phantom

Simulate shepp logan phantoms.

To Generate phantoms. You can call the following functions with the desired phantom shape as input:

  • modified_shepp_logan
  • shepp_logan
  • yu_ye_wang

You can generate a custom phantom by specifying a list of ellipsoid parameters by calling the phantom function. Ellipsoid parameters are as follows:

  • A : value inside the ellipsoid
  • a, b, c : axis length of the ellipsoid (in % of the cube shape)
  • x0, y0, z0 : position of the center (in % of the cube shape)
  • phi, theta, psi : Euler angles defining the orientation (in degrees)

Alternatively, you can generate only one ellipsoid by calling the ellipsoid function.

Examples

To generate a phantom cube of size 32 * 32 * 32:

>>> from siddon.phantom import *
>>> my_phantom = shepp_logan((32, 32, 32))
>>> assert my_phantom[16, 16, 16] == -0.8

Notes

You can take a look at those links for explanations: http://en.wikipedia.org/wiki/Imaging_phantom http://en.wikipedia.org/wiki/Ellipsoid http://en.wikipedia.org/wiki/Euler_angles This module is largely inspired by : http://www.mathworks.com/matlabcentral/fileexchange/9416-3d-shepp-logan-phantom

Original Author: Nicolas Barbey

mr_utils.test_data.phantom.phantom.phantom(shape, parameters_list, dtype=<class 'numpy.float64'>)[source]

Generate a cube of given shape using a list of ellipsoid parameters.

Parameters:
  • shape (tuple of ints) – Shape of the output cube.
  • parameters_list (list of dictionaries) – List of dictionaries with the parameters defining the ellipsoids to include in the cube.
  • dtype (data-type, optional) – Data type of the output ndarray.
Returns:

cube – A 3-dimensional ndarray filled with the specified ellipsoids.
Return type:

ndarray

See also

shepp_logan()
Generates the Shepp Logan phantom in any shape.
modified_shepp_logan()
Modified Shepp Logan phantom in any shape.
yu_ye_wang()
The Yu Ye Wang phantom in any shape.
ellipsoid()
Generates a cube filled with an ellipsoid of any shape.

Notes

http://en.wikipedia.org/wiki/Imaging_phantom

mr_utils.test_data.phantom.phantom.shepp_logan(shape, **kargs)[source]

Generates a Shepp-Logan phantom with a given shape and dtype

Parameters:
  • shape (3-tuple of ints) – Shape of the 3d output cube.
  • dtype (data-type) – Data type of the output cube.
Returns:

cube – 3-dimensional phantom.
Return type:

ndarray
mr_utils.test_data.phantom.phantom.modified_shepp_logan(shape, **kargs)[source]

Generates a Modified Shepp-Logan phantom with a given shape and dtype

Parameters:
  • shape (3-tuple of ints) – Shape of the 3d output cube.
  • dtype (data-type) – Data type of the output cube.
Returns:

cube – 3-dimensional phantom.
Return type:

ndarray
mr_utils.test_data.phantom.phantom.yu_ye_wang(shape, **kargs)[source]

Generates a Yu Ye Wang phantom with a given shape and dtype

Parameters:
  • shape (3-tuple of ints) – Shape of the 3d output cube.
  • dtype (data-type) – Data type of the output cube.
Returns:

cube – 3-dimensional phantom.
Return type:

ndarray
mr_utils.test_data.phantom.phantom.ellipsoid(parameters, shape=None, out=None, coordinates=None)[source]

Generates a cube filled with an ellipsoid of any shape.

Parameters:
  • parameters (list of dictionaries) – List of dictionaries with the parameters defining the ellipsoids to include in the cube.
  • shape (tuple of ints, optional) – Shape of the output cube.
  • out (array_like) – If None, initialized to all zeros.
  • coordinates (list) – List of coordinates
Returns:

out – The ellipsoid.
Return type:

array_like

Notes

If out is given, fills the given cube instead of creating a new one.