NerveMshCreator

class nrv.fmod.FEM.mesh_creator.NerveMshCreator(Length=10000, Outer_D=5, Nerve_D=4000, y_c=0, z_c=0, ver_level=2)[source]

Class allowing to generate Nerve shape 3D gmsh mesh with labeled physical domain Contains methodes dealing with the mesh geometries, physical domains and feilds Inherit from MshCreator class. see MshCreator for further detail

Attributes

NerveMshCreator.domains_1D

Identifiers of one-dimensional physical domains.

NerveMshCreator.domains_2D

Identifiers of two-dimensional physical domains.

NerveMshCreator.domains_3D

Identifiers of three-dimensional physical domains.

NerveMshCreator.n_core

Number of Gmsh threads used for mesh generation.

NerveMshCreator.n_domains

Number of registered physical domains.

Methods

NerveMshCreator.__init__([Length, Outer_D, ...])

initialisation of the NerveMshCreator

NerveMshCreator.add_CUFF([ID, x_c, ...])

Add CUFF electrode to the mesh

NerveMshCreator.add_CUFF_MEA([ID, N, x_c, ...])

NerveMshCreator.add_CUFF_MP([ID, N, x_c, ...])

Add MultiPolar CUFF electrodes to the mesh

NerveMshCreator.add_LIFE([ID, x_c, y_c, ...])

Add LIFE electrode to the mesh

NerveMshCreator.add_axon(ID)

Add an axon to the mesh.

NerveMshCreator.add_box([x, y, z, ax, ay, az])

add a box to the mesh

NerveMshCreator.add_cone([x, y, z, L, R1, R2])

add a x-oriented cone to mesh entities

NerveMshCreator.add_cylinder([x, y, z, L, R])

add a x-oriented cylinder to mesh entities

NerveMshCreator.add_domains(obj_IDs, phys_ID)

add domains (ID + name) to a goupe of entities Caution: as to be used after all entities are placed

NerveMshCreator.add_electrode(elec_type[, ...])

NerveMshCreator.add_from_cshape(shape[, ...])

genertate a volume by extruding a utils.geom._cshape.CShape along

NerveMshCreator.add_line(X0, X1)

add a line to the mesh

NerveMshCreator.add_point([x, y, z])

add a point to the mesh

NerveMshCreator.compute_domains()

Associate geometric entities with physical domains.

NerveMshCreator.compute_entity_domain()

link all geometrical entities to corresponding physical domains

NerveMshCreator.compute_geo()

Compute the mesh geometry

NerveMshCreator.compute_mesh()

Compute mesh geometry, domains and resolution and then generate the mesh

NerveMshCreator.compute_res()

Build the mesh-refinement fields associated with the nerve geometry.

NerveMshCreator.fragment([IDs, dim, verbose])

Fragmentation of the mesh important to link entities to each other

NerveMshCreator.generate()

genetate the mesh

NerveMshCreator.get_faces([com, bd])

update and return list of mesh face (optional: with their center of mass)

NerveMshCreator.get_info([verbose])

Collect and optionally print basic mesh statistics.

NerveMshCreator.get_mesh_info([verbose])

Deprecated alias of get_info().

NerveMshCreator.get_obj()

update and return list of mesh entities

NerveMshCreator.get_parameters()

Export the current mesh-creator configuration as a dictionary.

NerveMshCreator.get_res()

return the global resolution saved (usefull when no field are set)

NerveMshCreator.get_volumes([com, bd])

update and return list of mesh volumes (optional: with their center of mass)

NerveMshCreator.load(data[, mshfname, blacklist])

Generic loading method for NRV class instance

NerveMshCreator.refine_entities(ent_ID, ...)

refine mesh resolution in a list of faces or volumes IDs

NerveMshCreator.refine_min(feild_IDs)

refine mesh resolution taking the minimum value for a list of refinment fields

NerveMshCreator.refine_threshold(ent_ID, ...)

refine mesh resolution in a list of faces or volumes IDs

NerveMshCreator.refinement_callback(...)

Add a call back function which is apply to the mesh size defined by fields and return the final mesh size

NerveMshCreator.remove_fascicles([ID])

remove a fascicle of the FEM simulation

NerveMshCreator.reshape_axon(d[, y, z, ID, ...])

Reshape a axon of the FEM simulation

NerveMshCreator.reshape_fascicle([d, y_c, ...])

Reshape a fascicle of the FEM simulation

NerveMshCreator.reshape_nerve([Nerve_D, ...])

Reshape the nerve of the FEM simulation

NerveMshCreator.reshape_outerBox([Outer_D, ...])

Reshape the size of the FEM simulation outer box

NerveMshCreator.rotate(volume, angle[, x, ...])

rotate volume

NerveMshCreator.save([fname, save, blacklist])

Return extracellular context as dictionary and eventually save it as json file NB: caution, first argument is fname to match with MshCreator.save arguments

NerveMshCreator.save_geom(fname)

save only the mesh geometry in a .brep file

NerveMshCreator.set_chara_blen([i])

from gmsh: Extend characteristic lengths from the boundaries inside the surface/volume

NerveMshCreator.set_gnd_facet([outfacet, ...])

Set which of the outer facet should be the ground (element 1)

NerveMshCreator.set_ncore([i])

_summary_

NerveMshCreator.set_parameters(**kawrgs)

Generic method to set any attribute of NRV_class instance

NerveMshCreator.set_res(new_res)

set the global resolution saved (usefull when no field are set)

NerveMshCreator.set_verbosity([i])

from gmsh: Level of information printed on the terminal and the message console.

NerveMshCreator.visualize([fname])

Open the generated mesh in the Gmsh GUI.