svmbir.phantom

Functions:

gen_microscopy_sample(num_rows, num_cols)	Generate a microscopy sample phantom.
gen_microscopy_sample_3d(num_rows, num_cols, ...)	Generate a 3D microscopy sample phantom.
gen_shepp_logan(num_rows, num_cols)	Generate a Shepp Logan phantom.
gen_shepp_logan_3d(num_rows, num_cols, ...)	Generate a 3D Shepp Logan phantom based on below reference.
nrmse(image, reference_image)	Compute the normalized root mean square error between image and reference_image.

svmbir.phantom.gen_microscopy_sample(num_rows, num_cols)

Generate a microscopy sample phantom.

Parameters:

• num_rows – int, number of rows.

• num_cols – int, number of cols.

Returns:

out_image – 2D array, num_rows*num_cols

svmbir.phantom.gen_microscopy_sample_3d(num_rows, num_cols, num_slices)

Generate a 3D microscopy sample phantom.

Parameters:

• num_rows – int, number of rows.

• num_cols – int, number of cols.

• num_slices – int, number of slices.

Returns:

out_image – 3D array, num_slices*num_rows*num_cols

svmbir.phantom.gen_shepp_logan(num_rows, num_cols)

Generate a Shepp Logan phantom.

Parameters:

• num_rows – int, number of rows.

• num_cols – int, number of cols.

Returns:

out_image – 2D array, num_rows*num_cols

svmbir.phantom.gen_shepp_logan_3d(num_rows, num_cols, num_slices)

Generate a 3D Shepp Logan phantom based on below reference.

Kak AC, Slaney M. Principles of computerized tomographic imaging. Page.102. IEEE Press, New York, 1988. https://engineering.purdue.edu/~malcolm/pct/CTI_Ch03.pdf

Parameters:

• num_rows – int, number of rows.

• num_cols – int, number of cols.

• num_slices – int, number of slices.

Returns:

out_image – 3D array, num_slices*num_rows*num_cols

svmbir.phantom.nrmse(image, reference_image)

Compute the normalized root mean square error between image and reference_image.

Parameters:

• image – Calculated image

• reference_image – Ground truth image

Returns:

Root mean square of (image - reference_image) divided by RMS of reference_image