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Redesign EITForward(mesh, protocol) API #46

@liubenyuan

Description

@liubenyuan

The latest dev branch is working on a redesign (not backward compatible) version of EITForward class. This new design isolate,

  1. mesh (including pts: coordinates of nodes, tri: the connection of simplices, perm: permittivity, el_pos: electrode positions, ref: reference node),
  2. and the measurement protocol (ex_mat: excitation matrix (Neumann BC only, yet), step: voltage difference electrode, parser: measurement order).

For example,

# forward simulation
fwd = EITForward(mesh, protocol)
v0 = fwd.solve_eit()
v1 = fwd.solve_eit(perm_new, init=True)
# EIT imaging
algo = JAC(mesh, protocol)
ds = algo.solve(v1, v0, normalize=True)

The mesh and protocol can be a dict, or a dataset(#44), if the code block for building these two data structures (mesh, protocol) are intuitive to use, i.e., see the construction code of mesh and protocol in examples.

This new version (maybe 2.0) of pyeit will be release based on these two milestones:

  • simple, clean and easy to use API for EIT forward and inverse simulations,
  • large scale Forward simulation using a fine-grained Head/Thorax phantoms.

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