r16'))
>>> mask = ants.get_mask(r16)
>>> mat = ants.get_neighborhood_in_mask(r16, mask, radius=(2,2))