Note

This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.

3.3.5. fmralign.alignment_methods.OptimalTransportAlignment

class fmralign.alignment_methods.OptimalTransportAlignment(solver='sinkhorn_epsilon_scaling', metric='euclidean', reg=1, max_iter=1000, tol=0.001)

Compute the optimal coupling between X and Y with entropic regularization, using the pure Python POT (https://pythonot.github.io/) package.

Parameters:

solverstr (optional)

solver from POT called to find optimal coupling ‘sinkhorn’, ‘greenkhorn’, ‘sinkhorn_stabilized’,’sinkhorn_epsilon_scaling’, ‘exact’ see POT/ot/bregman on Github for source code of solvers

metricstr (optional)

metric used to create transport cost matrix, see full list in scipy.spatial.distance.cdist doc

regint (optional)

level of entropic regularization

Attributes:

Rscipy.sparse.csr_matrix

Mixing matrix containing the optimal permutation

__init__(solver='sinkhorn_epsilon_scaling', metric='euclidean', reg=1, max_iter=1000, tol=0.001)