mc_trans_mat¶

poreana.diffusion.mc_trans_mat(link, step, kwargs={}, is_norm=False, is_diagonal=False, is_length=True, limit=0)¶

This function plots the occupation of a normalized transition matrix as a heatmap. To normalize the transition matrix the number of the frame are used. This means that all entries in the transition matrix are divided by the total number of frames which are used to estimate the matrix.

Parameters:

link: string: Link to the diffusion hdf5, obj or yml data file generated by the sample routine poreana.sample.Sample.init_diffusion_mc() or the MC run poreana.mc.MC.run()
step: integer: Step length for which the transition matrix is to be displayed
kwargs: dict, optional: Dictionary with plotting parameters
is_norm: bool,optional: Normalized the transition with the number for frames
is_diagonal: bool, optional: Set the matrix diagonal to zero
is_length: bool, optional: x axis is output in box length
limit: float, optional: Set the lowest occupancy value for calculating the width of occupancy